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28 Mar 2009

Volume 130, Issue 12, Articles (12xxxx)

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Polyamorphism in tin tetraiodide

Kazuhiro Fuchizaki, Takaki Hase, Akihiro Yamada, Nozomu Hamaya, Yoshinori Katayama, and Ken-ichi Funakoshi

J. Chem. Phys. 130, 121101 (2009); http://dx.doi.org/10.1063/1.3109691 (4 pages) | Cited 4 times

Online Publication Date: 27 March 2009

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The discovery of a first-order phase transition in fluid phosphorus aroused renewed interest in polyamorphism in liquids with a locally tetrahedral molecular structure. We have performed in situ synchrotron x-ray diffraction measurements on tin tetraiodide, which consists of SnI4 tetrahedral molecules at ambient pressure, and established that the liquid forms existing above and below 1.5 GPa, where the slope of the melting curve of the solid phase changes abruptly, have different structures. This discovery offers evidence of thermodynamically stable polyamorphism in general compounds as well as in elements. A possible phase diagram that includes the two amorphous states already found is proposed based on the pseudobinary regular solution model. The vertex-to-face orientation between the nearest molecules plays a key role in the transition from the low-pressure to the high-pressure liquid phase.
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61.25.Em Molecular liquids
65.20.-w Thermal properties of liquids
64.70.Ja Liquid-liquid transitions
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Unusual dynamical arrest in polymer grafted nanoparticles

A. K. Kandar, S. Srivastava, J. K. Basu, M. K. Mukhopadhyay, S. Seifert, and S. Narayanan

J. Chem. Phys. 130, 121102 (2009); http://dx.doi.org/10.1063/1.3090484 (5 pages) | Cited 6 times

Online Publication Date: 30 March 2009

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We present results of temperature dependent measurements of dynamics of polymer grafted nanoparticles with high grafting density with star polymerlike morphology. We observed for the low grafting density and hence low functionality sample, a dynamically arrested state with lowering of temperature, similar to what was conjectured earlier. However the high grafting density sample shows liquidlike relaxation at all measured temperatures. Possible origin of dynamical arrest in the two grafting density sample is discussed.
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61.25.he Polymer solutions
61.20.Gy Theory and models of liquid structure
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Hydrogen-bond mediated transitional adlayer of glycine on Si(111)7×7 at room temperature

L. Zhang, A. Chatterjee, M. Ebrahimi, and K. T. Leung

J. Chem. Phys. 130, 121103 (2009); http://dx.doi.org/10.1063/1.3106762 (5 pages) | Cited 6 times

Online Publication Date: 30 March 2009

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The growth of glycine film by thermal evaporation on Si(111)7×7 at room temperature has been studied by X-ray photoemission. In contrast to common carboxylic acids, glycine is found to adsorb on Si(111)7×7 dissociatively through cleavage of a N–H bond instead of O–H bond. The intricate evolution of the observed N 1s features at 399.1, 401.4, and 402.2 eV with increasing film thickness demonstrates the existence of a transitional adlayer between the first adlayer and the zwitterionic multilayer. This transitional adlayer is estimated to be 1–2 adlayer thick and is characterized by the presence of intermolecular N⋯HO hydrogen bond. An intramolecular proton transfer mechanism is proposed to account for the adsorption process through the amino group.
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81.05.Lg Polymers and plastics; rubber; synthetic and natural fibers; organometallic and organic materials
68.55.am Polymers and organics
79.60.Dp Adsorbed layers and thin films
68.43.-h Chemisorption/physisorption: adsorbates on surfaces
82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
81.15.-z Methods of deposition of films and coatings; film growth and epitaxy
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Structures and harmonic vibrational frequencies for excited states of diatomic molecules with CCSD(R12) and CCSD(F12) models

