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Molecular Spintronic from a Theoretical Point of View
Carlo Adamo
Laboratoire d’Electrochimie et Chimie Analytique,
Ecole Nationale Supérieure de Chimie de Paris, 11 rue P. et M. Curie,
Paris F-75231 Cedex05, France
Devices related to spintronics are intended to manipulate the spin of the electron rather than its charge and, up-to-now, are related to semiconductor (S-C) technology. In this contribution we will present an ab-initio analysis of photoactive multi-spin molecular systems expected to undergo an intramolecular alignment of their spins upon light excitation. This photomagnetic effect is worth considered as the transposition of the coherence of spins (obtained in S-C devices) at the molecular level.

In particular using DFT and Time Dependent DFT (TD-DFT), we investigated the photochemical properties and the mechanism of magnetic exchange coupling (at the ground and excited state) of a series of organic [1,2] and organometallic [3] Photo-Molecular devices (PMD).

References
[1] Ciofini, I.; Lainé, P.P.; Zamboni, M.; Daul, C.A.; Marvaud, V.; Adamo, C.; Chem. Eur. J. 2007, 13, 5360-5377.
[2] Teki, Y.; Miyamoto, S.; Iimura, K.; Nakatsuji, M.; Miura, Y. J. Am. Chem. Soc. 2000, 122, 984-985.
[3] Ciofini, I.; Lainé, P.P.; Bedioui, F.; Adamo, C. J. Am. Chem. Soc., 2004, 126, 10763-10777.
Molecular Dynamics Simulation of NMR Lineshape Anisotropy of Guest Molecules within Inclusion Complexes
Saman Alavi, Peter Dornan, and Tom K. Woo
Department of Chemistry, University of Ottawa, Ottawa, Ontario Canada
Nonspherical cages in inclusion compounds can result in non-uniform motion of guest species in these cages and anisotropic lineshapes in NMR spectra of the guest. We present a methodology to calculate lineshape anisotropy of guest species in cages based on molecular dynamics simulations of the inclusion compound. The methodology is valid for guest atoms with spin 1/2 nuclei and does not depend on the temperature and type of inclusion compound or guest species studied. As an example, the nonspherical shape of the structure I (sI) clathrate hydrate large cages leads to preferential alignment of linear CO2 molecules in directions parallel to the two hexagonal faces of the cages. The angular distribution of the CO2 guests in terms of a polar angle θ and azimuth angle φ and small amplitude vibrational motions in the large cage are characterized by molecular dynamics simulations at different temperatures in the stability range of the CO2 sI clathrate. The experimental 13C NMR lineshapes of CO2 guests in the large cages show a reversal of the skew between the low temperature (77 K) and the high temperature (238 K) limits of the stability of the clathrate. In this work, we determine the angular distributions of the guests in the cages by the classical MD simulations of the sI clathrate and calculate the 13C NMR lineshapes over a range of temperatures. Good agreement between experimental lineshapes and calculated lineshapes is obtained. No assumptions regarding the nature of the guest motions in the cages are required.
The pKa computations of substituted aryl seleninic acids and aryl selenenic acids
S. Tahir Ali ,1,2 Walter M. F. Fabian1,Sajjad Karamat1,3 and Sajid Jahangir1,2
1Institut für Chemie, Karl-Franzens-Universität Graz, Heinrichstrasse 28, 8010 Graz, Austria.
2Department of Chemistry, Federal Urdu University of Arts, Science & Technology, Gulshan-e-Iqbal Science Campus, Karachi, Pakistan.
3Department of Chemistry, Quaid-e-Azam University, Islamabad, Pakistan.
The pKa and structures of a series of small molecules containing Se atom are calculated via Density Functional Method. [B3LYP/6-31G(d,p) and 6-31+G(d,p)] This series of compounds under consideration include substituted aryl seleninic acids and aryl selenenic acids. The pKa values of seleninic acids Ar-SeO2H and selenenic acids Ar-SeOH were calculated by using a thermodynamic cycle. The results are in reasonable agreement with the experimentally known pKa values (R2 > 0.92). The basis set 6-31G(d,p) used for pKa computations is not capable to provide a reasonable agreement with the experimental values. Additions of diffuse functions [6-31+G(d,p)] significantly improve the results. Reasonable trends but not absolute pKa values are obtained. The correlation seems to be better described by B3LYP/6-31+G(d,p) than B3LYP/6-31G(d,p) as indicated by the correlation coefficient R2 in benzene seleninic acids while in benzene selenenic acids the correlation seems to be better described by B3LYP/6-31G(d,p) than B3LYP/6-31+G(d,p) as indicated by the correlation coefficient R2.
The movement of ions and ionizable side chains in membranes.
Toby W. Allen
Department of Chemistry,
University of California, Davis
Biological membranes are traditionally pictured as low dielectric slabs that present large energetic barriers to polar and charged molecules. We investigate the interactions of ions and ionizable protein side chains with lipid bilayers to provide free energy and pKa profiles. Fully atomistic molecular dynamics simulations reveal that the membrane undergoes deformations that dictate membrane permeation energetics; lowering barriers for charged species and maintaining near-aqueous-phase pKa’s. We compare to available experimental partitioning data and carry out quantum mechanical calculations and polarizable membrane simulations to demonstrate surprising accuracy of these models. These studies have implications for many membrane-based biological processes, including the gating mechanisms of voltage gated ion channels.
Quantum study of beryllium interaction with tungsten (100) surface
A.Allouche
Physique des Interactions Ioniques et Moléculaires,
CNRS and Université de Provence,
Campus Scientifique de Saint Jérôme, service 242, 13397 Marseille Cedex 20 - FRANCE
Beryllium, tungsten and carbon are planned as wall cladding materials for the future international tokamak (ITER). Be and W will be the dominant components and therefore the formation of binary Be-W alloys under plasma action is one of the most important issues in plasma-wall interaction processes at the first wall. This article proposes a first principles DFT study of beryllium atoms retention in tungsten. In a first step the beryllium adsorption energy is calculated on W(100) surface, and then the barrier to inclusion into the bulk. For each calculation the electronic structure of the formed compound is analyzed through density of states (DOS) calculation.
Families of fully nonlocal kinetic energy density functionals: some new proposals
J. E. Alvarellos and D. Garcia-Aldea
Departamento de Fisica Fundamental. UNED.
Apartado 60.141. E-28080 Madrid (Spain).
Following recent ideas on the construction of kinetic energy density functionals that reproduce the linear response function of the homogeneous electron gas, we present some families of them:
- the more traditional approach where the nonlocal terms have the structure of the Thomas-Fermi functional
- the new approach, with a nonlocal term based on the von Weizsacker functional

In order to test the quality of these functionals, we will focus our attention on both the total kinetic energy and the local behavior of the kinetic energy density. The new functionals are capable of giving better local behavior than the GGA semilocal functionals, yielding at the same time accurate total kinetic energies.

We must remark that almost all the functionals discussed in the paper, when using an adequate reference density, can be evaluated as a single integral in momentum space, with a quasilinear scaling for the computational cost.

References
D. Garcia-Aldea and J. E. Alvarellos, J. Chem. Phys. 127, 144109 (2007).
D. Garcia-Aldea and J. E. Alvarellos, Phys. Rev. A 76, 052504 (2007).
D. Garcia-Aldea and J. E. Alvarellos, Phys. Rev. A 77, 022502 (2008).
Multiscale Modeling Workflow to Drive Performance of PEM Fuel Cells
L. Subramanian, A. Andersen, D. Rigby, J. L. Gavartin, J. Wescott, J. Srinivasan, P. Gestoso-Souto and W. Shirley
Accelrys, 10188 Telesis Court, Suite 100, San Diego, CA 92121, USA
As well evidenced by numerous recent publications the traditional monoscale modeling, be it in the macroscopic, FEM realm or in the microscopic, atomistic modeling realm has proven to be inadequate to study materials, their structure and their behavior. It is clear that a multiscale modeling approach is necessary to gain insight into the fundamental chemistry and physics of the system and tie this to the engineered behavior. A key to deriving powerful benefits from multiscale modeling is to be able to define, implement, and validate workflows relevant to the system across time and length scales. Data management and knowledge extraction enabled through pipelining technology will be discussed in the context of Fuel Cell catalyst and membrane design. The approach and its application will be illustrated with a select number of illustrative, non-proprietary examples



Correlated Sampling for the Neon Dimer in Diffusion Quantum Monte Carlo
James B. Anderson
Department of Chemistry and Department of Physics
Pennsylvania State University, USA
Correlated sampling for correction calculations in DQMC may be coupled with correlated sampling in VQMC to obtain high accuracies in the differences in energies for similar systems. The method succeeds because the differences in weights for correlated walkers in DQMC are minimized. Calculations for Ne dimers and separated Ne atom pairs yield accurate values for the interaction energies of Ne atoms.
Approximate London dispersion energy functional based on the range-separated hybrid (RSH) + MP2 approach
János ÁNGYÁN
Equipe Modélisation Quantique et Cristallographique, LCM3B, Nancy-University - CNRS, B.P. 239, F-54506 Vandoeuvre-les-Nancy
One of the major challenges for present-day density functionals is to provide a seamless representation of London dispersion interactions in density functional calculations. Recently, we have shown that in a range-separated hybrid DFT framework, where the short-range exchange-correlation is treated by appropriate functionals and the long-range exchange and correlation is described by wave function methods, in particular by Hartee-Fock followed by second order perturbation theory, one retrieves not only the van der Waals minimum, but also the asymptotically correct 1/R6 behavior of the potential energy. An advantage of this approach that one does not need any partition of interacting subsystems, making thus possible to describe intramolecular long-range dynamic correlation effects and intermolecular interactions in the same framework. Based on a local MP2 type Ansatz, it is shown that the long-range MP2 energy can be approximated using information taken from occupied orbitals only. This approach opens the way for a rapid, non-empirical estimation of London dispersion forces based on density functional calculations.
Computation of NMR parameters for materials
Jochen Autschbach
Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
This talk consists of two parts. The first, main, part is concerned with NMR computations for carbon nanotubes (CNTs). NMR is becoming increasingly important as an experimental tool to study the properties of CNT samples, but it remains difficult to obtain well resolved spectra. Accordingly, theoretical support is needed for predictions, and to help with the assignment of NMR spectra. We will discuss a number of theoretical studies of CNT NMR that we have undertaken during the past 4 years, with emphasis on the chemical shift range for narrow to medium diameter CNTs, and effects from covalent functionalization and defects on the NMR spectra. In the second part, we will showcase some recently developed theoretical tools to analyze NMR shielding and J-coupling tensors for elements from all parts of the periodic table. EFG tensor analyses will also be discussed briefly.
Selective Rotational Control in Molecular Mixtures
Ilya Sh. Averbukh, Sharly Fleischer, and Yehiam Prior
Department of Chemical Physics, The Weizmann Institute of Science,
Rehovot 76100, Israel

Molecular alignment by ultrashort laser pulses is attracting increasing attention motivated by various applications spanning from optical phase modulation and control of high harmonic generation to potential novel schemes for molecular analysis and separation. We demonstrate selective rotational manipulation of molecules in mixtures of molecular isotopes [1] and spin isomers [2]. The alignment is observed in time-resolved Four Wave Mixing experiment. The process involves application of two time-delayed, ultrashort laser pulses (~50fs) applied to the molecular mixture. The first pulse imparts torque to all of the molecules in the mixture, and due to rotational quantum revivals, one observes a series of aligned and anti-aligned states (parallel and perpendicular to the direction of the laser field polarization). Depending on the time delay between the pulses, the second pulse can enhance or significantly reduce the effect of the first pulse i.e. enhance or decrease the rotational energy of the rotating molecules. The selective alignment of a single component in a mixture is based on choosing the right time for the application of the second pulse. In the case of molecular isotopes, we exploit the slight difference in the moment of inertia (due to the difference in the isotope mass) and corresponding difference in rotational periodicity. In the case of spin isomers, there are no differences in the mechanical properties of the para and ortho spin isomers. However, the Pauli principle correlates the symmetry of the spin and rotational wave functions and induces differences in the time dependence of the spin isomer angular distributions. Since rotational states of different symmetries (even/odd) evolve out of phase at quarter revival times, we used this difference to affect the para and ortho isomers selectively. Moreover, using multi-pulse excitation with crossed polarization, unidirectional rotation may be attained [3], providing additional means for selective manipulations in molecular mixtures.

[1] Sharly Fleischer, Ilya. Sh. Averbukh and Yehiam Prior, Phys.Rev. A 74, 041403 (2006).
[2] Sharly Fleischer, Ilya. Sh. Averbukh and Yehiam Prior, Phys.Rev. Lett., 99, 093002 (2007).
[3] Sharly Fleischer, Ilya. Sh. Averbukh and Yehiam Prior, (to be published)
Excitation energies with time-dependent density matrix theory
Evert Jan Baerends, K. J. H. Giesbertz, O. V. Gritsenko, K. Pernal
Theoretical Chemistry, Vrije Universiteit, Amsterdam
Time-dependent density functional theory in its current adiabatic implementations exhibits three striking failures: a) totally wrong behavior of the excited state surface along a bond-breaking coordinate; b) lack of doubly excited configurations, affecting again excited state surfaces; c) much too low charge transfer excitation energies. We address these problems with time-dependent density matrix theory (TDDMFT).1,2 For two-electron systems the exact exchange-correlation functional is known in DMFT, hence exact response equations can be formulated. This affords a study of the performance of TDDMFT in the TDDFT failure cases mentioned (which are all strikingly exhibited by prototype two-electron systems such as dissociating H2 and HeH+). At the same time, adiabatic approximations, which will eventually be necessary, can be tested without being obscured by approximations in the functional. We find:3 a) In the fully non-adiabatic (ω-dependent, exact) formulation of linear response TDDMFT, it can be shown that LR-TDDMFT is able to provide exact excitation energies; in particular the first order (linear response) formulation does not prohibit the correct representation of doubly excited states; b) Within previously formulated simple adiabatic approximations2 the bonding-to-antibonding excited state surface as well as charge transfer excitations are described without problems, but not the double excitations; c) An adiabatic approximation is formulated in which also the double excitations are fully accounted for.

1. K. Pernal, O. Gritsenko and E. J. Baerends, Phys. Rev. A 75, 012506 (2007)
2. K. Pernal, K. J. H. Giesbertz, O. Gritsenko and E. J. Baerends, J. Chem. Phys. 127, 21401 (2007)
3. K. J. H. Giesbertz, E. J. Baerends, K. Pernal, O. Gritsenko, J. Chem. Phys., to be published
Is Bigger Really Better? Coupled-Cluster Theory for Larger Molecules
Rodney J. Bartlett, Andrew Taube, Tom Hughes, Tomasz Kus, Victor Lotrich, Norbert Flocke
Quantum Theory Project
University of Florida
Gainesville, FL, USA, 32611-5500
Today, single reference coupled-cluster theory typically provides the benchmark results for molecules with several atoms. This includes ground state energies, structures, properties, and transition states; and with its EOM-CC extensions, those for excited states. These results are also achieved within a virtually ‘black-box’ form, as CC theory has few choices except basis set, level of correlation, and the mean field reference function, which could be Hartree-Fock, Brueckner, Kohn-Sham, Natural Determinant, or something else. The next frontier for coupled-cluster theory is to make such well characterized and calibrated methods applicable to larger molecules. After all, the rationale for CC theory is its size-extensivity, which enables quantum chemistry to give meaningful results all the way to infinite systems. However, achieving meaningful large molecule CC results depends upon a variety of complementary strategies.

The simplest is to reduce the virtual space in large CC calculations by using frozen natural orbitals (FNO). Without any meaningful error, such a transformation will save over an order of magnitude in CCSD, CCSD(T), and ΛCCSD(T) calculations, and ~ 2 orders of magnitude in CCSDT. However, to apply this tool effectively requires the development of analytical gradient techniques which makes studies of potential energy surfaces with several minima and transition states amendable to high-level study. An illustration for the unimolecular dissociation of nitroethane illustrates the method.

The second is to develop parallel CC programs that can scale over hundreds and thousands of processors. The newly written ACES III is such a program that shows exceptional performance and functionality, with the same ease of ‘black-box’ application. All memory handling and message passing are achieved with a new super-instruction assembler language (SIAL) separating those details from the quantum chemistry being programmed. Illustrations for some molecules of biochemical interest will be presented.

Finally, our natural linear scaling CC method will be described as a way to provide highly correlated results for very large molecules, from local units. Many variants of the same basic idea have had some success, but our approach differs in some essential elements, and is directed at capturing the ultimate transferability we see in chemistry. We consider transferable energies, densities, and response properties.
Finite-size, geometry, and many-electron effects in strong field ionization
D. Bauer,1 S.V. Popruzhenko,1,2 and M. Ruggenthaler1
1 Max-Planck-Institut for Nuclear Physics, Heidelberg, Germany

2 Moscow Engineering Physics Institute, Moscow, Russia
Ionization rates, photoelectron-, and high harmonic-spectra of complex, finite-size systems such as clusters or fullerenes in intense laser fields are discussed. Using various numerical approaches we are able to disentangle finite-size from many-electron effects. For instance, the finite size influences the cut-offs in the photoelectron spectra for both "direct" and rescattered electrons, in particular at long wavelengths. Many-electron effects significantly alter high-order harmonic generation (HOHG) spectra through the presence of plasmon excitations, which then decay.

Since the recollision of photoelectrons is responsible for almost all of the interesting strong-field effects such as HOHG or high-order above-threshold ionization spectra and nonsequential double ionization, the questions arise whether (i) recolliding electrons may excite collective modes and (ii) if so, whether this excitation is efficient enough to be seen in the HOHG spectra. If yes, "tomographic" imaging schemes of complex molecules relying on HOHG are unlikely to reveil clear structural information.

In our presentation we shall discuss these questions with the help of simple models and results from time-dependent density functional theory (TDDFT) calculations.

This work was supported by the Deutsche Forschungsgemeinschaft.
Unified Density-Functional Treatment of Dynamical, Nondynamical, and Dispersion Correlations
Axel D. Becke, Erin R. Johnson, and Felix Kannemann
Department of Chemistry, Dalhousie University, Halifax, NS, B3H4J3, Canada
We have derived real-space density-functional models for all three correlation types of importance in chemistry: dynamical, nondynamical, and dispersion, and have unified them in an approach called “DF07” [J. Chem. Phys. 127, 124108 (2007)]. DF07 will be summarized and recent thermochemical benchmark results will be presented, including tests on transition-metal complexes.

The models underlying DF07 are post-exact-exchange, thus free of the many well-known failures of local GGA-type exchange approximations. Computation of the exact exchange energies and exact exchange-energy densities required by DF07 is costly, however, and a GGA-type reformulation is desirable. Our first steps in this direction will be discussed.
Triple-phase Boundary in Catalyst Layers
Peter Berg
Faculty of Science,
University of Ontario Institute of Technology,
Oshawa, Ontario, Canada
In PEM fuel cells, the triple-phase boundary (TPB) forms an important part of the catalyst layer microstructure. At the cathode pore level, a mathematical model is developed to describe the TPB between ionomer, air pore and C/Pt particles and its reaction-diffusion processes. We investigate the reaction kinetics near the TPB and how liquid water affects the distribution of the reaction rate along the C/Pt particles. The ultimate goal is to maximize platinum utilization, optimize the reaction kinetics, and establish a micro-macro link between local reaction kinetics and the macroscopic Butler-Volmer equation in terms of liquid water content.
Novel Findings in the Jahn-Teller Effect Theory.
Implications in Electronic Structure Calculations
Isaac B Bersuker
Institute for Theoretical Chemistry, Department of Chemistry & Biochemistry, The University of Texas at Austin, Austin, Texas, USA
Several important recent findings in the Jahn-Teller effect (JTE) theory are discussed, especially those related to ab initio calculations. The main basic result is the proof of the general validity of the JTE as the only source of instabilities and distortions of high-symmetry configurations of polyatomic systems. The immediate implication is that when unstable states are considered the excited electronic states that produce the instability of the ground state should be involved in the calculations, at least via the basis sets chosen to well represent all the mixing states. It is shown that when molecular systems are distorted, but there are no apparent degeneracies or close in energy states the JTE are “hidden” in the excited states of the undistorted configuration, even when the energy gap to these states is very large. For the example of the ozone molecule (which has no degenerate ground state, neither in the distorted obtuse-triangular nor in the undistorted regular triangular configurations, and it has no low-lying excited states) the distortion is shown to emerge from the JTE in the excited E state situated at ~8.3 eV above the ground state. The JT stabilization energy is more than ~9 eV which makes the distorted configuration the lowest in energy. For molecular systems with half-closed-shell electronic configurations e2 and t3 (formed by degenerate orbitals e and t), which produce totally symmetric charge distribution and are not subject to the JTE, distortions were shown to occur due to a strong pseudo JT mixing of two excited states. Again, the pseudo JT stabilization energy in these cases is larger than the energy gap to the ground state, and the distortion is accompanied by orbital disproportionation. In some systems this produces two coexisting states, low-spin distorted and high-spin undistorted, and a novel phenomenon: JT-induced spin-crossover. Distinguished from the known spin-crossover in transition metal compounds the JT-induced spin-crossover takes place in a large variety of molecular systems from different classes including organic compounds, and it has a much lower rate of relaxation between the two states; this makes them candidates for single-molecule materials for electronic devices.
Heterogeneous Atmospheric Chemistry at Night
Lori M. Cosman, Simone Gross, Jackson Mak, Daniel A. Knopf, Allan K. Bertram
Department of Chemistry, University of British Columbia
Laboratory, fieldwork, and modeling studies have conclusively shown that interactions between gas-phase species and atmospheric aerosol particles (termed heterogeneous atmospheric chemistry) can significantly influence the chemistry of the atmosphere. Although a significant amount of research has focused on heterogeneous atmospheric chemistry during the last two decades, this field is still in its infancy, especially in comparison with gas-phase atmospheric chemistry.

This talk will focus on heterogeneous atmospheric chemistry that can occur during the night. N2O5 hydrolysis on aqueous particles coated with organic monolayers will be discussed. Surface-active organic molecules (organic molecules that have both a hydrophobic group and a hydrophilic group) are common constituents of aqueous particles in the atmosphere. Several researchers have suggested that these organic molecules form organic monolayers on the surface of atmospheric aqueous particles. Using a newly constructed flow cell, we have investigated the effect of these organic monolayers on N2O5 hydrolysis.
Counter-intuitive analytical results for diffusion in nanostructures
Sergey M. Bezrukov
National Institutes of Health, Bethesda, MD 20892-0924, USA
Experimentally, we study fluctuations in small, about hundred pA ionic currents through nanopores of biological origin to detect and analyze single molecules of different nature (e.g., Physical Review Letters, 2006, 97:018301).

Theoretically, we explore the consequences of interactions between the pore and the translocating molecules within the framework of a continuum diffusion model for the particle dynamics in the channel (Journal of Physical Chemistry, 2000, 113:8206-8211 and Physical Review Letters, 2008, 100:038104 with the references therein). Several of our findings are quite counter-intuitive (e.g., Biophysical Journal, 2005, 88:L17-L19 and Physical Review Letters, 2006, 97:020601). Three of the examples to be discussed in the talk are: (i) “Sticking” to the channel slows down translocation (a particle spends more time in the channel) but increases the flux; (ii) “Uphill” and “downhill” particle translocation times (and their distributions) are identical; (iii) An optimal channel should exhibit the most pronounced binding on the side that is opposite to the side of the oncoming particles.
A Little Dipole Goes a Long Way: Electric Control of Ultracold Collisions
John L. Bohn
JILA and NIST, University of Colorado
As the temperature of a molecular gas is lowered to the sub-milliKelvin level, long-range forces become increasingly important in the dynamics of molecular interactions. For neutral, dipolar species, the dipole-dipole interaction is the dominant long-range force. It can affect collisions on length scales of hundreds or thousands of Bohr radii in a cold gas. In this talk I will discuss various consequences of this interaction, including prospects for exploiting it to control collision dynamics. Applications will include shielding of collisions; shelving molecular pairs in long-range states; and suppressing chemical reactivity.

This work was supported by the NSF.
Molecular dynamics of rare events: from phase transitions to protein folding
P.G. Bolhuis
van 't Hoff Institute for Molecular Sciences
University of Amsterdam
The Netherlands
Many processes in nature occur via rare but important events. For instance, nucleation phenomena, chemical reactions in solution, but also protein conformational changes such as folding, can occur on a long time scale compared to the fundamental time-step in atomistic molecular dynamics (MD). These long timescales are mostly caused by free energy barriers. Techniques such as umbrella sampling or Metadynamics can overcome these barriers, but need a proper reaction coordinate, which is not a priori known in complex systems. Parallel tempering a.k.a. replica exchange MD (REMD) can overcome barriers without knowledge of the reaction coordinate, but often suffers from convergence problems. Besides, all of these methods cannot give insight in kinetics. The Transition Path Sampling (TPS) method harvests an ensemble of trajectories connecting an reactant and product state and does not rely on a priori defined reaction coordinates. Besides the mechanism, it also gives access to the kinetics.

In this presentation, I will review the basic ideas and algorithms of TPS, and summarize recent developments, such as transition interface sampling, path replica exchange and likelihood maximization. Further, I will show some applications of the methodology to crystal nucleation, protein folding and conformational changes of signalling proteins.
Quantum Melting and Superfluidity of Hydrogen Clusters
Massimo Boninsegni
Department of Physics
University of Alberta
Clusters of para-hydrogen and ortho-deuterium, comprising between up to 50 molecules, have been extensively studied by computer simulations based on the continuous-space Worm Algorithm, which allows one to go down to temperatures as low as a few hundredths of a K. These clusters display an intriguing interplay of liquid- and solid-like behavior as a function of both temperature and cluster size. In this sense, their physics is far richer than that of helium clusters. An intriguing phenomenon predicted by our simulations is Quantum melting, whereby clusters in some size range (roughly between 22 and 30 molecules) are observed to go from rigid, solid-like, to essentially structureless and liquid-like as the temperature is lowered, due to the onset of quantum exchange cycles involving all the molecules in the cluster. At low temperature these clusters turn superfluid; their local superfluid response has been analyzed, and found to be essentially uniform throughout the system in the zero-temperature limit, even in clusters with a pronounced shell structure. In particular, exchanges involving molecules in the inner and outer shells are shown to be underlying the superfluid response. The relationship between the local superfluid and Bose condensate densities has also been investigated.
Experimental Indications of Tunneling in Organic and Organometallic Reactions -- Calculations Indicate Where to Look and What to Look For
G. Robert Shelton, Ayan Datta, David A. Hrovat, and Weston Thatcher Borden
Department of Chemistry, University of North Texas, Box 305070, Denton, Texas 76203-5070
Non-zero rates at cryogenic temperatures and a curved Arrhenius plot are just two of the indications of the importance of tunneling in a reaction. Calculations on reactions, in which tunneling is predicted to play a large role, show that a highly temperature-dependent primary H/D kinetic isotope effect (KIE) and primary and secondary KIEs that are non-multiplicative, provide reliable and, in general, more easily obtained indications of tunneling than curved Arrhenius plots. Examples will be drawn from calculations on a variety of organic and organometallic reactions.
The packing landscape and liquid-liquid phase transition of confined hard discs.
S. S. Ashwin and R. K. Bowles
Department of Chemistry
University of Saskatchewan
Saskatoon, SK, Canada
We calculate the complete inherent structure landscape, for a system of hard discs of diameter σ confined between two line separated by a distance 1.866 < H/σ < 2. Confinement in this range allows next nearest particle contacts which leads to a variety locally jammed packing environments that can be mapped onto two sets of incompatible nearest neighbour tiles. It also prevents particles from passing which eliminates the possibility of collective particle motion leading to unjamming. As a result, we can construct all the collectively jammed packings for the system by considering all the combinations of compatible tiles that result in locally jammed configurations and we enumerate them using the transfer matrix method. We also use molecular dynamics simulations to show that this system exhibits a unique entropy driven second-order liquid-liquid phase transition where the low density fluid maps to inherent structures made from one set of tiles, while the high density fluid maps to inherent structures constructed from the other. Analysis of the jammed packings reveals that it is not sufficient to described the inherent strucuture distribution solely in terms the number of jammed states with a given packing fraction because the underlying order of the different fluids distinguishes between jammed packings of the same density. Our work provides an interpretation of how the ideal glass is related to the distribution of packings that takes into account of the constraints required to maintain a system in the metstable branch and how these impact nature of the accessible inherent structures.
Insight into the Structure and Properties of DNA
from the Topology of the Electron Density
Russell J. Boyd
Department of Chemistry, Dalhousie University
Halifax, Nova Scotia, Canada, B3H 4J3
Some recent applications of the analysis of the topological properties of the electron density to a variety of topics will be summarized. In particular, I will discuss our work on models for enzyme catalysis, extended weak interactions in DNA and quadruplex formation of the human telomere. The latter is a repetitive unit found at the end of chromosomes. Successive rounds of replication shorten the telomere until a certain critical length is reached, at which point the genetic material is no longer viable and various cell death mechanisms are invoked. However, telomerase is a specialized enzyme that is capable of extending telomeres and has been found particularly active within tumour cells, possibly contributing to their immortality. These tracts of DNA have a high guanine content, allowing them to form higher order structures based on the propensity of guanine to form quartets. Ultimately, quadruplexes can be formed in which several quanine quartets stack upon one another, connected by loop segments in various arrangements. Fortunately, once the telomere forms these higher order structures, telomerase is no longer able to recognize it as a substrate. Our current study investigates a basket-type quadruplex, consisting of three stacked quartets linked by two edgewise and one diagonal loop. The theory of atoms in molecules is used to study the atomic properties of the quadruplex as compared to its unfolded, single-stranded counterpart.


Computational photochemistry of complex biological systems: photoabsorption properties of asFP595 fluorescent protein
Ksenia B. Bravaya,1 Anastasia V. Bochenkova,1 Alexander A. Granovsky,1
Alexander V. Nemukhin1,2

1 Department of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation

2 N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russian Federation
Photoswitchable fluorescent proteins which can be reversibly switched between dark and fluorescent states under the light irradiation in the particular spectral region present a promising tool for living cell imaging and 3D data storage. In this study high level multiconfigurational quantum chemistry methods implemented in the framework of the hybrid QM/MM approach are used for modeling optical properties of the photoswitchable asFP595 fluorescent protein [1]. The augmented multiconfigurational quasidegenerate perturbation theory technique (aug-MCQDPT2) based on the original MCQDPT2 method [2] is employed for estimations of vertical S0-S1 excitation energies. The obtained new data are of importance for further studies of the asFP595 photoswitching mechanism.
Both isolated chromophore and the asFP595 protein are used as model systems to study the environmental influence on the photoabsorption properties. All relevant protonation states of the chromophore are considered. The aug-MCQDPT2 technique applied to the related red fluorescent protein chromophore in the gas phase provides the quantitative estimation of the experimentally observed absorption maxima position within 20 nm. The same accuracy is expected for the asFP595 chromophore. This methodology implemented in the framework of the QM/MM technique is used for modeling photoabsorption of the asFP595 protein. Computed estimates of the vertical excitation energies of the asFP595 protein are used for interpretation of the experimental absorption spectrum. The protein species with the chromophore in the anionic form are demonstrated to be responsible for the main absorption bands in both dark and fluorescent states of asFP595. A hypothesis on the photoswitching mechanism is suggested.

1. Lukyanov, K. A.; Fradkov, A. F.; Gurskaya, N. G.; Matz, M. V.; Labas, Y. A.; Savitskyi, A. P.; Markelov, M. L.; Zaraisky, A.G.; Zhao, X.; Fang, Y.; Tan, W.; Lukyanov, S. A. J. Biol. Chem. 2000, 275, 25879–25882.
2. Nakano, H. J. Chem. Phys. 1993, 99, 7983-7992

This work was partly supported by the Science and Innovation Federal Russian Agency (project # 02.522.11.2002), by the Program for Molecular and Cell Biology from Russian Academy of Sciences, and by the grant from the Russian Foundation for Basic Research (project #08-03-00914-a). A.B. and K.B. acknowledge financial support form the Russian Science Support Foundation.
Theoretical Description of Smart Catalysis on Enzymes with Iron-oxo Core
Ewa Broclawik,1 Tomasz Borowski1 and Mariusz Radon2
1Institute of Catalysis, Polish Academy of Sciences, Krakow, Poland
2Faculty of Chemistry, Jagiellonian University, Krakow, Poland
Enzymatic iron sites activated by molecular oxygen to Fe=O (iron-oxo) form are responsible for a variety of oxidation reactions. Two major factors should be considered in theoretical modeling of enzymatic oxidation reactions: intricate though flexible electronic structure of oxyferryl active sites with variable radical character, and steric constraints, responsible for high selectivity. In this presentation we address two problems: (i) challenges posed to quantum chemistry by the ground state electronic structure of Cpd I (heme), and (ii) steric demands to perform the three consecutive processes, hydroxylation, cyclization and desaturation on a single iron–oxo site in Clavaminic Acid Synthase (non-heme).

The location of a radical in the ground state of Cpd I either on the porphyrin ring, or on a lone pair of the axial S from cysteine, crucial for predicting and understanding its reactivity, was investigated by the advanced QM methodology, multi-state CASPT2 to calculate the properties of low lying states for a reliable model [1]. Our calculations showed porphyrin radical character of Cpd I and confirmed validity of simple B3LYP modeling in this case.

A reliable structure of the FeIV=O-succinate-substrate complex in Clavaminic Acid Synthase (CAS) based on MD structure served for B3LYP investigation of molecular mechanism of clavaminic acid biosynthesis [2]. This study shows how a novel mechanism that involves O-radical fragmentation overcomes steric hindrance and helps to make smart catalysis comprising three distinctly different steps on a single active site.

[1] M. Radon, E. Broclawik, J. Chem. Theory Comput. 2007, 3, 728-734.
[2] T. Borowski, S. de Marothy, E. Broclawik, C. Schofield, PEM Siegbahn, Biochemistry 2007, 46, 3682-3691
Plasmonic Nanostructures for Enhanced Spectroscopy and Biosensing
Alexandre G. Brolo
Department of Chemistry, University of Victoria, P.O.Box 3065, Victoria, BC, Canada, V8W 3V6
email: agbrolo@uvic.ca
Nanohole arrays milled in thin films of noble metal show an increase of light transmission at certain wavelengths. This phenomenon is called extraordinary optical transmission, and is due to the excitation of surface plasmons (SPs) by grating coupling. The conditions for surface plasmon resonance (SPR) depend on the dielectric constant at the interface. The adsorption of molecular species then shifts the resonance condition forming the principle for the SP-based sensors. In this work, we will report on our progress to the development of an integrated microfluidic system containing nanohole arrays as sensor elements. We will also discuss nanohole-based schemes for surface-enhanced Raman scattering. Finally, we will present preliminary results on the application of single-molecule SERS in electrochemical environment.
Coherent Control in Open Quantum Systems
Paul Brumer
Chemical Physics Theory Group
Department of Chemistry
University of Toronto
Toronto, On, Canada
The quantum control of the dynamics of isolated molecular systems has been shown, both computationally and experimentally, to be highly successful. The challenge now lies in the control of systems in contact with an external environment, where decoherence can destroy quantum interference effects. We will discuss recent developments in the control of molecular processes in open quantum systems, with examples chosen from general control theorems, controlled electrical currents in nanowires, controlled optical gain thresholds in semiconductor quantum dots, and controlled decoherence in nanomechanical resonators.

Complex Symmetric Forms, Jordan Blocks, Microscopic Self-Organization and the Laws of Relativity
Erkki J. Brändas
Department of Quantum Chemistry, Uppsala University, Uppsala, Sweden
The justification and rationale for analytically continuing quantum mechanics into the complex plane are established and examined1. This extension is described by a complex symmetric representation, which is derived and demonstrated to include general Jordan block forms of Segrè characteristics larger than one1,2. The relation to microscopic self-organization through the emergence of these forms is demonstrated1. Various applications in physics and chemistry1-4, where these “triangular units” occur are pointed out including a simple relation with the Klein-Gordon-Dirac relativistic theory confirming some dynamical features of both the special and the general relativity theory3,4.

1 Brändas, E., 1995, Relaxation Processes and Coherent Dissipative Structures, In: Lippert, E and Macomber, J. D. (Eds) Dynamics during Spectroscopic Transitions
(Berlin: Springer Verlag) 148-193; ibid. Applications of CSM Theory, 194-241.
2 Brändas, E., 2008, Complex Symmetric Forms and the Emergence of Jordan Blocks in Analytically Extended Quantum Theory, Int. J. Comp. Math., in press.
3 E. Brändas, Are Einstein’s Laws of Relativity a Quantum Effect?in Frontiers in Quantum Systems in Chemistry and Physics, eds. by J. Maruani et. al, Kluwer Academic Publishers, Vol. 18, (in press) 2008.
4 E. Brändas, Quantum Mechanics and the Special- and General Theory of Relativity, Adv. Quant. Chem. 54, (2008) 115-132.
Chemistry in Solution: Adaptive QM/MM Simulations
Rosa E. Bulo, Lucas Visscher
Department of Theoretical Chemistry, Faculty of Sciences,
Vrije Universiteit Amsterdam
De Boelelaan 1083,
1081HV Amsterdam,
The Netherlands
Computational chemistry at a multi-scale level enables the detailed study of complicated processes in large systems that mimic experiment. It can combine an accurate description of a reactive region at quantum mechanical level with the description of inactive regions at lower levels of accuracy. What is missing in the multi-scale toolbox is a rigorous adaptive method for the molecular dynamics investigation of systems in which material is allowed to flow across the border between QM and MM regions. The development of such a method affords, among many other things, accurate investigation of chemical reactions in solution. A scheme like this needs to fulfill a certain set of conditions. 1) As in all accurate molecular dynamics simulations the total energy should be conserved. 2) The chosen adaptive QM/MM potential should properly describe the system under investigation. 3) The simulation should not become too expensive. A single solution that fulfills all criteria can easily result in a very complicated potential energy description, involving steep energy changes at the border between regions. We present a simple scheme that meets all above requirements and reduces fast fluctuations in the potential to a minimum.
Semiclassical origins of density functional theory
Kieron Burke
Department of Chemistry and Physics, University of California, Irvine, USA
I will explain a new approach to thinking about density functional theory, showing that its success is closely related to semiclassical approximations. This approach explains the need to generalize gradient approximations, and led to the recent PBEsol (Phys. Rev. Lett. 100, 136406(2008)). I will also outline a promising alternative to orbital-free density functional theory that greatly improves upon the usual density functional approach.
Quantum Monte Carlo for realistic chemical systems
Michel Caffarel
Laboratoire de Chimie et Physique Quantiques CNRS-IRSAMC,
Université de Toulouse, France.
In this talk I discuss recent applications of the Fixed-Node Diffusion Monte Carlo (FN-DMC) approach to some realistic chemical problems. The systems studied include transition-metal containing molecules (CuCl2, Cr2, hemocyanin, etc.), polyoxygen species (such as the O4 molecule) and organic molecules (acrolein, polyacetylene). We discuss various importants aspects associated with the use of QMC for realistic chemical problems: the problem of calculating reliable small differences of energies within the fixed-node approximation, the visualization of the electronic distributions via charge and spin densities, the construction of maximum probability domains, or the use of the Electron Pair Localization Function (EPLF).
References:
(1) M. Caffarel, R. Hernandez-Lamoneda, A. Scemama, and A. Ramirez-Solis, Phys. Rev. Lett. 99, 153001 (2007)
(2) T. Bouabca, M. Caffarel, N. Ben Amor, and D. Maynau ``A quantum Monte Carlo study of the n ----> π* (CO) transition in propenal: Role of the nodal hypersurfaces'', preprint
(3) R. Assaraf, M. Caffarel, and A. Scemama, Phys. Rev. E 75, 035701 (2007).
(4) A. Scemama, M. Caffarel, A. Savin, J. Comput. Chem. 28, 442 (2007).
(5) M. Caffarel, A. Scemama, and Alejandro Ramirez-Solis, ``Bonding in tetraoxygen: Analyzing the O4 ----> O2(X3Σg-) + O2(X3Σg-) reaction using the Electron Pair Localization Function'', preprint.
H2O Nucleation Around Noble Metal Cations
P. Calaminici1, P.E. Oropeza Alfaro1, M. Juarez Flores1, A.M. Koster1, M. Beltran2, J.U. Reveles3, S.N. Khanna3
1 Departamento de Quimica, CINVESTAV,Av. Instituto Politecnico Nacional 2508, A.P. 14-740, Mexico D.F. 07000, Mexico
2 Instituto de Investigaciones en Materiales, UNAM, A.P. 70-360, Mexico D.F. 04510, Mexico
3 Physics Department, Virginia Commonwealth University, Richmond VA 23284-2000 U.S.A.
First principle electronic structure calculations have been carried out to investigate the ground state geometry, electronic structure and binding energy of noble metal cations (H2O)n+ clusters containing up to 10 H2O molecules. The calculations are performed with the density functional theory code deMon2k [1]. Due to the very flat potential energy surface of these systems special care to the numerical stability of energy and gradient calculation must be taken. The comparison of the results obtained with Cu+, Ag+ and Au+ will be discussed. This investigation provides insight into the structural arrangement of the water molecules around these metals and a microscopic understanding of the observed incremental binding energy in the case of the gold cation based on collision induced dissociation experiments.

[1] A.M. Koster, P. Calaminici, M.E. Casida, R. Flores-Moreno, G. Geudtner, A. Goursot, T. Heine, A. Ipatov, F. Janetzko, J. Martin del Campo, S. Patchkovskii, J.U. Reveles, A. Vela and D.R. Salahub, deMon2k, The deMon Developers, Cinvestav, 2006
Thermodynamics and Kinetics of Elementary Steps in Catalysis
Charles T. Campbell
Department of Chemistry
University of Washington
Seattle, WA 98195-1700 USA
A survey of experimental and theoretical results concerning the thermodynamics and kinetics of surface chemical reactions of importance in catalysis will be presented. Topics include: (1) microcalorimetry studies of adsorption energies of small molecules and metal atoms on single crystal surfaces, and their comparison to values calculated using DFT; (2) studies of catalyst sintering kinetics; (3) systematic trends in pre-exponential factors for the rate constants of surface reactions; (4) a method for analyzing multi-step reaction mechanisms that mathematically quantifies the extent to which each elementary step controls the rate; and (5) proof that the adhesion energy of a compound (e.g., a metal oxide) to any interface it likes to wet (for example, the metal underlying an oxide coating) allows it to be thermodynamically stable in ultrathin film form (1-2 nm) at conditions far removed from the range of bulk stability (e.g., at 1000-fold lower O2 pressure).

Related papers:
1. Energetics of Cyclohexene Adsorption and Reaction on Pt(111) by Low-Temperature Microcalorimetry, O. Lytken, W. Lew, J. J.W. Harris, E. K. Vestergaard and C. T. Campbell, J. Am. Chem. Soc. (in press).
2. A Kinetic Model for Sintering of Supported Metal Particles with Improved Size-dependent Energetics, and Applications to Au on TiO2(110), S. C. Parker and C. T. Campbell, Phys. Rev. B 75, Art. No. 035430 (2007).
3. n-Alkanes on Pt(111) and on C(0001) / Pt(111): Chain Length-dependence of Kinetic Desorption Parameters, S. L. Tait, Z. Dohnálek, C. T. Campbell, B. D. Kay, J. Chem. Phys. 125, Art. No. 234308 (2006).
4. Finding the Rate-Determining Step in a Mechanism: Comparing DeDonder Relations with the “Degree of Rate Control”, C. T. Campbell, J. Catal. 204, 520-4, 2001
5. Transition metal oxides: extra thermodynamic stability as thin films, Charles T. Campbell, Physical Review Letters 96, 066106 (2006).

• Work supported by NSF and DOE-OBES Chemical Sciences Division.
Electronic transition energies: A study of the performances of 26 DFT functionals, CIS, CIS(D), RPA and EOM-CCSD methods compared to experiments.
Marco Caricato1,2, Gary W. Trucks1, Mike J. Frisch1 and Kenneth B. Wiberg2
1Gaussian, Inc., USA

2Department of Chemistry, Yale University, USA
This work reports a comparison among wavefunction and DFT single reference methods for vertical electronic transition energy calculations towards singlet states. A series of 11 small organic molecules are used as test cases, where accurate experimental data in gas phase are available. We compared CIS, RPA, CIS(D), EOM-CCSD and 26 density functionals of the type LSDA, GGA, M-GGA, H-GGA, HM-GGA and with separated short and long range exchange. The list of functionals is obviously not complete, but it spans more than 20 years of DFT development. Large differences in the results were found between the various functionals. The aim of this work is therefore to shed some light on the performance of the plethora of functionals available and compare them with some traditional wavefunction based methods on a molecular property of large interest as the transition energy.
Theoretical simulations of Resonant Inelastic X-Ray Scattering spectra in K-shell Cl Core-Excited chlorinated molecules
Stephane Carniato
Laboratoire de Chimie Physique,
Matiere et Rayonnement, UMR 7614 du CNRS, Universite Pierre et Marie Curie, 11, rue Pierre et Marie Curie, 75231 Paris Cedex 05, France
Computing potential energy surfaces (PES) is a major and essential task in theoretical physical chemistry. While the technique is well suited for ground and low lying excited states, accurate ab-initio calculations for core-excited states is less usual. However, knowledge of these PES is crucial for molecular dynamics studies after x-ray absorption. Experimental determination of the potentials would be extremely valuable but is yet to be achieved.

A key point for experimental exploration of core-excited PES from x-ray measurements is high spectral resolution, which is limited both by physical and instrumental factors. Continuous technical advances have improved the spectral resolution of x-ray spectrometers [1,2], leaving only two physical limitations as major factors, namely, lifetime and vibrational broadening. However, the lifetime broadening is very large (~0.5-1 eV) for inner shells with binding energies in the tender-hard x-ray region, i.e., 10 times larger than for inner shells in the soft x-ray region, and is comparable to, or larger than, the vibrational spacing of small molecules. This, in such case, reduces strongly the resolution obtainable for mapping PES using regular x-ray absorption techniques. X-ray Raman scattering has an great advantage over x-ray absorption: it provides lifetime-broadening removed resolution [3,4]. Furthermore, vibrational broadening in Resonant x-ray Raman scattering (RXRS) is quenched when PES involved in the process are parallel: (1) away from resonance if both ground and final states potential surfaces are parallel; (2) on resonance if the core-excited and final states are parallel. As recently reported by Simon et al.[5] RXRS measurements in tender X-region can greatly take advantage of this effect to investigate ultrafast molecular dynamics. High resolution decay spectra obtained with long-pulse synchrotron light pulses coupled with calculations based on the concept of an effective duration time of the scattering process provide a unique look at very short time nuclear dynamics a posteriori [6,7] which opens a new way of studying nuclear dynamics of core-excitation of polyatomic molecules, and will attract considerable attentions.

Based on theoretical simulations, the purpose of this presentation is to show how x-ray Raman technique can provide a tool to map the PES of core-excited states, using the concept of effective duration time of the x-ray scattering process. We will propose a scheme where selected vibrational states are populated by strong infrared (IR) laser pulses, and x-ray Raman scattering probes the core-excited states [8].

It will be also shown that angular polarized RIXS analysis of the Kα X-ray Raman scattering spectra opens a unique opportunity for giving with precision 2p-1 partition in spin-orbit component. In particular, supported by theoretical calculations we will show that small deviation of the spin-orbit ratio in 2p inner-shell absorption spectra between HCl and CF3Cl can be interpretated as molecular field and fine singlet-triplet exchange splitting effects.

Finally, related with observation of femtosecond-scale nuclear dynamics observed using RXRS (nuclear motion of a few picometers) for diatomic (HCl) molecule [5], and property for potential energy surface mapping detailed before, we will discuss how we expect that vibrational population inversion by femto-second laser pump followed by RIXS probing source [8] could evidence change in spin-orbit ratio.

References:
[1] J. Nordgren et al.,Rev. Sci. Instrum. 60, 1690 (1989).
[2] S. Brennan et al., Rev. Sci. Instrum. 60, 2243 (1989).
[3] P. Eisenberger et al., Phys. Rev. Lett. 36, 623 (1976).
[4] S. Aksela et al., Phys. Rev. Lett. 74, 2917 (1995).
[5] M. Simon, L. Journel, R. Guillemin, W.C. Stolte, I. Minkov, F. Gel'mukhanov, P. Salek, H. Agren,S. Carniato, R. Taieb, A. C. Hudson, and D. Lindle, Phys. Rev. A 73, 020706 (2006).
[6] F. Gel'mukhanov and H. Agren, Phys. Rep. 312, 87 (1999).
[7] F. Gel'mukhanov et al., Phys. Rev. A 59, 380 (1999).
[8] Carniato S., Taieb R., Guillemin R., Journel L., Simon M. and
Gel'mukhanov F., Chem. Phys. Lett., 439, 402 (2007).
Theoretical Investigation of self-assembled peptide Nanostructures for Biotechnological and Biomedicine Applications.
Jennifer A. Carvajal1, Tahir Cagin1,2
[1] Chemical Engineering, Texas A&M University, USA
[2] Materials Science and Engineering. Texas A&M University, USA
Self-assembled peptide nanostructures represents a key materials in the area of Biotechnology and Biomedicine due to the wide set of applications, ranging from molecular Bioelectronics to Drug Delivery. Peptides constitute one of the most useful building blocks in nature, with excellent chemical-physical stability and diversity.

Conformational Properties of Peptide Nanotubes such as structural stability, thermodynamic properties and transport properties of water within the tubes, were studied by using molecular dynamics simulation techniques. The cyclic peptide nanotube is composed initially of peptide subunits, cycle [-(L-Gln-D-Ala-l-Glu-D-Ala)2-], which adopt a low-energy ring-shaped conformation, where all backbone amide functionalities lay approximately perpendicular to the flat plane. The transport of water was favored compared with equivalent nano-channels, such CNTs, due the hydrophilic character of the hollow tubular zones of the peptide nanotubes. The prediction of conformational properties for Peptide Nanostructures will help to optimize material design. This should benefit the rational design of applicable Peptide based materials.
DFT STUDY OF THE σ-π AND π-π INTERACTIONS BETWEEN HETEROAROMATIC POLYCYCLIC MOLECULES: IMPLICATIONS ON ASPHALTENE STABILITY
Olga Castellanor1 and Humberto Soscún2
1PDVSA Intevep. LOS TEQUES, Apdo. 76343, Venezuela. castellanool@pdvsa.com

2Centro Nacional de Tecnología Química, Ministerio del Poder Popular para Ciencia y Tecnología CNTQ, Esquina El Chorro, Torre MCT. Apdo. 1010, Caracas, Venezuela. hsoscun@mct.gob.ve
The asphaltenes fraction is the heaviest and most polar part of the crude oil and it is the responsible for many operational problems in the oil industry. The asphaltenes fraction, which is dominated by molecular interactions, contains polyaromatic condensed rings with short aliphatic chains and polar heteroatoms such as nitrogen and sulphur. In order to understand at molecular level the origin of the interactions between asphaltenes molecules, in this work, we study the energetic stabilities of a series of heteroaromatic polycyclic complexes with two and three fused rings. Nafthalene (N), quinoline (Q) and benzothiophene (BT) were the bicyclic molecules chosen, whereas anthracene (A), acridine (Ac) and dibenzothiophene (DBT) were selected to model the three ring systems.
We study the optimized structures and interaction energies of the complexes formed between the two ring and three ring molecules, taking into account the σ-π and π-π possible interactions. The interaction energies were obtained by varying the minimum atomic distance (contact distance) between the interacting species from 0.2 to 8.0 Å. Three possible interactions were considered (parallel-parallel, anti parallel and T-Shape).
All the calculations were carried out using Density Functional Theory (DFT) with the self-consistent GGA Perdew-Wang 91 functional. The values of interaction energies at equilibrium point for the bicyclic ring complexes go from -4,47 Kcal/mol (N-BT) to -0.51 kcal/mol(Q-Q) and for the three ring complexes the range of the interaction energies goes from -6.07 kcal/mol (A-DBT) to -0.60 kcal/mol (DBT-DBT). For the studied complexes, we found that the strongest interaction energy corresponds to the A-DBT complex with a value of -6,07 kcal/mol. We can conclude that the interaction energies depend of the electronic nature of the heteroatom on the aromatic ring. The presence of sulphur S induces energetic stability to the complexes, meanwhile the nitrogen N induces repulsion when they interact with an aromatic non heteroatom molecule. Therefore, we can say that asphaltenes stability could increase with the content of sulfur atoms in the aromatic systems.
On the Interaction of Magnetic Iron Clusters with Hydrocarbons:
Fe4–Methane, Fe4-Propane, and Fe6-(Benzene)n, n=1,2,3 and 4
Miguel Castro, Alfredo Guevara, and Israel Valencia
Departamento de Física y Química Teórica, DEPg. Facultad de Química
Universidad Nacional Autónoma de México, México D.F., C.P. 04510, México

In this work was studied, by means of Density Functional Theory, the interaction of unsaturated and saturated hydrocarbons with the superparamagnetic iron clusters. The studied systems were Fe4–CH4, Fe4-C3H8, and Fe6-(Benzene)n, n=1,2,3 and 4. All-electron calculations were realized with the BPW91/6-311++G(2d,2p) method. In the 2S=14 (S=total spin) Fe4-CH4 ground state CH4 and C3H8interacts with Fe4 forming two weak CH---Fe bonds. For the higher 2S=12 and 10 energy states, in addition to CH---Fe, weak Fe---C bonding appears. The vibrational pattern of CH4 and C3H8 are perturbed significantly, and their dipole moments show a big increase. Thus, Fe4 is able to activate the C-H bonds of these unsaturated hydrocarbons, which is important for the efficiency of the combustion processes. The interaction of benzene with Fe6 clusters also will be discussed. The results indicate that the adsorption of benzene produces a considerable reduction of the magnetic moment of the cluster. Also the ionization energies and electron affinities are reduced. These behaviors are rationalized in terms of the C-Fe σ bond formation.
Computation of the conductivity of dense liquid hydrogen using Quantum Monte Carlo
Fei Lin1, D. M. Ceperley1, Miguel Morales1, Carlo Pierleoni2
1 University of Illinois Urbana-Champaign, USA
2 Universita di Laquila, Italy
The properties of warm dense hydrogen are crucial for understanding the giant planets and other related objects recently observed and for experiments concerning inertially confined fusion. Some of the outstanding questions are: how does hydrogen go from a molecular liquid to an atomic liquid. Is it a phase transition or a crossover? How high is the melting temperature of the crystal versus the pressure? Is there a low temperature liquid at high pressure? Experimental probes are limited; diamond anvil experiments to about 3Mbars and shock studies to the Hugoniot curve.

In recent years, we have developed a new method, Coupled Electron-Ion Monte Carlo [1], to allow coupled simulations of correlated electrons using reptation quantum Monte Carlo and ions at lower temperatures. We have performed simulations of dense hydrogen down to temperatures of 300K[2-3] and for pressures from 100KBar to 10MBars.

In this contribution, we discuss computation of the conductivity with the Kubo formula and quantum Monte Carlo. In this approach, one needs to compute the excitation energies of the dense liquid, and the current-current matrix elements. To compute these, we use reptation quantum Monte Carlo and use the Correlation Function Monte Carlo[4] to determine estimates of these quantities. Even with the sign problem, and limited averaging over protonic configurations, the results are in reasonable agreement with shock wave measurements[5] and show the insulator-metal transition.


1. C. Pierleoni and D. M. Ceperley, ChemPhysChem, 6 1872 (2005); Lecture Notes in Physics, 703, 641-683 (2006).
2. C. Pierleoni, D. M. Ceperley and M. Holzmann, Phys Rev. Letts. 93, 146402 (2004).
3. K. Delaney, C. Pierleoni and D. M. Ceperley, Phys. Rev. Letts. 97, 235702 (2006).
4. D. M. Ceperley and B. Bernu, J. Chem. Phys. 89, 6316 (1988).
5. S. T. Weir, A. C. Mitchell, and W. J. Nellis, Phys. Rev. Lett. 76, 1860 (1996); W. J. Nellis, S. T. Weir, and A. C. Mitchell, Phys. Rev. B 59, 3434 (1999).
Transition Metal Clusters: the Next Frontier of Ab Initio Approach
Grzegorz Chalasinski
Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszawa, Poland

Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
Transition metal (TM) clusters are of great importance as models and precursors of variety of metallic aggregates: from small clusters, to larger nanostructures, and the bulk. Because of their complex electronic structure, related to intra- and inter-shell electron-correlation and relativistic effects, the clusters elude approximate approaches that neglect any of these factors, and present unprecedented challenge for quantum chemistry. We will discuss these issues starting from the perspective of TM-helium interactions that expose the intricate anisotropy of TM atoms in weak interactions, and helps to evaluate the usefulness of different ab initio methods. The metal-helium interactions are presently also of practical interest as helium is the buffer gas employed to cool candidates for Bose-Einstein condensates (BEC). Next, we will have a look into the realm of TM dimers with the emphasis on the spin-parallel forms that, again, are of importance in the quest for BEC, but also relevant in the context of spinpolarized metallic state. Finally, we will have a glance at atomic metal trimers and anomalous many-body interactions that render them unique, and particularly difficult objects to examine.
Principles of Cooperative and Noncooperative Protein Folding
Hue Sun Chan
Departments of Biochemistry, and of Molecular Genetics
University of Toronto, Toronto, Ontario M5S 1A8 CANADA
http://biochemistry.utoronto.ca/chan/bch.html
Many small single-domain proteins undergo cooperative, switch-like folding/unfolding transitions with very low populations of intermediate, i.e., partially folded, conformations. Contrary to widely held expectations, the experimental phenomenon of cooperative, two-state-like folding is not accounted for by common notions about driving forces for folding. I will highlight how protein chain models with pairwise additive interactions are insufficient to account for the folding cooperativity of natural proteins, and how models with nonadditive local-nonlocal coupling may rationalize cooperative folding rates that are well correlated with native topology. To understand protein structure and function in general, however, it is important to also realize that not all proteins fold cooperatively. Recent experiments indicated that some proteins may fold noncooperatively in a "downhill," one-state manner; and appreciable variations in folding cooperativity were detected among natural proteins with approximately forty residues. The latter observation suggested that the behaviors of those proteins are valuable for delineating the contributing factors to folding cooperativity. To explore the role of native topology in a protein's propensity to fold cooperatively, we compared folding/unfolding thermodynamics simulated using three classes of native-centric coarse-grained chain models with different interaction schemes. We found a robust, experimentally valid rank ordering of model folding cooperativity independent of the interaction schemes tested, arguing strongly that native topology places significant constraints on how cooperatively a protein can be physically designed to fold.

Background references
Chan, Shimizu and Kaya (2004) Methods Enzymol 380, 350-379
Knott and Chan (2006) Proteins 65, 373-391
Ultrafast Electronuclear Dynamics of H2 Double Ionization
Eric Charron, Sebastien Saugout, Christian Cornaggia, and Annick Suzor-Weiner
Universite Paris-Sud - CNRS
LPPM Batiment 210
91405 Orsay cedex
France
We will present a detailed account of the ultrafast electronic and nuclear dynamics of H2 laser-induced double ionization. We have studied this process using a time-dependent wave packet approach that goes beyond the fixed nuclei approximation. The double ionization pathways are analyzed by following the evolution of the total wave function during and after the pulse. The rescattering of the first ionized electron produces a coherent superposition of excited molecular states which presents a pronounced transient H+H- character. This attosecond excitation is followed by field-induced double ionization and by the formation of short-lived autoionizing states which decay via double ionization. These two double ionization mechanisms may be identified by their signatures imprinted in the kinetic-energy distribution of the ejected protons.
Promise and peril in the simulation of nucleic acid structure, dynamics and interactions
Thomas E. Cheatham, III
Department of Medicinal Chemistry
Department of Pharmaceutics and Pharmaceutical Chemistry
College of Pharmacy
University of Utah
Salt Lake City, UT, USA 84124
Computers keep getting faster allowing ever longer simulations of nucleic acid structure. As we push farther, we expose limitations in the methods, the force fields and the simulation workflow. We will discuss some of the problems found over the past few years including incorrect RNA loop geometries, anomolous crystallization, and outline our attempts to improve the force fields and simulation methods. Finally we hope to discuss emerging plans to improve or facilitate the simulation workflow including running the simulations, processing the large sets of resulting data, and ultimately dissemination. This work is supported by NIH 1R01-GM081411, NIH 1R01-GM079383, and NSF LRAC MCA01S027.
Photoelectrocatalysis of Titanium Oxide Based Nanomaterials
Aicheng Chen
Department of Chemistry, Lakehead University, Canada
Photocatalysis has gained considerable attention in recent years owing to its widespread environmental applications in air purification, water disinfection and hazardous waste remediation. In this presentation, we report on the synthesis of different TiO2-based nanomaterials and their photoelectrocatalytic activities. The kinetics of the photoelectrocatalytic degradation of nitrophenols on TiO2 nanotubes was studied by in situ UV-Vis spectroscopy and chemometrics. A partial least squares (PLS) model was built up to determine the concentration profiles of the nitrophenols during the photoelectrocatalytic oxidation. Our study has shown that UV-vis spectroscopy coupled with PLS calibration can be used to in situ monitor the concentration changes, providing a novel approach to studying the competitive effects of organic pollutants during the photo-electrochemical treatment of wastewater. To further improve the photocatalytic activity of TiO2 nanomaterials, we have successfully synthesized F-doped and C-doped TiO2 nanostructures. The electronic states of anatase titania crystal with or without doped carbon were calculated in order to understand how carbon is doped into TiO2 nanostructures. The fabricated F-doped and C-doped TiO2 nanomaterials show enhanced visible light response and exhibit much higher photoelectrochemical activity for water-splitting and the photo-degradation of organic pollutants than P-25, which is currently considered to be one of the best commercial TiO2 photocatalysts.
Time-dependent density-functional theory for open system and its application to molecular electronics
GuanHua Chen
Department of Chemistry, The University of Hong Kong
We have developed a rigorous TDDFT formalism for open systems. It is based on the equation of motion for reduced single-electron density matrix. The resulting method has been used to simulate the transient currents through molecular devices.
First Principle Study of Torsional Potential Energy Surface of
sec-Butyl Radical
Yakun Chen and Yan Alexander Wang
Department of Chemistry, University of British Columbia, Canada
First principle calculations using spin polarized HF, MP2, CCSD and a variety of density functionals(DFs) with different basis sets are carried out to investigate the conformation of sec-butyl radical. All the wave function theory (WFT) methods employed predict a cis-like stable conformation with dihedral angle of about 47 degrees in addition to more stable trans-like and gauche conformations. On the other hand, most of the popular DF methods predict only the latter two equlilibrium structure. Using the WFT methods, the sec-butyl is found to overcome a very low energy barrier along the torsional potential energy curve from cis-like to gauche conformation. The inclusion of exact exchange and asymtotically corrected correlation functionals is found important for DF methods to locate this cis-like structure. The basis set effect is also discussed using popular B3LYP and MP2 Hamiltonians. Compared to the available hyperfine coupling constants of muoniated radical isotopmers, the existence of cis-like conformation is confirmed and the vibrational correction is found to be crucial to the stability prediction among the conformations of muoniated sec-butyl radical.
Theoretical Study on Orbital Dependent Magnetic Properties of Molecular Clusters with Unquenched Orbital Angular Momentum
Fan Wang, Bing-Wu Wang, Zhi-Da Chen
Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
In molecular magnetism the magnetic properties for a number of the magnetic coupling systems have been extensively investigated based on Ising and Heisenberg models. However, the situation is quite different for the systems involved in the unquenched orbital angular momentum, and the “spin-only” description from both the models proves to be invalid. In general, the orbitally dependent exchange interactions, orbital magnetic contributions and spin-orbit coupling should be taken into account in the models. In order to shed light on magnetic properties of the magnetic coupling molecular cluster containing the constituent metal ion with unquenched orbital angular momentum, we first introduce a general effective Hamiltonian. On the basis of the irreducible tensor operator approach to solve Hamiltonian we have coded a program package BJMAG, where a new coupling scheme to further make Hamiltonian matrix block diagonalization was used and we proposed a new numerical self-consistent method to calculate inter-cluster interaction to describe low-temperature magnetic behavior.

