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28 Dec 2010

Volume 133, Issue 24, Articles (24xxxx)

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J. Chem. Phys. 133, 244105 (2010); http://dx.doi.org/10.1063/1.3507878 (10 pages)

Harald Oberhofer and Jochen Blumberger
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Communication: Decoherence in a nonequilibrium environment: An analytically solvable model

Craig C. Martens

J. Chem. Phys. 133, 241101 (2010); http://dx.doi.org/10.1063/1.3507870 (4 pages)

Online Publication Date: 27 December 2010

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We describe an analytically solvable model of quantum decoherence in a nonequilibrium environment. The model considers the effect of a bath driven from equilibrium by, for example, an ultrafast excitation of a quantum chromophore. The nonequilibrium response of the environment is represented by a nonstationary random function corresponding to the fluctuating transition frequency between two quantum states coupled to the surroundings. The nonstationary random function is characterized by a Fourier series with the phase of each term starting initially with a definite value across the ensemble but undergoing random diffusion with time. The decay of the off-diagonal density matrix element is shown to depend significantly on the particular pattern of initial phases of the terms in the Fourier series, or equivalently, the initial phases of bath modes coupled to the quantum subsystem. This suggests the possibility of control of quantum decoherence by the detailed properties of an environment that is driven from thermal equilibrium.
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03.65.Yz Decoherence; open systems; quantum statistical methods
02.30.Lt Sequences, series, and summability
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Communication: Polarization-angle-scanning two-dimensional infrared spectroscopy of antiparallel β-sheet polypeptide: Additional dimensions in two-dimensional optical spectroscopy

Jun-Ho Choi and Minhaeng Cho

J. Chem. Phys. 133, 241102 (2010); http://dx.doi.org/10.1063/1.3522765 (4 pages)

Online Publication Date: 28 December 2010

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A theoretical description of polarization-angle-scanning (PAS) two-dimensional infrared (2DIR) spectroscopy, where the incident beam polarization directions are considered to be novel dimensions in coherent two-dimensional (2D) optical spectroscopy, is presented. To shed light on the underlying principles and to illustrate a potential use of this measurement method, we investigate the PAS 2DIR spectroscopy of an alanine-based antiparallel β-sheet, using the relationships between cross-peak amplitudes and incident beam polarization directions and carrying out numerical simulations. The numerically simulated PAS 2DIR spectra of the antiparallel β-sheet show that the magnitude and sign of the cross peak reflecting the correlation between the two characteristic amide I vibrations change for varying beam polarization directions. This suggests that each individual cross peak in a given 2D spectrum can be selectively eliminated with an appropriate beam polarization configuration, which in turn provides information on the transition dipole angle and possibly on the structure of coupled multichromophoric systems. This novel measurement method combining the polarization-angle-scanning technique with 2D vibrational or electronic spectroscopy would be a useful tool for probing structural changes of nonequilibrium molecular systems and to investigate transfers of population and coherence by monitoring the time-dependent changes of angles between transition dipoles.
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87.15.M- Spectra of biomolecules
87.14.ef Peptides
87.15.B- Structure of biomolecules
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Communication: Ionization potentials in the limit of large atomic number

Lucian A. Constantin, John C. Snyder, John P. Perdew, and Kieron Burke

J. Chem. Phys. 133, 241103 (2010); http://dx.doi.org/10.1063/1.3522767 (4 pages) | Cited 1 time

Online Publication Date: 29 December 2010

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By extrapolating the energies of nonrelativistic atoms and their ions with up to 3000 electrons within Kohn–Sham density functional theory, we find that the ionization potential remains finite and increases across a row of the periodic table, even as Z → ∞. The local density approximation for the exchange contribution becomes more accurate (or even exact) in this limit. Extended Thomas–Fermi theory matches the shell average of both the ionization potential and density change.
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71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.10.Ca Electron gas, Fermi gas
71.45.Gm Exchange, correlation, dielectric and magnetic response functions, plasmons
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Communication: Evidence of hydrated electrons injected by a metallic electrode in a high voltage system

