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28 Aug 2011

Volume 135, Issue 8, Articles (08xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 135, 084501 (2011); http://dx.doi.org/10.1063/1.3624366 (8 pages)

Letif Mones, Peter J. Rossky, and László Turi
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Communication: Uncovering molecule-TiO2 interactions with nonlinear spectroscopy

Stephen A. Miller, Brantley A. West, Anna C. Curtis, John M. Papanikolas, and Andrew M. Moran

J. Chem. Phys. 135, 081101 (2011); http://dx.doi.org/10.1063/1.3631339 (4 pages)

Online Publication Date: 22 August 2011

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Femtosecond transient grating experiments are used to investigate electronic structures and transport mechanisms in dye-sensitized nanocrystalline TiO2 films. This study examines two molecular sensitizers spanning the weak (a phosphonated Ruthenium complex) and strong (catechol) molecule-TiO2 coupling regimes. It is shown that strong molecule-TiO2 interactions give rise to photoinduced vibrational coherences at the interface between species. We suggest that the amplitudes of these coherences reflect the molecule-TiO2 coupling strength and signify the delocalization of excited state wavefunctions.
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73.21.-b Electron states and collective excitations in multilayers, quantum wells, mesoscopic, and nanoscale systems
78.66.Li Other semiconductors
63.22.Dc Free films
68.55.ag Semiconductors
78.47.da Excited states
71.10.Li Excited states and pairing interactions in model systems
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Communication: Highly accurate ozone formation potential and implications for kinetics

Richard Dawes, Phalgun Lolur, Jianyi Ma, and Hua Guo

J. Chem. Phys. 135, 081102 (2011); http://dx.doi.org/10.1063/1.3632055 (4 pages) | Cited 1 time

Online Publication Date: 24 August 2011

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Atmospheric ozone is formed by the O + O2 exchange reaction followed by collisional stabilization of the O3* intermediate. The dynamics of the O + O2 reaction and to a lesser extent the O3 stabilization depend sensitively on the underlying potential energy surface, particularly in the asymptotic region. Highly accurate Davidson corrected multi-state multi-reference configuration interaction calculations reported here reveal that the minimal energy path for the formation of O3 from O + O2 is a monotonically decaying function of the atom-diatom distance and contains no “reef” feature found in previous ab initio calculations. The absence of a submerged barrier leads to an exchange rate constant with the correct temperature dependence and is in better agreement with experiment, as shown by quantum scattering calculations.
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82.33.Tb Atmospheric chemistry
82.20.Fd Collision theories; trajectory models
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
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Communication: A density functional with accurate fractional-charge and fractional-spin behaviour for s-electrons

Erin R. Johnson and Julia Contreras-García

J. Chem. Phys. 135, 081103 (2011); http://dx.doi.org/10.1063/1.3630117 (4 pages)

Online Publication Date: 25 August 2011

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We develop a new density-functional approach combining physical insight from chemical structure with treatment of multi-reference character by real-space modeling of the exchange-correlation hole. We are able to recover, for the first time, correct fractional-charge and fractional-spin behaviour for atoms of groups 1 and 2. Based on Becke's non-dynamical correlation functional [A. D. Becke, J. Chem. Phys. 119, 2972 (2003)]10.1063/1.1589733 and explicitly accounting for core-valence separation and pairing effects, this method is able to accurately describe dissociation and strong correlation in s-shell many-electron systems.
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31.15.ej Spin-density functionals
31.15.V- Electron correlation calculations for atoms, ions and molecules
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
31.15.eg Exchange-correlation functionals (in current density functional theory)
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Communication: Imaging wavefunctions in dissociative photoionization