The ground state 4T1g of the octahedral high-spin Co(II) ion is orbitally degenerate, so the Co(II)-clusters reveal strong orbital dependent magnetic properties. As representative systems three Co(II)-clusters: [Co3(Hbzp)6][ClO4]2•2CH3OH•H2O(1), [Co4L(N3)4(CH3CN)4](ClO4)4•2H2O(2) and [Co3(L-N2O)4(CH3OH)2]•2B(ph)4•2H2O(3) have been synthesized and studied by using BJMAG. We first performed the best-fit procedure for experimentally variable-temperature magnetic susceptibilities. In order to further elucidate the individual role of each interaction in the employed model, the effects of the key factors governing the magnetic properties on variable-temperature magnetic susceptibilities were examined in detail.

[1] Wang F, Chen ZD*, Chem. Phys. 2006, 327, 427-433.
[2] Wang F, Wang BW*, Wang MW, Chen ZD*, Chem. Phys. Lett. 2008, 454, 177-183.
Monitoring and Risk Assessment of PAHs
in Cooked Fish and Shellfish
Jangduck Choi, Soojung Hu, Kwangho Lee, and Dongmi Choi
New Hazard Chemical Division, Department of Food Safety Evaluation , Korea Food & Drug Administration.
The following concentrations of some PAHs were investigated ; [benzo(a)anthracene, chrysene, benzo(b)fluoranthene, benzo(k)fluoranthene, benzo(a)pyrene, dibenzo(a,h)anthracene, benzo(g,h,i)perylene, indeno(1,2,3-c,d)pyrene] in fish(n=168) and shellfish(n=40). The methodology involved saponification and extraction with n-hexane, clean-up on Sep-Pak Florisil Cartridges and determination by HPLC/FLD(High Performance Liquid Chromatography /Fluorescence Detector). Overall method recoveries for 8 PAHs spiked into these products ranged from 88 to 112%. The mean levels of benzo(a)anthracene, chrysene, benzo(b)fluoranthene, benzo(k)fluoranthene, benzo(a)pyrene, dibenzo(a,h)anthracene, benzo(g,h,i)perylene and indeno(1,2,3-c,d)pyrene in cooked fish were ND, ND, 0.0009, ND, 0.01, ND, ND, ND and in cooked shellfish were 1.84, 3.51, 0.81, 0.38, 0.39, 0.04, 0.20, ND, respectively. This study used both TEFs(Toxic Equivalency Factors) proposed by U.S.EPA for carcinogenic effects. For the exposure assessment of PAHs by ingestion of cooked fish and shellfish, the average body weight for each age group seperating as 1-6 yrs, 7-12 yrs, 13-19 yrs, 20-64 yrs, and 64-79 yrs and average intake from report on national health and nutrition survey was used.
Aqueous multiscale organization and its influence upon ion sorption to mineral surfaces
Aurora Clark*, Matthew Wander, Brandon Kvamme, Adriana Dinescu**
*Washington State University, Department of Chemistry
**Idaho National Laboratory
In general, the environmental chemistry of Ln(III) is of less concern than for actinide contaminants. However the aqueous:mineral interfacial behavior of Ln(III) can serve as a surrogate for actinide species and yield fundamental insight into the factors that influence the free energy of ion adsorption in the absence of redox phenomena. Recently we have used density functional theory to characterize the thermodynamic and structural features of aqueous Ln(III) across the entire series.[1-2] This ab initio information has been used to develop highly optimized classical potentials for the Ln(III)-water interaction, allowing for potential of mean force simulations to be performed for the adsorption of Ln(III) to the 001 surface of quartz. Trends in the free energy of ion adsorption and its correlation to structural (re)organization of water along the reaction pathway will be discussed in this work.

[1] Clark, A. E. “Density Functional and Basis Set Dependence of Hydrated Ln(III) Properties.”J. Comp. Theor. Chem. 2008 ASAP article.
[2] Dinescu, A.; Clark, A. E. “Thermodynamic and Structural Features of Aqueous Ce(III).” J. Phys. Chem. A. 2008, accepted.
Design and Synthesis of Optimal Bimodal Porous Catalysts
Marc-Olivier Coppens
Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, U.S.A.

Recent years have witnessed a revolution in our abilities to impose the structure of porous materials at the nanoscale. Properties like nanopore size and atomistic structure of the pore surface directly influence the intrinsic function of nanoporous materials, e.g., the intrinsic activity and selectivity in heterogeneous catalysis. To have a large specific surface area, these materials enclose an enormous array of interconnected nanopores. Because diffusion through these pores is slow, the benefits of nanoscale control are lost if the larger scales are neglected. Larger pore channels are needed to transport molecules toward and away from the catalytic sites, fast enough to counter diffusion limitations. The questions are what the size distribution of these pores should be, how they should be spatially distributed, and how these bimodal, hierarchical materials are most conveniently manufactured? This paper will address the optimization of the multi-scale pore structure of porous materials, from pore surface roughness to the largest pore channels traversing a particle, in order to meet a desired target, such as maximum yield or selectivity in a chemical process. Diffusion through the pores is studied using methods from statistical physics. The multi-scale optimization is based on explicit pore network models, as well as continuum models, multi-grid methods being particularly powerful. It will be demonstrated that significantly more might be achieved with much less material, in a way that is practically realizable. For example, twice the amount of nitrogen oxides can be removed from exhaust gases, with half the amount of catalyst at typical commercial operating conditions.
New correlation functionals for DFT calculations
Vincent TOGNETTIa, Pietro CORTONAb and Carlo ADAMOa
a Laboratoire d’Electrochimie et de Chimie Analytique, UMR 7575, Ecole Nationale Supérieure de Chimie de Paris, 11 rue P. et M. Curie, F-75231 Paris Cedex 05, France.
b Laboratoire Structure, Propriété et Modélisation des Solides, UMR 8580, Ecole Centrale Paris, Grande Voie des Vignes, F-92295 Chatenay-Malabry, France.
A crucial step of any DFT calculations is the choice of the approximate functionals to be used. In standard calculations, one has to select an expression for the exchange-correlation energy. In addition, if the calculations are performed in the framework of the subsystem formulation of the DFT [1], an approximate expression for the so-called non-additive kinetic energy is also required. In this communication I will focus on the correlation energy, a functional for which two new approximations have been recently proposed [2,3]. The first one is a local functional which was derived by applying a Colle-Salvetti-like approach to the homogeneous electron gas. Quite unusually, an expression for the kinetic part of the correlation energy was at first obtained. Then, the total correlation energy was deduced by means of the virial theorem. The second functional belongs to the GGA family and was deduced by an approach similar to that adopted by Perdew, Burke, and Ernzerhof [4]: an analytical expression depending on the density, the reduced density gradient, and the relative spin-polarization was chosen and the constants appearing in it were determined without fitting reference data, but requiring that some physical constraints are satisfied. Both these functionals will be described and their performances will be analyzed and compared with those of the standard LDA and of GGA or hybrid functionals. Improvements are found for a variety of properties including some ones for which the orbital-free methods are proved to be particularly appropriate.

[1] P. Cortona, Phys. Rev. B 44, 8454 (1991).
[2] S. Ragot and P. Cortona, J. Chem. Phys. 121, 7671 (2004).
[3] V. Tognetti, P. Cortona, and C. Adamo, J. Chem. Phys. 128, 034101 (2008).
[4] J. P. Perdew, K. Burke and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996).
Investigation of Peierls instability in polyacetylene and carbon nanotubes using exact exchange functionals
Michel Côté(1), Guillaume Dumont(1), Paul Boulanger(1) and Matthias Ernzerhof(2)
(1) Département de physique, (2) Département de chimie, Université de Montréal
We present a first-principles study of Peierls distortions in trans-polyacetylene, polyacene and armchair (n,n) carbon nanotubes. All calculations were done within density-functional theory using a gaussian basis set. We show that while density only functionals (LDA, GGA) cannot reproduce the experimentally mesured dimerization in trans-polyactetylene, hybrid functionals including Hartree-Fock exchange can give the correct geometry. These findings suggest that armchair (n,n) carbon nanotubes could have a nonsymmetric ground state; in contradiction with what is commonly accepted. Indeed, the B3LYP functional (which includes 20% of exact exchange) opens a gap of 0.26 eV and 0.12 eV for the (3,3) and (6,6) carbon nanotubes respectively. Accordingly, dimerization amplitudes of 0.005 Angstroms and 0.002 Angstroms are obtained. It is found that the dimerization and the band gap are proportional to the the amount of exact exchange included in the functional.
Local Coupled Cluster Theory and Optical Activity
T. Daniel Crawford and Nicholas J. Russ
Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, U.S.A.
The most significant obstacle to the application of advanced quantum chemical methods such as coupled cluster theory to large molecules is the "polynomial scaling wall" -- the high-degree polynomial scaling of methods such as coupled-cluster theory with the size of the system. Although methods that diminish this wall by exploiting the localizability of electron correlation have yielded impressive results for energetics and potential surfaces, their efficacy for numerous other properties remains unclear. This paper will discuss recent progress in our group1 toward the development of locally correlated coupled cluster models for chiroptical response, viz. optical rotation and circular dichroism spectra of large chiral molecules.2

1 T.D. Crawford, M.C. Tam, and M.L. Abrams, J. Phys. Chem. A 111, 12057-12068 (2007).
2 N.J. Russ and T.D. Crawford, Phys. Chem. Chem. Phys. 10, 3345 (2008).

Water Adsorption and Ice Nucleation on Kaolinite: A Grand Canonical Monte Carlo study.
T. Croteau, A. K. Bertram, G. N. Patey
Department of Chemistry, University of British Columbia, Canada
Adsorption of water and possible ice nucleation is studied using the grand canonical Monte Carlo (GCMC) method on four defect-free kaolinite surfaces as a function of relative humidity at 298 K and 235 K. Results for both the SPC/E and TIP5P-E water models are compared and demonstrate that the Si-surface is hydrophobic and that the Al-surface ((001) plane) and both protonated and unprotonated edges ((100) plane) are hydrophilic. The edges most strongly adsorb even at very low relative humidities. This suggests that kaolinite particles might play a role in heterogeneous chemistry involving water. Adsorption on the Al-surface exhibits properties of a first-order process with evidence of collective behavior, whereas adsorption on the edges is essentially continuous and appears dominated by strong water lattice interactions. Only for the Al-surface are some hexagonal rings formed amongst the water molecules. However, the dimensions of the rings match the surface rather than hexagonal ice ( Ih). Consequently, a misfit of 14 % is calculated between hexagonal pattern of water adsorbed on the Al-surface and the basal plane of ice Ih which suggest that kaolinite particles are not to be expected to be good ice nuclei based on a match with ice Ih. The presence of "active sites" such as cracks, pores, steps, etc., is a possible explanation for ice nucleation on kaolinite.
Properties of Quantum Clusters in their Ground State
Javier Cuervo,1 Pierre-Nicholas Roy1 and Massimo Boninsegni2
1Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
2Department of Physics, University of Alberta, Edmonton, Alberta, Canada, T6G 2J1
The energetics, structure and imaginary-time dynamics of Pure and binary mixtures of clusters of paraH2 and orthoD2 molecules have been studied by means of the Path integral ground state (PIGS) Monte Carlo method. We have found that these systems display rich behavior of the chemical potential as a function of their size, shell structure loosely based in Mackay and anti-Mackay moieties, size-driven structural transitions and dynamical behavior even in their ground state. The solid- and liquid-like character of these systems was scrutinized and it was determined that at certain sizes clusters change from a liquid-like phase to a rigid phase. The dynamical properties of these systems were studied using imaginary-time correlation functions. Properties such as rate constants and excited states can be potentially obtained using this methodology.
O, Proton(s), Where Art Thou?
Qiang Cui
Dept. of Chem. Univ. of Wisc. Madison, 1101 Univ. Ave. Madison,
WI 53706
In this talk, I'll discuss several topics inspired by our long-term goal of understanding proton pumping in biomolecular systems using theoretical techniques. As stringent tests for the theoretical methods and computational protein model for complex biomolecular systems, pKa calculations are carried out using "brutal-force" QM/MM free energy perturbation methods for titritable amino acids in different protein environments. These include surface-exposed and buried residues in soluable proteins and buried residues in membrane proteins. The magnitude of errors introduced by the lack of electronic polarization in the MM force field, limited accuracy in the QM method, approximations in the solvent boundary condition as well as the impact of sampling are discussed. The calibrated QM/MM method is then applied to study the pKa of hydronium in two proton
pumps, bacterirhodopsin and cytochrome c oxidase; the results are discussed in the context of pumping mechanisms of these systems. Finally, QM/MM simulations are used to analyze the infrared spectra for the proton release group (PRG) in bacteriorhodopsin, and the results provide an alternative explanation for the interesting diffuse band identified experimentally.
Ion atom collisions in ultracold gases


Alexander Dalgarno
Harvard Smithsonian Center for Astrophysics
60 Garden Street
Cambridge Ma 02138 USA
The form of the interaction between a positive ion and a neutral atom or molecule is discussed and application is made to collisions of ions with their parent atoms.Scattering lengths and charge exchange cross sections are calculated for the several isotopes of ytterbium.The modifications to the theory that are needed to obtain a realistic description of near-resonance charge exchange in collisions in which the particles are different isotopes are considered and the results of calculations of the scattering lengths for collisions of the ions H+ and D+ with the atoms D and H are presented.
The Chemistry of the Early Universe
Alex Dalgarno
Harvard-Smithsonian Center for Astrophysics
A summary is given of the molecular processes that occurred in the early Universe and that lead to the formation of the first stars. Attention is drawn to some of the uncertainties.
Koopmans’ theorem and single excitation CI for open shell systems
Ernest R. Davidson1 and Boris N. Plakhutin2

1Department of Chemistry, University of Washington
Seattle, Washington, 98195 USA

2Laboratory of Quantum Chemistry, Boreskov Institute of Catalysis
Russian Academy of Sciences, Novosibirsk 630090, Russia
It is easy to generalize Koopmans’ original derivation to obtain the ionization energy and electron affinity from canonical orbital energies of ROHF wavefunctions. The same derivation points out the fallacy in using UHF orbital energies even when there is no spin polarization. Extension to frozen orbital CIS makes it clear which states might be meaningful and which will be nonsense. Even though density function theory does not provide wave functions, use of approximate functionals should be expected to cause the same failings in TD-DFT as KT and CIS does for wave function methods for open shell systems.
Long Range Electron Transfer in PHM : "Like a Bridge Over Troubled Water"
Aurélien de la Lande
Institute of Biocomplexity and Informatics
University of Calgary, Canada
Long range electron transfers (ET) are a class of chemical reactions frequently observed in biological media, for instance in the respiratory chain or in enzymatic cycles. Those so-called non-adiabatic reactions are usually understood within the framework of Marcus Theory of electron transfer. However the detailed way how enzymes control the tunnelling of the electron between redox cofactors is still a matter of discussions. The theoretical understanding is generally delicate because of the large number of atoms taking part to the "reaction coordinate" which exhibit motions of several time-scales. Particularly interesting are the nanosecond fluctuations of the medium separating the two redox cofactors.
In this presentation, we will present a contribution to this problematic in the case of Peptidylglycine α-hydroxylating monooxygenase (PHM). This curproenzyme catalyzes the stereospecific hydroxylation of glycine-extended peptides by insertion of an oxygen atom into a C — H bond. PHM contains two copper centres, designated as CuM and CuH, which are separated by a solvent cleft. Both provide an electron during the catalytic cycle to complete O2 reduction. According to previous biochemical studies, the CuM active site is considered as the reactive one: O2 coordination occurs followed by rupture of C — H substrate bond. On the other hand, the CuH centre plays the role of an electron donor for the following long range electron transfer step. Actually, the detailed mechanism for this step is unclear in spite of biochemical data suggesting the participation of the water molecules separating the copper sites.

The ET step is investigated by means of Molecular Dynamics Simulations (MDS) using the DYNAMO library and the OPLS force field. Our simulations render a plausible pathway for the electron to tunnel. This pathway involves a water molecule strongly maintained by some PHM residues and the substrate through the formation of a net of hydrogen bonds. The efficiency of this pathway is evaluated within the framework of Marcus theory by calculating dynamic electronic coupling with the Beratan's Pathway model. Simulations of mutated enzymes are also presented and chemically account for the mutated enzyme activities. When existing, alternative ET pathways are proposed and are calculated in fair agreement with experimental trends.
Kinetic energy for D-dimensional trapped particles
J.S. Dehesa, R. Gonzalez-Ferez, P. Sanchez-Moreno, R.J. Yañez
Department of Atomic, Molecular and Nuclear Physics, and Institute Carlos I for Theoretical and Computational Physics, University of Granada, Spain
The kinetic energy of non-relativistic single-particle systems with arbitrary D-dimensional central potentials is found to be bounded from below by means of the orbital hyperangular quantum number, the dimensionality and some radial and logarithmic expectation values. Beyond the intrinsic physico-mathematical interest of this problem, we want to contribute to the current development of the theory of independent particles confined in spherically symmetric traps with non-standard dimensions. The latter has been motivated by the recent experimental achievements of the evaporative cooling of dilute (i.e. almost non-interacting) fermions in magnetic traps.
D-dimensional uncertainty relations, Fisher information and kinetic energy
J.S. Dehesa, R. Gonzalez-Ferez, E. Romera and P. Sanchez-Moreno
Department of Atomic, Molecular and Nuclear Physics, and Institute Carlos I for Theoretical and Computational Physics, University of Granada, Spain
There exist various mathematical realizations of the Heisenberg uncertainty principle, which depend on spreading measures used to quantify the position and momentum uncertainties. The most popular one, but possibly the weakest, is the variance-based Heisenberg-Kennard. The information-theoretic-based uncertainty relations have been shown to be more appropriate and general. Bialynicki-Birula et al. have proposed uncertainty relations for the Shannon and Renyi entropies as uncertainty measures. Here we present an uncertainty relation for D-dimensional quantum systems with central potentials, which is based on the Fisher information measure. This measure, in contrast to Heisenberg and Shannon quantities, has a local character since it is given as a gradient functional of the corresponding quantum-mechanical probability density. The main characteristics of the Fisher-information-based uncertainty relation will be discussed, and some physical applications will be shown. Moreover, this relation is conjectured for general systems in the form F(ρ) F(γ) ≥ 4D2, where F(ρ) and F(γ) are the Fisher information measures in the two reciprocal spaces. Finally, the kinetic energy of the system is found to be bound on both sides by the position Fisher information measure.
Information-theoretic properties of Rydberg atoms with different dimensionalities
J.S. Dehesa, S. Lopez-Rosa and R.J. Yañez
Department of Atomic, Molecular and Nuclear Physics, and Institute Carlos I for Theoretical and Computational Physics, University of Granada, Spain
Multidimensional Rydberg atoms are not only important by themselves but also because they play a very important role to study the interface of classical-quantum mechanics and for their numerous applications in nanotechnology, quantum computation and D-dimensional physics. The spectroscopic properties of these systems have received much attention in the last few years [1]. Here we investigate the spreading properties of three-dimensional highly excited hydrogenic systems in position and momentum spaces far beyond the standard deviation and the power moments, by means of the information-theoretic measures (Shannon entropy, Fisher information) of the corresponding quantum-mechanical probability densities for both ground and excited states [2-3]. Emphasis will be done to circular, Rydberg and Rydberg circular states of three-dimensional atoms.

[1] S.R. Lundeen, Adv. At. Mol. Opt. Phys. 52 (2005) 161-208.

[2] J.S. Dehesa, S. Lopez-Rosa, B. Olmos and R.J. Yañez, J. Math. Phys. 47 (2006) 052104.

[3] J.S. Dehesa, S. Lopez-Rosa, A. Martinez and R.J. Yañez, Information theory of D-dimensional hydrogenic systems: Spreading properties. Application to Rydberg atoms. Preprint 2008.
Design of electronic kinetic functionals: Combining analytical theory and Monte Carlo sampling
L. Delle Site
Max-Planck-Institute for Polymer Research, Theory Group, Mainz (Germany)
Conceptually, the crucial point of the OFDFT approach, is that it is in principle exact, provided that the kinetic functional is rigorous. This means that the design of valid kinetic functionals would allow to explore the full power of the Hohenberg-Kohn theorem for extended systems. In this perspective the search for a rigorous kinetic functional becomes the primary goal for a valid application of this method. Here I report on some theoretical developments in the design of a (possible) robust kinetic functional based on basic physical principles and some rigorous mathematical prescriptions. When combined with computational tools, as the Monte Carlo sampling, these analytical results become of very practical use for the design of local kinetic functionals. Here I will report the test case of a uniform gas of interacting spinless particles.


References:
L.Delle Site, Journal of Physics A:Math.Gen. 39, 3047 (2006)
L.Delle Site, Journal of Physics A:Math.Theo. 40, 2787 (2007)
L.M.Ghiringhelli and L.Delle Site, Phys. Rev. B, 77, 073104 (2008)
Investigation of Chitosan from Squid Pen as Scar Remover
Merlina A. Delorino,1 and Salvacion P. Cresidio,Ph.D.2
1Colegio de San Juan de Letran-Calamba, Philippines

2Centro Escolar University, Manila, Philippines
Marine resources, such as crabs, shrimps, and squids are tapped for food production, which result to coastal waste of canning industries. Management of coastal waste is one of the major problems of tropical countries like the Philippines. One way to solve such problem is to look for application and uses of these waste materials. The quest for better biomaterials to meet a myriad of challenges in treating skin disorders has evoked great enthusiasm among researchers. The utilization of materials from nature could be the answer to a variety of needs in skin treatment or improving its appearance.

The main thrust of this study was the investigation of chitosan from squid pen in the formulation of scar remover. The characterization of prepared chitosan was done by determining the viscosity-average molecular weight (MV), degree of deacetylation (DD) and scanning of prepared chitosan films nanostructure. Using Brookfield viscometer with RV number 6 spindle and Mark Houwink equation, the viscosity-average molecular weight was calculated. The spectra of chitosan films were obtained using Impact 400 Nicolet FTIR with a frequency range of 4000-400cm-1. The nanostructure of the prepared chitosan films were scanned using Olympus CK40 phase contrast microscope coupled with camera at 20x magnification. Preparation of chitosan films demonstrated significantly different viscosity and average molecular weight which is one of the important parameters which could influence the performance of chitosan as scar remover. The effectiveness of the formulated product was evaluated by comparing it with a commercial product. Evaluation of the product was based on the personal perception of the respondents and not based on the assessment of panelists. The scar remover cream was formulated using the prepared chitosan as active ingredient.

Dopant-Modulated Reaction Mechanisms: Trimethylene Sulfide-Derived Nanostructure Formation on p- and n-Type H-Silicon(100)-2x1.
Gino A. DiLabio
National Institute for Nanotechnology,
National Research Council of Canada
11421 Saskatchewan Drive
Edmonton, Alberta
Canada
T6G 2M9
The nanoscale structuring of molecules on silicon surfaces is one approach for combining the tuneable properties of chemical species with the functionality of semiconductor materials. In this presentation, the growth characteristics of trimethylene sulfide (TMS) on p- and n-type H-Si(100)-2x1. The nanostructures formed by TMS on either surface are indistinguishable by scanning tunneling microscopy (STM). However, high-resolution electron energy loss spectroscopy (HREELS) and modeling by density functional theory indicate that the molecular attachment mechanism differs with dopant type. The results show that TMS adds to a surface silicon dangling bond through the formation of a Si-S bond on p-type silicon and through the formation of a Si-C bond on n-type silicon. In both cases, the added TMS undergoes ring opening following covalent bond formation with the surface. The different ring-opened radicals are able to abstract a hydrogen atom from one of two neighboring silicon dimers. The overall reaction produces TMS-derived nanostructures that grow via a square-wave pattern on the neighboring edges of two dimer rows.
Quantum Monte Carlo Study of the Two-Dimensional Homogeneous Electron Gas
Neil Drummond and Richard Needs
TCM Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK
We have used quantum Monte Carlo (QMC) methods to study the zero-temperature phase diagram of the two-dimensional homogeneous electron gas, achieving higher accuracy than earlier QMC studies. We find a transition from a paramagnetic Fermi fluid to a triangular Wigner crystal at density parameter rs=33(1) a.u. Our results show that a fully spin-polarised fluid is never stable, in contradiction with the conclusions of earlier studies. We have also searched for a recently proposed “hybrid” phase,1 but have not found it.

1 H. Falakshahi and X. Waintal, Phys. Rev. Lett. 94, 046801 (2005); X. Waintal, Phys. Rev. B 73, 075417 (2006).
Theoretical study of intramolecular and assisted by water proton transfer reaction
Fernanda Duarte and Alejandro Toro-Labbe
QTC, Departamento de Química Física, Facultad de Química,
Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860,Casilla 306, Correo 22, Santiago, Chile.
We present a detailed theoretical study, employing the B3LYP/6-31++ G (d,p) level of theory, of the proton transfer reaction in the systems HC(O)SH→HC(S)OH in gas phase[1] and assisted by water. The reactions are analyzed in terms of the reaction force[2] and reaction electronic flux[3].

The barrier heights for the H2O-assisted reaction is two times lower than that of the reference reaction, thus stresing the importance of the catalytic effect of the H2O molecule, that modifies considerably both electronic and structural properties along the reaction path.

References
[1] Gutiérrez-Oliva S.;Herrera B.;Toro-Labbé A.;Chermette H. J. Phys. Chem. A 109:1748, 2005.
[2] Toro-Labbé A. J. Phys. Chem. A, 103:4398, 1999.
[3] Herrera B.; Toro-Labbé A. J. Phys. Chem. A, 111 :5921, 2007.
Electronic structure of alkali dimers and trimers. Prospects for alignment and orientation effects.
R. Guérout1, M. Aymar1, J. Deiglmayr1,2, O. Dulieu1
1 Laboratoire Aimé Cotton, CNRS, Univ Paris-Sud 11, Bât. 505, 91405 Orsay, France
2 Physikalisches Institut, Universität Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
The rapid development of experimental techniques to produce cold and ultracold molecules [1] opens the ways to manipulate them or to control their formation dynamics using external fields, and to explore their interactions with surrounding particles. In most cases, the detailed knowledge of the internal molecular structure is required to guide such studies and to interpret their results. For several years now our group carries out systematic theoretical investigations on alkali molecular systems, using a quantum chemistry approach based on pseudopotentials for atomic core representation, Gaussian basis sets, and effective potentials for core polarization [2]. Potential curves and permanent and transition dipole moments have been obtained for all alkali pairs, both homonuclear and heteronuclear [2, 3], which are relevant for ultracold molecule formation processes. We also designed a novel approach for the treatment of molecular spin-orbit interaction.
The manipulation of heteronuclear alkali molecules with electrostatic or strong off-resonant laser fields is governed by their dipole moment and their static polarizability. We computed the variations with internuclear distance and with vibrational index of the static dipole polarizability tensor for all homonuclear and heteronuclear alkali dimers [4], and for alkali hydrides, in their electronic ground state and in their lowest triplet state. Polarizabilities are extracted from electronic energies using the finite-field method. For the heaviest species Rb2, Cs2, Fr2, for all heteronuclear alkali dimers, and for CsH, such results are presented for the first time. We found that for all alkali pairs, the parallel and perpendicular components of the ground state polarizabilities at the equilibrium distance Re scale as Re3. In addition we will present scenarios for the permanent alignment of ultracold heteronuclear molecules [4], based on combinations of static electric fields and strong laser fields [5].
Once ultracold molecular samples are dense enough, the interaction between atoms and molecules become observable [6]. We present preliminary results on the calculation of potential energy surfaces for alkali trimers involving heavy alkali species (Rb, Cs) at arbitrary geometries and symmetries. Using effective core potentials, it is possible to carry out full configuration interaction calculations for the valence electrons and hence accurately take into account all electronic interactions. The accuracy of our method is checked on Li3, for which the quartet surface of the ground state is available from other works [7]. We will present for the first time calculations for the quartet potential surface of cesium trimer. Results for other symmetries will be presented as well.

[1] Special issues of Eur. Phys. J. D, 31 (2004) and of J. Phys. B, 39 (2006)
[2] M. Aymar and O. Dulieu, J. Chem. Phys. 122, 204302 (2005)
[3] M. Aymar and O. Dulieu, Mol. Phys. 105, 1733 (2007)
[4] J. Deiglmayr, M. Aymar, R. Wester, M. Weidemüller, and O. Dulieu, J. Chem. Phys. Submitted.
[5] B. Friedrich and D. Herschbach, J. Phys. Chem. A 103, 10280 (1999)
[6] N. Zahzam et al, Phys. Rev. Lett. 96, 023202 (2006) ; P. Stanuum et al, Phys. Rev. Lett. 96, 0232021 (2006);
[7] M. Cvitas et al, Phys. Rev. Lett. 94, 200402 (2005)
Exploring Conductance Switching Properties of Molecular and Nano Scale Devices - A Computational Approach.
Barry D Dunietz
Department of Chemistry, University of Michigan
A computational approach is used and developed to study electron transport through molecular and nano scale devices. New models and methods are employed to describe the dynamics of electron transport under the influence of time dependent perturbations. Quantum interferences affecting the TD conductance are analyzed.

We also discuss our modeling of several recent high-profile experimental studies achieving molecular scale conductance which provide some intriguing insight at the molecular structural level on the functionality of the conducting devices. The studies involve metal recognition properties of short peptides or fabricated molecular sockets based on surface confined terpyridine ligands. If time permits we will describe the required structural features for a gating field to tune the conductance of a molecular conjugated system.
Tuning chemistry in Ionic Liquid Crystals
Alasdair Dunlap-Smith and Khashayar Ghandi
Department of Chemistry, Mount Allison University, Canada
Several ionic liquids have been evaluated for their influence on free radical chemistry. The cyclohexadienyl radical was studied with transverse field and avoided level-crossing muon spin resonance. Special attention has been given to anisotropic mesophases of these compounds. These mesophases were characterized with Differential Scanning Calorimetry (DSC), Polarized Optical Microscopy (POM) and 1H NMR. The interpretation of NMR data was confirmed using quantum calculations. Initial results include a previously uncharacterized Smectic A phase for methyl trioctadecyl ammonium Bromide, the observed influence of this mesophase on cyclohexadienyl radicals, and inverse temperature dependence for radical formation in isotropic 1-methyl-3-dodecyl imidazolium Iodide.
A Charge-Dependent Continuum Model of Solvation Accurate for Ions
Michel Dupuis, Donald M. Camaioni, Bojana Ginovska
Pacific Northwest National Laboratory
Dielectric continuum solvation models are widely used because they are a computationally efficacious way to simulate accurately equilibrium properties of solutes. However existing schemes for defining cavities are unable to consistently predict accurately ion solvation, especially anions. In this presentation we will highlight a new model (CD-COSMO for Charge-Dependent COSMO) model whereby the cavity is defined by simple empirically-based expressions involving the effective atomic charges of the solute atoms (derived from molecular electrostatic potential). Inherent to this approach, the cavity definitions reflect the strength of specific solute-water interactions. The approach is illustrated for a number of test cases, including the determination of acidities of an amine base, a study of the tautomerization equilibrium of a zwitterionic molecule (glycine), and the calculation of solvation energies of transition states toward a full characterization of reaction pathways in aqueous phase.
The electronic structure of surfaces and interfaces: DFT approach
I.S. Elfimov and G.A. Sawatzky
Advanced Materials and Process Engineering Laboratory (AMPEL), UBC
Beginning from the late 30s it has been recognized that the correlations between the electrons in the partially filled orbitals of transition metals are the source of a whole variety of interrelated phenomena such as metal-insulator transitions, orbital (or Jahn-Teller) ordering, charge ordering, lattice and magnetic polarons, etc. During the last several decades, these effects and the possibility to control them by external fields (e.g. magnetic and electric fields, pressure, and substrate-induced stress) has caused enormous amount of interests on transition metal-based materials among scientists and engineers. In the last few years an intense search has started for new materials in nanostructured form, exhibiting highly desired magnetic, electrical and magneto electric effects. In general, this is carried out by modifying existing materials, and trying various combinations of compounds, which already have similar properties in the bulk form. Simultaneously, the latest development in theoretical studies of electronic, magnetic and structural properties, based on Density Functional Theory, has also shown great successes on bulk materials. A combination of the theoretical and experimental approaches in the new nanostructure paradigm can strongly benefit the whole field of material science.

For example, DFT calculations of neutral (100) and (110) surfaces in MgO and NiO show that the change of Madelung potential at the surface caused by the breakdown in the lattice periodicity leads not only to a simple reduction of forbidden gap, but also forms surface states of specific symmetry, which have strong influence on the properties of the rest of material resulting in possible magnetic transition in the case of NiO thin films. They also predict an insulator to metal transitions at the polar (111) surface of ultra thin films of SrO, where charge carriers in an O 2p band order ferromagnetically, resulting in a very unique ferromagnetic metallic system. Interfaces are another very distinct example where the so-called polar catastrophe plays an important role, and results in a metallic conductivity at the interface between two simple band insulator SrGeO3 and LaAlO3.
Intermediate Hamiltonian multi-reference Hilbert-space Coupled Cluster method: theory and pilot applications
E. Eliav, A. Borschevsky, K. R. Shamasundar and U. Kaldor
School of Chemistry, Tel Aviv University, 69978 Tel Aviv, Israel
A reformulation of the multi-root multireference Hilbert-space coupled cluster (CC) method, based on extrapolated intermediate Hamiltonian (XIH) techniques, previously introduced in the frame of Fock-space CC [1] is presented. The method uses size-extensive complete active space description and the efficient intermediate-Hamiltonian technique to solve the intruder states problem. The new approach has several methodological and computational advantages, based on possibility to introduce different extrapolation procedures from the approximate intermediate Hamiltonian to the precise effective Hamiltonian. It opens a door for substantial increase of precision of standard multireference CC methods and for calculation of a large number of electronic states not accessible previously by the Hilbert-space coupled cluster approach.
Pilot applications of the modified Hilbert-space CC program [2] are presented, including excitation energies of Be and some other atomic and molecular systems. For the first time model spaces with several dozens of Slater determinants were used in the Hilbert-space multi-root calculations. Excellent agreement with experiment and significant improvement compared with standard multireference coupled cluster approaches are obtained.

References:
1.Ephraim Eliav; Marius J. Vilkas, Yasuyuki Ishikawa, Uzi Kaldor. J. Chem. Phys., 122(22), 224113/1-224113/5 (2005).
2. Shamasundar, K. R. , PhD thesis, NCL, Pune, India, 2004
Construction of a GGA exchange-correlation hole from a correlation factor ansatz
Matthias Ernzerhof1 and Hilke Bahmann2
1Department of Chemistry, University of Montreal, Canada

2Department of Chemistry, University of Wuerzburg, Germany
The Perdew-Burke-Ernzerhof (PBE) [1] approximation to the exchange-correlation energy is employed as a starting point for the construction of an approximate, spherically averaged exchange-correlation hole. In a first step, we develop a new model for the PBE exchange hole. This model satisfies the homogeneous electron gas limit, it is normalized and yields the correct small-gradient limit in the system average. A correlation factor [2], i.e., a function multiplying the exchange hole, is proposed that turns the exchange into an exchange-correlation hole. The correlation factor has a simple form and its parameters are determined through a number of known conditions that ought to be satisfied by a GGA exchange-correlation hole. The homogeneous-electron-gas limit of the new hole model is compared to the LSD hole [3].
[1] J.P. Perdew, K. Burke, M. Ernzerhof, PRL 77, 3865 (1996); 78, 1396(E) (1997).
[2] P. Gori-Giorgi, J.P. Perdew, PRB 66, 165118 (2002).
[3] J.P. Perdew, Y. Wang, PRB 46, 12947 (1992).
Bond dissociation- and correlation effects in molecular electronic devices
A. Goker, F. Goyer, and M. Ernzerhof
Department of Chemistry, University of Montreal, Canada
We present a simple model for a fundamental process in molecular electronics: the change in conductance upon bond breaking. In our model, a diatomic molecule is attached to spin-polarized contacts. Employing a Hubbard Hamiltonian, electron interaction is explicitly considered in the molecule and neglected in the contacts, enabling us to study the impact of electron interaction on the molecular conductance. In the limit where the electron repulsion is strong compared to the binding energy (as it is the case upon dissociation) electron transmission in strongly suppressed compared to the non-interacting case. On the other hand, the spin-polarized contacts introduce a coupling between the molecular singlet and triplet states, as a consequence of which, the energy gap between resonances is reduced.
Achieving Accurate Thermochemistry in State Specific Multireference Coupled Cluster Theory
Francesco A. Evangelista
Center for Computational Chemistry, University of Georgia, USA
In order to extend the applicability of current multireference coupled cluster methods to real chemical systems two major problems need to be addressed: the first is estimating the complete basis set limit of the electronic energy, while the second is increasing the accuracy of electron correlation treatment. These two problems are investigated in the context of state specific multireference coupled cluster theory using the sufficiency conditions advanced by Mukherjee (Mk-MRCC). To deal with the first issue a rigorous second order perturbation theory based on Mk-MRCC is developed, while the accuracy of Mk-MRCC with singles and doubles is improved by including higher excitations in the cluster operator. In my talk I will describe and present applications of the newly developed Mk-MRPT2. I will also discuss two schemes containing triple excitations: Mk-MRCCSDT-n and Mk-MRCCSDT which include approximate and full triples, respectively.
Self-Organization of Modular Protein Domains and its Role in the Assembly and Regulation of Protein Kinases
José Faraldo-Gómez
Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics, Germany
Allosteric enzymes such as non-receptor tyrosine kinases (NRTK) are key in the propagation of cellular signals in diverse contexts, including cell growth and adaptive immunity. Structurally, these modular proteins comprise a catalytic domain and a series of regulatory domains, which reversibly assemble/disassemble to enable the inactivation/activation of the kinase. As in protein folding, therefore, regulation of these multi-domain enzymes is presented with the problem of conformational search. Following an extensive, state-of-the-art computational analysis, and based on existing biochemical and biophysical data, we conclude that the assembly and regulation of NRTK critically relies on the ability of the inter-domain linkers to spatially organize the various functional domains, so as to promote the formation of specific domain-domain interfaces. These linker regions are thus not mere flexible connectors along the polypeptide chain, as has been widely assumed. Instead, they appear to be evolutionarily fine-tuned, from a physico-chemical and structural standpoint, to facilitate the exploration of conformational space during assembly, and would therefore be crucial for the appropriate regulation of NRTK function.

This research has been in part conducted in the laboratory of Benoît Roux (Cornell, Chicago), funded by NIH-CA-93577
Theoretical studies of one- and two-photon absorption properties for two series of three-branched fluorenylene-vinylene compounds with different centers (B, N) and peripheral substituted groups
Ji-Kang Feng,1,2 De-Ming Han1
1State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, China
2College of Chemistry, Jilin University, China
Two series of three-branched fluorenylene-vinylene compounds with different centers (B, N) and peripheral substituted groups were investigated. The equilibrium geometries and electronic structures were obtained by using the density functional theory B3LYP and 6-31G basis set. The one- and two-photon absorption properties of all the molecules were studied theoretically with a ZINDO-SOS method in detail. It can be seen that the maximum one-photon absorption (OPA) intensities and the maximum two-photon absorption (TPA) cross sections values are gradually increased with the stronger electron-donating capability [H﹤OH﹤N(CH3)2] or electron-accepting one (H﹤CHO﹤NO2). This indicates that intramolecular charge transfer from the center to the peripheral substituted groups (or vice versa) plays a very important role on the TPA. In addition, comparing the two molecules with different centers (B and N) and the same H peripheral group, one can see that the molecule with B center has larger TPA cross section than the latter.
First principles approach to the calculation of Mössbauer isomer shift
Michael Filatov and Reshmi Kurian
Theoretical Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, NL-9747 AG Groningen, the Netherlands
A quantum chemical computational scheme for the calculation of the isomer shift in Mössbauer spectroscopy is developed and applied to the calculations on a number of transition metal atoms and iron and tin complexes. Within the new theoretical scheme, the isomer shift is treated as a derivative of the total electronic energy with respect to the radius of a finite nucleus. The explicit use of a finite nucleus model in the calculations enables one to incorporate straightforwardly the effects of relativity and electron correlation. The results of calculations carried out for a set of iron and tin complexes as well as for a number of atoms and atomic ions show high reliability of the new method. The use of high level ab initio methods within the new scheme offers a possibility to obtain more accurate parameters of the nuclear γ-transitions from comparison with the experimentally measured Mössbauer isomer shifts.
Relativistic variational calculations for complex atomic systems
Charlotte Froese Fischer
Vanderbilt University, Nashville, TN 37235, USA
National Institute of Standards and Technology, Gaithersburg, MD 20899-8422, USA
Atomic data (energy levels, wavelengths, transition probabilities, hyperfine structure constants, electron affinities, isotope shift effects) are needed, for example, in astrophysical applications, fusion diagnostics, and plasma modelling. Often the needs are for atoms with complex spectra consisting of numerous lines but they may also be benchmark calculations where the inclusion of correlation and relativistic effects are particularly demanding.

Variational methods that optimize the orbital basis have advantages.In these methods, a radial orbital (RO) basis, that depends only on nl (or nlj) quantum numbers, is determined by the application of the variational procedure to an energy expression derived using the non-relativistic or Dirac-Coulomb Hamiltonian followed by a configuration interaction calculation for effects omitted at the variational stage. These broad approaches have been implemented in the Atomic STructure Package (ATSP2K)[1] and the General Relativistic Atomic Structure Package (GRASP2K)[2]. Both have some limitations. In the former the occupation of subshells with l >3 is restricted to at most two whereas in GRASP2K, subshells with j> 7/2 are restricted to at most two electrons. Both these codes rely on very general angular momentum codes for the evaluation of matrix elements for a variety of operators [3].

This talk will reviews factors that are beneficial when variational procedures are developed for complex atoms, ions, or anions. Systematic methods are recommended for assessing accuracy and
controlling the size of the calculation. Some examples will be presented.

References
[1] C. Froese Fischer, G. Tachiev, G. Gaigalas, M. R. Godefroid, An MCHF atomic-structure package for large-scale calculations, Comput. Phys. Commun. 176 559-579 (2007).
[2] P. Jönsson, X. He, C. Froese Fischer, and I. P. Grant, The grasp2K relativistic atomic structure package, Comput. Phys. Commun. 176, 597-692 (2007).
[3] G. Gaigalas, Z. Rudzikas, and C. Froese Fischer, An efficient approach for spin-angular integrations in atomic structure calculations, J. Phys. B: At. Mol. Opt. Phys. 30, 3747-3771 (1997).


Ultracold collisions of spin-polarized metastable hydrogen atoms
Robert C. Forrey
Department of Physics, Penn State University at Berks
The status of ab initio calculations of very low temperature cross sections for collisions between two spin-polarized metastable hydrogen atoms is discussed. Degeneracy between the 2s and 2p states produces long-range coupling that is non-vanishing at first order in perturbation theory. The degeneracy is lifted by the Lamb shift and fine structure splittings. Multiple adiabatic potential curves yield a set of coupled equations that must be solved at low energies. The electrostatic dipole-quadrupole interaction produces non-adiabatic radial coupling between (2s,2p) and (2p,2p) states. The Coriolis interaction yields non-adiabatic angular coupling that must be accounted for when working in a body-fixed frame. All of these contributions may be handled in a space-fixed atomic gauge that is particularly convenient for a spin-polarized system. The latest theoretical results are compared with an existing experiment.
Multi-scale modelling of coupled degradation mechanisms in PEFC environments: new theoretical insights and experimental validation
Alejandro A. Franco
Atomic Energy Commission of France(CEA)/LITEN/Department of Hydrogen Technologies/PEFC Components Lab, 17 rue des Martyrs, 38000 Grenoble, France.
It is largely observed that the nano/microstructure properties of PEFC catalyst layers (Pt and Pt-alloy-based) evolve during the Membrane-Electrodes Assembly (MEA) operation [1]. These spatiotemporal nano/microstructure changes are strongly dependent on the electrodes operating conditions (given by the dynamic nominal current, the reactant pressures and humidity, the cell temperature…), and translate into the cell potential degradation. PEFC lifetime is sometimes limited to 300-500 hours under some severe power drive-cycle operating conditions representative of automotive applications [2]. Because of the strong coupling between the different physicochemical phenomena taking place in the interlinked materials constituting the MEA, interpretation of ageing experiments is difficult, and analysis through physical modelling becomes crucial in order to establish microstructure-performance relationships, to elucidate MEA degradation mechanisms, and to help improving both PEFC electrochemical performance and durability. However, at present too little modelling work addressing PEFC degradation has been reported.

In this talk I discuss a new dynamic mechanistic theoretical approach of coupled electrochemical ageing processes in Pt- and Pt-M alloys-based PEFC MEA, on the basis of a recent modular multi-scale non-equilibrium thermodynamics model developed by us, allowing providing link between atomistic (ab initio) and macroscopic modelling studies [3-8]. The approach couples cathodic catalyst oxidation/dissolution/electrochemical ripening [7-10], dissolved metal ions diffusion/electro-migration/re-crystallization in the ionomer and cathodic carbon catalyst-support corrosion [11-12] with a novel description of the nano-scale electrochemical catalyst/electrolyte interface in presence of non-equilibrium electro-catalytic processes [4, 7-8] and a micro-scale transfer description of reactants, charges and water within the MEA.

On a physical basis, the model describes the feedback between the instantaneous performance and the intrinsic material ageing processes [11]: thus, the approach allows predicting cell potential transient behaviour (degradation) and MEA durability. This model provides new insights on the interplaying (synergies) between the different ageing phenomena and analyses the MEA response sensitivity to operating conditions, initial catalyst/C/ionomer loadings, initial electrodes micro-structure and temporal evolution of the electro-catalytic activity.

The model is numerically solved by using a Matlab® in-house computational code, and predicts temporal evolution of experimental observables (e.g. instantaneous polarisation curves, electrochemical impedance spectroscopy, cyclic voltammetry…). All the predictions are validated with in-situ [2] and ex-situ [13] experiments performed with dedicated half-cells and mono-cells with model electrodes (i.e. with well-controlled aggregates morphology and distribution [7-8, 14]) under different operating conditions: these in-house experiments include aging tests (e.g. > 500 h) as well as TEM/HR-TEM observations and XPS micro-structural characterisations before and after operation.

In this talk, I will illustrate the approach capabilities by discussing results focused on the study of:

• the impact of water transport on performance degradation and durability
• the identification of static and dynamic MEA power-cycles favouring synergies between Pt dissolution and C degradation mechanisms [15]
• the cumulative effect of the partial exposure of the anode catalyst to oxygen (induced by transient PEM crossover or fuel starvation) on transient PEFC performance, as well as the role of the initial cathode Pt loading on the carbon micro-structural ageing [11]
• the impact of long-term (e.g. > 500 h) CO anodic injection on performance and cathode nano/micro-structure evolution and carbon corrosion under power-cycled conditions [16]
• the impact of initial PtxCoy catalysts nano-structure on instantaneous electrochemical response and degradation [7-8]
• the impact of initial PtxCoy-oxidation state on instantaneous electrochemical response and clusters degradation [7-8]
• the impact of operating conditions on the PtxCoy-clusters instantaneous electrochemical response and degradation [7-8].

The approach proposed here is now being used at the CEA to optimize home-made PEFC MEA operating conditions and properties for improved performance and durability [17].

Acknowledgements. This work is being funded by the French National Research Agency (ANR-PAN H network) under the OPTICAT, DVD-AME and POLIMPAC projects.

References
[1] P. Ferreira, G. la O', Y. Shao-Horn, D. Morgan, R. Makharia, S. Kocha, H. Gasteiger; J. Electrochem .Soc., 152, A2256 (2005).
[2] S. Escribano, R. Jamard, A. Morin, S. Solan, L. Guetaz; in Proceedings of the 16th World Hydrogen Energy Conference (Lyon, June 13-16, 2006), paper #S19-583 (in conference CD) (2006).
[3] A.A. Franco, “ A physical multiscale model of the electrochemical dynamics in a polymer electrolyte fuel cell – An infinite dimensional Bond Graph approach”; PhD Thesis Université Claude Bernard Lyon-1 (France) no. 2005LYO10239 (2005).
[4] A. A. Franco, P. Schott, C. Jallut, B. Maschke, J. Electrochem. Soc., 153, A1053 (2006).
[5] A.A. Franco, P. Schott, C. Jallut, B. Maschke, Fuel Cells: From Fundamentals to Systems, Wiley-VCH, 7, 99 (2007).
[6] W. Bessler, A.A. Franco, “Multi-scale electro-kinetic concepts in fuel cells modelling”, paper in preparation (2008).
[7] A.A. Franco, S. Passot, P. Fugier, “Transient multi-scale modelling of PtxCoy catalysts degradation in PEFC environments”, oral communication (abstract #309), 213th Meeting of the Electrochemical Society, Phoenix (US), May 18-23 (2008).
[8] A.A. Franco, S. Passot, S. Mailley, E. Billy, L. Guetaz, N. Guillet, E. De Vito, P. Fugier, “Degradation of nano-structured PtxCoy catalysts in PEFC: new insights from an hybrid Monte Carlo-non-equilibrium thermodynamics approach”, paper in preparation (2008).
[9] A.A. Franco, M. Tembely, J. Electrochem. Soc., 154 (7) B712 (2007).
[10] A.A. Franco, ECS Transactions, 6, (10) 1 (2007) Chicago (Ed. V. Ramani).
[11] A.A. Franco, M. Gerard, J. Electrochem. Soc., 155 (4) B367 (2008).
[12] A.A. Franco, M. Gerard, “Transient model of carbon catalyst-support corrosion in a PEFC: multi-scale coupling with Pt electro-catalysis and impact on performance degradation”, oral communication (abstract #1160), 213th Meeting of the Electrochemical Society, Phoenix (US), May 18-23 (2008).
[13] N. Guillet, L. Roue, S. Marcotte, J. Applied Electrochemistry, 36, 8 (2006).
[14] S. Mailley et al., FR Patent WO/2007/088292 (2007).
[15] A. A. Franco, S. Passot, M. Guinard, M. Gerard, “Coupling of ageing mechanisms in PEFC environments: new insights from a multi-scale modelling investigation ”, accepted for oral comm. in the 59th Annual Meeting of the International Society of Electrochemistry, Sevilla (Spain), September 7-12 (2008)
[16] O. Lemaire, M. Guinard, B. Barthe, N. Guillet, A.A. Franco, “PEFC anode long-term CO contamination impact on intrinsic catalyst and C-support ageing mechanisms: new advances on durability understanding”, accepted for oral comm.. in the 59th Meeting of the International Society of Electrochemistry, Sevilla, September 7-12 (2008).
[17] A.A. Franco; “Transient Multi-scale Modeling of Coupled Ageing Mechanisms in PEFC - A theoretical tool for experimental interpretation and advanced MEA design” invited talk and in Proceedings of the 3rd Annual conference “Durability and Performance 2007”, American Knowledge Foundation, Miami (Florida, US), November 15-16 (2007).
Molecules in electric fields: eigenstates, collisions, motions
Bretislav Friedrich
Fritz-Haber-Institut der Max-Planck-Gesellschaft
Faradayweg 4-6, D-14195 Berlin, Germany
We'll show that combined electrostatic and radiative fields can greatly amplify the directional properties, such as axis orientation and alignment, of symmetric top molecules. We consider all four symmetry combinations of the prolate and oblate inertia and polarizability tensors, as well as the collinear and perpendicular (or tilted) geometries of the two fields. Two mechanisms are found to be responsible for the amplification of the molecules' orientation: (a) permanent-dipole coupling of the opposite-parity tunneling doublets created by the oblate polarizability interaction in collinear static and radiative fields; (b) hybridization of the opposite parity states via the polarizability interaction and their coupling by the permanent dipole interaction to the collinear or perpendicular static field. In perpendicular fields, the oblate polarizability interaction, along with the loss of cylindrical symmetry, is found to preclude the wrong-way orientation, causing all states to become high-field seeking with respect to the static field. The adiabatic labels of the states in the tilted fields depend on the adiabatic path taken through the parameter space comprised of the permanent and induced-dipole interaction parameters and the tilt angle between the two field vectors.

We'll present an analytic model of thermal state-to-state rotationally inelastic collisions of polar molecules in electric fields. The model is based on the Fraunhofer scattering of matter waves and requires Legendre moments characterizing the "shape" of the target in the body-fixed frame as its input. The electric field orients the target in the space-fixed frame and thereby effects a striking alteration of the dynamical observables: both the phase and amplitude of the oscillations in the partial differential cross sections undergo characteristic field-dependent changes that transgress into the partial integral cross sections. As the cross sections can be evaluated for a field applied parallel or perpendicular to the relative velocity, the model also offers predictions about steric asymmetry. We exemplify the field-dependent quantum collision dynamics with the behavior of the Ne-OCS and Ar-NO systems. A comparison with the close-coupling calculations available for the latter system [Chem. Phys. Lett. 313, 491 (1999)] demonstrates the model's ability to qualitatively explain the field dependence of all the scattering features observed.

Stark deceleration relies on time-dependent inhomogeneous electric fields which repetitively exert a decelerating force on polar molecules. Fourier analysis reveals that such fields, generated by an array of field stages, consist of a superposition of pairwise counter-propagating partial waves with well-defined phase velocities. Molecules whose velocities come close to the phase velocity of a given wave get a ride from that wave. For a square-wave temporal dependence of the Stark field, the phase velocities of the waves are found to be odd-fraction multiples of a fundamental phase velocity. We'll present the dynamics due to any of the waves as well as due to their mutual perturbations and interferences. A detailed comparison with classical trajectory simulations and with experiment demonstrates that the analytic “wave model” encompasses all the longitudinal physics encountered in a Stark decelerator.

Efficient Approach to Molecular RPA Correlation Energies
Filipp Furche
Department of Chemistry, University of California, Irvine, USA
The random phase approximation (RPA) [1] is emerging as a promising starting point for correlated ground state energy calculations in Kohn-Sham density functional theory: Molecular RPA correlation energies are size-consistent, compatible with exact exchange, capture long-range dispersion, and yield reasonably accurate atomization energies [2,3]. A major drawback of present RPA-based correlation treatments is their high computational cost which scales as the sixth power of the system size. In this talk, I will introduce a new, fully analytical approach to RPA correlation energies free of numerical integrations. I will present newly developed iterative algorithms that substantially reduce the cost of RPA correlation energy calculations. As a result, RPA based correlation treatments become competitive with second-order Moller-Plesset (MP2) calculations. I will analyze the new expression for the RPA correlation energy from a density functional and from a wavefunction perspective.

References:

[1] J. Dobson, in Time-dependent density functional theory, ed. by M. Marques, F. Nogueira, A. Rubio, K. Burke, and E. K. U. Gross, Springer, Berlin, 2006.
[2] F. Furche, Phys. Rev. B 64 (2001), 195120.
[3] F. Furche and T. Van Voorhis, J. Chem. Phys. 122 (2005), 164106.
QM or MM? Development of a Next Generation Force Field for Biomacromolecules
Jiali Gao
Department of Chemistry and Digital Technology Center, University of Minnesota, Minneapolis, MN 55455, USA
Molecular dynamics simulation has become a powerful tool for studying biochemical properties. At the heart of these calculations is the potential energy function that describes intermolecular interactions in the system, and often it is the accuracy of the potential energy surface that determines the reliability of simulation results. The current generation of force fields was essentially established in the 1960s; while the accuracy has been improved tremendously by systematic parameterization, little has changed in the formalism. The explicit polarization (X-Pol) potential that we describe in this paper is an electronic structure-based polarization force field, designed for molecular dynamics simulations and modeling of biopolymers. In this approach, molecular polarization and charge transfer effects are explicitly treated by a combined quantum mechanical and molecular mechanical (QM/MM) scheme, and the wave function of the entire system is variationally optimized by a double self-consistent field (DSCF) method. We illustrate the possibility of parametrizing the X-Pol potential to achieve the desired accuracy as that from MM force fields, and demonstrate the feasibility of carrying out molecular dynamics (MD) simulation of solvated proteins. We use a system consisting of 14281 atoms, including the protein bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions, to show the efficiency of an electronic structure-based force field in atomistic simulations. In this model, an approximate electronic wave function for the entire system is variationally optimized to yield the minimum Born-Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant. The new-generation X-POL force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible.
Enhanced sampling simulations for protein folding and aggregation
Yi Qin Gao
Department of Chemistry, Texas A&M University
A self-adaptive enhanced sampling method has been developed and applied to structure and thermodynamics calculations for biological systems. This method has the advantage of both replica exchange and multi-canonical simulations. It has been shown effective for the sampling of configuration of large and complex systems, and it has been applied in studies of the thermodynamics and folding pathways of small proteins using all atom models. These simulations allowed folding and unfolding processes of proteins to be studied with low computational cost and led to a more quantitative understanding of the protein folding mechanism.

The method was also applied in Monte Carlo simulations on proteins with different folding motifs and structures (simple alpha proteins, beta proteins, as well as multi-domain proteins with mainly alpha, beta, or both components), using recently developed coarse-grained polypeptide models. These studies have been used to understand the physics of protein-protein interaction and protein aggregation. Monte Carlo simulations making use of the newly developed self-adaptive enhanced sampling methods were performed to understand the molecular mechanism of polypeptides/small protein aggregation.
Asymptotics-based sub-linear scaling algorithms for Density Functional Theory
Carlos J. García-Cervera,1 Jianfeng Lu2 and Weinan E2,3
1Mathematics Department, University of California, Santa Barbara

2Program in Applied and Computational Mathematics, Princeton University

3Mathematics Department, Princeton University
I will discuss asymptotic-based algorithms for the study of the electronic structure of materials, in the context of density functional theory. I will illustrate the ideas using the orbital-free formulation, and if time permits, for Kohn-Sham DFT as well.

This is joint work with Weinan E (Princeton University), and Jianfeng Lu (Princeton University).
Charge transfer, double and bond-breaking excitations with time-dependent density matrix functional theory
K.J.H. Giesbertz, O.V. Gritsenko and E.J. Baerends
Afdeling Theoretische Chemie, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
Time-dependent density functional theory in its current adiabatic implementations exhibits three remarkable failures: a) totally wrong behavior of the excited state surface along a bond-breaking coordinate; b) lack of doubly excited configurations, affecting again excited state surfaces; c) much too low charge transfer excitation energies. These TDDFT failure cases are all strikingly exhibited by prototype two-electron systems such as dissociating H2 (zero σg -> σu excitation energy at R -> infinity, missing lowest excited state (a double excitation) at R > 2.5 Bohr) and HeH+ (charge transfer excitations). The exact density matrix functional being known in two-electron systems, the performance of time-dependent density matrix theory can be tested in those systems. We find for TDDMFT that: a) The first order (linear response) formulation does not prohibit the correct representation of doubly excited states; b) Within previously formulated simple adiabatic approximations the bonding-to-antibonding excited state surface as well as charge transfer excitations are described without problems, but not the double excitations; c) An adiabatic approximation is formulated in which also the double excitations are fully accounted for.
Resolutions of the Coulomb Operator
Sergey A. Varganov, Andrew T.B. Gilbert and Peter M.W. Gill
Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia
The Resolution of the Identity (RI) is widely used in many-body algorithms. It expresses the completeness of a set of functions fi( r) that possess the familiar orthonormality property.

