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28 Jun 2011

Volume 134, Issue 24, Articles (24xxxx)

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J. Chem. Phys. 134, 244501 (2011); http://dx.doi.org/10.1063/1.3593064 (14 pages)

Haruka Kyakuno, Kazuyuki Matsuda, Hitomi Yahiro, Yu Inami, Tomoko Fukuoka, Yasumitsu Miyata, Kazuhiro Yanagi, Yutaka Maniwa, Hiromichi Kataura, Takeshi Saito, Motoo Yumura, and Sumio Iijima
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Communication: Universality of the melting curves for a wide range of interaction potentials

Sergey A. Khrapak, Manis Chaudhuri, and Gregor E. Morfill

J. Chem. Phys. 134, 241101 (2011); http://dx.doi.org/10.1063/1.3605659 (4 pages) | Cited 1 time

Online Publication Date: 23 June 2011

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We demonstrate that the melting curves of various model systems of interacting particles collapse to (or are located very close to) a universal master curve on a plane of appropriately chosen scaled variables. The physics behind this universality is discussed. An equation for the emerging “universal melting curve” is proposed. The obtained results can be used to approximately predict melting of various substances in a wide range of conditions.
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64.70.dj Melting of specific substances
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Communication: A new spectroscopic window on hydroxyl radicals using UV + VUV resonant ionization

Joseph M. Beames, Fang Liu, Marsha I. Lester, and Craig Murray

J. Chem. Phys. 134, 241102 (2011); http://dx.doi.org/10.1063/1.3608061 (4 pages) | Cited 1 time

Online Publication Date: 24 June 2011

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A 1 + 1′ multiphoton ionization (MPI) detection scheme for OH radicals is presented. The spectroscopic approach combines initial excitation on the well-characterized A2Σ+–X2Π band system with vacuum ultraviolet (VUV) ionization via autoionizing Rydberg states that converge on the OH+ A3Π ion state. Jet-cooled MPI spectra on the (1,0) and (2,0) bands show anomalous rotational line intensities, while initial excitation on the (0,0) band does not lead to detectable OH+ ions. The onset of ionization with the (1,0) band is attributed to an energetic threshold; the combined UV + VUV photon energies are above the first member of the autoionizing (A3Π)nd Rydberg series. Comparison of the OH 1 + 1′ MPI signal with that from single photon VUV ionization of NO indicates that the cross section for photoionization from OH A2Σ+, v′ = 1 is on the order of 10−17 cm2.
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33.80.Eh Autoionization, photoionization, and photodetachment
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
33.70.Fd Absolute and relative line and band intensities
33.20.Sn Rotational analysis
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Communication: Linear-expansion shooting techniques for accelerating self-consistent field convergence

Yan Alexander Wang, Chi Yung Yam, Ya Kun Chen, and GuanHua Chen

J. Chem. Phys. 134, 241103 (2011); http://dx.doi.org/10.1063/1.3609242 (4 pages)

Online Publication Date: 30 June 2011

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Based on the corrected Hohenberg-Kohn-Sham total energy density functional [Y. A. Zhang and Y. A. Wang, J. Chem. Phys. 130, 144116 (2009)]10.1063/1.3104662, we have developed two linear-expansion shooting techniques (LIST)– direct LIST (LISTd) and indirect LIST (LISTi), to accelerate the convergence of self-consistent field (SCF) calculations. Case studies show that overall LISTi is the most robust and efficient algorithm for accelerating SCF convergence, whereas LISTd is advantageous in the early stage of an SCF process. More importantly, LISTi outperforms Pulay's direct inversion in the iterative subspace (DIIS) [P. Pulay, J. Comput. Chem. 3, 556 (1982)]10.1002/jcc.540030413 and its two recent improvements, energy-DIIS [K. N. Kudin, G. E. Scuseria, and E. Cancès, J. Chem. Phys. 116, 8255 (2002)]10.1063/1.1470195 and augmented Roothaan-Hall energy-DIIS [X. Hu and W. Yang, J. Chem. Phys. 132, 054109 (2010)]10.1063/1.3304922.
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31.15.xr Self-consistent-field methods
31.15.E- Density-functional theory
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A multiconfigurational time-dependent Hartree-Fock method for excited electronic states. I. General formalism and application to open-shell states