Carlos Eduardo Perles and Pedro Luiz Onófrio Volpe

J. Chem. Phys. 133, 241104 (2010); http://dx.doi.org/10.1063/1.3529422 (4 pages) | Cited 1 time

Online Publication Date: 30 December 2010

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In this work it a strong evidence of the hydrated electrons production was shown in a film of condensed water, by directing the injection of electrons in localized and/or delocalized water electronic states using a system of high voltage made in laboratory. The results show that the water layers on the silica particles are electrically charged by injection of electrons from a metal electrode when silica is placed in high electric field. This charging process also appears to depend on the thickness of these water layers and of the spatial arrangement required by the silica surface.
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79.05.+c Solvated electrons
71.55.Jv Disordered structures; amorphous and glassy solids
72.15.Rn Localization effects (Anderson or weak localization)
73.20.Fz Weak or Anderson localization
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back to top Theoretical Methods and Algorithms

Sampling rare events in nonequilibrium and nonstationary systems

Joshua T. Berryman and Tanja Schilling

J. Chem. Phys. 133, 244101 (2010); http://dx.doi.org/10.1063/1.3525099 (10 pages) | Cited 3 times

Online Publication Date: 22 December 2010

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Although many computational methods for rare event sampling exist, this type of calculation is not usually practical for general nonequilibrium conditions, with macroscopically irreversible dynamics and away from both stationary and metastable states. A novel method for calculating the time-series of the probability of a rare event is presented which is designed for these conditions. The method is validated for the cases of the Glauber–Ising model under time-varying shear flow, the Kawasaki–Ising model after a quench into the region between nucleation dominated and spinodal decomposition dominated phase change dynamics, and the parallel open asymmetric exclusion process. The method requires a subdivision of the phase space of the system: it is benchmarked and found to scale well for increasingly fine subdivisions, meaning that it can be applied without detailed foreknowledge of the physically important reaction pathways.
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47.55.db Drop and bubble formation
47.11.-j Computational methods in fluid dynamics
05.50.+q Lattice theory and statistics (Ising, Potts, etc.)
02.50.Cw Probability theory
47.70.Nd Nonequilibrium gas dynamics

A simple protocol for the probability weights of the simulated tempering algorithm: Applications to first-order phase transitions

Carlos E. Fiore and M. G. E. da Luz

J. Chem. Phys. 133, 244102 (2010); http://dx.doi.org/10.1063/1.3519813 (7 pages) | Cited 2 times

Online Publication Date: 22 December 2010

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The simulated tempering (ST) is an important method to deal with systems whose phase spaces are hard to sample ergodically. However, it uses accepting probabilities weights, which often demand involving and time consuming calculations. Here it is shown that such weights are quite accurately obtained from the largest eigenvalue of the transfer matrix—a quantity straightforward to compute from direct Monte Carlo simulations—thus simplifying the algorithm implementation. As tests, different systems are considered, namely, Ising, Blume–Capel, Blume–Emery–Griffiths, and Bell–Lavis liquid water models. In particular, we address first-order phase transition at low temperatures, a regime notoriously difficulty to simulate because the large free-energy barriers. The good results found (when compared with other well established approaches) suggest that the ST can be a valuable tool to address strong first-order phase transitions, a possibility still not well explored in the literature.
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05.50.+q Lattice theory and statistics (Ising, Potts, etc.)
05.70.Fh Phase transitions: general studies

Nonlocal van der Waals density functional: The simpler the better

Oleg A. Vydrov and Troy Van Voorhis

J. Chem. Phys. 133, 244103 (2010); http://dx.doi.org/10.1063/1.3521275 (9 pages) | Cited 11 times

Online Publication Date: 22 December 2010

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We devise a nonlocal correlation energy functional that describes the entire range of dispersion interactions in a seamless fashion using only the electron density as input. The new functional is considerably simpler than its predecessors of a similar type. The functional has a tractable and robust analytic form that lends itself to efficient self-consistent implementation. When paired with an appropriate exchange functional, our nonlocal correlation model yields accurate interaction energies of weakly-bound complexes, not only near the energy minima but also far from equilibrium. Our model exhibits an outstanding precision at predicting equilibrium intermonomer separations in van der Waals complexes. It also gives accurate covalent bond lengths and atomization energies. Hence the functional proposed in this work is a computationally inexpensive electronic structure tool of broad applicability.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
33.15.Fm Bond strengths, dissociation energies
33.15.Dj Interatomic distances and angles
31.15.xr Self-consistent-field methods