In the first part of my lecture, I will discuss functions that possess an analogous property called Coulomb-orthonormality and which permit us to resolve the two-particle Coulomb operator into a sum of products of one-particle functions.

In the second part of the lecture, I will present and discuss numerical applications of this resolution in the context of quantum chemistry.
First Principles Based Applications in Catalysis, Nanoelectronics, Fuel Cells, Materials Science, and Pharma
William A. Goddard, III
Materials and Process Simulation Center (MSC)
California Institute of Technology (139-74)
Pasadena, CA 91125
Advances in theoretical and computational chemistry are making it practical to consider fully first principles (de novo) predictions of important systems and processes in the Chemical, Biological, and Materials Sciences. Our approach to applying first principles to such systems is to build a hierarchy of models each based on the results of more fundamental methods but coarsened to make practical the consideration of much larger length and time scales. Connecting this hierarchy back to quantum mechanics enables the application of first principles to the coarse levels essential for practical simulations of complex systems.

We will highlight some recent advances in methodology and will illustrate them with recent applications to problems involving Catalysis, Nanoelectronics, Fuel Cells, and materials science selected from
•Mechanism of dioxygen reduction reaction on Pt alloy and non Pt fuel cell cathodes
•New Materials for Reversible hydrogen storage
•De novo Force Fields (from QM) to describe reactions and phase transitions (ReaxFF)
•Si and CNT nanowires for Nanoelectronics switches and interconnects
•Dynamics of Highly excited electronic systems applied to plasma etching of materials
•The mechanism underlying superconductivity in cuprates and FeAsMO systemss
•Predicted 3D structures of G-Protein Coupled Receptors (GPCRs)
•Predicted selective agonists and antagonists to specific GPCRs
Orbital-dependent functionals, new opportunities in DFT
Andreas Goerling
Lehrstuhl fuer Theoretische Chemie
Universitaet Erlangen-Nuernberg
Erlangen, Germany
The concept of orbital-dependent functionals in DFT is presented [1]. The optimized effective potential (OEP) method for constructing local multiplicative exchange-correlation potentials is considered and questions of its numerical stability are discussed [2,3]. A numerical stable OEP approach based on Gaussian basis sets is introduced [4]. As examples of the new opportunities offered by orbital-dependent functionals, a multi-configuration OEP approach for density-functional treatment of static correlation is presented [5] and a magnetization-current density-functional theory for a unified treatment of spin-orbit interactions, currents, and magnetic fields is introduced [6,7].

[1] A. Goerling, J. Chem. Phys., 123, 062203 (2005).
[2] A. Goerling, A. Hesselmann, M. Jones, and M. Levy,
J. Chem. Phys. 128, 104104 (2008).
[3] A. Hesselmann and A. Goerling, Chem. Phys. Lett. 455, 110 (2008).
[4] A. Hesselmann, A. W. Goetz, F. Della Sala, and A. Goerling,
J. Chem. Phys. 127, 054102 (2007).
[5] M. Weimer, F. Della Sala, and A. Goerling,
J. Chem. Phys. 128, 144109 (2008).
[6] S. Rohra and A. Goerling, Phys. Rev. Lett., 97, 013005 (2006).
[7] S. Rohra, E. Engel, and A. Goerling, cond-mat/0608505.
Controlling Many-body Systems with Periodic Driving Fields
Jiangbin Gong
Department of Physics and Centre of Computational Science and Engineering, National University of Singapore, Singapore
Controlled evolution of ultracold atomic and molecular systems is of importance to ultracold chemistry. In particular, the self-interaction of a Bose-Einstein condensate (BEC) presents challenges and new opportunities for many-body quantum control. Here we focus on how adiabatic passage techniques may be still used to control the highly nonlinear mean-field dynamics of a BEC. For example, we show that a periodic driving field may totally suppress the so-called nonlinear Landau-Zener tunneling probability, thus allowing for complete adiabatic population inversion in the presence of strong nonlinearity. We shall also demonstrate that nonlinear Floquet states associated with the driven mean-field dynamics of a BEC can be used for effective and robust adiabatic control. Indeed, using a simple model of a BEC in a double-well potential plus a symmetry-breaking driving field, it is shown that nonlinearity-induced degeneracy of nonlinear Floquet states leads to an interesting phenomenon called "nonlinear anholonomy", in the sense that the system can be placed on a different Floquet state after adiabatically moving along a closed path in the parameter space.
Application and Evaluation of Calix[4]arene-capped beta-Cyclodextrin-bonded Silica Particles as Chiral Stationary Phase for Chiral Drug Separation in Liquid Chromatography
Sennappan Kanagamani Thamarai, Ying Wei, and Yinhan Gong*
Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 119074. Tel: (65)-65158498. Fax: (65)-67751160. E-mail: obggy@nus.edu.sg
Development and application of new chiral stationary phases (CSPs) with high enantioselectivities to separate chiral molecules is one of the most active areas of liquid chromatography (LC). Many chiral separations have been accomplished using beta-cyclodextrin-type bonded silica particles as CSPs in LC. However, one drawback in utilizing beta-cyclodextrins (beta-CD) has been the low binding constants for most guest molecules. The physical chemistry calculation showed that this type of CSP could not separate of chiral isomers of some drug compounds, e.g, warfarin, etc. The main aim of this study is to design, prepare and apply new CSP with high enantioselectivity to separate chiral drug compounds. Calix[4]arene-capped (3-(2-O-beta-cyclodextrin)-2-hydroxypropoxy)-propylsilyl-appended silica particles (C4CD-HPS), a novel type of substituted beta-cyclodextrin-bonded chiral stationary phase, have been synthesized and used to separate chiral drugs in HPLC. This new type of CSP has a chiral selector with two recognition sites: calix[4]arene and beta-CD. The chromatographic behavior of C4CD-HPS has been studied with some chiral drug compounds under both normal and reversed-phase conditions. The results show that C4CD-HPS has excellent enantioselectivity for a wide range of chiral aromatic compounds including warfarin due to the cooperative functioning of the calix[4]arene and beta-CD.
First principles studies of the liquid-vapor interfaces of metals and alloys
David J. Gonzalez, Luis E. Gonzalez
Departamento de Fisica Teorica, Universidad de Valladolid, 47011 Valladolid, SPAIN
We report results of molecular dynamics simulations of the liquid-vapor (LV) interfaces in several liquid metals and alloys. The study has been performed by the orbital-free ab initio molecular dynamics (OF-AIMD) method where the forces acting on the nuclei are computed from the electronic structure which, in turn, is calculated within the density functional theory (DFT). The electronic structure undergoes drastic changes at the LV interface and therefore is important to ensure that the forces on the ions accurately reflect the electronic structure in their surroundings.

The OF-AIMD method uses an explicit, albeit approximate density functional for the electronic kinetic energy. This leads to a substantial simplification over the Kohn-Sham method of DFT which achieves greater accuracy but at the cost of much greater computational expense. The OF-AIMD method makes possible the simulation of much greater samples for longer times.

For each system, the study has been performed by using samples of 2000/3000 particles in a slab geometry with periodic boundary conditions. The longitudinal ionic density profiles (DP) exhibit a pronounced stratification extending several atomic diameters into the bulk. In the alloy, the partial ionic DP's clearly reflect the tendency to migrate towards the surface by the ions with the component with the lower surface tension. The self-consistent valence electronic DP also shows oscillations although weaker than the ionic ones. Comparison is made with the available experimental data.
Monohydration of Nucleic Acid Bases. A Comparison of the Results of Molecular Mechanics and Correlated Quantum Mechanics Calculations.
Eduardo González,1 J. Francisco Meléndez,2 Alexandra Deriabina1and Valery Poltev1
1Facultad de Ciencias Físico-Matemáticas, Universidad Autónoma de Puebla, México

2Facultad de Ciencias Quimicas, Universidad Autónoma de Puebla, México
A correct description of interactions of a single water molecule with the nucleic acid bases is crucial for simulations of nucleic acid structure, functions and interactions with other biologically important molecules. The interaction energies and mutual base - base positions for the four DNA bases can be calculated by two groups of computational methods, molecular mechanics (MM) and quantum mechanics (QM). The simulation of nucleic acid fragments in water surroundings is possible with MM only. Potential functions of molecular mechanics are adjusted to reproduce experimental data on hydration enthalpy of single base - single water interactions and of enthalpy of hydration of the bases. These data are not sufficient to determine all the parameters. To check a validity of MM calculations we perform correlated ab initio QM calculations for different local energy minima of water-base interactions with various basis sets. The minima with a single hydrogen bond and with two hydrogen bonds, when water molecule is H-bonded to the base H-bond donor and H-bond acceptor, obtained by QM calculations are close to those obtained via MM in energies and mutual base - water positions. However, we fail to reproduce via QM calculations with rather extended basis sets mutual base-water positions for some local minima with two water donor - base acceptor H-bonds obtained by MM method. Reasons of such a discrepancy are analyzed and correlations between calculated and experimental characteristics of the base monohydration are discussed.
Orbital-free ab initio simulations of interfaces between liquid metals
and solid metals: inflluence of surface geometry and mobility.
Luis E. Gonzalez and David J. Gonzalez
Departamento de Fisica Teorica. Universidad de Valladolid. 47011 Valladolid. SPAIN
The understanding of the properties of liquid metals in contact with a solid wall is of both physical and technological interest. Through the use of orbital-free ab initio molecular dynamics we analyze the structure of 2000 atoms of a liquid metal (Al, Na or Li) in contact with a metallic wall described atomistically.

For liquid Al, the solid is modeled as an array of Al atoms fixed at the sites of an fcc lattice, somehow simulating a metallic material with a much higher melting temperature. We study how the liquid structure is affected by the orientation of the wall surface (100, 111 and 110).

A further step in the studies is taken by considering real solid metals (whose atoms move) on which the liquid metals lay. In particular we consider Liquid Li in contact with the (110) surface of solid fcc Ca, and liquid Na on the (110) surface of solid bcc Ba.

The choice of systems is dictated by the requirement of a small change in the mean electron density across the solid-liquid interface so as to analyze only the influence of the geometry and mobility of the solid surface on the properties of the liquid in a consistent way through the different systems.
The spherically and system-averaged pair density in the strong-interaction limit of density functional theory
Paola Gori-Giorgi,1 Michael Seidl,2 Andreas Savin1
1Laboratoire Chimie Theorique, CNRS and University Paris VI, 4 Place Jussieu, 75005 Paris, France

2Institute of Theoretical Physics, University of Regensburg, D-93040 Regensburg, Germany
The correlation energy in density functional theory can be expressed exactly in terms of the change in the probability of finding two electrons at a given distance r12 (spherically and system-avergaed pair density, often known as intracule density) when the electron-electron interaction is multiplied by a real parameter &lambda varying between 0 (Kohn-Sham system) and 1 (physical system). In this process, usually called adiabatic connection, the one-electron density is (ideally) kept fixed by a suitable local one-body potential. Here we investigate the intracule density in the large &lambda limit of the adiabatic connection. This strong-interaction limit of density functional theory turns out to be, like the opposite non-interacting Kohn-Sham limit, mathematically simple and can be entirely constructed from the knowledge of the one-electron density. Comparison of our results with the same quantities calculated in the opposite limit, the non-interacting Kohn-Sham system, provides useful insight on the nature of electronic correlation in density functional theory.
On the production of a molecular Rydberg gas and its transformation to a cold plasma

Jonathan P. Morrison, Christopher J. Rennick, James S. Keller*, and Edward R. Grant
Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1 Canada
*Department of Chemistry, Kenyon College,Gambier, Ohio 43022-9623 USA
We report the spontaneous formation of a plasma from a gas of cold Rydberg molecules. Double resonant laser excitation promotes nitric oxide, cooled to 1 K in a seeded supersonic molecular beam, to single Rydberg states extending as deep as 80 cm-1 below the lowest ionization threshold. The density of excited molecules in the illuminated volume is as high as 1 x 1013 cm3. This population evolves to produce prompt free electrons and a durable cold plasma of electrons and intact NO+ ions.
Surface Reactions in Heterogeneous Atmospheric Chemistry and Environmental Catalysis
Vicki H. Grassian
Department of Chemistry
University of Iowa
Iowa City, IA 52242
One of the greatest challenges in fully understanding the environment and environmental consequences of human activity comes from the molecular complexity of the natural and human-impacted environment. This presentation discusses recent experimental and theoretical studies designed to advance the molecular level understanding of the chemistry that occurs on oxide and carbonate surfaces in the atmosphere. Here the role of adsorbed water in the chemistry of oxide and carbonate surfaces with atmospheric gases such as SO2, NO2, HNO3 and CO2 will be discussed. Furthermore, efforts to find methods to remove these gases from the atmosphere using novel nanomaterials are also explored through combined experiment and theory.
First-principles investigations of electrocatalysis and corrosion
Jeffrey Greeley
Center for Nanoscale Materials
Argonne National Laboratory
United States
In recent years, the increasing sophistication of computational surface science methodologies has begun to permit the analysis, using first-principles techniques, of electrocatalytic reactions of interest in fuel cells. In this talk, I will briefly present a simple-yet-powerful approach to such analyses, and I will show how the approach can be applied to a series of problems of interest in both fundamental and applied electrochemistry. The systems of interest are related to both the activity and stability of electrocatalytic materials; they include the oxygen reduction reaction, the electrooxidation of simple alcohols, and metal dissolution/deposition in acids.
Issues in the Imaging of Molecular Orbitals through HHG or Photoionization
Chris H. Greene^1, Zachary B. Walters2, and Stefano Tonzani3
1,2Department of Physics and JILA, University of Colorado, Boulder, CO 80309-0440

3Department of Chemistry, Northwestern University, Evanston, IL 60208-3113
This presentation explores the theory of imaging of molecular orbitals in a photoionization or high-harmonic generation experiment. Some of the limitations of the plane-wave approximation are documented through the study of simple model problems in one dimension. Prospects for seeing evidence of nonperturbative modifications of the electron-rescattering wavefunction will also be discussed.
The radiative lifetime of OH, NH, and metastable CO
Gerrit C. Groenenboom
Theoretical Chemistry
Institute for Molecules and Materials
Radboud University Nijmegen
Heyendaalseweg 135
6525 AJ Nijmegen
In the last decade, many cold molecule techniques were developed. These techniques are now being used to measure molecular properties with unprecedented accuracy, providing benchmark numbers and posing a challenge to ab initio theory.

The Stark deceleration technique has been used to decelerate and trap electrostatically the vibrationally excited hydroxyl radical OH(X2 Π, v=1) [1] and metastable CO(a3 Π) [2]. The radiative lifetimes of these species were measured directly in the time domain. The results are compared to the results of new high level ab initio calculations. Good agreement was found for the OH( v=1) lifetime and the new dipole function was used to recompute the OH Meinel system [3]. The combined experimental and theoretical results for metastable CO imply that the accepted lifetime data for the A1Π state of CO must be revised.

The radiative lifetime of vibrationally excited NH( v=1) was determined in a buffer gas cooling experiment [4]. The result is in perfect agreement with a new ab initio calculation, but both theoretical and experimental results differ considerably from literature results.

[1] S. Y. T. van de Meerakker, N. Vanhaecke, M. P. J. van der Loo, G. C. Groenenboom, and G. Meijer, Phys. Rev. Lett. 95, 013003 (2005)
[2] J. J. Gilijamse, S. Hoekstra, S. A. Meek, M. Metsälä, S. Y. T. van de Meerakker, G. Meijer, and G. C. Groenenboom, J. Chem. Phys., 127, 221102 (2007)
[3] M. P. J. van der Loo and G. C. Groenenboom, J. Chem. Phys. 126, 114314 (2007), ibid. 128, 15992 (2008)
[4] W. C. Campbell, G. C. Groenenboom, H.-I Lu, E. Tsikata, and J. M. Doyle, Phys. Rev. Lett., 100, 083003 (2008)
High harmonic generation from multiple orbitals in N2
Markus Guehr, Brian K. McFarland, Joseph P. Farrell and Philip H. Bucksbaum
Stanford PULSE Center, Physics Department, Stanford University, CA 94305, USA and Stanford Linear Accelerator Center, Menlo Park, CA 94025, USA
We have observed simultaneous high harmonic generation (HHG) from two molecular electronic orbitals, the highest occupied molecular orbital (HOMO) and the next lower bound HOMO-1 in N2. The HOMO-1 is revealed through enhancements in the HHG signal at characteristic alignment angles of the molecular axis to the polarization of the harmonic driving pulse. The angular alignment is accomplished by impulsive rotational excitation of a cold and dense N2 beam by a nonresonant femtosecond laser pulse. During a rotational revival, the molecules undergo a rapid change in orientation with respect to the polarization of a second laser which produces HHG. While low order harmonics (15-25) show a weakening of the harmonic signal if the molecular axis stands preferentially perpendicular to the harmonic generation polarization, at higher harmonic orders a peak appears that is highly visible in this configuration. We attribute the weakened amplitude in the low harmonic to ionization and recombination of the HOMO and the peak at higher harmonics to ionization and recombination of the HOMO-1. The peak prominent at higher harmonics shows three important features predicted by our quantum simulations and simple ionization arguments: it has an extended cutoff; it is strongest when the molecular axes are near 90o to the harmonic generation polarization; and it is most prominent near the cutoff.

We furthermore show phase measurements for the harmonics generated on N2 and Ar. We observe a characteristic phase jump of π at the Cooper minimum of Ar and a phase jump of 0.4 π at the 25 harmonic of N2.
Bridging time-scales in polymer dynamics: coarse-graining and multiscale modeling
Marina G. Guenza
Department of Chemistry and Institute of Theoretical Science
University of Oregon, Eugene, OR 97403 USA
The dynamics of macromolecules is characterized by the presence of several length scales and related time scales in which relevant phenomena take place. This defines the complex nature of the liquid and renders its theoretical treatment a difficult matter. The necessity of developing theoretical approaches that can describe in a comprehensive manner properties observed at many different length scales is a fundamental challenge in polymer physics and biophysics.

Theoretical models play a pivotal role in building the infrastructure that allows one to model these multiscale properties. We present methods to coarse-grain the structure of soft-matter systems, which provide effective potentials that are input to multiscale simulations. We also present methods to coarse-grain the dynamics of macromolecules in dilute solutions and in the melt state. Theoretical predictions for the dynamics of polymer liquids and proteins show quantitative agreement with experimental data.
Implicit Solvent Models for Coupled-Cluster Theory
Steven R. Gwaltney and Kanchana S. Thanthiriwatte
Department of Chemistry, Center for Environmental Health Sciences, and HPC2 Center for Computational Sciences, Mississippi State University, Mississippi State, MS 39762, USA
We report our recent progress on developing methods to include the effects of solvation in high-level electronic structure calculations. First, we will discuss our fully self-consistent coupled-cluster singles and doubles (CCSD) Onsager type model. After presenting some benchmark results, we will discuss the application of this approach to the nitration of benzene and show how solvation effects may affect the mechanism of the reaction. Finally, we will present preliminary results from our recent work combining the reference interaction site model (RISM) description of solvent structure with a CCSD description of the solute (RISM-CCSD).
Hydrogen Tunneling and Protein Motion in Enzyme Reactions
Sharon Hammes-Schiffer
Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802 USA
Theoretical studies of proton, hydride, and proton-coupled electron transfer reactions in enzymes will be presented. We have developed theoretical approaches that include the quantum mechanical effects of the active electrons and transferring proton(s), as well as the motions of the entire solvated enzyme. The proton-coupled electron transfer reaction catalyzed by the enzyme lipoxygenase will be discussed. The experimentally measured deuterium kinetic isotope effect of 80 at room temperature is found to arise from the small overlap of the reactant and product proton vibrational wavefunctions in this nonadiabatic reaction. The calculations illustrate that the proton donor-acceptor vibrational motion and the reorganization of the protein, substrate, and cofactor play vital roles in this enzyme reaction. The hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase will also be discussed. An analysis of the simulations leads to the identification and characterization of a network of coupled motions that extends throughout the enzyme and represents conformational changes that facilitate the charge transfer process. Mutations distal to the active site are shown to significantly impact the catalytic rate by altering the conformational motions of the entire enzyme and thereby changing the probability of sampling conformations conducive to the catalyzed reaction.
Hybrid quantum/classical molecular dynamics of hydrogen transfer reactions in enzymes
Sharon Hammes-Schiffer
Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802 USA
Hybrid quantum/classical molecular dynamics methods for simulating proton and hydride transfer reactions in solution and enzymes will be presented. These approaches include electronic and nuclear quantum effects, as well as the motions of the entire solvated enzyme. Recently developed methods for enhanced sampling and the efficient generation of potentials of mean force will be discussed. A comparison of methods including nuclear quantum effects through grid-based and path integral approaches will also be presented. The accuracy and reliability of these methods are assessed by comparison to exact quantum dynamical calculations for model systems and comparison to experimental data for complex enzyme systems.
Attosecond resolution quantum dynamics for atoms and molecules in strong laser fields
Ke-Li Han
State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
A parallel quantum electron and nuclei wave packet computer method has been developed to study laser–atom/molecule interaction in the nonperturbative regime with attosecond resolution. The nonlinear phenomena occurred in that regime can be studied with the code in a rigorous way by numerically solving the time-dependent Schrödinger equation of electrons and nuclei. Time-propagation of the wave functions is performed using a split-operator approach, and based on a sine discrete variable representation. Photoelectron spectra for hydrogen and kinetic-energy spectra for molecular hydrogen ion in linearly polarized laser fields are calculated using a flux operator scheme, which testifies the validity and the high efficiency of this method.
Simplified Quantum Monte Carlo Trial Function Design for “Difficult” Systems
John A.W. Harkless1, Floyd A. Fayton1, Ainsley A. Gibson2, and Joseph S. Francisco3
1Department of Chemistry, Howard University, Washington, DC, 20059
2Advanced Research Computing, Georgetown University, Washington, DC, 20057
3Department of Chemistry and Department of Earth & Atmospheric Sciences, Purdue University, West Lafayette, IN 47907-2084

Current and ongoing work in applying simplified trial function design to “difficult” systems has met with varied degrees of success. We report results from applying quantum Monte Carlo (QMC) to the energetics of S4, N2, O2, C2, and select transition metal systems. The S4 results estimate the energy gap between the C2v and D4h conformers, atomization and bond energies, as well as selected excited states. Singlet and triplet electronic excitations are estimated for N2, O2, C2. The ionization potential and electron affinities of Sc-Cu will be reported as well. The overall effectiveness and accuracy of our variational and diffusion Monte Carlo results are compared against other available theory and experiment.
Measuring chirality in NMR in the presence of a static electric field.
Robert A. Harris*(1), Jamie D. Walls(2), Cynthia J.Jameson(3)
(1) Department of Chemistry, University of California, Berkeley
(2) Department of Chemistry, Harvard University
(3) Department of Chemistry, University of Illinois, Chicago
Simple symmetry arguments are presented to show that an isotropic nuclear spin Hamiltonian in the presence of a static, homogeneous electric field supports chirality. However,the eigenvalues of said Hamiltonian are not chiral; hence chirality is not manifest in the usual NMR experiments. We show that the response to certain pulse sequences exhibit chirality.
A Jahn-Teller analysis of K3 and Rb3 in the electronic states
12E´and 12E´´
Andreas W. Hauser,1 Carlo Callegari,1 Wolfgang E. Ernst1 and Pavel Soldán2
1 Institute of Experimental Physics, Graz University of Technology, Petersgasse 16, A-8010 Graz, Austria

2 Charles University in Prague, Faculty of Mathematics and Physics, Department of Chemical Physics and Optics, Ke Karlovu 3, CZ-12116 Prague 2, Czech Republic
The doublet ground states of the alkali trimers are paradigmatic for the
E × e type Jahn-Teller problem, which describes the interaction of a two-fold degenerate electronic state with a two-fold degenerate vibration [I.B. Bersuker, Chem. Rev. 101, 1067-1114 (2001)].

In this study the homonuclear trimers of potassium and rubidium are investigated in their Jahn-Teller distorted doublet 12E´ (1B2/1A1 in C2v symmetry) ground states and 12E´´ (2B1/1A2) excited states at the CCSD(T) and CASPT2 level of theory. Two-dimensional cuts of the ground state PES are presented and analyzed in terms of the theory of Jahn-Teller potentials. We extract the corresponding parameters for both molecules in both states via nonlinear fits of the PES as a function of the Qx (symmetric bending mode) and Qs (breathing mode) normal coordinates.

With inclusion of spin-orbit coupling the Jahn-Teller effect is partially quenched. We make use of the ECP-LS technique to calculate the splittings and apply the methodology of Barckholtz and Miller to provide an analytical description for the corresponding states of both trimers [T. A. Barckholtz and T. A. Miller, Int. Rev. in Phys. Chem. 17, No. 4, 435-524 (1998)].
Tractable Valence Space Models for Strong Electron Correlations
Martin Head-Gordon
Department of Chemistry,
University of California, and,
Chemical Sciences Division,
Lawrence Berkeley National Laboratory
Berkeley CA 94720
USA
Strong correlations can be viewed as those arising within a valence orbital active space. One reasonable definition of such a space is to supply one correlating orbital for each valence occupied orbital. Exact solution of the Schrodinger equation in this space is exponentially difficult with its size, and therefore approximations are imperative. The most common workaround is to truncate the number of orbitals defining the active space, and then solve the truncated problem, as is done in CASSCF. An important alternative is to systematically approximate the Schrödinger equation in the full valence space, for example by using coupled cluster theory. I shall discuss some recent advances in low-scaling coupled cluster models for valence correlations, and some chemical applications to biradicaloid and bond-breaking problems using these methods.
Coherent Control with Shaped Femtosecond Pulses: Applications to CARS
X.G. Xu, S.O Konorov, John W. Hepburn, V. Milner
The Laboratory for Advanced Spectroscopy and Imaging Research (LASIR)
Department of Chemistry
University of British Columbia
This talk will describe the general features of coherent control with shaped, broadband, femtosecond pulses. Recent work in our laboratory has focussed on coherent population transfer and CARS spectroscopy using shaped tuneable femtosecond pulses. The talk by Valery Milner in this session will describe the coherent population transfer experiments, while this talk will focus on using broadband femtosecond pulses for high resolution CARS spectroscopy. In recent publications, we have described the use of shaped broadband pulses to completely characterize, with high energy resolution, molecular vibrations(1), and the use of noise auto-correlation to record a high resolution CARS spectrum(2). Extensions of this work into coherent control of CARS intensities and all-optical processing of femtosecond CARS to produce a high resolution spectrum will be used to illustrate the power of femtosecond CARS.
(1)X.G. Xu, S.O. Konorov, S. Zhdanovitch, J.W. Hepburn, and V. Milner, J. Chem. Phys. 126, 091102 (2007)
(2)X.G. Xu, S.O. Konorov, J.W. Hepburn, and V. Milner, Nature Physics 4, 125-129 (2008)
Computational Studies of Unbridged Dizinc Compounds
Steven S. Hepperle and Yan Alexander Wang
University of British Columbia, Vancouver, British Columbia, Canada, V6T1Z4
It has been four years since the first synthesis of the dizinc compound Zn25-C5(CH3)5)2 from Zn(η5-C5(CH3)5)(η1-C5(CH3)5) and Zn(C2H5)2, and since then numerous theoretical papers have been published regarding the properties of this molecule. However, the mechanism of this reaction has yet to be elucidated. We have used Kohn-Sham computational methods coupled with MP2 single-point energies to study a variety of different mechanistic possibilities for the formation of Zn25-C5(CH3)5)2. In order to understand the plausibilities of each of these mechanisms, they will be further compared with pseudo-mechanisms for the synthesis of Zn25-C5H5)2 (which does not form experimentally). From these comparisons, a suitable rationalization of the role the methyl groups play in the formation of Zn25-C5(CH3)5)2 can be inferred. Also, it has been found that only certain ZnR2 reagents (R= C2H5, C6H5) react to form Zn25-C5(CH3)5)2, and an analysis of this experimental data may also be included in this work.
Unraveling the electronic states of DNA multimers using novel methods based on time-dependent density functional theory
John M. Herbert
Department of Chemistry
Ohio State University
Columbus, OH
For small organic chromophores, time-dependent density functional theory (TD-DFT) offers a reasonably accurate means to calculate excitation energies for the lowest few valence excited states, and at the same time this method is computationally tractable in much larger systems. This talk will detail the catastrophic problems (namely, the appearance of a multitude of spurious charge-transfer states, along with spurious intensity stealing) that are encountered when TD-DFT with standard functionals is applied to large molecules, clusters, or condensed-phase environments. In an effort to alleviate this problem, and to facilitate TD-DFT calculations in systems that exhibit real charge-transfer states, our group has begun to experiment with long-range-corrected DFT, in which the Hartree-Fock exchange interaction is turned on (and local DFT exchange is turned off) asymptotically, in order to achieve the correct 1/R asymptotic decay of the exchange-correlation potential. We are using this and other new techniques to understand the complicated electronic structure of single- and double-stranded DNA, where it appears that ππ* excitons and also charge-transfer excimer states both exist at comparable energies near the Franck-Condon geometry. Sorting out the excited-state potential energy surfaces is crucial to understanding DNA's intrinsic photostability.
OH
Kersti Hermansson
Materials Chemistry, The Ångström Laboratory,Uppsala University, Box 538, S-751 21 Uppsala, Sweden
I will discuss the calculation of OH frequencies in ionic aqueous solutions and in crystalline solids, absolute frequencies as well as frequency shifts.

O-H stretching vibrational frequencies are known to be very sensitive to intermolecular interaction. IR and Raman spetroscopies are therefore two of the major research tools for characterization of the local structure and bonding around water and OH groups.
Theoretical calculations can provide much insight here, and help disentangle the various contributions to the OH frequency downshift (down or up).

The calculation of OH frequencies in liquid solutions is particularly challenging since it requires an adequate treatment of the temperature effects, the interatomic interactions, the (anharmonic) vibrations, and access to a reliable structural model. We are using a 4-step "QM + MD + QM + QM' strategy to address these computational difficulties, and I will present results for the first hydration shell around mono- and multi-valent metal ions in aqueous solution.
Interference induced by static magnetic fields in ultracold collisions
Felipe Herrera and Roman Krems
Department of Chemistry, University of British Columbia, Vancouver,
B.C. V6T 1Z1, Canada
We propose a general method for inducing interference between scattering wave functions in atomic and molecular collisions at ultracold temperatures, by using a dc magnetic field. The scheme is based on the preparation of collision partners in coherent superpositions of Zeeman states. The magnetic field is used to induce interference between two incident incoming channels. As an illustrative example, we consider ultracold collisions between Li and Cs atoms, and show that ratios of state resolved collision cross sections can be enhanced significantly by engineering the preparation of the initial coherent superpositions.
Molecular Theory for Large Systems
Takahito Nakajima, Takao Tsuneda, and Kimihiko Hirao
Department of Applied Chemistry, School of Engineering,
The University of Tokyo
With the emergence of peta-scale computing platforms we are entering a new period of modeling. The computer simulations can be carried out for larger, more complex, and more realistic systems than ever before. DFT may be the only tool that enables us to carry out accurate simulations for larger systems such as biomolecules and nanomaterials with reasonable computational cost.

The evaluation of Coulomb integrals is very often the most time consuming step for DFT with GGA functionals. A linear-scaling implementation of the Gaussian and finite-element Coulomb (GFC) method is presented for the rapid computation of the electronic Coulomb potential [1]. Coulomb integrals can be evaluated by solving the Poisson equation. The fast multipole method is utilized for the evaluation of the Poisson equation boundary condition [2]. The method realizes a linear scaling with system size for both one-dimensional polyalanine chains and three-dimensional diamond fragments. It makes molecular quantum calculations affordable for very large systems involving several thousands of basis functions.

Although hybrid GGA improves the accuracy, it makes the calculation more expensive since the fast algorithms for Coulomb integrals cannot be employed for HF exchange. The hybrid DFT application to large systems is limited. Recently we have developed the dual-level approach to DFT [3]. The scheme is based on the low sensitivity of the electron density to the choice of the functional and the basis set. The dual-level DFT works quite well and the large reduction of the computer resources can be achieved. Hybrid functional can now be applied to very large systems.

The first-order molecular properties are well predicted by GGA functionals. However, induced or response properties require correction for the asymptotic behavior. The failure arises from the wrong long range behavior due to the local character of the approximate exchange- correlation functionals. By splitting the Coulomb interaction into short-range and long-range components following Savin’s idea, we have proposed a new hybrid GGA functional with correct long-range electron- electron interactions [4]. Hybrid GGA has good energetics, good Rydberg behavior, good CT predictions, and good optical response. Van der Waals interactions are also described accurately [5]. The scheme was applied to planar aromatic systems (dimers and trimers of coronene, circum coronene, and circum circum coronene) to estimate -stacking energies.

References
[1] Y.Kurashige, T. Nakajima and K.Hirao, J.Chem.Phys., 126, 144106 (2007).
[2] M. Watson,Y.Kurashige, T. Nakajima and K.Hirao, J.Chem.Phys., in press.
[3] T.Nakajima and K.Hirao, J.Chem.Phys., 124, 184108 (2006).
[4] Y.Tawada,T.Tsuneda,S.Yanagisawa,T.Yanai and K.Hirao, J.Chem.Phys. 120, 8425 (2004).
[5] T.Sato, T.Tsuneda and K.Hirao, J.Chem.Phys., 123, 104307 (2005).
Future Directions in Coupled-Cluster and Perturbation Theories
So Hirata
Quantum Theory Project, Department of Chemistry and Department of Physics, University of Florida
We propose four research directions that we consider the most important and fruitful in coupled-cluster and perturbation theories: (1) Automated derivation and implementations, (2) Flexible basis sets (including explicitly-correlated approaches and the use of grids), (3) Linear or low-rank cost-scaling algorithms for large molecules and solids, and (4) Extensions to other many-body problems such as molecular vibrations. We will present our contributions along these directions. This work is supported by U.S. Department of Energy, Office of Basic Energy Sciences (DE-FG02-04ER15621).
Low variance trial wave-functions for Quantum Monte Carlo with numerically stable analytical gradients over exponential orbitals.
Peter Reinhardt(1) and Philip Hoggan* in collaboration with Roland Assaraf(1)
* Presenter, LASMEA, UMR CNRS 6602, University Blaise Pascal, 24 Avenue des Landais, Clermont-Ferrand.

(1) LCT, University Pierre et Marie Curie, Jussieu, Paris.
Trial wave-functions used in Quantum Monte Carlo (QMC) calculations are demonstrated to require the correct nuclear cusp and exponential decay. It is also advantageous to possess the correct nodal structure of the molecular orbitals for the ground state system. These conditions are seen to be catered for by Sturmian basis functions.

The trial wave-function can conveniently include electron correlation, which is frequently implemented 'a posteriori' using a Jastrow factor in the internuclear variable. The possibility of Sturmian including geminal basis functions in this variable is briefly mentioned. Anti-symmetrized spinorbital and geminal products of Coulomb Sturmians provide compact low variance explicitly correlated trial wave-functions for QMC.

Graphic examples of electron density and its gradient will be shown including the chlorine atom and the water molecule in ETO basis sets readily available (Thakkar, ADF) and more extended examples. These are contrasted with results in a gaussian basis.
Keywords: Coulomb potential, Coulomb Sturmians, explicit correlation.
Initial steps towards a parameter-free simulation for material properties: Electronic couplings in transport processes
Chao-Ping Hsu
Institute of Chemistry, Academia Sinica,
128 Academia Rd. Sec. 2 Nankang, Taipei, 115 Taiwan ROC
In simulations for the charge or photon energy transporting properties, it is often necessary to employ empirically fitted parameters. However in designing new molecular systems to improve device performances, it is necessary to use a predictive scheme without unknown empirical parameter. The rate of charge transfer (CT) and excitation energy transfer (EET) between two molecules in a material directly affect its charge mobility, exciton diffusion, and spectroscopic characteristics. The rates of these processes can be described by the Fermi golden rule and its extensions, where the rates typically depend on the squared amplitude of electronic coupling factor. To obtain such an electronic coupling (an off-diagonal matrix element) out of eigenstate solutions that typical quantum calculations yield, it is necessary to develop proper theoretical definitions and computational schemes. The first part of this presentation will consist of recent progresses in the methodologies that can characterize electronic coupling values for parameter-free simulations. In particular, we have recently developed new schemes for a general class of molecules in their CT and EET processes. The organic dyes used in dye-sensitized solar cells (DSSCs) were also under investigation. The second part of the presentation will include our recent results, where a positive correlation between the device performance and the amount of charge separation upon photo excitation is seen.
Ultracold molecules: production and control
Jeremy M. Hutson
Department of Chemistry, University of Durham, South Road,
Durham, DH1 3LE, England
There have been enormous advances over the last few years in methods to produce cold molecules, below 1 K, and ultracold molecules, below 1 mK. This talk will briefly outline recent experimental advances and then turn to the challenges that they pose for theoretical chemical physics. We need to understand the interactions and collisions of molecules at very low energies. In addition, since ultracold molecules will be controlled with electric and magnetic fields, it is crucial to include these in the calculations. The small splittings due to nuclear spins are also very important.

There are two different classes of experiment directed at ultracold molecules. In indirect methods, molecules are produced directly in laser-cooled atomic gases. These methods have already produced molecules at nK temperatures. The initial experiments produced molecules very near dissociation, but it is now realistic to expect that a dense gas of ultracold molecules in their ground state will be produced in a matter of months. The talk will describe recent calculations on the (remarkably complex) energy levels of Cs2 in magnetic fields, both near dissociation [1] and in low-lying states [2].

In direct methods, molecules are cooled from room temperature. These methods can be applied to many more species than direct methods, but have not yet produced trapped molecules below about 10 mK. One of the most promising methods to cool such molecules further is sympathetic cooling, in which the molecules are cooled by contact with a laser-cooled atomic gas at μK temperatures. The talk will describe recent calculations designed to help choose a good system for sympathetic cooling experiments [3].

[1] J. M. Hutson, E. Tiesinga, and P. S. Julienne. Avoided crossings between bound states of ultracold Cesium dimers. arXiv:physics/0806.2583 (2008).

[2] J. Aldegunde and J. M. Hutson. The hyperfine energy levels of alkali metal dimers: low-lying rotational states of homonuclear molecules in magnetic fields. In preparation (2008).

[3] P. S. Zuchowski and J. M. Hutson. The prospects for producing ultracold NH3 molecules by sympathetic cooling: a survey of interaction potentials. arXiv:physics/0805.1705 (2008).
Atomic Structures of Carbon Nanotubes
Sumio Iijima1,2,3
1National Institute of Advanced Industrial Science and Technology /Nanotube Research Center, Japan
2NEC, Japan
3Faculty of Science and Technology, Meijo University, Japan
Controlling the structures of carbon nanotubes has been an important issue in many research areas such as optical property measurements, electron transport, mechanical property etc. and elucidation of tubule growth mechanism as well as industrial applications (for instance separation of semiconducting and metallic). Among many characterization techniques the most straightforward one is high resolution electron microscopy (HRTEM), particularly at the atomic level resolution. The development of the spherical aberration correction devices enables us to visualize individual carbon atoms on a single graphene sheet, providing directly chiral indices (n, m) of any single or double walled carbon nanotube. Another application of the HRTEM to nano-carbon materials is to direct molecular structure determination of single molecules such as higher fullerene molecules and metallofullerenes, that will be a good complementary method to synchrotron X-ray diffraction method. More important emphasis will be on in-situ observation of dynamic morphological-changes in carbon nanotubes under various conditions (heat, current directions, presence of metal catalysts etc). The new technique revealed the electro-migration and diffusion of atomic defects such as atomic carbon vacancy and “interstitial” that takes place on the graphene sheets. The information thus obtained forms an important basis of understanding various unique properties of carbon nanotubes.

Z. Liu, et al., Phys. Rev. Lett., 95, 187406(2005). K. Suenaga, et al. Nature Nanotech. 2, 358 (2007).
Z. Liu, et al. Nature Nanotech.,422 (2007). Y. Sato, et al., Nano Lett, 7, 3704 (2007). C. Jin, et al.,
Nature Nanotech.3, 17 (2008). C. Jin, et al., Nano Lett. 8, 1127(2008).
Condensation of a Miscible Vapour onto a Liquid Nano-droplet
Levent Inci,1 and Richard K. Bowles1
1Department of Chemistry, University of Saskatchewan, Canada
The condensation of a vapour onto a liquid nano-droplet is an important atmospheric process that allows the cloud condensation nuclei to grow. We study a Lennard-Jones binary mixture consisting of a non-volatile liquid nano-droplet surrounded by a miscible solvent vapour phase using Molecular Dynamics (MD) simulations. Preliminary investigations of the nucleation of the vapour particles onto the nano-droplet show that two distinct processes : First, the nucleation of thin film around the nano-droplet which appears to be dominated by large fluctuations in the size of largest cluster suggesting nucleation occurs by non-classical mechanism, possibly involving the coalescence of smaller embryos on the surface of the droplet and this process is followed by a subsequent growth of the droplet.
2D Spectrochemical Series of ML6 Metal Complexes for Controlling the Ligand Field Splitting
Tomohiko Ishii,1 Shino Tsuboi,1 Genta Sakane2 and Masahiro Yamashita3
1Department of Advanced Materials Science, Faculty of Engineering, Kagawa University, Takamatsu, JAPAN

2Department of Chemistry, Faculty of Science, Okayama University of Science, Okayama, JAPAN

3Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, JAPAN
Metal complexes are very attractive compounds because of their physical properties such as the electronic, magnetic and the optical phenomena can be explained by means of the ligand field splitting of the d- and/or f-electron orbitals of the central metal atom. The physical properties can be controlled continuously by changing the substituent of the ligand molecules. So many coordination chemists are studying how to control freely the ligand field splitting width by changing the chemical modification to the ligand. There are some basically textbook examples of the ligand field splitting such as the crystal field theory, ligand field theory, Tanabe-Sugano diagram, and the Tsuchida's spectrochemical series, as following,

CO > CN > PPh3 > NO2 > SO32– > phen > bpy > en > NH3 > py > CH3CN > ONO > NCS > OH2 > C2O42– > ONO2 > OSO32– > OCHO > OH > OCO22– > OCOR > S2O32– > F > N3 > Cl > SCN > S2– > Br > I ,

that is the most powerful strategic system for the metal complexes including the bidentate ligands with almost of trivalent cobalt (Co(III)) and chrome (Cr(III)). But these theoretical systems are not appropriate for many other complexes. On the other hand, the central metal dependence of the spectrochemical series has also been reported, as following,

Pt4+ > Ir3+ > Pd4+ > Ru3+ > Rh3+ > Mo3+ > Mn4+ > Co3+ > Fe3+ > V2+ > Fe2+ > Co2+ > Ni2+ > Mn2+ ,

should be suitable for the hexaammine complexes [M(NH3)6]n+ and the hexaaqua ones [M(H2O)6]n+. Unfortunately, it is also well knows that the metal atom dependence of the spectrochemical series is not suitable for any other ligand molecules except in the cases of these ammonia and water. There are no developments of the discussions of ligand field splitting and the spectrochemical series during these 30-40 years, whereas the Tsuchida's spectrochemical series mentioned above was reported more than 70 years ago. Therefore, we are trying to review the ligand dependence and/or metal dependence of the spectrochemical series separately, and the concept of the novel universal spectrochemical series, which can be applied for any combinations of the central metals and the ligand molecules, should be introduced.

Quantum wavepacket ab initio molecular dynamics: Applications to vibrational properties in hydrogen-bonded clusters and hydrogen tunneling in biological enzymes
Srinivasan S. Iyengar
Department of Chemistry and Department of Physics,
Indiana University,
800 E. Kirkwood Ave.,
Bloomington, IN-47405.
USA
http://www.indiana.edu/~ssiweb/
This talk is arranged in three parts: The first part of the talk deals with the discussion of a computational methodology developed within our group. The approach combines quantum wavepacket dynamics with ab initio molecular dynamics and is potentially useful in studying problems where nuclear quantum effects can play an important role. Computational bottlenecks and associated solutions are also discussed. The second and third portions of the talk deal with applications of this approach that result in interesting insights in (a) hydrogen tunneling in biological enzymes, and (b) solvation structure, dynamics, and simulation of vibrational spectroscopy in hydrogen-bonded molecular clusters.
First Principles Studies on the Electrode/Electrolyte-Interface
Timo Jacob
Universität Ulm, Albert-Einstein-Allee 47, D-89069 Ulm, Germany
In order to obtain a deeper understanding of the processes underlying electrocatalytic reactions an atomistic view is required. However, compared to experimental setups under UHV conditions, electrochemical reactions occur in a multi-component environment and under conditions of finite temperature, pressure, and electrode potential. Here it is necessary not to study the entire system, but to separate out the influence of particular external parameters, such as the composition of the system, temperature, pressure, or electrode potential and to investigate the induced changes on the atomic level.

In order to describe electrochemical interfaces we recently formulated the extended ab initio atomistic thermodynamics method, which allows calculating ( p,T,φ)-phase diagrams from first principles. On the basis of this approach we will first discuss the possibilities and limitations of theoretical approaches to electrochemistry. Afterwards, we will focus on the oxygen reduction reaction (ORR) and successively include environmental parameters, showing that a pure and perfect catalyst surface, which is often used to study this reaction, is clearly incomplete.

Finally, calculations on alternative catalyst materials (Pt-based alloys and nano-structured Ir) that experimentally show enhanced reaction rates are discussed. We find that the electrode potential is also an important parameter for actively tuning electrode morphologies and nanostructuring.
Investigation of chiroptical properties of Benzodiazepines through theoretical methods and experimental data
Sajid Jahangir,1,2 Walter M. F. Fabian1 Khalid Mohammad Khan3 and S. Tahir Ali1,2
1Institut für Chemie, Karl-Franzens Universität Graz, Heinrichstr. 28, A-8010 Graz, Austria
2Department of Chemistry, Federal Urdu University of Arts, Science and Technology Gulshan-i-Iqbal Campus Karachi, Pakistan
3International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
The Boltzmann weighted circular dichroism spectra of 4-Methyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazipin-2-one (R and S configuration), 4-Methyl-5-acetyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazipin-2-one (R configuration) and 4,5-Dimethyl-1-acetyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazipin-2-one (R configuration) are simulated on the basis of electronic excitation energies (wavelength) and rotational strengths R (cgs). Ten conformation of each analogue are obtained by Sybyl simulated annealing at force field MMFF94s. All the conformers are optimized by B3LYP/6-31G(d) level of theory. Electronic excitation energies (wavelength) and rotational strengths R (cgs) are calculated by time dependent density functional theory using density functional B3PW91 and bases set TZVP. The experimental and calculated CD spectra are compared and influence of H-, CH3- and CH3CO- group on CD spectra is determined.


Toxicity of Lead: Quantum-Mechanical Exploration of Lead Poisoned Zinc Fingers
Andrzej A. Jarzecki
City University of New York, Brooklyn College
We report on a systematic quantum-mechanical study aimed at elucidating the essential connections between lead coordination preferences and lead toxicity at the molecular level. We have demonstrated – in agreement with experimental data – that lead binds tightly, especially to cysteine-rich sites, and it introduces new coordination preferences and structures that do not stabilize the proper form of structural zinc-binding domains. Electronic structure calculations, along with the molecular orbital analysis, have revealed that the classical interpretation of major role of stereochemically active lone-pair orbital in the observed structural diversity of lead complexes might be too simplistic. We have proposed that the optimal arrangement of lead’s ligand is modulated by the extant od s-p orbital mixing and electronic stabilization of lone-pair orbital, which is differently influenced by sulfur and nitrogen donor atoms. Computed structural parameters were found to be in excellent agreement with crystallographic and EXEFS data. Computed UV spectra have identified characteristic UV bands for lead poisoned peptides observed at around 260 nm and 330 nm. The bands have been definitively assigned as ligand-to-metal charge-transfer bands. Direct comparison of computed UV spectra with model peptides strongly suggests a possibility of mixed (tetra- and tri-coordinated lead) structural domains coexisting in the poisoned protein environment.

In light of these results, we have concluded that sensitive structural and dynamic probes of lead domain formation, such as resonance Raman (RR) spectroscopy guided by theoretical calculations could become an essential tool to advance our understanding of lead poisoning mechanisms.

Our initial simulations of RR spectra have been focused on cysteine-rich lead domains. These results indicate that a specific structure and coordination mode of lead in cysteine-rich lead domains might be detectable by RR spectroscopy. We have predicted that when the excitation wavelength is in resonance with UV lead bands, the appreciable enhancement of vibrational modes is found not only for expected Pb-S stretching and bending modes, but also for characteristic C-S stretching and CH2 bending modes of coordinated cysteine. Even more importantly, computed RR intensities for lead domains show unique patterns, and therefore, they might be successfully applied to identify and to monitor structure and coordination of lead in poisoned proteins.

Analysis of the Origin of Catalytic Activity of Platinum in Electrochemical Reactions Involving Hydrogen
Gregory Jerkiewicz
Queen's University, Department of Chemistry
90 Bader Lane
Kingston, Ontario
K7L 3N6, Canada
The future hydrogen economy, which involves the use of H2 as a renewable fuel and an energy carrier, drives the interest in various aspects of hydrogen electrochemistry. In the context of hydrogen generation and utilization in electrochemical devices, platinum is one of the most important catalytic metals. Specifically, Pt is an extremely active metallic catalyst for the H2 generation through water electrolysis (it lies at the apex of the electrochemical “volcano relation”), H2 electro-oxidation, and electrocatalytic hydrogenation of unsaturated organic compounds. However, the origin of platinum’s exceptional catalytic activity is not well understood, although factors such as chemical inertness, mechanical stability and strength, electronic properties, and adsorption behavior, just to mention a few, are recognized to play an important role. Clearly, the origin of platinum’s catalytic properties needs to be understood in order to develop guidelines and criteria for the smart design and manufacture of cheap, abundant alternatives. This contribution overviews the results of long-term, meticulous research on the interfacial behavior of Pt under electrochemical conditions, and presents new results and concepts. In particular, the concept of the potential of minimum mass is introduced and its importance to electrochemistry is analyzed. The role of the under-potentially deposited H (Hupd) in several electrode processes involving H is discussed. The origin of OHads, that is believed to participate in the electro-oxidation of COads, is studied.
In-situ electrochemical quartz-crystal nanobalance (EQCN) study of the behavior of Pt in aqueous H2SO4, HClO4 and NaOH reveals that the interfacial mass reaches a minimum at 0.045 V, as the applied potential is scanned from +1.50 V to –0.20 V, or vice versa. The minimum is referred to as the potential of minimum mass (Emm or pmm) and its value (0.045 VSHE) for this system coincides with the completion of adsorption of Hupd and the commencement of electrolytic H2 generation. The value of Emm, that is different from the potential of zero charge (pzc = 0.27 V), and the structure of the Pt/electrolyte interface in the vicinity of 0.045 VSHE are discussed in terms of interactions of Hupd, Hopd, anions, and H2O molecules with Pt. The saturation layer of Hupd that develops prior to the onset of the H2 generation (also called the hydrogen evolution reaction, HER) modifies platinum’s hydrophilic properties, possibly facilitating the adsorption of over-potentially deposited H (Hopd). The EQCN analysis also reveal an increase of interfacial mass in the potential region of HER that is assigned to hydrogen bonding-like interactions between Hopd and H2O molecules in the double-layer.
Re-examination of the mechanism of Pt electro-oxidation that involves in-situ EQCN, ex-situ Auger electron spectroscopy (AES), cyclic-voltammetry (CV), and long-term anodic polarization measurements reveals that the process does not involve OHads as an intermediate; on the contrary, it results in the direct formation of PtO. The growth of PtO is treated theoretically using oxide growth theories (theory I: interfacial escape of the metal cation from the metal into the oxide; theory II: interfacial place exchange between Pt surface atoms and Oads adatoms). The absence of OHads as an intermediate raises important questions with respect to the origin of OH that is believed to be operative in the electro-oxidation of COads through the formation of the (Pt–CO∙∙∙OH–Pt)≠ activated complex.
Delocalization Errors in Density Functionals and Implications for Diels-Alder Reactions
Erin R. Johnson, Paula Mori-Sánchez, Aron J. Cohen, and Weitao Yang
Department of Chemistry, Duke University, Durham, NC, 27708
Diels-Alder reactions involve the cycloaddition of a substituted alkene to a conjugated diene. This class of reactions is extremely important in organic chemistry and occurs via a concerted mechanism. While computational methods now approach chemical accuracy for many organic reactions, recent work by Houk and coworkers revealed that popular Density-Functional Theory (DFT) methods yield unusually large errors in the thermochemistry (and barriers) of Diels-Alder reactions. This is surprising because the closed-shell reactants and products are precisely the type of organic chemical species generally thought to be well-described by DFT. This work investigates the performance of several density functionals for the thermochemistry of Diels-Alder reactions. The observed errors arise because most popular functionals suffer from delocalization error and therefore have an energetic bias against localized densities. We correlate the errors in Diels-Alder reaction energies with the repulsion energy between the bridgehead carbon atoms in the bicyclic reaction products. Two functionals free from electron delocalization error yield significantly more accurate results. We conclude that this class of functional can ensure correct prediction of the exothermicity of Diels-Alder reactions. More generally, functionals free from delocalization error should be used for theoretical studies of reactions where there is a loss of extended conjugation or formation of highly branched or cage-like moieties.
Multimillion-To-Billion Atom Molecular Dynamics Simulations of Deformation, Fracture and Nanoindentation in Silica Glass
Rajiv K. Kalia, Aiichiro Nakano, and Priya Vashisht
Collaboratory for Advanced Computing and Simulations
University of Southern California, Los Angeles, CA 90089-0242, USA

Cavitation is a ubiquitous form of damage in the ductile fracture of metallic alloys. However, recent Atomic Force Microscopy studies of stress corrosion cracking and molecular dynamics (MD) simulations of dynamic fracture reveal that the key damage mechanism during crack extension in “brittle” glasses also involves cavitation, albeit at the nanometer scale. In this talk, I will present results of our multimillion-to-billion atom MD simulations on: (1) nucleation, growth and coalescence of damage nanocavities in dynamic fracture of amorphous silica; (2) deformation and breakup mechanisms for nanovoids in shearing silica glass; and (3) defect migration and recombination in nanoindentation of amorphous silica.
Approximate coupled-cluster singles, doubles, triples, and quadruples methods
Mihály Kállay1 and Jürgen Gauss2
1Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Budapest P.O.Box 91, H-1521 Hungary
2Institut für Physikalische Chemie, Universität Mainz, D-55099 Mainz, Germany
The theory and implementation of approximate coupled-cluster singles, doubles, triples, and quadruples (CCSDTQ) methods are discussed for general single determinant reference functions. While the extension of iterative approximate models to the non-Hartree--Fock case is straightforward, the generalization of perturbative approaches is not trivial. In contrast to the corresponding perturbative triples methods, there are several additional terms required for non-Hartree--Fock reference functions, and there are several possibilities to derive approximations to these terms. However, it is difficult to develop an approach that is consistent with the canonical Hartree--Fock-based theory. Several approximations have been implemented and their performance for total energies and heats of formation has been assessed. The numerical results show that the performance of the methods does not depend strongly on the approximations assumed. Furthermore, the new perturbative quadruples methods, when applied to canonical Hartree--Fock reference functions, outperform the existing ones without increasing the computational costs.
Methods of Fermion Monte Carlo
M. H. Kalos
Lawrence Livermore National Laboratory, Livermore CA, 94551, USA
Our research has been aimed at a method that solves the Schroedinger equation in imaginary time for fermions systems, and that has no uncontrolled approximations, such as a fixed node. We use walkers that carry plus and minus signs, usually organized as populations of pairs of opposite signs. To avoid the exponential decay of Monte Carlo signal-to-nose ratio, it is necessary to cancel close pairs. In high-dimensional spaces, diffusing walkers rarely come close enough to cancel, but this is overcome by correlating the diffusion of the walkers in an appropriate way. One must also remove the "plus-minus" symmetry, so that the asymptotic joint distribution of plus and minus walkers is not symmetric under the exchange of walkers of opposite signs and therefore has a non-zero overlap with an antisymmetric projection function. This symmetry can be broken in several ways: by the use of importance functions that are different for plus and minus walkers; by the use of an asymmetric importance function that depends on the coordinates of both walkers; by the addition of an external asymmetric many-body potential; and by the breaking and reforming of the links that join plus to minus walkers, optimized using an asymmetric cost function.

Orbital-free effective embedding potential at nuclear cusp
Juan Maria Garcia Lastraa, Jakub W. Kaminskib, Tomasz A. Wesolowskib
aUniversidad del Pais Vasco
Departamento de Fisica de Materiales
E-20018 Donostia-San Sebastian, Spain

bUniversite de Geneve, Departement de Chimie Physique
30, quai Ernest-Ansermet,
CH-1211 Geneve 4, Switzerland

One of the crucial components of the orbital-free effective embedding potential in one electron equations for embedded orbitals (see eq. 20-21 in [1]) is the term vt[&rhoA,&rhoB] arising from the non-additivity of the kinetic energy. Previously we have shown that the use of Gradient Expansion Approximation to obtain the analytical expression for vt[&rhoA,&rhoB] is not a good strategy[2]. It does not recover the proper behaviour of vt[&rhoA,&rhoB] near the nuclei and violates the exact limit condition when &rhoA->0 and
density of the environment &rhoB comprises two electrons[3]. A new approximation to vt[&rhoA,&rhoB] obeying the considered properties is constructed. A special test procedure is applied to investigate the quality of the obtained approximation on a set of the model complexes.

[1] T. A. Wesolowski, A. Warshel J. Phys. Chem., 1993, 97, 8050.
[2] Y. A. Bernard, M. Dulak, J. W. Kaminski, T. A. Wesolowski J. Phys A: Math. Gen., 2008, 41, 055302.
[3] J.M. Garcia Lastra, J. W. Kaminski, T. A. Wesolowski, Phys. Rev. A, 2008, submitted
GGAs and Van der Waals Interactions in Density-Functional Theory
Felix Kannemann and Axel D. Becke
Department of Chemistry, Dalhousie University, Halifax, NS, B3H4J3, Canada
There is considerable debate, indeed confusion, in the DFT literature regarding exchange-correlation GGAs and their applicability to van der Waals interactions. Pure Hartree-Fock exchange gives repulsive noble-gas interactions. Popular GGAs of pure exchange type, however, exhibit everything from apparent binding to overly excessive repulsion. Lacks and Gordon, in Phys. Rev. A 47, 4681 (1993), assessed exchange GGAs for their ability to reproduce Hartree-Fock repulsion energies in He2 and Ne2. We have extended their assessment to the six pair interactions between He, Ne, and Ar. One GGA in particular, without any adjustment of parameters whatsoever, reproduces Hartree-Fock repulsion energies with remarkable accuracy.

This exchange GGA may be combined with dynamical correlation GGAs and the dispersion model of Becke and Johnson [J. Chem. Phys. 124, 174104 (2006) and 127, 154108 (2007)] to yield noble-gas vdW binding-energy curves of excellent quality.
Quantum Transport, Decoherence and Surface-Hopping Dynamics
Raymond Kapral
Chemical Physics Theory Group,
Department of Chemistry, University of Toronto,
Toronto, ON M5S 3H6 Canada
The transport properties of quantum mechanical systems can be expressed in terms of autocorrelation functions whose computation involves sampling from equilibrium quantum initial distributions and quantum evolution of observables. Chemical reaction rate constants, excited state relaxation rates, diffusion and other transport coefficients can be obtained in this way. It is difficult to simulate the quantum dynamics of large, complex, many-body systems. To surmount this difficultly, the calculation of such statistical properties will be cast in a framework that employs full quantum equilibrium sampling with mixed quantum-classical evolution of observables. The quantum-classical evolution differs from that in standard surface-hopping methods and accounts for quantum coherence. In standard surface-hopping schemes for nonadiabatic dynamics evolution is assumed to take place on single Born-Oppenheimer surfaces, interspersed by hops between these surfaces. The basis of such approaches will be analyzed in the context of mixed quantum-classical dynamics by accounting for the decoherence of the quantum degrees of freedom by the environment. The implications of quantum versus classical initial sampling on the computation of correlation functions using surface-hopping dynamics will be discussed. The theory will be applied to the computation of condensed phase proton transfer reaction rates.
Simple Dynamics for Complex Systems
Raymond Kapral
Chemical Physics Theory Group, Department of Chemistry,
University of Toronto, Toronto, ON M5S 3H6 Canada
The investigation of the dynamics of complex systems often requires knowledge of time evolution on physically relevant long distance and time scales. This is a challenging task for computer simulation. This fact has prompted the development of a number of different coarse-grain molecular dynamics methods. A method that combines a full molecular dynamics description of a part of the system with a mesoscopic treatment of the remaining degrees of freedom will be described. This method, called multiparticle collision dynamics, idealizes the collisions that occur in the system but retains the most important features of full molecular dynamics, namely, it conserves mass, momentum and energy and preserves phase space volumes. The method will be illustrated by computations on the dynamics of model protein molecular machines that convert chemical energy into cyclic conformational changes, and the dynamics of synthetic self-propelled particles in solution.
Molecular structure and dynamics observed using ultrashort-pulse extreme-ultraviolet light
Henry C. Kapteyn and Margaret M. Murnane
Department of Physics and JILA,and NSF Engineering Research Center for Extreme-Ultraviolet Science and Technology,University of Colorado at Boulder and NIST, Boulder, CO 80309
Light pulses from a femtosecond laser can be coherently upconverted to generate light in the extreme-ultraviolet and soft x-ray regions of the spectrum using high-order harmonic generation. Advances in laser technology, combined with a better understanding of the high harmonic process,[1] have made it possible make use of this ultrashort-pulse source of ionizing radiation for a variety of application experiments[2]. For example, recently, we have done the first direct time-resolved studies of molecular fragmentation resulting from ionization,[3] and have probed the angle-dependent photoionization cross section of laser-aligned molecules.[4] The high-order harmonic generation process itself also can be used to probe molecular structure.[5] In this talk I will give an overview of experiments in this area done in our group, and will discuss the technology and future prospects for tabletop-scale ultrafast x-ray sources.