R. P. Miranda, A. J. Fisher, L. Stella, and A. P. Horsfield

J. Chem. Phys. 134, 244101 (2011); http://dx.doi.org/10.1063/1.3600397 (10 pages)

Online Publication Date: 22 June 2011

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The solution of the time-dependent Schrödinger equation for systems of interacting electrons is generally a prohibitive task, for which approximate methods are necessary. Popular approaches, such as the time-dependent Hartree-Fock (TDHF) approximation and time-dependent density functional theory (TDDFT), are essentially single-configurational schemes. TDHF is by construction incapable of fully accounting for the excited character of the electronic states involved in many physical processes of interest; TDDFT, although exact in principle, is limited by the currently available exchange-correlation functionals. On the other hand, multiconfigurational methods, such as the multiconfigurational time-dependent Hartree-Fock (MCTDHF) approach, provide an accurate description of the excited states and can be systematically improved. However, the computational cost becomes prohibitive as the number of degrees of freedom increases, and thus, at present, the MCTDHF method is only practical for few-electron systems. In this work, we propose an alternative approach which effectively establishes a compromise between efficiency and accuracy, by retaining the smallest possible number of configurations that catches the essential features of the electronic wavefunction. Based on a time-dependent variational principle, we derive the MCTDHF working equation for a multiconfigurational expansion with fixed coefficients and specialise to the case of general open-shell states, which are relevant for many physical processes of interest.
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31.15.xr Self-consistent-field methods
31.50.Df Potential energy surfaces for excited electronic states
03.65.Ge Solutions of wave equations: bound states

A multiconfigurational time-dependent Hartree-Fock method for excited electronic states. II. Coulomb interaction effects in single conjugated polymer chains

R. P. Miranda, A. J. Fisher, L. Stella, and A. P. Horsfield

J. Chem. Phys. 134, 244102 (2011); http://dx.doi.org/10.1063/1.3600404 (13 pages)

Online Publication Date: 22 June 2011

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Conjugated polymers have attracted considerable attention in the last few decades due to their potential for optoelectronic applications. A key step that needs optimisation is charge carrier separation following photoexcitation. To understand better the dynamics of the exciton prior to charge separation, we have performed simulations of the formation and dynamics of localised excitations in single conjugated polymer strands. We use a nonadiabatic molecular dynamics method which allows for the coupled evolution of the nuclear degrees of freedom and of multiconfigurational electronic wavefunctions. We show the relaxation of electron-hole pairs to form excitons and oppositely charged polaron pairs and discuss the modifications to the relaxation process predicted by the inclusion of the Coulomb interaction between the carriers. The issue of charge photogeneration in conjugated polymers in dilute solution is also addressed.
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71.20.Rv Polymers and organic compounds
71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)
71.15.Pd Molecular dynamics calculations (Car-Parrinello) and other numerical simulations
71.38.-k Polarons and electron-phonon interactions
71.35.-y Excitons and related phenomena
71.15.Qe Excited states: methodology

Quantum effects in energy and charge transfer in an artificial photosynthetic complex

Pulak Kumar Ghosh, Anatoly Yu. Smirnov, and Franco Nori

J. Chem. Phys. 134, 244103 (2011); http://dx.doi.org/10.1063/1.3600341 (13 pages) | Cited 2 times

Online Publication Date: 23 June 2011

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We investigate the quantum dynamics of energy and charge transfer in a wheel-shaped artificial photosynthetic antenna-reaction center complex. This complex consists of six light-harvesting chromophores and an electron-acceptor fullerene. To describe quantum effects on a femtosecond time scale, we derive the set of exact non-Markovian equations for the Heisenberg operators of this photosynthetic complex in contact with a Gaussian heat bath. With these equations we can analyze the regime of strong system-bath interactions, where reorganization energies are of the order of the intersite exciton couplings. We show that the energy of the initially excited antenna chromophores is efficiently funneled to the porphyrin-fullerene reaction center, where a charge-separated state is set up in a few picoseconds, with a quantum yield of the order of 95%. In the single-exciton regime, with one antenna chromophore being initially excited, we observe quantum beatings of energy between two resonant antenna chromophores with a decoherence time of ∼100 fs. We also analyze the double-exciton regime, when two porphyrin molecules involved in the reaction center are initially excited. In this regime we obtain pronounced quantum oscillations of the charge on the fullerene molecule with a decoherence time of about 20 fs (at liquid nitrogen temperatures). These results show a way to directly detect quantum effects in artificial photosynthetic systems.
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82.50.Hp Processes caused by visible and UV light
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.20.Rp State to state energy transfer
36.40.Cg Electronic and magnetic properties of clusters
33.80.-b Photon interactions with molecules
34.70.+e Charge transfer

A comparison of accelerators for direct energy minimization in electronic structure calculations

