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7 Feb 2013

Volume 138, Issue 5, Articles (05xxxx)

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J. Chem. Phys. 138, 054901 (2013); http://dx.doi.org/10.1063/1.4789267 (14 pages)

Alexander Winkler, Peter Virnau, Kurt Binder, Roland G. Winkler, and Gerhard Gompper
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Communication: Transfer of more than half the population to a selected rovibrational state of H2 by Stark-induced adiabatic Raman passage

Nandini Mukherjee, Wenrui Dong, John A. Harrison, and Richard N. Zare

J. Chem. Phys. 138, 051101 (2013); http://dx.doi.org/10.1063/1.4790402 (4 pages)

Online Publication Date: 4 February 2013

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By using Stark-induced adiabatic Raman passage (SARP) with partially overlapping nanosecond pump (532 nm) and Stokes (683 nm) laser pulses, 73% ± 6% of the initial ground vibrational state population of H2 (v = 0, J = 0) is transferred to the single vibrationally excited eigenstate (v = 1, J = 0). In contrast to other Stark chirped Raman adiabatic passage techniques, SARP transfers population from the initial ground state to a vibrationally excited target state of the ground electronic surface without using an intermediate vibronic resonance within an upper electronic state. Parallel linearly polarized, co-propagating pump and Stokes laser pulses of respective durations 6 ns and 4.5 ns, are combined with a relative delay of ∼4 ns before orthogonally intersecting the molecular beam of H2. The pump and Stokes laser pulses have fluences of ∼10 J/mm2 and ∼1 J/mm2, respectively. The intense pump pulse generates the necessary sweeping of the Raman resonance frequency by ac (second-order) Stark shifting the rovibrational levels. As the frequency of the v = 0 → v = 1 Raman transition is swept through resonance in the presence of the strong pump and the weaker delayed Stokes pulses, the population of (v = 0, J = 0) is coherently transferred via an adiabatic passage to (v = 1, J = 0). A quantitative measure of the population transferred to the target state is obtained from the depletion of the ground-state population using 2 + 1 resonance enhanced multiphoton ionization (REMPI) in a time-of-flight mass spectrometer. The depletion is measured by comparing the REMPI signal of (v = 0, J = 0) at Raman resonance with that obtained when the Stokes pulse is detuned from the Stark-shifted Raman resonance. No depletion is observed with either the pump or the Stokes pulses alone, confirming that the measured depletion is indeed caused by the SARP-induced population transfer from the ground to the target state and not by the loss of molecules from photoionization or photodissociation. The two-photon resonant UV pulse used for REMPI detection is delayed by 20 ns with respect to the pump pulse to avoid the ac Stark shift originating from the pump and Stokes laser pulses. This experiment demonstrates the feasibility of preparing a large ensemble of isolated molecules in a preselected single quantum state without requiring an intermediate vibronic resonance.
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33.57.+c Magneto-optical and electro-optical spectra and effects
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Ta Mass spectra
33.70.Jg Line and band widths, shapes, and shifts
33.80.-b Photon interactions with molecules
33.80.Be Level crossing and optical pumping
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
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Communication: Biexciton generation rates in CdSe nanorods are length independent

Roi Baer and Eran Rabani

J. Chem. Phys. 138, 051102 (2013); http://dx.doi.org/10.1063/1.4790600 (4 pages)

Online Publication Date: 6 February 2013

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We study how shape affects multiexciton generation rates in a semiconducting nanocrystal by considering CdSe nanorods with varying diameters and aspect ratios. The calculations employ an atomistic semiempirical pseudopotential model combined with an efficacious stochastic approach applied to systems containing up to 20 000 atoms. The effect of nanorod diameter and aspect ratio on multiexciton generation rates is analyzed in terms of the scaling of the density of trion states and the scaling of the Coulomb couplings. Both show distinct scaling from spherical nanocrystals leading to a surprising result where the multiexciton generation rates are roughly independent of the nanorod length.
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71.35.-y Excitons and related phenomena
73.21.-b Electron states and collective excitations in multilayers, quantum wells, mesoscopic, and nanoscale systems
71.15.Dx Computational methodology (Brillouin zone sampling, iterative diagonalization, pseudopotential construction)
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An accurate and linear-scaling method for calculating charge-transfer excitation energies and diabatic couplings