[1] H. Kapteyn, O. Cohen, I. Christov, and M. Murnane, "Harnessing attosecond science in the quest for coherent X-rays," Science, vol. 317, pp. 775-778, Aug 2007.
[2] R. L. Sandberg, C. Y. Song, P. W. Wachulak, D. A. Raymondson, A. Paul, B. Amirbekian, E. Lee, A. E. Sakdinawat, C. La-O-Vorakiat, M. C. Marconi, C. S. Menoni, M. M. Murnane, J. J. Rocca, H. C. Kapteyn, and J. W. Miao, "High numerical aperture tabletop soft x-ray diffraction microscopy with 70-nm resolution," Proceedings of the National Academy of Sciences of the United States of America, vol. 105, pp. 24-27, Jan 2008.
[3] E. Gagnon, P. Ranitovic, A. Paul, C. L. Cocke, M. M. Murnane, H. C. Kapteyn, and A. S. Sandhu, "Soft x-ray driven femtosecond molecular dynamics," Science, vol. 317, pp. 1374-1378, 2007.
[4] I. Thomann, R. Lock, V. Sharma, E. Gagnon, S. T. Pratt, H. C. Kapteyn, M. M. Murnane, and W. Li, "Direct Measurement of the Transition Dipole for Single Photoionization of N2 and CO2," Journal of Physical Chemistry A, vol. To be published, 2008.
[5] X. Zhou, R. Lock, W. Li, N. Wagner, M. M. Murnane, and H. C. Kapteyn, "Molecular Recollision Interferometry in High Harmonic Generation," Physical Review Letters, vol. 100, p. 073902, 22 February 2008 2008.
Perspectives on the continuum models for PEFC catalyst layers
Kunal Karan
Queen's-RMC Fuel Cell Research Centre,
and Dept of Chemical Engineering

Queen's University, Kingston, Canada K7L 5L9
Although electro-catalysis for polymer electrolyte fuel cells (PEFCs) has been a central focus of fuel cell researchers for past two decades, the role of catalyst layer microstructure on the overall fuel cell performance and durability has garnered attention only in the past 5-7 years. At a molecular/atomic level, the charge-transfer reaction rate is a function of the local potentials (chemical, electronic, ionic, thermal). On a micro-scale, the catalyst layer represents spatially distributed system wherein the local potentials vary. Continuum models have been utilized to capture/describe the distribution of these potentials and, consequently, that of the local and overall electrochemical reaction rates. These models differ in the description of catalyst layer microstructure, i.e. the shape and spatial distribution of various constituents – ionomer, electrocatalyst+support, and pores - of the catalyst layers. Owing to a number of unknown or ‘tunable’ parameters, the overall current-voltage predictions from the different models may not vary significantly from each other and, in fact, resemble the experimentally observed trends. However, the physics described by the models may be very different. As such, the validity of the models is debatable.

The presentation will summarize, critique and contrast the current approaches employed in continuum-based modeling of PEFC catalyst layer.
Dynamics and kinetics in lipid-based assemblies
Mikko Karttunen
Department of Applied Mathematics, The University of Western Ontario, London (ON), Canada
In this talk, I will discuss self-assembly and dynamics in systems consisting of lipids and/or surfactants and peptides. My focus will be on lipid diffusion in lipid bilayers and the self-assembly of charged micellar systems, and I will demonstrate how the
assembly can be controlled by electrostatic interactions. Formation and break-up of vesicles and micelles are of fundamental importance in a variety of biological processes and in applications such as drug delivery. Here, we have used atomic scale molecular dynamics simulations to study the physical mechanisms that control the behaviour of those systems.
X-ray spectrum emitted from a blackbody flying with a relativistic speed
Jun Kawai
Department of Materials Science and Engineering, Kyoto University, Japan
The author and others have been studying similarity among electron beam excited X-ray blemsstrahlung, synchrotron radiation, and blackbody radiation. This is important for the quantitative elemental analysis of microarea using an electron probe microanalyzer (EPMA). The X-ray blemsstrahlung and synchrotron radiation are similar to the blackbody radiation of 107 K. Similarity between the synchrotron radiation and a blackbody of temperature T flying with a relativistic speed v (< 0) will be discussed in the present poster. The Planck’s equation modified due to the Doppler effect, where the photon energy observed at the forward direction is essentially the blackbody radiation with much lower temperature 104 K. The synchrotron radiation is well approximated by a gray-body radiation [1], where the difference from the Bose-Einstein statistics may be due to the self-absorption effect.

[1] T. Tanigaki, J. Kawai, X-Ray Spectrom., 36, 321 (2007).
Fundamental Understanding of Magnetism based on the Accurate Solution of Many-Body Coulombic System
Yoshiyuki Kawazoe, Takayuki Oyamada, Kenta Hongo, and Hiroshi Yasuhara
Institute for Materials Research, Tohoku University, Sendai, 980-8577, Japan
Traditionally, based on the Slater’s perturbation theory, the stability of the highest spin-multiplicity state, following the Hund’s multiplicity rule, has been interpreted as being ascribed to a lowering in the electron-electron Coulomb repulsive interaction Vee, i.e., exchange energy. In fact, this conventional interpretation is incorrect even at the stage of the Hartree-Fock (HF) approximation, which has already been reported for the low-lying excited states of the helium isoelectronic systems and light molecules by sophisticated calculations involving correlation as well as by HF. The misinterpretation arises from the assumption that all the multiplicity states belonging to the same configuration have quite the same set of HF orbitals. It gives the same kinetic energy T and the same nucleus-electron attractive Coulomb interaction Vne for any two states and hence ascribes the total energy difference between the two to the difference in Vee, exchange energy. The assumption is invalid since it violates the virial theorem 2T+V=0 (assuming P=0), which should exactly hold for the Coulombic many body systems, based on the scaling in the three dimensional space. It says that T and V are not free, they are related. Based on the virial theorem, total energy of the system E=T+V=-T=V/2.

The correct interpretation can be achieved from such calculations as fulfill the virial theorem. The stability of the highest multiplicity state is ascribed to a lowering in Vne that is gained at the cost of increasing Vee as well as T. The appearance of the highest possible spin polarization in the ground state of various atoms and molecules is interpreted as being a consequence of the predominance of Vne. We have confirmed the above interpretation by diffusion quantum Monte Carlo method. This finding is very important, because this result indicates that the origin of magnetism should not be explained by the exchange interaction, but mainly by the difference in Vne.

By such a high accuracy numerical calculation, we can now predict the materials properties without any experimental observations. Accordingly, we can assure the quality of our computational results for materials design, which has never been established especially for so-called strongly correlated systems, for which normally Hubbard model is applied, but by the model kinetic energy T is decreased and it contradicts to the virial theorem.

By using present supercomputers, such high accuracy calculations are possible up to 100 electron systems. We now can check the accuracy of numerical calculations and have good confidence to predict new materials before experiments. A paradigm shift from “explanation” to “prediction” is realized. Exchange-correlation potentials are carefully selected to be able to predict new materials by the first principle calculations. Some of the examples, e.g. silicon fulllerenes, will be indicated in the presentation. Molecular dynamics calculation based on the first principle calculations have been performed to predict dynamics-related physical and chemical properties of new materials. Ferroelectric properties and other interesting functional materials will also be introduced.
Nonadiabatic Quantum-Classical Dynamics of a System Containing a Conical Intersection
Aaron Kelly, and Raymond Kapral
Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Canada
Conical intersections are thought to play a major role in controlling the dynamical outcomes of many interesting chemical and biological processes. The influence of local environmental degrees of freedom on a charge transfer process near a conical intersection are investigated using a model developed to represent isomerization of a retinal analogue in a polarizable medium. The full quantum evolution of this system was approximated by mixed quantum-classical Liouville dynamics, and a Trotter based hybrid MC/MD simulation algorithm was employed to solve the resulting equations of motion. The results of this study are compared with other existing nonadiabatic simulation methods, such as Tully's surface hopping approach.
Numerical Analysis of Solutions of Boltzmann Equation Utilizing Quadrature Discretization Method
Saheba Khurana and Mark Thachuk
Department of Chemistry
University of British Columbia
Vancouver, Canada
The study of ion mobility using models based on principles of kinetic theory will be carried out. Calculations will be done when the ions in the bath gas reach a steady state average velocity and solutions to the Boltzmann equation will be obtained using the quadrature discretization method (QDM). The QDM is a mathematical method of finding solutions of integral and differential equations. Numerical analysis will be conducted on the results obtained from the above mentioned procedure. The intention will to apply the results to the random shaped bodies which undergo collisional-induced rotational alignment and eventually include arbitrary fields and study the behavior under such conditions.
BS-DFT and BS-HDFT studies on Cr-Cr quadruple bond based on energy decomposition analysis
Yasutaka Kitagawa, Yasuyuki Nakanishi, Toru Saito, Takashi Kawakami, Mitsutaka Okumura,and Kizashi Yamaguchi*
Department of Chemistry, Graduate School of Science, Osaka University
1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
*Center for Quantum Science and Technology under Extreme Conditions, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
A density functional theory (DFT) method has been applied to various systems and been showing successful results. However it still has an unsatisfactory point on strong electron correlation systems with degenerate valence orbitals. A metal-metal bonding is one of the typical cases of them. Ab initio calculations of those systems have been a difficult task because two different types of electron correlation effects, i.e. dynamical correlation and non-dynamical correlation, must be taken into consideration.

Recent trends of the computational approach for such strongly correlating systems are the use of broken symmetry (BS) DFT and BS hybrid DFT (HDFT) calculations. In this study, we examined how BS DFT (or BS HDFT) reproduced electron correlation effects in metal-metal bonding systems. In order to elucidate what UDFT (or UHDFT) expressed as correlation energies, total energy was decomposed into kinetic energy, nuclear-nuclear potential, nuclear-electron potential and electron-electron potential based on energy decomposition analysis and they were compared with ones of UHF, CASSCF and so on. In addition, an energy gap between lowest spin state and highest spin state was also examined with respect to calculations of effective exchange intagrals (J).
Surface Modification Strategies Based on Polymer Brushes
Jayachandran N. Kizhakkedathu
Centre for Blood Research, Department of Pathology and Laboratory Medicine, University of BC, Vancouver, BC V6T 1Z3, Canada
The control of the surface properties materials is central to many areas of research and key to numerous commercially important biotechnology applications, ranging from biomaterials to immunoassays. The covalent grafting of polymer chains at one end to surface at relatively high density produce ‘polymer brushes’ leads to the steric crowding of chains at the interface results in the extension of chains away from the surface. These structures provide one intriguing method to control the interfacial properties. Surface initiated Atom Transfer Radical Polymerization (ATRP), controlled/living polymerization technique, offers a unique opportunity to control properties of grafted polymer layers such as molecular weight, graft density, hydrodynamic thickness etc. Another advantage of ATRP is that, it offers mild experimental conditions for polymer grafting. In this presentation, we will discuss the applications of surface initiated ATRP to produce well-defined polymer brushes from synthetic surfaces. We will also discuss the physical and chemical properties of polymer grafted surfaces and its influence on stimuli responsiveness and interactions with biological fluids such as blood or plasma. This will enable us to find correlations between the physical structures the grafted polymer layers and properties of interfaces.
Temperature induced dissociation of Aβ monomers from amyloid fibril
Takako Takeda and Dmitri K. Klimov
Department of Bioinformatics and Computational Biology,
George Mason University, USA
All-atom molecular dynamics is used to study the temperature induced dissociation of Aβ monomers from the amyloid fibril. The free energy landscape of monomers on the surface of Aβ fibril is mapped by applying free energy disconnectivity graphs. The results suggest that Aβ monomers sample diverse set of low free energy states with different degree of association with the fibril. Generally, Aβ monomers with partially formed fibril-like interactions have the lowest free energies. Overall, Aβ amyloid protofilaments appear to be highly resistant to thermal dissociation. Monomer dissociation from the fibril edge proceeds via multiple stages and pathways. The simulation findings are discussed in the context of recent experimental results.
New Model Core Potentials: Development, Calibration, and Applications
Tao Zeng,1 Hirotoshi Mori,2 Eisaku Miyoshi,3 and Mariusz Klobukowski1
1 Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
2 Division of Advanced Sciences, Ochanomizu University, Tokyo 112-8610, Japan
3 Graduate School of Engineering Sciences, Kyushu University, Fukuoka 816-8580, Japan
The Model Core Potential (MCP) [1] is a useful tool in computational quantum chemistry because it preserves the nodal structure of the valence atomic orbitals. It may be particularly useful in the relativistic quantum chemistry [2].

Three new MCPs: mcp-Nzp (N = d, t, q) were designed for the main-group elements [3] and the quality of results obtained using them is expected to be comparable with those from all-electron calculations with cc-pVNZ basis sets (N = D, T, Q). We will discuss systematic validation of the new MCPs: the three families of MCPs and corresponding basis sets were used with HF, MP2, CCSD, CCSD(T), and DFT methods to optimize structures of small molecules containing main-group atoms of the first five rows of the periodic table. The relative errors with respect to the experimental values were calculated for all molecules in two categories: equilibrium bond lengths and bond angles. The qualities of the MCPs in combination with various computational methods will be quantitatively presented.

Recently, the new MCPs were prepared for the transition metal elements from the first [4] and second [5] rows, and preliminary results from molecular calculations will be presented. These new MCPs use an extended number of subshells in the valence space. In order to study the chemical importance of the consecutive core subshells of Au, we parameterized four new families of MCPs with different valence shells for Au. In the new MCPs, the electrons in 5p5d6s, 4f5p5d6s, 5s5p5d6s, and 5s4f5p5d6s subshells are treated explicitly. The properties of small molecules containing Au (AuH and Au2) were studied using the new MCPs in order to establish whether a subshell should be included in the MCP.

[1] Klobukowski, M.; Huzinaga, S.; Sakai, Y. Model Core Potentials: Theory and Applications. In Computational Chemistry: Reviews of Current Trends, Vol. 3; Leszczynski, J., Ed.; World Scientific, Singapore: 1999.
[2] Lovallo, C. C.; Klobukowski, M. Chem. Phys. Lett. 2003, 368, 589.
[3] Miyoshi, E.; Mori, H.; Hirayama, R.; Osanai, Y.; Noro, T.; Honda, H.; Klobukowski, M. J. Chem. Phys. 2005, 122, 074104.
[4] Osanai, Y.; Mon, M. S.; Noro, T.; Mori, H.; Nakashima, H.; Klobukowski, M.; Miyoshi, E. Chem. Phys. Lett. 2008, 452, 210.
[5] Osanai, Y.; Soejima, E.; Noro, T.; Mori, H.; Mon, M. S.; Klobukowski, M.; Miyoshi, E. Chem. Phys. Lett. 2008 (in press).
Multiconfiguration perturbation theory using generalized Møller-Plesset partitioning and its application to APSG reference function
Masato Kobayashi,1,2 Ágnes Szabados,1 Péter R. Surján1 and Hiromi Nakai2
1Laboratory of Theoretical Chemistry, Institute of Chemistry, Loránd Eötvös University, H1518 Budapest P.O.B. 32., Hungary

2Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, Tokyo 169-8555, Japan
We propose a novel perturbation theory (PT) starting from a multiconfigurational (MC) zero-order wave-function. To span the configuration space, the theory employs biorthogonal vector sets together with skew projectors. At difference with previous formulations, the present construction operates with the Fockian corresponding to a single principal determinant. The theory provides a simple, generalized Møller-Plesset (MP) second-order correction to improve any reference function, corresponding either to a complete or incomplete model space. Computational demand of the procedure is determined by the iterative inversion of the Fockian, similarly to single reference MP theory calculated in a localized basis. A numerical application to APSG (antisymmetrized product of strongly-orthogonal geminals) reference function gives accurate dissociation curves at the same level as the multi-reference MP theory adopting the adequate active space.
Coupled cluster approaches for modeling large molecular systems in various environments
K. Kowalski, M. Valiev, N. Govind, P.D. Fan. W.A. de Jong
William R Wiley Environmental Molecular Sciences Laboratory and Chemical Sciences Division,
Pacific Northwest National Laboratory
The coupled-cluster (CC) methodology has become a leading formalism not only in gas-phase calculations but also in modeling systems for which the inclusion of the surrounding environment is critical for a comprehensive understanding of complex photochemical reactions. At the same time it has been proven that high-level CC formalisms are capable of providing highly adequate characterization of excitation energies and excited-state potential energy surfaces. With the ever increasing power of computer platforms and highly scalable codes, very accurate QM/MM calculations for large molecules (defining the quantum region) can be routinely performed in the foreseeable future even with iterative methods accounting for the effect of triples ( CCSDT-n/EOMCCSDT-n). We will discuss several components of recently developed and implemented CC methodologies in NWChem. This includes: (1) Novel iterative/non-iterative methods accounting for the effect of triply excited configurations, (2) Massively parallel implementations of the CC theories based on the manifold of singly and doubly excited configurations. Several examples will illustrate how these approaches can be used in multiscale QM/MM framework.
Dynamics and Electron Transfer in Peptides
Heinz-Bernhard Kraatz
Department of Chemistry
The University of Western Ontario
An understanding of the fundamental properties that govern redox processes in biological systems remains elusive at the molecular level. To this end, electron transfer (ET) studies from an electro-active ferrocene group (Fc) through structurally well-defined peptide spacers to a surface using electrochemical techniques is a useful approach to evaluate the electronic properties of peptides. Since peptides are readily attached to gold surfaces exploiting the high affinity of thiols and disulfides for gold, our work largely focuses on the study of structurally well-defined peptide-cysteamine conjugates or peptides containing a cystein residue. Progress has been made on helical peptides, although many questions remain regarding the structural rigidity of helical peptides on surfaces. Here a series of helical Fc-peptide films were studied and their ET rates were determined. A linear relationship between kET and donor-acceptor distance was observed. However, these peptides are not rigid units but appear highly flexible and thus their dynamic properties have to be taken into account. To this effect, two Fc-peptide films were studied using electrochemical surface plasmon resonance and reveal that reorientations within the think film concomitant with the oxidation of the Fc-label were significant.
Tracer diffusion in rough sphere fluids
Olga Kravchenko, Ruslan Sokolowski, Gren Patey and Mark Thachuk
Chemistry Department, University of British Columbia
Molecular dynamics was employed in order to investigate diffusion properties of a tracer particle in a rough sphere fluid that possesses convertible energy of rotation. We are particularly interested in examining the region between molecular and hydrodynamics regimes and find the boundary conditions adopted by the system. In this study we use the perfectly rough sphere model, which allows us to introduce rotation of individual particles into our system and observe the effect of this rotaion on boundary conditions in the rough sphere fluid in comparison with smooth sphere fluid.
First principles statistical mechanics of single polymer molecules: from PEG to DNA
H.J. Kreuzer
Department of Physics
Dalhousie University
Halifax, NS
A first principles theory based on (i) first principles (density functional theory) calculations of the potential energy surfaces of the polymer conformers yielding their geometry and their energetics, and (2) the proper statistical mechanics allows the parameter-free calculation of the thermodynamic properties of single polymer strands. For the statistical mechanics we succeeded to formulate and solve a Green's function approach (transfer matrix method) in the presence of an external force field. We give a detailed discussion of force-extension curves (the mechanical equation of state) and the role of fluctuations in both the Helmholtz and the Gibbs ensemble. This is particularly relevant when experiments are done with the Atomic Force Microscope. Applied to poly(ethylene glycol) molecules we achieve quantitative agreement with experimental data, both in hexadecane and in water. Lately we have looked at complex molecules. I will show results for Dextran where we included the boat-chair transition rigorously. Stretching Titin is another case of great complexity where a proper account of bondbreaking must also be included leading to some unforeseen features that greatly effect the interpretation of experimental data. Lastly, I report on a complete description of stretching DNA including the BS transition and also its melting at high forces/extensions.
On the use of the exact exchange optimized effective potential method for static response properties
Mykhaylo Krykunov, Tom Ziegler
Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada
In the present work we have questioned a belief that the better Kohn-Sham orbital energies and smaller HOMO-LUMO gaps, produced from the exact exchange optimized effective potential (EXX-OEP) method, might significantly improve the paramagnetic contribution to the NMR chemical shifts in comparison with the Hartree-Fock (HF) method. First of all, we have shown analytically that if there is such a local potential that produces the HF energy, and the Kohn-Sham orbitals are obtained as a result of separate rotations of the occupied and virtual HF orbitals, any static magnetic property obtained from the coupled perturbed HF method is identical to that one which is obtained from the EXX-OEP approach. It is also shown that such a theorem is valid for the improved virtual orbitals method.

To test this statement we have employed several variants of the EXX-OEP method, based on the expansion of the local exchange potential into a linear combination of fit functions, for the calculation of the NMR chemical shifts for the set of small molecules containing C, H, N, O, and F. Comparison of the deviation between experimental and calculated chemical shifts from the HF, the EXX-OEP and the CEDA approximation to the EXX-OEP methods has shown that for carbon, hydrogen, and fluorine the EXX-OEP methods do not yield any improvement over the HF method. For nitrogen and oxygen we have found that the EXX-OEP performs better that the HF method.

However, in the limit of infinite basis and a perfect fit of the HF potential the EXX-OEP and the HF methods would afford the same chemical shifts. Unfortunately, without a perfect fit the chemical shifts from the EXX-OEP strongly depend on the fit convergence. In our opinion, the EXX-OEP should not be used for response properties as it is numerically unstable and not an improvement over the HF.
Probing Open-Shell Wave Functions by Photoelectron Imaging: Dyson Orbitals within Equation-of-Motion Coupled-Cluster Formalism
Anna I. Krylov
Dept. of Chemistry, USC
Angular distribution of photoelectrons (PAD) contains information about electronic wave functions and thus can be used to determine the nature of the state, as well as monitor its changes in the course of reactions. However, the interpretation of PADs in terms of molecular orbital composition of the ionized state is not straightforward. PADs are related to the so called Dyson orbitals, which can be interpreted as states of the leaving electron. Calculation of Dyson orbitals for the ground and excited states within equation-of-motion formalism is described and illustrated by examples.

[1] C.M. Oana and A.I. Krylov, J. Chem. Phys., 127, 234106 (2007)
Zigzag Graphene Nanoribbons with sp3 Edges
Konstantin N. Kudin
Princeton Institute for Science and Technology of Materials (PRISM), Princeton University, Princeton, New Jersey 08544
I will talk about an ab initio study of zigzag graphene nanoribbons with saturated edges. Such ribbons could possibly form during graphite oxidation. Compared to the previously studied ribbons with all carbons of sp2 type, in these structures edge carbons have either two H or two F atoms, and are of sp3 type. The electronic structure of this new type of ribbons is quite diverse. In narrower ribbons the closed shell electronic state is the most stable one. In wider ribbons a state with antiferromagentically spin-polarized edges is the lowest in energy, similarly to the ribbons with all sp2 type carbons. A notable feature of narrower ribbons is significant single-double carbon bond alternation across the ribbon, which has a distinct Raman spectra signature.
Tracing ultrafast electronic processes in real time and space
Alexander I. Kuleff and Lorenz S. Cederbaum
Theoretische Chemie, PCI, Universität Heidelberg
Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
An ab initio method for multielectron wave-packet propagation is presented [1]. It gives the possibility to describe fully ab initio the dynamics of various de-excitation processes taking into account all electrons of the system and their correlation. The approach is equally suitable for tracing in real time and space the electron dynamics of both decaying and non-decaying electronic states. As an example, the evolution of the electronic cloud throughout the interatomic Coulombic decay (ICD) process in the rare gas cluster NeAr following Ne2 s ionization is computed and analyzed [2].


[1] A. I. Kuleff, J. Breidbach, and L. S. Cederbaum, J. Chem. Phys. 123, 044111 (2005).

[2] A. I. Kuleff and L. S. Cederbaum, Phys. Rev. Lett. 98, 083201 (2007).
Analytical modeling of fuel cells and stacks: Results, challenges and perspectives
A.A.Kulikovsky
Institute for Energy Research - Fuel Cells
Forschungszentrum Juelich, GmbH
Results of analytical modeling of PEFC, DMFC and SOFC cells and stacks performed in Juelich will be reported. We start with the simple 1D+1D model of a hydrogen cell and show how this model explains several interesting features of cell operation. Analogous model of DMFC results in effect of formation of internal "jumper", which short-circuits cell electrodes and reduces OCV. Experimental investigation of this effect reveals new regimes of cell operation and leads to a novel method for DMFC performance recovery. We will discuss models of heat and current transport in DMFC and SOFC stacks. The models give simple relations for temperature shape in stacks and warn about thermal instability of stack operation. Challenges and perspectives for this type of modeling will be discussed.
Ligand Binding and Protein Reorganization in the Glutamate Receptors
Maria Kurnikova
Chemistry department
Carnegie Mellon University, Pittsburgh, PA, USA
The ionotropic glutamate receptors are localized in the pre- and postsynaptic membrane of neurons in the brain. Activation by the principal excitatory neurotransmitter glutamate allows the ligand binding domain to change conformation, communicating opening of the channel for ion conduction. The free energy of the GluR2 S1S2 ligand binding domain (S1S2) closure transition was computed using a combination of thermodynamic integration and umbrella sampling modeling methods. A path that involves lowering the charge on E705 was chosen to clarify the role of this binding site residue. Continuum electrostatic interactions in S1S2 are used to show E705, located in the ligand binding cleft, stabilizes the closed conformation of S1S2. Hybrid continuum electrostatics/MD calculations along the chosen closure transition pathway reveal solvation energies, as well as electrostatic interaction energies between two lobes of the protein increase the relative energetic difference between the open and the closed conformational states. By analyzing the role of several cross-cleft contacts as well as other binding site residues we demonstrate how S1S2 interactions facilitate formation of the closed conformation of the ligand binding domain. Ligand protein interaction is analysed using continuuum electrostatics/MD calculations as well as a hybrid QM/MM approach.
Crystallizing Molecular Liquids: From Techniques to Understanding
P.G. Kusalik
Department of Chemistry, University of Calgary, 2500 University Dr. N.W., Calgary, Alberta, T2N 1N4
The formation and growth of crystals from liquids or solutions are important physical processes, yet a detailed microscopic understanding of these processes has remained elusive. Molecular simulation offers a very powerful tool with which to probe their microscopic mechanisms. This paper will begin with a brief review of the key issues around the question of how nature finds order, particularly in the light of models such are classical nucleation theory and the protein folding funnel. I will then explore how these models relate to detailed observations we have made in our own simulations of the (heterogeneous) crystal growth of ice and in the (homogeneous) nucleation of atomic and simple molecular systems. I will then describe a novel technique we have developed and employed in our simulations, based on configurational temperatures, that can be effectively used to dramatically enhance, by many orders of magnitude, the rates of crystallization observed in molecular simulations. I will specifically examine the detailed microscopic structural properties of the states sampled by our systems during the process of their phase transitions.
N-Particle Density Matrix-Based Quantum Monte Carlo
Jörg Kussmann,1 Christian Ochsenfeld,2 and James B. Anderson1
1Department of Chemistry, Pennsylvania State University, USA

2Theoretical Chemistry, University of Tübingen, Germany
A reformulation of Quantum Monte Carlo (QMC) methods in the basis of the N-particle density matrix ( N-PDM) is presented.1,2 For systems with a non-vanishing band gap these methods provide an aymptotical linear-scaling behavior for the evaluation of the local energy. Basic aspects of the reformulation including the effect of density matrix truncation, scaling behavior, and implementation of the fixed-node approximation are discussed. Furthermore, employing multi-configuration density matrices3 and accounting for the electron-nuclear cusp condition4 is described. With these tools at hand, a general and efficient application of this density matrix-based approach becomes possible for any trial function-based QMC method.

1. J. Kussmann, H. Riede, and C. Ochsenfeld, Phys. Rev. B 75, 165107 (2007).
2. J. Kussmann and C. Ochsenfeld, J. Chem. Phys. 128, 134104 (2008).
3. J. Kussmann and J. B. Anderson, in preparation.
4. J. Kussmann and C. Ochsenfeld, Phys. Rev. B 76, 115115 (2007).
Simulations of ammonium transport in AmtB protein using a polarizable force field
Guillaume Lamoureux
Department of Chemistry and Biochemistry, Concordia University, Canada
Bacteria, yeast and plants under low ammonium concentrations express proteins from the Amt/MEP family that have a high affinity for ammonium and facilitate its transport across the membrane. Despite a number of x-ray structures of Amt/MEP proteins now available, the nature of the chemical species found along the permeation pathway remains highly ambiguous. Experiments in bacteria suggest a net transport of NH3, but experiments in plants suggest a net transport of NH4+.

Using molecular dynamics simulations, we examine the relative stabilities of various conformations of water, ammonia (NH3) and ammonium (NH4+) in the pore of Escherichia coli's AmtB. We account for the high cooperativity of cation-π interactions between NH4+ and the aromatic residues lining the AmtB pore by using a polarizable force field based on classical Drude oscillators.

Impedance of porous electrodes
Andrzej Lasia
Département de chimie, Université de Sherbrooke,
Sherbrooke, Québec, J1K 2R1
Electrochemical Impedance Spectroscopy, EIS, is an excellent technique to study interfacial electrochemical processes. It is also sensitive to surface geometry and is used to study porous electrodes. EIS is a very sensitive technique but it can be used only after dc electrochemical and physical characterization of the electrode material. It is often used to study the fuel cells which contain porous electrode assemblies.
In general, dc and ac potential and concentration gradients develop in the pore leading to numerical solutions of the problem. The simplest model involves a cylindrical pore but solutions for pores of any geometry might be obtained numerically.
The solutions will be presented for the ideally polarized electrode, in the presence of red-ox species but in the absence of the dc current, in the presence of dc current involving dc potential, dc concentration gradients only and the general case involving both gradients. Next model of the distribution of pore sizes and the continuous pores model will be mentioned [1,2].

[1] A. Lasia, Modern Aspects of Electrochemistry, B. E. Conway, J. Bockris, and R.E. White, Eds., Kluwer Academic/Plenum Publishers, New York, 1999, Vol. 32, p. 143.

[2] A. Lasia, “Impedance of porous electrodes”, Modern Aspects of Electrochemistry, M. Schlesinger, Ed., vol. 43, in print.
Theory of Non-Markovian Rate Processes
Ji-Hyun Kim and Sangyoub Lee
Department of Chemistry,
Seoul National University,
Seoul 151-747,
South Korea
Starting from a multidimensional reaction kinetic equation with a general time evolution operator and a reaction sink function K, we derive formally exact expressions for the survival probability, reaction time distribution, and mean reaction time by using the projection operator technique. These rate expressions are given in the rational function form with the irreducible memory function as the key ingredient. This approach has an advantage over the direct perturbation approaches that use the reaction term as the small parameter, in that the irreducible memory function has a structure that can be perturbatively treated with (K-) as the small parameter. The well-known Wilemski-Fixman type rate expressions are reproduced as the zeroth-order approximation from the present theory. Practical methods for evaluating the formal rate expressions are presented, and the results calculated for a model of electron transfer in non-Debye solvents are compared with computer simulations. It is found that the present approach is very promising for the study of non-Markovian dispersive kinetics.
Zero-width resonances in intense field molecular photodissociation
R Lefebvre
Laboratoire de Photophysique Moleculaire
Universite Paris-Sud, Campus d'Orsay
91405 Orsay, France
We have been exploring [1,2] the possibility to base a control of molecular photodissociation on the existence of zero-width resonances for certain critical field intensities. The photodissociation rate as a function of time for a Floquet state evolving from a field-free vibrational state, for a sufficiently adiabatic pulse, can be calculated with a cw field with the intensity of the pulse at time t. An interesting feature arises for some of the states: the resonance width passes through a null value. The explanation resides in a mechanism involving two different interfering paths contributing in a destructive way to the outgoing scattering amplitude. For an initial molecular state consisting of a mixture of several states, after the end of the pulse a state with a width going through a zero value may have the largest survival probability.
Depending on the laser frequency different molecular Floquet states present this property of a zero width. This opens the possibility
to populate selectively a given molecular state



[1] O. Atabek, R. Lefebvre and X.Gadea, Phys. Rev. A 74, 063412(2006).
[2] O. Atabek, R. Lefebvre, C. Lefebvre and T.T. Nguyen-Dang, Phys. Rev. A 77, 043413(2008)

Heat transport in proteins
David M Leitner
Department of Chemistry
University of Nevada, Reno
Energy flows anisotropically through the residues and vibrational states of globular proteins, in some cases serving as signaling pathways between distant binding sites on the molecule. We discuss calculations of rates and pathways for vibrational energy flow and heat transport in a number of protein molecules. These include computation of anharmonic decay rates of vibrational modes, anomalous diffusion of energy transported by the vibrational modes of a protein, and computation of thermal transport coefficients. Anharmonicity significantly enhances thermal transport in proteins. Computed anharmonic decay rates compare well with available experimental rates, for instance, in the amide I region, where the computed rates match the data measured by pump-probe spectroscopy from 10 K to 310 K. Over this temperature range the experimental amide I lifetimes are nearly independent of temperature. We find that lifetimes of most higher frequency vibrational modes of proteins vary little with temperature, consistent with a propensity for localized modes of a protein close in space to be typically separated by several hundred wave numbers.
Some Recent Developments in Quantum Monte Carlo
William A. Lester, Jr.
Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California at Berkeley, Berkeley, CA 94720-1460, USA
and
Chemical Sciences Division, Lawrence Berkeley National Laboratory
Berkeley, CA 94720, USA
The quantum Monte Carlo method has become recognized for its capability of describing the electronic structure of atomic, molecular and condensed matter systems to high accuracy. This talk will focus on new developments connected with trial function construction and extension of the approach to a QM/MM (quantum mechanics/molecular mechanics) formulation for the inclusion of solvent. This work was supported by the Director, Office of Science, Office of Basic Energy Sciences, Chemical Sciences Division of the U.S. Department of Energy under Contract No. DE-AC03-76SF00098, and by the CREST Program of the U. S. National Science Foundation. The calculations were carried out at the U. S. National Energy Research Supercomputer Center (NERSC).
Nonadiabatic Excitation and Electron Impact Cooling During Gas Phase Laser Filamentation
Robert J. Levis
Department of Chemistry, Temple University, Philadelphia, USA
Shaped strong field lasers can be used to control the location and spatial extent of laser filaments in both solution phase and gas phase media. Such filaments create coherent bandwidth sufficient to support single cycle pulses in the visible. This talk will delineate experiments concerning the coherent control of the filamentation process. Investigations of the mechanism of filament production and subsequent electron dynamics in the laser-induced plasma have also been measured using femtosecond four wave scattering experiments. An impact excitation cooling mechanism will be presented to explain the filament dynamics as a function of noble gas IP, molecule vibrational structure, and laser intensity.

"On a General Theory of Hybrids for Exchange and Correlation, and Degeneracies in DFT"
Mel Levy
Department of Chemistry
Duke University
Durham, North Carolina 27708

Hybrid functionals have been among the most successful for approximating exchange and correlation. A brief history of the development of hybrids, with and without the separation of long-range and short-range interactions, will be given in terms of electron-electron repulsion contributions along the adiabatic connection and in terms of representations in which these repulsions do not explicitly appear. Then an understanding of hybrids will be provided through integration by parts [1] along the adiabatic connection and use will also be made of coordinate scaling.

Although the original proof of the Hohenberg-Kohn variational theorem required non-degeneracies, the variational theorem was long ago extended to include degeneracies[2]through the use of the constrained-search formulation. Degeneracy is the major cause of pure-state non-v-representability [3,4]. But the connections, due to degeneracies, between non-interacting ensembles and the existence of holes [5] below the Fermi level are not at all well known. For this reason, these connections will be discussed in terms of convergence difficulties in self-consistent calculations.

1. M Levy, A J Cohen, P Mori-Sanchez and W Yang, unpublished.
2. M Levy, Proc. Natl. Acad. Sci. (USA) 76, 6062 (1979).
3. M Levy, Phys Rev A 26, 1200 (1982).
4. E H Lieb, Int. J Quantum Chem 24, 243 (1983).
5. M Levy and J P Perdew, in "Density Functional Methods in Physics", eds. R M Dreisler and J da Providencia (Plenum: New York, 1985).



Free Energy of Nonequilibirum Polarization with Constrained Equilibrium Approach
Li Xiang-Yuan
College of Chemical Engineering, Sichuan University,Chengdu 610065,P. R. China
The thermodynamic principle for a nonequilibrium state[1] is adopted to reformulate the nonequilibrium free energy in condensed matter. By applying an extra electric field, the nonequilibrium polarization can be made a constrained equilibrium state1, and the novel expression for nonequilibrium salvation energy has been obtained as a new form that account for the potebtial energy of the nonequilibrium polarization in the imposed extra electric field which is used to maintain the constrained equilibrium. This implies that all the expressions of nonequilibrium salvation energy[2], including that formulated by the authors in recent years [3,4], are incorrect. According to the new form of the nonequilibrium salvation energy, the solvent reorganization energy is given by half the product of the extra field and the nonequilibrium part of the polarization. Suppose a two-sphere case in which an electron transfers from one site to another, a quite different two-sphere model is developed. Comparing with the traditional Marcus model [2], one can immediately draw a conclusion that the solvent reorganization energy predicted by Eq.(4) should be scaled down by a factor close to 1/2. Typically, for water, this factor takes a value of 0.556. Further, for the nonpolar solvent, this factor drops to an even smaller value. This implies the nonpolar organic solvent will apply much weaker influence than predicted by Marcus model on ET kinetics. Therefore, the longstanding problems that Marcus model overestimates the solvent reorganization energy[5-9] are nicely solved.

References
1. M.A. Leontovich, An Introduction to Thermodynamics , 2nd ed. (Gittl Publ., Moscow, 1950, in Russian).
2 R. A. Marcus, J. Chem. Phys. 24, 979(1956).
3 X.-Y. Li, and K.-X. Fu, J. Comput. Chem. 25, 500(2004).
4. X.-Y. Li, and K.-X. Fu, J. Theor. Comput. Chem. 4, 907(2005).
5 M. D. Johnson, J. R. Miller, N. S. Green, G. L. Closs, J. Phys. Chem. 93, 1173(1989).
6.B. P. Paulson, J. R. Miller, W.-X. Gan, and G. Closs, J. Am. Chem. Soc. 127, 4860(2005).
7. S. J. Formasinho, L.G. Arnaut, and R. Fausto, Prog. Reaction Kinetics 23, 11(1998).
8 C. Serpa, P.. S. Gomes, L. G. Arnaut, J. S. de Melo, and S. J. Formosinho, ChemPhysChem 7, 2533(2006).
9. J. R. Reimers, Z.-L. Cai, N. S. Hush, Chem. Phys. 319, 39 (2005).
Physical Basis Underlying Metal Function in Proteins
Leon Lee and Carmay Lim
Institute of Biomedical Sciences
Academia Sinica
Nearly half of all proteins contain metal ions, which perform a wide variety of functions associated with life processes. In this talk, I will first present a brief overview of our work on unraveling the physico-chemical basis governing metal binding affinity, selectivity, and function in proteins. As an example, I will describe our recent studies revealing the molecular principles underlying structural and catalytic Zn−sites in proteins. Based on these principles, I will describe a simple method to distinguish the two types of sites and to verify the catalytic role of Zn2+. Finally, I will discuss how the physical bases revealed aid in designing potential drug molecules that target Zn−proteins.
Relativistic Many-Body-Perturbation Procedures
Ingvar Lindgren, Sten Salomonson, and Daniel Hedendahl
Physics Department, University of Gothenburg, Göteborg, Sweden
The standard approach to relativistic many-body calculations has for at least three decades been based on the projected Dirac-Coulomb (DC) or Dirac-Coulomb-Breit (DCB) approximations. Here, the negative-energy solutions of the Dirac equation are eliminated by projection operators, and in the DCB case the instantaneous Breit interaction is included. This approximation contains all effects to order α2 Rydbergs. The procedure is not relativistically covariant, and effects of retardation, virtual-electron-positron-pair creation and radiative effects (self energy, vacuum polarization and vertex correction), so-called QED effects, which are of order α3 and higher, are left out.

Contributions to the energy due to leading QED effects and very recently also most second-order effects can be evaluated by S-matrix formulation or related techniques [1,2], but it has until now not been possible to include these effects into the wave function and merge them into a many-body perturbative (MBPT) procedure. The covariant-evolution procedure, recently developed by the Göteborg group [3], can serve as the basis for such a merger.

The new procedure makes it, in principle, possible for the first time to combine QED corrections with electron correlation to arbitrary order, effects that can also be of order α3. The procedure is now being implemented, and it has been shown that the effect of electron correlation on first-order QED (retardation and virtual pairs) for He-like neon dominates heavily over second-order QED effects, which are of order α4 and higher [4]. The procedure can be treated very much like standard MBPT, but the diagram evaluation leads to a modification of the standard Goldstone rules.

The only true covariant procedure for bound-state calculation that has been available so far is the Bethe-Salpeter equation (BSE), which as such is not suitable as a basis for many-body perturbative calculations. It has been demonstrated that our new procedure, carried to infinite order, leads for two-particle systems to BSE, demonstrating its relativistic covariance [5]. The procedure can therefore, in principle, be regarded as a Rayleigh-Schrödinger-based perturbative (linked-diagram) expansion of the Bethe-Salpeter equation, applicable to many-body systems, also in the multi-reference (quasi-degenerate) case.

References
[1] P. J. Mohr, G. Plunien, and G. Soff, Phys. Rep. 293, 227 (1998).
[2] V. M. Shabaev, Phys. Rep. 356, 119 (2002).
[3] I. Lindgren, S. Salomonson, and B. Åsén, Phys. Rep. 389, 161 (2004).
[4] D. Hedendahl, S. Salomonson, and I. Lindgren (to be published).
[5] I. Lindgren, S. Salomonson, and D. Hedendahl, Phys. Rev. A 73, 056501 (2006).
Building a biomimetic membrane at electrode surfaces
Jacek Lipkowski
Department of Chemistry, University of Guelph, Guelph, Ontario, N1G 2W1
I will describe electrochemical, neutron reflectivity, infrared reflection absorption spectroscopy (IRRAS) and scanning probe microscopy (STM and AFM) studies of the structure of phospholipids bilayers deposited onto a metal electrode at the metal-solution interface. I will show how vesicles of phospholipids fuse to form bilayers at the electrode surface. What the stability of these films is in the presence of electric fields that are comparable in magnitude to the fields acting on biological membranes. How these fields affect ordering of molecules within the membrane and how they cause a phase transition from the liquid crystalline to the gel state. I will also show how the electric field affects the stability of mixed bilayers composed of phospholipids and cholesterol, incorporation of peptides into the bilayer.

The metal electrode surface, covered by a bilayer of phospholipids, can be charged and electric fields on the order of 108V/m can be applied to these films. The fields have comparable magnitude to the fields acting on biological membranes. It can be used to manipulate organic molecules within the bilayer membrane. By turning a knob on the control instrument one can force phase transitions in the film of organic molecules or force them to disperse or to aggregate at the surface. We use electrochemical techniques to control the physical state of the film while the spectroscopic, surface imaging and neutron scattering techniques are employed to study conformational
Several Problems in Modeling of MEAs of PEM Fuel Cells
Zhong-Sheng (Simon) Liu
Institute for Fuel Cell innovation
National Research Council Canada
4250 Wesbrook Mall
Vancouver, BC, Canada
V6T 1W5

Simon.Liu@nrc-cnrc.gc.ca
Modeling and simulation provide an effective and economic way to reveal physical and electrochemical processes inside a membrane-electrode-assembly (MEA)of PEM fuel cells. In this talk we present several problems, which limit the accuracy, reliability and scope of modeling approaches. These problems are mainly about the constitutive assumptions that are being used for modeling of mass transport phenomena inside MEAs.
New Generation Relativistic Electronic Structure Theory
Wenjian Liu
Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
Any quantum chemical or physical calculations should be concerned with two issues: the choice of Hamiltonian and then the choice of method for correlating the motion of the particles. And it is clear that, any ‘good’ theory for a certain class of problem must fulfill all the three criteria:
(1) Simple. The true physics and the underlying laws are all simple and beautiful, e.g., the Newton equation, the Maxwell equation, the Schrödinger equation (SE), the Dirac equation (DE), as well as the mass-energy relationship (E=mc2), to name just a few.
(2) Accurate. One should get the right answer for the right reason, without relying on error compensation.
(3) Efficient. For the same accuracy, the cheaper the better. Reversely, given the same efficiency, the more accurate the better.

Up to date, most quantum chemical and physical calculations have been based on the SE. Such calculations have turned out to be very successful in analyzing experiments. However, it must be realized that the SE describes an artificial world in which light travels at infinite speed. Instead, only the DE built upon the special theory of relativity represents our real world. Since all experiments are carried out in the real world, in principle only the DE can validate and predict experiments. As a matter of fact, the SE can faithfully be applied only to the ground states of systems composed of light elements, say, up to Z=36. According to the above criteria, the SE is not a ‘good’ theory. On the other hand, the DE is also not a ‘good’ theory because it tends to overshoot chemistry and ordinary physics: Its negative energy states have nothing to do with chemistry and ordinary physics. To get a ‘good’ theory, the following four questions have to be addressed. If the point of departure is the DE, (Q1) can we find an exact two-component (2C), electron-only theory? (Q2) can the computational effort of the DE be reduced down to that of a 2C counterpart? If the point of departure is the SE, (Q3) can we find an optimal scalar relativistic equation that is as simple as the SE? Finally, starting from the midpoint of the DE and SE, (Q4) can we find an equation that can seamlessly fuse the two equations such that heavy and light elements in the system can be treated differently?

All the four questions have nicely been answered, based on the simple idea of “from atoms to molecule”1-3 rather than on mathematical tricks. It can now be claimed that relativity in chemistry has been solved, 80 years after Dirac though.

References:
1. W. Kutzelnigg and W. Liu, J. Chem. Phys. 123, 241102 (2005).
2. W. Liu and D. Peng, J. Chem. Phys. 125, 044102 (2006).
3. D. Peng, W. Liu, Y. Xiao, and L. Cheng, J. Chem. Phys. 127, 104106 (2007).
Absorption and transport properties of near-field coupled plasmons and molecules
Kenneth Lopata and Daniel Neuhauser
Department of Chemistry and Biochemistry, University of California, Los Angeles, U.S.A.
We present a simple computational approach for describing, in both time and frequency domains, the dynamics of combined plasmon and molecular excitations. The plasmon excitations are treated classically and the molecular excitations are treated using a linear response random phase approximation. Two model systems are discussed. Firstly, we show how the position and location of the molecule with respect to a linear array of gold nanoparticles can be monitored using polarized absorption spectroscopy. Secondly, we demonstrate how the molecule can be used to gate plasmon transport through a nanoparticle junction. Such arrangements can act as either sensors or switch components in plasmonic circuits.
Understanding the melting process in free sodium clusters.
A. Aguado, J. M. López, and S. Núñez
Dpt. Física Teórica, Atómica y Óptica. Universidad de Valladolid.
47005 Valladolid. Spain
There is a fundamental interest in understanding the analog of the melting phase transition in small atomic clusters. Classical arguments predict that melting temperatures of small particles should show a monotonic decrease from the bulk limit as their sizes shrink.

However, Jarrold and co-workers [1] have demonstrated that small gallium and tin clusters melt at temperatures higher than the bulk melting temperature. Also, calorimetry experiments by Haberland and co-workers [2] show that the size dependence of melting temperature is not monotonic for Na clusters.

Employing an orbital-free version of density-functional-theory, which expresses the energy as an explicit functional of the valence electron density, and pseudopotentials to represent the ionic field acting on the valence electrons, we have performed isokinetic Born-Oppenheimer Molecular dynamics runs, in which the average kinetic energy is kept constant by velocity rescaling and the atomic forces are evaluated from the Hellmann-Feynman theorem.

The irregular size dependence of the melting temperatures Tm observed in the calorimetry experiments on sodium clusters is quantitatively reproduced and interpreted by the MD simulations.

We will also show recent results on the melting-like transition of sodium clusters of small size. Na25 shows a peculiar post-melting transition, associated to the progressive dissappearance of the radial atomic layering of the liquid cluster as it is heated. For small clusters, the loss of radial layering can imply a substantial change in the relative number of internal and surface atoms, and therefore has a signature in the heat capacity.

[1] A. A. Shvartsburg and M. F. Jarrold, Phys. Rev. Lett 85, 2530 (2000); G. A. Breaux et al Phys. Rev. Lett 91, 215508 (2003)
[2] M. Schmidt et al., Phys. Rev. Lett. 79, 99 (1997); Nature (London) 393, 238 (1998); C.R. Physique 3, 327 (2002); Phys. Rev. Lett. 90, 103401(2003); R. Kusche et al., Eur. Phys. J. D 9, 1 (1999).
Quantum Simulation of Materials at Micron Scales and Beyond
Qing Peng1, Xu Zhang1, Linda Hung2, Emily A. Carter2,3 and Gang Lu1


1Department of Physics and Astronomy,
California State University Northridge, Northridge, CA, USA
2Program in Applied and Computational
Mathematics, Princeton University, Princeton, New Jersey, USA
3Department of Mechanical and Aerospace
Engineering, Princeton University, Princeton, New Jersey, USA


We present a novel multiscale modeling approach that can simulate multi-million atoms effectively via density functional theory. The method is based on the framework of the quasicontinuum (QC) approach with orbital-free density functional theory (OFDFT) as its sole energetics formulation. The local QC part is formulated by the Cauchy-Born hypothesis with OFDFT calculations for strain energy and stress. The nonlocal QC part is treated by an OFDFT-based embedding approach, which couples OFDFT nonlocal atoms to local region atoms. The method - QCDFT- is applied to a nanoindentation study of an Al thin film, and the results are compared to a conventional QC approach. The results suggest that QCDFT represents a new direction for the quantum simulation of materials at length scales that are relevant to experiments.

Some Recent Advances in the Exact Non-Born-Oppenheimer Treatment of Hookean Three- and Four-Particle Systems
Xabier Lopez,1 J.M. Ugalde,1 L. Echevarria,2 and E.V. Ludena3
1Donostia International Physics Center (DICP) and Kimika Fakultatea, Euskal Herrico Unibertsitatea, Posta Kutxa 1072, 20080 Donostia, Euskadi, Spain.
2Departamento de Quimica, Universidad Simon Bolivar, Sartenejas, Venezuela.
3Centro de Quimica, Instituto Venezolano de Investigaciones Cientificas, IVIC, Apartado 21827, Caracas 1020-A, Venezuela.
The Hookean systems under consideration are formed by three and four charged particles with arbitrary masses where the interaction between the particles with the same charge is Coulombic and that between particles with different charges is harmonic.

Based on the exact non-Born-Oppenheimer solutions for these systems, we examine the problem of the definition of molecular structure, which in the Born-Oppenheimer treatment is given in terms of the topological characteristics of the one-particle density. We show that for these systems, which include on the same footing nuclear and electronic motion, there is not a unique definition of the one-particle density on account of the arbitrariness of the choice of the origin of coordinates. We explore the topology of the density under different choices and analyze in this context the notion of molecular structure.

We obtain the exact non-Born-Oppenheimer solutions for the Hookean model of dipositronium (a four particle system formed by two electrons and two positrons) and for the family of systems formed by two positive and two negative particles, all with the same mass M. In particular, for all these systems we discuss the effect of symmetry on the wave function (spatial, spin, and charge and parity exchange) as well as the relationship between mass and the type of correlation function (between particles with the same charge) appearing in the exact solutions.

Finally, we consider these Hookean model systems in the presence of external magnetic fields as feasible models for single and double quantum dots. In this context we examine the effect of the dot radius and the external magnetic field on the correlation between particles with the same charge and in particular we analyze the phenomenon of particle localization leading to the arisal of Wigner-type molecules.
Optimization of nodal hypersurfaces in quantum Monte Carlo
Arne Lüchow
Institute of Physical Chemistry,
RWTH Aachen University,
52056 Aachen, Germany
Over the last few years, quantum Monte Carlo methods have shown to be applicable to a wide range of quantum chemical problems with high accuracy, including excited states and weak interactions. QMC can retain the inherent favorable scaling of Monte Carlo methods in these applications. Recent results are discussed with the emphasis on new ways to control the fixed-node error of diffusion quantum Monte Carlo by optimization of the nodal hypersurfaces of a trial function.
Development of a Polarizable Empirical Force Field Based on the Classical Drude Oscillator.
Alexander D. MacKerell, Jr.
Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
Ongoing efforts in our laboratory are developing a polarizable force field based on the classical Drude oscillator for a range of molecules representative of biological systems, with emphasis on proteins, lipids and nucleic acids. A central theme in these efforts is the accurate treatment of both atomic interactions as well as condensed phase properties. To achieve this goal target data for optimization of the non-bond parameters includes a variety of quantum mechanical and experimental condensed phase properties. An overview of this approach, including results for a variety of small molecules, peptides, lipids and nucleic acids will be presented.
Charge-transfer at the electrochemical interface: a simulation study
Paul A. Madden
School of Chemistry, University of Edinburgh, UK
The understanding of the electrochemical interface is one of the few domains of physical chemistry on which the modern methods of theoretical chemistry, electronic structure calculations and computer simulation, have had little impact. The interface between an electrode and a coulombic liquid is a particularly interesting challenge; it is often analysed by appeal to the double-layer ideas, yet the validity of these dilute electrolyte solution concepts in the pure ionic liquid is easily challenged. Here computer simulations of a molten salt at a model metallic electrode maintained at a constant electrical potential are described. The interactions between the ions and their interactions with the electrode are obtained from first-principles calculations. The free-energy surfaces for oxidised and reduced species invoked in the Marcus Theory of Electron Transfer are calculated. The physical factors which cause them to be affected by the proximity of the redox species to the interface are identified.

Reference: Electrochemical charge transfer at a metallic electrode: A simulation study; S.K. Reed, P.A. Madden and A. Papadopoulos, J. Chem. Phys., 128, 124701 (2008).
A Size-Extensive State-Specific Multi-Reference Coupled Cluster Theory with Incomplete Model Spaces and Its Approximate Variants.
Rahul Maitra1, Dipayan Datta1, Sanghamitra Das1 and Debashis Mukherjee1
1Raman Center for Atomic, Molecular and Optical Sciences, Indian Association for the Cultivation of Science, Kolkata, India
In this poster, we present a rigorously size-extensive State- Specific Multi-reference Coupled Cluster (SS-MRCC) theory, based on an arbitrary incomplete active space (IAS). This extension of the parent theory using a complete active space (CAS) reduces the computational cost considerably. The essentials of the formalism build on an earlier work of Mukherjee (Chem. Phys. Letters 125 (1986) 207), where it was shown how by eliminating the components of an effective operator providing a size-extensive energy on diagonalization requires use of extra operators inducing internal excitations, whose nature is such that they can induce excitations outside the IAS by the action on at least one model function. With this constraint, the effective operator is 'closed' in the sense of inducing transitions only within the IAS. To achieve this, the simplest procedure is to abandon the traditional choice of the intermediate normalization of the wave operator.
We also present some useful approximate variants of the full-blown SS-MRCC theory with IAS, like the State-Specific Multi-Reference Coupled Electron Pair like Approximations (SS-MRCEPA) and also the perturbative approximations(SS-MRPT). Pilot applications to some prototypical systems will be presented to illustrate the performance of the theories. Size-extensivity of the energy in our formalism will guarantee size-consistency if we choose the IAS carefully, so that it admits of the product separability into fragments at the active space level. Some useful IAS satisfying such a requirement is provided by the quasi-complete active space and some special types of RAS.
Quantum transitions in Lennard-Jones clusters
Vladimir Mandelshtam
UC Irvine
I will present our most recent numerical results on thermodynamics of quantum Lennard Jones (LJ) clusters.

The classical LJ(n) clusters had been studied previously and very extensively, particularly in our group:
J. Chem. Phys. 2006, 124, 20451;
J. Phys. Chem. , 2007, 111, 10284.

The above numerical results demonstrate how complex these systems can be (even without taking into account the quantum effects), having a number of structural motifs that are thermodynamically stable for different ranges of the size n and temperature T.

The quantm effects change the critical parameters (n and T) as we demonstrated for the case of neon clusters:
J. Chem. Phys. 2005, 122, 154305;
Phys. Rev Lett. 2006, 96, 113401

Our most recent results explore the evolution of the ground state (i.e., the zero temperature case) of the LJ(n,L) cluster as a function of its size n and the de Boer quantum delocalization length L. The corresponding "phase diagram" that we constructed shows the stability ranges for the competing structural motifs. An increase of L has an effect similar to heating and as such may induce structural transformations.

Tomographic Imaging of Molecular Orbitals from High-Order
Harmonic Spectra: Challenges in Theory
Richard Taïeb, Jérémie Caillat and Alfred Maquet
Laboratoire de Chimie Physique-Matière et Rayonnement,
(UMR 7614 du CNRS)
Université Pierre et Marie Curie,
11, Rue Pierre et Marie Curie, 75231 Paris Cedex 05, France.
A few years ago, it has been shown that one could reconstruct the spatial dependence of the 3σg Highest-Occupied Molecular orbital (HOMO) in N2 through the analysis of the harmonic spectra generated by molecules oriented in space [1]. The conceptual framework of the approach is based on the so-called "Strong-Field Approximation" treatment of the harmonic generation process that links the harmonic phases and amplitudes to the ones of the bound-free molecular dipole. Then the HOMO of the molecule can be deduced from a tomographic analysis of the harmonic signals originating from molecules with different alignments in space with respect to the polarization of the pump laser, see [2] and references therein. Further generalizations of these pioneering results are under active investigations from both the experiment and theory sides. For recent results obtained in CO2, see [3]. So far, the agreement between theory and experiment is not completely satisfactory.
In our presentation, we shall address several issues directly related to the theoretical treatment of this class of processes and we shall discuss different strategies under development aiming at filling the gap between theory and experiment.

[1] Itatani, J; Levesque, J; Zeidler, D, et al.
Tomographic imaging of molecular orbitals
NATURE 432, 867-871 (2004)

[2] Lein, M
Molecular imaging using recolliding electrons
JOURNAL OF PHYSICS B-ATOMIC MOLECULAR AND OPTICAL PHYSICS 40, R135-R173 (2007)

[3] Bouttu, W; Haessler, S; Merdji, H; Breger, G; Waters, G; Stankiewicz, M; Frasinski, L.J.; Taïeb, R; Caillat, J; Maquet, A; Monchicourt, P; Carré, B. and Salières, P
Coherent control of attosecond emission from aligned molecules
NATURE PHYSICS in press (2008)

Experiment-motivated theoretical studies of reaction rates:'on water' organic reactions, isotope fractionation and single-molecule fluctuations
Rudolph A. Marcus
Noyes Laboratory of Chemical Physics
California Institute of Technology
MC 127-72
Pasadena CA 91125
Much of theoretical chemistry has involved equations and their application to experiments, Debye, Debye-Hückel, TST, Kramers, LCAO, RRKM, among others. In fortunate circumstances one can, as in a theory of electron transfer reactions, relate different experiments to each other without adjustable parameters, as well as make predictions. A major focus more recently has been on computations for individual systems, on the specific rather than on the generic. The computations have permitted the treatment of certain experiments in a detailed fashion not possible earlier. In some cases computations served as numerical experiments yielding new insights, as in an analysis of classical and quantum trajectories in the literature of a simple H+H2 reaction, leading to the coining of a new term, vibrational adiabaticity.1

Recent formulations of theory in the analytic/computational domain will be described, using several of the following examples: mass-independent isotope effect in ozone formation,2 catalysis of certain organic on-water reactions,3 intermittent fluorescence of nanoparticles,4 single-molecule properties of proteins,5 temperature independence of the H/D kinetic isotope effect for some enzymes operating under their natural conditions,6 and an abnormal Arrhenius pre-exponential factor for a thermophilic enzyme operating below its “break-point” temperature.6

It will be interesting to see how the interplay between experiment, analytic theory and computation develops in future theoretical chemistry. The emphasis in this talk will be on puzzles, arising from experiments in search of theory.

