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21 May 2012

Volume 136, Issue 19, Articles (19xxxx)

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J. Chem. Phys. 136, 191101 (2012); http://dx.doi.org/10.1063/1.4718380 (4 pages)

Gerald R. Kneller, Konrad Hinsen, and Paolo Calligari
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Communication: A minimal model for the diffusion-relaxation backbone dynamics of proteins

Gerald R. Kneller, Konrad Hinsen, and Paolo Calligari

J. Chem. Phys. 136, 191101 (2012); http://dx.doi.org/10.1063/1.4718380 (4 pages)

Online Publication Date: 15 May 2012

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We present a model for the local diffusion-relaxation dynamics of the Cα-atoms in proteins describing both the diffusive short-time dynamics and the asymptotic long-time relaxation of the position autocorrelation functions. The relaxation rate spectra of the latter are represented by shifted gamma distributions, where the standard gamma distribution describes anomalous slow relaxation in macromolecular systems of infinite size and the shift accounts for a smallest local relaxation rate in macromolecules of finite size. The resulting autocorrelation functions are analytic for any time t ⩾ 0. Using results from a molecular dynamics simulation of lysozyme, we demonstrate that the model fits the position autocorrelation functions of the Cα-atoms exceptionally well and reveals moreover a strong correlation between the residue's solvent-accessible surface and the fitted model parameters.
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87.15.ap Molecular dynamics simulation
87.15.Vv Diffusion
87.15.R- Reactions and kinetics
87.15.H- Dynamics of biomolecules
87.14.ej Enzymes
87.15.M- Spectra of biomolecules
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back to top Theoretical Methods and Algorithms

Replica exchange with nonequilibrium switches: Enhancing equilibrium sampling by increasing replica overlap

Andrew J. Ballard and Christopher Jarzynski

J. Chem. Phys. 136, 194101 (2012); http://dx.doi.org/10.1063/1.4712028 (11 pages)

Online Publication Date: 15 May 2012

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We describe a replica exchange strategy where trial swap configurations are generated by nonequilibrium switching simulations. By devoting simulation time to the switching simulations, one can systematically increase an effective overlap between replicas, which leads to an increased exchange acceptance rate and less correlated equilibrium samples. In this paper, we derive our method for a general class of stochastic dynamics, and discuss various strategies for enhancing replica overlap through novel dynamical schemes and prudent choices of switching protocols. We then demonstrate our method on a model system of alanine dipeptide in implicit solvent, characterizing decreases in data correlations and gains in sampling efficiency.
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87.14.ef Peptides
02.50.Ey Stochastic processes
87.15.H- Dynamics of biomolecules

A new multiscale modeling method for simulating the loss processes in polymer solar cell nanodevices

Anton Pershin, Sergii Donets, and Stephan A. Baeurle

J. Chem. Phys. 136, 194102 (2012); http://dx.doi.org/10.1063/1.4712622 (11 pages)

Online Publication Date: 15 May 2012

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The photoelectric power conversion efficiency of polymer solar cells is till now, compared to conventional inorganic solar cells, still relatively low with maximum values ranging from 7% to 8%. This essentially relates to the existence of exciton and charge carrier loss phenomena, reducing the performance of polymer solar cells significantly. In this paper we introduce a new computer simulation technique, which permits to explore the causes of the occurrence of such phenomena at the nanoscale and to design new photovoltaic materials with optimized opto-electronic properties. Our approach consists in coupling a mesoscopic field-theoretic method with a suitable dynamic Monte Carlo algorithm, to model the elementary photovoltaic processes. Using this algorithm, we investigate the influence of structural characteristics and different device conditions on the exciton generation and charge transport efficiencies in case of a novel nanostructured polymer blend. More specifically, we find that the disjunction of continuous percolation paths leads to the creation of dead ends, resulting in charge carrier losses through charge recombination. Moreover, we observe that defects are characterized by a low exciton dissociation efficiency due to a high charge accumulation, counteracting the charge generation process. From these observations, we conclude that both the charge carrier loss and the exciton loss phenomena lead to a dramatic decrease in the internal quantum efficiency. Finally, by analyzing the photovoltaic behavior of the nanostructures under different circuit conditions, we demonstrate that charge injection significantly determines the impact of the defects on the solar cell performance.
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88.40.hj Efficiency and performance of solar cells
88.40.jr Organic photovoltaics

Equation of state of charged colloidal suspensions and its dependence on the thermodynamic route

Thiago E. Colla, Alexandre P. dos Santos, and Yan Levin

J. Chem. Phys. 136, 194103 (2012); http://dx.doi.org/10.1063/1.4718367 (7 pages)

Online Publication Date: 16 May 2012

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The thermodynamic properties of highly charged colloidal suspensions in contact with a salt reservoir are investigated in the framework of the renormalized Jellium model (RJM). It is found that the equation of state is very sensitive to the particular thermodynamic route used to obtain it. Specifically, the osmotic pressure calculated within the RJM using the contact value theorem can be very different from the pressure calculated using the Kirkwood-Buff fluctuation relations. On the other hand, Monte Carlo simulations show that both the effective pair potentials and the correlation functions are accurately predicted by the RJM. It is suggested that the lack of self-consistency in the thermodynamics of the RJM is a result of neglected electrostatic correlations between the counterions and coions.
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82.70.Dd Colloids
61.20.Ja Computer simulation of liquid structure
82.70.Kj Emulsions and suspensions
64.30.-t Equations of state of specific substances