Michele Pavanello, Troy Van Voorhis, Lucas Visscher, and Johannes Neugebauer

J. Chem. Phys. 138, 054101 (2013); http://dx.doi.org/10.1063/1.4789418 (12 pages)

Online Publication Date: 1 February 2013

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Quantum–mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those charge transfer excitations that take place between non-covalently bound molecules. In particular, we present a method that scales linearly with the number of non-covalently bound molecules in the system and is based on a two-pronged approach: The molecular electronic structure of broken-symmetry charge-localized states is obtained with the frozen density embedding formulation of subsystem density-functional theory; subsequently, in a post-SCF calculation, the full-electron Hamiltonian and overlap matrix elements among the charge-localized states are evaluated with an algorithm which takes full advantage of the subsystem DFT density partitioning technique. The method is benchmarked against coupled-cluster calculations and achieves chemical accuracy for the systems considered for intermolecular separations ranging from hydrogen-bond distances to tens of Ångstroms. Numerical examples are provided for molecular clusters comprised of up to 56 non-covalently bound molecules.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.20.Ln Semiclassical theory of reactions and/or energy transfer
34.70.+e Charge transfer
31.15.E- Density-functional theory
31.15.xr Self-consistent-field methods
33.15.Dj Interatomic distances and angles

Coupling of kinetic Monte Carlo simulations of surface reactions to transport in a fluid for heterogeneous catalytic reactor modeling

C. Schaefer and A. P. J. Jansen

J. Chem. Phys. 138, 054102 (2013); http://dx.doi.org/10.1063/1.4789419 (9 pages)

Online Publication Date: 1 February 2013

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We have developed a method to couple kinetic Monte Carlo simulations of surface reactions at a molecular scale to transport equations at a macroscopic scale. This method is applicable to steady state reactors. We use a finite difference upwinding scheme and a gap-tooth scheme to efficiently use a limited amount of kinetic Monte Carlo simulations. In general the stochastic kinetic Monte Carlo results do not obey mass conservation so that unphysical accumulation of mass could occur in the reactor. We have developed a method to perform mass balance corrections that is based on a stoichiometry matrix and a least-squares problem that is reduced to a non-singular set of linear equations that is applicable to any surface catalyzed reaction. The implementation of these methods is validated by comparing numerical results of a reactor simulation with a unimolecular reaction to an analytical solution. Furthermore, the method is applied to two reaction mechanisms. The first is the ZGB model for CO oxidation in which inevitable poisoning of the catalyst limits the performance of the reactor. The second is a model for the oxidation of NO on a Pt(111) surface, which becomes active due to lateral interaction at high coverages of oxygen. This reaction model is based on ab initio density functional theory calculations from literature.
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82.20.Fd Collision theories; trajectory models
31.15.E- Density-functional theory
34.10.+x General theories and models of atomic and molecular collisions and interactions (including statistical theories, transition state, stochastic and trajectory models, etc.)
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions

Many-body dispersion interactions from the exchange-hole dipole moment model

A. Otero-de-la-Roza and Erin R. Johnson

J. Chem. Phys. 138, 054103 (2013); http://dx.doi.org/10.1063/1.4789421 (10 pages) | Cited 1 time

Online Publication Date: 1 February 2013

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In this article, we present the extension of the exchange-hole dipole moment model (XDM) of dispersion interactions to the calculation of two-body and three-body dispersion energy terms to any order, 2l-pole oscillator strengths, and polarizabilities. By using the newly-formulated coefficients, we study the relative importance of the higher-order two-body and the leading non-additive three-body (triple-dipole) interactions in gas-phase as well as in condensed systems. We show that the two-body terms up to R−10, but not the terms of higher-order, are essential in the correct description of the dispersion energy, while there are a number of difficulties related to the choice of the damping function, which precludes the use three-body triple-dipole contributions in XDM. We conclude that further study is required before the three-body term can be used in production XDM density-functional calculations and point out the salient problems regarding its use.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

Signatures of discrete breathers in coherent state quantum dynamics

Kirill Igumenshchev, Misha Ovchinnikov, Panagiotis Maniadis, and Oleg Prezhdo

J. Chem. Phys. 138, 054104 (2013); http://dx.doi.org/10.1063/1.4788618 (11 pages)

Online Publication Date: 1 February 2013

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In classical mechanics, discrete breathers (DBs) – a spatial time-periodic localization of energy – are predicted in a large variety of nonlinear systems. Motivated by a conceptual bridging of the DB phenomena in classical and quantum mechanical representations, we study their signatures in the dynamics of a quantum equivalent of a classical mechanical point in phase space – a coherent state. In contrast to the classical point that exhibits either delocalized or localized motion, the coherent state shows signatures of both localized and delocalized behavior. The transition from normal to local modes have different characteristics in quantum and classical perspectives. Here, we get an insight into the connection between classical and quantum perspectives by analyzing the decomposition of the coherent state into system's eigenstates, and analyzing the spacial distribution of the wave-function density within these eigenstates. We find that the delocalized and localized eigenvalue components of the coherent state are separated by a mixed region, where both kinds of behavior can be observed. Further analysis leads to the following observations. Considered as a function of coupling, energy eigenstates go through avoided crossings between tunneling and non-tunneling modes. The dominance of tunneling modes in the high nonlinearity region is compromised by the appearance of new types of modes – high order tunneling modes – that are similar to the tunneling modes but have attributes of non-tunneling modes. Certain types of excitations preferentially excite higher order tunneling modes, allowing one to study their properties. Since auto-correlation functions decrease quickly in highly nonlinear systems, short-time dynamics are sufficient for modeling quantum DBs. This work provides a foundation for implementing modern semi-classical methods to model quantum DBs, bridging classical and quantum mechanical signatures of DBs, and understanding spectroscopic experiments that involve a coherent state.
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03.65.Sq Semiclassical theories and applications
02.10.Ud Linear algebra
03.65.Fd Algebraic methods