1. RAM J.Chem.Phys. 43,1598 (1965)
2. Y.Q. Gao & RAM J.Chem.Phys. 116,137 (2002) and 127,Art.No. 244318 (2007)
3. Y. Jung & RAM J.Am.Chem.Soc. 129,5492 (2007)
4. J. Tang & RAM, J.Chem.Phys., 123,Art.No.05470 (2005); P. Frantsuzov & RAM Phys.Rev.B, 72,155321 (2005).
5. M. K. Prakash & RAM, Proc.Nat.Acad.Sci.USA, 104,15982 (2007) and J.Phys.Chem.B, 112,399 (2008)
6. RAM, in “Quantum Tunneling in Enzyme Catalyzed Reactions,” R. Allemann, ed. (to be published 2008)
The localization / delocalization dilemma in the electronic structure of d- and f-element oxides
Richard L. Martin
Theoretical Division, MSB268, Los Alamos National Laboratory, Los Alamos, NM 87545

The electronic structure of many of the oxides containing d− and f-elements has long been a challenge for theory. For example, the traditional workhorses of density functional theory, the local density approximation (LDA) and the generalized gradient approximations (GGA), predict most of these systems to be metallic, when in fact they are insulators with band gaps of several eV. These problems reflect the localization/delocalization dilemma faced in systems with weak overlap and seem to be largely overcome by the new generation of hybrid density functionals developed for molecular studies. Only recently has it been possible to apply these functionals to solids but in the cases studied thus far we find a distinct improvement. The hybrid functionals predict the correct insulating ground state, band gap, lattice constant and magnetic behavior at 0K, where known. I will review the origin of the problem, how hybrid functionals differ from traditional ones, and recent applications to MnO, CeO2, Ce2O3, and the actinide oxide series AnO2, An = Th ... Es.
Simulating materials with chemical detail at IBM: From biophysics to high-tech applications
Glenn Martyna
Physical Science Division
IBM TJ Watson Research Center
The goal of simulation studies is to provide insight into important systems of scientific and technical interest. Today, appoaching these systems involves treating accurately complex heterogeneous interfaces. The modeling of nanostructures is reviewed with application to problems in engineering, physics, and biochemistry. In particular, studies of perpendicular magnetic recording, buckytube field effect transistors, phase change memories and the properties of biometic systems are discussed along with the novel parallel algorithms and mathematical physics underlying the computations.
Electron Correlation and Nuclear Motion Corrections to the
Ground-State Energy of Helium Isoelectronic Ions, from Li to Kr
R. L. Pavlov,a,b J. Maruani,b I. M. Mihailov,c Ch. J. Velchev,a and M. Dimitrova-Ivanovich a
a Institute for Nuclear Research and Nuclear Energy, Bulgarian Academy of Sciences, 72 Tsarigradsko Chaussee, 1784 Sofia, Bulgaria
b Laboratoire de Chimie Physique, CNRS and UPMC, 11 Rue Pierre et Marie Curie, 75005 Paris, France
c Institute of Solid State Physics, Bulgarian Academy of Sciences,
72 Tsarigradsko Chaussee, 1784 Sofia, Bulgaria
Nonrelativistic energies for the ground state of Helium isoelectronic ions for Z = 3-54 are computed. Calculations are performed using explicitly correlated wavefunctions of a generalized Hylleraas type. The variational procedure used allows solving the two-electron Schrödinger equation with a practically unlimited number of parameters for trial wavefunctions expanded in products of positive powers of the Hylleraas coordinates. A nonconventional optimization procedure, involving nonlinear programming, is applied. The contribution of the various terms is assessed, including nuclear finite mass and ‘polarization’ corrections. Our results are compared to other theoretical results. Combined with noncorrelated relativistic energies, they yield a good agreement with available experimental data.

FIGURE
Relative magnitudes of various corrections to the ionization energies of He isoelectronic ions.

TABLE
A few results measured and computed using our procedure.

IP / au 6C4+ 7N5+ 8O6+ 9F7+ 10Ne8+ 11Na9+ 12Mg10+ 13Al11+ 14Si12+
Meas. 14.4087 20.2878 27.1688 35.0530 43.9522 54.0919 64.7401 76.7590 ******
Comp. 14.4088 20.2877 27.1692 35.0545 43.9443 53.8404 64.7439 76.6568 89.5805

Nano-scale Modeling of Catalyst Layers for PEM Fuel Cells
Tetsuya Mashio,1 Kourosh Malek,2 Atsushi Ohma,1 Kouichi Yamaguchi,1 and Kazuhiko Shinohara1
1Fuel Cell Laboratory, Nissan Research Center, Nissan Motor Co., Ltd., Japan

2National Research Council Canada, Institute for Fuel Cell Innovation, Canada
Polymer electrolyte membrane (PEM) fuel cells are a very promising power source for automotive use. Significant issues that must be addressed in order to commercialize fuel cell vehicles (FCVs) include reducing the cost and improving power density. Pt particles in catalyst layers (CLs) might not be adequately utilized due to the random structures of each components such as Pt particles, ionomer, and carbon particles in CLs and non-uniform distributions of reactants and reaction rates during a fuel cell operation. Therefore, optimization of the structures as a result of understanding the mechanism of the three phase boundary formation and mass transport in the molecular level is expected to be one solution to these issues.
The structure of the CLs in different scales was clarified based on the ex-situ measurement results. Important parameters in nano scale were discussed on the basis of the insights from the simple model using a finite element method. Morphology of ionomer and transport properties of water and hydronium ion in the vicinity of a graphitized carbon sheet were analyzed by molecular dynamics simulations under the neutral/uncharged conditions. The impact of functional groups was investigated under the charged conditions, and the effect of the porous structure of the carbon was also discussed.
Anti-Hermitian Part of the Contracted Schrodinger Equation for
the Direct Calculation of Two-electron Reduced Density Matrices
David A. Mazziotti
Department of Chemistry and The James Franck Institute, The University of Chicago, USA
Two-electron reduced density matrices (2-RDMs) have recently been directly calculated by solving the anti-Hermitian contracted Schrödinger equation (ACSE) to obtain 95–100% of the ground-state correlation energy of atoms and molecules with the accuracy increasing with the size of the one-electron basis set [1-7]. In this lecture we will discuss the ACSE and its comparison to the contracted Schrodinger equation (CSE) with regard to cumulant reconstruction of RDMs, the role of Nakatsuji’s theorem, and the structure of the wavefunction [3]. The ACSE can treat both single- and multi-reference correlation effects [6]. Applications to be discussed include the potential energy surfaces of HF, H2O, and C2, the cis and trans isomers of HO3- [7], and the reaction of bicylobutane to form 1,3-butadiene. Computed 2-RDMs very closely satisfy known N-representability conditions.

[1] D. A. Mazziotti, Phys. Rev. Lett. 97, 143002 (2006).
[2] D. A. Mazziotti in Two-electron Reduced-Density-Matrix Mechanics with Application to Many electron Atoms and Molecules, edited by D. A. Mazziotti, Advances in Chemical Physics Vol. 134 (John Wiley and Sons, New York, 2007), p. 331.
[3] D. A. Mazziotti, Phys. Rev. A 75, 022505 (2007).
[4] D. A. Mazziotti, J. Chem. Phys. 126, 184101 (2007).
[5] C. Valdemoro, L. M. Tel, D. R. Alcoba, and E. Perez-Romero, Theor. Chem. Acc. 118, 503509 (2007).
[6] D. A. Mazziotti, Phys. Rev. A 76, 052502 (2007).
[7] D. A. Mazziotti, J. Phys. Chem. A 111, 12635 (2007).
Electron Transport in Molecular Monolayers between Metallic Conductors
Richard L. McCreery, Adam Bergren, Sergio Jimenez, Andrew Bonifas,
Haijun Yan

University of Alberta
National Institute for Nanotechnology
Ohio State University
The prospect of using molecules as components in electronic circuits has both enormous potential and enormous challenges. It is possible that molecular circuits will enhance silicon-based microelectronics, yielding faster, denser, and cheaper electronic devices with possibly new functions not possible with conventional semiconductors. Our approach to the problem is based on a layer of molecules covalently oriented between a conducting substrate and a metallic top contact1-4. We use Raman and UV-Vis spectroscopy to probe the structure of the molecules in live molecular junctions, in which molecules are subjected to unusually large electric fields (e.g. 107 V/cm)5-8. The behavior of molecules as circuit components is strongly dependent on temperature, molecular structure and bonding to the contacts, and it is possible to monitor chemical changes in molecular junctions during operation. The focus of the presentation is on electron transport in carbon/molecule/copper electronic junctions, in particular the factors which control the current/voltage characteristics of the devices.

(1) McCreery, R. L.; Viswanathan, U.; Kalakodimi, R. P.; Nowak, A. M.; Carbon/molecule/metal molecular electronic junctions: the importance of "contacts"; Faraday Discussions 2006, 131, 33.
(2) McCreery, R.; Wu, J.; Kalakodimi, R. J.; Electron Transport and Redox Reactions in Carbon Based Molecular Electronic Junctions; Phys. Chem. Chem. Physics. 2006, 8, 2572.
(3) McGovern, W. R.; Anariba, F.; McCreery, R.; Importance of oxides in carbon/molecule/metal molecular junctions with titanium and copper top contacts; J. Electrochem Soc 2005, 152, E176.
(4) Anariba, F.; Steach, J.; McCreery, R.; Strong Effects of Molecular Structure on Electron Transport in Carbon/molecule/Copper Electronic Junctions; J. Phys. Chem B 2005, 109, 11163.
(5) Nowak, A.; McCreery, R.; In-Situ Raman Spectroscopy of Bias-Induced Structural Changes in Nitroazobenzene Molecular Electronic Junctions; J. Am. Chem. Soc. 2004, 126 16621.
(6) Kalakodimi, R. P.; Nowak, A.; McCreery, R. L.; Carbon/Molecule/Metal and Carbon/Molecule/Metal Oxide Molecular Electronic Junctions; Chem. Mater. 2005, 17, 4939.
(7) McCreery, R. L.; Analytical challenges in molecular electronics; Analytical Chemistry 2006, 78, 3490.
(8) Bonifas, A. P.; McCreery, R. L.; In-Situ Optical Absorbance Spectroscopy of Molecular Layers in Carbon Based Molecular Electronic Devices; Chem. Mater. 2008, 20, 3849.
Cold Collisions of OH with He
Edmund Meyer, Manuel Lara and John Bohn
JILA, NIST and Deptartment of Physics, University of Colorado, Boulder
Cooling polar molecules is the next big step in achieving control of the microscopic world. The rich structure of diatomic molecules, as compared to atoms, presents a new level of difficulty in attaining such a feat. Possibilities for state-changing collisions can be fairly high due to small nuances in the structure of the molecule. Most studies up till now focus on cold collisions (mK range) between He and molecules in Σ symmetries, meaning zero electronic orbital angular momentum about the internuclear axis. The interest in He is due to the advancement and success of buffer gas cooling. Our understanding of energy transfer in cold collisions will be broadened by considering molecules in other symmetries. To this end, we consider cold collisions of a molecule in Π symmetry, meaning one unit of electronic orbital angular momentum. The way in which energy is shuffled in this type of molecule is funadamentally different than previous studies due to the change in Hund's case from (b) to (a). We present the first calculations of cold collisions of He with diatomic molecules in Π symmetries. We focus primarily on the collisions between He and OH, which is a molecule of much interest to both the experimental and theoretical groups working in the field of cold collisions of molecules.
Spontaneous Resolution by Parity Violation - Could it be Observable?
Mojmír Kývala, Jakub Chalupský, Zdeněk Havlas, and Josef Michl
Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic
Ever since the beginnings of stereochemistry in the second half of the 19th century, chemists have been firmly convinced that at equilibrium two enantiomers (mirror image molecules) are present in an exact 1:1 ratio. For half a century, physicists have known that this belief is incorrect, because of a small parity violating term in the Hamiltonian. However, calculations suggest that the anticipated deviation from exact energetic equivalence is far too small to be detected, and that for all practical purposes the chemists’ belief is correct. Attempts to detect molecular consequences of parity violation have concentrated on small-molecule spectroscopy, not on deviations from a 1:1 ratio at equilibrium (spontaneous resolution). They have not yet succeeded to our knowledge, but success in the foreseeable future appears possible.

We have asked a related but different question: might there not be some molecular structures, perhaps quite complicated, for which the effect of parity violation would be large enough for spontaneous resolution to be observable by the chemists’ usual tools, such as measurement of optical activity as a function of temperature? For this purpose we have converted the usual approximate non-relativistic expression for the parity violation energy into a very simple model that provides qualitative insight, and analyzed the conditions under which a relatively large parity violation term would be expected. Guided by the results, we have performed two-component relativistic calculations for selected candidates and found some for which the energy difference between enantiomers is of the order of microjoules/mol. This is a small energy difference, but is several orders of magnitude larger than any computed previously for chiral molecules that were chosen more or less randomly. It appears possible that our effort will ultimately result in prediction of molecular structures for which spontaneous resolution will actually be observable by today’s tools.
Model for simulating coupled electronic and nuclear dynamics in liquids
Thomas F. Miller, III
Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, USA
We describe our recent efforts to simulate the coupled dynamics of electrons and nuclei in the condensed phase. The ring polymer molecular dynamics (RPMD) model is used to simulate the diffusion of an excess electron in supercritical helium over a range of fluid densities. The accuracy of the RPMD model is tested against numerically exact path integral statistics through the use of analytical continuation techniques. At fluid densities approaching those of typical liquids, the RPMD model provides an accurate description for the fast, highly quantum mechanical dynamics of the excess electron. In this regime where the dynamics of the electron is strongly coupled to the dynamics of the atoms in the fluid, trajectories that can reveal diffusive motion of the electron must be long in comparison to βh-.
Using the Initial Value Representation of Semiclassical Theory to Add Quantum Effects to Classical Molecular Dynamics Simulations

William H. Miller
Department of Chemistry
University of California
Berkeley, CA 94707
USA
Semiclassical (SC) theory provides a good description of essentially all quantum effects (interference/coherence, tunneling and other classically forbidden processes, symmetry effects of identical particles, quantization of bounded motion, etc.) in molecular dynamics; this has long been appreciated and validated by many applications to small molecular systems [cf. Adv. Chem. Phys. 25, 69-177 (1974)]. Since SC theory is built on the classical trajectories of the dynamical system, it should in principle be possible to use it also to add quantum effects to classical molecular dynamics simulations of complex molecular systems (i.e., those with many degrees of freedom), e.g., chemical reactions in solution, in clusters, in bio-molecular or any complex environment. The practical implementation of SC theory for systems with many degrees of freedom is based on various initial value representations (IVRs), which have recently undergone a re-birth of interest in this regard. This talk reviews the basic idea of the SC-IVR approach and describes a variety of recent applications that have been carried out using it. For some recent overviews, see Proc. Nat. Acad. Sci. 102, 6660-6664 (2005) and J. Chem. Phys. 125, 132305.1-8 (2006).
Quantum State Manipulation with Ultra-Short Laser Pulses
Valery Milner
Department of Chemistry and the Laboratory for Advanced Spectroscopy and Imaging Research (LASIR), University of British Columbia, Canada
Fast and efficient transfer of atoms and molecules from one quantum state to another is important in many areas of science.
High-resolution spectroscopy, metrology, quantum computing and state-selective chemistry (to name just a few examples) all rely on the ability to prepare the system of interest in a well defined target state, while tolerating instrumental noise, de-coherence, and other imperfections of the environment. In this talk, I will describe our recent progress in achieving this goal with ultrafast lasers. I will show how by matching the temporal shape of a laser pulse to the dynamics of a system, one can perform fast and robust excitation of the desired coherent superposition of states on a femtosecond time scale.
Multi-Step Modelling of Giant Polyoxometalates:
Structure and Dynamics of (H2O)100 Encapsulated Water Cluster
Pere Miró,1 Tamoghna Mitra,2 Adrian-Raul Tomsa,2 Alice Merca,2 Hartmut Bögge,2 Achim Müller,2 Josep Bonet Ávalos,3 Josep Maria Poblet,4 and Carles Bo1,4
1Institute of Chemical Research of Catalonia (ICIQ), Tarragona (Spain)
2Faculty Chemistry, University of Bielefeld, Bielefeld (Germany)
3Department of Chemical Engineering, ETSEQ, University Rovira i Virgili, Tarragona (Spain)
4Department of Inorganic and Physical Chemistry, University Rovira i Virgili, Tarragona (Spain)
During the last decade, the chemistry of polyoxometalates (POMs) enabled the growing of impressive new giant structures such as those reported by Müller and coworkers.[1] A striking feature of those nanocapsules is that encapsulated water molecules show a highly ordered multilayer structure. For instance, the (H2O)100 cluster in [(Mo{Mo5}O21{H2O}6)12(Mo2O4SO4)30]72- characterized by X-ray shows three layers that correspond to two dodecahedron and a distorted rhombicosidodecahedron.[2] We will show in this communication how the high symmetry (Ih) of these capsules allowed the determination of their electronic structures by means of DFT-based methods, and deriving parameters that were then used to carry out classical molecular dynamics simulations. Following our previous experience with smaller systems,[3] the above mentioned nanocapsule and the new [(Mo{Mo5}O21{H2O}6)12(Mo2O4HCO2)30]42- have been studied. Our simulations reproduce the same multilayer structure as seen experimentally, and also reveal the dynamic behaviour of these water clusters.

[1] Müller, A.; Shah, S. Q. N.; Bögge, H.; Schmidtmann, M. Nature 1999, 397 (6714), 48-50.
[2] Müller, A.; Krickemeyer, E.; Bögge, H.; Schmidtmann, M.; Roy, S.; Berkle, A. Angew. Chem. Int. Ed 2002, 41, 3604
[3] López, X.; Nieto-Draghi, C.; Bo, C.; Bonet Avalos, J.; Poblet, J. M. J. Phys. Chem. A 2005, 109, 1216. Leroy, F.; Miró, P.; Poblet, J. M.; Bonet Avalos, J.; Bo, C. J. Phys. Chem. B 2008, in press.
Geometry of wave functions for quantum systems: nodal structures and many-body effects
Lubos Mitas*
North Carolina State University
For fermions in continuous space the fixed-node diffusion Monte Carlo methods proved to be very successful for many practical, large-scale calculations of real or model systems. The major remaining barrier for improving upon the fixed-node approximation is our limited accuracy and knowledge of the nodes of fermionic trial functions. The fermion nodes of many-body wavefunctions are notoriously difficult to improve and many of their properties, including nodal cell topologies and exact shapes, have been puzzling or not clearly understood. We explicitly prove that for d>1 the nondegenerate fermionic ground states have the minimal number of two nodal cells for any system size under rather general conditions. For systems with interactions the proof is based on exploring the properties of BCS wavefunctions. The same property is demonstrated for temperature density matrices in d>1. These proofs have inspired search for trial wavefunctions which demonstrably possess the correct nodal topologies. To this end, we have proposed and tested pfaffian wavefunctions with both singlet and triplet pairing orbitals in a single and easy to evaluate form as an efficient way to capture the correct topological properties. The recent results and further progress in this direction will be discussed.

*In collaboration with M. Bajdich, K. E. Schmidt, J. Kolorenc, S. Hu and K. Rasch.
Destabilized Magnesium-based Alloy Thin Films as Model Systems for Hydrogen Storage
David Mitlin*, Chris T. Harrower*, Julian Haagsma*, Colin Ophus*, Babak Shalchi*, Mohsen Danaie*, Mouna Saoudi**, Helmut Fritzsche**
*Chemical and Materials Engineering, University of Alberta, Edmonton AB, Canada
and
NRC National Institute for Nanotechnology, Edmonton AB, Canada

**National Research Council Canada, SIMS, Canadian Neutron Beam Centre, Chalk River Laboratories, Chalk River ON, Canada
The key for achieving 100 °C - range hydrogen sorption is to have favorable thermodynamics, i.e. a hydrogen binding energy near 30 kJ/mol. Metallic magnesium possesses sufficient gravimetric and volumetric sorption capacity, but has unfavorable thermodynamics (-77 kJ/mol α-MgH2 formation energy) and poor kinetics. In this presentation I will discuss our general methodology for tuning the hydrogen sorption thermodynamics of magnesium, through alloy design. We use a thin films approach to create a range of destabilized magnesium-based alloys and of accompanying catalytic layers. Thin films make for ideal “model” systems that may be used for accurately and rapidly screening a variety of matrix and catalyst formulations. Because of the small diffusion distances, films also allow for better separation of system thermodynamics from the kinetics. The synthesized films were tested volumetrically through multiple adsorption-desorption cycles. The microstructures were characterized by neutron reflectometry and x-ray diffraction. We show that alloying magnesium with light elements that have weak hydrogen interaction, such as aluminum, is a very effective method for lowering the sorption temperature to near ambient. At certain compositions, the addition of aluminum promotes the high-pressure γ-MgH2 phase at the expense of the equilibrium α-MgH2. At other compositions, the sorbed microstructure is a composite of α-MgH2 intermixed with α-AlH3. We also demonstrate that there is critical temperature above which the palladium catalyst caps are not stable, reacting with the underlying material and losing their efficacy. Additionally, there will be a discussion of the processing and sorption kinetics of MgH2 - metal catalyst - carbon nanotube (CNT) powder composites, and of direct TEM characterization of milled MgH2.
On the Origin of the trans – influence in Square Planar d8 -complexes. A Theoretical Study
Mariusz Mitoraj, 1,2 Hongjuan Zhu2 Artur Michalak1 and Tom Ziegler2
1Department of Theoretical Chemistry, Faculty of Chemistry, Jagiellonian University, R.Ingardena 3, 30-060 Cracow, Poland


2Department of Chemistry, University of Calgary,
2500 University Dr NW, Calgary, Alberta Canada
The trans influence of ligands T in trans-[Ni(Cl)2NH3T]n complexes with T- = B(Me)2-, H-, CP-, CH2CH3-, CN-, HCC-, Cl-, F- for n=-1 and T = PF3, PH3, P(CH3)3, CO for n=0 has been analyzed with the help of the Extended Transition State (ETS) energy decomposition scheme and as well as the Natural Orbitals for Chemical Valence (NOCV) method.

The TCl2Ni-NH3 bond is made up of the bonding interaction between the empty sigma-Ni acceptor orbital on the [TCl2Ni]n fragment and the sigma- NH3 donor orbital. The sigma-Ni orbital is in turn an out-of-phase combination between dz2 on the metal and an occupied sigma-T orbital: sigma-Ni= dz2-C1*sigma-T. It has been shown that the trans influence is related to the contribution (C1) to sigma-Ni from sigma-T. Thus the smaller the contribution C1 to sigma-Ni the larger the overlap and the stronger the TCl2Ni-NH3 bond. The contribution C1 is in turn related to the orbital energy ε(sigma-T) of T. Thus the lower ε(sigma-T) is, the smaller is C1. There is thus an inverse relation between the trans influence of a ligand T and its electronegativity.
Theoretical Methods to Study the Electron Transfer Effect
Yirong Mo
Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
Electron transfer (ET) processes play a fundamental role in all chemical and biochemical reactions. Notably, the qualitative Marcus-Hush two-state model has been widely employed to study ET processes. However, it remains a challenge to develop robust theoretical methods to derive the energy profiles of the diabatic states at the ab initio level and correlate the ET rate with physical quantities such as the electronic coupling element and reorganization energies. As the popular molecular orbital (MO) theory cannot derive the wavefunction for a diabatic state self-consistently due to its delocalization nature, we proposed an efficient variant of the ab initio valence bond (VB) theory, called block-localized wave function (BLW) method which takes the advantages of both the MO and VB theories. Most recently, we have extended the BLW method to the DFT level and implemented it in the quantum mechanical software GAMESS. The BLW method can be used to study the intramolecular electron delocalization (e.g., aromaticity or hyperconjugation in ethane) and intermolecular electron transfer effects (e.g., energy decompositions in terms of electrostatic, polarization and charge transfer effects). Based on the BLW method, we further propose a two-state method to investigate electron transfer processes in gaseous and condensed phases. Comparison between the BLW-based two-state method and other qualitative two-state models will be presented and examples will be provided to illustrate the potentials and applicability of the new two-state method, which can be used to establish the correlation of the electron transfer efficiency with the donor/acceptor and bridge groups and the media effect for DBA complexes, and explore the structure-property relationships in non-linear optical materials.

References:
1) Mo, Y., Song, L., Lin, Y., “The block-localized wavefunction (BLW) method at the density functional theory (DFT) level”, J. Phys. Chem. A, 111(34), 8291-8301 (2007). (Cover Feature Article)
2) Mo, Y., “A two-state model based on the block-localized wavefunction (BLW) method”, J. Chem. Phys., 126, 224104 (2007).
3) Mo, Y., Gao, J., “Theoretical analysis of the rotational barrier of ethane”, Acc. Chem. Res., 40(2), 113-119 (2007).
4) Song, L.; Lin, Y.; Liu, M.; Cao, Z.; Wu, W.; Mo, Y., “Theoretical study of the interchain conductivity in poly(p-phenylene)”, in preparation.
Spectroscopic Investigation of Superfluidity of Molecular Hydrogen (H2).
Takamasa Momose
Department of Chemistry and Department of Physics and Astronomy, The University of British Columbia, Vancouver, Canada.
Quantum clusters of molecular hydrogen have been attracted great attention both theoretically and experimentally because of its possible superfluid phase. Parahydrogen has been predicted to undergo Bose-Einstein condensate (BEC) and to exhibit a superfluid phase below 4 K, but it has not been observed yet due to the freezing of bulk hydrogen systems at 13.8K. Clusters of molecular hydrogen are very appealing system for the observation of possible superfluid phase of molecular hydrogen, because clusters are known to exhibit significantly lower freezing temperature than their bulk systems. Here, we report our recent investigation of large (N=100 - 100,000) hydrogen clusters at very low temperature (0.4 K) using superfluid He droplet spectroscopy. Laser induced fluorescence (LIF) of probe molecules doped in these hydrogen clusters showed clear evidence of non-rigidity of hydrogen clusters at 0.4 K. The observed spectra showed clear dependence on the cluster size as well as on the ortho-para concentration of hydrogen molecules. We have also examined the property of large hydrogen clusters at 4 K created by the expansion of cold, compressed hydrogen gas into vacuum. We will discuss the properties of large hydrogen clusters and possible superfluid phase of molecular hydrogen based on our observed spectra. Recent theoretical investigation of molecular sperfluidity will also be reviewed.
Vaporization-Exchange Modeling of Water Transport through Nafion
Charles Monroe,1 Tatiana Romero,2 Walter Mérida,2 and Michael Eikerling1
1 Department of Chemistry, Simon Fraser University, Canada

2 Department of Mechanical Engineering, University of British Columbia, Canada

1,2 National Research Center Canada Institute for Fuel Cell Innovation (NRC-IFCI), Canada
The understanding of water transport through ionomer membranes is widely recognized as a critical factor in the design or optimization of polymer electrolyte fuel cells. Rates of water transport through partially hydrated ionomers may be determined by interfacial processes, such as evaporation/condensation or adsorption, as well as bulk processes, such as diffusion or percolation. A model is applied to sorption experiments involving ionomer slabs with one face contacting stagnant water or saturated water vapor and the opposite face exposed to a well mixed flowing gas. The transport parameters that describe interfacial and bulk processes are quantified separately by examining how the total water flux depends on the gas flow rate and membrane thickness. For practical Nafion membranes, which typically have thicknesses of 100 μm or less, water transport rates are found to be limited by vaporization-exchange kinetics between the ionomer and adjacent gas phases, rather than by bulk diffusion or percolation.
Darboux transform for spatially dependent mass Schrödinger equations:

Isospectral potentials for the free-particle potential model.
J. Morales1, G. Ovando1,2, J. J. Peña1 and G. Ares de Parga2.
1Universidad Autónoma Metropolitana – Azc., Departamento de CB-Area de FAMA, Av. San Pablo 180, Reynosa Azcapotzalco, 02200 México, D. F.

2Escuela Superior de Física y Matemáticas, IPN, Unidad Profesional Adolfo López Mateos,
Zacatenco, Edificio 9, 07738 México, D.F.
The Darboux proposition is based on the covariance properties of ordinary and partial differential equations with respect to a gauge transformation in the special case of the Sturm-Liouville relationship. In this work, the one-dimensional Schrödinger equation with a position-dependent mass (SEPDM) is reduced, via a canonical transformation approach, into a Schrödinger-like equation with a position-independent mass (SLEPIM) for an effective potential that incorporates the spatially dependent mass. Thus, taking advantage on the similarity between the SLEPIM and the Sturm-Liouville differential equation it is proposed the application of the Darboux transform to the SEPDM problem in order to find the partner isospectral potentials. Explicitly, as useful example, it is considered the special case of the free particle potential model as former potential of the SEPDM, which leads to a Riccati equation for the equivalent of the Witten W(u)superpotential. In that case, the choice of an ansatz for W(u)leads to different isospectral partners, that fulfill the SEPDM for specific position-dependent mass distributions such as occurs with harmonic-type isospectral potentials for m(x)=1/(2(αx2+1)1/2). Beyond the applications considered in this work as examples, the proposal is general and can be straightforwardly used in the search of those exactly solvable SEPDM and their isospectral partners that could be useful in the quantum chemical treatment of condensed matter studies.
Growth Process of Single-Walled Carbon Nanotubes from Metal Cluster:
Density Functional Tight-Binding Molecular Dynamics Simulation
Yasuhito Ohta,1 Yoshiko Okamoto,1 Stephan Irle2, and Keiji Morokuma1
1Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
2Institute for Advanced Research and Department of Chemistry, Nagoya University, Nagoya 464-8602, Japan
The authors previously performed quantum chemical molecular dynamics (QM/MD) simulations based on the density functional tight binding (DFTB) method and proposed the “shrinking hot giant fullerene” mechanism for formation of fullerenes from small carbon clusters [1]. This method enabled us to study nonequilibrium processes involving bond breaking and formation of many-body molecular systems. They also performed QM/MD study on the mechanism of carbon nanotube growth from the SiC surface [2]. Synthetic techniques of the mass production of single walled carbon nanotubes (SWNTs) have been making significant progress since their discovery in 1993. Transition metals such as Fe, Co, Ni, Mo, Y play an essential role as catalysts for SWNT synthesis. However, the mechanism for the growth process of SWNTs still remains unclear. In the present study [3], we investigated the growth process of SWNTs using the DFTB molecular dynamics method. An open-ended nanotube was attached to the transition metal clusters, which are composed of Fe atoms, and carbon atoms were continuously bombarded around the boundary between the nanotube and metal atoms. We observed an efficient growth of the attached nanotube. Introduction of the electronic temperature to take into account the multiple degeneracy of transition metal d orbitals was a key to the success. We explore the essential steps of the growth process by changing the size of the metal clusters, density of feedstock molecules, and temperature.

[1] S. Irle, G. Zheng, Z. Wang, and K. Morokuma, J. Phys. Chem. B, 2006, 110, 14531-14545.
[2] Z. Wang, S. Irle, G. Zheng, M. Kusunoki, and K. Morokuma, J. Phys. Chem. C, 2007, 111, 12960-12972.
[3] Y. Ohta, Y. Okamoto, S. Irle, and K. Morokuma, ACS Nano, in press.
First-Principles Evaluation of Coulomb and Exchange Parameters for DFT+U Calculations
Nick J. Mosey,1 Peilin Liao,2 and Emily A. Carter3
1 Department of Chemistry, Queen's University, Kingston, Ontario, Canada

2 Department of Chemistry, Princeton University, Princeton, New Jersey

3 Department of Mechanical and Aerospace Engineering and Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey
Strongly-correlated electron materials are characterized by the presence of partially-filled d or f shells near the Fermi level. The electrons in these states are inherently localized, leading to a high degree of correlation between their motions. This narrows the associated bandwidths, causing the material to be an insulator and inducing a whole host of interesting electronic and magnetic properties. DFT calculations incorrectly characterize these materials as metals or small-gap insulators. This error can be traced to large self-interaction errors for the localized electrons. The DFT+U method attempts to correct this error by applying a parameterized Hartree-Fock-like potential to the localized states. The parameters that enter into this potential correspond to the Coulomb (U) and exchange (J) interactions between localized electrons on the same atom. Typically, U and J are treated as empirical parameters that are fit to experimental data, which is not suitable for calculations of novel materials. Here, we will present an approach for obtaining these parameters directly from Hartree-Fock calculations. Application of the method to transition metal oxides demonstrates that it yields values of U and J that are similar to empirical estimates of these parameters. In addition, the calculated values of U and J exhibit the proper dependence on various properties (e.g. ionic charge and spin state) of the transition metal ions.
Relativistic and QED treatment of long-range resonant interactions
between like atoms
Wojciech Skomorowski, Tatiana Korona, and Robert Moszynski
Department of Chemistry
University of Warsaw
Pasteura 1
02-093 Warsaw
Poland
Theory of long-range relativistic interactions between identical atoms in their ground and excited states is formulated with a special emphasis on the spin-orbit interactions. It is shown that the relativistic resonant interaction between like atoms, one in the ground 1S state and the other in an excited 3L state, shows an R-(2L+1) behavior. Other contributions to the resonant relativistic potential are also considered and a complete treatment of the Casimir-Polder retardation effects within the long-wavelength quantum electrodynamics formalism is reported. Numerical results illustrating these theoretical developments are presented on the example of the calcium and strontium diatomic molecules. The accuracy of the results is proven by comparison of the computed and measured lifetimes for the electronically excited states of these atoms, and of the computed and measured transition frequencies in the high-resolution photoassociation spectra. The transition frequencies in the ultracold regime, from the rovibrational continuum of the ground electronic state to the long-range rovibrational levels of the excited electronic states corresponding to the 1S+3P dissociation, and bound by spin-orbit interactions, represent a very stringent test for the present heoretical developments.
Development of a Novel Spin-free Combinatoric Open-shell Coupled Cluster (COS-CC) Theory to Single-reference CSFs: Application to a Doublet State
Dipayan Datta and Debashis Mukherjee
Department of Physical Chemistry,
and the Raman Center of Atomic, Molecular and Optical Sciences

Indian Association for the Cultivation of Science
Calcutta 700 032, INDIA.
I will present in this talk a compact spin-free coupled cluster (CC) theory for simple open-shell configurations, like doublets and biradicals, which are not necessarily single determinants. A new cluster Ansatz for the wave-operator is introduced, in which the cluster operators with direct valence spectator scatterings are replaced by closed-shell-like single and double excitation operators. The cluster operators with exchange valence spectator scatterings and the pure valence excitation operators are allowed to contract among themselves through the spectator orbitals. The novelty of the Ansatz is in the choice of a suitable automorphic factor accompanying each composite of non-commuting operators, ensuring that each such composite appears only once. This leads to CC equations which terminate exactly at the quartic power of the cluster amplitudes for the so-called 'direct term', reminiscent of the closed-shell CC theory, and upto a finite power determined by the number of open shells for the 'normalization term'. As a pilot example application, I will show results for the state energies of several doublet states, and assess the performance of the theory by comparing with the benchmark full CI result in the same basis sets. The results show the power and the efficacy of the method.
Chemical Reactions at Ultracold Temperatures
Balakrishnan Naduvalath
Department of Chemistry
University of Nevada Las Vegas
Las Vegas, NV 89154, USA
The development of techniques for cooling and trapping of a wide variety of atomic and molecular species in recent years has opened up exciting opportunities for probing and controlling atomic and molecular collisions with unprecedented precision. In contrast to thermal energy collisions, ultracold collisions offer fascinating and unique opportunities to study molecular encounters in the extreme quantum regime where the entire collision can be dominated by a single partial wave. Inelastic and reactive processes often exhibit high selectivity at ultracold temperatures where a specific quantum state is populated as a result of the collision process. In the cold and ultracold regimes, the perturbations introduced by external electric and magnetic fields are significant compared to the collision energies and external control of chemical reactions using electric and magnetic fields is of considerable experimental and theoretical interest. In this talk, I will give an overview of recent progress in quantum dynamical studies of inelastic and reactive collisions at ultracold temperatures with an emphasis on tunneling dominated reactions.

Laser control of photodissociation process in diatomic molecule
K. Sugimori1, A. Tawada2, M. Sano2, S. Taniguchi2, H. Nagao2, and
K. Nishikawa2

1Kinjo University, Kasama,Hakusan, 924-8511, Japan

2Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
Abstract. In this work, we simulate the laser-induced photodissociation of the OH molecule, and focus on the control of the wavepacket generated on the continuum state from the bound state by laser pulse. This photodissociation process is induced by the multiphoton absorption, and involves the above-threshold dissociation(ATD) due to the continuum–continuum transition by the intense laser field. This optical process includes the information of all discrete vibrational states and the dissociative continuum state substantially, so we treat all the bound–bound, the bound–continuum and the continuum–continuum transitions equivalently. Here we are interested in the control of the ATD spectrum, so we use the laser pulse with the non-resonant frequency. First we investigate the laser pulse with the optimal laser parameters to effectively generate the ATD process, which involves several peaks of the ATD spectrum corresponding to the multiphoton absorption. To control this spectrum, i.e., to generate the single ATD spectrum effectively, we use two-color laser pulses with ? and 2? frequencies. By changing the laser intensity and the phase difference of two lasers, we control the photodissociation process to efficiently generate the simple ATD spectrum. This means the generation of the atomic beam with the definite energy. In our simulation, to numerically solve the Schrödinger equation, we adopt the split-operator method, which conserves the norm of the state vector. Moreover, we can take into account implicitly but completely for the continuum state in the photoassociation process. and can treat both discrete and continuum states simultaneously and correctly. In order to analyze the continuum state involved, we show the effective method by means of the quasicontinuum state on the Morse potential obtained by numerically diagonalizing the total system without the external field.
Kinetic energy and Fisher information
A. Nagy
Department of Theoretical Physics
University of Debrecen
H--4010 Debrecen, Hungary
There is a long-standing interest towards accurate kinetic energy functionals in orbital-free density functional theory. We have recently shown that the local kinetic energy can be used as the fundamental descriptor for molecular systems [1]. In this ansatz, the electron density must be expressed as the functional of the local kinetic energy.

It has been pointed out by Sears, Parr and Dinur[2] more than twenty years ago that there is an intimate relationship between the kinetic energy functional and the Fisher information [3]. The talk will focus on further studies of Fisher information and its relationship to the kinetic energy [4,5]

[1] P. W. Ayers and A. Nagy, J. Chem. Phys. 126, 144108 (2007).
[2] S. B. Sears, R. G. Parr and U. Dinur, Israel J. Chem.19, 165 (1980).
[3] R. A. Fisher, Proc. Cambridge Philos. Soc. 22, 700 (1925).
[4] A. Nagy, Chem. Phys. Lett. 449, 212 (2007).
[5] A. Nagy and S. B. Liu, Phys. Lett. A 372, 1654 (2008).
Linear scaling correlated techniques based on divide-and-conquer method
Hiromi Nakai
Department of Chemistry and Biohemistry,
School of Advanced Science and Engineering, Waseda University,
3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
The divide-and-conquer (DC) method, which was proposed by Yang et al. [1,2], is one of the linear-scaling techniques, avoiding explicit diagonalization of the Fock matrix and reducing the Fock elements. The DC method was applied mainly to pure density functional theory (DFT) or semi-empirical molecular orbital (MO) calculations. We have applied the DC method to the Hartree-Fock (HF) and hybrid HF/DFT calculations [3,4]. Reliability of the DC-HF and DC-hybrid HF/DFT has been confirmed when adopting an adequate cut-off radius, which defines the localization region in the DC formalism.

Next, we have proposed an alternative linear-scaling scheme for obtaining the second-order Møller-Plesset perturbation (MP2) and coupled-cluster with singles and doubles (CCSD) energies based on the DC technique. Those methods, which we call DC-MP2 [5] and DC-CCSD [6], evaluate the correlation energies of the total system by summing up DC subsystem contributions. The energy density analysis (EDA) [7] scheme plays an important role to estimate the non-redundant correlation energies of the individual subsystems. Numerical assessments have confirmed that the DC-based correlation method must be a real breakthrough as a practical recipe to perform accurate quantum chemical calculations of large systems such as biomolecules and functional nanomaterials.

[1] W. Yang, Phys. Rev. Lett., 66, 1438 (1991).
[2] W. Yang and T.-S. Lee, J. Chem. Phys., 103, 5674 (1995).
[3] T. Akama, M. Kobayashi, and H. Nakai, J. Comput. Chem., 28, 2003 (2007).
[4] T. Akama, A. Fujii, M. Kobayashi, H. Nakai, Mol. Phys., 19-22, 2799 (2007).
[5] M. Kobayashi, Y. Imamura, and H. Nakai, J. Chem. Phys., 127, 074103 (2007).
[6] M. Kobayashi, and H. Nakai, J. Chem. Phys., submitted (2008). [7] H. Nakai, Chem. Phys. Lett., 363, 73 (2002).
Solving the Schrödinger Equation and the Dirac-Coulomb Equation
Hiroshi Nakatsuji
Quantum Chemistry Research Institute, Kyodai Katsura Venture Plaza, Goryo Oohara 1-36, Nishikyo-ku, Kyoto 615-8245, Japan
Schrödinger equation provides a governing principle of chemistry, biology, and physics of matter. So, if we can solve the Schrödinger equation accurately, quantum chemistry would become a central science of these fields, giving confident theoretical predictions towards experiments. Though this was simply a dream for over 80 years, a route of realizing this dream has been found in our laboratory. Actually, the general method of solving the Schrödinger equation can be explained with very simple mathematics. Similar method is also useful for solving the Dirac-Coulomb equation. By extending this entirely new approach, we want to remove too much empiricism from chemistry.

[1] P. A. M. Dirac, Proc. Roy. Soc. (London), A123, 714 (1929).
[2] H. Nakatsuji, J. Chem. Phys. 113, 2949 (2000).
[3] H. Nakatsuji and E. R. Davidson, J. Chem. Phys. 115, 2000 (2001).
[4] H. Nakatsuji, Phys. Rev. Lett. 93, 030403 (2004).
[5] H. Nakatsuji and H. Nakashima, Phys. Rev. Lett. 95, 050407 (2005).
[6] H. Nakatsuji, Bull. Chem. Soc. Jap. 78, 1705 (2005).
[7] H. Nakatsuji, Phys. Rev. A, 72, 062110 (2005).
[8] Y. Kurokawa, H. Nakashima, and H. Nakatsuji, Phys. Rev. A, 72, 062502 (2005).
[9] H. Nakashima and H. Nakatsuji, J. Chem. Phys. 127, 224104-1-14 (2007).
[10] H. Nakatsuji, H. Nakashima, Y. Kurokawa, and A. Ishikawa, Phys. Rev. Lett. 99, 240402 (2007).
[11] A. Ishikawa, H. Nakashima, and H. Nakatsuji, J. Chem. Phys. 128, 124103 (2008).
[12] H. Nakashima and H. Nakatsuji, J. Chem. Phys. 128, 154107 (2008).
[13] H. Nakashima, Y. Hijikata, and H. Nakatsuji, J. Chem. Phys. 128, 154108 (2008).
The Hyperconjugation Effect
Felipe Fleming1, Andre Gustavo Horta Babrosa2, Marco Antonio Chaer Nascimento,1
1 Instituto de Química, Universidade Federal do Rio de Janeiro, Brazil

2Instituo de Química, Universidade Federal Fluminense,Niteroi, Brazil
The term hyperconjugation was first introduced by Mulliken [1] although the idea of extra-conjugation effects had been previously used by Wheland [2]. While Mulliken made use exclusively of the molecular orbital approach, Wheland made a systematic comparison between the HLSP (Heitler-London-Slater-Pauling) method, latter coined as the VB-method, and the HMH (Hund-Mulliken-Hückel) method, or the MO method, as known today. Since at that time it was not yet feasible to perform full quantum-mechanical calculations, the discussion was mostly qualitative. Latter on Mulliken [3] tried to quantify the contribution of hyperconjugation to different properties of conjugated and saturated compounds. Form their analysis, the hyperconjugation effect in the VB model would correspond to introducing some ionic structures in the VB wave function, or to extending conjugation (electronic delocalization) in the MO model. Since then, this effect became very popular among organic chemists and the VB picture has been used, in a qualitative way, to explain all sort of unexpected behavior. More recently this effect has become also very popular among MO users in relation to the NBO. According to this type of analysis, the hyperconjugation effect manifests itself as a charge transfer from the conjugated system to the saturated unit. In this paper we will examine quantitatively this effect, using both the MO and VB approaches, to analyze the presence of hyperconjugation in molecules generally used to illustrate this effect, namely: propylene, methyl-acetylene and toluene. We also examined the ethane molecule in order to investigate a recent proposal that the preference for the staggered configuration is due to hyperconjugation effect. From the comparison between SOGVB and CAS-SCF wave functions, which differ only by the absence, in the first one, of configurations corresponding to charge transfer, we will show that there is no evidence for such effect on any of the molecules investigated. Also, from the VB point of view, we found no contributions of ionic structures in the GMS [4] wave functions of the molecules investigated. (CNPq, FAPERJ)

[1] R.S. Mulliken, J. Chem. Phys. 7, 339 (1939)
[2] G.W. Wheland, J. Chem. Phys. 2, 474 (1934)
[3] R.S. Mulliken, C.A. Rieke, W.G. Brown, J. Am. Chem. Soc. 63, 41 (1941)
[4] E. Hollauer, M.A.C. Nascimento, J. Chem. Phys. 99, 1207 (1993)
Quantum-classical dynamics in the mapping basis
Ali Nassimi and Raymond Kapral
Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada.
Since the introduction of the idea of mapping over fictitious harmonic oscillators for the study of angular momentum by Schwinger, mapping (as an exact quantum mechanical method) has been used in various contexts mainly to change discreet quantum states to continuous ones and then apply semi- classical or linearization approximations to study the dynamics. In this work, we construct a method for evaluating physical properties of quantum-classical systems using a mapping basis. The quantum-classical Liouville equation is an accurate governing equation of motion for many chemical and biochemical systems. The simulation of this equation is often carried out in a specific basis for the subsystem degrees of freedom. In this work this equation of motion is cast in the mapping basis. This enables us to evaluate physical system properties as a function of time which in turn enables us to evaluate average values. As an example of the application of this method, we present calculations for the average value of the population difference in a spin-boson system (a two state system bilinearly coupled to a bath of harmonic oscillators). Our simulations are able to reproduce the exact quantum results for this model and our method is easily adapted to simulate a quantum system coupled to an arbitrary many-body bath.
Multiscale Modeling of Self-Assembled Polyelectrolyte Membranes
Alexander V. Neimark
Dept. of Chemical and Biochemical Engineering
Rutgers, The State University of New Jersey
98 Brett Road, Piscataway, NJ 08854-8058
Email: aneimark@rutgers.edu
Web: http://sol.rutgers.edu/aneimark.html
Polyelectrolyte membranes often possess a hierarchical structure. They are built of nanoscale hydrophilic and hydrophobic blocks arranged in self-assembled mesoscopic structures. Depending on the system and the environmental conditions, these self-assembled structures may have either regular symmetric or disordered fractal morphologies. Transport, mechanical, and rheological properties of a self-assembled system depend not only on its chemical composition but also on its morphology. Thus, the structure formation is the key problem that is to be considered toward a better understanding of engineering properties of self-assembled systems. The hierarchical structure of polymer systems implies a hierarchical structure of a suite of modeling tools, which must span many orders of magnitude of spatial and temporal scales. I will present an overview of multiscale simulation methods employed in our group, which enable us to describe the macroscopic properties of complex systems from ab-initio quantum mechanical calculations of electron density to atomistic molecular dynamics and Monte Carlo simulations to coarse-grained mesocsopic methods of dissipative particle dynamics. The methods will be illustrated on the example of structure formation and transport in polyelectrolyte membranes, such as Nafion and sulphonated block-copolymers, which are employed in fuel cells and protective clothing.

Computational studies of high boron content elastomers. Current and Future Work.
Christopher J. Nelson,1,2, Marc Meads,2 Christine J. Cardin,2 Howard M. Colquhoun2.

1 Computational Chemistry Team, MSRD, DRAS, AWE, Aldermaston, Reading, RG7 4PR, UK.
2 School of Chemistry, The University of Reading, Whiteknights, Reading, RG6 6AD, UK.
Although widely available since the 1970's, there is still a lack of understanding at the nano-scale of Dexsil-type compounds. This lack of understanding is mainly due to the way in which the polysiloxane-carborane chains interact with one another in both the crystalline and amorphous phases. In this work, we aim to explore the complex dexsil-type structure using a combination of theoretical and experimental techniques. We present details of the development of an interatomic potential to describe the polysiloxane-carborane unit and results from recent Molecular Dynamics calculations evaluating the potential. We also present the crystal structure of a new synthetic polymer we have synthesised.

©Crown Copyright 2008/MoD
Correlated Quantum Dynamics of Many Electron Systems with
Wave Function Based Methods
Mathias Nest
University Potsdam,
Theoretical Chemistry,
Potsdam, Germany
In this talk, the possibilities of simulating the correlated dynamics of several electrons with wave function-based electronic structure methods will be discussed. The focus will be on explicitly time-dependent versions of CASSCF (leading to MCTDHF), and configuration interaction (leading to TD-CI).

The correlated motion of electrons plays an essential role in many branches of physics and chemistry, like photoelectron spectroscopy, higher harmonic generation, etc. This is even more so, since laser pulses on the attosecond time scale allow to study the time-resolved dynamics of electron systems out of equilibrium. These experiments need to be complemented on the theoretical side, and require the development of new methods of electron dynamics. In this talk, applications to the control of electronic motion and electron thermalization/relaxation are discussed. Additionally, an outlook to electronic quantum dynamics with the reduced two-electron density matrix 2RDM is given.
Photophysical Properties of Natural Light-Harvesting Complexes Studied by Subsystem Density Functional Theory
Johannes Neugebauer
ETH Zurich,
Laboratorium fuer Physikalische Chemie,
Wolfgang-Pauli-Strasse 10, HCI
8093 Zurich, Switzerland
The theoretical investigation of pigments in light-harvesting complexes requires the characterization of excited states of very large systems, since the absorption properties of the chromophores are influenced by pigment-environment as well as pigment-pigment interactions. A recently proposed subsystem approach [1] to time-dependent density functional theory (TDDFT), which is based on the generalization of frozen-density embedding to excited states [2], is applied in order to study both protein-pigment interactions and excitonic couplings as occurring in the light-harvesting complex LH2 of purple bacteria [3]. It is shown that this approach is suitable to describe such effects, and in particular that it can reproduce the characteristic features of excitonically coupled chromophores in absorption and circular dichroism spectra. In contrast to conventional supermolecular calculations on coupled chromophores, it is more efficient and easily allows for the extraction of phenomenological coupling constants as occurring in model theories of excitation energy transfer. This approach can thus be of great value in the interpretation of energy transfer pathways in light-harvesting systems.

[1] J. Neugebauer, J. Chem. Phys. 126 (2007), 134116.
[2] M.E. Casida, T.A. Wesolowski, Int. J. Quantum Chem. 96 (2004), 577.
[3] J. Neugebauer, J. Phys. Chem. B 112 (2008), 2207.
Orbital-Free Hydrodynamic Tensor DFT and Extensions Towards Covalent Systems
Daniel Neuhauser
UCLA, Chemistry and Biochemistry Department
We first review a new effort, Hydrodynamical Tensor DFT (HTDFT). In HTDFT the fundamental variables are the density, current, stress tensor, and a few other tensors (as many as desired). A systematic set of equations is derived for these tensors, and is terminated, for both ground and time-dependent system, by enforcing the last term (last "cummulant") to yield a good time-independent and eventually time-dependent response for homogenous systems. The resulting method is a little more than an order of magnitude more expensive in memory than purely density-based methods, but is systematically improvable. The second half of the talk review further extensions that should be able to handle covalent systems in consistent ways, using ideas developed in orbital free methods.
Electrocatalysis from First Principles: Mechanisms and Site Requirments for the Electroxidation of Oxygenates
Matthew Neurock
Departments of Chemical Engineering and Chemistry
University of Virginia, Charlottesville VA, United States
Electrocatalysis is controlled by the elementary reactions that occur at the interface between the electrode and the solution phase along with the electrochemical potential that results across this interface. Elucidating the electrochemical behavior at this interface, however, presents a considerable challenge due to complexity of the surface chemistry, the explicit atomic and molecular structure of the solution phase at the interface, the presence and formation different ions and their specific location in solution or on the surface, and the surface potentials and electric fields that results as a function of the surface reactivity. First principles based simulations of electrocatalysis tend to be limited due the size of the systems required to appropriately model the interfacial structure, and by the fact that ab initio methods are typically constant charge rather than constant potential systems. We have developed a new approach by which we can begin to simulate the elementary pathways and kinetics for constant potential systems. The approach was used to simulate the electrocatalytic oxidation of methanol and formic acid and the electrocatalytic reduction of oxygen for direct alcohol fuel cells, as well as to identify promising new electrocatalytic materials for both the anode and the cathode.
A combined R-matrix eigenstate basis set and finite-differences propagation method for the time-dependent Schrödinger equation: the one-elecron case
L. A.A. Nikolopoulos, J. Parker, K. T. Taylor
Department of Applied Mathematics and Theoretical Physics
The Queen's University of Belfast, BT7 1NN Belfast,UK
In this work we present the theoretical framework for the solution of the time-dependent Schrödinger equation (TDSE) of atomic systems under strong electromagnetic fields with the configuration space of the electron's coordinates separated artificially over two regions, that is region (I) and (II). In region (I) the solution of the TDSE is obtained by an R-matrix basis set representation of the time-dependent wavefunction. In region (II) a grid representation of the wavefunction is considered and propagation in space and time is obtained through the finite-differences method [1]. In both regions, a high-order explicit scheme is employed for the time propagation.While, in a purely hydrogenic system no approximation is involved due to this separation, in multielectron systems the validity and the usefulness of the present method relies on the basic assumption of the R-matrix theory [2], namely that beyond a certain distance {[}encompassing region (I)] the ejected electron is distinguishable from the other electrons and there evolves effectively as a one-electron system. The method is developed for single active electron systems with the R-matrix eigenstates expanded on a set of B-splines basis set [3] and applied to the case of the hydrogen being the ideal systems for all the unnecessary multi-electron complications to be absent.



References,
[1] K. J. Meharg, J.S. Parker and K.T. Taylor, J. Phys. B, 38,237,(2005)
[2] P. G. Burke and K. Berrington, Atomic and Molecular Processes: An R-matrix approach, (IOP Publishing, Bristol 1993)
[3] L. A.A. Nikolopoulos, Phys. Rev. A, 73, 043408, (2006)
Theoretical Study of Structural and Magnetic Properties of Aluminum Nanoclusters
T. V. B Phung, T. Hashimoto, K. Nishikawa and H. Nagao
Division of Mathematical and Physical Science,
Graduate School of Natural Science and Technology,
Kanazawa University, Kakuma, Kanazawa 920-1192, Japan.
Stability and magnetization of Aln clusters are investigated using ab initio density functional calculations based on plane-wave and the all electron projector augmented-wave (PAW) method. We present stable structures of small-sized Aln (n = 2-17) clusters obtained from optimization with binding energy and magnetization which are good agreement with experiment data. The size dependence of binding energy and magnetization are clarified. From noncollinear magnetic properties of Al3 and Al5 clusters, the distribution of spin structure in the ground state is delocalized. We found in the range of 13 ≤ n ≤ 55, the transition between icosahedral and truncated decahedral of Aln clusters occurred. For large clusters, we discuss the stability of Aln cuboctahedral clusters with up to 923 atoms based on the size dependent binding energy. The coefficients corresponding to surface and edge energies for cuboctahedral Aln clusters have estimated, and we could obtained the cohesive energy of bulk system, Ec = 3.418 eV, close to experiment value through the fitting function of size dependent binding energy. Finally, we discuss the magnetization of cuboctahedral Aln clusters in relation to shell structure. When the size of cluster is enlarged, the distribution of magnetization shows the spin density becomes largest at the outmost shell. From Al147 to Al923 clusters, electrons in the center and innermost shell might be similar to the bulk.

Keywords: Aluminum nanoclusters, magnetization, ab initio DFT calculation

References

[1] Alonso, J. A. Structures and properties of atomic nanocluster 2005, Imperial College Press.
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Developing Computational Tools for Peptidomimetic Inhibitors of Protein-Protein interactions
Masha Niv
Institute of Biochemistry, Food Science and Nutrition
Faculty of Agricultural, Food and Environmental Quality Sciences,
The Hebrew University of Jerusalem,
Rehovot 76100, Israel
As productivity of drug discovery efforts declines, novel approaches to rational drug design are being introduced. Emerging paradigms include the targeting of protein-protein interactions (PPIs) via proteinomimetic and peptidomimetic compounds. Our goal is to develop and utilize computational tools that are appropriate for the design of specific inhibitors of protein-protein interactions. Examples of rational design of selective peptidomimetic kinase inhibitors will be presented[1], and a peptide docking approach, PDZdock[2], as well as protein motif-based approach, Scan2S[3, 4], will be described.


[1] M. Y. Niv et al., J Biol Chem 279, 1242 (2004).
[2] M. Y. Niv and H. Weinstein, J Am Chem Soc 127, 14072 (2005).
[3] M. Y. Niv et al., Proteins (2007).
[4] L. Skrabanek and M. Y. Niv, Proteins (in press).


Redox Energetics, Geometries, and Spectroscopic Properties of Iron-Sulfur Clusters from Simple Electron Transfer to Multielectron Catalysis in Nitrogenase
Louis Noodleman,1 Vladimir Pelmenschikov, 1 Wenge Han,1 James A. Fee,1 and 1David A. Case 1
1Department of Molecular Biology, The Scripps Research Institute,
La Jolla, CA, USA
We will examine electronic structure and redox energetics for iron-sulfur clusters starting from Fe2S2 and Fe4S4 centers in electron transfer proteins and ending with the first steps in the catalytic cycle of the FeMo cofactor cluster of the nitrogenase enzyme, which reduces molecular nitrogen (N2) to ammonia plus hydrogen. The principal computational tool is spin polarized density functional theory (DFT) using the broken symmetry (BS) method for treating spin-coupling. DFT predictions of Mossbauer and hyperfine properties strongly augment calculations of redox energetics and geometries for understanding early steps of the nitrogenase catalytic cycle. Supported by NIH Grant GM39914.
On a manifestly covariant mechanics
M. Nooijen, L. M. Huntington
University of Waterloo, Waterloo Ontario
While the many-electron Dirac equation yields highly accurate results in relativistic quantum chemistry it is not manifestly Lorentz invariant. Quantum field theory is regarded as the remedy for a consistent relativistic quantum mechanics, but this is very hard to apply to chemical problems in practice.

In this talk I will explore a manifestly covariant many-particle classical mechanics with action-at-a-distance potentials with the aim to create a starting point for a mathematically consistent relativistic quantum mechanics that closely follows the classical-quantum Hamiltonian formulation of Schroedinger's equation.

This investigation seems to give rise to a 'mid-life' crises of my understanding of physical theories, leading e.g. to a Lorentz-invariant Newtonian mechanics, and a relativistic mechanics in which linear and and angular momentum are only conserved in a special "synchronous" reference frame in conflict with the principle of relativity.

At the end of this talk I will try to convey the importance of a "computable physics" , which is to be designed to facilitate computing while compromising on agreement with experiment.



The Concept of Ergodicity in Chemistry - A Statistical Mechanical Approach to Dynamics, Reactions and Chemical Bonding
Sture Nordholm
Department of Chemistry, University of Gothenburg, Sweden
There is tremendous progress in the application of theoretical methods to chemistry and chemical physics. Most of it is of computational character and approaches chemical phenomena from a detailed microscopic point of view with the goal of minimizing approximation. Quantum chemistry is the best example but the progress in probing dynamical phenomena by classical trajectory and quantum mechanical wavepacket and scattering methods is also of this kind. There is an alternative approach based on statistical mechanics which uses assumptions of thermal or microcanonical equilibration to find approximate theories that capture the global essence of reality without having to resolve the local and microscopic details. I will briefly recall how this approach has yielded the famous transition state and RRKM theories of chemical reaction rates. I will then show how further progress has been made by focussing on the concept of ergodicity of dynamics which is implicitly or explicitly used in most present theories. The possibility of achieving refined and more realistic theory rests on the ability to resolve nonergodic effects. I will show how this can be done to improve the understanding of the collisional energy transfer mechanism which activates or deactivates reactants in gas phase chemical reactions. I will then argue that nonergodic effects and slow internal electron transfer in atoms and molecules strain atoms and molecules and explain their reactivity and tendency to form covalently bonded structures. This reinterpretation of the central bonding mechanism of chemistry will be based on an analysis of the general success of nearly all forms of quantum chemistry and particularly of the dramatic failure of the original density functional theory of Thomas and Fermi. - Detailed mechanical and approximative statistical mechanical approaches are found to be complementary in the unravelling of the central bonding and reaction mechanisms of chemistry.
Molecular Mechanism of Monovalent Cation Selectivity in the Na+-dependent Amino Acid Transporters
Sergei Noskov1,2 and David Caplan1,2
1 Institute for Biocomplexity and Informatics, Department of Biological Sciences2, University of Calgary, Canada
The x-ray structures of LeuT and Glt, bacterial homologues of Na+/Cl--dependent amino-acid transporters, provides a great opportunity to better understand the molecular basis of monovalent cation. Both proteins possess ion-binding sites selective for Na+ over K+ and Li+. Extensive QM/MM minimization combined with all-atom free energy molecular dynamics simulations of the LeuT and Glt transporters embedded in an explicit membrane are performed at different temperatures and various occupancy states of the binding sites to dissect the molecular mechanism of ion selectivity. In this work, we demonstrate that there is a collective effect of multiple binding sites on a total selectivity for Na+ over Li+. The role of local connectivity, site rigidity, atomic polarization and partial charge transfer in monovalent cation selectivity is discussed.
Molecular modeling of the short-side-chain perfluorosulfonic acid fuel fell membrane: hydration, structure, and transport
Stephen J. Paddison
Department of Chemical and Biomolecular Engineering
University of Tennessee
spaddison@utk.edu
The short-side-chain (SSC) perfluorosulfonic acid (PFSA) membrane exhibits higher proton conductivity than Nafion 1100 when prepared at equivalent weights (EWs) of about 800. We have undertaken a broad suite of multiscale molecular modeling studies of this ionomer including, electronic structure and QM/MM calculations of oligomeric fragments, classical molecular dynamics and dissipative particle dynamics simulations of the hydrated ionomer with systems ranging in size from several 103 to 107 atoms. These studies have elucidated insight into the local and extended structure of the polymer, distinctions in the hydrated morphology as a function of both water content and EW, and the dissociation and diffusion of hydrated protons and water molecules. Results from these investigations will be discussed in the context of understanding how polymer chemistry may be used to synthesize fuel cell membranes with superior properties.
Quasidegeneracy and coupled-cluster methods: Some recent developments
Josef PALDUS1,2 and Xiangzhu LI1
1 Department of Applied Mathematics, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1

2 Department of Chemistry and Guelph-Waterloo Center for Graduate Work in Chemistry, Waterloo-Campus, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
Single-reference (SR) coupled-cluster (CC) methods that employ at most one- and two-body cluster amplitudes [e.g., CCSD or CCSD(T)] account well for a dynamic correlation thanks to the exponential Ansatz for the wave operator, but are unable to properly describe static and/or non-dynamic correlation effects arising due to the degeneracy and/or quasi-degeneracy of a reference configuration, respectively. Consequently, these methods often fail when employed to describe such important phenomena as the breaking of genuine chemical bonds or properties of open-shell systems in general. In such cases, the role of higher-than-pair clusters can no longer be ignored, while their explicit consideration is computationally unaffordable and their perturbative treatment, as in CCSD(T), breaks down.