Spin densities from subsystem density-functional theory: Assessment and application to a photosynthetic reaction center complex model

Alisa Solovyeva, Michele Pavanello, and Johannes Neugebauer

J. Chem. Phys. 136, 194104 (2012); http://dx.doi.org/10.1063/1.4709771 (14 pages)

Online Publication Date: 16 May 2012

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Subsystem density-functional theory (DFT) is a powerful and efficient alternative to Kohn–Sham DFT for large systems composed of several weakly interacting subunits. Here, we provide a systematic investigation of the spin-density distributions obtained in subsystem DFT calculations for radicals in explicit environments. This includes a small radical in a solvent shell, a π-stacked guanine–thymine radical cation, and a benchmark application to a model for the special pair radical cation, which is a dimer of bacteriochlorophyll pigments, from the photosynthetic reaction center of purple bacteria. We investigate the differences in the spin densities resulting from subsystem DFT and Kohn–Sham DFT calculations. In these comparisons, we focus on the problem of overdelocalization of spin densities due to the self-interaction error in DFT. It is demonstrated that subsystem DFT can reduce this problem, while it still allows to describe spin-polarization effects crossing the boundaries of the subsystems. In practical calculations of spin densities for radicals in a given environment, it may thus be a pragmatic alternative to Kohn–Sham DFT calculations. In our calculation on the special pair radical cation, we show that the coordinating histidine residues reduce the spin-density asymmetry between the two halves of this system, while inclusion of a larger binding pocket model increases this asymmetry. The unidirectional energy transfer in photosynthetic reaction centers is related to the asymmetry introduced by the protein environment.
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31.15.ej Spin-density functionals
31.15.es Applications of density-functional theory (e.g., to electronic structure and stability; defect formation; dielectric properties, susceptibilities; viscoelastic coefficients; Rydberg transition frequencies)
87.15.ag Quantum calculations
87.15.M- Spectra of biomolecules
82.50.Hp Processes caused by visible and UV light
87.16.-b Subcellular structure and processes

Hybrid coupled cluster methods: Combining active space coupled cluster methods with coupled cluster singles, doubles, and perturbative triples

Zhuangfei Kou, Jun Shen, Enhua Xu, and Shuhua Li

J. Chem. Phys. 136, 194105 (2012); http://dx.doi.org/10.1063/1.4716185 (8 pages)

Online Publication Date: 16 May 2012

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Based on the coupled-cluster singles, doubles, and a hybrid treatment of triples (CCSD(T)-h) method developed by us [J. Shen, E. Xu, Z. Kou, and S. Li, J. Chem. Phys. 132, 114115 (2010)10.1063/1.3359851; J. Shen, E. Xu, Z. Kou, and S. Li, J. Chem. Phys. 133, 234106 (2010)10.1063/1.3518100; J. Shen, E. Xu, Z. Kou, and S. Li, J. Chem. Phys. 134, 044134 (2011)10.1063/1.3541250], we developed and implemented a new hybrid coupled cluster (CC) method, named CCSD(T)q-h, by combining CC singles and doubles, and active triples and quadruples (CCSDtq) with CCSD(T) to deal with the electronic structures of molecules with significant multireference character. These two hybrid CC methods can be solved with non-canonical and canonical MOs. With canonical MOs, the CCSD(T)-like equations in these two methods can be solved directly without iteration so that the storage of all triple excitation amplitudes can be avoided. A practical procedure to divide canonical MOs into active and inactive subsets is proposed. Numerical calculations demonstrated that CCSD(T)-h with canonical MOs can well reproduce the corresponding results obtained with non-canonical MOs. For three atom exchange reactions, we found that CCSD(T)-h can offer a significant improvement over the popular CCSD(T) method in describing the reaction barriers. For the bond-breaking processes in F2 and H2O, our calculations demonstrated that CCSD(T)q-h is a good approximation to CCSDTQ over the entire bond dissociation processes.
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31.15.bw Coupled-cluster theory
33.15.-e Properties of molecules

Trapping photon-dressed Dirac electrons in a quantum dot studied by coherent two dimensional photon echo spectroscopy

O. Roslyak, Godfrey Gumbs, and S. Mukamel

J. Chem. Phys. 136, 194106 (2012); http://dx.doi.org/10.1063/1.4707182 (12 pages)

Online Publication Date: 17 May 2012

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We study the localization of dressed Dirac electrons in a cylindrical quantum dot (QD) formed on monolayer and bilayer graphene by spatially different potential profiles. Short lived excitonic states which are too broad to be resolved in linear spectroscopy are revealed by cross peaks in the photon-echo nonlinear technique. Signatures of the dynamic gap in the two-dimensional spectra are discussed. The effect of the Coulomb induced exciton-exciton scattering and the formation of biexciton molecules are demonstrated.
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71.35.-y Excitons and related phenomena
78.47.jf Photon echoes

