# <span class=strong>Reception and Poster Session</span><br/><br/><br><b>Poster submissions welcome from all participants</b>

Monday, January 12, 2009 - 5:40pm - 7:00pm

Lind 400

**Improved united-atom models for perfluorinated**

self-assembled monolayers

Saulo Vázquez (University of Santiago de Compostela)

Several united-atom (UA) force fields for perfluorinated self-assembled monolayer (FSAM) surfaces are proposed. These UA models of FSAM are based on a preceding force field, and the modifications done in this work involved the type of potential function and parameters used to represent the nonbonded interactions among the united atoms of the FSAM chains, which have been shown to play a key role in the energy transfer that takes place in collisions of gases with self-assembled monolayers.**Coherent and optimal control of adiabatic motion of ions**

in a trap

Dmitri Babikov (Marquette University)

Vibrational motion of ions in a linear trap can be efficiently controlled by creating small anharmonicity of the trapping potential and using optimally shaped MHz pulses to induce the desired states-to-state transitions. In this work the motional quantum states of ions in an anharmonic trap were calculated numerically using expansion over the basis set of Hermit polynomials. The Optimal Control Theory is employed in order to optimize shaped pulses for the major quantum gates, such as NOT, CNOT, Pi-rotation and the Hadamard transform.**Memory, hysteresis and oscillation induced by multiple**

covalent modifications and its

application to circadian rhythm of Cyanobacteria

Isamu Ohnishi (Hiroshima University)

No transcription-translation feedback system of circadian clock by

KaiC protein's

phosphorylation is very interesting and also significant as a kind of

core cycle of the

circadian rhythm in Cyanobacteria. In order to understand the

oscillation phenomena,

we pay attention to a function of memory in a cell level. A standard

structure of such a

binary digit of memory is presented by use of multiple covalent

modifications in this

presentation. A key idea is bistability of covalent modification

states which creates

hysterecally and digitally switching mechanism between them. By use of

this kind of

memory, we see the circadian oscillation be realized. In fact, by deterministic

simulations as well as by stochastic simulation, it is shown that the

system obtains

stable circadian oscillations, and shown that multiplicity of

modification sites reinforces

the stability of memory in several senses. Moreover, it is reported

that this model

explains well several molecular biologically experimental facts about

period's change by

use of mutants of Kai proteins in the circadian rhythm of Cyanobacteria.**A self-consistent, polarizable, electron-water potential for use in hydrated-electron simulations**

Leif Jacobson (The Ohio State University)

Previously Turi and Borgis have parameterized an electron-water interaction potential in the static exchange approximation to yield a one-electron pseudopotential that has been applied to the study of anionic water clusters and the bulk hydrated electron. This potential has been used solely in conjunction with the Simple Point Charge (SPC) water model which is known to yield poor results for neutral water clusters. We re-parameterize the pseudopotential to be used with the polarizable AMOEBA water model to yield a potential in which the one-electron density polarizes the water molecules and vice versa in a fully self-consistent manner. The resulting model Hamiltonian is considerably more accurate for reproducing vertical electron binding energies (VEBEs), cluster geometries, and relative isomer energies when compared to ab initio results. The role of self-consistent polarization is particularly pronounced in clusters where the excess electron is bound in the interior of the cluster.**Infrared spectroscopy and dynamics of the Zundel cation**

Oriol Vendrell-Romagosa (Ruprecht-Karls-Universität Heidelberg)

Results are presented on the dynamics and IR spectroscopy of the Zundel

(H5O2+) cation. The full-dimensional (15D) quantum simulations are

performed with the multiconfiguration time-dependent Hartree (MCTDH)

method.

We investigate the IR spectroscopy of H5O2+ and various of its

isotopomers, namely D5O2+, HD4O2+ and DH4O2+ isotopomers, and provide a

comparison to recent experiments on these systems. Dramatic changes in the

dynamics and spectroscopy of the clusters are observed upon isotopic

substitution.

Accurate measurements of IR spectra of protonated water clusters prepared

in the gas phase has become possible in recent years. The aim of our

theoretical studies is to sheed light on interpretation of these complex

spectra, provide useful physical insight in the dynamics of the hydrated

proton, and last but not least, to advance in the description of complex

molecular systems and clusters by full quantum methods.**A model for the photo-orientation of a molecular sample irradiated with**

polarized light

Maurizio Persico

Molecules irradiated by polarized light have a maximum excitation

probability when their transition dipole vector is parallel to the light

polarization. An excited molecule, because of its internal motions and

of the interactions with the chemical environment, will change its

orientation. As a consequence, a molecular sample gets oriented when

irradiated, but the spontaneous rotational diffusion tends to restore the

isotropic conditions. We have set up a stochastic model to represent

the photo-induced anisotropy and its development in time. The

calculation uses as input the results of single chromophore surface

hopping simulations. The method is tested on azobenzene and shows the

interplay of photo-orientation, rotational diffusion, and

photoisomerization.**Solvation dynamics in supercritical fluoroform**

Francesca Ingrosso (Université de Nancy I (Henri Poincaré))