Effective local potentials for excited states

Viktor N. Staroverov and Vitaly N. Glushkov

J. Chem. Phys. 133, 244104 (2010); http://dx.doi.org/10.1063/1.3521492 (9 pages)

Online Publication Date: 22 December 2010

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The constrained variational Hartree–Fock method for excited states of the same symmetry as the ground state [Chem. Phys. Lett. 287, 189 (1998)] is combined with the effective local potential (ELP) method [J. Chem. Phys. 125, 081104 (2006)] to generate Kohn–Sham-type exact-exchange potentials for singly excited states of many-electron systems. Illustrative examples include the three lowest 2S states of the Li and Na atoms and the three lowest 3S states of He and Be. For the systems studied, excited-state ELPs differ from the corresponding ground-state potentials in two respects: They are less negative and have small additional “bumps” in the outer electron region. The technique is general and can be used to approximate excited-state exchange-correlation potentials for other orbital-dependent functionals.
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31.15.xr Self-consistent-field methods
31.50.Df Potential energy surfaces for excited electronic states

Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set

Harald Oberhofer and Jochen Blumberger

J. Chem. Phys. 133, 244105 (2010); http://dx.doi.org/10.1063/1.3507878 (10 pages) | Cited 2 times

Online Publication Date: 22 December 2010

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We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn–Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken–Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q−) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, (〈|H ab |2〉)1/2 = 6.7 mH, is significantly higher than the value obtained for the minimum energy structure, |H ab | = 3.8 mH. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q− in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level.
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34.70.+e Charge transfer
34.20.Gj Intermolecular and atom-molecule potentials and forces
31.15.E- Density-functional theory
31.15.at Molecule transport characteristics; molecular dynamics; electronic structure of polymers

Multidimensional optical spectroscopy of a single molecule in a current-carrying state

S. Rahav and S. Mukamel

J. Chem. Phys. 133, 244106 (2010); http://dx.doi.org/10.1063/1.3517218 (12 pages) | Cited 1 time

Online Publication Date: 23 December 2010

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The nonlinear optical signals from an open system consisting of a molecule connected to metallic leads, in response to a sequence of impulsive pulses, are calculated using a superoperator formalism. Two detection schemes are considered: coherent stimulated emission and incoherent fluorescence. The two provide similar but not identical information. The necessary superoperator correlation functions are evaluated either by converting them to ordinary (Hilbert space) operators which are then expanded in many-body states, or by using Wick's theorem for superoperators to factorize them into nonequilibrium two point Green's functions. As an example we discuss a stimulated Raman process that shows resonances involving two different charge states of the molecule in the same signal.
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33.80.Be Level crossing and optical pumping
42.65.Jx Beam trapping, self-focusing and defocusing; self-phase modulation
33.20.Fb Raman and Rayleigh spectra (including optical scattering)
33.50.Dq Fluorescence and phosphorescence spectra
31.15.-p Calculations and mathematical techniques in atomic and molecular physics

Density-functional expansion methods: Evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations

Timothy J. Giese and Darrin M. York

J. Chem. Phys. 133, 244107 (2010); http://dx.doi.org/10.1063/1.3515479 (10 pages) | Cited 2 times

Online Publication Date: 28 December 2010

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We extend the Kohn–Sham potential energy expansion (VE) to include variations of the kinetic energy density and use the VE formulation with a 6-31G* basis to perform a “Jacob's ladder” comparison of small molecule properties using density functionals classified as being either LDA, GGA, or meta-GGA. We show that the VE reproduces standard Kohn–Sham DFT results well if all integrals are performed without further approximation, and there is no substantial improvement in using meta-GGA functionals relative to GGA functionals. The advantages of using GGA versus LDA functionals becomes apparent when modeling hydrogen bonds. We furthermore examine the effect of using integral approximations to compute the zeroth-order energy and first-order matrix elements, and the results suggest that the origin of the short-range repulsive potential within self-consistent charge density-functional tight-binding methods mainly arises from the approximations made to the first-order matrix elements.
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31.15.E- Density-functional theory
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions

Comparison of one-particle basis set extrapolation to explicitly correlated methods for the calculation of accurate quartic force fields, vibrational frequencies, and spectroscopic constants: Application to H2O, N2H+, NO2+, and C2H2

Xinchuan Huang, Edward F. Valeev, and Timothy J. Lee

J. Chem. Phys. 133, 244108 (2010); http://dx.doi.org/10.1063/1.3506341 (15 pages) | Cited 6 times

Online Publication Date: 28 December 2010

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One-particle basis set extrapolation is compared with one of the new R12 methods for computing highly accurate quartic force fields (QFFs) and spectroscopic data, including molecular structures, rotational constants, and vibrational frequencies for the H2O, N2H+, NO2+, and C2H2 molecules. In general, agreement between the spectroscopic data computed from the best R12 and basis set extrapolation methods is very good with the exception of a few parameters for N2H+ where it is concluded that basis set extrapolation is still preferred. The differences for H2O and NO2+ are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C2H2, however, a known one-particle basis set deficiency for C–C multiple bonds significantly degrades the quality of results obtained from basis set extrapolation and in this case the R12 approach is clearly preferred over one-particle basis set extrapolation. The R12 approach used in the present study was modified in order to obtain high precision electronic energies, which are needed when computing a QFF. We also investigated including core-correlation explicitly in the R12 calculations, but conclude that current approaches are lacking. Hence core-correlation is computed as a correction using conventional methods. Considering the results for all four molecules, it is concluded that R12 methods will soon replace basis set extrapolation approaches for high accuracy electronic structure applications such as computing QFFs and spectroscopic data for comparison to high-resolution laboratory or astronomical observations, provided one uses a robust R12 method as we have done here. The specific R12 method used in the present study, CCSD(T)R12, incorporated a reformulation of one intermediate matrix in order to attain machine precision in the electronic energies. Final QFFs for N2H+ and NO2+ were computed, including basis set extrapolation, core-correlation, scalar relativity, and higher-order correlation and then used to compute highly accurate spectroscopic data for all isotopologues. Agreement with high-resolution experiment for 14N2H+ and 14N2D+ was excellent, but for 14N16O2+ agreement for the two stretching fundamentals is outside the expected residual uncertainty in the theoretical values, and it is concluded that there is an error in the experimental quantities. It is hoped that the highly accurate spectroscopic data presented for the minor isotopologues of N2H+ and NO2+ will be useful in the interpretation of future laboratory or astronomical observations.
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33.20.Tp Vibrational analysis
33.20.Sn Rotational analysis
31.15.bw Coupled-cluster theory
33.15.Fm Bond strengths, dissociation energies

Aggregation work at polydisperse micellization: Ideal solution and “dressed micelle” models comparing to molecular dynamics simulations

S. V. Burov and A. K. Shchekin

J. Chem. Phys. 133, 244109 (2010); http://dx.doi.org/10.1063/1.3519815 (9 pages)

Online Publication Date: 28 December 2010

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General thermodynamic relations for the work of polydisperse micelle formation in the model of ideal solution of molecular aggregates in nonionic surfactant solution and the model of “dressed micelles” in ionic solution have been considered. In particular, the dependence of the aggregation work on the total concentration of nonionic surfactant has been analyzed. The analogous dependence for the work of formation of ionic aggregates has been examined with regard to existence of two variables of a state of an ionic aggregate, the aggregation numbers of surface active ions and counterions. To verify the thermodynamic models, the molecular dynamics simulations of micellization in nonionic and ionic surfactant solutions at two total surfactant concentrations have been performed. It was shown that for nonionic surfactants, even at relatively high total surfactant concentrations, the shape and behavior of the work of polydisperse micelle formation found within the model of the ideal solution at different total surfactant concentrations agrees fairly well with the numerical experiment. For ionic surfactant solutions, the numerical results indicate a strong screening of ionic aggregates by the bound counterions. This fact as well as independence of the coefficient in the law of mass action for ionic aggregates on total surfactant concentration and predictable behavior of the “waterfall” lines of surfaces of the aggregation work upholds the model of “dressed” ionic aggregates.
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82.70.Dd Colloids
82.70.Uv Surfactants, micellar solutions, vesicles, lamellae, amphiphilic systems, (hydrophilic and hydrophobic interactions)
61.20.Ja Computer simulation of liquid structure