W. Scott Hopkins and Stuart R. Mackenzie

J. Chem. Phys. 135, 081104 (2011); http://dx.doi.org/10.1063/1.3632103 (4 pages)

Online Publication Date: 26 August 2011

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The dissociative ionization dynamics of excited electronic states of the xenon dimer, Xe2, have been studied using velocity map ion imaging (VMI). A one-colour, (2+1) resonant excitation scheme was employed to first excite and then ionize selected vibrational levels of the Xe2 6p 2[1/2]0 0g+ Rydberg state. Cationic fragments were then detected by the VMI. The data provide an outstanding example of the reflection principle in photodissociation with the full nodal structure of the Rydberg state wavefunctions clearly observed in the final Xe+ kinetic energy distributions without the need for scanning the excitation energy. Fitting of the observed distributions provides detailed and precise information on the form of the Xe2+ I(1/2g) potential energy curve involved which is in excellent agreement with the results of photoelectron imaging studies [Shubert and Pratt, J. Chem. Phys. 134, 044315 (2011) 10.1063/1.3533361]. Furthermore, the anisotropy of the product angular distributions yields information on the evolution of the electronic character of the ionic state with internuclear separation, R. The combination of the nature of dissociative ionization and the extent of the bound state wavefunctions provide information over an unusually wide range of internuclear separation R (ΔR > 0.75 Å). This would normally require scanning over a considerable energy region but is obtained in these studies at a fixed excitation energy.
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33.80.Eh Autoionization, photoionization, and photodetachment
33.80.Gj Diffuse spectra; predissociation, photodissociation
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
31.50.Df Potential energy surfaces for excited electronic states
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Communication: Efficient counterpoise corrections by a perturbative approach

Jia Deng, Andrew T. B. Gilbert, and Peter M. W. Gill

J. Chem. Phys. 135, 081105 (2011); http://dx.doi.org/10.1063/1.3632054 (4 pages) | Cited 1 time

Online Publication Date: 26 August 2011

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We investigate the use of Hartree-Fock and density functional perturbative corrections for estimating the counterpoise correction (CPC) for interaction energies at the self-consistent field level. We test our approach using several popular basis sets on the S22 set of weakly bound systems, which can exhibit large basis set superposition errors. Our results show that the perturbative approaches typically recover over 95% of the CPC and can be up to twelve times faster to compute than the conventional methods and therefore provide an attractive alternative to calculating CPCs in the conventional way.
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31.15.xp Perturbation theory
31.15.xr Self-consistent-field methods
31.15.E- Density-functional theory
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Communication: Extended multi-state complete active space second-order perturbation theory: Energy and nuclear gradients

Toru Shiozaki, Werner Győrffy, Paolo Celani, and Hans-Joachim Werner

J. Chem. Phys. 135, 081106 (2011); http://dx.doi.org/10.1063/1.3633329 (4 pages)

Online Publication Date: 30 August 2011

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The extended multireference quasi-degenerate perturbation theory, proposed by Granovsky [J. Chem. Phys. 134, 214113 (2011)], is combined with internally contracted multi-state complete active space second-order perturbation theory (XMS-CASPT2). The first-order wavefunction is expanded in terms of the union of internally contracted basis functions generated from all the reference functions, which guarantees invariance of the theory with respect to unitary rotations of the reference functions. The method yields improved potentials in the vicinity of avoided crossings and conical intersections. The theory for computing nuclear energy gradients for MS-CASPT2 and XMS-CASPT2 is also presented and the first implementation of these gradient methods is reported. A number of illustrative applications of the new methods are presented.
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31.15.xp Perturbation theory
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.bw Coupled-cluster theory
31.50.-x Potential energy surfaces
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Reciprocity in the degeneracies of some tetra-atomic molecular ions

Erika Bene, Tamás Vértesi, and Robert Englman

J. Chem. Phys. 135, 084101 (2011); http://dx.doi.org/10.1063/1.3625917 (6 pages) | Cited 1 time

Online Publication Date: 22 August 2011

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Various ab initio computations, as, e.g., in G. J. Halász and Á. Vibók, Int. J. Quantum Chem. 111, 342 (2011), have shown that in molecules of the type (HCCH)+, when the extremal H atoms are distorted from a linear form but maintain a planar geometry, a pair of conical intersections (ci) occur at such positions that the ratios of the distortional coordinates of the two atoms are in the two ci's reciprocals of each other. These computations have here been extended to locate the ci's also for HCNH. The two groups of results are explained by simple analytic perturbational expressions for the energy differences of the lowest adjacent electronic states, with inclusion of excited state effects.
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31.15.A- Ab initio calculations
33.15.Bh General molecular conformation and symmetry; stereochemistry