In principle, it is a multi-reference (MR) version of CC theory that provides an adequate formalism for handling of quasi-degeneracy. Unfortunately, its general implementation at either the valence universal (VU) or state universal (SU) level is far from being straightforward. Consequently, more and more emphasis has been lately given to its state-selective or state-specific versions, which focus on one state at a time. An alternative way to overcome the shortcommings of the standard CCSD and CCSD(T) approaches is to employ the so-called internally (ic) or externally corrected (ec) CCSD methods. The former rely entirely on the CC formalism while the latter ones exploit some non-CC wave function(s) as a source of information about higher-than-pair clusters. Although we have exploited the concept of ec-approaches at both the SR and MR levels, we shall focuss here on the former ones, in particular on the so-called reduced MR (RMR) CCSD and CCSD(T) methods exploiting the complementarity of CC and CI descriptions.

Following a brief exposition of these techniques and of their underlying concepts, we will illustrate their performance on a number of very challenging problems, such as the triple-bond breaking in N2, the singlet-triplet splitting in diradicals, and the symmetry breaking in the ABA-type molecules. Time permitting, we will address the computation of reaction barrier heights and the structure of transition metal compounds. We also hope to briefly report on a recently developed ic-version of the RMR-type approaches, the so-called partially-linearized (pl) MR CCSD methods.
Building NEP: An open-source numerical experiment platform for simulation of molecules in strong laser fields.
Serguei Patchkovskii,1 Sergei Yurchenko2, Thomas Heine3, Michael Spanner1, and Olga Smirnova1
1Steacie Institute for Molecular Sciences, NRC Canada, Ottawa, Ontario, Canada

2Institut für Physikalische Chemie, Dresden Technical University, Dresden, Germany

3School of Science and Engineering, Jacobs University, Bremen, Germany
A wide variety of phenomena arise in atoms and molecules subjected to strong laser fields. As a result, numerical simulations in this field often rely on "disposable" computer codes, written with a single physical problem in mind. For the last few years, we have been developing a numerical toolkit, which can be used to assemble a computer model of the desired strong-field process from standard, inter-operable blocks. The toolkit supports uniform Cartesian and cylindrical grids, and includes an interface to a quantum chemistry code (GAMESS-US). Graphical analysis capability is provided through an interface to the OpenDX scientific visualization package. We will show a number of applications utilizing the toolkit, including 3D simulations of laser-induced electron diffraction [1], full-dimensional (2D cylindrical) simulations of XUV probing of attosecond recollision [2], calculation of exchange-corrected recombination matrix elements in molecules using plane wave [3] and adiabatic eikonal-Volkov [4,5] continuum solutions, implementation of MO-ADK ionization amplitudes, and calculation of time-dependent eikonal-Volkov continuum wavefunctions [6]. We expect to open the toolkit and most of the accompanying applications to the strong-field community as an open-source Numerical Experiment Platform (NEP) later this year.


1. S. N. Yurchenko, S. Patchkovskii, I. V. Litvinyuk, P. B. Corkum and G. L. Yudin, PRL 93, 223003 (2004).
2. O. Smirnova, S. Patchkovskii and M. Spanner, PRL 98, 123001 (2007).
3. S. Patchkovskii, Z. X. Zhao, T. Brabec and D. M. Villeneuve, PRL 97, 123003 (2006); ibid 219901 (2006); JCP 126, 114306 (2007).
4. O. Smirnova, A. S. Mouritzen, S. Patchkovskii and M. Y. Ivanov, J Phys. B: At. Mol. Opt. Phys. 40, F197 (2007).
5. O. Smirnova, S. Patchkovskii, M. Y. Ivanov, submitted.
6. M. Spanner, S. Patchkovskii, O. Smirnova, in preparation.
Water Adsorption in Inhomogeneous Environments: Nanopores and Surfaces
G.N. Patey, G. Lakatos, T. Croteau, A.K. Bertram
Department of Chemistry, University of British Columbia
Grand canonical Monte Carlo simulations are used to examine the adsorption of water into cylindrical nanopores with and without ions. Ion-bearing nanopores are found to fill at reservoir chemical potentials (pressures) well below that of saturated water vapor. The threshold chemical potential is found to be sensitive to both the size of the channel and the ion species, with the anion-bearing pores filling at lower chemical potentials. Filling occurs through an ion-water cluster route, and hysteresis is not observed upon desorption. This contrasts with the situation for ion-free pores. Nanopores of nonuniform diameter are also considered, and nonuniformities are shown to significantly influence the adsorption isotherms, leading in some cases to multiple filling transitions. Finally, water adsorption on different clay (kaolinite) surfaces will be briefly discussed. Particular attention will be focussed on possible explanations of kaolinites ability to nucleate ice under atmospheric conditions.
Charge Transfer in Wet Double Strand DNA
Michele Pavanello1, Maksym Volobuyev2, Benedetta Mennucci3 and Ludwik Adamowicz1
1Department of Chemistry, the University of Arizona, Tucson, Arizona
2Chemistry Department, Kharkiv Polytechnic Institute, Kharkiv, Ukraine
3Dipartimento di Chimica e Chimica industriale,Università di Pisa, Pisa, Italy
Because of its implications in cancer-related studies and nano-technological applications, charge transfer in DNA has recently received considerable attention from the scientific community. We have developed a novel method capable of describing the charge dynamics in double strand DNA of various lengths. In this model the solvent, and therefore its interaction with the DNA, is allowed to evolve in a time-dependent fashion.
The magnitude of the solvent effect is determined in two alternative ways. The first one, purely quantum-mechanical, models the solvent as a continuum using the Polarizable Continuum Model implemented in the commercial GAUSSIAN 03 suite of programs, whereas the second method is a hybrid between quantum and molecular mechanics and it explicitly considers the solvent molecules, exploiting the ONIOM module of GAUSSIAN 03.
Preliminary results show that the charge transfer is slowed by about 20% when the solvent effect is taken into account. In addition, if the DNA base pairs are completely submersed in water the charge transfer between them does not occur. We therefore infer that in biological systems the interactions of the DNA base pairs with their non-aqueous surrounding is an important factor in the charge migration phenomenon. Although these findings are preliminary, they shed light upon a multitude of solvation effects largely underestimated by the current literature.
Very Accurate Calculations of Small Molecules within the Born-Oppenheimer Approximation
Michele Pavanello, Wei Cheng-Tung, and Ludwik Adamowicz
Department of Chemistry, the University of Arizona, Tucson, Arizona
Explicitly Correlated Gaussians with floating centers have been used to expand the electronic wavefunctions of small molecular systems, like H2 , H3+, He2 and (H2)2. The wavefunctions are optimized according to the principle of minimum energy using analytical gradients. The accuracy achieved for the calculation of the energy falls within a tenth of a nano-hartree.
The wavefunctions obtained are used to calculate important molecular properties, such as one-electron densities and Electric Field Gradients (EFGs) at the nuclei. For the H3+ molecular ion our calculations are the most accurate to date.
Application of the novel Fermion Monte Carlo Algorithm with second stage importance sampling.
Francesco Pederiva1, Malvin H. Kalos2, Randolph Q. Hood2
1 Department of Physics, University of Trento, via Sommarive 14, I-38100 Povo - Trento, and INFM/CNR DEMOCRITOS National Simulation Center, Trieste (Italy).
2 Lawrence Livermore National Laboratory, Livermore, CA 94550 (USA)
The original Fermion Monte Carlo algorithm (M.H. Kalos and F. Pederiva, Phys. Rev. Lett. 85, 3547 (2000)) has been improved by the introduction of a second stage importance sampling. This procedure modifies the branching of the pairs of signed walkers in order to favor configurations of the pairs contributing with positive sign to the estimators, while keeping averages unbiased.

As a test case we present results on the homogeneous two-dimensional electron gas with N=10 and N=26 electrons. For the N=26 case, in particular, starting from nodes defined by a Slater determinant of plane waves we recover the transient estimate result of Kwon et al. (Phys. Rev. B 53, 7376 (1996)) which was obtained starting from backflow single particle functions. A discussion on the application to chemical systems will also be presented.
Promising Fifth-Rung Density Functional: Dobson’s ISTLS with Tests for Uniform Gases, Planar Surfaces, and Quantum Wells
John P. Perdew ,1 L. A. Constantin ,1 J. M. Pitarke ,2 J. F. Dobson ,3 and A. Garcia-Lekue4
1Department of Physics and Quantum Theory Group, Tulane University, New Orleans, LA 70118 USA
2CIC nanoGUNE Consolider, Mikeletegi Pasealekua 56, E-2009 Donostia, Basque Country, Spain
3Nanoscale Science and Technology Centre, Griffith University, Nathan, Queensland 4111, Australia
^[4}Donostia International Physics Center (DIPC), Manuel de Lardizabal Pasealekua, E-20018 Donostia, Basque Country, Spain
The fifth and highest rung of the Jacob’s Ladder classification of approximate density functionals for the exchange-correlation energy employs as inputs all occupied and unoccupied Kohn-Sham orbitals. The simplest fifth-rung functionals are based on the random phase approximation (RPA) or various corrections thereto. In the 1960’s, Singwi, Tosi, Land and Sjoelander (STLS) proposed for the uniform electron gas a generalization of RPA with a more realistic pair density. Recently Dobson et al. [1] have proposed an Inhomogeneous STLS approximation which is nonempirical and one-electron self-interaction free. Unlike RPA, ISTLS predicts an accurate correlation energy for the uniform electron gas in three or two dimensions . We also find that it predicts an accurate surface energy for jellium [2], and a realistic variation of energy from a wide quasi-two-dimensional quantum well (describable by semi-local density functionals such as the generalized gradient approximation) down to the zero-thickness or true two-dimensional limit [3]. Semi-local functionals fail to describe this “dimensional crossover”. Although ISTLS is not an easy functional to implement for real molecules and solids, such tests may be worth the effort. As a first step in this direction, we propose tests of ISTLS for spherical atoms, to determine to what extent this approximation (and also RPA) is many-electron self-interaction free [4].

[1] J. F. Dobson, J. Wang, and T. Gould, Phys. Rev. B 66, 081108 (R) (2002).
[2] L. A. Constantin, J. M. Pitarke, J. F. Dobson, A. Garcia-Lekue, and J. P. Perdew,
Phys. Rev. Lett. 100, 036401 (2008).
[3] L. A. Constantin, J. P. Perdew, and J. M. Pitarke, “Collapse of the Electron Gas to Two Dimensions in Density Functional Theory”, submitted.
[4] A. Ruzsinszky, J. P. Perdew, G. I. Csonka, O. A. Vydrov, and G. E. Scuseria, J. Chem. Phys. 126, 104102 (2007).
Hidden Charge 2e Boson in Doped Mott Insulators
Philip Phillips
Loomis Laboratory of Physics, University of Illinois, 1110 W. Green St.,
Urbana, Il. 61801-3080
We construct the low energy theory of a doped Mott insulator, such as the high-temperature superconductors, by explicitly integrating over the degrees of freedom far away from the chemical potential. For either hole or electron doping, a charge 2e bosonic field emerges at low energy. The charge 2e boson mediates dynamical spectral weight transfer across the Mott gap and creates a new charge e excitation by binding a hole. The presence of a new low-energy charge e excitation represents a fundamental breakdown of Fermi liquid theory as this excitation has no correspondence with the spectrum in the free system. As a result of this new excitation, a bifurcation of the electron dispersion below the chemical potential obtains as is observed recently in angle-resolved photoemission on Pb-doped Bi2Sr2CaCu2O8+&delta (Pb2212). In addition, we show that the 1) mid-infrared band in the optical conductivity, 2) the T2 contribution to the thermal conductivity, 3) the pseudogap, 4)insulating behaviour away from half-filling, 5) the high and low-energy kinks in the electron dispersion and 6) T-linear resistivity all derive from the charge 2e boson.

1.) R. G. Leigh, P. Phillips, and T. -P. Choy, Phys. Rev. Lett. vol. 99, 46404 (2007).

2.) T. -P. Choy, R. G. Leigh, P. Phillips, and P. D. Powell, Phys. Rev. B, vol. 77, 14512 (2008).

3.) T. -P. Choy, R. G. Leigh, and P. Phillips, Phys. Rev. B, vol. 77, 104524 (2008)
Renormalized Coupled-Cluster Methods: Theoretical Foundations and Extension to Open-Shell and Large Systems
Piotr Piecuch,1,2 Marta Włoch,1,3 Jeffrey R. Gour,1 and Wei Li1
1Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
2Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, USA
3Department of Chemistry, Michigan Technological University, Houghton, Michigan, USA
The development of practical single-reference electronic structure methods that could be applied to at least some of the most frequent multi-reference situations, such as single bond breaking, radicals, and biradicals, and that could provide a balanced description of dynamical and non-dynamical correlation effects with a more or less black-box effort is an important goal of contemporary quantum chemistry. We will discuss some of our efforts toward the development of such procedures. Specifically, we will focus on the ideas that have resulted in the discovery and development of renormalized coupled-cluster approaches [1-3]. The renormalized coupled-cluster methods, such as CR-CCSD(T), CR-CCSD(TQ), and the recent size extensive formulation of CR-CCSD(T), termed CR-CC(2,3), which are all derived from the asymmetric energy expressions that define the method of moments of coupled-cluster equations and which are available in the GAMESS package, represent a new generation of single-reference approaches that eliminate the failures of conventional coupled-cluster approximations, such as CCSD(T), whenever non-dynamical correlation effects become more significant. Moreover, the CR-CC(2,3) approach is as accurate as CCSD(T) when non-dynamical correlation effects are small. We will show that the relatively inexpensive renormalized coupled-cluster methods provide an accurate and balanced description of reaction pathways involving bond breaking, radicals, and biradicals, singlet-triplet gaps in biradical and magnetic systems, and excited states dominated by one- and two-electron transitions, enabling one to address interesting mechanistic problems in organic and bioinorganic chemistries, and photochemistry, where other methods that one can afford encounter difficulties. Although we will largely focus on the extension of the CR-CC(2,3) approach to open-shell systems [3], we will also mention the development of the CR-CC(2,3) and other coupled-cluster methods for large molecular systems with hundreds of atoms [4] through the use of the linear scaling parallel and vectorized algorithms employing the local correlation ansatz termed ‘cluster-in-molecule’ [5]. We will emphasize that the renormalized coupled-cluster methods extend the applicability of conventional single-reference quantum-chemical approaches of the CCSD(T) type to bond breaking, reaction pathways, and excited states with an ease of a black-box calculation that can be performed by experts as well as non-experts.

[1] (a) Kowalski, K.; Piecuch, P. J. Chem. Phys. 2000, 113, 18. (b) Piecuch, P.; Kowalski, K. In Computational Chemistry, Reviews of Current Trends; Leszczyński, J., Ed.; World Scientific: Singapore, 2000; Vol. 5, p. 1. (c) Piecuch, P.; Kowalski, K.; Pimienta, I. S. O.; McGuire, M. J. Int. Rev. Phys. Chem. 2002, 21, 527. (d) Piecuch, P.; Kowalski, K.; Pimienta, I. S. O.; Fan, P.-D.; Lodriguito, M.; McGuire, M. J.; Kucharski, S. A.; Kuś, T.; Musiał, M. Theor. Chem. Acc. 2004, 112, 349.
[2] (a) Piecuch, P.; Włoch, M. J. Chem. Phys. 2005, 123, 224105. (b) Piecuch, P.; Włoch, M.; Gour, J.R.; Kinal, A. Chem. Phys. Lett. 2006, 418, 467. (c) Włoch, M.; Lodriguito, M.; Piecuch, P.; Gour, J. R. Mol. Phys. 2006, 104, 2149.
[3] (a) Włoch, M.; Gour, J.R.; Piecuch, P. J. Phys. Chem. A 2007, 111, 11359. (b) Piecuch, P.; Gour, J.R.; Włoch, M.; Int. J. Quantum Chem. 2008, 108, 2128.
[4] (a) Li, W.; Piecuch, P.; Gour, J.R.; Li, S., in preparation. (b) Li, W.; Piecuch, P.; Gour, J.R., in preparation.
[5] (a) Li, S.; Ma, J.; Jiang, Y. J. Comp. Chem. 2002, 23, 237. (b) Li, S.; Shen, J.; Li, W.; Jiang, Y. J. Chem. Phys. 2006, 125, 074109.
Progress towards quantitative molecular modelling: development of new generation force fields.
Jean-Philip Piquemal

Laboratoire de Chimie Théorique,
Université Pierre et Marie Curie, UMR 7616 CNRS,
CC 137, 4 Place Jussieu, 75252 Paris Cedex 05, France.
jpp@lct.jussieu.fr
In this talk, we will discuss the methodologies presently available to evaluate many-body interactions in biological systems. We will present a new energy decomposition scheme based on localized orbitals1 as well as and extension of the topological analysis of the Electron Localization Function (ELF) to the computation of chemically intuitive distributed electrostatic moments.2 Implications for the design of accurate next generation polarisable force fields will be discussed.3


References

1) P. Reinhardt, J-P Piquemal and A. Savin, 2008, submitted.
2) J. Pilmé and J-P Piquemal, J. Comput. Chem., 2008, XX, XXX, online, DOI 10.1002/jcc.20904
3) a) J-P. Piquemal, G. A. Cisneros, P. Reinhardt, N. Gresh and T. A. Darden, J. Chem. Phys., 2006, 124, 104101; b) N. Gresh, G. A. Cisneros, T. A. Darden and J-P Piquemal, J. Chem. Theory. Comput., 2007, 3, 1960.


Ice Formation Funnel: Stepwise Ordering of Water during Crystallization
Payman Pirzadeh, Peter Kusalik
Department of Chemistry, University of Calgary, Alberta, CANADA
Protein folding is an activated process which starts with formation of local native bonds and flows through internal long range interactions that minimize a protein’s free energy to result in a final native structure. This phenomenon has been understood using a model called the protein folding funnel, which describes changes in conformational order-parameters (protein structure) in parallel with thermodynamic variables such as free energy and entropy. Since proteins are complicated structures with hundreds degrees of freedom, the analysis and interpretation of their actual folding funnel is very difficult. In this molecular simulation study, we explore liquid water systems as they crystallize; this is a simpler activated process that we might expect to exhibit similar phenomenology as it orders. Our simulation results show that initially some local structures, i.e. hydrogen bonded clusters or rings, are formed in the liquid phase. These rings tend to be short-lived and essentially uncorrelated structures. As one approaches the ice-water interface, the population of certain sized rings and their positional correlation changes; for instance, the number of coupled five-seven member rings initially increases at the interface region and then vanishes in the solid phase while the number of coupled six-six member rings, which are the building blocks of ice, continually increases at the cost of other ring sizes. By analogy with proteins, although with the advantage of a much smaller number of degrees of freedom, we are able to show that formation of ice can also be seen to take place in stages where these stages correspond to specific levels of order.
An alternative formulation of the Mukherjee's state-specific MRCC theory with simpler coupling terms
Jiri Pittner
J. Heyrovsky Institute,
Academy of Sciences of the Czech Republic,
Dolejskova 3,
CZ-18223 Praha
An alternative formulation of the Mukherjee's state-specific MRCC theory will be presented, which leads to amplitude equations fully equivalent to the original ones, but containing an explicitly energy-dependent term analogous to the Brillouin-Wigner MRCC equations. Besides manifesting the close relationship between the two MRCC methods, this formulation leads to a simpler form of the coupling terms, which contain a single exponential of the cluster operator rather than a product of two exponentials.
We have recently implemented the Mukherjee's MRCC theory at the SD and SD(T) levels in the Aces II program. Results of first calculations providing assessment of the accuracy and comparison with previous MR BWCCSD(T) results will be shown.
Symmetry-adapted spectroscopic parameters (“integral invariants”) for the atomic dN and icosahedral hN states
Boris N. Plakhutin
Laboratory of Quantum Chemistry, Boreskov Institute of Catalysis, Russian Academy of Sciences
We report recent developments in the theory of "integral invariants" [1] which is an extension of the classic Slater-Racah atomic theory to high-symmetry nonlinear molecules. The main attention is paid to analysis of the specific group-theoretical paradox called a “ non-Bethe’s term splitting ” [2] that follows from both the atomic theory [3] and the theory of integral invariants [2,4] when comparing the energy spectra of the states arising from two related electronic configurations,
[(10)N, O+(5)] ↔ [ dN, O+(3)], (1)
and
[ dN, O+(3)] ↔ [ hN, ( I, Ih)], (2)
respectively, where (10) is the fivefold degenerate irrep of the orthogonal group O+(5). The essence of the “non-Bethe’s term splitting” is that the position of split dN states (1) on the energy scale relative to the position of the parent (10)N states represented in terms of the Racah’ spectroscopic parameters does not obey the familiar Bethe’ conditions, and the same is for the states (2).

In this work we first define the fundamental (symmetry-adapted) spectroscopic parameters for the atomic d and icosahedral h shells. The energy spectra of the states (1) and (2) represented in terms of the new parameters, called ' integral invariants ', take amazingly simple and physically clear form, free of the discussed “paradox”. The numerical values of these parameters were estimated from ROHF and FCI-RAS calculations of atom Mn and endofullerene Mn@C60 ( Ih}).
This work was supported by the RFBR (grant No. 06-03-32587) and by the grant for Fundamental Researches of the Chemistry and Material Science Section of the Russian Academy of Sciences.

References:

[1] B.N. Plakhutin, in: Reviews of Modern Quantum Chemistry (World Scientific, 2002), Vol. I, pp. 16-42.
[2] B.N. Plakhutin, J. Chem. Phys. 119 (2003) 11429.
[3] G. Racah, Phys. Rev. 76 (1949) 1352.
[4] B.N. Plakhutin and R. Carbó-Dorca, Phys. Lett. A, 267 (2000) 370; ibid, 279 (2001) 102.

Multiplet structure of charged metal endofullerenes M@C60+q (M = Mn, Cr, Fe) with electronic configuration hN
A.V. Moskvin,1 A.V. Novikov,2 N.N. Breslavskaya,3 and B.N. Plakhutin 1
1 Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia
2 Institute of Computational Mathematics and Mathematical Geophysics RAS, Novosibirsk, Russia
3 Institute of General and Inorganic Chemistry RAS, Moscow, Russia
Multiplet structure of cations C60q+ ( Ih) and of charged metal endofullerenes M@C60q+ ( Ih) having the electronic configuration hN was studied in a number of previous works [1-3]. The common drawback of the structures reported in [1-3] is that the position of the hN states on the energy scale does not correlate with the position of the respective parent atomic dN states, as required by the group theory [4]. In practice, this drawback leads to some non-physical predictions such as the so called “non-Bethe’s” splitting of dN states [1] and/or the incorrect shift of the groups of hN states on the energy scale with respect to each other [2-3] (for a discussion, see Ref. 4).
Here we report the multiplet structure of charged metal endofullerenes M@C60q+ ( Ih) (M = Mn, Cr, Fe) based on the use of the new symmetry-adapted spectroscopic parameters (“integral invariants”) for the icosahedral h shell [5]. Numerical values of these parameters have been derived from non-empirical ROHF and FCI-RAS (Full CI in the Restricted Active Space) calculations of metal endofullerenes M@C60q+ ( Ih) having the open-shell configuration hN.

Special attention is paid to analysis of the position of the hN states on the energy scale with respect to the position of the parent atomic dN states and of the specific character of splitting of degenerate atomic 2H ( d3) and 2P ( d3) states in the icosahedral field.

This work was supported by the RFBR (grant No. 06-03-32587) and by the grant for Fundamental Researches of the Chemistry and Material Science Section of the Russian Academy of Sciences.

References:

[1] B. N. Plakhutin and R. Carbó-Dorca, Phys. Lett. A, 267 (2000) 370.
[2] A.V.Nikolaev and K.H.Michel, J. Chem. Phys., 117 (2002) 4761.
[3] M. Wierzbowska, M. Luders, and E. Tosatti, J. Phys. B. 37 (2004) 2685.
[4] B. N. Plakhutin, J. Chem. Phys. 119 (2003) 11429.
[5] B. N. Plakhutin, published in this book.
Multiscale modeling for proteins and DNA
Steven Plotkin1
1Department of Physics, University of British Columbia
I will summarize and illustrate our recent developments in coarse-grained computational models of biomolecules. With sufficiently accurate models, the vast array of biomolecular phenomena can become a theoreticians playground, where the rich diversity of biological mechanism or pathology can be quantified physico-chemically and correspondingly elucidated or predicted. I will focus on the phenomena of protein folding and misfolding, as well as DNA dynamics in translocation. I will also pose and then answer a specific fundamental question inspired by biomolecular self-organization and structural comparison, namely how to generalize the notion of distance to higher dimensional objects such as polymers.
Langevin dynamics beyond the linear approximation
A. V. Plyukhin
University of Saskatchewan
The standard form of the Langevin equation, describing the evolution of a slow degree of freedom in a complex many-body system, involves the dissipating force which is linear in velocity. Such a description usually corresponds to the lowest order approximation in a small parameter, which controls the slowness of a targeted degree of freedom. Beyond the lowest order, the dissipative force contains non-linear corrections. Though small, these corrections may result in the subtle effects of the interplay of noise and nonlinearity, which are completely washed out when one uses the conventional linear Langevin equation. For example, in an ensemble of non-interactive Brownian particles a finite average velocity may temporary develop, even if it is zero initially. Another intriguing issue is ergodic properties: beyond the linear approximation the relaxation to the Boltzmann-Gibbs equilibrium was demonstrated only for idealized, truly Markovian models. I shall outline the recent progress in the field and the problems to be solved.

Structure and Properties of Molecular Crystals from Accurate First Principles Intermolecular Potentials
Rafal Podeszwa,1,2 Betsy M. Rice,3 and Krzysztof Szalewicz2
1 Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland

2 Department of Physics and Astronomy, University of Delaware, Newark, DE 19716, USA

3 The U.S. Army Research Laboratory, Aberdeen Proving Ground, Maryland 21005, USA
Symmetry-adapted perturbation theory (SAPT) based on Kohn-Sham orbitals and frequency-dependent density susceptibilities [SAPT(DFT)] [1,2] has been shown to provide a similar accuracy of interaction energies as high-level wave-function-based methods [1,3] with a greatly reduced computational cost [2,4]. The SAPT(DFT) method is particularly useful for systems with a dominant dispersion component since the supermolecular DFT approach fails completely in this case. In particular, π-π interactions has been modeled with very good accuracy [5, 6].

We demonstrate [7] that intermolecular potentials obtained with SAPT(DFT) provides sufficient accuracy and numerical efficiency for predicting properties of two molecular crystals: cyclotrimethylene trinitramine (RDX) and benzene. The SAPT(DFT) potential of the RDX dimer [8] was used in simulations of several hypothetical RDX crystal structures. The results of the simulations showed that the structure corresponding to the experimental crystal lattice has the lowest energy. For the benzene crystal, the SAPT(DFT)-based potential [5], together with three-body SAPT(DFT) non-additive corrections [9], yielded the lattice energy accurate to within a few percent of the experimental values, significantly better than other methods based on first principles [10]. The decomposition of the energy shows large importance of the dispersion interaction in the crystal binding of both systems.

[1] A. J. Misquitta, R. Podeszwa, B. Jeziorski, and K. Szalewicz, J. Chem. Phys. 123, 214103 (2005).
[2] R. Podeszwa, R. Bukowski, and K. Szalewicz, J. Chem. Theory Comput. 2, 400 (2006).
[3] R. Podeszwa and K. Szalewicz, Chem. Phys. Lett. 412, 488 (2005).
[4] R. Bukowski, R. Podeszwa, and K. Szalewicz, Chem. Phys. Lett. 414, 111 (2005).
[5] R. Podeszwa, R. Bukowski, and K. Szalewicz, J. Phys. Chem. A 110, 10345 (2006).
[6] R. Podeszwa and K. Szalewicz, Phys. Chem. Chem. Phys. 10, in press, DOI: 10.1039/b719725j (2008).
[7] R. Podeszwa, B. M. Rice, and K. Szalewicz, to be published.
[8] R. Podeszwa, R. Bukowski, B. M. Rice, and K. Szalewicz, Phys. Chem. Chem. Phys. 9, 5561 (2007).
[9] R. Podeszwa and K. Szalewicz, J. Chem. Phys. 126, 194101 (2007).
[10] W. B. Schweizer and J. D. Dunitz, J. Chem. Theory Comput. 2, 288 (2006).
The semiclassical route to quantum dynamics in real time
Eli Pollak
Chemical Physics Department
Weizmann Institute of Science
76100, Rehovoth, Israel

eli.pollak@weizmann.ac.il
One of the central challenges facing theoretical Chemistry and Physics is the computation of quantum dynamics in complex systems. Due to the oscillatory nature of quantum mechanical properties, this problem has remained elusive even with present state of the art computational facilities. The problem is two fold. One must solve for the dynamics, and this should be done on the fly using present day ab-initio codes. The need for a general methodology cannot be overstated, since the ability of computing quantum dynamics in real time would impact our understanding of diverse topics, such as spectroscopy, molecular reaction dynamics, solid state physics, ab-initio quantum chemistry, quantum computation, Bose-Einstein condensates to name a few.

In this talk I will discuss the semiclassical initial value representation approach. Using a novel time dependent perturbation theory, I will show that the semiclassical approximation to the exact quantum propagator may be considered to be the zero-th order term in a time dependent perturbation theory expansion of the exact propagator. This leads to profound new insight into quantum dynamics. Exact quantum dynamics may be obtained purely from classical paths. Deep tunneling is effected through coherent classical paths. New and efficient approximate semiclassical propagators may be used to improve convergence properties.

A distinct advantage of semiclassics is that it needs only local information on the force field and so is in principle amenable to on the fly ab-initio computations. A first example of ab-initio semiclassical dynamics will be presented for the absorption spectrum of formaldehyde. Additional applications will include a comparison with the classical Wigner approximation, vibrational relaxation and the general semiclassical theory for dissipative systems.
Proline and Glycine Control Protein Self-Organization into Elastomeric or Amyloid Fibrils
Régis Pomès
Molecular Structure and Function, Hospital for Sick Children, and Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
Elastin is the polymeric extracellular matrix protein which provides extensible tissues, such as large arteries and lung alveoli, with the propensity for elastic recoil. In contrast, amyloid fibrils are a pathogenic state of proteins associated with tissue degeneration in numerous debilitating diseases, including Alzheimer’s disease, transmissible spongiform encephalopathies, and type II diabetes. Although both elastin-like and amyloid-like materials result from the aggregation and self-organization of proteins into fibrils, the molecular basis of their differing physical properties is poorly understood. Here we study the structural properties of monomeric and aggregated states of a set of peptides modeled after elastin-like and amyloidogenic sequences using molecular simulations. We demonstrate that elastin-like and amyloid-like peptides are separable on the basis of peptide-peptide hydrogen bonding and backbone hydration. The comparison of similar sequences indicates that these properties are modulated by proline and glycine. Accordingly, the analysis of diverse sequences, including those of elastin, amyloids, spider silks, wheat gluten, lizard egg shells, and insect resilin, reveals a threshold in proline and glycine composition above which amyloid formation is impeded and elastomeric properties become apparent. The predictive capacity of this threshold is confirmed by the self-assembly of recombinant peptides into either amyloid or elastin-like fibrils. Our findings support a unified model of protein aggregation in which hydration and conformational disorder are fundamental requirements for elastomeric function.
Coulomb-corrected trajectories in strong-field ionization
S.V. Popruzhenko1,2 and D. Bauer1
1 Max Planck Institute for Nuclear Physics, Postfach 103980,69029 Heidelberg, Germany, e-mail: dbauer@mpi-hd.mpg.de

2 Moscow Engineering Physics Institute, Kashirskoe Shosse 31, 115409, Moscow, Russia, e-mail: poprz@theor.mephi.ru
We report on a newly developed theory of strong field multiphoton ionization of atoms, which is based on the commonly accepted strong field approximation [1] and incorporates the effects of the long-range Coulomb field of the atomic residual to an extend that, we believe, was never achieved before. To account for the Coulomb field effects we use the technique of classical trajectories propagating in imaginary time and space (complex quantum trajectories) [2]. The result is an acceptably simple semi-analytical theory of ionization in fields of arbitrary polarization, applicable in the tunneling as well as in the multiphoton regime where the Keldysh parameter γ is small or large with respect to unity, respectively. An essential advantage of the theory is that it deals with complex trajectories instead of wave functions. In this way our method can be considered complementary to another recently presented new approach to the same problem based on the use of the Eikonal-Volkov approximation for wave functions [3].

We present several comparisons between predictions of our theory and exact numerical results obtained from the solution of the time-dependent Schroedinger equation. This includes:
(i) asymmetric angular distributions for ATI in an elliptically polarized field;
(ii) interference structures of ATI spectra in a linearly polarized field;
(iii) total ionization rates of atoms and ions in an intense high-frequency field when the Keldysh parameter γ>>1, and
(iv) laser-induced population of Rydberg states in short intense laser pulses.

For the cases (i)--(iii) we demonstrate quantitative agreement with exact numerical results and show that the effect of the Coulomb field is of principal importance. In particular, we show that in the multiphoton limit the Coulomb-induced enhancement of the total ionization rate appears to be an even more pronounced orders-of-magnitude effect than is known for the tunneling limit. For the effects (i) and (iv) we also present comparisons of our results with available data and formulate what kind of measurements are desirable to provide more instructive comparisons with the theory.

This work was supported by the Deutsche Forschungsgemeinschaft.

[1] L.V. Keldysh, Zh. Eksp. Teor. Fiz. V.47, 1945 (1964) [Sov. Phys.- JETP V.25, 1307]; F.H.M. Faisal, J. Phys. B V.6, L89 (1973); H.R. Reiss, Phys. Rev. A V.22, 1786 (1980).

[2] P. Salieres, B. Carre, L. Le Deroff, et al., Science V.292 (5518), 902 (2001); V.S. Popov, Phys. Usp. V.47, 855 (2004).

[3] Olga Smirnova, Michael Spanner and Misha Ivanov, Phys. Rev. A V.77, 033407 (2008).
DYNAMICS ON THE NANOSCALE: Time-domain ab initio studies of quantum dots and carbon nanotubes.
Oleg V. Prezhdo
Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
Device miniaturization requires an understanding of the dynamical response of materials on the nanometer scale. A great deal of experimental and theoretical work has been devoted to characterizing the excitation, charge, spin, and vibrational dynamics in a variety of novel materials, including carbon nanotubes, quantum dots, conducting polymers, inorganic semiconductors and molecular chromophores. We have developed state-of-the-art non-adiabatic molecular dynamics techniques and implemented them within time-dependent density functional theory in order to model the ultrafast photoinduced processes in these materials at the atomistic level, and in real time.

The electron-phonon interactions in carbon nanotubes (CNT) determine the response times of optical switches and logic gates, the extent of heating and energy loss in CNT wires and field-effect transistors, and even a superconductivity mechanism. Our ab initio studies of CNTs directly mimic the experimental data and reveal a number of unexpected features, including the fast intrinsic intraband relaxation and electron-hole recombination, the importance of defects, the dependence of the relaxation rate on the excitation energy and intensity, and a detailed understanding of the role of active phonon modes.

Quantum dots (QD) are quasi-zero dimensional structures with a unique combination of molecular and bulk properties. As a result, QDs exhibit new physical properties such as carrier multiplication, which has the potential to greatly increase the efficiency of solar cells. The electron-phonon and Auger relaxation in QDs compete with carrier multiplication. Our detailed studies of the competing processes in PbSe QDs rationalize why carrier multiplication was first observed in this material.

Our real-time atomistic simulations create a detailed picture of these materials, allow us to compare and contrast their properties, and provide a unifying description of quantum dynamics on the nanometer scale.
On calculating protein-ligand absolute binding free energies and entropies through exhaustive search
Enrico O. Purisima and Hervé Hogues
Biotechnology Research Institute
National Research Council of Canada
6100 Royalmount Avenue, Montreal, Quebec H4P 2R2 Canada
In previous work we developed a force field-based scoring function that uses solvated interaction energies (SIE) to predict absolute binding free energies (JCIM, 47, 122). A mean unsigned error of 1.3 kcal/mol was obtained for a diverse fitting data set of 99 protein-ligand complexes. However, an empirical scaling factor of about 0.1 was required to bring the SIE to the same range as the experimental binding free energies. We hypothesized that this was due to enthalpy-entropy compensation and noted that the degree of compensation was close to what Gilson and coworkers had observed in their calculations. In this work, we explore the role of configurational entropy in reducing the magnitude of the binding free energy. We use exhaustive conformational search for constructing the partition function, allowing direct calculation of the binding free energy and entropic contribution. As an illustrative test case we consider the binding of a series of small nonpolar ligands to an internal cavity in the L99A mutant of T4 lysozyme.
Intramolecular Quantum Chemical Kinetics and Symmetry Breakings from High Resolution Spectroscopy
Martin Quack
ETH Zurich, Laboratory of Physical Chemistry, CH-8093 Zurich, Switzerland, Martin@Quack.ch
Intramolecular quantum dynamical primary processes form the basis for the kinetics of chemical reactions. We shall introduce the topic with a discussion of the great variety of time scales on which these processes occur and how they can be naturally ordered by means of successive symmetry breakings [1, 2, 3].

In the main part of the lecture, we shall report on recent progress in the Zurich project on the quantum dynamics of parity violation in chiral molecules. After our discovery [4, 5, 6] that parity violating energy differences &Deltapv E in enantiomers of chiral molecules are typically one to two orders of magnitude larger than anticipated on the basis of older theoretical work, the prospects for doing successful experiments along the lines proposed more than two decades ago [7] look very good, indeed. We shall summarize the current status of our spectroscopic and theoretical work as well as of alternative approaches in other laboratories (see also the recent review [3]).

If time permits, we shall also discuss the implications for biomolecular homochirality [8] as well as for the study of fundamental symmetry violations such as the speculative CPT-symmetry violation [1, 9], and ISTCP-symmetry violation [10].

References:
[1] Quack, M., "Molecular femtosecond quantum dynamics between less than yoctoseconds and more than days: Experiment and theory", Chapter 27 in "Femtosecond Chemistry, Proc. Berlin Conf. Femtosecond Chemistry, Berlin (March 1993)", Manz, J.; Woeste, L., Eds. Verlag Chemie: Weinheim, 1995; pp 781-818.
[2] Quack, M., "Recent Results in Quantum Chemical Kinetics from High Resolution Spectroscopy" in "Computation in Modern Science and Engineering: Proceedings of the International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007), Corfu, Greece, 25-30 September 2007", AIP Conference Proceedings 963, Simos, T. E.; Maroulis, G., Eds. American Institute of Physics: 2007; Vol. 2, Part A, pp 245-248.
[3] Quack, M.; Stohner, J.; Willeke, M., Annu. Rev. Phys. Chem. 2008, 59, 741-769.
[4] Bakasov, A.; Ha, T. K.; Quack, M., "Ab initio calculation of molecular energies including parity violating interactions" in "Chemical Evolution, Physics of the Origin and Evolution of Life, Proc. of the 4th Trieste Conference (1995)", Chela-Flores, J.; Raulin, F., Eds. Kluwer Academic Publishers: Dordrecht, 1996; pp 287-296.
[5] Bakasov, A.; Ha, T. K.; Quack, M., J. Chem. Phys. 1998, 109, (17), 7263-7285.
[6] Berger, R.; Quack, M., J. Chem. Phys. 2000, 112, (7), 3148-3158.
[7] Quack, M., Chem. Phys. Lett. 1986, 132, (2), 147-153.
[8] Quack, M., Angew. Chem. Int. Ed. (Engl.) 2002, 114, 4618-4630.
[9] Quack, M., "Electroweak quantum chemistry and the dynamics of parity violation in chiral molecules" in "Modelling Molecular Structure and Reactivity in Biological Systems, Proc. 7th WATOC Congress, Cape Town January 2005", Naidoo, K. J.; Brady, J.; Field, M. J.; Gao, J.; Hann, M., Eds. Royal Society of Chemistry: Cambridge, 2006; pp 3 – 38.
[10] Quack, M., Abstract for the Sixth Congress of the International Society for Theoretical Chemical Physics (ISTCP-VI), Plenary Lecture (Vancouver, 19 – 24 July 2008)
QM/QM Electronic Embedding Models for Materials Chemistry
Krishnan Raghavachari, Hrant P. Hratchian and Priya V. Parandekar
Department of Chemistry
Indiana University
Bloomington, IN 47405
The development of accurate and broadly applicable models for large molecules/materials continues to be a significant challenge facing the quantum chemistry community. Hybrid models, such as the popular ONIOM-based QM/QM schemes (where the central region and the surrounding region are partitioned and treated with two different levels of theory), offer a promising avenue for modeling large systems. However, in almost all QM/QM applications published in the literature thus far, only a mechanical embedding scheme is used and coupling between the two regions is treated only mechanically with the wavefunction in the central region unaffected by the electronic structure of the surrounding region. We are presently developing a sequence of electronic embedding schemes for more realistic simulations. The resulting hierarchy, where the treatment ranges from simple point charge embedding to interaction integrals in the Hamiltonian matrix, will be discussed. We will also describe our current development status and present results from initial applications to materials studies.
Path-Integral Monte Carlo Approach to Few-Electron Molecules
Ilkka Kylänpää, Markku Leino and Tapio T. Rantala
Department of Physics, Tampere University of Technology
P.O.Box 692, FI-33101 Tampere, Finland
Evaluation of the electronic structure of matter is the fundamental problem addressed in quantum chemistry. Approximations to the many-electron quantum state are conventionally searched with methods based on either the wave function formalism (starting from Hartree–Fock, HF) or the density-functional theory (DFT). Both of these approaches rely on numerical solutions of the Schrödinger equation in some form. Here, we present an alternative approach based on quantum Monte Carlo (QMC) and carry out some testing with simple few-electron molecules.

Path-Integral Monte Carlo (PIMC) approach is based on direct evaluation of the quantum statistical density matrix of the many-electron system. This approach entails some specific features. As the conventional electronic structure approaches are “not good” at including many-body phenomena of electrons, but the treatment of exchange being more straightforward, for PIMC the case is opposite. Many-body effects are almost trivially included, but counting exchange interaction is more involved. Furthermore, finite temperature a mixed state instead of pure eigenstates has to be assumed. Also, Born–Oppenheimer approximation can be declined and quantum dynamics of nuclei can be straightforwardly included.

We present PIMC electronic structure and derive related molecular properties for some simple test cases: hydrogen atom, molecule and molecular ion [1]. We also demonstrate and evaluate the small effects from coupling of nuclear and electronic dynamics, finite-temperature and electronic correlations. Finally, the advantages and draw-backs of the method will be critically assessed.

[1] I.Kylänpää, M. Leino and T.T. Rantala, Phys.Rev. A 76, 052508 (2007).
Polynomial scaling of spin problem
Vitaly A Rassolov
Department of Chemistry and Biochemistry
University of South Carolina
One of the main challenges of quantum chemistry is exponential scaling of the ground state energy search. In most cases of chemical interest the electrons are strongly quantized. This makes it possible to use mean field approximation (or a single determinant starting point), with various corrections. We argue that one of the main disadvantages of a single determinant is its inability to describe spin couplings correctly, either in spin-restricted, or in spin-unrestricted versions. There has been developed many schemes that reduce errors of spin description. To the best of our knowledge they are either approximate, or scale exponentially with system size. We show that it is possible to have a practical model with rigorously correct spin description and with polynomial scaling.
Extreme applications of attosecond laser pulses: Tracing incoherent or coherent dynamics
Jan M Rost
Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
With the advent of attosecond laser pulse technology, the question arises what it can be used for, similarly as in the early days of femtosecond laser pulses. We will demonstrate the potential of two completely different applications.
The first one is to use attosecond laser pulses to observe ultrafast transient dynamics which is over when particles reach the detectors. Consequently, such processes have escaped observation so far. As an example we will discuss the internal charging of a rare gas cluster during illumination with a strong femtosecond laser pulse. This charging, taking of the order of 10 fs, can be traced by appropriately delayed attosecond pulses [1].

Secondly, we will discuss a comb of electronic wavepackets, created by an attosecond pulse train in the presence of a strong infrared laser field. This highly coherent electron dynamics leads to intricate effects in the single ionization of atoms or molecules when the delay of the attosecond pulse train with respect to the infrared laser is varied [2].

[1] Ionut Georgescu, Ulf Saalmann and Jan M. Rost, Phys. Rev. Lett. 99, 183002 (2007)

[2] P. Johnsson, J. Mauritsson, T. Remetter, A. L’Huillier and K. J. Schafer, Phys. Rev. Lett.
99, 233001 (2007); Paula Riviere, Camilo Ruiz and Jan M Rost, Phys. Rev. A 77, 033421
(2008)
Improving Reptation quantum Monte Carlo
Wai Kong Yuen,1 Robert D. Giacometti2 and Stuart M. Rothstein2,3
Brock University, St. Catharines, Ontario, L2S 3A1 CANADA

1 Department of Mathematics
2 Department of Chemistry
3 Department of Physics
Since its publication, the reptation quantum Monte Carlo algorithm of S. Baroni and S. Moroni (1999 Phys. Rev. Lett. 82, 4745) has been applied to several important problems in physics. After discussing the algorithm's mathematical foundations, we propose two new ones based on relaxing some of its assumptions, and illustrate their facility for estimating properties of small molecules.
Ab initio Study of Interfacial Structure and Dynamics in Polymer Electrolyte Membranes
Ata Roudgar, Sudha P. Narasimachary and Michael Eikerling
Department of Chemistry, Simon Fraser University, Burnaby, Canada
Transport properties and stability of proton-conducting polymer electrolyte membranes (PEM) depend on chemical architecture, phase separation at the mesoscale, and random morphology at the macroscale. Understanding these relations is vital for the design of advanced PEM. Our calculations focus on the concerted dynamics of flexible charged sidechains, water molecules, and protons inside PEMs. We performed ab initio calculations for a model that consists of a 2D hexagonal array of flexible acidic surface groups (SG) with fixed endpoints and one water molecule per SG. We vary separations dCC of SG and explore corresponding interfacial conformations and the strength of water binding. At small dCC the minimally hydrated is strongly correlated and it weakly interacts with an additional water molecule (< 0.1eV). At a critical SG separation of dCCts~6.7Å we found a transition between highly correlated and cluster-like conformations of surface groups. This transition includes proton transfer. We have identified hydronium translation, surface group rotation, and surface group tilting as collective coordinates that trigger this transition. We explored transition paths by calculating contour plots of the total energy as a function of these three collective coordinates for 3 values of dCC around dCCts~6.7Å. The barrier-energy at dCC=dCCts is 0.55~eV. In order to explore proton exchange between the surface layer and adjacent water molecules we have added an additional layer of 14 water molecules. Our result at dCCts shows that SG weakly interact with second water layer (~0.1 eV/SG). Overall, results of our calculations provide valuable fundamental insights into proton transport mechanisms in PEMs at elevated temperature and minimal hydration that we plan to exploit in view of advanced membrane design.
Simulating the Unbiased Reaction Dynamics of Catalytic Reactions through Path Sampling
Christopher N. Rowley and Tom. K. Woo
Centre for Catalysis Research and Innovation
Department of Chemistry
University of Ottawa
DFT calculations have become indispensable for organometallic chemistry, serving as a tool to find detailed reaction mechanisms. Finite-temperature effects are known to be significant in many of these reactions, although they are indiscernible to routine calculations. Using molecular dynamics directly is often impractical, as >μs waiting times are typical. Transition path sampling is an innovative technique to overcome these timescale limitations.1 Given an initial reactive trajectory,2 an ensemble of short, dynamical trajectories is harvested using a Monte Carlo algorithm. We have applied this technique to two prominent organometallic reactions.3

(1) Dellago, C.; Bolhuis, P. G.; Geissler, P. L. Adv. Chem. Phys. 2002, 123, 1-78.
(2) Rowley, C. N.; Woo, T. K. J. Chem. Phys. 2007, 126, 024110/1-024110/8.
(3) Rowley, C. N.; Woo, T. K.; J. Am. Chem. Soc. 2008, 130, 7218-7219.


Dopant rotation in superfluid clusters
Pierre-Nicholas Roy and Nikolai Blinov
Department of Chemistry, University of Alberta
Novel approaches for the study of molecular dynamics in complex systems will be presented. A particularly challenging problem is the inclusion of quantum mechanical effects in molecular simulations. We will focus on doped quantum clusters where one can observe the onset of superfluid behavior at the nanoscale. Quantum Monte Carlo techniques are used in this case in order to obtain imaginary time correlation functions that can, in turn, be related to spectroscopic signatures. We will discuss the importance of the inclusion of rotational degrees of freedom when estimating effective rotational inertia and superfluid response.
Estimating ice growth rates in molecular dynamics simulations
Dmitri Rozmanov, Peter Kusalik
Department of Chemistry, University of Calgary, Alberta, Canada
The heterogeneous crystal growth of a solid phase can be seen as the dynamic competition between melting and crystal formation at the interface. The macroscopic outcome of which is determined by the specific location of the system in the condition-space relative to its phase diagram.

In this work, ice growth was investigated using steady state non-equilibrium classical molecular dynamics simulations and TIP4P-2005 water model. Three different systems of growing 0001 (basal) faces of hexagonal ice containing 960, 1800 and 2880 water molecules were studied at temperatures of 2, 6, 12 and 23 K below the melting temperature of the model under the atmospheric pressure.

Statistics from 120 ns simulation trajectories were collected for these systems. The original trajectories were split into segments of shorter length and growth rated were estimated using those segment. The probability distributions of the ice growth rates obtained using segments of different lengths were statistically analyzed in order to estimate the time scale for reliable determination of such rates. A normal Gaussian distribution was assumed for the variance of the rates. It was shown that the process of ice growth is truly stochastic in nature, and that simulations of several tens of nanoseconds are required to obtain growth rates within 99% confidence interval even at optimal growth conditions. For the bigger system the maximum average growth rate of 0.7+-0.25 A/ns was obtained at the 12 K undercooling.
Non-sequential double ionization above and below classical recollision threshold
Artem Rudenko
Max-Planck Advanced Study Group, Center for Free Electron Laser Science, Notkestrasse 85, 22607 Hamburg, Germany
Non-sequential double ionization (NSDI) of atoms by intense linearly polarized laser radiation remains in the focus of strong-field physics as one of the central and most controversial topics despite intensive experimental and theoretical research for more than two decades. Though it is nowadays generally accepted that the main underlying mechanism of this reaction is a recollision between the first emitted electron and its parent ion, the current understanding of NSDI, in particular, of the sub-cycle dynamics of the recollision event, is still far from being complete. Several experimental advances made within the last year, including studies on wavelength dependence of NSDI [1,2], first fully-differential data for He target [3,4], and latest measurements on Ar well below the classical recollision threshold [5] shed some new light on this problem, and set further challenges for theory. In this contribution we will overview these results, and discuss questions which remain open, in particular, the interrelation between the different types of classical trajectories, 'antenna-like' recollision-induced excitations, and sub-threshold NSDI.

[1] O. Herrwerth et al., New J. Phys. 10 025007 (2008).
[2] A.S. Alnaser et al., J. Phys. B 41 031001 (2008).
[3] A. Staudte et al., Phys. Rev. Lett. 99, 263002 (2007).
[4] A. Rudenko et al., Phys. Rev. Lett. 99, 263003 (2007).
[5] Y. Liu et al., Phys. Rev. Lett., in press (2008).
An accurate ab-initio anatomy of a full diatomic potential energy curve:
The fluorine molecule
Klaus Ruedenberg and Laimutis Bytautas
Department of Chemistry and Ames Laboratory USDOE
Iowa State University, Ames, IA, 50011, USA
Using the recently developed method of Correlation Energy Extrapolation By Intrinsic Scaling (CEEIS), the full ab-initio ground state potential energy curve of the 18-electron fluorine molecule has been obtained with an accuracy of about 0.2 millihartree from about 1 to 3 Angstrom, the equilibrium distance being near 1.4A. Full configuration interaction energies were determined for the non-relativistic correlated wavefunctions, extrapolated to the complete basis set limits, and complemented by the contributions due to spin-orbit coupling and scalar relativistic effects. An even-tempered gaussian expansion provided an excellent fit, from which the vibration-rotation spectrum was calculated. The full experimental spectrum of 22 vibrational levels, measured earlier at the Herzberg Laboratory, was recovered with a mean absolute deviation of about 5 wavenumbers, the rotational constants were recovered within 0.002 wavenumbers. The dissociation energy was obtained within 30 wavenumbers of the experimental value.

The unexpectedly rapid decay from –61mh at 1.4A towards less than –0.5 millihartree at 3A was elucidated by expressing the energy as the sum of the energy of the uncorrelated, but properly dissociating wavefunction and the correlation energy. At longer ranges, the former became exactly identical with the interaction between the quadrupoles of the fluorine atoms, while the latter became exactly identical with the London dispersion interaction. The former are repulsive, due to the quadrupole alignments in the groundstate, and proportional r-5; the latter are attractive and proportional r-6. There moreover is an additional repulsive force due to the loss of spin-orbit coupling upon bond formation. As a result of these antagonistic interactions, the potential energy curve has a hump at about 4A, with a value of about +0.04 millihartree. The descent of the potential towards the minimum, when the atoms approach each other from infinity, begins therefore only at internuclear distances less than about twice the equilibrium distance and is then much steeper than the conventionally presumed quasi-exponential decay. It has in fact Gaussian character.

In addition, several Pi-states lie a few tenths of a millihartree below the ground state in the long-range region. This is because, in Pi-states, the atomic quadrupoles are aligned in such a manner as to yield an attraction. Since these states are repulsive at shorter ranges, they cross the groundstate state at about 3Å. Spin-orbit-coupling-assisted non-adiabatic mixing of these states will therefore be needed to determine the energies of the highest two or three vibrational ground state levels.

For none of the lower states, does the total potential exhibit dispersion-type long-range behavior. The complications of the physics and the quantitative behavior beyond twice the equilibrium distance create difficulties in determining the dissociation energy by extrapolation from the ground-state spectroscopic information.
Diminished gradient dependence of density functionals: Constraint satisfaction and self-interaction correction
Adrienn Ruzsinszky,1 John P. Perdew,1 Gábor I. Csonka,2 Oleg A. Vydrov3 and Gustavo E. Scuseria3

1Department of Physics and Quantum Theory Group, Tulane University, New Orleans, Louisiana 70118
2Department of Chemistry, Budapest University of Technology and Economics, H-1521 Budapest, Hungary
3Department of Chemistry, Rice University, Houston, Texas 77005
The Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation [1] for the exchange correlation energy functional has two nonempirical constructions, based on satisfaction of universal exact constraints on the hole density or on the energy. We show here that, by identifying one possible free parameter in exchange and a second in correlation, we can continue to satisfy these constraints while diminishing the gradient dependence [2] almost to zero (i.e., almost recovering the local spin density approximation or LSDA). This points out the important role played by the Perdew-Wang 1991 nonempirical hole construction in shaping PBE and later constructions. Only the undiminished PBE is good for atoms and molecules, for reasons we present, but a somewhat diminished PBE could be useful for solids; in particular [3], the surface energies of solids could be improved. Even for atoms and molecules, a strongly diminished PBE works well when combined with a scaled-down self-interaction correction [4] (although perhaps not significantly better than LSDA). This shows that the undiminished gradient dependence of PBE and related functionals works somewhat like a scaled-down selfinteraction correction to LSDA. Recently Odashima and Capelle [5] have stressed that electron densities of real atoms, molecules and solids have exact exchange-correlation energies that are always significantly higher than the Lieb-Oxford lower bound. Their work also suggests that a diminished gradient dependence (more like LSDA) may be acceptable.


[1] J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 77, 3865 (1996)
[2] G. I. Csonka, O. A. Vydrov, G. E. Scuseria, A. Ruzsinszky, and J. P. Perdew, J. Chem. Phys. 126, 244107 (2007).
[3] J.P. Perdew, A. Ruzsinszky, G.I. Csonka, L.A. Constantin, X. Zhou, O.A. Vydrov, G.E. Scuseria, and K. Burke, Phys. Rev. Lett. 100, 136406 (2008).
[4] O. A. Vydrov, G. E. Scuseria, A. Ruzsinszky, J. P. Perdew, and G. I. Csonka, J. Chem. Phys. 124, 094108 (2006).
[5] M. Odashima and K. Capelle, J. Chem. Phys. 127, 054106 (2007).
Molecules in Intense Ultrashort Laser Pulses: Influence of Nuclear Geometry and Orientation
Alejandro Saenz
Humboldt-Universität zu Berlin, Institut für Physik, AG Moderne Optik, Hausvogteiplatz 5-7, 10117 Berlin, Germany
Based on simple models of tunneling ionization and experimental evidence, it was until about a decade ago believed that the single ionization of neutral molecules is practically identical to the one of atoms and depends basically only on the ionization potential. More advanced and detailed experiments revealed, however, that many molecules show a different ionization behavior and are, in fact, more difficult to ionize than atoms with the same ionization potential.

Models of various degree of sophistication have been used to explain these differences and to predict also molecular effects in high-harmonic generation. The latter may in turn open a pathway to study molecular dynamics (both of nuclei and electrons) on a sub-femtosecond time scale. This requires, however, a thorough understanding of the molecular behavior in intense ultrashort laser pulses in order to relate an experimental signal to a structural change.

In this talk a report will be given about our recent progress in the investigation of molecules in intense laser pulses. This includes the full solution of the time-dependent Schrödinger equation (TDSE) describing the two electrons in molecular hydrogen within the fixed-nuclei approximation in which both electrons and their interaction is included in full dimensionality. Very recently, we were even able to provide for the first time also results for a perpendicular orientation of the molecular axis with respect to the laser field. Furthermore, results of our new approach that describes in principle arbitrary molecules within the fixed-nuclei single-active-electron approximation will be presented. The results of these ab-initio treatments are used for an investigation of the validity of the interpretations of molecular effects that are based on simplified strong-field models.

Quantum mechanics and molecular mechanics: could they/should they play a key role in systems biology? What’s possible? What’s not
Dennis Salahub
Department of Chemistry
IBI - Institute for Biocomplexity and Informatics
ISEEE – Institute for Sustainable Energy, Environment and Economy
University of Calgary
2500 University Drive NW
Calgary, Alberta T2N 1N4
Canada
One viewpoint of the still emerging field of systems biology sees integration along one axis involving system size (and perhaps some dynamics) going from macromolecules (proteins, DNA, RNA, etc) to cells, to tissues, to organs, to organisms, etc. This is sometimes called computational biology. Another axis looks at kinetic models at growing levels of complexity going from pathways, to modules to full genetic regulatory networks. This is taken to lie in the general field of bioinformatics. There is an almost unpopulated chasm between the two communities pursuing these two approaches.

In this lecture I will argue that a starting point at even a finer level of resolution is necessary if one is to fill the gap between the two axes. I will attempt to describe the state-of-the-art of atomistic multi-scale approaches including those that use quantum mechanics to describe chemical reactions. I will review the pertinent molecular dynamics literature. Following that I will give a few results for nano-bio systems that are now being calculated using Density Functional Theory (DFT). Although modern DFT is fast, it is still not fast enough for applications in biology so we are paying attention to so-called reactive force fields (ReaxFF) which try to capture the essence of quantum mechanical calculations through parametrization against DFT calculations on full chemical reaction paths.

Turning to the other axis, I will summarize recent results on protein production regulated by genetic networks that incorporate the main steps in the transcription and translation processes. The Gillespie algorithm is used to solve the (effective) chemical master equation.

The seminar will finish with our first (baby-step) attempts to fill the gap by looking at the mechanism of transcription involving metallo-proteins with Mg ions in the active site. The project uses both DFT and the ReaxFF force field. We hope, in the fullness of time, to be able to feed calculated information on reaction rates into the Gillespie (or other) algorithm and, hence, have the behavior of the regulatory network guided by the underlying atomistic and electronic mechanisms.
Dependence of HOMO-LUMO gap of DNA Basepair Steps on Twist angle: A Density Functional Approach.
Sudipta Samanta, Tanushri Saha Dasgupta and Jaydeb Chakrabarti
S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700098, India.
Stacking energy along with the density of states (DOS) of all the 10 unique DNA base-pair steps (bp step) are calculated using density functional theory within the ultrasoft pseudopotential plane wave method and local density approximation for the exchange-correlation functional. To know the contribution of different atoms on DOS we have further the projected Density of states (pDOS) for all ten unique dinucleotide bp steps. We have found that atoms of the purine bases, of a particular bp steps contribute significantly on HOMO state and atoms of the pyrimidine bases contribute significantly on LUMO state. we have also studied how the variation of HOMO-LUMO gap of different bp steps with twist angle, and have shown that such twisted geometry can be used as a tool for band gap engineering and manipulation of optical properties of DNA bp steps. Our study shows that for some of the bp steps (purine-purine) is highly sensitive to variation in twist angle.
Correlation energies obtained using one-particle operators
Claudine Gutlé,1 Francois Colonna2 and Andreas Savin2
1 Laboratoire Interuniversitaire des Systèmes Atmosphériques, CNRS UMR 7583 and Universités Paris 7 et Paris 12, 94010 Créteil, France

2 Laboratoire de Chimie Théorique, CNRS UMR 7616 and Université Pierre et Marie
Curie, 75252 Paris, France
Density functional or density matrix functional theory show that the correlation energy can be obtained from one-particle operators.