A quadratically convergent VBSCF method

Zahid Rashid and Joop H. van Lenthe

J. Chem. Phys. 138, 054105 (2013); http://dx.doi.org/10.1063/1.4788765 (9 pages)

Online Publication Date: 1 February 2013

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A quadratically convergent valence bond self-consistent field method is described where the simultaneous optimisation of orbitals and the coefficients of the configurations (VB structures) is based on a Newton-Raphson scheme. The applicability of the method is demonstrated in actual calculations. The convergence and efficiency are compared with the Super-CI method. A necessary condition to achieve convergence in the Newton-Raphson method is that the Hessian is positive definite. When this is not the case, a combination of the Super-CI and Newton-Raphson methods is shown to be an optimal choice instead of shifting the eigenvalues of the Hessian to make it positive definite. In the combined method, the first few iterations are performed with the Super-CI method and then the Newton-Raphson scheme is switched on based on an internal indicator. This approach is found computationally a more economical choice than using either the Newton-Raphson or Super-CI method alone to perform a full optimisation of the nonorthogonal orbitals.
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31.15.xw Valence bond calculations
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.xr Self-consistent-field methods

Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency

Baron Peters, Peter G. Bolhuis, Ryan G. Mullen, and Joan-Emma Shea

J. Chem. Phys. 138, 054106 (2013); http://dx.doi.org/10.1063/1.4775807 (13 pages)

Online Publication Date: 1 February 2013

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We propose a method for identifying accurate reaction coordinates among a set of trial coordinates. The method applies to special cases where motion along the reaction coordinate follows a one-dimensional Smoluchowski equation. In these cases the reaction coordinate can predict its own short-time dynamical evolution, i.e., the dynamics projected from multiple dimensions onto the reaction coordinate depend only on the reaction coordinate itself. To test whether this property holds, we project an ensemble of short trajectory swarms onto trial coordinates and compare projections of individual swarms to projections of the ensemble of swarms. The comparison, quantified by the Kullback-Leibler divergence, is numerically performed for each isosurface of each trial coordinate. The ensemble of short dynamical trajectories is generated only once by sampling along an initial order parameter. The initial order parameter should separate the reactants and products with a free energy barrier, and distributions on isosurfaces of the initial parameter should be unimodal. The method is illustrated for three model free energy landscapes with anisotropic diffusion. Where exact coordinates can be obtained from Kramers-Langer-Berezhkovskii-Szabo theory, results from the new method agree with the exact results. We also examine characteristics of systems where the proposed method fails. We show how dynamical self-consistency is related (through the Chapman-Kolmogorov equation) to the earlier isocommittor criterion, which is based on longer paths.
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82.20.Db Transition state theory and statistical theories of rate constants
65.40.G- Other thermodynamical quantities

The Schrödinger equation with friction from the quantum trajectory perspective

Sophya Garashchuk, Vaibhav Dixit, Bing Gu, and James Mazzuca

J. Chem. Phys. 138, 054107 (2013); http://dx.doi.org/10.1063/1.4788832 (7 pages)

Online Publication Date: 1 February 2013

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Similarity of equations of motion for the classical and quantum trajectories is used to introduce a friction term dependent on the wavefunction phase into the time-dependent Schrödinger equation. The term describes irreversible energy loss by the quantum system. The force of friction is proportional to the velocity of a quantum trajectory. The resulting Schrödinger equation is nonlinear, conserves wavefunction normalization, and evolves an arbitrary wavefunction into the ground state of the system (of appropriate symmetry if applicable). Decrease in energy is proportional to the average kinetic energy of the quantum trajectory ensemble. Dynamics in the high friction regime is suitable for simple models of reactions proceeding with energy transfer from the system to the environment. Examples of dynamics are given for single and symmetric and asymmetric double well potentials.
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03.65.Ge Solutions of wave equations: bound states
03.65.Ta Foundations of quantum mechanics; measurement theory
02.30.Hq Ordinary differential equations

Structural fluctuation of protein in water around its native state: A new statistical mechanics formulation