Kurt Baarman and Joost VandeVondele

J. Chem. Phys. 134, 244104 (2011); http://dx.doi.org/10.1063/1.3603445 (6 pages)

Online Publication Date: 23 June 2011

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We compare three different methods for direct energy minimization in electronic structure calculations where the gradient of the energy functional with respect to the molecular orbitals is available. These methods make use of the preconditioned gradient to increase robustness. An orbital transformation is used to ensure that the orthogonality constraint on the orbitals remains satisfied when using standard minimization methods. In addition, we propose an adaptive scheme for estimating the curvature of the energy functional to increase the performance of a line search free quasi-Newton method. We show that the performance of all methods is similar when robustness of the methods is ensured.
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31.15.E- Density-functional theory
31.10.+z Theory of electronic structure, electronic transitions, and chemical binding

Index k saddles and dividing surfaces in phase space with applications to isomerization dynamics

Peter Collins, Gregory S. Ezra, and Stephen Wiggins

J. Chem. Phys. 134, 244105 (2011); http://dx.doi.org/10.1063/1.3602465 (19 pages)

Online Publication Date: 23 June 2011

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In this paper, we continue our studies of the phase space geometry and dynamics associated with index k saddles (k > 1) of the potential energy surface. Using Poincaré-Birkhoff normal form (NF) theory, we give an explicit formula for a “dividing surface” in phase space, i.e., a codimension one surface (within the energy shell) through which all trajectories that “cross” the region of the index k saddle must pass. With a generic non-resonance assumption, the normal form provides k (approximate) integrals that describe the saddle dynamics in a neighborhood of the index k saddle. These integrals provide a symbolic description of all trajectories that pass through a neighborhood of the saddle. We give a parametrization of the dividing surface which is used as the basis for a numerical method to sample the dividing surface. Our techniques are applied to isomerization dynamics on a potential energy surface having four minima; two symmetry related pairs of minima are connected by low energy index 1 saddles, with the pairs themselves connected via higher energy index 1 saddles and an index 2 saddle at the origin. We compute and sample the dividing surface and show that our approach enables us to distinguish between concerted crossing (“hilltop crossing”) isomerizing trajectories and those trajectories that are not concerted crossing (potentially sequentially isomerizing trajectories). We then consider the effect of additional “bath modes” on the dynamics, by a study of a four degree-of-freedom system. For this system we show that the normal form and dividing surface can be realized and sampled and that, using the approximate integrals of motion and our symbolic description of trajectories, we are able to choose initial conditions corresponding to concerted crossing isomerizing trajectories and (potentially) sequentially isomerizing trajectories.
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82.30.Qt Isomerization and rearrangement
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Fd Collision theories; trajectory models

Padé spectrum decompositions of quantum distribution functions and optimal hierarchical equations of motion construction for quantum open systems

Jie Hu, Meng Luo, Feng Jiang, Rui-Xue Xu, and YiJing Yan

J. Chem. Phys. 134, 244106 (2011); http://dx.doi.org/10.1063/1.3602466 (10 pages) | Cited 1 time

Online Publication Date: 23 June 2011

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Padé spectrum decomposition is an optimal sum-over-poles expansion scheme of Fermi function and Bose function [J. Hu, R. X. Xu, and Y. J. Yan, J. Chem. Phys. 133, 101106 (2010)]10.1063/1.3484491. In this work, we report two additional members to this family, from which the best among all sum-over-poles methods could be chosen for different cases of application. Methods are developed for determining these three Padé spectrum decomposition expansions at machine precision via simple algorithms. We exemplify the applications of present development with optimal construction of hierarchical equations-of-motion formulations for nonperturbative quantum dissipation and quantum transport dynamics. Numerical demonstrations are given for two systems. One is the transient transport current to an interacting quantum-dots system, together with the involved high-order co-tunneling dynamics. Another is the non-Markovian dynamics of a spin-boson system.
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05.30.Jp Boson systems
05.30.Fk Fermion systems and electron gas
03.75.Lm Tunneling, Josephson effect, Bose-Einstein condensates in periodic potentials, solitons, vortices, and topological excitations
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion

Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures

John D. Chodera, William C. Swope, Frank Noé, Jan-Hendrik Prinz, Michael R. Shirts, and Vijay S. Pande