Ionization energy of atoms obtained from GW self-energy or from random phase approximation total energies

Fabien Bruneval

J. Chem. Phys. 136, 194107 (2012); http://dx.doi.org/10.1063/1.4718428 (10 pages)

Online Publication Date: 17 May 2012

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A systematic evaluation of the ionization energy within the GW approximation is carried out for the first row atoms, from H to Ar. We describe a Gaussian basis implementation of the GW approximation, which does not resort to any further technical approximation, besides the choice of the basis set for the electronic wavefunctions. Different approaches to the GW approximation have been implemented and tested, for example, the standard perturbative approach based on a prior mean-field calculation (Hartree-Fock GW@HF or density-functional theory GW@DFT) or the recently developed quasiparticle self-consistent method (QSGW). The highest occupied molecular orbital energies of atoms obtained from both GW@HF and QSGW are in excellent agreement with the experimental ionization energy. The lowest unoccupied molecular orbital energies of the singly charged cation yield a noticeably worse estimate of the ionization energy. The best agreement with respect to experiment is obtained from the total energy differences within the random phase approximation functional, which is the total energy corresponding to the GW self-energy. We conclude with a discussion about the slight concave behavior upon number electron change of the GW approximation and its consequences upon the quality of the orbital energies.
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34.50.Fa Electronic excitation and ionization of atoms (including beam-foil excitation and ionization)
31.15.xr Self-consistent-field methods
31.15.E- Density-functional theory

Potential flux landscapes determine the global stability of a Lorenz chaotic attractor under intrinsic fluctuations

Chunhe Li, Erkang Wang, and Jin Wang

J. Chem. Phys. 136, 194108 (2012); http://dx.doi.org/10.1063/1.4716466 (13 pages)

Online Publication Date: 18 May 2012

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We developed a potential flux landscape theory to investigate the dynamics and the global stability of a chemical Lorenz chaotic strange attractor under intrinsic fluctuations. Landscape was uncovered to have a butterfly shape. For chaotic systems, both landscape and probabilistic flux are crucial to the dynamics of chaotic oscillations. Landscape attracts the system down to the chaotic attractor, while flux drives the coherent motions along the chaotic attractors. Barrier heights from the landscape topography provide a quantitative measure for the robustness of chaotic attractor. We also found that the entropy production rate and phase coherence increase as the molecular numbers increase. Power spectrum analysis of autocorrelation function provides another way to quantify the global stability of chaotic attractor. We further found that limit cycle requires more flux and energy to sustain than the chaotic strange attractor. Finally, by detailed analysis we found that the curl probabilistic flux may provide the origin of the chaotic attractor.
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82.40.Bj Oscillations, chaos, and bifurcations
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
05.45.-a Nonlinear dynamics and chaos
82.20.-w Chemical kinetics and dynamics

Ab initio quantum dynamics using coupled-cluster

Simen Kvaal

J. Chem. Phys. 136, 194109 (2012); http://dx.doi.org/10.1063/1.4718427 (15 pages)

Online Publication Date: 18 May 2012

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The curse of dimensionality (COD) limits the current state-of-the-art ab initio propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functions to vary in an adaptive fashion as well, thereby creating a highly flexible, polynomially scaling approximation to the time-dependent Schrödinger equation. The method inherits size-consistency and extensivity from the CC method. The method is dubbed orbital-adaptive time-dependent coupled-cluster, and is a hierarchy of approximations to the now standard multi-configurational time-dependent Hartree method for fermions. A numerical experiment is also given.
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31.15.bw Coupled-cluster theory
31.15.xr Self-consistent-field methods
31.15.A- Ab initio calculations
05.30.Fk Fermion systems and electron gas

Generalized Gibbs state with modified Redfield solution: Exact agreement up to second order

Juzar Thingna, Jian-Sheng Wang, and Peter Hänggi

J. Chem. Phys. 136, 194110 (2012); http://dx.doi.org/10.1063/1.4718706 (11 pages)

Online Publication Date: 18 May 2012

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A novel scheme for the steady state solution of the standard Redfield quantum master equation is developed which yields agreement with the exact result for the corresponding reduced density matrix up to second order in the system-bath coupling strength. We achieve this objective by use of an analytic continuation of the off-diagonal matrix elements of the Redfield solution towards its diagonal limit. Notably, our scheme does not require the provision of yet higher order relaxation tensors. Testing this modified method for a heat bath consisting of a collection of harmonic oscillators we assess that the system relaxes towards its correct coupling-dependent, generalized quantum Gibbs state in second order. We numerically compare our formulation for a damped quantum harmonic system with the nonequilibrium Green's function formalism: we find good agreement at low temperatures for coupling strengths that are even larger than expected from the very regime of validity of the second-order Redfield quantum master equation. Yet another advantage of our method is that it markedly reduces the numerical complexity of the problem; thus, allowing to study efficiently large-sized system Hilbert spaces.
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03.65.Ta Foundations of quantum mechanics; measurement theory
03.65.Ge Solutions of wave equations: bound states
02.30.-f Function theory, analysis