We present a molecular dynamics simulation study of solvation and collective polarizability dynamics supercritical fluoroform at a series of densities at constant temperature, slightly above the critical temperature, T_c. Our solvation dynamics studies were designed to represent the time-dependent frourescence Stokes shift for the chromophore coumarin 153. The equilibrium and nonequilibrium solvation responses were calculated. We found strong density dependence of solvation time correlations, with slower decay at lower densities and more pronounced for the excited-state than for the ground-state response. As for the nonequilibrium response, we showed that the inclusion of the interaction between the solute charge density and solvent induced dipoles improves the agreement with available experimental data. Preliminary results of an investigation of collective polarizability anisotropy relaxation in pure supercritical fluoroform are also presented. We focus on the nuclear response observable in optical Kerr effect and show that the results at higher densities are sensitive to the model used for the interaction-induced polarizability.**Mechanistic simulation of the autocatalytic isopeptide bond**

formation in pili with QM/MM minimum free energy path method

Xiangqian Hu (Duke University)

We studied the detailed reaction mechanism of autocatalytic intramolecular isopeptide bond formations in pili of Gram-negative bacteria with the recently developed QM/MM minimum free-energy path (QM/MM-MFEP) method. The scrutinized reaction mechanism consists of at least three steps in which proton transfers occur prior to and after the formation of the intramolecular isopeptide bond. Preliminary results revealed crucial roles of an active-site Glu residue in both the proton transfer reactions and the formation of the intramolecular isopeptide bond. Our results will provide important information for identifying and designing new vaccine candidates that can be applied to the bacterial

pilus.**Analysis of structured populations in aquaculture**

József Farkas (University of Stirling)

Farmed and wild salmonid fish are subject to parasitism from a number of

copepod parasites of the family Caligidae. These sea lice are damaging,

causing reduced growth and appetite, wounding and susceptability to

secondary infections. Economic losses due to this type of parasites are

high, with a value in excess of US $100 million globally. The life history

of the parasite involves a succession of ten distinct developmental stages

from egg to adult. In the present talk I will focus on the mathematical

analysis of a nonlinear partial differential equation model with

distributed states-at-birth, which type of model is intended to desribe

the dynamics at the first chalimus stage of the parasite.**Born-Oppenheimer corrections near a Renner-Teller intersection**

Mark Herman (University of Minnesota, Twin Cities)

We perform a rigorous mathematical analysis of the bending modes of

a linear triatomic molecule that exhibits the Renner-Teller effect.

Assuming the potentials are smooth, we prove that the wave functions

and energy levels have asymptotic expansions in powers of epsilon,

where the fourth power of epsilon is the ratio of an electron mass to the mass of a

nucleus. To prove the validity of the expansion, we must prove

various properties of the leading order equations and their

solutions. The leading order eigenvalue problem is analyzed in

terms of a parameter b, which is equivalent to the parameter

originally used by Renner. Perturbation theory and finite

difference calculations suggest that there is a crossing involving the ground bending vibrational

state near b=0.925. The crossing involves two states with

different degeneracy.**Quantum transition state theory applied to collinear reactions**

Arseni Goussev (University of Bristol)Roman Schubert (University of Bristol)

We apply a recently developed quantum version of Transition State Theory based on Quantum Normal Forms (QNF) to simple collinear reactions. We find that the normal form converges quickly for molecules which are not too light.**Many-body theory of surface-enhanced Raman scattering**

David Masiello (Northwestern University)

Joint work with George C. Schatz.

A many-body Green's function approach to the microscopic theory

of surface-enhanced Raman

scattering is presented. Interaction ects between a general

molecular system and a spatially

anisotropic metal particle supporting plasmon excitations in

the presence of an external radiation

field are systematically included through many-body

perturbation theory. Reduction of the

exact ects of molecular-electronic correlation to the level of

Hartree-Fock mean-field theory is

made for practical initial implementation, while description of

collective oscillations of conduction

electrons in the metal is reduced to that of a classical plasma

density; extension of the former to

a Kohn-Sham density-functional or second-order Møller-Plesset

perturbation theory is discussed;

further specialization of the latter to the random-phase

approximation allows for several salient

features of the formalism to be highlighted without need for

numerical computation. Scattering and

linear-response properties of the coupled system subjected to

an external perturbing electric field

in the electric-dipole interaction approximation are

investigated. Both damping and finite-lifetime

ects of molecular-electronic excitations as well as the

characteristic fourth-power enhancement

of the molecular Raman scattering intensity are elucidated from

first principles. It is demonstrated

that the presented theory reduces to previous models of

surface-enhanced Raman scattering and

leads naturally to a semiclassical picture of the response of a

quantum-mechanical molecular system

interacting with a spatially anisotropic classical metal

particle with electronic polarization

approximated by a discretized collection of electric dipoles.**A quantum chemist’s view of molecular conduction via**

the reduced density matrix

Joseph Subotnik (Tel Aviv University)