An orbital-invariant and strictly size extensive post-Hartree-Fock correlation functional

Christian Kollmar and Frank Neese

J. Chem. Phys. 135, 084102 (2011); http://dx.doi.org/10.1063/1.3624567 (8 pages)

Online Publication Date: 22 August 2011

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A strictly size extensive post-Hartree-Fock correlation functional being invariant with respect to orbital transformations within the occupied and virtual subspaces is presented. While avoiding the necessity to solve additional Z vector equations for the calculation of properties and energy gradients, this functional reproduces almost exactly the results of coupled-cluster singles doubles (CCSD) calculations. In particular, it is demonstrated that the method is rigorous in the sense that it can be systematically improved by the perturbative inclusion of triple excitations in the same way as CCSD. As to the computational cost, the presented approach is somewhat more expensive than the CCSD if the energy is variationally optimized with respect to both the orbitals and the excitation amplitudes. Replacement of orbital optimization by the Brueckner condition reduces the computational cost by a factor of two, thus making the method less expensive than CCSD.
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31.15.xr Self-consistent-field methods
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How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?

Ramon Grima, Philipp Thomas, and Arthur V. Straube

J. Chem. Phys. 135, 084103 (2011); http://dx.doi.org/10.1063/1.3625958 (16 pages) | Cited 1 time

Online Publication Date: 22 August 2011

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The chemical Fokker-Planck equation and the corresponding chemical Langevin equation are commonly used approximations of the chemical master equation. These equations are derived from an uncontrolled, second-order truncation of the Kramers-Moyal expansion of the chemical master equation and hence their accuracy remains to be clarified. We use the system-size expansion to show that chemical Fokker-Planck estimates of the mean concentrations and of the variance of the concentration fluctuations about the mean are accurate to order Ω−3/2 for reaction systems which do not obey detailed balance and at least accurate to order Ω−2 for systems obeying detailed balance, where Ω is the characteristic size of the system. Hence, the chemical Fokker-Planck equation turns out to be more accurate than the linear-noise approximation of the chemical master equation (the linear Fokker-Planck equation) which leads to mean concentration estimates accurate to order Ω−1/2 and variance estimates accurate to order Ω−3/2. This higher accuracy is particularly conspicuous for chemical systems realized in small volumes such as biochemical reactions inside cells. A formula is also obtained for the approximate size of the relative errors in the concentration and variance predictions of the chemical Fokker-Planck equation, where the relative error is defined as the difference between the predictions of the chemical Fokker-Planck equation and the master equation divided by the prediction of the master equation. For dimerization and enzyme-catalyzed reactions, the errors are typically less than few percent even when the steady-state is characterized by merely few tens of molecules.
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82.20.Pm Rate constants, reaction cross sections, and activation energies
82.30.Nr Association, addition, insertion, cluster formation
82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
87.14.ej Enzymes

Breaking the carbon dimer: The challenges of multiple bond dissociation with full configuration interaction quantum Monte Carlo methods