Bongsoo Kim and Fumio Hirata

J. Chem. Phys. 138, 054108 (2013); http://dx.doi.org/10.1063/1.4776655 (11 pages)

Online Publication Date: 4 February 2013

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A new statistical mechanics formulation of characterizing the structural fluctuation of protein correlated with that of water is presented based on the generalized Langevin equation and the 3D-reference interaction site model (RISM)/RISM theory of molecular liquids. The displacement vector of atom positions, and their conjugated momentum, are chosen for the dynamic variables for protein, while the density fields of atoms and their momentum fields are chosen for water. Projection of other degrees of freedom onto those dynamic variables using the standard projection operator method produces essentially two equations, which describe the time evolution of fluctuation concerning the density field of solvent and the conformation of protein around an equilibrium state, which are coupled with each other. The equation concerning the protein dynamics is formally akin to that of the coupled Langevin oscillators, and is a generalization of the latter, to atomic level. The most intriguing feature of the new equation is that it contains the variance-covariance matrix as the “Hessian” term describing the “force” restoring an equilibrium conformation, which is the second moment of the fluctuation of atom positions. The “Hessian” matrix is naturally identified as the second derivative of the free energy surface around the equilibrium. A method to evaluate the Hessian matrix based on the 3D-RISM/RISM theory is proposed. Proposed also is an application of the present formulation to the molecular recognition, in which the conformational fluctuation of protein around its native state becomes an important factor as exemplified by so called “induced fitting.”
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87.15.Ya Fluctuations
87.14.E- Proteins
87.15.B- Structure of biomolecules
87.15.hp Conformational changes
36.20.Ey Conformation (statistics and dynamics)
36.20.Hb Configuration (bonds, dimensions)

The orbital-specific virtual local triples correction: OSV-L(T)

Martin Schütz, Jun Yang, Garnet Kin-Lic Chan, Frederick R. Manby, and Hans-Joachim Werner

J. Chem. Phys. 138, 054109 (2013); http://dx.doi.org/10.1063/1.4789415 (10 pages) | Cited 2 times

Online Publication Date: 4 February 2013

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A local method based on orbital specific virtuals (OSVs) for calculating the perturbative triples correction in local coupled cluster calculations is presented. In contrast to the previous approach based on projected atomic orbitals (PAOs), described by Schütz [J. Chem. Phys. 113, 9986 (2000)]10.1063/1.1323265, the new scheme works without any ad hoc truncations of the virtual space to domains. A single threshold defines the pair and triple specific virtual spaces completely and automatically. It is demonstrated that the computational cost of the method scales linearly with molecular size. Employing the recommended threshold a similar fraction of the correlation energy is recovered as with the original PAO method at a somewhat lower cost. A benchmark for 52 reactions demonstrates that for reaction energies the intrinsic accuracy of the coupled cluster with singles and doubles excitations and a perturbative treatment of triples excitations method can be reached by OSV-local coupled cluster theory with singles and doubles and perturbative triples, provided a MP2 correction is applied that accounts for basis set incompleteness errors as well as for remaining domain errors. As an application example the interaction energies of the guanine-cytosine dimers in the Watson-Crick and stacked arrangements are investigated at the level of local coupled cluster theory with singles and doubles and perturbative triples. Based on these calculations we propose new complete-basis-set-limit estimates for these interaction energies at this level of theory.
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31.15.bw Coupled-cluster theory
82.20.-w Chemical kinetics and dynamics
31.15.xp Perturbation theory

Going beyond the frozen core approximation: Development of coordinate-dependent pseudopotentials and application to Na 2+

Argyris Kahros and Benjamin J. Schwartz

J. Chem. Phys. 138, 054110 (2013); http://dx.doi.org/10.1063/1.4789425 (9 pages)

Online Publication Date: 4 February 2013

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Mixed quantum/classical (MQC) simulations treat the majority of a system classically and reserve quantum mechanics only for a few degrees of freedom that actively participate in the chemical process(es) of interest. In MQC calculations, the quantum and classical degrees of freedom are coupled together using pseudopotentials. Although most pseudopotentials are developed empirically, there are methods for deriving pseudopotentials using the results of quantum chemistry calculations, which guarantee that the explicitly-treated valence electron wave functions remain orthogonal to the implicitly-treated core electron orbitals. Whether empirical or analytically derived in nature, to date all such pseudopotentials have been subject to the frozen core approximation (FCA) that ignores how changes in the nuclear coordinates alter the core orbitals, which in turn affects the wave function of the valence electrons. In this paper, we present a way to go beyond the FCA by developing pseudopotentials that respond to these changes. In other words, we show how to derive an analytic expression for a pseudopotential that is an explicit function of nuclear coordinates, thus accounting for the polarization effects experienced by atomic cores in different chemical environments. We then use this formalism to develop a coordinate-dependent pseudopotential for the bonding electron of the sodium dimer cation molecule and we show how the analytic representation of this potential can be used in one-electron MQC simulations that provide the accuracy of a fully quantum mechanical Hartree-Fock (HF) calculation at all internuclear separations. We also show that one-electron MQC simulations of Na 2+ using our coordinate-dependent pseudopotential provide a significant advantage in accuracy compared to frozen core potentials with no additional computational expense. This is because use of a frozen core potential produces a charge density for the bonding electron of Na 2+ that is too localized on the molecule, leading to significant overbinding of the valence electron. This means that FCA calculations are subject to inaccuracies of order ∼10% in the calculated bond length and vibrational frequency of the molecule relative to a full HF calculation; these errors are fully corrected by using our coordinate-dependent pseudopotential. Overall, our findings indicate that even for molecules like Na 2+, which have a simple electronic structure that might be expected to be well-treated within the FCA, the importance of including the effects of the changing core molecular orbitals on the bonding electrons cannot be overlooked.
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31.15.xr Self-consistent-field methods
33.15.Mt Rotation, vibration, and vibration-rotation constants