We present a very simple model for numerically describing the steady state dynamics of a system interacting with continua of states representing a bath. Our model can be applied to equilibrium and non-equilibrium problems. For a one-state system coupled to two free electron reservoirs, our results match the Landauer formula for current traveling through a molecule. More significantly, we can also predict the non- equilibrium steady state population on a molecule between two out-of-equilibrium contacts. While the method presented here is for one-electron Hamiltonians, we outline how this model may be extended to include electron-electron interactions and correlations, an approach which suggests a connection between the conduction problem and the electronic structure problem.**Calculating solution redox free energies with Ab initio QM/MM**

minimum free energy path method

Xiancheng Zeng (Duke University)

A quantum mechanical/molecularmechanical minimum free energy path

(QM/MM-MFEP) method was developed to calculate the redox free energies

of large systems in solution with greatly enhanced efficiency for

conformation sampling. The QM/MM-MFEP method describes the

thermodynamics of a system on the potential of mean force (PMF)

surface of the solute degrees of freedom. The MD sampling is only

carried out with the QM subsystem fixed. It thus avoids on-the-fly

QM calculations and overcomes the high computational cost of the

direct ab initio QM/MM molecular dynamics (MD) needed for sampling.

The enhanced efficiency and uncompromised accuracy of this approach

are especially significant for biochemical systems. The QM/MM-MFEP

method thus provides an efficient approach to free energy simulation

of complex electron transfer reactions.**Non–adiabatic scattering wave functions in a simple**

Born–Oppenheimer model

George Hagedorn (VPI and SU)

No Abstract**Symmetry-broken independent-particle models in Born-Oppenheimer**

molecular dynamics of chemical bond dissociation

Igor Schweigert (Naval Research Laboratory)

Joint work with Brett I. Dunlap.

Simulating chemical bond dissociation dynamics requires

electronic

structure methods to seamlessly describe the transition

from the initial closed-shell configuration to an open-shell

intermediate.

Direct-dynamic simulations of the RO-NO2 bond dissociation

in nitric

esters are presented to demonstrate the importance of using

unrestricted single-determinant methods and

spin-symmetry-broken orbitals. Challenges in locating the symmetry-broken

electronic potential energy surface in the course of a reactive

trajectory are discussed. The second derivative of the unrestricted energy

with respect to nuclear displacement is shown to be

discontinuous at the onset of symmetry breaking, in analogy with the

discontinuous specific heat in the Landau theory of second-order phase

transitions.**Tunneling dynamics in a double well within the approximate**

quantum trajectories framework

Sophya Garashchuk (University of South Carolina)

Quantum-mechanical (QM) effects in molecular dynamics –

zero-point energy, tunneling and nonadiabatic dynamics –

are

essential for accurate description and understanding of

reactions in complex molecular systems.

Since the exact solution of the Schrödinger equation for such

systems in full dimension is neither feasible nor necessary,

the trajectory-based approaches have special appeal: classical

description is often appropriate for dynamics of heavy

particles such as nuclei, and cheap – methods of molecular

mechanics are routinely applied to high-dimensional systems of

hundreds of atoms. The challenge is to include quantum effects

on dynamics of the trajectories.

We use the de Broglie-Bohm formulation of the Schrodinger

equation to formulate a semiclassical trajectory method. QM

effects are included through the quantum force due to

localization of the trajectory ensemble, acting on the

trajectories in addition to the classical forces. A cheap

approximation to the quantum potential makes the method

practical in many dimensions and captures dominant quantum

effects in semiclassical systems.

The latest development is a description of the double well

dynamics – a prototype of the proton transfer

reactions – which exhibits hard quantum effect of tunneling. This is

achieved by combining the approximate quantum trajectory

dynamics with the population amplitudes in the reactant and

product wells. The trajectories are driven by the asymptotic

classical potentials, while the population amplitudes are

described in a small basis. The method is exact if these

reactant/product potentials are harmonic and the basis size is

sufficiently large. In the semiclassical regime trajectory

dynamics is approximate, and the basis size can be as small as

two functions. The approach is fully compatible with the

trajectory description of multidimensional systems capturing

quantum tunneling along the reactive coordinate and ZPE flow

among all degrees of freedom.**Azobenzene in solution: excited state dynamics simulation**

Maurizio Persico

We present a set of surface hopping simulations of the excited state

decay and photoisomerization of azobenzene, in vacuo and in two solvents

of different viscosity, methanol and ethylene glycol. We are able to

reproduce the experimental quantum yields and the fluorescence

transients (both intensity and anisotropy). We bring out the effects of

solvation on the photodynamics and propose a new interpretation of

recent experiments.**Partial differential equations in chemical dynamics**

with finite elements

Craig Michoski (The University of Texas at Austin)

We introduce some mathematical analysis in the form of existence and uniqueness results for chemically miscible compressible classical systems of equations. Then we show some extensions to chemical reactor systems, where chemical kinetics and intermolecular diffusion is taken into consideration, and applied to atmospheric chemistry. Finally we show an extension to quantum hydrodynamic systems of equations, used to model chemical reactions.