George H. Booth, Deidre Cleland, Alex J. W. Thom, and Ali Alavi

J. Chem. Phys. 135, 084104 (2011); http://dx.doi.org/10.1063/1.3624383 (14 pages)

Online Publication Date: 22 August 2011

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The full configuration interaction quantum Monte Carlo (FCIQMC) method, as well as its “initiator” extension (i-FCIQMC), is used to tackle the complex electronic structure of the carbon dimer across the entire dissociation reaction coordinate, as a prototypical example of a strongly correlated molecular system. Various basis sets of increasing size up to the large cc-pVQZ are used, spanning a fully accessible N-electron basis of over 1012 Slater determinants, and the accuracy of the method is demonstrated in each basis set. Convergence to the FCI limit is achieved in the largest basis with only O[107] walkers within random errorbars of a few tenths of a millihartree across the binding curve, and extensive comparisons to FCI, CCSD(T), MRCI, and CEEIS results are made where possible. A detailed exposition of the convergence properties of the FCIQMC methods is provided, considering convergence with elapsed imaginary time, number of walkers and size of the basis. Various symmetries which can be incorporated into the stochastic dynamic, beyond the standard abelian point group symmetry and spin polarisation are also described. These can have significant benefit to the computational effort of the calculations, as well as the ability to converge to various excited states. The results presented demonstrate a new benchmark accuracy in basis-set energies for systems of this size, significantly improving on previous state of the art estimates.
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31.15.vn Electron correlation calculations for diatomic molecules
33.15.Fm Bond strengths, dissociation energies

An approximate density-functional method using the Harris-Foulkes functional

G. D. Bellchambers and F. R. Manby

J. Chem. Phys. 135, 084105 (2011); http://dx.doi.org/10.1063/1.3625433 (6 pages)

Online Publication Date: 22 August 2011

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We present a method which uses the results of a molecular Kohn-Sham calculation at a reference geometry to approximate the energy at many different geometries. The Kohn-Sham electron density of the reference geometry is decomposed into atomic fragments, which move with the nuclei to approximate the density at a new geometry and the energy is evaluated with the Harris-Foulkes functional. Preliminary results for a biological quantum-mechanics/molecular-mechanics trajectory are promising: the errors of reference-geometry Harris-Foulkes (compared to full self-consistent Kohn-Sham) for the PBE exchange-correlation functional have the same magnitude as the difference between the energies of PBE and BLYP.
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87.14.ej Enzymes
87.15.B- Structure of biomolecules
31.15.eg Exchange-correlation functionals (in current density functional theory)

On the accuracy of the state space restriction approximation for spin dynamics simulations

Alexander Karabanov, Ilya Kuprov, G. T. P. Charnock, Anniek van der Drift, Luke J. Edwards, and Walter Köckenberger

J. Chem. Phys. 135, 084106 (2011); http://dx.doi.org/10.1063/1.3624564 (8 pages) | Cited 1 time

Online Publication Date: 23 August 2011

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We present an algebraic foundation for the state space restriction approximation in spin dynamics simulations and derive applicability criteria as well as minimal basis set requirements for practically encountered simulation tasks. The results are illustrated with nuclear magnetic resonance (NMR), electron spin resonance (ESR), dynamic nuclear polarization (DNP), and spin chemistry simulations. It is demonstrated that state space restriction yields accurate results in systems where the time scale of spin relaxation processes approximately matches the time scale of the experiment. Rigorous error bounds and basis set requirements are derived.
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76.60.Es Relaxation effects
76.70.Fz Double nuclear magnetic resonance (DNMR), dynamical nuclear polarization
76.30.-v Electron paramagnetic resonance and relaxation

Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory

Miho Isegawa, Jiali Gao, and Donald G. Truhlar

J. Chem. Phys. 135, 084107 (2011); http://dx.doi.org/10.1063/1.3624890 (13 pages)

Online Publication Date: 23 August 2011

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Molecular fragmentation algorithms provide a powerful approach to extending electronic structure methods to very large systems. Here we present a method for including charge transfer between molecular fragments in the explicit polarization (X-Pol) fragment method for calculating potential energy surfaces. In the conventional X-Pol method, the total charge of each fragment is preserved, and charge transfer between fragments is not allowed. The description of charge transfer is made possible by treating each fragment as an open system with respect to the number of electrons. To achieve this, we applied Mermin's finite temperature method to the X-Pol wave function. In the application of this method to X-Pol, the fragments are open systems that partially equilibrate their number of electrons through a quasithermodynamics electron reservoir. The number of electrons in a given fragment can take a fractional value, and the electrons of each fragment obey the Fermi–Dirac distribution. The equilibrium state for the electrons is determined by electronegativity equalization with conservation of the total number of electrons. The amount of charge transfer is controlled by re-interpreting the temperature parameter in the Fermi–Dirac distribution function as a coupling strength parameter. We determined this coupling parameter so as to reproduce the charge transfer energy obtained by block localized energy decomposition analysis. We apply the new method to ten systems, and we show that it can yield reasonable approximations to potential energy profiles, to charge transfer stabilization energies, and to the direction and amount of charge transferred.
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34.70.+e Charge transfer
31.15.E- Density-functional theory
31.50.-x Potential energy surfaces