Modeling molecular response in uniform and non-uniform electric fields

Michael Morris and Meredith J. T. Jordan

J. Chem. Phys. 138, 054111 (2013); http://dx.doi.org/10.1063/1.4788833 (9 pages)

Online Publication Date: 4 February 2013

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The response of a molecule to an electric field E, often a model of environment, can be expressed in terms of a sum of power series expansions. We investigate the accuracy and limits of applicability of this expression using one-, two-, and three-dimensional models of the hydrogen-bonded complex, ClH:NH3. Energetic, structural, and vibrational spectroscopic characteristics are determined at first- and second-order in E and ∇E and compared with ab initio values for a range of uniform and non-uniform electric fields chosen to simulate molecular environments. It is found that even at field strengths large enough to cause dramatic structural change in the complex, energetic, structural, and vibrational spectroscopic characteristics are accurately calculated using only terms linear in E and ∇E. These results suggest that knowledge of the zero-field molecular potential energy, dipole, and quadrupole moment surfaces may be sufficient to accurately model the interaction of a molecule with a wide range of chemical environments.
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33.20.Tp Vibrational analysis
31.15.ae Electronic structure and bonding characteristics
31.30.jp Electron electric dipole moment
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

Generalized Born forces: Surface integral formulation

Federico Fogolari, Alessandra Corazza, and Gennaro Esposito

J. Chem. Phys. 138, 054112 (2013); http://dx.doi.org/10.1063/1.4789537 (11 pages)

Online Publication Date: 5 February 2013

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Generalized Born (GB) models offer a convenient alternative to Poisson-Boltzmann based models. In the last decade, the GB radii computed based on the exact results obtained for a charge embedded in a conducting sphere have proven to be accurate also for the complex molecular shapes of proteins. The surface integral formulation of the theory has been much less explored than the volume integral formulation. In this work, we provide the exact equations for the GB solvation forces in the surface integral formulation, which are non-trivial due to the non-negligible dependence of GB radii on atomic positions and due to the discontinuity in the derivative of the solvent accessible surface point positions with respect to atomic positions. The equations derived here provide a useful reference for developing faster approximations.
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87.14.E- Proteins
87.15.B- Structure of biomolecules
02.30.-f Function theory, analysis
36.20.Hb Configuration (bonds, dimensions)
82.30.Nr Association, addition, insertion, cluster formation

NMR chemical shift as analytical derivative of the Helmholtz free energy

Willem Van den Heuvel and Alessandro Soncini

J. Chem. Phys. 138, 054113 (2013); http://dx.doi.org/10.1063/1.4789398 (10 pages)

Online Publication Date: 5 February 2013

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We present a theory for the temperature-dependent nuclear magnetic shielding tensor of molecules with arbitrary electronic structure. The theory is a generalization of Ramsey's theory for closed-shell molecules. The shielding tensor is defined as a second derivative of the Helmholtz free energy of the electron system in equilibrium with the applied magnetic field and the nuclear magnetic moments. This derivative is analytically evaluated and expressed as a sum over states formula. Special consideration is given to a system with an isolated degenerate ground state for which the size of the degeneracy and the composition of the wave functions are arbitrary. In this case, the paramagnetic part of the shielding tensor is expressed in terms of the g and A tensors of the electron paramagnetic resonance spin Hamiltonian of the degenerate state. As an illustration of the proposed theory, we provide an explicit formula for the paramagnetic shift of the central lanthanide ion in endofullerenes Ln@C60, with Ln = Ce3+, Nd3+, Sm3+, Dy3+, Er3+, and Yb3+, where the ground state can be a strongly spin-orbit coupled icosahedral sextet for which the paramagnetic shift cannot be described by previous theories.
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36.40.Mr Spectroscopy and geometrical structure of clusters
33.35.+r Electron resonance and relaxation
33.25.+k Nuclear resonance and relaxation