Construction of high-dimensional neural network potentials using environment-dependent atom pairs

K. V. Jovan Jose, Nongnuch Artrith, and Jörg Behler

J. Chem. Phys. 136, 194111 (2012); http://dx.doi.org/10.1063/1.4712397 (15 pages)

Online Publication Date: 18 May 2012

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An accurate determination of the potential energy is the crucial step in computer simulations of chemical processes, but using electronic structure methods on-the-fly in molecular dynamics (MD) is computationally too demanding for many systems. Constructing more efficient interatomic potentials becomes intricate with increasing dimensionality of the potential-energy surface (PES), and for numerous systems the accuracy that can be achieved is still not satisfying and far from the reliability of first-principles calculations. Feed-forward neural networks (NNs) have a very flexible functional form, and in recent years they have been shown to be an accurate tool to construct efficient PESs. High-dimensional NN potentials based on environment-dependent atomic energy contributions have been presented for a number of materials. Still, these potentials may be improved by a more detailed structural description, e.g., in form of atom pairs, which directly reflect the atomic interactions and take the chemical environment into account. We present an implementation of an NN method based on atom pairs, and its accuracy and performance are compared to the atom-based NN approach using two very different systems, the methanol molecule and metallic copper. We find that both types of NN potentials provide an excellent description of both PESs, with the pair-based method yielding a slightly higher accuracy making it a competitive alternative for addressing complex systems in MD simulations.
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34.20.Cf Interatomic potentials and forces
31.15.E- Density-functional theory
31.15.A- Ab initio calculations

The three-electron harmonium atom: The lowest-energy doublet and quadruplet states

Jerzy Cioslowski, Krzysztof Strasburger, and Eduard Matito

J. Chem. Phys. 136, 194112 (2012); http://dx.doi.org/10.1063/1.4717461 (8 pages)

Online Publication Date: 21 May 2012

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Calculations of sub-μhartree accuracy employing explicitly correlated Gaussian lobe functions produce comprehensive data on the energy E(ω), its components, and the one-electron properties of the two lowest-energy states of the three-electron harmonium atom. The energy computations at 19 values of the confinement strength ω ranging from 0.001 to 1000.0, used in conjunction with a recently proposed robust interpolation scheme, yield explicit approximants capable of estimating E(ω) and the potential energy of the harmonic confinement within a few tenths of μhartree for any ω ⩾ 0.001, the respective errors for the kinetic energy and the potential energy of the electron-electron repulsion not exceeding 2 μhartrees. Thanks to the correct ω → 0 asymptotics incorporated into the approximants, comparable accuracy is expected for values of ω smaller than 0.001. Occupation numbers of the dominant natural spinorbitals and two different measures of electron correlation are also computed.
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31.50.-x Potential energy surfaces
31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.xr Self-consistent-field methods

The multiscale coarse-graining method. VIII. Multiresolution hierarchical basis functions and basis function selection in the construction of coarse-grained force fields

Avisek Das and Hans C. Andersen

J. Chem. Phys. 136, 194113 (2012); http://dx.doi.org/10.1063/1.4705384 (15 pages)

Online Publication Date: 21 May 2012

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The multiscale coarse-graining (MS-CG) method is a method for determining the effective potential energy function for a coarse-grained (CG) model of a molecular system using data obtained from molecular dynamics simulation of the corresponding atomically detailed model. The coarse-grained potential obtained using the MS-CG method is a variational approximation for the exact many-body potential of mean force for the coarse-grained sites. Here we propose a new numerical algorithm with noise suppression capabilities and enhanced numerical stability for the solution of the MS-CG variational problem. The new method, which is a variant of the elastic net method [Friedman et al., Ann. Appl. Stat. 1, 302 (2007)]10.1214/07-AOAS131, allows us to construct a large basis set, and for each value of a so-called “penalty parameter” the method automatically chooses a subset of the basis that is most important for representing the MS-CG potential. The size of the subset increases as the penalty parameter is decreased. The appropriate value to choose for the penalty parameter is the one that gives a basis set that is large enough to fit the data in the simulation data set without fitting the noise. This procedure provides regularization to mitigate potential numerical problems in the associated linear least squares calculation, and it provides a way to avoid fitting statistical error. We also develop new basis functions that are similar to multiresolution Haar functions and that have the differentiability properties that are appropriate for representing CG potentials. We demonstrate the feasibility of the combined use of the elastic net method and the multiresolution basis functions by performing a variational calculation of the CG potential for a relatively simple system. We develop a method to choose the appropriate value of the penalty parameter to give the optimal basis set. The combined effect of the new basis functions and the regularization provided by the elastic net method opens the possibility of using very large basis sets for complicated CG systems with many interaction potentials without encountering numerical problems in the variational calculation.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
31.50.-x Potential energy surfaces
31.15.xv Molecular dynamics and other numerical methods
31.15.xt Variational techniques