The theoretical current-voltage dependence of a non-degenerate disordered organic material obtained with conductive atomic force microscopy

Cristiano F. Woellner, José A. Freire, Michele Guide, and Thuc-Quyen Nguyen

J. Chem. Phys. 135, 084108 (2011); http://dx.doi.org/10.1063/1.3626871 (7 pages)

Online Publication Date: 24 August 2011

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We develop a simple continuum model for the current voltage characteristics of a material as measured by the conducting atomic force microscopy, including space charge effects. We address the effect of the point contact on the magnitude of the current and on the transition voltages between the different current regimes by comparing these with the corresponding expressions obtained with planar electrodes.
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72.20.Ht High-field and nonlinear effects
72.80.Le Polymers; organic compounds (including organic semiconductors)

Using the charge-stabilization technique in the double ionization potential equation-of-motion calculations with dianion references

Tomasz Kuś and Anna I. Krylov

J. Chem. Phys. 135, 084109 (2011); http://dx.doi.org/10.1063/1.3626149 (13 pages) | Cited 1 time

Online Publication Date: 24 August 2011

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The charge-stabilization method is applied to double ionization potential equation-of-motion (EOM-DIP) calculations to stabilize unstable dianion reference functions. The auto-ionizing character of the dianionic reference states spoils the numeric performance of EOM-DIP limiting applications of this method. We demonstrate that reliable excitation energies can be computed by EOM-DIP using a stabilized resonance wave function instead of the lowest energy solution corresponding to the neutral + free electron(s) state of the system. The details of charge-stabilization procedure are discussed and illustrated by examples. The choice of optimal stabilizing Coulomb potential, which is strong enough to stabilize the dianion reference, yet, minimally perturbs the target states of the neutral, is the crux of the approach. Two algorithms of choosing optimal parameters of the stabilization potential are presented. One is based on the orbital energies, and another – on the basis set dependence of the total Hartree-Fock energy of the reference. Our benchmark calculations of the singlet-triplet energy gaps in several diradicals show a remarkable improvement of the EOM-DIP accuracy in problematic cases. Overall, the excitation energies in diradicals computed using the stabilized EOM-DIP are within 0.2 eV from the reference EOM spin-flip values.
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34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
31.15.xr Self-consistent-field methods

Least constraint approach to the extraction of internal motions from molecular dynamics trajectories of flexible macromolecules

Guillaume Chevrot, Paolo Calligari, Konrad Hinsen, and Gerald R. Kneller

J. Chem. Phys. 135, 084110 (2011); http://dx.doi.org/10.1063/1.3626275 (8 pages)

Online Publication Date: 24 August 2011

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We propose a rigorous method for removing rigid-body motions from a given molecular dynamics trajectory of a flexible macromolecule. The method becomes exact in the limit of an infinitesimally small sampling step for the input trajectory. In a recent paper [G. Kneller, J. Chem. Phys. 128, 194101 (2008)]10.1063/1.2902290, one of us showed that virtual internal atomic displacements for small time increments can be derived from Gauss’ principle of least constraint, which leads to a rotational superposition problem for the atomic coordinates in two consecutive time frames of the input trajectory. Here, we demonstrate that the accumulation of these displacements in a molecular-fixed frame, which evolves in time according to the virtual rigid-body motions, leads to the desired trajectory for internal motions. The atomic coordinates in the input and output trajectory are related by a roto-translation, which guarantees that the internal energy of the molecule is left invariant. We present a convenient implementation of our method, in which the accumulation of the internal displacements is performed implicitly. Two numerical examples illustrate the difference to the classical approach for removing macromolecular rigid-body motions, which consists of aligning its configurations in the input trajectory with a fixed reference structure.
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36.20.Ey Conformation (statistics and dynamics)
31.15.xv Molecular dynamics and other numerical methods
87.10.Tf Molecular dynamics simulation
87.15.H- Dynamics of biomolecules
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)