Adiabatic connections can be used as a guide for constructing approximations to correlation energy expressions.

Such functionals were tested against accurate calculations in atoms.
The Evanescent NCCO Radical
Henry F. Schaefer III
Center for Computational Chemistry, The University of Georgia, Athens, Georgia 30602, USA
The NCCO radical is considered likely to be an important species in combustion chemistry. However, its identification, particularly via infrared spectscopy, has proved to be severely challenging. By combining theory with experiment this long-standing problem has finally been resolved.
Exploring Potential Energy Surfaces by Ab Initio Molecular Dynamics
H. Bernhard Schlegel
Department of Chemistry
Wayne State University
Detroit, Michigan 48202 USA
In Born-Oppenheimer molecular dynamics (BOMD), each time the forces on the nuclei are needed in the integration of the classical equations of motion, a converged electronic structure calculation is carried out. Bond additivity corrections are used to improve the potential energy surface for the ab initio molecular dynamics studies. For the reaction of formaldehyde radical anion with methyl chloride, one transition state leads to two different products. Since the bifurcation in the reaction path occurs after the transition state, molecular dynamics is needed to study the branching ratio. Another reaction in which the branching ratio has been explored by ab initio molecular dynamics is the keto-enol isomerization and dissociation of acetone radical cation. Dynamics favors the dissociation of the newly formed methyl group, and the branching ratio depends on the initial energy. Born-Oppenheimer molecular dynamics has also been used to explore the dissociation of acetylene and allene dications.
Quantum free energy differences from non-equilibrium path integrals
Jeremy Schofield1, Ramses van Zon1, Gilles H. Peslherbe2 and Lisandro Hernandez de la Pena2,3
1Chemical Physics Theory Group, Department of Chemistry, University of Toronto
2 Center for Research in Molecular Modeling and
Department of Chemistry and Biochemistry, Concordia University
3 Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois
In this talk we discuss how the imaginary-time path integral representation of the canonical partition function of a quantum system and non-equilibrium work fluctuation relations can be combined to yield methods for computing free energy differences in quantum systems using non-equilibrium processes. The path integral representation is isomorphic to the configurational partition function of a classical field theory, to which a natural but fictitious Hamiltonian dynamics is associated. It is shown that if this system is prepared in an equilibrium state, after which a control parameter in the fictitious Hamiltonian is changed in a finite time, then formally the Jarzynksi non-equilibrium work relation and the Crooks fluctuation relation are shown to hold, where work is defined as the change in the energy as given by the fictitious Hamiltonian. Since the energy diverges for the classical field theory in canonical equilibrium, two regularization methods are introduced which limit the number of degrees of freedom M to be finite. The convergence of the work distribution as M tends to infinity is demonstrated analytically for a system composed of quantum particle trapped in a harmonic well of uniformly changing strength, leading to finite results for the free energy difference when the Jarzynski non-equilibrium work relation or the Crooks fluctuation relation are used. The numerical applicability of the methods is also demonstrated for a quartic double-well potential with varying asymmetry. A general parameter-free smoothing procedure for the work distribution functions is useful in this context.

Few-electron dynamics in the interaction with strong fields
Armin Scrinzi
Vienna U. of Technology
Photonics Institute
Simple single active electron models have been highly successful in describing the interaction of strong laser fields with atoms and have inspired a large number of experiments. Still, the validity and predictive power of these models for few-electron atoms and in particular for molecules remains to be investigated. There are only few (semi-)analytical models that include electron correlation. Alternatively, the numerical integration of the time-dependent Schroedinger equation (TDSE) is a challenging task because of the exponential growth of the problem size with the particle number, which has largely limited computations to n=2 active electrons.

In recent years, we have developed the MCTDHF (Multi-Configuration Time-Dependent Hartree-Fock) method for the solution of the TDSE for atoms and molecules in IR laser fields. The method scales like n4 with the number of active electrons, as opposed to the exponential scaling encountered in direct discretizations of the TDSE. Different from time-dependent density-functional theory, which has an even more favorable n2-scaling, MCTDHF allows for the straight forward computation of two-electron observables and for systematic convergence studies.

As examples, we show calculations of the strong field ionization of linear molecules with up to 6 active electrons, electron-assisted laser ionization of an atom, high harmonic generation on a diatomic
4-electron molecule, and the XUV-IR pump-probe ionization of Helium. While for our parameters, the effects of electron correlation on ionization are rather straight forward and can be incorporated into simple models, we find dramatic qualitative modifications of the high harmonic spectrum by multi-electron effects. For the pump-probe scenario, we find find significant crosstalk between the XUV pump and the IR probe pulses.
Nonlocal exact exchange: range separation, hybridization, and local variants
Gustavo E. Scuseria
Department of Chemistry, Rice University, Houston, Texas 77005, USA
This presentation will address our current efforts to develop more accurate exchange-correlation forms for density functional theory. There are two leading themes in our current work: range separation and local weights. On the first theme, we will present a three-range hybrid functional and discuss the rationale for the success of screened functionals like HSE and LC-wPBE. On the second theme, the emphasis will be on new metrics for local hybridization and local range separation.
Complex spectroscopic properties in complex materials from first principles
Daniel Sebastiani
Max Planck Institute for Polymer Research, Mainz (Germany)
The determination of intra- and intermolecular conformations of supramolecular assemblies has always been and still is a challenge for modern chemistry and physics. First-principles calculations of spectroscopic magnetic resonance parameters have the potential to elucidate microscopic structure in a variety of extended systems, ranging from molecular crystals over covalently and hydrogen-bonded nanotubes to liquids and solvated molecules.

Spectroscopic parameters are highly sensitive to the effect of weak interactions, such as hydrogen bonding and the proximity of aromatic moieties. In particular, delocalized electronic states give rise to unique fingerprints in terms of the reaction of the orbitals to external fields. The calculation of the spectroscopic signatures of such packing effects are often more accurate than the direct determination of the corresponding structural features via ab-initio calculations.

In disordered systems like liquids, the experimentally observable properties are computed as ensemble averages over trajectories obtained from sampling Car-Parrinello molecular dynamics simulations. This technique further allows for the direct computational evaluation of the temperature dependence of experimentally accessible spectroscopic properties.

Multi-Objective Optimization of Polymer Electrolyte Fuel Cells
M. Secanella, A. Sulemanb, N. Djilaib, D. Songa and S. Liua
aNational Research Council Canada, Institute for Fuel Cell Innovation, 4250 Wesbrook Mall, Vancouver, B.C., Canada
bUniversity of Victoria, Institute for Integrated Energy Systems and Dept. of Mechanical Engineering, Victoria, B.C. Canada
Improvements in performance, reliability and durability as well as reductions in production cost, remain critical prerequisites for the commercialization of polymer electrolyte fuel cells. In this work, a computational framework for fuel cell analysis and optimization is presented as an innovative alternative to the time consuming trial-and-error process currently used for fuel cell design. The framework is based on a two-dimensional through-the-channel isothermal, isobaric and single-phase membrane electrode assembly (MEA) model. The model input parameters are the manufacturing parameters used to build the MEA: platinum loading, platinum to carbon ratio, electrolyte content and gas diffusion layer porosity. The governing equations of the fuel cell model are solved using Netwon's algorithm and the adaptive finite element method in order to achieve quadratic convergence and a mesh independent solution respectively. The analysis module is used to solve the optimization problem of maximizing performance while minimizing the production cost of the MEA. To solve this problem a gradient-based optimization algorithm is used in conjunction with analytical sensitivities. The presented computational framework is the first attempt in the literature to combine highly efficient analysis and optimization methods to perform optimization in order to tackle large-scale problems. The framework presented is capable of solving a complete MEA optimization problem with state-of-the-art electrode models in approximately 30 minutes. The optimization results show that it is possible to achieve Pt-specific power density for the optimized MEAs of 0.21 gPt/kW. This value is below the DoE target for large-scale implementation, 0.4 gPt/kW, and demonstrates the potential of using numerical optimization for fuel cell design. In future work, the optimization framework and the fuel cell models will be improved upon and the optimization results will be validated against experimental data. The optimization problem will be expanded to include geometric parameters. The fuel cell model will be improved upon by including the effects of the microstructure and two-phase flow on both the electrode and membrane models.
Simulation Studies of a Charged Protein-Ligand Complex in the Gas Phase: from Intrinsic Intermolecular Interactions to Water Dynamics
Mikyung Seo, Elena N. Kitova, John S. Klassen and Pierre-Nicholas Roy
Alberta Ingenuity Centre for Carbohydrate Science and Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
Detailed theoretical studies of charged protein-ligand complexes raise fascinating questions regarding the nature of binding and the preservation of specific interactions when they are ionized and placed in the gas phase. We recently reported that intrinsic intermolecular interactions can be preserved under the conditions of gas-phase mass spectrometry experiments [ J. Am. Chem. Soc., 130, 1214 (2008)]. It is of great interest to extend our study to investigate dynamics of water molecules in the charged and hydrated protein-ligand complex in the gas phase. These water molecules are originally present in the crystal structure of the complex and participate in hydrogen bonds with the complex. A series of molecular dynamics simulations were performed in the gas phase at the +8 charge state of the complex composed of a single chain variable fragment (scFv) of the monoclonal antibody Se 155-4 and the trisaccharide ligand, Gal[Abe]Man, including those “crystallographic” water molecules. The simulations were carried out over a wide temperature range with the aim of understanding varying hydrogen bond dynamics of individual water molecules. Bond lifetime correlation functions were calculated for all specific hydrogen bonds between the water molecules and complex. Our analysis showed that the water molecules have different hydrogen bond lifetimes at different temperatures.
Stochastic Formulation of Quantum Dissipative Dynamics*
Jiushu Shao
College of Chemistry, Beijing Normal University, China
The quantum dynamics of dissipative systems is rigorously described by stochastic differential equations, the analogue to the traditional Langevin equation. The influence of the environment on the system of interest is fully characterized by the bath-induced stochastic field. This formulation can be implemented directly for random simulation or employed to develop a deterministic algorithm a la hierarchical equations for calculating the reduced density matrix. Moreover, one may take both advantages of the random and deterministic treatments to elaborate a powerful combination approach.

The mixed random-deterministic scheme has been successfully used to calculate the time evolution of the spin-boson model at zero temperature from weak to moderate dissipation. The obtained results including the coherent-incoherent transition are consistent with the conventional wisdom. This approach, for a better numerical performance, is further modified by converting a certain part of the random treatment to the deterministic one. It is observed that for strong dissipation the population in the localized state obeys a simple rate dynamics where the time scale in the scaling limit does not change in the regime of incoherent motion. A theoretical analysis within the stochastic description to understand the critical change of the dynamics is developed.

1) J. Shao, J. Chem. Phys. 120, 5053 (2004)
2) Y. Yan, F. Yang, Y. Liu, and J. Shao, Chem. Phys. Lett. 395, 216 (2004)
3) Y. Zhou, Y. Yan, and J. Shao, Europhys. Lett. 72, 334 (2005)
4) J. Shao, Chem. Phys. 322, 187 (2006)
5) Y. Zhou and J. Shao, J. Chem. Phys. 128, 034106 (2008)
6) J. Shao, unpublished.


*Supported by the National Natural Science Foundation of China and 973 Program of the Ministry of Science and Technology of China.
Adiabatic Raman transfer as a measurement tool in creation of cold molecules.
Evgeny Shapiro
Department of Chemistry, The University of British Columbia.
Deeply bound translationally and vibrationally cold diatomic molecules can be created by a laser-driven Raman adiabatic passage. Here, one uses two types of laser pulses. The “pump” pulse couples the initial state, which can be either an incoming wave packet of two colliding trapped atoms or a loosely bound Feshbach molecule, with an intermediate excited molecular state. The “dump” couples the intermediate with the target molecular state. Reminiscent of the standard STIRAP routine, an efficient population transfer is achieved by sending the pulses in the “counterintuitive” order: The dump starts before the pump. In this talk I will describe how the pulse shaping and exploiting multi-pathway interferences allow measuring the initial multichannel wave function in a laser-controlled wave packet basis [1], and how they can be used to obtain a wealth of spectroscopic information about the molecule one is working with [2].

[1] E.A. Shapiro, Moshe Shapiro, “Adiabatic Raman photoassociation with shaped laser pulses”. To appear in “Cold molecules: theory, experiment and application”, R.V. Krems, B. Friedrich and W.C. Stwalley, eds.
[2] E.A. Shapiro, A. Pe’er, J. Ye, M. Shapiro, Phys. Rev. Lett., 101, 023601 (2008).
Derivation of the coordinate-momentum commutation relations and the quantum dynamical equations from Canonical Invariance, the third law of thermodynamics and the "beginning of time".
Moshe Shapiro
Dept. of Chemistry
University of British Columbia
Vancouver V6T1Z1
Canada
We show that the coordinate-momentum commutation relations and the relativistic and non-relativistic quantum dynamical equations can all be derived from the classical principle of Canonical Invariance and the linearity of the correspondence between physical observables and quantum operators. The implications of this derivation to accelerating quantum relativistic systems, the third law of thermodynamics, and what may be viewed as the "beginning of time" are discussed.
Methods for Non-bonded Interactions
C. David Sherrill
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
Non-bonded interactions govern self-assembly, biomolecular structure, drug recognition, and crystal structures of neutral molecules. Unfortunately, such interactions have proven challenging to model reliably. To better understand the physics of non-bonded interactions, our group has published potential energy curves near the ab initio limit for several prototypes of common non-bonded interactions, namely, pi-pi (benzene dimer), CH/pi (benzene-methane), S/pi (H2S-benzene), and heteroatom-pi (pyridine dimer and pyridine-benzene). Using these data as benchmarks, we have assessed the reliability and efficiency of wide variety of approximate models, including empirical force fields, next-generation density functional models, empirically-corrected density functional theory, and spin-component-scaled second-order Møller-Plesset perturbation theory (SCS-MP2). We have also examined the effectiveness of various ancillary approximations, such as resolution-of-the-identity or density-fitting approximations for the integrals. For situations where high accuracy is desired but the cost of perturbative triples may become prohibitive, we have introduced a spin-component-scaled coupled-cluster singles and doubles (SCS-CCSD) approach which faithfully reproduces coupled-cluster with perturbative triples, CCSD(T), for non-bonded interactions, but which has the same computational cost as CCSD.
A model for air-side PEM fuel cell contamination
Zheng Shi, Datong Song, Kalid Fatih, Hui, Li, Yanghua Tang, Jianlu Zhang, Zhenwei Wang, Shaohong Wu, Zhong-Sheng Liu, Haijiang Wang, Jiujun Zhang
Institute for Fuel Cell Innovation, National Research Council Canada
A general air-side feed stream contamination model is developed to describe the transient and steady state behaviour of PEM fuel cell in the presence of air-side feed stream impurities. The model is based on electrode and surface chemical reaction kinetics. The model is further employed in the study of air-side toluene contamination. Experimental data of toluene contamination at different current densities (0.2, 0.5, 0.74 and 1A/cm2) and contamination levels (1, 5 and 10ppm) were used to validate the model. The toluene contamination effects on fuel cell performance are discussed in light of the modeling results. The model reveals that with 7ppm toluene, 100mV performance drop at 1A/cm2 can be expected. Toluene blocks the catalyst surface, with 7ppm toluene at current density of 0.5A/cm2, the free catalyst coverage can be reduced from about 60% to 24%.
Quantal cumulant dynamics for many-body systems
Yasuteru Shigeta
Department of Physics, Graduate School of Pure and Applied Sciences, Tsukuba University, Japan
The many-body quantum simulation is limited to some degree, because it costs too much. Therefore it is desirable to establish an efficient simulation scheme with lower costs for it in order to understand the many-body quantum phenomena. Instead of the full quantum dynamics, a variety of methods based upon semi-classical and quantal dynamics has been proposed. Recently, we have developed a quantal cumulant dynamics (QCD) in order to treat large quantum systems with low costs. The key ideas are that a coordinate shift operator acting on a potential operator is introduced and that a cumulant expansion technique is applied to evaluate the expectation value of the shift operator. In this work, we derive the coupled equations of motion of coordinates, momenta, cumulants that consist of symmetric-ordered products of the coordinate and the momentum fluctuation operators. Then the methodology is generalized to treat many-body systems. We introduce the cumulant of the internal coordinates and conjugate momenta and derive equations of motion of them along with those of coordinates and momenta. We apply the methodology to describe quantum nature of structural transitions of Morse clusters. We have evaluated a Lindemann index of small quantum clusters and observed quantum isotope effects on their melting behavior. The quantum effects shallow the potential and elongate the equilibrium distance of the Morse potential. These features result in increase of transition temperatures of freezing and melting toward those of classical ones.
Conceptual Unfoundedness of Hybridization and the Nature of the Spherical Harmonics
George P. Shpenkov
FIRMUS S.A.R.L.
33, boulevard Princesse Charlotte
MC 98000 MONACO
The quantum mechanical concept of hybridization is based on mixing the 'real' and 'imaginary' parts of complex wave functions. The erroneousness of such an operation, resulted in the notion of electron configuration of atoms, is revealed in this work. The true nature of spherical harmonics and important results originated from analyzing the above concept are presented here as well.
Rereading Langer’s influential 1937 JWKB paper: the unnecessary Langer transformation; the ambiguous ħ; the power of Borel summation
Harris J. Silverstone
Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
In the Abstract of his influential 1937 paper, Langer [1] attacked the JWKB analysis of the radial wave equation as “uncritical and in error,” and “when correctly applied the [JWKB] theory yields the formulas” in which (l+1/2)2 replaced l(l+1), now often called the Langer modification, and justified via the “Langer transformation,” r=ex, ψ(r)=ex/2u(x). Taken through first order in ħ, the modified JWKB wave function behaved like rl+1 at the origin, in contrast with the unmodified r1/2+√(l(l+1)), and the energy levels obtained in first order were exact (as if to all orders). Langer’s analysis stimulated several extensions and arguably inconsistent generalizations. Krieger and Rosenzweig [2] in 1967 pushed Langer’s solution to third order but concluded “there is no effective potential [in the r variable] ... which will give rise to the correct result ...” beyond first order. Beckel and Nakhleh [3] in 1963 found a value of K to replace l(l+1) so that the third-order JWKB wave function went like rl+1. Fröman and Fröman [4] in 1974 extended Beckel and Nakhleh’s idea to 9th order. Seetharaman and Vasan [5] in 1984 found the complete generalization to any order and showed that in infinite order, K should be exactly l(l+1), i.e., no Langer modification. Hainz and Grabert [6] in 1999 found a different way to get the rl+1 behavior in all orders by decomposing the centrifugal potential into a zeroth and first-order term with respect to ħ via ħ2 l(l+1)=L2 +ħL. They concluded that no Langer modification was necessary with their decomposition. Most surprising, Dahl and Schleich [7] in 2004 observed that the Langer modification in Langer’s derivation came completely from the r-1/2 in r-1/2ψ(r)=u(x), and that the exponential transformation was completely unnecessary. They concluded, “[Langer’s] analysis may, in fact, be considered as nothing more than a somewhat complicated way of solving [the wave equation for r-1/2ψ(r), in which the radial laplacian is “two-dimensional”] by the JWKB method.” So simple a revelation of a complete generalization took 67 years to discover.

Why are there several incompatible solutions and how can they be compared in a unified framework? Three ideas are salient. The first is that ħ is treated ambiguously and inconsistently: the ħ in the kinetic energy drives the expansion, while the ħ in the centrifugal potential is passive, implicit, intrinsic, but never expanded. The different solutions differ in how ħ is split between these two roles. The second is the Borel summability of the JWKB expansions [8-14], which gives each expansion precise analytic meaning. The third is a sharp tool by Aoki, Kawai and Takei to obtain the r = 0 behavior of the JWKB wave function.

When the implicit ħi is distinguished from the expansion ħ (by the subscript “i”), the Aoki-Kawai-Takei technique permits finding the exponent of r before the two are set equal. In the original analysis (Kramers) the exponent multiplied by ħ is ħ/2+(ħi2 l(l+1)+ħ2 /4)1/2. With Hainz and Grabert, the product is ħi l+ħ. With Dahl and Schleich (and Langer via the exponential transformation), the product is ħ/2+ ħi (l+1/2). With the two ħ’s distinguished, one can give a most simple generalization of the Langer substitution: ħi2 l(l+1) should be replaced by ħi2 (l+1/2)2 - ħ2 /4.

[1] R. E. Langer, Phys. Rev. 51, 669 (1937).
[2] J. B. Krieger and C. Rosenzweig, Phys. Rev. 164, 171 (1967).
[3] C. L. Beckel and J. Nakhleh, J. Chem. Phys. 39, 94 (1963).
[4] N. Fröman and P. O. Fröman, Nuovo Cimento B 20, 121 (1974).
[5] M. Seetharaman and S. S. Vasan, J. Phys. A 17, 2485 (1984). Also, M. Robnik and L. Salasnich, J. Phys. A 30, 1719 (1997); V. Romanovski and M. Robnik, Nonlinear Phenomena in Complex Systems 3, 214 (2000).
[6] J. Hainz and H. Grabert, Phys. Rev. A 60, 1698 (1999).
[7] J. P. Dahl and W. P. Schleich, J. Phys. Chem. A 108, 8713 (2004).
[8] A. Voros, Ann. Inst. Henri Poincaré 39, 211 (1983).
[9] H. J. Silverstone, Phys, Rev. Lett. 55, 2523 (1985).
[10] T. Aoki, T. Kawai and Y. Takei, Sugaku Expositions 8, 217 (1995). Originally appeared in Japanese in Sugaku 45, 299 (1993); T. Aoki, T. Kawai and Y. Takei, in Special Functions, ICM-90 Satellite Conference Proceedings, ed. by M. Kashiwara and T. Miwa (Springer-Verlag, Berlin, 1991), pp. 1–29.
[11] T. Kawai and Y. Takei, Algebraic Analysis of Singular Perturbation Theory. Translations of Mathematical Monographs 227 (2005), American Mathematical Society. (Originally published in Japanese in 1998 from Iwanami. Translated by Goro Kato.); T. Kawai and Y. Takei, in Analyse Algébrique des Perturbations Singulière. I: Méthodes Résurgentes, ed. by L. Boutet de Monvel (Hermann, Paris, 1994), p. 85.
[12] E. Delabaere, H. Dillinger and F. Pham, J. Math. Phys. 38, 6126 (1997).
[13] E. Delabaere and F. Pham, Ann. Inst. Henri Poincaré Phys. Théor. 71, 1 (1999).
[14] T. Koike, Publ. RIMS, Kyoto Univ. 36, 297 (2000); T. Koike, RIMS Kokyuroku 1159, 100 (2000); T. Koike. On the solutions of eigenvalue problems for the Coulomb potential in exact WKB analysis. Preprint.
HHG spectroscopy of polyatomic molecules
Olga Smirnova , Serguei Patchkovskii and Misha Ivanov
SIMS, NRC Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6 Canada,
We analyse how different observables of the high harmonic generation (HHG) spectroscopy can be used to reveal electronic dynamics in polyatomic molecules. We use the example of CO2 molecule and show how phase and amplitude measurements of harmonic light can be used to disentangle the contribution of different molecular orbitals to HHG process.

The controversy between the experimental data [1,2] and detailed measurements [3] have shown that the "molecular structure-related" minimum in the experimental high harmonic generation (HHG) spectra from CO2 molecule is sensitive to the experimental parameters such as the laser intensity. This sensitivity has first indicated the complexity of the underlying process, which far exceeds the two-center interference picture. In that picture, the position of the interference minimum in the HHG spectrum would be intensity-independent. We show that the intensity dependence of the so-called "structure-related" minimum is related to multi-electron dynamics and the contribution of different orbitals (or the hole states of the molecular ion) to the HHG spectra.
According to the three-step model, the HHG emission amplitude factorizes into those of strong-field ionization, electron propagation in the continuum and recombination. Which of these three processes is responsible for the severe deviations from the single-active electron predictions?
One typically assumes that the HHG emission is dominated by one path-way: ionization from HOMO and subsequent recombination to HOMO, denoted as HOMO-> HOMO. Indeed, strong-field ionization is exponentially sensitive to the ionization potential Ip, and lower-lying orbitals have higher Ip. We show that strong angular dependence of the ionization rates and the balance between the recombination and the ionization amplitudes for different molecular orbitals lead to almost equal contributions of several alternative pathways, such as HOMO-1-> HOMO-1 (involving the \tilde A 2Πu state of the cation) and HOMO-2 ->HOMO-2 (involving the \tilde B 2Σ+u$ state), i.e. ionization from and recombination to orbitals below HOMO. (Counting the orbitals, we do not include their degeneracy).
Controlling the angle of the molecular alignment, one controls the relative contribution of these additional channels into the total HHG signal. HOMO-> HOMO channel dominates for low energy part of the spectra, while others lead to higher cut-off and dominate the high energy part of the spectra. The minimum in HHG spectrum does not reflect the structure of any particular orbital, but is determined by the interplay of HHG emission from different channels. Changing the laser intensity one distorts the balance between the channels and the harmonic minimum shifts.
We acknowledge partial financial support from NSERC SRO 5796-299409/03 grant.

1. T. Kanai ,S. Minemoto, H. Sakai, Nature 435, 470 (2005)
2. C. Vozzi et al Phys. Rev. Lett. 95, 153902 (2005)
3. Y. Mairesse, N. Dudovich, P. Corkum and D. Villeneuve (unpublished)
Transition pathways of small titanium-oxygen clusters on the rutile (100) surface
Roger Smith, Edward Sanville, Louis Vernon, Steven Kenny
Department of Mathematical Sciences, Loughborough University, Loughborough, LE11 3TU, UK
We present energetic and geometric data for transitions between adsorption sites of small titanium and oxygen clusters on the rutile (110) surface. This is an important problem in thin film deposition since the rate at which particles arrive on the surface can be small compared to the possibility of diffusion of adsorbed species over the surface. In such cases the growth of the film is diffusion dominated rather than being governed by the kinetics of the arriving particles. The small clusters include the titanium and oxygen atoms, TiO, O2, and TiO2 clusters. The transition pathways were calculated using density functional theory, a Qeq charge transfer empirical potential of Hallil, et al. [1] and in some cases a fixed charge empirical model. The DFT calculations used the local density approximation, (LDA), or spin-polarised local density approximation functional, (LSDA) where appropriate. A triple-numeric set of local basis functions was used, with two polarisation functions present on each atom, (TNDP). The transition pathways were optimised using the nudged elastic band method, (NEB) [2].

Reasonable agreement between the DFT and Qeq models was found with regard to the small cluster binding sites upon the surface, with some exceptions. An adsorbed titanium atom was found to have two preferred binding sites, the upper and lower hollow sites. Both DFT and Qeq indicated a forward activation energy of 1-1.5 eV, and a reverse barrier of 0.6 eV. However, DFT indicated that an adsorbed oxygen atom has two stable binding sites, with transition activation energies ranging from 0.3 to 2.5 eV, while Qeq indicated the presence of only one stable binding site, with a translational energy barrier of just under 0.8 eV. The adsorbed TiO cluster was found to have two preferred binding sites, analogous to those for the adsorbed titanium atom, with similar transition energies ranging from 0.8 to 3.5 eV. With DFT, an adsorbed dioxygen molecule was found as a preferred binding site, with a translational energy barrier of 0.35 eV between adjacent equivalent sites. The Qeq model, however, does not predict the existence of this site. Finally, the TiO2 cluster was found by DFT to have a well-defined binding site, with diffusion energy barriers of 2.96 to 5.0 eV. In this case, the Qeq model predicted similar results, with a tendency to underestimate the energy barriers.

Dissociation pathways of TiO2 into separated adsorbed atoms were also calculated by DFT, with an energy barrier of complete dissociation of 11.5 eV. The relatively high energy barriers to diffusion and dissociation indicate that adsorbed clusters, (for example from surface growth processes such as magnetron sputtering), would tend to remain immobile at the site of initial impact at room temperature.

The formation and diffusion of two subsurface interstitial sites were examined using DFT. The barriers to subsurface interstitial formation were found to be 1.5-1.9 eV, with a barrier to diffusion of 1.2 eV. Work is now under way to model dynamic growth on this surface by impact of low energy atoms and ions (0-50 eV). The initial indications suggest high energy barriers to diffusion and therefore growth that is dominated by the kinetics of the interaction between the arriving particles and the surface; the latest results from these calculations will be presented at the meeting.

[1] Hallil, A.; Tetot, R.; Berthier, I.; Braems, I.; Creuze, J. Phys Rev B (2006), 73, 165406
[2] Henkelman G.; Jonsson H. J Chem Phys (2000) 113, 9978


Numerical Simulations of Non-adiabatic Attosecond Electron Dynamics
Stanley M. Smith
Center for Advanced Photonics Research and Department of Chemistry
Temple University, Philadelphia, PA 19122
Electron dynamics determine the outcome of the non-adiabatic laser-molecule interaction for short pulses on the order of three optical cycles. For these short pulses, the carrier envelope phase is an important factor in determining the excited states populated after the pulse. We have used modified midpoint unitary transform time-dependent Hartree-Fock (MMUT-TDHF) theory to study the electron dynamics of CO2 subjected to short three cycle pulses. The excited state spectrum of CO2 varies significantly depending on the carrier envelope phase. To investigate the differences, a windowed Fourier transform was used to probe the attosecond electron dynamics during the pulse. This analysis shows different excitation during the pulse leads to the change in excited state spectrum after the pulse.
A Systematical Investigation of Ionic Liquids
H.V. Spohr,1 and G.N. Patey1

1Department of Chemistry, University of British Columbia, Canada
Room temperature ionic liquids, consisting entirely of ions, are a new class of solvents. Their uses are widespread and applications are increasing, for example in analytics, separation, electrochemistry, synthesis, as engineering fluids or as performance additives. The advantages of room temperature ionic liquids are low volatilities, low flammabilities and the possibility to tune the properties of a specific liquid by slightly changing its molecular structure, for example side chains or functional groups. However, this customisability also poses the challenge of predicting the liquid properties from their molecular origins. We approach this challenge in a systematic way by isolating the most important molecular features of ionic liquids and conducting molecular dynamics simulations of simplified model systems. The first model examines the influence of the size disparity of the ions. While the ion size ratio is increased, the interionic distance and other parameters are kept constant to isolate the effects of size disparity. The second model scrutinises the effect of asymmetric charge placement within the ions. Both spherical ions have the same diameter, the only difference is the displacement of the cationic charge off the center of mass. The structural and dynamical properties of these model ionic liquids are presented.
The Infrared Spectrum of NO3
John F. Stanton
University of Texas at Austin
The NO3 radical has a long spectroscopic history that stretches back more than a century. Despite this, it is a fact that only two of its fundamental vibrations have been observed in the infrared, and one of them has arguably been misassigned. This talk presents a view of the spectra of NO3 from two different perspectives -- a diabatic and adiabatic representations -- and focuses on infrared observations below 2500 cm-1 as well as in the near-infrared between 7500-9000 cm-1. In addition, analytic calculation of diabatic couplings within the framework of equation-of-motion coupled-cluster theory are introduced and a few numerical examples given.
A family of model Kohn-Sham potentials for exact exchange
Viktor N. Staroverov
Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
Solving the exact-exchange optimized effective potential (OEP) equation to high accuracy is a nontrivial numerical problem. A pragmatic alternative to this procedure is to model the OEP directly as the sum of Slater's average exchange potential and a response correction using occupied Kohn-Sham orbitals as ingredients. We introduce a family of nonempirical approximations to the unknown response term motivated by the known second-order gradient expansion of the exact-exchange potential. Two previously proposed approximations to the response correction (the approximation of Harbola and Sen and the much more accurate Becke-Johnson model) are shown to be special cases of our general form at zeroth order. Inclusion of an explicit first-order term into the Becke-Johnson model yields an even more realistic approximation, as demonstrated by comparing the shapes and integrated exchange energies of these potentials to the exact OEP results.
The strengths and weaknesses of orbital-free materials simulation
M. J. Stott
Physics Dept., Queen's University
Schemes for simulating the structural properties of a collection of atoms are termed ab initio when the forces acting on the ions are obtained from a first principles treatment of the electrons. Ab initio schemes are usually based on density functional theory with the inscrutable effects of electron-electron interactions contained in an explicit functional of the electron density, the exchange-correlation energy, Exc[n], for which good approximations have been devised. This is the only approximation in Kohn-Sham schemes in which the electron kinetic energy, Ts, is calculated exactly in terms of a set of one-electron orbitals describing the individual electrons. For N atoms there are ~ N such orbitals to be calculated and this task limits the size of system that can be treated, and the time period over which the dynamics can be followed in a MD simulation. Orbital-free schemes use the electron density, n(r), rather than N orbitals to describe the electronic system, allowing great simplifications and very much more efficient calculations, which is a strength of the approach. But a weakness is the associated cost of an approximate electron kinetic energy. A further weakness is the limitation on the electron-ion interaction that can be used. Nevertheless, some systems are well suited to an orbital-free treatment e.g. those composed of so-called simple metals. The talk will discuss how the strengths may be exploited and the weaknesses remedied.
Insights into the mechanism of action of the cationic antimicrobial peptides aurein 2.2 and 2.3 from Australian Southern Bell frogs
Suzana K. Straus
Department of Chemistry, University of British Columbia,
Vancouver, BC, V6T 1Z1, CANADA
With the steady rise in the number of antibiotic-resistant Gram-positive bacteria, it has become increasingly important to find new bactericidal agents which are highly active and have novel and diversified mechanisms of action. Cationic antimicrobial peptides are an important class of peptides which target a wide range of microbes, such as bacteria and fungi. They are being explored as alternatives to currently used antibiotics, because of their unique property of displaying little to no antibiotic resistance effects.

We will present some of our recent results on two other members of the aurein peptide family, namely aurein 2.2-CONH2 (GLFDIVKKVVGALGSL-CONH2) and aurein 2.3-CONH2 (GLFDIVKKVVGAIGSL-CONH2), as well as an inactive version of aurein 2.3 with a carboxy C-terminus (aurein 2.3-COOH). We will demonstrate that these peptides adopt alpha-helical structure in the presence of membranes, regardless of their composition, using circular dichroism (CD) and solution state NMR. We will also illustrate how these peptides interact with model and bacterial membranes (using oriented CD, 31P NMR, differential scanning calorimetry, calcein release and DiSC35 assays) and provide insight into the mode of action of this class of compounds.
Calculation of Absolute Binding Affinities with Free Energy Perturbation Approach: Application to intracellular and extracellular drug binding to hERG1 channel
Julia Subbotina,1 Henry Duff 2 and Sergey Noskov1
1Institute for Biocomplexity and Informatics, Department of Biological Sciences, University of Calgary, Canada
2Faculty of Medicine, University of Calgary, Canada
The ability of the ligand to bind tightly to the receptor is a determining quantity to drug action efficiency. Thus, methodological development of the theoretical and experimental techniques to probe and evaluate absolute binding affinity or free energy of binding is a key to the design more effective pharmaceutical agents. However, accurate evaluation of the ligand binding to a protein a-priori possesses an evident challenge due to large number degrees of freedom in receptor, solvent and ligand itself to be considered. Here we present an application of the free energy simulation techniques to study ligand binding to a target potassium channel hERG1. Atomistic simulations combined with FEP techniques allow robust estimation for both free energy of ligand desolvation ( ΔGsolv) and free energy due to ligand-protein interactions at the binding site ( ΔGbind). The theoretical framework is similar to that developed before.1 To elucidate the potential human ether-go-go potassium ion channel (hERG) blockers we have performed molecular dynamics simulations for the number of possible conformations for three ligan-protein complexes. The set of parameters for binding drugs were developed by using the scope of parameterization protocols, based on extensive QM calculations.
The possibility of intracellular (IC) and extracellular (EC) binding for two high- and low-specificity hERG blockers (KN-93 and dofetilide) were explored in molecular details. It was found that for KN-93, but not for dofetilide, is possible to bind to the EC mouth of the channel, offering structural support to functional findings reported earlier as a plausible explanation for the drug activity.2

1 Jiyao Wang , Yuqing Deng, Benoît Roux. Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials. Biophys J 91:2798-2814 (2006).
2 Rezazadeh S, Claydon, T. W., Fedida, D. KN-93 (2-[N-(2-hydroxyethyl)]-N-(4-methoxybenzenesulfonyl)]amino-N-(4-chlorocinnamyl)-N-methylbenzylamine),a calcium/calmodulin-dependent protein kinase II inhibitor, is a direct extracellular blocker of voltage-gated potassium channels. J Pharm Exp Therap 317(1): 292-299 (2006).

Validity condition of Jarzynski's equation for boundary switching processes
Jaeyoung Sung
Department of Chemistry, Chung-Ang University, Seoul 156-756, Korea
Jarzynski’s equation (JE) has been known to relate free energy change of a system to statistical distribution of work done on the system for an arbitrary process. In the present work, we present the validity condition of JE for boundary switching processes. The validity condition of JE is examined for an example of spontaneous irreversible processes, for which, obviously, JE does not hold. We find that the free energy difference between two configurational states with different phase-space volume cannot be correctly estimated by JE for any adiabatic boundary switching process.
Multiconfigurational perturbative type studies
Ágnes Szabados, Zoltán Rolik and Péter R. Surján
Laboratory of Theoretical Chemistry, Loránd Eötvös University, Budapest, Hungary
Perturbation theory (PT) based on a multiconfigurational function is one of the currently established approaches to account for electron correlation in systems of inherently multireference character. There are numerous PT formulations belonging to this category, but only a few of them achieve all the criteria desirable for an ideal correlation approach: i) size-consistent; ii) intruder free; iii) orbital invariant; iv) modest computational cost.

A multiconfigurational PT framework (MCPT) developed in our laboratory ( J. Chem. Phys. 119, 1922; ibid. 122, 114104) is of relatively low cost and can be formulated in a size-consistent manner at second order. In the present study we investigate refinements of the theory with the aim of improving its accuracy as well as reducing its sensitivity to intruders. The most serious drawback of the theory in its present form is the dependence of correlation corrections on the choice of a Fermi-vacuum. We explore possible strategies to distill this behaviour and present pilot numerical calculations on test systems assessing the performance of the new theories.
Quantum Monte Carlo Combined with Fragment Molecular Orbital Method
Shigenori Tanaka
Graduate School of Human Development and Environment
Kobe University
By combining the quantum Monte Carlo (QMC) and fragment molecular orbital (FMO) methods, we have developed a novel ab initio methodology to calculate the total energy of biomolecules with good accuracy. Electronic correlation is taken into account using the Slater-Jastrow wave functions and the variational quantum Monte Carlo (VMC) method. We then calculated the energy of the whole system directly and by using the FMO method, finding that the combined QMC-FMO approach works very well. In addition to the total energy, we can estimate the inter-fragment interaction energies (IFIEs) on the basis of this method. Application examples will be shown for polypeptides and polynucleotides.

Design of chemically propelled nanodimer motors
Yu-Guo Tao and Raymond Kapral
Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Ontario M5S 3H6, Canada
The self-propelled motion of nanodimers fueled by a chemical reaction taking place under nonequilibrium steady state conditions is investigated[1,2]. The nanodimer consists of a pair of catalytic and chemically inactive spheres, in general with different sizes, with a fixed internuclear separation. The solvent in which the dimer moves is treated at a particle-based mesoscopic level using multiparticle collision dynamics. The directed motion of the dimer can be controlled by adjusting the interaction potentials between the solvent molecules and the dimer spheres, the internuclear separation, and sphere sizes. Dimers can be designed so that the directed motion along the internuclear axis occurs in either direction and is much larger than the thermal velocity fluctuations, a condition needed for such nanodimers to perform tasks involving targeted dynamics.


[1] Gunnar Rückner and Raymond Kapral, Phys. Rev. Lett. 98, 150603 (2007).
[2] Yu-Guo Tao and Raymond Kapral, J. Chem. Phys., 128, 164518 (2008).
Simulation studies of proton transport in ionomers
Philip L. Taylor and Elshad Allahyarov
Department of Physics,
Case Western Reserve University,
Cleveland, Ohio 44118-7079, U.S.A.

We have used molecular-dynamics simulations to study the morphological changes induced in a Nafion-like ionomer by the imposition of a strong electric field or a mechanical stress. In the case of a strong electric field, we observe the formation of structures aligned along the direction of the applied field. The polar head groups of the ionomer side chains assemble into clusters, which then form rod-like formations, and these cylindrical structures then assemble into a hexagonally ordered array aligned with the field direction. For semi-dry ionomers, at high current densities these rod-like clusters undergo an inner micro-phase separation, in which distinct wire-like lines of sulfonate head groups are accompanied by similar wire-like alignments of bound protons. Occasionally these lines of sulfonates and protons form a helical structure. Upon removal of the electric field, the hexagonal array of rod-like structures remains, but the microphase separation disappears below a certain threshold current. Uniaxial stretching of a recast Nafion film causes a preferential orientation of backbone segments in the direction of stretching. Our simulations of humid Nafion show that this has a strong effect on the proton conductivity, which is enhanced along the stretching direction, while the conductivity perpendicular to the stretching direction is strongly reduced. Stretching also causes the perfluorinated side chains to orient perpendicular to the stretching axis. We find the morphological changes in the stretched Nafion to be partly retained upon removal of the uniaxial stress.
Hunting for global minima of molecular clusters
Sergey Kazachenko and Ajit J. Thakkar
Department of Chemistry, University of New Brunswick, Fredericton NB E3B 6E2, Canada
Finding the global minimum of a potential energy surface of a molecular is a difficult problem because the number of minima increases exponentially with respect to the number of atoms in the system. Minima hopping is a recently developed global optimization method which offers several advantages over other popular methods. As a first step this method was implemented in TINKER. To improve performance, rotational and translational perturbations of the monomers were introduced as additional steps in the algorithm. The hydrogen bond topology plays an important role in water clusters, but minima hopping does not always find the best topology. Hence, a hydrogen bond topology optimization algorithm for water clusters was developed. Topology optimization can lower the energy of a cluster by as much as 2 kcal/mol. Minima hopping with the improvements mentioned above was applied to pure water clusters ranging from (H2O)6 to (H2O)34 using the TIP4P force field with subsequent reoptimization of the lowest 2000 structures using the AMOEBA and TTM2.1-F force fields.
Automatic Construction of Ab Initio Potential Energy Surfaces
Richard Dawes and Donald L. Thompson
Department of Chemistry
University of Missouri-Columbia
Columbia, Missouri 65211 USA
A highly accurate and efficient method for molecular global potential energy surface (PES) construction and fitting is demonstrated. An interpolating moving least-squares (IMLS) method using low-density ab initio potential, gradient, or Hessian values to compute PES parameters is shown to lead to an accurate and efficient PES representation. The method is automated and flexible so that a PES can be optimally generated for classical trajectories, spectroscopy, or other applications. Two main drivers for the fitting method have been developed thus far. The first is a PES generator designed primarily for spectroscopy applications. Using this method, the configuration space defined by a specified energy range is automatically fit to a predefined accuracy. A second approach is based on trajectory methods for computing reaction rates. In this approach, the configuration space that is dynamically accessible to a particular ensemble of trajectories is fit “on the fly.” Results that are indicative of the accuracy, efficiency, and scalability will be presented.
A converse approach to the calculation of NMR shielding tensors
Timo Thonhauser
Department of Physics
Wake Forest University
Winston-Salem, NC 27109
We propose an alternative approach for computing the NMR response in periodic solids that is based on a recently developed theory of orbital magnetization [1]. Instead of obtaining the shielding tensor from the response to an external magnetic field, we derive it directly from the orbital magnetization appearing in response to a microscopic magnetic dipole [2]. Our new approach is very general, and it can be applied to either isolated or periodic systems. The converse procedure has an established parallel in the case of electric fields, where Born effective charges are often obtained from the polarization induced by a sublattice displacement instead of the force induced by an electric field. Our novel approach is simple and straightforward to implement since all complexities concerning the choice of the gauge origin are avoided and the need for a linear-response implementation is circumvented. We have demonstrated its correctness and viability by calculating chemical shieldings in simple molecular systems, finding excellent agreement with previous theoretical and experimental results. Applications to more complex systems are currently in progress.

[1] T. Thonhauser, D. Ceresoli, D. Vanderbilt, and R. Resta, Phys. Rev. Lett. 95, 137205 (2005).
[2] T. Thonhauser, Arash A. Mostofi, Nicola Marzari, R. Resta, David Vanderbilt, arXiv:0709.4429v1.
A Self-Consistent and Environmental-Dependent Hamiltonian and its Applications to Dynamics of Carbon Onions
Wei Quan Tian*, Ming Yu, Chris Leahy, Chakram S. Jayanthi, and Shi-Yu Wu
Department of Physics, University of Lousiville, Louisville, Kentucky, 40292, USA
As the drastic increase of computational cost for first principles methods with system size even with aid of linear scaling strategies, application of such methods in nanosicence modeling is limited. On the other hand, without electronic structure modeling, the quantum effect important for correctly describing nanosystems is hardly captured. A self-consistent (SC) and environment-dependent (ED) multicenter Hamiltonian in the framework of linear combination of atomic orbitals (LCAO) with quantum effect [1] will be discussed in the present talk. The parameters of this semi-empirical Hamiltonian are constructed by fitting them to the ab-initio properties of small clusters and the bulk system that are calculated either using Gaussian-2003 or VASP. The semi-empirical Hamiltonian thus constructed allows us to study nanoscale structures consisting of thousands of atoms, especially, when linear scaling algorithms are used in tandem with the molecular dynamics based on this Hamiltonian. The applications of this new method to the dynamics of fullerene and fullerene onion nanoparticles show the predictive power of SCED/LCAO in nanomaterial modeling and can shed light on the formation of big cage (or fullerene) structures from onion structures.

[1]. C. Leahy, M. Yu, C. S. Jayanthi, and S. –Y. Wu, Phys. Rev. B, 2007, 74, 155408.

* Permanent address: State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
Coarse-grained simulations of lung surfactant, membranes, and nanoparticles
Peter Tieleman
University of Calgary, Department of Biological Sciences
Many biologically interesting phenomena occur on a time scale that is too long to be studied by atomistic simulations. Coarse-grained (CG) molecular modeling allows computer simulations to be run on length and time scales that are 2–3 orders of magnitude larger compared to atomistic simulations, providing a bridge between the atomistic and the mesoscopic scale. The MARTINI force field is a general force field for biomolecular simulation that currently includes parameters for a broad range of lipids and for proteins. I will briefly discuss the MARTINI force field and then focus on two applications that are out of reach for atomistic simulations: the behavior of fullerenes near lipid membranes and the collapse properties of lung surfactant models.

Recent toxicology studies suggest that nanosized aggregates of fullerene molecules can enter cells and alter their functions, and also cross the blood–brain barrier. However, the mechanisms by which fullerenes penetrate and disrupt cell membranes are not known. Our simulations show that the fullerene molecules rapidly aggregate in water but disaggregate after entering the membrane interior. The permeation of a solid-like fullerene aggregate into the lipid bilayer is thermodynamically favoured and occurs on the microsecond timescale. High concentrations of fullerene induce changes in the structural and elastic properties of the lipid bilayer, but these are not large enough to mechanically damage the membrane.

Lipid monolayers at an air-water interface can be compressed laterally, but beyond a certain threshold they become unstable and collapse. Lipid monolayer collapse plays an important role in the regulation of surface tension at the air-liquid interface in the lungs. We have simulated monolayer collapse using molecular dynamics simulations. Collapse begins with buckling of the monolayer, followed by folding of the buckle into a bilayer in the water phase. Folding leads to an increase in the monolayer surface tension, which reaches the equilibrium spreading value. Immediately after their formation, the bilayer folds have a flat semi-elliptical shape, in agreement with theoretical predictions. The folds undergo further transformation and form either flat circular bilayers or vesicles. The transformation pathway depends on macroscopic parameters of the system that can be calculated from simulations and depend on system composition and temperature. Transformation into a vesicle reduces the energy of the fold perimeter and is facilitated for softer bilayers, e.g. those with a higher content of unsaturated lipids or at higher temperatures.

References
[1] L. Monticelli et al, J. Chem. Theo. Comp. 4,819-834; Marrink et al, J. Phys. Chem. B 111, 7812 (2007)
[2] L. Monticelli et al., Nature Nanotechnology 3, 363-368
[3] S. Baoukina et al., Proc. Natl. Acad. Sci., in press
Theoretical and Experimental Vibrational Characterizations of Amine-Coated Silver Nanoparticles
Motoi Tobita,1 and Yusuke Yasuda2
1Advanced Research Laboratory, Hitachi, Ltd., Tokyo, Japan

2Materials Research Laboratory, Hitachi, Ltd., Ibaraki, Japan
Vibrational spectra of neutral and cationic amines on a silver surface were studied by using experimental and theoretical methods in combination. This work provides a prescription for identifying the charged state of amine on silver nanoparticles. In regards to the experiment, the infra-red (IR) spectrum of silver nanoparticles (Ag-NPs) coated by neutral octylamine was measured by Fourier transformed IR. In regards to the calculations, vibrational spectra of neutral and cationic octylamine, adsorbed on a silver surface were obtained by density-functional BPW91 calculations. The calculations show that amines of different charged states, i.e., neutral or cationic, can clearly be distinguished by the characteristic frequencies of N-H stretching and wagging modes. A comparison between the calculated and experimentally measured spectra of the Ag-NPs revealed that the amine in the synthesized Ag-NPs actually takes the neutral form. In addition, the synthesized Ag-NPs are shown to contain a non-negligible amount of residual ascorbic acid as well as some oxidized amines. In one of the IR spectra of amine-coated Ag-NPs measured prior to this study, the amine was found to be likely to take the cationic form. The current study demonstrates that a combination of theoretical calculations and experiments will help in characterizing the structure and constitution of organic species adsorbed on a metal surface.
The Role of Gold Adatoms in Self-Assembled Monolayers of Thiol on Au(111)
Edmanuel Torres, P. Ulrich Biedermann, Alexander T. Blumenau
Max-Planck Institut fuer Eisenforschung GmbH, Max-Planck-Str. 1, 40237 Duesseldorf, Germany
Self-assembled monolayers (SAM's) of thiol on gold surfaces are of great interest not only because the number potential applications in fields such as molecular electronics, nanotechnology or biosciences, but also because their intrinsic phenomenon of self assembly can be studied. The development of future applications of alkanethiol SAM's in nanosciences requires reproducible methods that strongly depend on the understanding of the binding mechanism of the molecules on the metallic surfaces and the preferred structures. However, in spite of intense studies during the last two decades attempting to understand the self assembling mechanism and the spatial arrangement of the alkanethiol molecules on the surfaces, experiment and theoretical calculations have persistently disagreed: In particular the discussion whether the molecules adsorb on top or at a site close to the bridge site has been one of the most remarkable controversy [1, 2]. The fact that surface reconstructions were not considered could be the origin of the controversial results. A recent STM/DFT study at very low coverage discovered a gold adatom in between two thiol molecules [3]. This was further supported by a PED/GXRD/DFT study at high density coverage [4]. Later theoretical investigations taking gold adatoms into account in thiol-SAM structures have shown better agreement with experiments [5, 6]. In the present work, we have systematically studied adatoms and surface vacancy structures and compared their binding and surface energies. Structural differences between the (√3×√3)R30o also known as α-phase, and the c(4×2) superlattices were investigated. While our results for the alpha phase show that molecules are directly bound to an unreconstructed Au(111) surface on a bridge site slightly shifted to the fcc hollow position, for c(4×2) calculations involving gold adatoms suggest a quasi top position to be the favourable adsorption site. In particular we found that gold atoms added to an α-phase induce a phase transition that ends up in a new c(4×2). Simulated STM images of our most favourable structure including adatoms and vacancies exhibit the zig-zag modulation in intensity, which is characteristic for the δ-phase c(4×2) superstructure. It can be clearly seen that differences not only stem from the inequivalent positions of the S atoms with respect to the surface but also result from variations in tilting and precession angles with respect to the α-phase.

[1] Vericat, C.; Vela, M. E.; Salvarezza, R. C. Phys. Chem. Chem. Phys. 2005, 7, 3258-3268.
[2] Vericat, C.; Vela, M. E.; Benitez, G. A.; Gago, J. A. M.; Torrelles, X.; Salvarezza, R. C. J. Phys.: Cond. Matt. 2006, 18, R867-R900.
[3] Maksymovych, P.; Sorescu, D. C.; Yates, J. T. Phys. Rev. Lett. 2006, 97, 146103.
[4] Mazzarello, R.: Cossaro, A.: Verdini, A.: Rousseau, R.: Casalis, L.: Danisman, M. F.: Floreano, L.: Scandolo, S.: Morgante, A.: Scoles, G. Phys. Rev. Lett. 2007, 98, 016102.
[5] Nagoya, A.; Morikawa, Y. J. Phys.: Cond. Matt. 2007, 19, 365245.
[6] Wang, J.-g.; Selloni, A. J. Phys. Chem. C 2007, 111, 12149-12151.
Algebraic Approach to Electronic Spectroscpy and Dynamics
Mohamad Toutounji
United Arab Emirates University
Lie algebra, Zassenhaus, and parameter differentiation techniques are utilized to break up the exponential of a bilinear Hamiltonian operator into a product of noncommuting exponential operators by the virtue of the theory of Wei and Norman J. [Wei, E. Norman, J. Math. Phys. 4, 575 (1963); J. Wei; E. Norman, Proc. Amer. Math. Soc., 15, 327 (1964)]. There are about three different ways to find the Zassenhaus exponents, namely binomial expansion, Suzuki formula, and q-exponential transformation. A fourth, and most reliable method, is provided. Since linearly displaced and distorted (curvature change upon excitation/emission) Hamiltonian and spin-boson Hamiltonian may be classified as bilinear Hamiltonians, the presented algebraic algorithm (exponential operator disentanglement exploiting six-dimensional Lie algebra case) should be useful in spin-boson problems. The linearly displaced and distorted Hamiltonian exponential is only treated here. While the spin-boson model is used here only as a demonstration of the idea, the herein approach is more general and powerful than the specific example treated. The optical linear dipole moment correlation function is algebraically derived using the above mentioned methods and coherent states. Coherent states are eigenvectors of the bosonic lowering operator and not of the raising operator While exp( ) translates coherent states, exp( ) operation on coherent states has always been a challenge, as has no eigenvectors. Three approaches, and the results, of that operation are provided. Linear absorption spectra are derived, calculated, and discussed. The linear dipole moment correlation function for the pure quadratic coupling case is expressed in terms of Legendre polynomials to better show the even vibronic transitions in the absorption spectrum. Comparison of the present line shapes to those calculated by other methods is provided. Franck-Condon factors for both linear and quadratic coupling are exactly accounted for by the herein calculated linear absorption spectra. This new methodology should easily pave the way to calculating the four-point correlation function, F(t1,t2,t3,t4), of which the optical nonlinear response function may be procured, as evaluating F(t1,t2,t3,t4) is only evaluating the optical linear dipole moment correlation function iteratively over different time intervals, which should allow calculating various optical nonlinear temporal/spectral signals.
TDDFT Excitation Energies: An Evaluation and a Diagnostic Test
Michael J G Peach1, Peter Benfield1, Trygve Helgaker2, David J Tozer1
1 Department of Chemistry, Durham University, Durham, UK
2Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, Norway

http://www.dur.ac.uk/d.j.tozer
We present a critical assessment [1] of the performance of DFT exchange-correlation functionals for calculating local, Rydberg, and intramolecular charge-transfer (CT) electronic excitation energies. The degree of spatial overlap between the occupied and virtual orbitals involved in an excitation is measured using a quantity Λ, and the extent to which excitation energy errors correlate with Λ is quantified.

The coulomb-attenuated CAM-B3LYP [2] functional provides by far the best overall performance; no correlation is observed between excitation energy errors and Λ, reflecting the good quality, balanced description of all three categories of excitation. By contrast, a clear correlation is observed for representative GGA and hybrid functionals, allowing a simple diagnostic test to be proposed for judging the reliability of a general excitation from these functionals – when Λ falls below a prescribed threshold, excitations are likely to be in very significant error.

The study highlights the ambiguous nature of the term ‘charge transfer’, providing insight into the observation that while many CT excitations are poorly described by GGA and hybrid functionals, others are accurately reproduced. For GGA and other local functionals, we also demonstrate that the extensive errors in asymptotic intermolecular CT excitations can be quantitatively understood from a consideration of the integer discontinuity [3].


[1] MJG Peach, P Benfield, T Helgaker, DJ Tozer, J. Chem. Phys. 128 044118 (2008)
[2] T Yanai, DP Tew, and NC Handy, Chem. Phys. Lett. 393 51 (2004)
[3] JP Perdew, RG Parr, M Levy, JL Balduz, Phys. Rev. Lett. 49 1691 (1982)

Recent Progress on Development of Orbital-free Kinetic Energy Density Functionals for Materials Simulations
S.B.Trickey1, V.V.Karasiev1,2, R.S. Jones3,
and F.E. Harris1,4

1 Quantum Theory Project, Dept. of Physics and Dept. of Chemistry
Univ.of Florida, Gainesville, FL 32611

2 Centro de Quimica, Instituto Venezolano de
Investigaciones Cientificas, IVIC,
Apartado 21827, Caracas 1020-A, Venezuela

3 Dept. of Physics, Loyola College in Maryland,
4501 N. Charles Street, Baltimore, MD 21210

4 Dept.of Physics, Univ. of Utah, Salt Lake City UT 84112
The appeal of orbital-free density functional theory for materials simulations is the prospect of Born-Oppenheimer forces for first- principles molecular dynamics with a computational cost scaling as the relevant system volume rather than some power of the electron count Ne. Of course, the missing link is a reliable, orbital-free expression for the Kohn-Sham kinetic energy (KE) functional Ts. Despite their careful construction, earlier KE functionals of the gradient expansion or generalized gradient approximation (GGA) types do not yield acceptable interatomic forces even for simple diatomic and polyatomic molecules.

In previous work [1,2], we traced this difficulty primarily to the violation of the non-negativity constraint on the Pauli potential. We proposed the use of modified conjoint functionals parameterized to recover inter-atomic forces for very small training sets, without requiring that they also yield accurate total energies. The modified functionals, in common with GGA-type functionals, are singular at the nuclei, but the singularity is positive, leading to semi- quantitatively correct interatomic forces. After surveying that work, the talk will present our recent advances in developing simple semi-local KE functionals. By truncation of the gradient expansion and enforcement of non-singularity to that order, we are able to remove the unphysical singularities from the Pauli potential. The result is a set of so-called reduced density derivatives in terms of which new approximate functionals can be expressed. Results from some simple reduced derivative approximation (RDA) kinetic-energy functionals will be given.

[Work supported in part by US National Science Foundation ITR Grant DMR-0325553.]

1. V.V. Karasiev, S.B. Trickey, and F.E. Harris, J. Comp.-Aided Mat. Des. 13, 111 (2006).

2. "Recent Advances in Developing Orbital-free Kinetic Energy Functionals", V.V. Karasiev, R.S. Jones, S.B. Trickey, and F.E. Harris, in "New Developments in Quantum Chemistry", J.L. Paz and A.J. Hernandez, editors (Research Signpost, Kerala) [in press].

New Density Functonals for a Broad Range of Applications
Donald G. Truhlar and Yan Zhao
Department of Chemistry, University of Minnesota
207 Pleasant St. SE, Minneapolis, MN 55455
We have developed a suite of density functionals. The functional with broadest capability, M06, is uniquely well suited for good performance on both transition-metal and main group-chemistry; it also gives good results for barrier heights and noncovalent interactions. Another functional, M06-L, has no Hartree-Fock exchange; this allows for very fast calculations on large systems, and M06-L is especially good for transition-metal chemistry and NMR chemical shieldings. M08-2X has the very best performance for main-group thermochemistry, barrier heights, and noncovalent interactions. M06-HF has no self-interaction error and is the best functional for charge transfer spectroscopy. A general characteristic of the whole suite is the optimized inclusion of kinetic energy density and higher separate accuracy of medium-range exchange and correlation contributions with less cancellation of errors than previous functionals [1-4]; for example, the functionals are compatible with a range of Hartree-Fock exchange and, although one or another of them may be more highly recommended for one or another property or application, all four are better on average than the very popular B3LYP functional.
[1] "Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions," Y. Zhao, N. E. Schultz, and D. G. Truhlar, Journal of Chemical Theory and Computation 2, 364-382 (2006).
[2] "A New Local Density Functional for Main Group Thermochemistry, Transition Metal Bonding, Thermochemical Kinetics, and Noncovalent Interactions," Y. Zhao and D. G. Truhlar, Journal of Chemical Physics 125, 194101/1-18 (2006).
[3] “The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals,” Y. Zhao and D. G. Truhlar, Theoretical Chemistry Accounts 120, 215-241 (2008).
[4] "Density Functionals with Broad Applicability in Chemistry," Y. Zhao and D. G. Truhlar, Accounts of Chemical Research 41, 157-167 (2008).