Local CC2 response method for triplet states based on Laplace transform: Excitation energies and first-order properties

Katrin Freundorfer, Daniel Kats, Tatiana Korona, and Martin Schütz

J. Chem. Phys. 133, 244110 (2010); http://dx.doi.org/10.1063/1.3506684 (15 pages) | Cited 6 times

Online Publication Date: 28 December 2010

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A new multistate local CC2 response method for calculating excitation energies and first-order properties of excited triplet states in extended molecular systems is presented. The Laplace transform technique is employed to partition the left/right local CC2 eigenvalue problems as well as the linear equations determining the Lagrange multipliers needed for the properties. The doubles part in the equations can then be inverted on-the-fly and only effective equations for the singles part must be solved iteratively. The local approximation presented here is adaptive and state-specific. The density-fitting method is utilized to approximate the electron-repulsion integrals. The accuracy of the new method is tested by comparison to canonical reference values for a set of 12 test molecules and 62 excited triplet states. As an illustrative application example, the lowest four triplet states of 3-(5-(5-(4-(bis(4-(hexyloxy)phenyl)amino)phenyl)thiophene-2-yl)thiophene-2-yl)-2-cyanoacrylic acid, an organic sensitizer for solar-cell applications, are computed in the present work. No triplet charge-transfer states are detected among these states. This situation contrasts with the singlet states of this molecule, where the lowest singlet state has been recently found to correspond to an excited state with a pronounced charge-transfer character having a large transition strength.
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31.15.vj Electron correlation calculations for atoms and ions: excited states
31.15.ag Excitation energies and lifetimes; oscillator strengths

A smooth, nonsingular, and faithful discretization scheme for polarizable continuum models: The switching/Gaussian approach

Adrian W. Lange and John M. Herbert

J. Chem. Phys. 133, 244111 (2010); http://dx.doi.org/10.1063/1.3511297 (18 pages) | Cited 5 times

Online Publication Date: 28 December 2010

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Polarizable continuum models (PCMs) are a widely used family of implicit solvent models based on reaction-field theory and boundary-element discretization of the solute/continuum interface. An often overlooked aspect of these theories is that discretization of the interface typically does not afford a continuous potential energy surface for the solute. In addition, we show that discretization can lead to numerical singularities and violations of exact variational conditions. To fix these problems, we introduce the switching/Gaussian (SWIG) method, a discretization scheme that overcomes several longstanding problems with PCMs. Our approach generalizes a procedure introduced by York and Karplus [J. Phys. Chem. A 103, 11060 (1999)], extending it beyond the conductor-like screening model. Comparison to other purportedly smooth PCM implementations reveals certain artifacts in these alternative approaches, which are avoided using the SWIG methodology. The versatility of our approach is demonstrated via geometry optimizations, vibrational frequency calculations, and molecular dynamics simulations, for solutes described using quantum mechanics and molecular mechanics.
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31.15.xv Molecular dynamics and other numerical methods
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.50.-x Potential energy surfaces
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

An adaptive coupled-cluster theory: @CC approach

Dmitry I. Lyakh and Rodney J. Bartlett

J. Chem. Phys. 133, 244112 (2010); http://dx.doi.org/10.1063/1.3515476 (15 pages) | Cited 4 times

Online Publication Date: 28 December 2010

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A formulation of an adaptive coupled-cluster theory is presented. The method automatically “adjusts” to any state of an electronic system and converges to the full CI limit, thus being capable of describing both single- and multireference phenomena. Adaptivity is accomplished through a guided selection of a compact set of cluster amplitudes as required for a proper description of the electronic system under consideration. The approach suggested is of “black-box” type. A special importance-selection function (discriminatory function) is explicitly introduced for the guided selection of variables involved in the theoretical model. The method is tested on molecules which exhibit strong multireference character in the region of chemical bond elongation. An unambiguous comparison with formally exact full CI solutions shows that the method is capable of providing mHartee accuracy using a rather compact set of cluster amplitudes.
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31.15.bw Coupled-cluster theory
33.15.Fm Bond strengths, dissociation energies
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations

The flux-flux correlation function for anharmonic barriers

Arseni Goussev, Roman Schubert, Holger Waalkens, and Stephen Wiggins

J. Chem. Phys. 133, 244113 (2010); http://dx.doi.org/10.1063/1.3518425 (8 pages)

Online Publication Date: 28 December 2010

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The flux-flux correlation function formalism is a standard and widely used approach for the computation of reaction rates. In this paper we introduce a method to compute the classical and quantum flux-flux correlation functions for anharmonic barriers essentially analytically through the use of the classical and quantum normal forms. In the quantum case we show that for a general f degree-of-freedom system having an index one saddle the quantum normal form reduces the computation of the flux-flux correlation function to that of an effective one-dimensional anharmonic barrier. The example of the computation of the quantum flux-flux correlation function for a fourth order anharmonic barrier is worked out in detail, and we present an analytical expression for the quantum mechanical microcanonical flux-flux correlation function. We then give a discussion of the short-time and harmonic limits.
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82.20.Pm Rate constants, reaction cross sections, and activation energies

Escape from the potential well: Competition between long jumps and long waiting times

Bartłomiej Dybiec

J. Chem. Phys. 133, 244114 (2010); http://dx.doi.org/10.1063/1.3511722 (8 pages) | Cited 1 time

Online Publication Date: 28 December 2010

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Within a concept of the fractional diffusion equation and subordination, the paper examines the influence of a competition between long waiting times and long jumps on the escape from the potential well. Applying analytical arguments and numerical methods, we demonstrate that the presence of long waiting times distributed according to a power-law distribution with a diverging mean leads to very general asymptotic properties of the survival probability. The observed survival probability asymptotically decays like a power law whose form is not affected by the value of the exponent characterizing the power law jump length distribution. It is demonstrated that this behavior is typical of and generic for systems exhibiting long waiting times. We also show that the survival probability has a universal character not only asymptotically, but also at small times. Finally, it is indicated which properties of the first passage time density are sensitive to the exact value of the exponent characterizing the jump length distribution.
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05.60.-k Transport processes
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion

Crystal nucleation of hard spheres using molecular dynamics, umbrella sampling, and forward flux sampling: A comparison of simulation techniques

L. Filion, M. Hermes, R. Ni, and M. Dijkstra

J. Chem. Phys. 133, 244115 (2010); http://dx.doi.org/10.1063/1.3506838 (15 pages) | Cited 12 times

Online Publication Date: 29 December 2010

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Over the last number of years several simulation methods have been introduced to study rare events such as nucleation. In this paper we examine the crystal nucleation rate of hard spheres using three such numerical techniques: molecular dynamics, forward flux sampling, and a Bennett–Chandler-type theory where the nucleation barrier is determined using umbrella sampling simulations. The resulting nucleation rates are compared with the experimental rates of Harland and van Megen [Phys. Rev. E 55, 3054 (1997)], Sinn et al. [Prog. Colloid Polym. Sci. 118, 266 (2001)], Schätzel and Ackerson [Phys. Rev. E 48, 3766 (1993)], and the predicted rates for monodisperse and 5% polydisperse hard spheres of Auer and Frenkel [Nature 409, 1020 (2001)]. When the rates are examined in units of the long-time diffusion coefficient, we find agreement between all the theoretically predicted nucleation rates, however, the experimental results display a markedly different behavior for low supersaturation. Additionally, we examined the precritical nuclei arising in the molecular dynamics, forward flux sampling, and umbrella sampling simulations. The structure of the nuclei appears independent of the simulation method, and in all cases, the nuclei contains on average significantly more face-centered-cubic ordered particles than hexagonal-close-packed ordered particles.
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82.60.Nh Thermodynamics of nucleation

Understanding free-energy perturbation calculations through a model of harmonic oscillators: Theory and implications to improve the sampling efficiency by molecular simulation