Extension of the invariant environment refinement technique + reverse Monte Carlo method of structural modelling for interpreting experimental structure factors: The cases of amorphous silicon, phosphorus, and liquid argon

Orsolya Gereben and László Pusztai

J. Chem. Phys. 135, 084111 (2011); http://dx.doi.org/10.1063/1.3624839 (6 pages)

Online Publication Date: 24 August 2011

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The invariant environment refinement technique, as applied to reverse Monte Carlo modelling [invariant environment refinement technique + reverse Monte Carlo (INVERT + RMC); M. J. Cliffe, M. T. Dove, D. A. Drabold, and A. L. Goodwin, Phys. Rev. Lett. 104, 125501 (2010)10.1103/PhysRevLett.104.125501], is extended so that it is now applicable for interpreting the structure factor (instead of the pair distribution function). The new algorithm, called the local invariance calculation, is presented by the examples of amorphous silicon, phosphorus, and liquid argon. As a measure of the effectiveness of the new algorithm, the ratio of exactly fourfold coordinated Si atoms was larger than obtained previously by the INVERT-RMC scheme.
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61.43.Dq Amorphous semiconductors, metals, and alloys
61.20.Ja Computer simulation of liquid structure
61.25.-f Studies of specific liquid structures

Calculation of multiple initial state selected reaction probabilities from Chebyshev flux-flux correlation functions: Influence of reactant internal excitations on H + H2O → OH + H2

Bin Jiang, Daiqian Xie, and Hua Guo

J. Chem. Phys. 135, 084112 (2011); http://dx.doi.org/10.1063/1.3626525 (8 pages) | Cited 2 times

Online Publication Date: 24 August 2011

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A Chebyshev-based flux-flux correlation function approach is introduced for calculating multiple initial state selected reaction probabilities for bimolecular reactions. Based on the quantum transition-state theory, this approach propagates, with the exact Chebyshev propagator, transition-state wave packets towards the reactant asymptote. It is accurate and efficient if many initial state selected reaction probabilities are needed. This approach is applied to the title reaction to elucidate the influence of the H2O ro-vibrational states on its reactivity. Results from several potential energy surfaces are compared.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Kh Potential energy surfaces for chemical reactions

Pair correlation function integrals: Computation and use

Rasmus Wedberg, John P. O’Connell, Günther H. Peters, and Jens Abildskov

J. Chem. Phys. 135, 084113 (2011); http://dx.doi.org/10.1063/1.3626799 (9 pages)

Online Publication Date: 24 August 2011

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We describe a method for extending radial distribution functions obtained from molecular simulations of pure and mixed molecular fluids to arbitrary distances. The method allows total correlation function integrals to be reliably calculated from simulations of relatively small systems. The long-distance behavior of radial distribution functions is determined by requiring that the corresponding direct correlation functions follow certain approximations at long distances. We have briefly described the method and tested its performance in previous communications [R. Wedberg, J. P. O’Connell, G. H. Peters, and J. Abildskov, Mol. Simul. 36, 1243 (2010);10.1080/08927020903536366 Fluid Phase Equilib. 302, 32 (2011)]10.1016/j.fluid.2010.10.004, but describe here its theoretical basis more thoroughly and derive long-distance approximations for the direct correlation functions. We describe the numerical implementation of the method in detail, and report numerical tests complementing previous results. Pure molecular fluids are here studied in the isothermal-isobaric ensemble with isothermal compressibilities evaluated from the total correlation function integrals and compared with values derived from volume fluctuations. For systems where the radial distribution function has structure beyond the sampling limit imposed by the system size, the integration is more reliable, and usually more accurate, than simple integral truncation.
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31.15.B- Approximate calculations