The multiscale coarse-graining method. IX. A general method for construction of three body coarse-grained force fields

Avisek Das and Hans C. Andersen

J. Chem. Phys. 136, 194114 (2012); http://dx.doi.org/10.1063/1.4705417 (11 pages)

Online Publication Date: 21 May 2012

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The multiscale coarse-graining (MS-CG) method is a method for constructing a coarse-grained (CG) model of a system using data obtained from molecular dynamics simulations of the corresponding atomically detailed model. The formal statistical mechanical derivation of the method shows that the potential energy function extracted from an MS-CG calculation is a variational approximation for the true potential of mean force of the CG sites, one that becomes exact in the limit that a complete basis set is used in the variational calculation if enough data are obtained from the atomistic simulations. Most applications of the MS-CG method have employed a representation for the nonbonded part of the CG potential that is a sum of all possible pair interactions. This approach, despite being quite successful for some CG models, is inadequate for some others. Here we propose a systematic method for including three body terms as well as two body terms in the nonbonded part of the CG potential energy. The current method is more general than a previous version presented in a recent paper of this series [L. Larini, L. Lu, and G. A. Voth, J. Chem. Phys. 132, 164107 (2010)]10.1063/1.3394863, in the sense that it does not make any restrictive choices for the functional form of the three body potential. We use hierarchical multiresolution functions that are similar to wavelets to develop very flexible basis function expansions with both two and three body basis functions. The variational problem is solved by a numerical technique that is capable of automatically selecting an appropriate subset of basis functions from a large initial set. We apply the method to two very different coarse-grained models: a solvent free model of a two component solution made of identical Lennard-Jones particles and a one site model of SPC/E water where a site is placed at the center of mass of each water molecule. These calculations show that the inclusion of three body terms in the nonbonded CG potential can lead to significant improvement in the accuracy of CG potentials and hence of CG simulations.
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61.20.Ja Computer simulation of liquid structure
61.20.Gy Theory and models of liquid structure
61.20.Ne Structure of simple liquids
61.25.Em Molecular liquids

The multiscale coarse-graining method. X. Improved algorithms for constructing coarse-grained potentials for molecular systems

Avisek Das, Lanyuan Lu, Hans C. Andersen, and Gregory A. Voth

J. Chem. Phys. 136, 194115 (2012); http://dx.doi.org/10.1063/1.4705420 (12 pages)

Online Publication Date: 21 May 2012

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The multiscale coarse-graining (MS-CG) method uses simulation data for an atomistic model of a system to construct a coarse-grained (CG) potential for a coarse-grained model of the system. The CG potential is a variational approximation for the true potential of mean force of the degrees of freedom retained in the CG model. The variational calculation uses information about the atomistic positions and forces in the simulation data. In principle, the resulting MS-CG potential will be an accurate representation of the true CG potential if the basis set for the variational calculation is complete enough and the canonical distribution of atomistic states is well sampled by the data set. In practice, atomistic configurations that have very high potential energy are not sampled. As a result there usually is a region of CG configuration space that is not sampled and about which the data set contains no information regarding the gradient of the true potential. The MS-CG potential obtained from a variational calculation will not necessarily be accurate in this unsampled region. A priori considerations make it clear that the true CG potential of mean force must be very large and positive in that region. To obtain an MS-CG potential whose behavior in the sampled region is determined by the atomistic data set, and whose behavior in the unsampled region is large and positive, it is necessary to intervene in the variational calculation in some way. In this paper, we discuss and compare two such methods of intervention, which have been used in previous MS-CG calculations for dealing with nonbonded interactions. For the test systems studied, the two methods give similar results and yield MS-CG potentials that are limited in accuracy only by the incompleteness of the basis set and the statistical error of associated with the set of atomistic configurations used. The use of such methods is important for obtaining accurate CG potentials.
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31.50.-x Potential energy surfaces
34.20.Gj Intermolecular and atom-molecule potentials and forces
31.15.xt Variational techniques
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Full-dimensional quantum dynamics study of exchange processes for the D + H2O and D + HOD reactions