Development of polaron-transformed explicitly correlated full configuration interaction method for investigation of quantum-confined Stark effect in GaAs quantum dots

Christopher J. Blanton, Christopher Brenon, and Arindam Chakraborty

J. Chem. Phys. 138, 054114 (2013); http://dx.doi.org/10.1063/1.4789540 (6 pages)

Online Publication Date: 5 February 2013

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The effect of external electric field on electron-hole (eh) correlation in gallium arsenide quantum dots is investigated. The electron-hole Schrodinger equation in the presence of an external electric field is solved using explicitly correlated full configuration interaction method and accurate exciton binding energy and electron-hole recombination probability are obtained. The effect of the electric field was included in the 1-particle single component basis functions by performing variational polaron transformation. The quality of the wavefunction at small inter-particle distances was improved by using Gaussian-type geminal function that depended explicitly on the electron-hole separation distance. The parameters of the explicitly correlated function were determined variationally at each field strength. The scaling of total exciton energy, exciton binding energy, and electron-hole recombination probability with respect to the strength of the electric field was investigated. It was found that a 500 kV/cm change in field strength reduces the binding energy and recombination probability by a factor of 2.6 and 166, respectively. The results show that the eh-recombination probability is affected much more strongly by the electric field than the exciton binding energy. Analysis using the polaron-transformed basis indicates that the exciton binding should asymptotically vanish in the limit of large field strength.
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78.20.Jq Electro-optical effects
78.67.Hc Quantum dots
71.38.-k Polarons and electron-phonon interactions
71.70.Ej Spin-orbit coupling, Zeeman and Stark splitting, Jahn-Teller effect
72.20.Jv Charge carriers: generation, recombination, lifetime, and trapping
73.63.Kv Quantum dots

A relative entropy rate method for path space sensitivity analysis of stationary complex stochastic dynamics

Yannis Pantazis and Markos A. Katsoulakis

J. Chem. Phys. 138, 054115 (2013); http://dx.doi.org/10.1063/1.4789612 (16 pages)

Online Publication Date: 6 February 2013

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We propose a new sensitivity analysis methodology for complex stochastic dynamics based on the relative entropy rate. The method becomes computationally feasible at the stationary regime of the process and involves the calculation of suitable observables in path space for the relative entropy rate and the corresponding Fisher information matrix. The stationary regime is crucial for stochastic dynamics and here allows us to address the sensitivity analysis of complex systems, including examples of processes with complex landscapes that exhibit metastability, non-reversible systems from a statistical mechanics perspective, and high-dimensional, spatially distributed models. All these systems exhibit, typically non-Gaussian stationary probability distributions, while in the case of high-dimensionality, histograms are impossible to construct directly. Our proposed methods bypass these challenges relying on the direct Monte Carlo simulation of rigorously derived observables for the relative entropy rate and Fisher information in path space rather than on the stationary probability distribution itself. We demonstrate the capabilities of the proposed methodology by focusing here on two classes of problems: (a) Langevin particle systems with either reversible (gradient) or non-reversible (non-gradient) forcing, highlighting the ability of the method to carry out sensitivity analysis in non-equilibrium systems; and, (b) spatially extended kinetic Monte Carlo models, showing that the method can handle high-dimensional problems.
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05.70.Ce Thermodynamic functions and equations of state
02.50.Ey Stochastic processes
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
02.50.Ng Distribution theory and Monte Carlo studies
05.20.Dd Kinetic theory
02.50.Cw Probability theory
05.20.-y Classical statistical mechanics
05.70.Ln Nonequilibrium and irreversible thermodynamics

Accelerated direct semiclassical molecular dynamics using a compact finite difference Hessian scheme

Michele Ceotto, Yu Zhuang, and William L. Hase

J. Chem. Phys. 138, 054116 (2013); http://dx.doi.org/10.1063/1.4789759 (13 pages)

Online Publication Date: 6 February 2013

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This paper shows how a compact finite difference Hessian approximation scheme can be proficiently implemented into semiclassical initial value representation molecular dynamics. Effects of the approximation on the monodromy matrix calculation are tested by propagating initial sampling distributions to determine power spectra for analytic potential energy surfaces and for “on the fly” carbon dioxide direct dynamics. With the approximation scheme the computational cost is significantly reduced, making ab initio direct semiclassical dynamics computationally more feasible and, at the same time, properly reproducing important quantum effects inherent in the monodromy matrix and the pre-exponential factor of the semiclassical propagator.
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31.15.A- Ab initio calculations
31.50.-x Potential energy surfaces

Polarizability effects in molecular dynamics simulations of the graphene-water interface