Analytic energy gradients for the spin-free exact two-component theory using an exact block diagonalization for the one-electron Dirac Hamiltonian

Lan Cheng and Jürgen Gauss

J. Chem. Phys. 135, 084114 (2011); http://dx.doi.org/10.1063/1.3624397 (7 pages) | Cited 3 times

Online Publication Date: 24 August 2011

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We report the implementation of analytic energy gradients for the evaluation of first-order electrical properties and nuclear forces within the framework of the spin-free (SF) exact two-component (X2c) theory. In the scheme presented here, referred to in the following as SFX2c-1e, the decoupling of electronic and positronic solutions is performed for the one-electron Dirac Hamiltonian in its matrix representation using a single unitary transformation. The resulting two-component one-electron matrix Hamiltonian is combined with untransformed two-electron interactions for subsequent self-consistent-field and electron-correlated calculations. The “picture-change” effect in the calculation of properties is taken into account by considering the full derivative of the two-component Hamiltonian matrix with respect to the external perturbation. The applicability of the analytic-gradient scheme presented here is demonstrated in benchmark calculations. SFX2c-1e results for the dipole moments and electric-field gradients of the hydrogen halides are compared with those obtained from nonrelativistic, SF high-order Douglas-Kroll-Hess, and SF Dirac-Coulomb calculations. It is shown that the use of untransformed two-electron interactions introduces rather small errors for these properties. As a first application of the analytic geometrical gradient, we report the equilibrium geometry of methylcopper (CuCH3) determined at various levels of theory.
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31.15.xr Self-consistent-field methods
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.xp Perturbation theory

Velocity-scaling optimized replica exchange molecular dynamics of proteins in a hybrid explicit/implicit solvent

Jinan Wang, Weiliang Zhu, Guohui Li, and Ulrich H. E. Hansmann

J. Chem. Phys. 135, 084115 (2011); http://dx.doi.org/10.1063/1.3624401 (5 pages)

Online Publication Date: 25 August 2011

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We propose a scheme for replica exchange molecular dynamics of proteins in explicit solvent that minimizes the number of required replicas using velocity rescaling. Our approach relies on a hybrid method where the protein evolves at each temperature in an explicit solvent, but replica exchange moves utilize an implicit solvent term. The two terms are coupled through the velocity rescaling. We test the efficiency of this approach for a common test case, the trp-cage protein.
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87.15.ap Molecular dynamics simulation
87.15.hp Conformational changes
87.14.E- Proteins
87.15.R- Reactions and kinetics
87.15.N- Properties of solutions of macromolecules

Comparison of Brownian dynamics algorithms with hydrodynamic interaction

Ricardo Rodríguez Schmidt, José G. Hernández Cifre, and José García de la Torre

J. Chem. Phys. 135, 084116 (2011); http://dx.doi.org/10.1063/1.3626868 (10 pages)

Online Publication Date: 26 August 2011

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The hydrodynamic interaction is an essential effect to consider in Brownian dynamics simulations of polymer and nanoparticle dilute solutions. Several mathematical approaches can be used to build Brownian dynamics algorithms with hydrodynamic interaction, the most common of them being the exact but time demanding Cholesky decomposition and the Chebyshev polynomial expansion. Recently, Geyer and Winter [J. Chem. Phys. 130, 1149051 (2009)]10.1063/1.3089668 have proposed a new approximation to treat the hydrodynamic interaction that seems quite efficient and is increasingly used. So far, a systematic comparison among those approaches has not been clearly made. In this paper, several features and the efficiency of typical implementations of those approaches are evaluated by using bead-and-spring chain models. The different sensitivity to the bead overlap detected for the different implementations may be of interest to select the suitable algorithm for a given simulation.
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05.40.Jc Brownian motion
61.25.he Polymer solutions

A systematic formulation of the virial expansion for nonadditive interaction potentials