Bina Fu and Dong H. Zhang

J. Chem. Phys. 136, 194301 (2012); http://dx.doi.org/10.1063/1.4718386 (7 pages)

Online Publication Date: 16 May 2012

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The exchange processes of D + H2O and D + HOD reactions are studied using initial state-selected time-dependent wave packet approach in full dimension. The total reaction probabilities for different partial waves, together with the integral cross sections, are obtained both by the centrifugal sudden (CS) approximation and exact coupled-channel (CC) calculations, for the H2O(HOD) reactant initially in the ground rovibrational state. In the CC calculations, small resonance peaks in the reaction probabilities and quick diminishing of the resonance peaks with the increase of total angular momenta J do not lead to clear step-like features just above the threshold in the cross sections for the title reactions, which are different in other isotopically substituted reactions where the hydrogen atom was included as the reactant instead of the deuterium atom [B. Fu, Y. Zhou, and D. H. Zhang, Chem. Sci. 3, 270 (2012)10.1039/c1sc00684c; B. Fu and D. H. Zhang, J. Phys. Chem. A 116, 820 (2012)10.1021/jp211096q]. It is interesting that the shape resonance-induced features resulting from the reaction tunneling are significantly diminished accordingly in the reactions of the deuterium atom and H2O or HOD, owing to the weaker tunneling capability of the reagent deuterium atom in the title reactions than the reagent hydrogen atom in other reactions. In the CS calculations, the resonance peaks persist in many partial waves but cannot survive the partial-wave summations. The cross sections for the D′ + H2O → D′OH + H and D′ + HOD → D′OD + H reactions are substantially larger than those for the D′ + HOD → HOD′ + D reaction, indicating that the D′/H exchange reactions are much more favored than the D′/D exchange.
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82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.20.-w Chemical kinetics and dynamics
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions

A molecular H2 potential for heterogeneous simulations including polarization and many-body van der Waals interactions

Keith McLaughlin, Christian R. Cioce, Jonathan L. Belof, and Brian Space

J. Chem. Phys. 136, 194302 (2012); http://dx.doi.org/10.1063/1.4717705 (8 pages)

Online Publication Date: 17 May 2012

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A highly accurate aniostropic intermolecular potential for diatomic hydrogen has been developed that is transferable for molecular modeling in heterogeneous systems. The potential surface is designed to be efficacious in modeling mixed sorbates in metal-organic materials that include sorption interactions with charged interfaces and open metal sites. The potential parameters are compatible for mixed simulations but still maintain high accuracy while deriving dispersion parameters from a proven polarizability model. The potential includes essential physical interactions including: short-range repulsions, dispersion, and permanent and induced electrostatics. Many-body polarization is introduced via a point-atomic polarizability model that is also extended to account for many-body van der Waals interactions in a consistent fashion. Permanent electrostatics are incorporated using point partial charges on atomic sites. However, contrary to expectation, the best potentials are obtained by permitting the charges to take on values that do not reproduce the first non-vanishing moment of the electrostatic potential surface, i.e., the quadrupole moment. Potential parameters are fit to match ab initio energies for a representative range of dimer geometries. The resulting potential is shown to be highly effective by comparing to electronic structure calculations for a thermal distribution of trimer geometries, and by reproducing experimental bulk pressure-density isotherms. The surface is shown to be superior to other similarly portable potential choices even in tests on homogeneous systems without strong polarizing fields. The present streamlined approach to developing such potentials allows for a simple adaptation to other molecules amenable to investigation by high-level electronic structure methods.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
31.15.ap Polarizabilities and other atomic and molecular properties
31.50.Bc Potential energy surfaces for ground electronic states
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

Multielectron effects in high harmonic generation in N2 and benzene: Simulation using a non-adiabatic quantum molecular dynamics approach for laser-molecule interactions

Daniel Dundas

J. Chem. Phys. 136, 194303 (2012); http://dx.doi.org/10.1063/1.4718590 (17 pages)

Online Publication Date: 17 May 2012

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A mixed quantum-classical approach is introduced which allows the dynamical response of molecules driven far from equilibrium to be modeled. This method is applied to the interaction of molecules with intense, short-duration laser pulses. The electronic response of the molecule is described using time-dependent density functional theory (TDDFT) and the resulting Kohn-Sham equations are solved numerically using finite difference techniques in conjunction with local and global adaptations of an underlying grid in curvilinear coordinates. Using this approach, simulations can be carried out for a wide range of molecules and both all-electron and pseudopotential calculations are possible. The approach is applied to the study of high harmonic generation in N2 and benzene using linearly polarized laser pulses and, to the best of our knowledge, the results for benzene represent the first TDDFT calculations of high harmonic generation in benzene using linearly polarized laser pulses. For N2 an enhancement of the cut-off harmonics is observed whenever the laser polarization is aligned perpendicular to the molecular axis. This enhancement is attributed to the symmetry properties of the Kohn-Sham orbital that responds predominantly to the pulse. In benzene we predict that a suppression in the cut-off harmonics occurs whenever the laser polarization is aligned parallel to the molecular plane. We attribute this suppression to the symmetry-induced response of the highest-occupied molecular orbital.
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31.15.ee Time-dependent density functional theory
42.65.Ky Frequency conversion; harmonic generation, including higher-order harmonic generation
02.70.Bf Finite-difference methods
33.80.Eh Autoionization, photoionization, and photodetachment

Photoelectron spectroscopy and theoretical studies of UF5− and UF6−

Phuong Diem Dau, Jing Su, Hong-Tao Liu, Dao-Ling Huang, Fan Wei, Jun Li, and Lai-Sheng Wang