J. Chem. Phys. 134, 244107 (2011); http://dx.doi.org/10.1063/1.3592152 (14 pages)

Online Publication Date: 24 June 2011

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Dynamical averages based on functionals of dynamical trajectories, such as time-correlation functions, play an important role in determining kinetic or transport properties of matter. At temperatures of interest, the expectations of these quantities are often dominated by contributions from rare events, making the precise calculation of these quantities by molecular dynamics simulation difficult. Here, we present a reweighting method for combining simulations from multiple temperatures (or from simulated or parallel tempering simulations) to compute an optimal estimate of the dynamical properties at the temperature of interest without the need to invoke an approximate kinetic model (such as the Arrhenius law). Continuous and differentiable estimates of these expectations at any temperature in the sampled range can also be computed, along with an assessment of the associated statistical uncertainty. For rare events, aggregating data from multiple temperatures can produce an estimate with the desired precision at greatly reduced computational cost compared with simulations conducted at a single temperature. Here, we describe use of the method for the canonical (NVT) ensemble using four common models of dynamics (canonical distribution of Hamiltonian trajectories, Andersen thermostatting, Langevin, and overdamped Langevin or Brownian dynamics), but it can be applied to any thermodynamic ensemble provided the ratio of path probabilities at different temperatures can be computed. To illustrate the method, we compute a time-correlation function for solvated terminally-blocked alanine peptide across a range of temperatures using trajectories harvested using a modified parallel tempering protocol.
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82.20.Fd Collision theories; trajectory models
31.15.xv Molecular dynamics and other numerical methods
82.20.Wt Computational modeling; simulation

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

Jan-Hendrik Prinz, John D. Chodera, Vijay S. Pande, William C. Swope, Jeremy C. Smith, and Frank Noé

J. Chem. Phys. 134, 244108 (2011); http://dx.doi.org/10.1063/1.3592153 (14 pages)

Online Publication Date: 24 June 2011

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Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.
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87.15.R- Reactions and kinetics
82.30.-b Specific chemical reactions; reaction mechanisms
02.50.-r Probability theory, stochastic processes, and statistics
02.60.-x Numerical approximation and analysis

Ab initio study of excited state electronic circular dichroism. Two prototype cases: Methyl oxirane and R-(+)-1,1′-bi(2-naphthol)

Antonio Rizzo and Olav Vahtras

J. Chem. Phys. 134, 244109 (2011); http://dx.doi.org/10.1063/1.3602219 (13 pages)

Online Publication Date: 27 June 2011

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A computational approach to the calculation of excited state electronic circular dichroism (ESECD) spectra of chiral molecules is discussed. Frequency dependent quadratic response theory is employed to compute the rotatory strength for transitions between excited electronic states, by employing both a magnetic gauge dependent and a (velocity-based) magnetic gauge independent approach. Application is made to the lowest excited states of two prototypical chiral molecules, propylene oxide, also known as 1,2-epoxypropane or methyl oxirane, and R-(+)-1,1′-bi(2-naphthol), or BINOL. The dependence of the rotatory strength for transitions between the lowest three excited states of methyl oxirane upon the quality and extension of the basis set is analyzed, by employing a hierarchy of correlation consistent basis sets. Once established that basis sets of at least triple zeta quality, and at least doubly augmented, are sufficient to ensure sufficiently converged results, at least at the Hartree-Fock self-consistent field (HF-SCF) level, the rotatory strengths for all transitions between the lowest excited electronic states of methyl oxirane are computed and analyzed, employing HF-SCF, and density functional theory (DFT) electronic structure models. For DFT, both the popular B3LYP and its recently highly successful CAM-B3LYP extension are exploited. The strong dependence of the spectra upon electron correlation is highlighted. A HF-SCF and DFT study is carried out also for BINOL, a system where excited states show the typical pairing structure arising from the interaction of the two monomeric moieties, and whose conformational changes following photoexcitation were studied recently with via time-resolved CD.
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33.55.+b Optical activity and dichroism
31.15.xr Self-consistent-field methods
31.15.vq Electron correlation calculations for polyatomic molecules
31.15.E- Density-functional theory
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.ae Electronic structure and bonding characteristics

Benchmark of density functional theory methods on the prediction of bond energies and bond distances of noble-gas containing molecules