Di Wu

J. Chem. Phys. 133, 244116 (2010); http://dx.doi.org/10.1063/1.3511703 (14 pages) | Cited 1 time

Online Publication Date: 30 December 2010

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Free-energy perturbation calculation is frequently used to calculate free-energy differences because it is easy to implement and the computation is fast. However, the calculation is subject to large inaccuracies in some circumstances due to the insufficient sampling of the relevant tails of the energy-difference distributions. Here we expand this knowledge of insufficient sampling into a two-dimensional (2D) energy space using a model of harmonic oscillators. We show analytically the relation between the energies of the sampling system and those of the desired target energy spaces, which provide the basis to understand the difficulties in free-energy perturbation calculations. We clarify the reasons of the inaccurate calculation in the different harmonic cases that stem from the spatial separations of the reference and the target energy pairs located in the two-dimensional energy space. The potential-energy space introduced into this 2D energy-space model provides additional clues to improve the sampling efficiency. Based on this understanding, we propose two ways to calculate the free-energy differences using the two schemes of the distribution method. We show that the distribution method implemented in the appropriate energy space—the energy-difference space and the potential-energy space, respectively—can improve the calculation of free energies in different circumstances. This analysis implies that the sampling can be improved if it is directed toward the appropriate region in the potential-energy space, which is easily implemented in various types of free-energy calculations. To test this, we calculate the free-energy surface of alanine dipeptide in gas phase and in aqueous phase, respectively. We demonstrate that the free-energy surface calculation is improved when the biased sampling of the potential energy is integrated into the sampling scheme.
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31.50.-x Potential energy surfaces
05.70.Ce Thermodynamic functions and equations of state
31.15.xp Perturbation theory

A cutoff phenomenon in accelerated stochastic simulations of chemical kinetics via flow averaging (FLAVOR-SSA)

Basil Bayati, Houman Owhadi, and Petros Koumoutsakos

J. Chem. Phys. 133, 244117 (2010); http://dx.doi.org/10.1063/1.3518419 (6 pages)

Online Publication Date: 30 December 2010

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We present a simple algorithm for the simulation of stiff, discrete-space, continuous-time Markov processes. The algorithm is based on the concept of flow averaging for the integration of stiff ordinary and stochastic differential equations and ultimately leads to a straightforward variation of the the well-known stochastic simulation algorithm (SSA). The speedup that can be achieved by the present algorithm [flow averaging integrator SSA (FLAVOR-SSA)] over the classical SSA comes naturally at the expense of its accuracy. The error of the proposed method exhibits a cutoff phenomenon as a function of its speed-up, allowing for optimal tuning. Two numerical examples from chemical kinetics are provided to illustrate the efficiency of the method.
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82.20.Uv Stochastic theories of rate constants
02.30.Hq Ordinary differential equations
82.20.Fd Collision theories; trajectory models
02.50.Ga Markov processes
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Ground and excited electronic states of azobenzene: A quantum Monte Carlo study

M. Dubecký, R. Derian, L. Mitas, and I. Štich

J. Chem. Phys. 133, 244301 (2010); http://dx.doi.org/10.1063/1.3506028 (5 pages) | Cited 2 times

Online Publication Date: 22 December 2010

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Large–scale quantum Monte Carlo (QMC) calculations of ground and excited singlet states of both conformers of azobenzene are presented. Remarkable accuracy is achieved by combining medium accuracy quantum chemistry methods with QMC. The results not only reproduce measured values with chemical accuracy but the accuracy is sufficient to identify part of experimental results which appear to be biased. Novel analysis of nodal surface structure yields new insights and control over their convergence, providing boost to the chemical accuracy electronic structure methods of large molecular systems.
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31.15.vq Electron correlation calculations for polyatomic molecules
33.15.Bh General molecular conformation and symmetry; stereochemistry
02.70.Ss Quantum Monte Carlo methods

Metastable anions of dinitrobenzene: Resonances for electron attachment and kinetic energy release