J. Chem. Phys. 136, 194304 (2012); http://dx.doi.org/10.1063/1.4716182 (9 pages)

Online Publication Date: 17 May 2012

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The UF5− and UF6− anions are produced using electrospray ionization and investigated by photoelectron spectroscopy and relativistic quantum chemistry. An extensive vibrational progression is observed in the spectra of UF5−, indicating significant geometry changes between the anion and neutral ground state. Franck-Condon factor simulations of the observed vibrational progression yield an adiabatic electron detachment energy of 3.82 ± 0.05 eV for UF5−. Relativistic quantum calculations using density functional and ab initio theories are performed on UF5− and UF6− and their neutrals. The ground states of UF5− and UF5 are found to have C4v symmetry, but with a large U−F bond length change. The ground state of UF5− is a triplet state (3B2) with the two 5f electrons occupying a 5fz3-based 8a1 highest occupied molecular orbital (HOMO) and the 5fxyz-based 2b2 HOMO-1 orbital. The detachment cross section from the 5fxyz orbital is observed to be extremely small and the detachment transition from the 2b2 orbital is more than ten times weaker than that from the 8a1 orbital at the photon energies available. The UF6− anion is found to be octahedral, similar to neutral UF6 with the extra electron occupying the 5fxyz-based a2u orbital. Surprisingly, no photoelectron spectrum could be observed for UF6− due to the extremely low detachment cross section from the 5fxyz-based HOMO of UF6−.
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33.60.+q Photoelectron spectra
33.20.Tp Vibrational analysis
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
31.15.ae Electronic structure and bonding characteristics
31.15.E- Density-functional theory
31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions

Evolution of superhalogen properties in PtCln clusters

Jorly Joseph, Kalpataru Pradhan, Purusottam Jena, Haopeng Wang, Xinxing Zhang, Yeon Jae Ko, and Kit H. Bowen, Jr.

J. Chem. Phys. 136, 194305 (2012); http://dx.doi.org/10.1063/1.4719089 (7 pages)

Online Publication Date: 18 May 2012

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We have systematically calculated the ground state geometries, relative stability, electronic structure, and spectroscopic properties of PtCln (n = 1–7) clusters. The bonding in these clusters is dominated by covalent interaction. In neutral clusters, chlorine atoms are chemically bound to Pt up to n = 5. However, in neutral PtCl6 and PtCl7 clusters, two of the chlorine atoms bind molecularly while the remaining bind as individual atoms. In the negative ions, this happens only in the case of PtCl7 cluster. The geometries of both neutral and anionic clusters can be considered as fragments of an octahedron and are attributed to the stabilization associated with splitting of partially filled d orbitals under the chloride ligand field. The electron affinity of PtCln clusters rises steadily with n, reaching a maximum value of 5.81 eV in PtCl5. PtCln clusters with n ≥ 3 are all superhalogens with electron affinities larger than that of chlorine. The accuracy of our results has been verified by carrying out photoelectron spectroscopy experiments on PtCln− anion clusters.
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36.40.Mr Spectroscopy and geometrical structure of clusters
33.60.+q Photoelectron spectra
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Fm Bond strengths, dissociation energies

Rovibrational dynamics of the strontium molecule in the A1Σu+, c3Πu, and a3Σu+ manifold from state-of-the-art ab initio calculations

Wojciech Skomorowski, Filip Pawłowski, Christiane P. Koch, and Robert Moszynski

J. Chem. Phys. 136, 194306 (2012); http://dx.doi.org/10.1063/1.4713939 (13 pages)

Online Publication Date: 18 May 2012

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State-of-the-art ab initio techniques have been applied to compute the potential energy curves for the electronic states in the A1Σu+, c3Πu, and a3Σu+ manifold of the strontium dimer, the spin-orbit and nonadiabatic coupling matrix elements between the states in the manifold, and the electric transition dipole moment from the ground X1Σg+ to the nonrelativistic and relativistic states in the A+c+a manifold. The potential energy curves and transition moments were obtained with the linear response (equation of motion) coupled cluster method limited to single, double, and linear triple excitations for the potentials and limited to single and double excitations for the transition moments. The spin-orbit and nonadiabatic coupling matrix elements were computed with the multireference configuration interaction method limited to single and double excitations. Our results for the nonrelativistic and relativistic (spin-orbit coupled) potentials deviate substantially from recent ab initio calculations. The potential energy curve for the spectroscopically active (1)0u+ state is in quantitative agreement with the empirical potential fitted to high-resolution Fourier transform spectra [A. Stein, H. Knöckel, and E. Tiemann, Eur. Phys. J. D 64, 227 (2011)]10.1140/epjd/e2011-20229-6. The computed ab initio points were fitted to physically sound analytical expressions, and used in converged coupled channel calculations of the rovibrational energy levels in the A+c+a manifold and line strengths for the A1Σu+←X1Σg+ transitions. Positions and lifetimes of quasi-bound Feshbach resonances lying above the 1S0 + 3P1 dissociation limit were also obtained. Our results reproduce (semi)quantitatively the experimental data observed thus far. Predictions for on-going and future experiments are also reported.
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33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Vq Vibration-rotation analysis
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