Tuan A. Ho and Alberto Striolo

J. Chem. Phys. 138, 054117 (2013); http://dx.doi.org/10.1063/1.4789583 (9 pages)

Online Publication Date: 7 February 2013

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The importance of including the polarizability of both water and graphene in molecular dynamics simulations of the water/graphene system was quantified. A thin film of either rigid single point charge extended (SPC/E) water or polarizable simple 4-site water model with Drude polarizability (SWM4_DP) water on non-polarizable and polarizable graphene surfaces was simulated. The graphene surface was either maintained neutral or charged, positively and negatively. The results suggest that SPC/E and SWM4_DP water models yield very similar predictions for the water structural properties on neutral non-polarizable graphene, although they yield slightly different dynamical properties of interfacial water on neutral non-polarizable graphene. More pronounced were the differences obtained when graphene was modeled with a polarizable force field. In particular, the polarizability of graphene was found to enhance the number of interfacial SWM4_DP water molecules pointing one of their OH bonds towards the neutral surface. Despite this structural difference, the dynamical properties predicted for the interfacial SWM4_DP water were found to be independent on polarizability as long as the polarizability of a carbon atom is smaller than α = 0.878 Å. On charged graphene surfaces, the effect of polarizability of graphene on structural properties and some dynamical properties of SWM4_DP water is negligible because electrostatic forces due to surface charge dominate polarization forces, as expected. For all cases, our results suggest that the hydrogen bond network is insensitive to the polarizability of both water and graphene. Understanding how these effects will determine the accumulation of ions near neutral or charged graphene could have important implications for applications in the fields of energy storage and water desalination.
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61.48.Gh Structure of graphene
61.50.Lt Crystal binding; cohesive energy
61.43.Bn Structural modeling: serial-addition models, computer simulation

Quantum dynamical structure factor of liquid neon via a quasiclassical symmetrized method

Michele Monteferrante, Sara Bonella, and Giovanni Ciccotti

J. Chem. Phys. 138, 054118 (2013); http://dx.doi.org/10.1063/1.4789760 (10 pages)

Online Publication Date: 7 February 2013

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We apply the phase integration method for quasiclassical quantum time correlation functions [M. Monteferrante, S. Bonella, and G. Ciccotti, Mol. Phys. 109, 3015 (2011)10.1080/00268976.2011.619506] to compute the dynamic structure factor of liquid neon. So far the method had been tested only on model systems. By comparing our results for neon with experiments and previous calculations, we demonstrate that the scheme is accurate and efficient also for a realistic model of a condensed phase system showing quantum behavior.
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61.20.Ja Computer simulation of liquid structure
02.50.Ng Distribution theory and Monte Carlo studies

A variational formulation of electrostatics in a medium with spatially varying dielectric permittivity

Vikram Jadhao, Francisco J. Solis, and Monica Olvera de la Cruz

J. Chem. Phys. 138, 054119 (2013); http://dx.doi.org/10.1063/1.4789955 (13 pages)

Online Publication Date: 7 February 2013

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In biological and synthetic materials, many important processes involve charges that are present in a medium with spatially varying dielectric permittivity. To accurately understand the role of electrostatic interactions in such systems, it is important to take into account the spatial dependence of the permittivity of the medium. However, due to the ensuing theoretical and computational challenges, this inhomogeneous dielectric response of the medium is often ignored or excessively simplified. We develop a variational formulation of electrostatics to accurately investigate systems that exhibit this inhomogeneous dielectric response. Our formulation is based on a true energy functional of the polarization charge density. The defining characteristic of a true energy functional is that at its minimum it evaluates to the actual value of the energy; this is a feature not found in many commonly used electrostatic functionals. We explore in detail the charged systems that exhibit sharp discontinuous change in dielectric permittivity, and we show that for this case our functional reduces to a functional of only the surface polarization charge density. We apply this reduced functional to study model problems for which analytical solutions are well known. We demonstrate, in addition, that the functional has many properties that make it ideal for use in molecular dynamics simulations.
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87.15.Pc Electronic and electrical properties
36.20.Ey Conformation (statistics and dynamics)
87.14.-g Biomolecules: types
87.15.ap Molecular dynamics simulation

Combined-hyperbolic-inverse-power-representation of potential energy surfaces: A preliminary assessment for H3 and HO2

A. J. C. Varandas

J. Chem. Phys. 138, 054120 (2013); http://dx.doi.org/10.1063/1.4788912 (14 pages) | Cited 2 times

Online Publication Date: 7 February 2013

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The purpose is to fit an accurate smooth function of the many-body expansion type to a multidimensional large data set using a basis-set type method. By adopting a combined-hyperbolic-inverse-power-representation for the basis, the novel approach is tested in detail for the ground electronic state of tri-hydrogen and hydroperoxyl systems, assuming that their potential energy surfaces are single-sheeted representable. It is also shown that the method can be easily applicable to potential energy curves by considering as prototypes molecular oxygen and the hydroxyl radical.
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31.50.Bc Potential energy surfaces for ground electronic states
back to top Advanced Experimental Techniques