Jun Yang and Christof Hättig

J. Chem. Phys. 130, 124101 (2009); http://dx.doi.org/10.1063/1.3093947 (12 pages) | Cited 9 times

Online Publication Date: 23 March 2009

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The equation-of-motion coupled-cluster method for excited states with the singles-and-doubles model (CCSD) has been implemented for ansatz 2 of the explicitly correlated CCSD(R12) and CCSD(F12) methods as part of the program package Dalton. In this model, an orthonormal complementary auxiliary basis set is used for the resolution-of-identity approximation in order to calculate the three-electron integrals needed for CCSD(R12) and CCSD(F12). The additional CCSD(R12) or CCSD(F12) terms introduced within ansatz 2, which are not present in ansatz 1, are derived and discussed with regard to the extra costs needed for their computation. As a first application the basis set convergence of equilibrium bond lengths and harmonic vibrational frequencies has been investigated for some singlet excited states of the diatomic molecules N2, CO, BF, and BH. The calculated CCSD(F12) results show that the average absolute deviations of the bond lengths and frequencies from the basis set limits are below 0.1 pm and 5 cm−1 as well as 0.05 pm and 1 cm−1 for the triple- and quadruple-ζ basis sets, respectively. These deviations are shown to largely arise from the SCF basis set incompleteness errors.
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31.15.vj Electron correlation calculations for atoms and ions: excited states
31.15.bw Coupled-cluster theory
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Bh General molecular conformation and symmetry; stereochemistry

Quadratic canonical transformation theory and higher order density matrices

Eric Neuscamman, Takeshi Yanai, and Garnet Kin-Lic Chan

J. Chem. Phys. 130, 124102 (2009); http://dx.doi.org/10.1063/1.3086932 (12 pages) | Cited 20 times

Online Publication Date: 23 March 2009

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Canonical transformation (CT) theory provides a rigorously size-extensive description of dynamic correlation in multireference systems, with an accuracy superior to and cost scaling lower than complete active space second order perturbation theory. Here we expand our previous theory by investigating (i) a commutator approximation that is applied at quadratic, as opposed to linear, order in the effective Hamiltonian, and (ii) incorporation of the three-body reduced density matrix in the operator and density matrix decompositions. The quadratic commutator approximation improves CT’s accuracy when used with a single-determinant reference, repairing the previous formal disadvantage of the single-reference linear CT theory relative to singles and doubles coupled cluster theory. Calculations on the BH and HF binding curves confirm this improvement. In multireference systems, the three-body reduced density matrix increases the overall accuracy of the CT theory. Tests on the H2O and N2 binding curves yield results highly competitive with expensive state-of-the-art multireference methods, such as the multireference Davidson-corrected configuration interaction (MRCI+Q), averaged coupled pair functional, and averaged quadratic coupled cluster theories.
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31.15.bw Coupled-cluster theory
31.15.xp Perturbation theory
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations

Relativistic all-electron molecular dynamics simulations

Jens Thar and Barbara Kirchner

J. Chem. Phys. 130, 124103 (2009); http://dx.doi.org/10.1063/1.3086655 (12 pages) | Cited 5 times

Online Publication Date: 23 March 2009

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The scalar-relativistic Douglas–Kroll–Hess method is implemented in the Born–Oppenheimer molecular dynamics simulation package CP2K. Using relativistic densities in a nonrelativistic gradient routine is found to be a valid approximation of relativistic gradients. An excellent agreement between optimized structures and geometries obtained from numerical gradients is observed with an error smaller than 0.02 pm. Hydrogen halide dimers [(HX)2, with X = F, Cl, Br, I] serve as small test systems for first-principles molecular dynamics simulations. Relativistic effects are observed. That is, the amplitude of motion is larger, the frequency of motion is smaller, and the distances are larger in the relativistic picture. Several localization schemes are evaluated for different interatomic and intermolecular distances. The errors of these localization schemes are small for geometries which are similar to the equilibrium structure. They become larger for smaller distances, introducing a slight bias toward closed packed configurations.
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31.15.xv Molecular dynamics and other numerical methods
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Dj Interatomic distances and angles
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions

Multivariate frequency domain analysis of protein dynamics

Yasuhiro Matsunaga, Sotaro Fuchigami, and Akinori Kidera

J. Chem. Phys. 130, 124104 (2009); http://dx.doi.org/10.1063/1.3090812 (8 pages) | Cited 3 times

Online Publication Date: 23 March 2009

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Multivariate frequency domain analysis (MFDA) is proposed to characterize collective vibrational dynamics of protein obtained by a molecular dynamics (MD) simulation. MFDA performs principal component analysis (PCA) for a bandpass filtered multivariate time series using the multitaper method of spectral estimation. By applying MFDA to MD trajectories of bovine pancreatic trypsin inhibitor, we determined the collective vibrational modes in the frequency domain, which were identified by their vibrational frequencies and eigenvectors. At near zero temperature, the vibrational modes determined by MFDA agreed well with those calculated by normal mode analysis. At 300 K, the vibrational modes exhibited characteristic features that were considerably different from the principal modes of the static distribution given by the standard PCA. The influences of aqueous environments were discussed based on two different sets of vibrational modes, one derived from a MD simulation in water and the other from a simulation in vacuum. Using the varimax rotation, an algorithm of the multivariate statistical analysis, the representative orthogonal set of eigenmodes was determined at each vibrational frequency.
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87.15.H- Dynamics of biomolecules
87.15.ap Molecular dynamics simulation
87.14.E- Proteins

An efficient algorithm for the density-functional theory treatment of dispersion interactions

Jürgen Gräfenstein and Dieter Cremer

J. Chem. Phys. 130, 124105 (2009); http://dx.doi.org/10.1063/1.3079822 (16 pages) | Cited 33 times

Online Publication Date: 23 March 2009

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The quasi-self-consistent-field dispersion-corrected density-functional theory formalism (QSCF-DC-DFT) is developed and presented as an efficient and reliable scheme for the DFT treatment of van der Waals dispersion complexes, including full geometry optimizations and frequency calculations with analytical energy derivatives in a routine way. For this purpose, the long-range-corrected Perdew–Burke–Ernzerhof exchange functional and the one-parameter progressive correlation functional of Hirao and co-workers are combined with the Andersson–Langreth–Lundqvist (ALL) long-range correlation functional. The time-consuming self-consistent incorporation of the ALL term in the DFT iterations needed for the calculation of forces and force constants is avoided by an a posteriori evaluation of the ALL term and its gradient based on an effective partitioning of the coordinate space into global and intramonomer coordinates. QSCF-DC-DFT is substantially faster than SCF-DC-DFT would be. QSCF-DC-DFT is used to explore the potential energy surface (PES) of the benzene dimer. The results for the binding energies and intermolecular distances agree well with coupled-cluster calculations at the complete basis-set limit. We identify 16 stationary points on the PES, which underlines the usefulness of analytical energy gradients for the investigation of the PES. Furthermore, the inclusion of analytically calculated zero point energies reveals that large-amplitude vibrations connect the eight most stable benzene dimer forms and make it difficult to identify a dominating complex form. The tilted T structure and the parallel-displaced sandwich form have the same D0 value of 2.40 kcal/mol, which agrees perfectly with the experimental value of 2.40±0.40 kcal/mol.
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31.15.E- Density-functional theory
31.50.-x Potential energy surfaces
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
34.20.Gj Intermolecular and atom-molecule potentials and forces
33.20.Tp Vibrational analysis
31.15.xr Self-consistent-field methods

Calculation of long time classical trajectories: Algorithmic treatment and applications for molecular systems