Tai-Yuan Lai, Chun-Yu Yang, Hsiao-Jing Lin, Chang-Yu Yang, and Wei-Ping Hu

J. Chem. Phys. 134, 244110 (2011); http://dx.doi.org/10.1063/1.3603455 (8 pages) | Cited 1 time

Online Publication Date: 28 June 2011

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We have tested three pure density functional theory (DFT) functionals, BLYP, MPWPW91, MPWB95, and ten hybrid DFT functionals, B3LYP, B3P86, B98, MPW1B95, MPW1PW91, BMK, M05-2X, M06-2X, B2GP-PLYP, and DSD-BLYP with a series of commonly used basis sets on the performance of predicting the bond energies and bond distances of 31 small neutral noble-gas containing molecules. The reference structures were obtained using the CCSD(T)/aug-cc-pVTZ theory and the reference energies were based on the calculation at the CCSD(T)/CBS level. While in general the hybrid functionals performed significantly better than the pure functionals, our tests showed a range of performance by these hybrid functionals. For the bond energies, the MPW1B95/6-311+G(2df,2pd), BMK/aug-cc-pVTZ, B2GP-PLYP/aug-cc-pVTZ, and DSD-BLYP/aug-cc-pVTZ methods stood out with mean unsigned errors of 2.0−2.3 kcal/mol per molecule. For the bond distances, the MPW1B95/6-311+G(2df,2pd), MPW1PW91/6-311+G(2df,2pd), and B3P86/6-311+G(2df,2pd), DSD-BLYP/6-311+G(2df,2pd), and DSD-BLYP/aug-cc-pVTZ methods stood out with mean unsigned errors of 0.008−0.013 Å per bond. The current study showed that a careful selection of DFT functionals is very important in the study of noble-gas chemistry, and the most recommended methods are MPW1B95/6-311+G(2df,2pd) and DSD-BLYP/aug-cc-pVTZ.
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31.15.E- Density-functional theory
33.15.Dj Interatomic distances and angles
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
31.15.bw Coupled-cluster theory

Comparison of two adaptive temperature-based replica exchange methods applied to a sharp phase transition of protein unfolding-folding

Michael S. Lee and Mark A. Olson

J. Chem. Phys. 134, 244111 (2011); http://dx.doi.org/10.1063/1.3603964 (7 pages)

Online Publication Date: 28 June 2011

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Temperature-based replica exchange (T-ReX) enhances sampling of molecular dynamics simulations by autonomously heating and cooling simulation clients via a Metropolis exchange criterion. A pathological case for T-ReX can occur when a change in state (e.g., folding to unfolding of a protein) has a large energetic difference over a short temperature interval leading to insufficient exchanges amongst replica clients near the transition temperature. One solution is to allow the temperature set to dynamically adapt in the temperature space, thereby enriching the population of clients near the transition temperature. In this work, we evaluated two approaches for adapting the temperature set: a method that equalizes exchange rates over all neighbor temperature pairs and a method that attempts to induce clients to visit all temperatures (dubbed “current maximization”) by positioning many clients at or near the transition temperature. As a test case, we simulated the 57-residue SH3 domain of alpha-spectrin. Exchange rate equalization yielded the same unfolding-folding transition temperature as fixed-temperature ReX with much smoother convergence of this value. Surprisingly, the current maximization method yielded a significantly lower transition temperature, in close agreement with experimental observation, likely due to more extensive sampling of the transition state.
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87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.15.hm Folding dynamics
87.15.ap Molecular dynamics simulation
87.14.E- Proteins

Analytical evaluation of first-order electrical properties based on the spin-free Dirac-Coulomb Hamiltonian

Lan Cheng and Jürgen Gauss

J. Chem. Phys. 134, 244112 (2011); http://dx.doi.org/10.1063/1.3601056 (11 pages) | Cited 3 times

Online Publication Date: 28 June 2011

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We report an analytical scheme for the calculation of first-order electrical properties using the spin-free Dirac-Coulomb (SFDC) Hamiltonian, thereby exploiting the well-developed density-matrix formulations in nonrelativistic coupled-cluster (CC) derivative theory. Orbital relaxation effects are fully accounted for by including the relaxation of the correlated orbitals with respect to orbitals of all types, viz., frozen-core, occupied, virtual, and negative energy state orbitals. To demonstrate the applicability of the presented scheme, we report benchmark calculations for first-order electrical properties of the hydrogen halides, HX with X = F, Cl, Br, I, At, and a first application to the iodo(fluoro)methanes, CHnF3 − nI, n = 0–3. The results obtained from the SFDC calculations are compared to those from nonrelativistic calculations, those obtained via leading-order direct perturbation theory as well as those from full Dirac-Coulomb calculations. It is shown that the full inclusion of spin-free (SF) relativistic effects is necessary to obtain accurate first-order electrical properties in the presence of fifth-row elements. The SFDC scheme is also recommended for applications to systems containing lighter elements because it introduces no extra cost in the rate-determining steps of a CC calculation in comparison to the nonrelativistic case. On the other hand, spin-orbit contributions are generally small for first-order electrical properties of closed-shell molecules and may be handled efficiently by means of perturbation theory.
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31.15.bw Coupled-cluster theory
31.15.xp Perturbation theory
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure

Brueckner doubles coupled cluster method with the polarizable continuum model of solvation

Marco Caricato, Giovanni Scalmani, and Michael J. Frisch

J. Chem. Phys. 134, 244113 (2011); http://dx.doi.org/10.1063/1.3604560 (10 pages) | Cited 2 times

Online Publication Date: 28 June 2011

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We present the theory and implementation for computing the (free) energy and its analytical gradients with the Brueckner doubles (BD) coupled cluster method in solution, in combination with the polarizable continuum model of solvation (PCM). The complete model, called PTED, and an efficient approximation, called PTE, are introduced and tested with numerical examples. Implementation details are also discussed. A comparison with the coupled-cluster singles and doubles CCSD-PCM-PTED and CCSD-PCM-PTE schemes, which use Hartree-Fock (HF) orbitals, is presented. The results show that the two PTED approaches are mostly equivalent, while BD-PCM-PTE is shown to be superior to the corresponding CCSD scheme when the HF reference wave function is unstable. The BD-PCM-PTE scheme, whose computational cost is equivalent to gas phase BD, is therefore a promising approach to study molecular systems with complicated electronic structure in solution.
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31.15.bw Coupled-cluster theory
31.15.xr Self-consistent-field methods

Decoherence and surface hopping: When can averaging over initial conditions help capture the effects of wave packet separation?

Joseph E. Subotnik and Neil Shenvi

J. Chem. Phys. 134, 244114 (2011); http://dx.doi.org/10.1063/1.3603448 (8 pages) | Cited 3 times

Online Publication Date: 29 June 2011

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Fewest-switches surface hopping (FSSH) is a popular nonadiabatic dynamics method which treats nuclei with classical mechanics and electrons with quantum mechanics. In order to simulate the motion of a wave packet as accurately as possible, standard FSSH requires a stochastic sampling of the trajectories over a distribution of initial conditions corresponding, e.g., to the Wigner distribution of the initial quantum wave packet. Although it is well-known that FSSH does not properly account for decoherence effects, there is some confusion in the literature about whether or not this averaging over a distribution of initial conditions can approximate some of the effects of decoherence. In this paper, we not only show that averaging over initial conditions does not generally account for decoherence, but also why it fails to do so. We also show how an apparent improvement in accuracy can be obtained for a fortuitous choice of model problems, even though this improvement is not possible, in general. For a basic set of one-dimensional and two-dimensional examples, we find significantly improved results using our recently introduced augmented FSSH algorithm.
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42.50.Ar Photon statistics and coherence theory
42.25.Kb Coherence
03.65.-w Quantum mechanics
02.50.Ng Distribution theory and Monte Carlo studies

A general formulation for the efficient evaluation of n-electron integrals over products of Gaussian charge distributions with Gaussian geminal functions

Andrew Komornicki and Harry F. King

J. Chem. Phys. 134, 244115 (2011); http://dx.doi.org/10.1063/1.3600745 (19 pages) | Cited 1 time

Online Publication Date: 29 June 2011

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In this work, we present a general formulation for the evaluation of many-electron integrals which arise when traditional one particle expansions are augmented with explicitly correlated Gaussian geminal functions. The integrand is expressed as a product of charge distributions, one for each electron, multiplied by one or more Gaussian geminal factors. Our formulation begins by focusing on the quadratic form that arises in the general n-electron integral. Using the Rys polynomial method for the evaluation of potential energy integrals, we derive a general formula for the evaluation of any n-electron integral. This general expression contains four parameters ω, θ, v, and h, which can be evaluated by an examination of the general quadratic form. Our analysis contains general expressions for any n-electron integral over s-type functions as well as the recursion needed to build up arbitrary angular momentum. The general recursion relation requires at most n + 1 terms for any n-electron integral. To illustrate the general method, we develop explicit expressions for the evaluation of two, three, and four particle electron repulsion integrals as well as two and three particle overlap and nuclear attraction integrals. We conclude our exposition with a discussion of a preliminary computational implementation as well as general computational requirements. Implementation on parallel computers is briefly discussed.
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31.50.-x Potential energy surfaces
31.15.-p Calculations and mathematical techniques in atomic and molecular physics

Mixed quantum-classical simulations of charge transport in organic materials: Numerical benchmark of the Su-Schrieffer-Heeger model