New insights for accurate chemically specific measurements of slow diffusing molecules

Jianbo Hou and Louis A. Madsen

J. Chem. Phys. 138, 054201 (2013); http://dx.doi.org/10.1063/1.4789923 (8 pages)

Online Publication Date: 7 February 2013

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Investigating the myriad features of molecular transport in materials yields fundamental information for understanding processes such as ion conduction, chemical reactions, and phase transitions. Molecular transport especially impacts the performance of ion-containing liquids and polymeric materials when used as electrolytes and separation media, with applications encompassing battery electrolytes, reverse-osmosis membranes, mechanical transducers, and fuel cells. Nuclear magnetic resonance (NMR) provides a unique probe of molecular translations by allowing measurement of all mobile species via spectral selectivity, access to a broad range of transport coefficients, probing of any material direction, and investigation of variable lengthscales in a material, thus, tying morphology to transport. Here, we present new concepts to test for and guarantee robust diffusion measurements. We first employ a standard pulsed-field-gradient (PFG) calibration protocol using 2H2O and obtain expected results, but we observe crippling artifacts when measuring 1H-glycerol diffusion with the same experimental parameters. A mathematical analysis of 2H2O and glycerol signals in the presence of PFG transients show tight agreement with experimental observations. These analyses lead to our principal findings that (1) negligible artifacts observed with low gyromagnetic ratio (γ) nuclei may become dominant when observing high γ nuclei, and (2) reducing the sample dimension along the gradient direction predictably reduces non-ideal behaviors of NMR signals. We further provide a useful quantitative strategy for error minimization when measuring diffusing species slower than the one used for gradient calibration.
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66.10.C- Diffusion and thermal diffusion
76.60.-k Nuclear magnetic resonance and relaxation
back to top Atoms, Molecules, and Clusters

Photodissociation dynamics of the methyl perthiyl radical at 248 nm via photofragment translational spectroscopy

Neil C. Cole-Filipiak, Bogdan Negru, Gabriel M. P. Just, Dayoung Park, and Daniel M. Neumark

J. Chem. Phys. 138, 054301 (2013); http://dx.doi.org/10.1063/1.4789485 (5 pages)

Online Publication Date: 1 February 2013

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Photofragment translational spectroscopy was used to study the photodissociation of the methyl perthiyl radical CH3SS at 248 nm. The radical was produced by flash pyrolysis of dimethyl disulfide (CH3SSCH3). Two channels were observed: CH3 + S2 and CH2S + SH. Photofragment translational energy distributions indicate that CH3 + S2 results from C–S bond fission on the ground state surface. The CH2S + SH channel can proceed through isomerization to CH2SSH on the ground state surface but also may involve production of electronically excited CH2S.
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82.20.Kh Potential energy surfaces for chemical reactions
31.50.-x Potential energy surfaces
33.20.Lg Ultraviolet spectra

A comprehensive and comparative study of elastic electron scattering from OCS and CS2 in the energy region from 1.2 to 200 eV

H. Murai, Y. Ishijima, T. Mitsumura, Y. Sakamoto, H. Kato, M. Hoshino, F. Blanco, G. García, P. Limão-Vieira, M. J. Brunger, S. J. Buckman, and H. Tanaka

J. Chem. Phys. 138, 054302 (2013); http://dx.doi.org/10.1063/1.4788666 (12 pages)

Online Publication Date: 1 February 2013

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We report absolute differential cross sections (DCSs) for elastic electron scattering from OCS (carbonyl sulphide) and CS2 (carbon disulphide) in the impact energy range of 1.2–200 eV and for scattering angles from 10° to 150°. Above 10 eV, the angular distributions are found to agree quite well with our present calculations using two semi-phenomenological theoretical approaches. One employs the independent-atom model with the screening-corrected additivity rule (IAM-SCAR), while the other uses the continuum-multiple-scattering method in conjunction with a parameter-free exchange-polarization approximation. Since OCS is a polar molecule, further dipole-induced rotational excitation cross sections have been calculated in the framework of the first Born approximation and incoherently added to the IAM-SCAR results. In comparison with the calculated DCS for the S atom, atomic-like behavior for the angular distributions in both the OCS and CS2 scattering systems is observed. Integrated elastic cross sections are obtained by extrapolating the experimental measurements, with the aid of the theoretical calculations, for those scattering angles below 10° and above 150°. These values are then compared with the available total cross sections.
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34.50.Cx Elastic; ultracold collisions
33.15.Mt Rotation, vibration, and vibration-rotation constants
34.50.Gb Electronic excitation and ionization of molecules
34.80.Gs Molecular excitation and ionization
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