Atomic and molecular collisions in a magnetic field: mechanisms and control
T. V. Tscherbul,{^1} R. V. Krems2, and A. Dalgarno1
1ITAMP, Harvard-Smithsonian CfA, Cambridge, MA 02138, USA

2Department of Chemistry, University of British Columbia,
Vancouver B.C., V6T1Z1, Canada
A fundamental goal behind recent experiments with cold molecules is to understand the mechanisms of inelastic energy transfer and chemical reactions in the presence of electromagnetic fields. Here, we show that collisions of oxygen molecules can be efficiently manipulated by magnetic fields. The cross sections for spin relaxation in O2 - O2 collisions soar by five orders of magnitude as the external magnetic field is varied from 0 to 200 G, which suggests that evaporative cooling of molecules is only possible at low magnetic fields. Our results indicate that spin depolarization in molecule-molecule collisions is generally more efficient than in atom-molecule collisions.

Collision-induced transfer of polarization between the alkali metal atoms and He3 nuclei plays an important role in spin-exchange optical pumping [1], atomic magnetometry [2], and cryogenic cooling [3]. Here, we present quantum mechanical cross sections for spin exchange in collisions of Li, Na, and K atoms with He-3 based on the accurate ab initio calculations of the electron spin density. Our calculations indicate that previous models tend to overestimate the Fermi contact hyperfine interaction by a factor of around 10. We find that the calculated cross sections for spin exchange in Na - He and K - He collisions are in good agreement with earlier measurements performed at T = 373.15 K [4].

[1] T. G. Walker and W. Happer, Rev. Mod. Phys. 69, 629 (1997).
[2] D. Budker et al., Rev. Mod. Phys. 74, 1153 (2002).
[3] T. Hong et al., arxiv:0805.1416 (2008).
[4] T. G. Walker, Phys. Rev. A 40, 4959 (1989).

Enhanced conformational sampling and free energies via novel spatial-warping transformations and adiabatic dynamics
Mark E. Tuckerman
Department of Chemistry and Courant Institute of Mathematical Sciences
One of the computational grand challenge problems is to develop methodology capable of sampling conformational equilibria in systems with rough energy landscapes. If met, many important problems, most notably protein structure prediction, could be significantly impacted. In this talk, I will present a new approach in which molecular dynamics is combined with a novel variable transformation designed to warp configuration space in such a way that barriers are reduced and attractive basins stretched. The new method rigorously preserves equilibrium properties while leading to very large enhancements in sampling efficiency. The performance of the method is demonstrated on long polymer chains and simple protein models and is shown to significantly outperform replica-exchange Monte Carlo with only one trajectory. Finally, a new molecular dynamics approach for generateing multi-dimensional free-energy surfaces that employs adiabatic dynamics combined with multiple time-step integration to drive a set of extended phase-space variables as a means of enhancing the sampling of a subspace of collective variables will be presented.
MD and QMMM Binding Affinity Calculations Correlate with Cytotoxic Potency of Novel Colchicine Derivatives Against Cancer Cell Lines
J.A. Tuszynski, J. Mane, J.T. Huzil and L. Johnson
Division of Experimental Oncology
Cross Cancer Institute
11560 University Avenue
Edmonton, AB T6G 1Z2
Canada
Colchicine is a highly toxic plant-derived alkaloid which inhibits microtubule polymerization by binding to tubulin dimers. Currently, the chemotherapeutic value of colchicine is limited by its toxicity against normal cells. This could be remedied by derivatizing colchicine to preferentially bind tubulin isotypes or mutants which are more common in cancer cells than in normal body tissues, and particularly in those cancer types which are resistant to conventional therapies. In recent studies, it has been demonstrated that class III ß-Tubulin over-expression is associated with taxane-resistant subsets of non-small cell lung cancer, advanced ovarian cancer, breast cancer and cancers of unknown primary origin. In our study we used Quantum Mechanics Molecular Mechanics (QMMM) and Molecular Dynamics (MD) modeling to construct and assess derivatives of colchicine which will bind class III ß-Tubulin with increased affinity. Using QMMM and MD modeling techniques, 21 colchicine derivatives were designed to increase affinity for class III beta-Tubulin by offering a better steric fit into the binding pocket . These derivatives were subsequently synthesized by organic chemists at Oncovista Inc. of San Antonio, TX. The colchicine derivatives were then tested in MTS cytotoxicity assays against ten different cancer cell lines and one normal cell line, with differing characteristics and morphologies. Results were obtained by graphing the MTS absorbance readings, and calculating an EC50 Value (drug concentration at which 50% of the drug’s effects are seen) using sigmoidal dose-response analysis. Colchicine has an EC50 Value in the range of 10-7 M, and several of our novel derivatives (ie. CH-32, CH-34 and CH-35) were found to have EC50 Values in the range of 10-9 M, while other derivatives (ie. CH-6, CH-7 and CH-21) were found to have EC50 values in the range of 10-5 M to 10-6 M. These results indicate that some of our derivatives have more than 100 times greater cancer cell kill effectiveness than colchicine. Interestingly, comparative derivative cytotoxicity was found to correlate with theoretically predicted QMMM and MD bindign affinities. Successful derivatives warrant continued investigation, screening and development. We propose that our modeling approach may be used to design and test in silico any variety of drugs for specific targets such as vinca alkaloids, taxanes and peloruside.
Optimization of Many-Body Wave Functions
Julien Toulouse1 and Cyrus J. Umrigar2
1 Laboratoire de Chimie Theorique (UMR 7616), Universite Pierre et Marie Curie (Paris 6) and Centre National de la Recherche Scientifique, 4 place Jussieu, 75252 Paris, France
2 Laboratory of Atomic and Solid State Phyics,
Cornell University, Ithaca, NY 14853
Straightforward energy minimization methods for optimizing quantum Monte Carlo (QMC) wavefunctions are inefficient since they require a very large number of Monte Carlo configurations per variational parameter. Consequently until a few years ago, the variance-minimization method (minimization of the variance of the local energy) was the preferred method. Recently simple, robust and efficient methods for optimizing an arbitrary linear combination of the energy and the variance, including pure energy optimization, have been developed. Using these methods it is possible to optimize all the parameters in QMC wavefunctions (Jastrow, determinantal coefficients, orbital coefficients and basis function exponents). Wavefunctions with progressively larger numbers of variational parameters are found to have monotonically decreasing energies, not only in variational Monte Carlo but also in fixed-node diffusion Monte Carlo.

[1] C. J. Umrigar and Claudia Filippi, Phys. Rev. Lett. 94, 150201, (2005).
[2] C. J. Umrigar, Julien Toulouse, Claudia Filippi, S. Sorella, R. G. Hennig, Phys. Rev. Lett. 98, 110201 (2007).
[3] Julien Toulouse and C. J. Umrigar, J. Chem. Phys.} 126, 084102, (2007).
[4] Julien Toulouse and C. J. Umrigar, J. Chem. Phys. 128, 174101 (2008).
Computational Mutagenesis in Analysis of Protein Stability and Function: Effects of Hydration
Gregory M. Reck, Majid Masso and Iosif I. Vaisman


Department of Bioinformatics and Computational Biology, George Mason University, USA
Accurate predictive models for the impact of amino acid residue substitutions on protein stability provide important insights into protein structure and function. Such models are also valuable for the design and engineering of new proteins. Previously described methods have utilized properties of protein sequence or structure to predict the free energy change of mutants through the application of either computational energy-based approaches or machine learning techniques. However, accuracy associated with applying these methods separately is frequently far from optimal. We detail a computational mutagenesis technique based on a four-body, knowledge-based, statistical contact potential defined by Delaunay tessellation of amino acid residue locations only or with the inclusion of the locations of hypothetical water positions surrounding the protein. For any mutation due to a single amino acid replacement in a protein, the method provides an empirical normalized measure of the ensuing environmental perturbation occurring at every residue position. The residue environment based predictors of stability change are evaluated by applying machine learning tools to large training sets of mutants derived from diverse proteins that have been experimentally studied and described. Predictive models based on our combined approach for unhydrated and hydrated proteins are in many cases significantly outperform other existing models.
An accurate solution of the G-particle-hole hypervirial.
C. Valdemoro1, D. R. Alcoba2, L. M. Tel3, E. Pérez-Romero3
1 Instituto de Matemáticas y Física Fundamental,
CSIC, Serrano 123, 28006 Madrid, Spain
2 Facultad de Ciencias Exactas y Naturales,
Universidad de Buenos Aires, Ciudad Universitaria
1428 Buenos Aires, Argentina
3 Departamento de Química Física,
Universidad de Salamanca, 37008 Salamanca, Spain
The equation obtained by mapping the matrix representation of the Schrödinger equation with the 2-order correlation transition matrix elements into the 2-body space is the so called correlation contracted Schrödinger equation (CCSE) [1]. The form of this equation has been known for several years. As shown by Alcoba [1], the solution of the CCSE coincides with that of the Schrödinger equation. Here the attention is focused in the vanishing hypervirial of the G-particle-hole operator (GHV) [2]. By applying a time-like Heisenberg transformation to the G-particle-hole operator, a good approximation of the expectation value of this operator as well as of the GHV is obtained. A comparative analysis of the GHV and the anti-Hermitian part of the contracted Schrödinger equation (ACSE) [3] demonstrates that the stationary conditions of the former involve more degrees of freedom than those of the latter one and, consequently, they are harder to satisfy. The method is illustrated for the case of the Beryllium isoelectronic series as well as for the Li2 and BeH2 molecules. These results show that 99.04%-100.09% of the correlation energy is accounted for. The convergence of these calculations was more rapid when using the GHV than with the ACSE.


[1] D.R. Alcoba, Phys. Rev. A 65, 32519 (2002).

[2] D.R. Alcoba, C. Valdemoro, L.M. Tel, E. Pérez-Romero,
submitted for publication
.

[3] D.A. Mazziotti, Phys. Rev. Lett., 97, 143002 (2006).


Green-Kubo for solids
Henk van Beijeren
Institute for Theoretical Physics
Utrecht University
Green-Kubo formalism for the derivation of macroscopic dynamical equations can be developed straightforwardly with the aid of the Mori-Zwanzig projection operator formalism. The only (but crucial!) physical inputs are the hamiltonian plus the proper choice of a set of microscopic variables whose values on average will decay slowly. For simple fluids these "hydrodynamic densities" are the long wave length Fourier components of mass, momentum and energy density. In dielectric solids the mass density has to be extended to a set of displacement fields, describing the instantaneous deviations of atom and molecule positions from their average values. Application of the Green-Kubo formalism in this case reproduces the known phenomenological elastodynamic equations. Besides the usual microscopic expressions for elastic constants it produces expressions for the transport coefficients in terms of integrals over current-current time correlation functions. Mode-coupling results, including long time tails, may differ from the corresponding ones for fluids, due to the replacement of shear modes by transverse sound modes.
Complementary structure sensitive and insensitive catalytic relationships
Rutger A. van Santen
Schuit Institute of Catalysis
Laboratory of Inorganic Chemistry and Catalysis
Eindhoven University of Technology
The Netherlands
An important class of heterogeneous catalysts consists of transition metal particles dispersed on a high surface area support. When the support can be considered chemically inert, as can be the case when carbon is used as a support or sometimes also for alumina or siliceous supports, the support mainly acts as a dispersant of the metal particles.

Nearly half a century ago a remarkable dependence of catalytic rate on dispersion of the catalytically active particles was found for particular classes of reactions. With decreasing particle size three different types of behavior can be distinguished. Whereas some reactions appear to be independent of particle size (e.g. hydrogenation of unsaturated alkenes), others steeply increase with decreasing particle size (e.g. hydrogenolysis of alkanes) and quite interestingly some reactions show a maximum in activity when particle size decreases (e.g. carbon monoxide methanation). The typical range of particle sizes where these effects are observed vary between 2 and 20 nm. This is outside the range where metal particles start to behave as molecular clusters instead of as metallic particles.

Therefore the chemical reactivity of metal particles in this size range can be deduced from the reactivity differences of transition metal surfaces that have the same topology as the sites that occur on the metal particles. This provides an interesting link between surface science and heterogeneous catalysis.

Especially due to detailed computational quantum-chemical studies our understanding of the relation between surface structure and surface chemical reactivity has been significantly enhanced. As we will show detailed analysis of transition state energies and structures provides the key conceptual link between chemical reactivity and surface structure. It reveals new insights of the reasons why there are the three classes of structure sensitive and insensitive heterogeneous catalytic reactivity relationships.
Exploring Electron Transfer and Bond Breaking with Constrained DFT
Troy Van Voorhis
Department of Chemistry
Massachusetts Institute of Technology
77 Massachusetts Ave.
Cambridge, MA 02139
Electron transfer reactions are the centerpiece of artificial photosynthetic complexes, organic LEDs and essentially all of redox chemistry. This talk will highlight ongoing work being carried out in our group aimed at developing methods that can accurately simulate the reaction dynamics in these types of systems. Specifically, this talk will focus on the electronic structure problem inherent in describing electron transfer: How can we treat charge transfer states on the same footing with the electronic ground state? How do we make connections between a phenomenological picture like Marcus theory and a more rigorous approach like DFT? How do we describe bond formation (in particular proton transfer) that is often intimately connected with the process of electron transfer? Time permitting, we will mention some applications of these methods to organic light emission, photoinduced dynamics and/or redox catalysis.
Structural and dynamical properties of nanofluids using effective potentials
Ramses van Zon
Chemical Physics Theory Group
Department of Chemistry
University of Toronto
Toronto, Ontario, Canada
Suspensions of nanoparticles, so-called nanofluids, have a wide range of application, from cooling fluid to self-assembly. Effective potentials for nanoparticles will be presented which allow for a more efficient theoretical study of such systems. Even with the effective description, the difference in length scales between the nanoparticles and the fluid particles in the suspension can lead to problems in simulations of such systems. Strategies will be given which can minimize these problems. Two applications of the effective description will be discussed. The radial distribution functions are studied as an example of a structural property of the nanofluid, and it is shown how to make the most of limited statistics by using the so-called weighted residues method instead of the histogram method. The dynamics of displacements of individual particles in the nanofluids is the second application of the effective description. One of the results is that nanoparticles can exhibit near-Gaussian behaviour on time scales on the order of 5 to 10 picoseconds.
Multiscale Modeling of Self-Assembled Polyelectrolyte Membranes
Aleksey Vishnyakov, Alexander V. Neimark
Department of Chemical and Biochemical Engineering,
Rutgers, the State University of New Jersey
Polyelectrolyte membranes often possess a hierarchical structure. They are built of nanoscale hydrophilic and hydrophobic blocks arranged in self-assembled mesoscopic structures. Depending on the system and the environmental conditions, these self-assembled structures may have either regular symmetric or disordered fractal morphologies. Transport, mechanical, and rheological properties of a self-assembled system depend not only on its chemical composition but also on its morphology. Thus, the structure formation is the key problem that is to be considered toward a better understanding of engineering properties of self-assembled systems. The hierarchical structure of polymer systems implies a hierarchical structure of a suite of modeling tools, which must span many orders of magnitude of spatial and temporal scales. I will present an overview of multiscale simulation methods employed in our group, which enable us to describe the macroscopic properties of complex systems from ab-initio quantum mechanical calculations of electron density to atomistic molecular dynamics and Monte Carlo simulations to coarse-grained mesocsopic methods of dissipative particle dynamics. The methods will be illustrated on the example of structure formation and transport in polyelectrolyte membranes, such as Nafion and sulphonated block-copolymers, which are employed in fuel cells and protective clothing.
Geometry optimization with a noisy potential energy surface
Lucas K. Wagner
University of California, Berkeley
While density functional theory has been very successful in calculating minimum energy structures for molecular and solid systems, it fails in several regimes, including the excited state and weak-binding systems. Quantum Monte Carlo (QMC) is a particularly tempting method to improve on these deficiencies, since it offers highly accurate total energies for the ground state and an accurate description of selected excited states. However, QMC suffers from two major deficiencies: 1) forces are not easily calculated and 2) the energy is obtained with stochastic uncertainty, which makes optimization a challenging task. We evaluate several methods for overcoming these difficulties, and suggest a solution.
Energy Barriers for the Dissociation of Charged Protein Complexes in the Gas Phase
Surajith N. Wanasundara and Mark Thachuk
Department of Chemistry
University of British Columbia
2036 Main Mall, Vancouver, BC
V6T 1Z1, CANADA
Several electrospray ionization mass spectrometric (ESI-MS) studies have pointed out that the dissociation of protein complexes can lead to fragments with asymmetric charge to mass ratios. Free energy barriers for the dissociation of charged protein complexes can be used to understand this phenomenon. Relative free energy profiles for the dissociation of charged cytochrome c dimer were estimated by performing constrainted molecular dynamics simulations at selected fixed center of mass (COM) distances along the dissociation path. Mean number of overcrossings were also plotted with COM distance in order to understand the structural changes during dissociation.
Ab initio Simulation on Morphology and Site-dependent Reactivity of Pt Nanoparticles
Liya Wang, Ata Roudgar, Michael Eikerling
Department of Chemistry, Simon Fraser University
Institute for Fuel Cell Innovation, National Research Council Canada
Supported Pt nanoparticles are applied as electrocatalyst in polymer electrolyte fuel cells (PEFCs). Size, morphology, and surface structures determine stability and reactivity of these particles. We have performed ab initio calculations based on Density Functional Theory (DFT) on Pt particles with varying size (up to 150 atoms) and morphologies. The cohesive energy is calculated as a function of the number of atoms. Octahedron and truncated octahedron are found as the most stable particle morphologies in the range of 1.2-2 nm. The truncated cuboctahedron was selected for further studies of surface reactivity. Studies on oxygen atom adsorption were performed as a probe of electronic structure effects on the catalytic activity. An oxygen atom was moved over a grid of well-defined sites and geometry optimization calculations were performed at each point, with fixed lateral position of the oxygen and fixed atomic configuration of Pt. As a result we were able construct contour plots of adsorption energies for each crystalline nanofacet on the particle surface. In order to exploit the effect of particle reconstruction on adsorption energy, we performed full optimization calculations, in which all nuclear degrees of freedom are allowed to relax. Our results indicate that at adsorption energies are strongly spatially varying functions on each facet. The comparison of the adsorption energy between simulations with fixed particle structure and simulations involving particle reconstruction, reveals that in the latter case the adsorption energy increases from 0.5eV to 1.2eV depending on the adsorption site.
Chemistry of Single-Walled Carbon Nanotubes
Yan Alexander Wang
Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
yawang@chem.ubc.ca
The state of the art of creating single-vacancy defected and substitutionally doped single-walled carbon nanotubes (SWCNTs) has been done with “brutal” physical means under very high temperature of hundreds and thousands of degrees. Such extreme thermal treatments generally do not have a great degree of control over the positions of doping and substitution. Through employing density-functional theory, we have demonstrated the first example of synthesising substitutionally nitrogen-doped SWCNT via chemistry under mild conditions [1-3]. In the reaction of nitric oxide molecules with a defected SWCNT, the 5-1DB defect site can capture a nitrogen atom from a nitric oxide molecule, yielding a nitrogen-doped SWCNT. The same process can also provide a novel way to repair a damaged SWCNT. Our work opens promising perspectives in the development of nanostructured materials with new electronic properties.

To understand more about the reactivity of single-vacancy defected SWCNTs [3,4], we studied the interaction between ozone and carbon nanotubes in the presence of a vacancy and identified the most probable dissociation pathways of ozone to be the reaction involving the unsaturated active carbon atom at the vacancy defect site [3,5]. We thus offer a timely theoretical elucidation for the process of the ozonization of SWCNTs, which has been widely used to cut carbon nanotubes in experiments.

The search for novel nanocatalyst systems and sensors is currently a very active area of research. There are a number of ongoing experimental projects using carbon nanotubes as a metal catalyst support by coating carbon nanotubes with metal nanoparticles. We further explored the possibility of utilizing platinum-doped carbon nanotubes as sensors for small gas molecules and as nanocatalysts [2,3,6-8]. Our results will facilitate the experimental work in nanotube chemistry, enabling applications of SWCNTs in catalysis, chemical sensors, and fuel cells. During the studies of the adsorptions of small gas molecules on the platinum-doped carbon nanotube, we also identified a few novel nanotube-coordinated platinum complexes, which will be extremely useful for nanotube-metallic chemistry [7,8].

[1] “Chemical Reaction of Nitric Oxides with the 5-1DB Defect of the Single-Walled Carbon Nanotube,” L. V. Liu, W. Q. Tian, and Y. A. Wang, J. Phys. Chem. B 110, 1999-2005 (2006).

[2] “Electronic Properties and Reactivity of the Doped and Defected Single-Walled Carbon Nanotubes,” W. Q. Tian, L. V. Liu, and Y. A. Wang, in Handbook of Theoretical and Computational Nanotechnology, Vol. 9, edited by M. Rieth and W. Schommers (American Scientific, Valencia, California, USA, 2006), Chap. 10, p. 499-524.

[3] “Electronic Structure and Reactivities of Perfect, Defected, and Doped Single-Walled Carbon Nanotubes,” W. Q. Tian, L. V. Liu, Y.-K. Chen, and Y. A. Wang, J. Comput. Theor. Nanosci. 5, in press (2008).

[4] “Ab Initio Studies of the Vacancy Defected Fullerenes and Single-Walled Carbon Nanotubes,” L. V. Liu, W. Q. Tian, and Y. A. Wang, J. Chem. Phys., submitted (2007).

[5] “Ozonization at the Vacancy Defect Site of the Single-Walled Carbon Nanotube,” L. V. Liu, W. Q. Tian, and Y. A. Wang, J. Phys. Chem. B 110, 13037-13044 (2006).

[6] “Electronic Properties and Reactivity of Pt-Doped Carbon Nanotubes,” W. Q. Tian, L. V. Liu, and Y. A. Wang, Phys. Chem. Chem. Phys. 8, 3528-3539 (2006).

[7] “Novel Nanotube-Coordinated Platinum Complexes,” C. S. Yeung, L. V. Liu, and Y. A. Wang, J. Comput. Theor. Nanosci. 4, 1108-1119 (2007).

[8] “Adsorption of Small Gas Molecules onto Pt-doped Single-Walled Carbon Nanotubes,” C. S. Yeung, L. V. Liu, and Y. A. Wang, J. Phys. Chem. C 112, 7401-7411 (2008).
Asymptotic Behavior of Functional Derivatives of Kinetic-Energy Density Functionals
Yan Alexander Wang
Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
yawang@chem.ubc.ca
The “exchange-correlation derivative discontinuity” [1] has drawn quite considerable attention recently and many research groups have been designing new exchange-correlation density functionals and potentials based on such theoretical results. The backbone of the exchange-correlation derivative discontinuity arguments heavily relies on a particular value of the chemical potential, μ = − ( I+ A)/2, which is the negative of Mulliken’s electronegativity. Here, I and A are the first ionization potential and the first electron affinity of a bounded quantum chemical system under investigation, respectively. We have previously shown that the exact value of the chemical potential at an integer number of electrons is the negative of the first ionization potential, μ = − I, not the popular preference of the negative of Mulliken’s electronegativity [2].

For both non-interacting and fully interacting quantum chemical systems, we will further show that functional derivatives of kinetic-energy density functionals approach the exact functional derivative of the von Weizsäcker functional asymptotically, in both Hilbert and Fock spaces. Consequently, we confirm our initial assessment of the derivative discontinuity [2]: there is no derivative discontinuity of the exchange-correlation functional at an integer number of electrons and the functional derivative of the kinetic-energy density functional is solely responsible for the derivative discontinuity.

[1] J. P. Perdew, R. G. Parr, M. Levy, and L. J. Balduz, Jr., Phys. Rev. Lett. 49, 1691 (1982).

[2] F. E. Zahariev and Y. A. Wang, Phys. Rev. A 70, 042503 (2004).
Orbital-Corrected Orbital-Free Density Functional Theory
Yan Alexander Wang
Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
yawang@chem.ubc.ca
Density functional theory (DFT) has been firmly established as one of the most widely used first-principles quantum mechanical methods in many fields. Each of the two ways of solving the DFT problem, i.e., the traditional orbital-based Kohn-Sham (KS) and the orbital-free (OF) [1] schemes, has its own strengths and weaknesses. We have developed a new implementation of DFT, namely orbital-corrected OF-DFT (OO-DFT) [2], which coalesces the advantages and avoids the drawbacks of OF-DFT and KS-DFT and allows systems within different chemical bonding environment to be studied at a much lower cost than the traditional self-consistent KS-DFT method. For the cubic-diamond Si and the face-centered-cubic Ag systems, OO-DFT accomplishes the accuracy comparable to fully self-consistent KS-DFT with at most two non-self-consistent iterations [2] via accurately evaluating the total electronic energy before reaching the full self-consistency [2-5]. Furthermore, OO-DFT can achieve linear scaling by employing currently available linear-scaling KS-DFT algorithms and may provide a powerful tool to treat large systems of thousands of atoms within different chemical bonding environment much more efficiently than other currently available linear-scaling DFT methods. Our work also provides a new impetus to further improve OF-DFT method currently available in the literature.

[1] “Orbital-Free Kinetic-Energy Density Functional Theory,” Y. A. Wang and E. A. Carter, in Theoretical Methods in Condensed Phase Chemistry, edited by S. D. Schwartz (Kluwer, Dordrecht, 2000), p. 117-184.

[2] “Orbital-Corrected Orbital-Free Density Functional Theory,” B. Zhou and Y. A. Wang, J. Chem. Phys. 124, 081107 (2006). (Communication)

[3] “An Accurate Total Energy Density Functional,” B. Zhou and Y. A. Wang, Int. J. Quantum Chem. 107, 2995-3000 (2007).

[4] “Total Energy Evaluation in the Strutinsky Shell Correction Method,” B. Zhou and Y. A. Wang, J. Chem. Phys. 127, 064101 (2007).

[5] “Accelerating the Convergence of the Total Energy Evaluation in Density Functional Theory Calculations,” B. Zhou and Y. A. Wang, J. Chem. Phys. 128, 084101 (2008).
DFT and Force Field Studies of Tryptophan Metabolites and Their Interactions with Beta-Amyloid Peptide
Donald F. Weaver,1 Michael D. Carter1 and Christopher Barden1
1Department of Chemistry, Dalhousie University, Nova Scotia, Canada
Alzheimer's disease is a chronic progressive brain disease characterized by progressive loss of memory and cognitive abilities. Although the cause of Alzheimer's disease remains unelucidated, current evidence suggests that aberrant aggregation of beta-amyloid peptide is a primary cause. Following an in silico screening program, metabolites of tryptophan were identified as agents capable of binding to beta-amyloid peptide and inhibiting this protein misfolding process. Force field and DFT studies have been employed to explicitly model the interaction of various tryptophan metabolites with segments of the beta-amyloid peptide.
Structure of cytochrome P450s and personalized drug
Cheng-Cheng Zhang, Jing-Fang Wang, Jing-Yi Yan, Kuo-Chen Chou, Dong-Qing Wei*
College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
Cytochrome P450s are the most important enzymes responsible for phase I drug metabolism. The polymorphic nature of cytochrome P450s largely influences individual drug responses, drug-drug interactions and induces adverse drug reactions. By far, thirty crystal structures of eight mammalian cytochrome P450s (CYP 2C5, 2C8, 2C9, 3A4, 2D6, 2B4, 2A6 and 1A2) have been published. In this talk, we shall discuss the recent studies on the structures of cytochrome P450s: some characteristic features of these enzymes and many essential, conserved amino acids in the active sites have been identified. These results are of fundamental importance for drug development and understanding the metabolism for both endogenous and xenobiotic substrates. With the help of computational methods, the structural information will provide insights into personalization of drug treatments in both proper drug therapy and appropriate dosage of a certain drug.
Reactions in viscous media: Potential energy surfaces in solvent-solute coordinates
Manjinder Dhaliwal,1 Essex Edwards,1 Liam Huber,1 Michael Basilevsky,2 and Noham Weinberg1
1Department of Chemistry, University of the Fraser Valley, Abbotsford, BC V2S 7M8, Canada

2Photochemistry Center, Russian Academy of Sciences, Moscow 117421, Russia
A novel definition [1] of a solvent coordinate associated with a given reaction is formulated in terms of molecular-dynamic trajectories of the solvent and is applied to discuss the topography of potential energy and free energy surfaces of model isomerization reactions in solvent-solute coordinates. It is shown that the arrangement of the reactant and product valleys on these surfaces can vary from consecutive to parallel, depending on the strength of the solvent-solute interactions, thus switching [2] from Kramers-Grote-Hynes [3] to Agmon-Hopfield [4] regime.

[1] M. Dhaliwal, M.V. Basilevsky, N. Weinberg, J. Chem. Phys. 126, 234505 (2007)
[2] A.M. Berezhkovskii and V.Yu. Zitserman, Chem. Phys. Lett. 158, 369 (1989)
[3] H.A. Kramers, Physica (Amsterdam) 7, 284 (1940); R.F. Grote and J.T. Hynes, J. Chem. Phys. 73, 2715 (1980)
[4] N. Agmon and J.J. Hopfield, J. Chem. Phys. 78, 6947 (1983); 79, 2042 (1983)
Orbital-free effective embedding potential: universality, exact properties, approximations, and its use in numerical simulations.
Tomasz A. Wesolowski, Georgios Fradelos, Jakub A. Kaminski
Dopartment of Physical Chemistry
University of Geneva
30, quai Ernest-Ansermet
1211 GENEVE, Switzerland
We review our recent work concerning several issues related to the orbital-free effective embedding potential introduced originally for embedding a system of non-interacting electrons in a frozen-density environment [1]. This potential has been recently shown [2] to be also exact for embedding interacting electrons at certain conditions. The construction of a new non-empirical approximation to its kinetic-energy-dependent component, which relfects several among its exact properties [3], will be outlined. Applications of the orbital-free effective embedding potential in studies of environment-induced shifts of various observables determined by local features of the electronic structure will be reviewed [4].

[1] Wesolowski & Warshel J. Phys. Chem. 97 (1993) 8050.
[2] Wesolowski, Phys. Rev.A. 77 (2008) 012504.
[3] Kaminski et al. in preparation
[4] Fradelos et al, in preparation
Exactly solvable models of polymers subject to a force
Stu Whittington
Department of Chemistry, University of Toronto
Atomic force microscopy allows individual polymer molecules to be manipulated. For instance, a polymer in a compact phase can be extended or a polymer can be pulled off a surface at which it is adsorbed. We shall discuss several exactly solvable models of polymers subject to a force, including models of these two physical situations. For the case of random copolymers the situation is more complicated and even simple models cannot be solved completely. However, upper and lower bounds can be derived which give information about the nature of the phase diagram in the force-temperature plane.
Status, Challenges and Trends for Fuel Cells Going Forward
David P. Wilkinson1,2
1Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, B.C., Canada V6T 1Z3
2National Research Council, Institute for Fuel Cell Innovation, 4250 Wesbrook Mall, Vancouver, B.C., Canada V6T 1W5
Technical progress as well as investments in fuel cells for transportation, stationary, portable, and micro fuel cell applications have been significant in recent years. The present view is optimistic for fuel cell power generation and the status is presently at the field trial level, or early commercialization stage, moving into volume commercialization. Fuel cells and direct electrochemical fuels (including hydrogen) provide the promise of being one of the long-term solutions to the improvement of energy efficiency, energy sustainability, energy security and the reduction of greenhouse gases and urban pollution. However, fuel cells will need to be competitive on an economic and a performance basis with the established and highly developed internal combustion engine and other forms of power generation. Even though much progress has been made with the fuel cell significant technical challenges still remain today in a number of areas including reliability, durability, cost, operational flexibility, technology simplification and integration, fundamental understanding and life cycle impact. Fundamental understanding, new advanced materials and associated engineering design and modeling will be required to close these technical gaps. This presentation will provide a perspective on fuel cell technology today, research and development directions, and the scientific and engineering challenges the fuel cell community faces.
Protein Flexibility in Molecular Docking
Zunnan Huang and Chung F. Wong
Department of Chemistry and Biochemistry and Center for Nanoscience,
University of Missouri-Saint Louis,
One University Boulevard, St. Louis, Missouri 63121, USA.
Molecular docking is playing an increasingly important role in studying molecular recognition and in computer-aided drug design. Until recently, most previous work focused on assuming protein molecules to be completely rigid molecules. Unfortunately, this approximation does not always work well because many protein molecules are known to adopt different conformations depending on what ligands are bound to them. This talk shall review our recent efforts on developing molecular dynamics-based methods to incorporate protein flexibility in molecular docking. By using protein kinases and phosphatases as examples, we shall demonstrate how our models can improve ligand docking, study the different conformations of a protein that are induced by diverse ligands, and provide insights into docking pathways at the atomic level.
From Potential Energy Surface to Potential 3D Layout
Tao Wu,1 Qi Wang1 and Qunsheng Peng2
1Department of Chemistry, Zhejiang University, China

2State Key Laboratory of CAD&CG, Department of Mathematics,Zhejiang University, China
It is well understood that the potential energy surfaces plays a key role in the modern chemical dynamics. In the study of biopolymer dynamics, because of the complex of the systems, in many cases only one of its 1D simple versions - potential energy landscape or free energy landscape - could be used. Potential 3D layout, which is correspond to functionally important regions and plays key role in recognition, stabilization and adhesion, is missing. There are two challenges: 1.No general way in calculation. 2. Cannot be discerned by simple visual inspection of the dynamics. In this talk, a briefly introduction of the application of potential energy surfaces / potential energy landscape in transport dynamics, and protein adhesion dynamics on nanoscale surface textures is reported. Then, we will introduce the resent development of 3D potential layout in the study of protein stability in long time range.
On the Derivation of the Kohn-Sham Equation
Ping Xiang and Yan Alexander Wang
Department of Chemistry, University of British Columbia, Canada
Two ways of deriving the Kohn-Sham equation are implied in existing literature. However, both are shown to be incorrect since they would lead to a paradox. It is found that some plausible procedures which are common in literature give birth to this paradox. One theorem is proposed to elucidate the error of these procedures. Furthermore, it is shown that the paradox can be resolved by introducing some arbitrary constants in the Kohn-Sham effective potential.
Extending the applicability of B3LYP
Xin Xu, Jianming Wu, Ying Zhang and AnAn Wu
State Key Laboratory of Physical Chemistry of Solid Surfaces; Department of Chemistry, Xiamen University, Xiamen 361005, Fujian, ChinaState Key Laboratory of Physical Chemistry of Solid Surfaces; Center for Theoretical Chemistry, College for Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
Density functional theory (DFT) has become the method of choice for first principles quantum chemical calculations of the electronic structure and properties of many chemical systems. Based on the number of occurrences of functional names in the journal titles and abstracts analyzed from the ISI Web of Science (2007), B3LYP is by far the most popular density functional in chemistry, representing 80% of the total of occurrences of density functionals in the literature, in the period 1990-2006.

Is B3LYP good for everything? How can we go beyond B3LYP?

Our strategies fall into two categories. One is to design a systematic correction scheme on top of B3LYP, such that all B3LYP data, already and continuously built-up in the literature, can be used with higher accuracy and thus higher reliability at no extra cost as compared to B3LYP. The other is to develop new density functional. The new functional should maintain the advantage of B3LYP, while surmount its known difficulties, leading to a general functional with more predictive power.

In this talk, progress along these two lines in our group will be reported
Theoretical study of molecular mean structures at vibrational excited states
using quasi-classical direct ab initio MD
Tomonori Yamada1,2 and Misako Aida1,2
1 Department of Chemistry, Graduate School of Science, Hiroshima University, JAPAN
2 Center for Quantum Life Sciences, JAPAN
The recent progress of computer power has enabled high level ab initio MO calculations, and now searching for a bottom of a potential energy surface is routinely carried out by calculating potential energies and their gradients. Molecular structures in real systems are, however, distributed over all the possible coordinate spaces at certain vibrational states. The molecular conformations measured by experiments are their mean values, and they are different according to the vibrational eigenstates of the molecule. Furthermore, the definitions of the structures depend on the experimental methods [1,2]. Therefore, the theoretical methods are expected to be able to calculate the differently defined structures at vibrationl states including excited states. In this study, we calculate the atomic distances of OH and OD radicals at the ground and excited vibrational states with several definitions and compare the results with experimentally observed values.

For calculating mean structures, we used two methods; (a) quasi-classical direct ab initio molecular dynamics (MD) [3], and (b) quantum mechanical method using Fourier Grid Hamiltonian method (FGH) [4]. The methods (a) and (b) give classical and quantum mechanically averaged structures, respectively. The comparison between the results of classical and quantum mechanical methods are of interest. In this study, we show there is no difference between the mean structures obtained from these two methods, if the proper condition is applied to the classical method.

In addition, we show the calculated re, r0, rz , and rg structures of H2O using quasi-classical direct ab initio MD. The computational results agree well with the experimentally observed structures.

Reference
[1] T. Oka, J. Phys. Soc. Jpn., 15, 2274 (1960).
[2] K. Kuchitsu, K. Oyanagi, Faraday Discuss. Chem. Soc., 62, 20 (1977)
[3] T. Yamada, M. Aida, Chem. Phys. Lett., 752, 315 (2008).
[4] C.C. Marston, G.G. Balint-Kurti, J. Chem. Phys., 91, 3571 (1989).
Quantum Dynamics of Dissipative Systems
YiJing Yan
Department of Chemistry, Hong Kong University of Science and Technology, Kowloon, Hong Kong
Quantum dissipation theory (QDT) deals with the dynamics of a quantum system in contact with quantum bath surroundings. It is well known that the Feynman-Vernon influence functionals path integral formalism is exact for arbitrary strength of dissipation and memory effects of Gaussian fluctuating surroundings on the system. However, path integral formalism is generally quite inconvenient in both implementation and application, compared with its differential counterpart.

In this work, I will present a differential equivalent form of exact QDT, denoted as hierarchical equations of motion (HEOM) formalism [1,2], for boson versus fermion bath, and canonical versus grand canonical bath ensemble coupling cases. The theory admits also an arbitrary time-dependent external field driving. Two systems will be used to elaborate the HEOM formalism.

In an electron transfer (ET) system, the fluctuating surroundings serve as a canonical boson-bath ensemble, responsible for the system decoherence and energy relaxation. I will discuss the quantum versus classical solvation and related issues, based on the analytical results of HEOM for ET rates in Debye solvents [3].

In a quantum transport setup, a molecule or quantum dot is placed in contact with electrodes under applied bias voltage and/or gate voltage. Each electrode serves as a grand canonical fermion-reservoir bath at a given temperature and under the external applied chemical potential. The bath reservoir now is responsible not only for decoherence and energy relaxation, but also for the fermion particles ( i.e., electrons) transport in/out of the system. The HEOM-based quantum transport theory will be summarized [2], together with the calculated transient currents through a quantum dot system in response to various forms of external time-dependent applied voltage [4].

Support from Research Grants Council of Hong Kong Government is acknowledged.

[1] R. X. Xu, P. Cui, X. Q. Li, Y. Mo, Y. J. Yan, 122, 041103 (2005); R. X. Xu and Y. J. Yan, Phys. Rev. E, 75, 031107 (2007); J. S. Jin, S. Welack, J. Y. Luo, X. Q. Li, P. Cui, R. X. Xu, and Y. J. Yan, J. Chem. Phys. 126, 134113 (2007).
[2] J. S. Jin, X. Zheng, and Y. J. Yan, J. Chem. Phys. 128, 234703 (2008).
[3] P. Han, R. X. Xu, B. Q. Li, J. Xu, P. Cui, Y. Mo, and Y. J. Yan, J. Phys. Chem. B, 110, 11438 (2006); R. X. Xu, Y. Chen, P. Cui, H. W. Ke, and Y. J. Yan, J. Phys. Chem. A, 111, 9618 (2007).
[4] X. Zheng, J. S. Jin, and Y. J. Yan, submitted to Phys. Rev. B (2008).
Insights into Current Limitations of Density Functional Theory
Paula Mori-Sanchez, Aron J. Cohen, and Weitao Yang
Department of Chemistry, Duke University
Durham, NC 27708, USA
Density functional theory of electronic structure is widely and successfully applied in simulations throughout engineering and sciences. However, there are spectacular failures for many predicted properties, which can be traced to the delocalization error and static correlation error of commonly used approximations. These errors can be characterized and understood through the perspective of fractional charges and fractional spins introduced recently. Reducing these errors will open new frontiers for applications of density functional theory.

References

P. Mori-Sanchez, A. J. Cohen, and W. T. Yang, “Self-interaction-free exchange-correlation functional for thermochemistry and kinetics,” Journal of Chemical Physics, vol. 124, p. 091102, 2006.

P. Mori-Sanchez, A. J. Cohen, and W. T. Yang, “Many-electron self-interaction error in approximate density functionals,” Journal of Chemical Physics, vol. 125, p. 201102, 2006.

A. J. Cohen,P. Mori-Sanchez, , and W. T. Yang, “Development of exchange-correlation functionals with minimal many-electron self-interaction error,” Journal of Chemical Physics, vol. 126, p.191109, 2007.

A. J. Cohen, P. Mori-Sanchez, and W. T. Yang, “Fractional charge perspective on the band-gap in density-functional theory,” Physical Review B, vol. 77, p. 115123, 2008.

P. Mori-Sanchez, A. J. Cohen, and W. T. Yang, “Localization and delocalization errors in density functional theory and implications for band-gap prediction,” Physical Review Letters, vol. 100, p. 146401, 2008

A. J. Cohen, P. Mori-Sanchez, W. T. Yang, “Fractional spins and static correlation error in density functional theory”, Http://arXiv.org/abs/0805.1724.

Reaction Resonances in the F+H2 Reaction
Dong Hui Zhang and Xueming Yang*

State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
Reaction resonance is a frontier topic in chemical dynamics research, and it is also essential to the understanding of mechanisms of elementary chemical reactions. In this presentation, we will describe a recent combined experimental and theoretical study on the benchmark F+H2 reaction. Experimental evidence of reaction resonances has been detected in a full quantum state resolved reactive scattering study of the F+H2 reaction. Highly accurate full quantum scattering theoretical modeling shows that the reaction resonance is caused by two reaction resonance states. Further studies show that quantum interference is present between the two reaction resonance states for the forward scattering product. This study is a significant step forward in our understanding of chemical reaction resonances in the benchmark F+H2 system. Further experimental studies on the effect of H2 rotational excitation on dynamical resonances were carried out. Dynamical resonances on the F+H2(j=1) reaction have also been observed. A more recent study on the F+HD system has also been carried out. The isotope substitution actually provides an extremely sensitive probe to the reaction resonance potential surface in this important system.

Revelation of Large Cavity in Liquid Water in terms of(H2O)-7P ABEEM/MM Model
Dong-Xia Zhao, Ping Qian, and Zhong-Zhi Yang*
Chemistry and Chemical Engineering Faculty
Liaoning Normal University
Dalian, 116029
China
zzyang@lnnu.edu.cn
Cavity size distribution for liquid water has been explored in terms of molecular dynamics simulations based on the newly developed flexible-body and charge-fluctuating (H2O)-7P ABEEM/MM potential model. The molecular dynamics simulations were carried out at some temperatures. It is found that the cavity size distribution in liquid water shows large cavities and oscillating phenomenon. The large cavities remarkably occupy the most of the total void volume of the liquid, though the number of large cavities is a little percent of the total cavity number. By using a topological expression, a cavity can be expressed by a hydrogen bond network formed by a number of water molecules which surround the cavity, and the largest cavity has 36 surrounding water molecules. This kind of hydrogen bond network provides a basic approach to represent a cavity in liquid water. In order to gain the further insight into the effect of hydrogen bonds around the large cavity, the structural parameters and ABEEM charge distributions of water molecules of the whole water liquid have been calculated and compared with those of the cage around the large cavity. The implications of such findings have been analyzed and discussed in detail.

Reference
1.Yang, Z. Z.; Wu, Y.; Zhao, D. X. J. Chem. Phys. 2004, 120, 2541.
2.Wu, Y.; Yang, Z. Z. J. Phys. Chem. A 2004, 108, 7563.
3.Yang, Z. Z.; Li, X. J. Phys. Chem. A (Letters) 2005, 109, 3517.
4.Yang, Z. Z.; Li, X. J. Chem. Phys. 2005, 123, 094507.
5.Yang, Z. Z.; Zhang, Q. J. Comput. Chem. 2006, 27, 1.
6.Yang, Z. Z.; Qian, P. J. Chem. Phys. 2006, 125, 064311.

Acknowledgments
The authors greatly thank Professor Jay William Ponder for providing the Tinker program. This research has been aided by the grants from the National Natural Science Foundation of China (No. 20633050 and No. 20403007).
Pt-doped Single-Walled Carbon Nanotubes
Charles See Yeung, Lei Vincent Liu and Yan Alexander Wang
Department of Chemistry, University of British Columbia, Canada
Transition metal-doped single-walled carbon nanotubes (SWCNTs) have been studied within density functional theory. In particular, sidewall substitution of a C atom with a Pt atom results in a notable change in geometric and electronic properties. Pt-doped SWCNTs display enhanced ability to interact with small gas molecules in comparison to their undoped analogs and results in an exothermic adsorption process. The affinity of the interaction was observed to be dependent on molecular orientation. By analysis of the resulting nanotube–adsorbate complexes, we found that the presence of gases has a strong influence on the electronic structure of these macromolecules and hence suggests possible applications of this material in nanoelectronics and nanosensory technologies. The extended C framework surrounding the Pt atom can also be considered a supramolecular ligand in analogy to classical alkylplatinum(IV) complexes and may have important implications in the development of nanoscale catalysts.
Quantum Mechanical Simulations of Ribozyme Catalysis
Darrin M. York1
1Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
An area of intense experimental and theoretical research effort has been concentrated on elucidating how RNA molecules are able to catalyze complex biochemical reactions that rival the efficiency of many protein enzymes. A detailed understanding of the underlying mechanisms of these RNA enzymes, or ribozymes, provides insight into the inner workings of more complex cellular catalytic RNA machinery such as the ribosome. Ultimately, these insights may aid the rational design of new medical therapies that target viral, neurological and genetic disease, as well as the development of new bio/nanotechnology. Despite tremendous efforts from both experimental and theoretical research communities, many details about ribozyme mechanisms have remained elusive. In this talk, results of linear-scaling electronic structure and generalized macromolecular solvent boundary methods are applied with molecular simulations using new quantum mechanical models to study the mechanisms of phosphoryl transfer reactions in solution and in prototype ribozyme systems such as the hammerhead and hairpin ribozymes. These multi-scale models are able to simultaneously span large spatial domains and long time scales that are required to provide insight into the structure and dynamics leading to RNA catalysis. The results are compared with crystallographic data, kinetic measurements, thio and kinetic isotope effects and other biochemical data.
Molecular Dynamics Simulations of RNA
Darrin M. York1
1Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
Simulations of RNA present special challenges involving large conformational variations, long-range electrostatic forces and strong interactions with monovalent and divalent ions. In the case of certain RNA enzymes, this situation is further complicated by reactive chemical steps that are coupled with binding-induced conformational rearrangements to arrive at a catalytically pre-reactive conformation. The study of the mechanism thus involves both conformational and chemical steps that are highly coupled, and require long-time simulations to obtain a complete picture of the structure and dynamics and to extract meaningful thermodynamic and kinetic information. In order to make such calculations feasible, we have developed new linear-scaling Ewald and fast-multipole algorithms and generalized macromolecular solvent boundary methods based on a variational electrostatic projection technique that can be applied with either classical molecular simulation force fields or combined quantum mechanical/molecular mechanical methods. These methods are applied to study the conformational and chemical steps of the minimal sequence and full length hammerhead ribozyme, and the L1 ligase riboswitch.
Search for low leakage molecular diodes: nanoscale structural and electrical characterization of Au/alkyl monolayer/Si junctions
Hua-Zhong Yu
Department of Chemistry and 4D Labs, Simon Fraser University,
Burnaby, BC V5A 1S6, Canada; e-mail: hogan_yu@sfu.ca
With the ever-increasing demand for miniaturization of electronic devices, much focus has recently been devoted to the molecular modification of traditional semiconductor materials. Covalently-bonded, organic monolayers on silicon can be readily prepared from the photochemical reactions of hydrogen-terminated silicon with 1-alkenes; we have initially worked on understanding the formation and reactivity of -functionalized monolayers. We then explored both electrochemical and solid-state measurements as sensitive tools for the examination of their electrical properties. In particular, we have developed a protocol of using mercury drops as the top electrodes for the construction and testing of metal-molecule-semiconductor diode junctions, which relies on the fact that the high surface tension of the mercury inhibits metal film interaction and disruption of the monolayer. Both current-voltage and capacitance-voltage measurements have shown that n-alkyl monolayer-modified diode junctions possess higher effective barrier heights, lower ideality factors (i.e., close to unity), and better reproducibility than that of native oxide thin films.

For electronic devices to attain widespread practical application, a robust and practical method of making electrical contacts to the organic monolayers must be found. The most popular option is to use vacuum deposition to create a metal (e.g., Au) pad on the surface. We have obtained spectroscopic evidence that the molecular layers remain after such metal evaporation, although structural disruption was detected. The next task is to evaluate the effect of chain length and choice of end groups on the electrical performance of the metal-molecule-silicon junctions prepared with thermally-deposited Au contacts.
Developing efficient computational protocol for accurate electrostatic interaction in MD simulation of proteins
Chang G. Gi1, Ye Mei1, John Z.H. Zhang2
1Institute of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Nanjing University

2Department of Chemistry, New York University
Correct description of electrostatic interaction in proteins requires the proper treatment of electronic polarization of protein, which is quantum mechanical in nature and missing in the widely used molecular mechanics force fields. Here we show that a fragment-based quantum chemistry approach combined with continuum solvent model enables us to properly describe protein solvation and polarization and to derive polarized protein-specific charges for MD simulation of proteins. Extensive molecular dynamics simulations based on the new polarized protein-specific charges demonstrate that electronic polarization plays a critical role in stabilizing the structure and dynamics of proteins. We believe that the polarized protein-specific charges derived from first principle calculation will be of general and practical usage in theoretical and experimental study of protein structure and function.
Born-Oppenheimer Ab initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions
Yingkai Zhang
Department of Chemistry, New York University, New York, NY 10003
To simulate enzyme reactions, extensive sampling on a reasonably accurate potential energy surface is needed to obtain reliable results. We are pushing the envelope of on-the-fly Born-Oppenheimer MD simulations with ab initio QM/MM methods and umbrella sampling to determine free energy profiles of chemical reactions in complex systems. At each time step, the atomic forces as well as the total energy of the QM/MM system are calculated with the pseudobond ab initio QM/MM approach on-the-fly, and Newton equations of motion are integrated. This on-the-fly ab initio QM/MM MD approach, which takes account of dynamics of reaction active site and its environment on an equal footing, has been recently demonstrated to be feasible and successful in elucidating the catalytic power of SET7/9, understanding methylation state specificity of histone lysine methylation, and characterizing the Sir2 catalyzed nicotinamide cleavage reaction.
Perturbative Total Energy Evaluation in SCF Iterations---Tests on Molecular Systems
Yu Adam Zhang and Yan Alexander Wang
Department of Chemistry, University of British Columbia
The corrected Hohenberg-Kohn-Sham (cHKS) and corrected Harris (cHarris) total energy functionals we proposed before [J Chem Phys 2008, 128, 084101] have been extended to Hartree-Fock theory. Two common and one difficult molecular case studies with these functionals show that they are generally very useful in accelerating the SCF convergence.
Molecular Face
Dong-Xia Zhao and Zhong-Zhi Yang
College of Chemistry and Chemical Engineering, Liaoning Normal University
The spatial knowledge is the first one of all information about an object. Molecular shape and size, molecular van der Waals surface and/or solvent-accessible surface etc. have been widely studied and applied. This paper is to show that a molecular face (MF) for a molecule may be defined uniquely and intrinsically via the molecular intrinsic characteristic contours (MICC) with coding the molecular electron density (ED) as the fourth-dimension. The significant feature of an MF provides both molecular spatial appearance and its frontier electron density, being an intuitive picture as a molecular fingerprint or face. With simple examples, the physical significance for a MF is then demonstrated.

Reference

1.Z. Z. Yang, E. R. Davidson, Int. J. Quantum Chem. 62, 47 (1996).
2.D. X. Zhao, L. D. Gong, Z. Z. Yang, J. Phys. Chem. A, 109, 10121 (2005); Z. Z. Yang, D. X. Zhao, Y. Wu, J. Chem. Phys. 121, 3452 (2004); D. X. Zhao, Z. Z. Yang, J. Mol. Struct.: THEOCHEM, 579, 73 (2002)
3.Z. Z. Yang and D. X. Zhao, Chem. Phys. Lett. 292, 387 (1998); D. X. Zhao, Z. Z. Yang, Sci. China, Ser. B: Chem. 42, 391 (1999).
4.Z. Z. Yang, L. D. Gong, D. X. Zhao, M. B. Zhang, J. Comput. Chem. 26, 35 (2005); L. D. Gong, D. X. Zhao, Z. Z. Yang, J. Mol. Struct.: THEOCHEM 636, 57(2003).


Acknowledgement
This research is supported by the National Science Foundation of China (Grants No. 20403007, No. 20633050). The authors are very grateful to Prof. E. R. Davidson for his providing the MELD program and other kind helps.
Dynamic Coulomb blockade in single-lead quantum dots
Xiao Zheng, Jingshuang Jin and Yijing Yan*
Department of Chemistry, Hong Kong University of Science and Technology, Hong Kong
We investigate the transient dynamic response of an Anderson impurity quantum dot to a family of ramp-up driving voltage applied to the single coupling lead. Transient current is calculated based on a hierarchical equations of motion formalism for open dissipative systems [1, 2]. We have found that (a) in the adiabatic charging limit, the quasi-steady dynamics provide only partial information on the quantum dot energetic configuration; (b) With an appropriately chosen switch-on duration, all transitions among dot Fock states can be resolved distinctly through the resonance peaks of transient current in real time, and hence provide comprehensive information on the quantum dot energetic configuration; (c) In the instantaneous switch-on limit, the frequency-dependent response current spectrum reveals sensitively and faithfully the dot energetic configuration through the characteristic resonance signatures. This work thus highlights the significance and versatility of transient dynamics calculations.

[1] J. S. Jin, S. Welack, J. Y. Luo, X. Q. Li, P. Cui, R. X. Xu, and Y. J. Yan, J. Chem. Phys. 126, 134113 (2007).
[2] J. S. Jin, X. Zheng, and Y. J. Yan, J. Chem. Phys. 128, 234703 (2008).
Various quantum mechanical effects built into molecular
dynamics simulation with non-Born-Oppenheimer trajectory
Chaoyuan Zhu
Institute of Molecular Science, Department of Applied Chemistry, and Center for Interdisciplinary Molecular Science, National Chiao-Tung University, Hsinchu 300, Taiwan.
Molecular dynamics simulations typically treat nuclei as moving classically on a single adiabatic potential energy surface, and these simulation methods are not directly generalizable to non-Born-Oppenheimer molecular dynamical processes due to the inherently quantum mechanical nature of electronic transitions in systems. Semiclassical methods are unitized to build quantum mechanical effects into classical trajectories as non-Born-Oppenheimer trajectories. There are generally two kind of treatments in which quantum mechanical effects are dealt with by analytical theory and numerical formulation. Both ways are generally faced on two new problems; (1) how to treat non-Born-Oppenheimer trajectory that moves on multiple electronically potential energy surfaces and (2) how to simulate electronically nonadiabatic transition probability from one surface to another. Quantum mechanical effects including nonadiabatic transition, nonadiabatic tunneling, nonadiabatic coherence, and decoherence are analytically and/or numerically implemented into classical trajectories, namely non-Born-Oppenheimer trajectories that can be successfully incorporated with various mixed quantum-classical methods for modeling non-Born-Oppenheimer molecular dynamics.
The Application of Magnetically Perturbed Time-Dependent Density Functional Theory to Magnetic Circular Dichroism
T.Ziegler, M.Seth, M.Krykunov
Department of Chemistry, University of Calgary, Alberta Canada T2N 1N4
We introduce in the first part of the talk the perturbation of a constant magnetic field into time-dependent density functional theory (TDDFT) to obtain first order magnetic corrections to transition densities and excitation theory. The magnetically perturbed time-dependent density functional theory (MP-TDDFT) is used next to describe magnetic circular dicroism (MCD) that is induced into a molecule when light propagate in the direction of a constant magnetic field. We apply finally our MCD theory to main-group molecules, transition metal complexes and biological systems. Comments will also be given about the complications added to TD-DFT when dealing with open shell transition metal complexes.

References:
(a)M.Seth, T. Ziegler, A. Banerjee, J. Autschbach, S.J.A van Gisbergen, E.J. Baerends, J. Chem. Phys. 120, 10942-10954 (2004).
(b) M. Seth, M., J.Autschbach, T.Ziegler, J. Chem. Phys., 122, 094112-1-094112-7 (2005).
(c) M.Seth, T.Ziegler, J. Chem. Phys. 124, 144105-1-144105-12 (2006).
(d) M.Seth, A. Autschbach, T.Ziegler, J. Chem. Theory and Comput. 3, 434-447, (2007).
(e) M.Seth, T.Ziegler J. Chem. Phys. 127, 134108 (2007).
(f) M.Krykunov, M.Seth,T.Ziegler,J.Autschbach J. Chem. Phys. 127, 244102 (2007)
A revised electronic Hessian for approximate time-dependent density functional theory.
Tom Ziegler , Michael Seth, Mykhaylo Krykunov and Jochen Autschbach
Department of Chemistry, University of Calgary,University Drive 2500, Calgary, AB T2N-1N4, Canada

Time-dependent density functional theory (TD-DFT) at the generalized gradient (GGA) level of theory has revealed systematic errors in calculated excitation energies.This is especially the case for electron transitions between two separated regions of space or between orbitals of different spatial extend. It is suggested that these limitations can be attributed to the ground state Hessian . Thus for approximate DFT the Hessian G(DFT) can be used to describe changes in energy due to small (perturbations) of the electron density but not one-electron excitations involving the rearrangement of a full electron charge. This is in contrast to Hartree-Fock theory where G(HF) has a trust-region that is accurate for both small perturbations and one-electron excitations. The difference in the behavior of G(DFT) and G(HF) can be traced back to the fact that Coulomb and exchange terms that cancel in HF-theory not necessary do so in approximate DFT. Thus, the deficiency of for the calculation of excitation energies is likely to persist for all approximate DFT theories that suffer from self-interaction errors. It is however shown that one can derive a new matrix G(R-DFT) in which the self-interaction errors are taken properly into account by a revision of the diagonal elements in G(DFT). Further, the matrix G(R-DFT) is accurate for the same trust-region as G(HF) . With TD-DFT based on G(R-DFT) , energies for state-to-state transitions represented by a one-electron excitation (i--> a ) are approximately calculated as ΔE(ai)=E(ai) -E(o) . Here ΔE(ai) is the energy difference between the ground state Kohn-Sham Slater determinant E(o) and the energy E(ai) of a Kohn-Sham Slater determinant where i has been replaced by a . A discussion is finally given on the relation between TD-DFT based on G(R-DFT) and variational DFT- approaches (ΔSCF-DFT) to the calculation of excitation energies.
A new mathematical approach for the treatment of the vibrational isotope effect
Tomislav P. Živković
Institute Rudjer Bošković, Bijenička cesta 54, Zagreb, Croatia
Vibrational isotope effect can be efficiently treated within the formalism of the Low Rank Perturbation (LRP) method. In LRP this effect is treated within the harmonic approximation and under standard assumption that force field does not change upon isotopic substitutions. Within those approximations LRP is exact.
Consider a pair of two n-atom isotopic molecules A and B which are identical except for isotopic substitutions at r atoms. LRP replaces standard treatment of vibrational isotope effect which involves the solution of the 3nX3n matrix eigenvalue equation with a solution of a 3rX3r matrix equation. Since r is usually less than n, this results in the improved computational efficiency. LRP also provides a new conceptual insight into the regularities of the vibrational isotope effect. One finds that vibrational frequencies ωk and normal modes Ψk of the isotopomere B depend mainly on local properties involving region subject to the isotopic substitutions. The only global properties needed to obtain frequencies and normal modes of the isotopomer B are frequencies νi of the parent molecule A. Vibrational isotope effect does not depend on any fine details outside the region subject to the isotopic substitutions (such as force field constants, detailed geomettry, atomic masses, etc.).
Suggested method is illustrated by LRP treatment of out-of-plane vibrations of several planar molecules and their (H,D)-isotopomers. In particular, one finds that LRP frequencies agree with available experimental out-of-plane vibrational frequencies of benzene (H,D)-isotopomers better than reported DFT frequencies improves with scaling technique.
The Electric Field Gradient as a Probe of Electron Correlation and Orbital Ordering
J. W. Zwanziger
Department of Chemistry and Institute for Research in Materials, Dalhousie University, Halifax, NS B3H 4J3 Canada
Transition metal oxides such as CuO, Cu2O, LaTiO3 and YTiO3 show a variety of interesting phenomena such as antiferromagnetism and Mott-Hubbard metal-insulator transitions associated with strong electron correlations at the transition metal sites. Density functional theory within the local density approximation typically fails to reproduce these effects, but can be satisfactorily corrected using a Hubbard U term in the Hamiltonian, leading to the so-called LDA+U method. On the experimental side, the electric field gradient, observable by nuclear magnetic resonance or nuclear quadrupole resonance, is quite sensitive to these effects. We show how calculation of the electric field gradient together with LDA+U is implemented in a modern open-source DFT code, using the projector-augmented wave formalism, and then give examples of the above systems including comparison with experiment at both ambient and elevated pressures.
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