Linjun Wang, David Beljonne, Liping Chen, and Qiang Shi

J. Chem. Phys. 134, 244116 (2011); http://dx.doi.org/10.1063/1.3604561 (8 pages)

Online Publication Date: 29 June 2011

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The electron-phonon coupling is critical in determining the intrinsic charge carrier and exciton transport properties in organic materials. In this study, we consider a Su-Schrieffer-Heeger (SSH) model for molecular crystals, and perform numerical benchmark studies for different strategies of simulating the mixed quantum-classical dynamics. These methods, which differ in the selection of initial conditions and the representation used to solve the time evolution of the quantum carriers, are shown to yield similar equilibrium diffusion properties. A hybrid approach combining molecular dynamics simulations of nuclear motion and quantum-chemical calculations of the electronic Hamiltonian at each geometric configuration appears as an attractive strategy to model charge dynamics in large size systems “on the fly,” yet it relies on the assumption that the quantum carriers do not impact the nuclear dynamics. We find that such an approximation systematically results in overestimated charge-carrier mobilities, with the associated error being negligible when the room-temperature mobility exceeds ∼4.8 cm2/Vs (∼0.14 cm2/Vs) in one-dimensional (two-dimensional) crystals.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
71.35.Pq Charged excitons (trions)
71.38.-k Polarons and electron-phonon interactions
63.20.kd Phonon-electron interactions
72.20.Fr Low-field transport and mobility; piezoresistance

Development and application of the analytical energy gradient for the normalized elimination of the small component method

Wenli Zou, Michael Filatov, and Dieter Cremer

J. Chem. Phys. 134, 244117 (2011); http://dx.doi.org/10.1063/1.3603454 (11 pages) | Cited 2 times

Online Publication Date: 30 June 2011

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The analytical energy gradient of the normalized elimination of the small component (NESC) method is derived for the first time and implemented for the routine calculation of NESC geometries and other first order molecular properties. Essential for the derivation is the correct calculation of the transformation matrix U relating the small component to the pseudolarge component of the wavefunction. The exact form of ∂U/∂λ is derived and its contribution to the analytical energy gradient is investigated. The influence of a finite nucleus model and that of the picture change is determined. Different ways of speeding up the calculation of the NESC gradient are tested. It is shown that first order properties can routinely be calculated in combination with Hartree-Fock, density functional theory (DFT), coupled cluster theory, or any electron correlation corrected quantum chemical method, provided the NESC Hamiltonian is determined in an efficient, but nevertheless accurate way. The general applicability of the analytical NESC gradient is demonstrated by benchmark calculations for NESC/CCSD (coupled cluster with all single and double excitation) and NESC/DFT involving up to 800 basis functions.
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33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.bw Coupled-cluster theory
31.15.E- Density-functional theory
31.15.xr Self-consistent-field methods

Optimizing transition interface sampling simulations

Ernesto E. Borrero, Marcus Weinwurm, and Christoph Dellago

J. Chem. Phys. 134, 244118 (2011); http://dx.doi.org/10.1063/1.3601919 (9 pages) | Cited 1 time

Online Publication Date: 30 June 2011

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We demonstrate that a recently proposed adaptive optimization algorithm for forward flux sampling simulations [E. E. Borrero and F. A. Escobedo, J. Chem. Phys. 129, 024115 (2008)]10.1063/1.2953325 can be easily applied within the framework of transition interface sampling. This optimization algorithm systematically identifies the kinetic bottlenecks along the order parameter used to partition phase space via interfaces and improves the statistical accuracy of the reaction rate constant estimate. In different versions of the algorithm, the number or the placement of the interfaces (or both) are varied in order to allocate the numerical effort in a balanced way. The algorithm is demonstrated for a simple two-dimensional model and for the dipole flip transition of icelike structures inside carbon nanotubes. For these test systems, the optimization yielded an efficiency increase by a factor of 2-15.
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82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Wt Computational modeling; simulation
82.20.Db Transition state theory and statistical theories of rate constants
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Photoelectron imaging spectroscopy of nitroethane anions

Christopher L. Adams and J. Mathias Weber

J. Chem. Phys. 134, 244301 (2011); http://dx.doi.org/10.1063/1.3602467 (8 pages) | Cited 1 time

Online Publication Date: 22 June 2011

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We present low-energy velocity map photoelectron imaging results for bare and Ar solvated nitroethane anions. We report an improved value for the adiabatic electron affinity of nitroethane of (191 ± 6) meV which is used to obtain a C-NO2 bond dissociation energy of (0.589 ± 0.019) eV in nitroethane anion. We assign a weak feature at (27 ± 5) meV electron binding energy to the dipole-bound anion state of nitroethane. Photoelectron angular distributions exhibit increasing anisotropy with increasing kinetic energies. The main contributions to the photoelectron spectrum of nitroethane anion can be assigned to the vibrational modes of the nitro group. Transitions involving torsional motion around the CN bond axis lead to strong spectral congestion. Interpretation of the photoelectron spectrum is assisted by ab initio calculations and Franck-Condon simulations.
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33.60.+q Photoelectron spectra
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
33.20.Tp Vibrational analysis
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Fm Bond strengths, dissociation energies
31.15.ae Electronic structure and bonding characteristics