Robert Hellmann and Eckard Bich

J. Chem. Phys. 135, 084117 (2011); http://dx.doi.org/10.1063/1.3626524 (7 pages)

Online Publication Date: 26 August 2011

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A new formulation of the virial expansion for a classical gas is derived without the restriction to pairwise-additive interaction potentials. Explicit expressions up to the eighth virial coefficient, suitable for numerical evaluation, are given in the form of integrals over sums of cluster diagrams. Compared with previous approaches, the number of cluster diagrams increases more moderately with increasing order of the virial coefficient. Thus, the new formulation should be particularly useful for the computation of high-order virial coefficients.
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05.20.Jj Statistical mechanics of classical fluids
51.30.+i Thermodynamic properties, equations of state
02.60.-x Numerical approximation and analysis

Application of an efficient multireference approach to free-base porphin and metalloporphyrins: Ground, excited, and positive ion states

Rajat K Chaudhuri, Karl F. Freed, Sudip Chattopadhyay, and Uttam Sinha Mahapatra

J. Chem. Phys. 135, 084118 (2011); http://dx.doi.org/10.1063/1.3627153 (10 pages)

Online Publication Date: 26 August 2011

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The improved virtual orbital-complete active space configuration interaction (IVO-CASCI) method is applied to determine the geometries of the ground state of free-base porphin and its metal derivatives, magnesium and zinc porphyrins. The vertical excitation energies and ionization potentials are computed at these optimized geometries using an IVO-based version of multireference Möller-Plesset (IVO-MRMP) perturbation theory. The geometries and excitation energies obtained from the IVO-CASCI and IVO-MRMP methods agree well with experiment and with other correlated many-body methods. We also provide the ground state vibrational frequencies for free-base porphin and Mg-porphyrin. All frequencies are real in contrast to self-consistent field treatments which yield an imaginary frequency. Ground state normal mode frequencies (scaled) of free-base porphin and magnesium porphyrin from IVO-CASCI and complete active space self-consistent field methods are quite similar and are consistent with Becke-Slater-Hartree-Fock exchange and Lee-Yang-Parr correlation density functional theory calculations and with experiment. In addition, geometries are determined for low-lying excited state triplets and for positive ion states of the molecules. To our knowledge, no prior experimental and theoretical data are available for these excited state geometries of magnesium and zinc porphyrins. Given that the IVO-CASCI and IVO-MRMP computed geometries and excitation energies agree favorably with experiment and with available theoretical data, our predicted excited state geometries should be equally accurate.
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31.15.vj Electron correlation calculations for atoms and ions: excited states
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
31.15.xp Perturbation theory
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.xr Self-consistent-field methods
31.15.E- Density-functional theory

Closed-shell ring coupled cluster doubles theory with range separation applied on weak intermolecular interactions

Julien Toulouse, Wuming Zhu, Andreas Savin, Georg Jansen, and János G. Ángyán

J. Chem. Phys. 135, 084119 (2011); http://dx.doi.org/10.1063/1.3626551 (8 pages) | Cited 2 times

Online Publication Date: 26 August 2011

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We explore different variants of the random phase approximation to the correlation energy derived from closed-shell ring-diagram approximations to coupled cluster doubles theory. We implement these variants in range-separated density-functional theory, i.e., by combining the long-range random phase approximations with short-range density-functional approximations. We perform tests on the rare-gas dimers He2, Ne2, and Ar2, and on the weakly interacting molecular complexes of the S22 set of Jurečka et al. [P. Jurečka, J. Šponer, J. Černý, and P. Hobza, Phys. Chem. Chem. Phys. 8, 1985 (2006)10.1039/b600027d]. The two best variants correspond to the ones originally proposed by Szabo and Ostlund [A. Szabo and N. S. Ostlund, J. Chem. Phys. 67, 4351 (1977)10.1063/1.434580]. With range separation, they reach mean absolute errors on the equilibrium interaction energies of the S22 set of about 0.4 kcal/mol, corresponding to mean absolute percentage errors of about 4%, with the aug-cc-pVDZ basis set.
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31.15.bw Coupled-cluster theory
31.15.E- Density-functional theory
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