The electronic spectrum of Si3 I: Triplet D3h system

N. J. Reilly, D. L. Kokkin, X. Zhuang, V. Gupta, R. Nagarajan, R. C. Fortenberry, J. P. Maier, T. C. Steimle, J. F. Stanton, and M. C. McCarthy

J. Chem. Phys. 136, 194307 (2012); http://dx.doi.org/10.1063/1.4704672 (7 pages)

Online Publication Date: 18 May 2012

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We report the measurement of a jet-cooled electronic spectrum of the silicon trimer. Si3 was produced in a pulsed discharge of silane in argon, and the excitation spectrum examined in the 18 000–20 800 cm−1 region. A combination of resonant two-color two-photon ionization (R2C2PI) time-of-flight mass spectroscopy, laser-induced fluorescence/dispersed fluorescence, and equation-of-motion coupled-cluster calculations have been used to establish that the observed spectrum is dominated by the 13A1″ – math 3A2′ transition of the D3h isomer. The spectrum has an origin transition at 18 600± 4 cm−1 and a short progression in the symmetric stretch with a frequency of ∼445 cm−1, in good agreement with a predicted vertical transition energy of 2.34 eV for excitation to the 13A1″ state, which has a calculated symmetric stretching frequency of 480 cm−1. In addition, a ∼505 cm−1 ground state vibrational frequency determined from sequence bands and dispersed fluorescence is in agreement with an earlier zero-electron kinetic energy study of the lowest D3h state and with theory. A weaker, overlapping band system with a ∼360 cm−1 progression, observed in the same mass channel (m/z = 84) by R2C2PI but under different discharge conditions, is thought to be due to transitions from the (more complicated) singlet C2v ground state (1A1) state of Si3. Evidence of emission to this latter state in the triplet dispersed fluorescence spectra suggests extensive mixing in the excited triplet and singlet manifolds. Prospects for further spectroscopic characterization of the singlet system and direct measurement of the energy separation between the lowest singlet and triplet states are discussed.
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33.50.Dq Fluorescence and phosphorescence spectra
33.80.Eh Autoionization, photoionization, and photodetachment
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
31.15.bw Coupled-cluster theory
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Ta Mass spectra

Laser-induced enhancement of tunneling in NHD2

Matthieu Sala, Stéphane Guérin, Fabien Gatti, Roberto Marquardt, and Hans-Dieter Meyer

J. Chem. Phys. 136, 194308 (2012); http://dx.doi.org/10.1063/1.4718591 (11 pages)

Online Publication Date: 21 May 2012

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We apply and explore techniques aiming at enhancing the tunneling by laser fields, originally developed for a one-dimensional model, to a complete six-dimensional vibrational model of the inversion motion in NHD2. The computational study is performed with the multi-configuration time-dependent Hartree method. Assuming an ideal three-dimensional alignment we obtain a driven tunneling time twenty times smaller than the natural one, in rather good agreement with an oversimplified three-state model. In the case of one-dimensional alignment, a linearly polarized field leads to a poor enhancement of the tunneling probability, after averaging over the rotation about the alignment axis, whereas a circularly polarized field improves the rotationally averaged tunneling probability at the end of the pulse.
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33.80.Be Level crossing and optical pumping
31.15.xr Self-consistent-field methods
33.20.Tp Vibrational analysis
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Resonant inelastic x-ray scattering of CeB6 at the Ce L1- and L3-edges

Lijia Liu, Tsun-Kong Sham, Hisashi Hayashi, Noriko Kanai, Yuki Takehara, Naomi Kawamura, Masaichiro Mizumaki, and Robert A. Gordon

J. Chem. Phys. 136, 194501 (2012); http://dx.doi.org/10.1063/1.4716180 (8 pages)

Online Publication Date: 15 May 2012

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We report a resonant inelastic x-ray scattering (RIXS) study of crystalline CeB6. Ce Lα1,2 RIXS was measured with excitation energies resonant with the Ce L3-edge. A lifetime-broadening suppressed x-ray absorption near-edge structure (LBS-XANES), which successfully reproduced the Lα1,2 RIXS spectra over wide ranges of excitation and emission energies, was simulated using the SIM-RIXS program. A pre-edge structure in the LBS-XANES can be resolved, and many-body effects were suggested in the Lα1,2 RIXS around the Ce L3-edge energy. No convincing signs of Ce (II) or Ce (IV) states were observed in the LBS-XANES. Ce Lγ4 RIXS was measured at 302 K and 28 K with excitation energies across the Ce L1-edge. The interactions of p-valence electrons between Ce and B6 were found to be considerably small, regardless of temperature. Thus, the electronic state of CeB6 was concluded to be suitably described as a nominally Ce(4f 1)3+(e−)(B6)2− system with some hybridization among all valence orbitals of Ce and B.
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78.70.Ck X-ray scattering
78.70.Dm X-ray absorption spectra
71.20.Ps Other inorganic compounds
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