Non-linear dynamics of the photodissociation of nitrous oxide: Equilibrium points, periodic orbits, and transition states

Frederic Mauguiere, Stavros C. Farantos, Jaime Suarez, and Reinhard Schinke

J. Chem. Phys. 134, 244302 (2011); http://dx.doi.org/10.1063/1.3601754 (12 pages) | Cited 1 time

Online Publication Date: 24 June 2011

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The diffuse vibrational bands, observed in the ultraviolet photodissociation spectrum of nitrous oxide by exciting the molecule in the first 1A′ state, have recently been attributed to resonances localized mainly in the NN stretch and bend degrees of freedom. To further investigate the origin of this localization, fundamental families of periodic orbits emanating from several stationary points of the 1A′ potential energy surface and bifurcations of them are computed. We demonstrate that center-saddle bifurcations of periodic orbits are the main mechanism for creating stable regions in phase space that can support the partial trapping of the wave packet, and thus they explain the observed spectra. A non-linear mechanical methodology, which involves the calculation of equilibria, periodic orbits, and transition states in normal form coordinates, is applied for an in detail exploration of phase space. The fingerprints of the phase space structures in the quantum world are identified by solving the time dependent Schrödinger equation and calculating autocorrelation functions. This demonstrates that different reaction channels could be controlled if exact knowledge of the phase space structure is available to guide the initial excitation of the molecule.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
82.60.Hc Chemical equilibria and equilibrium constants
33.20.Lg Ultraviolet spectra
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
82.20.Kh Potential energy surfaces for chemical reactions
31.50.-x Potential energy surfaces

Gas phase solvatochromic effects of phenol and naphthol photoacids

Anna Melnichuk and Rodney J. Bartlett

J. Chem. Phys. 134, 244303 (2011); http://dx.doi.org/10.1063/1.3603456 (11 pages)

Online Publication Date: 27 June 2011

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A quantum chemical study of spectral shifts by single molecule solvation of phenol, α-naphthol, and β-naphthol is presented. The methods employed include the equation-of-motion coupled cluster, the similarity transformed equation-of-motion coupled cluster, single excitation configuration-interaction, and time-dependent density functional theory. Based on the calculations, there is no evidence that there is significant charge-transfer between the solute and the solvent. Instead, it appears that the observed solvation redshift is due to the nature of the excited state on the solute molecule.
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34.70.+e Charge transfer
31.50.Df Potential energy surfaces for excited electronic states
33.70.Jg Line and band widths, shapes, and shifts
31.15.bw Coupled-cluster theory
31.15.ee Time-dependent density functional theory
31.15.vj Electron correlation calculations for atoms and ions: excited states

Sulfur 1s near-edge x-ray absorption fine structure (NEXAFS) of thiol and thioether compounds

Shirin Behyan, Yongfeng Hu, and Stephen G. Urquhart

J. Chem. Phys. 134, 244304 (2011); http://dx.doi.org/10.1063/1.3602218 (7 pages) | Cited 1 time

Online Publication Date: 27 June 2011

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The speciation and quantification of sulfur species based on sulfur K-edge x-ray absorption spectroscopy is of wide interest, particularly for biological and petroleum science. These tasks require a firm understanding of the sulfur 1s near-edge x-ray absorption fine structure (NEXAFS) spectra of relevant species. To this end, we have examined the gas phase sulfur 1s NEXAFS spectra of a group of simple thiol and thioether compounds. These high-resolution gas phase spectra are free of solid-state broadening, charging, and saturation effects common in the NEXAFS spectra of solids. These experimental data have been further analyzed with the aid of improved virtual orbital Hartree–Fock ab initio calculations. The experimental sulfur 1s NEXAFS spectra show fine features predicted by calculation, and the combination of experiment and calculation has been used to improve assignment of spectroscopic features relevant for the speciation and quantification of the sulfur compounds.
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33.20.Rm X-ray spectra
31.15.xr Self-consistent-field methods
31.15.ap Polarizabilities and other atomic and molecular properties
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