A. Mauracher, S. Denifl, A. Edtbauer, M. Hager, M. Probst, O. Echt, T. D. Märk, P. Scheier, T. A. Field, and K. Graupner

J. Chem. Phys. 133, 244302 (2010); http://dx.doi.org/10.1063/1.3514931 (9 pages)

Online Publication Date: 22 December 2010

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Attachment of free, low-energy electrons to dinitrobenzene (DNB) in the gas phase leads to DNB− as well as several fragment anions. DNB−, (DNB-H)−, (DNB-NO)−, (DNB-2NO)−, and (DNB-NO2)− are found to undergo metastable (unimolecular) dissociation. A rich pattern of resonances in the yield of these metastable reactions versus electron energy is observed; some resonances are highly isomer-specific. Most metastable reactions are accompanied by large average kinetic energy releases (KER) that range from 0.5 to 1.32 eV, typical of complex rearrangement reactions, but (1,3-DNB-H)− features a resonance with a KER of only 0.06 eV for loss of NO. (1,3-DNB-NO)− offers a rare example of a sequential metastable reaction, namely, loss of NO followed by loss of CO to yield C5H4O− with a large KER of 1.32 eV. The G4(MP2) method is applied to compute adiabatic electron affinities and reaction energies for several of the observed metastable channels.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Fm Bond strengths, dissociation energies

Microwave spectra, structure, and dynamics of the weakly bound complex, N2 CO2

Daniel J. Frohman, Edwin S. Contreras, Ross S. Firestone, Stewart E. Novick, and William Klemperer

J. Chem. Phys. 133, 244303 (2010); http://dx.doi.org/10.1063/1.3517061 (6 pages)

Online Publication Date: 23 December 2010

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The Fourier transform microwave spectra of the various isotopologs of the weakly bound complex of carbon dioxide with the most abundant molecule in the atmosphere, nitrogen, have been measured. The structure of the complex has been determined and evidence for the inversion of the N2 is presented. The molecule is T-shaped, with the OCO forming the cross of the T, a structure consistent with that deduced from a previous rotationally resolved infrared experiment. A significant wide-amplitude bending motion of the N2 is deduced from the values of the (nearly identical) nuclear quadrupole coupling constants of the nitrogen nuclei. The spectroscopic results are compared with high-quality ab initio calculations. We examine the consequences of the N2 CO2 complex formation in the atmosphere upon the greenhouse warming potential of carbon dioxide.
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33.20.Bx Radio-frequency and microwave spectra
33.25.+k Nuclear resonance and relaxation

Dynamics and mechanism of the non-adiabatic transitions from the ungerade I2(D0+u) state induced by collisions with rare gas atoms

M. E. Akopyan, E. I. Khadikova, S. S. Lukashov, S. A. Poretsky, A. M. Pravilov, A. A. Buchachenko, and Yu. V. Suleimanov

J. Chem. Phys. 133, 244304 (2010); http://dx.doi.org/10.1063/1.3517503 (10 pages) | Cited 1 time

Online Publication Date: 28 December 2010

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The stepwise three-photon two-color laser excitation scheme is used for selective population of the first-tier ion-pair D0+u state of molecular iodine. Collection and analysis of the luminescence after the excitation of the vD = 6, 8, 13 and 18 vibronic levels of the D state in the pure iodine vapor and the gas-phase mixtures with He, Ar and Xe provide the total and, whenever possible, partial rate constants for the collision-induced non-adiabatic transitions to the other ion-pair states of the first tier. Comparison with the analogous data obtained previously for the non-adiabatic transitions from the E0+g state reveals the similarity between two cases. For He, the D ↔ E transitions are preferable, whereas for Ar and Xe transitions to the D′ and β states dominate at vD = 6, 8 and 13, in accord with the statistical considerations. Efficient population of the δ state at vD = 18 in Ar and Xe is the most prominent non-statistical feature observed. The vibrational product state distributions for the D → E transitions are also obtained. In contrast to the previously studied E → D transition, they show significant positive vibronic energy transfer. The measurements for He and Ar are accompanied by the quantum scattering calculations that reproduce well the main qualitative features of the experimental results.
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33.80.Wz Other multiphoton processes
82.20.Pm Rate constants, reaction cross sections, and activation energies
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
33.50.-j Fluorescence and phosphorescence; radiationless transitions, quenching (intersystem crossing, internal conversion)
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