Hartmut Schwetlick and Johannes Zimmer

J. Chem. Phys. 130, 124106 (2009); http://dx.doi.org/10.1063/1.3096294 (11 pages) | Cited 3 times

Online Publication Date: 23 March 2009

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We study the problem of finding a path that joins a given initial state with a final one, where the evolution is governed by classical (Hamiltonian) dynamics. A new algorithm for the computation of long time transition trajectories connecting two configurations is presented. In particular, a strategy for finding transition paths between two stable basins is established. The starting point is the formulation of the equation of motion of classical mechanics in the framework of Jacobi’s principle; a shortening procedure inspired by Birkhoff’s method is then applied to find geodesic solutions. Numerical examples are given for Müller’s potential and the collinear reaction H2+H→H+H2.
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82.20.Nk Classical theories of reactions and/or energy transfer
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Db Transition state theory and statistical theories of rate constants

Nonadiabatic coupling vectors within linear response time-dependent density functional theory

Ivano Tavernelli, Enrico Tapavicza, and Ursula Rothlisberger

J. Chem. Phys. 130, 124107 (2009); http://dx.doi.org/10.1063/1.3097192 (10 pages) | Cited 15 times

Online Publication Date: 24 March 2009

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A method is developed to compute the nonadiabatic coupling vectors (NACVs) between electronic ground and excited states as well as between any possible pair of excited states within the framework of linear response time-dependent density functional theory (TDDFT) in the adiabatic approximation. The development is an extension to our previous work on surface hopping dynamics [ E. Tapavicza et al., Phys. Rev. Lett. 98, 023001 (2007) ] for which we improve the description of the TDDFT approximation of the excited state wavefunctions by means of linear response orbitals. The method is first validated on the H+H2 system that has a region of strong coupling near the conical intersection at the equilateral geometry. These results confirm the quality and the numerical efficiency of the approach, which has an accuracy comparable to the one achieved with wavefunction-based methods. Finally, we apply the method to the calculation of the NACVs of protonated formaldimine (NH2CH2+) along a surface hopping trajectory initiated in the second excited state.
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31.15.E- Density-functional theory
31.50.Df Potential energy surfaces for excited electronic states

A Chebychev propagator for inhomogeneous Schrödinger equations

Mamadou Ndong, Hillel Tal-Ezer, Ronnie Kosloff, and Christiane P. Koch

J. Chem. Phys. 130, 124108 (2009); http://dx.doi.org/10.1063/1.3098940 (12 pages) | Cited 6 times

Online Publication Date: 24 March 2009

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A propagation scheme for time-dependent inhomogeneous Schrödinger equations is presented. Such equations occur in time dependent optimal control theory and in reactive scattering. A formal solution based on a polynomial expansion of the inhomogeneous term is derived. It is subjected to an approximation in terms of Chebychev polynomials. Different variants for the inhomogeneous propagator are demonstrated and applied to two examples from optimal control theory. Convergence behavior and numerical efficiency are analyzed.
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03.65.Ge Solutions of wave equations: bound states
02.30.Yy Control theory
02.10.De Algebraic structures and number theory
02.30.Hq Ordinary differential equations
02.60.Lj Ordinary and partial differential equations; boundary value problems

Highly accurate tau-leaping methods with random corrections

Yucheng Hu and Tiejun Li

J. Chem. Phys. 130, 124109 (2009); http://dx.doi.org/10.1063/1.3091269 (20 pages) | Cited 3 times

Online Publication Date: 24 March 2009

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We aim to construct higher order tau-leaping methods for numerically simulating stochastic chemical kinetic systems in this paper. By adding a random correction to the primitive tau-leaping scheme in each time step, we greatly improve the accuracy of the tau-leaping approximations. This gain in accuracy actually comes from the reduction in the local truncation error of the scheme in the order of τ, the marching time step size. While the local truncation error of the primitive tau-leaping method is O(τ2) for all moments, our Poisson random correction tau-leaping method, in which the correction term is a Poisson random variable, can reduce the local truncation error for the mean to O(τ3), and both Gaussian random correction tau-leaping methods, in which the correction term is a Gaussian random variable, can reduce the local truncation error for both the mean and covariance to O(τ3). Numerical results demonstrate that these novel methods more accurately capture crucial properties such as the mean and variance than existing methods for simulating chemical reaction systems. This work constitutes a first step to construct high order numerical methods for simulating jump processes. With further refinement and appropriately modified step-size selection procedures, the random correction methods should provide a viable way of simulating chemical reaction systems accurately and efficiently.
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82.20.Uv Stochastic theories of rate constants
82.20.Wt Computational modeling; simulation
02.50.Ey Stochastic processes
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion

Electrostatic correlations in colloidal suspensions: Density profiles and effective charges beyond the Poisson–Boltzmann theory

Alexandre P. dos Santos, Alexandre Diehl, and Yan Levin

J. Chem. Phys. 130, 124110 (2009); http://dx.doi.org/10.1063/1.3098556 (4 pages) | Cited 12 times

Online Publication Date: 24 March 2009

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A theory is proposed which allows us to calculate the distribution of the multivalent counterions around a colloidal particle using the cell model. The results are compared with the Monte Carlo simulations and are found to be very accurate in the two asymptotic regimes, close to the colloidal particle and far from it. The theory allows to accurately calculate the osmotic pressure and the effective charge of colloidal particles with multivalent counterions.
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82.70.Dd Colloids
82.70.Kj Emulsions and suspensions
82.39.Wj Ion exchange, dialysis, osmosis, electro-osmosis, membrane processes

Comparison between integrated and parallel tempering methods in enhanced sampling simulations

Lijiang Yang, Qiang Shao, and Yi Qin Gao

J. Chem. Phys. 130, 124111 (2009); http://dx.doi.org/10.1063/1.3097129 (8 pages) | Cited 4 times

Online Publication Date: 24 March 2009

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Recently, we introduced an integrated tempering approach to enhance sampling in the energy and configuration space for large systems. In this paper, we show that this new method has a higher efficiency than bias potential and generalized ensemble methods, such as accelerated molecular dynamics and replica-exchange molecular dynamics (parallel tempering) methods, in yielding thermodynamic averages. Particularly, the sampling efficiencies in both energy and configuration spaces are compared in details between integrated and parallel tempering methods. Related issues regarding the efficiency involved in the usage of the parallel tempering method are also discussed.
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87.15.ap Molecular dynamics simulation
87.14.E- Proteins
31.15.xv Molecular dynamics and other numerical methods

Replica exchange statistical temperature Monte Carlo

Jaegil Kim, Thomas Keyes, and John E. Straub

J. Chem. Phys. 130, 124112 (2009); http://dx.doi.org/10.1063/1.3095422 (10 pages) | Cited 6 times

Online Publication Date: 24 March 2009

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The replica exchange statistical temperature Monte Carlo algorithm (RESTMC) is presented, extending the single-replica STMC algorithm [ J. Kim, J. E. Straub, and T. Keyes, Phys. Rev. Lett. 97, 050601 (2006) ] to alleviate the slow convergence of the conventional temperature replica exchange method (t-REM) with increasing system size. In contrast to the Gibbs–Boltzmann sampling at a specific temperature characteristic of the standard t-REM, RESTMC samples a range of temperatures in each replica and achieves a flat energy sampling employing the generalized sampling weight, which is automatically determined via the dynamic modification of the replica-dependent statistical temperature. Faster weight determination, through the dynamic update of the statistical temperature, and the flat energy sampling, maximizing energy overlaps between neighboring replicas, lead to a considerable acceleration in the convergence of simulations even while employing significantly fewer replicas. The performance of RESTMC is demonstrated and quantitatively compared with that of the conventional t-REM under varying simulation conditions for Lennard-Jones 19, 31, and 55 atomic clusters, exhibiting single- and double-funneled energy landscapes.
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31.15.xv Molecular dynamics and other numerical methods
34.20.Cf Interatomic potentials and forces
05.10.Ln Monte Carlo methods
36.40.-c Atomic and molecular clusters
02.70.Uu Applications of Monte Carlo methods

A new electronic structure method for doublet states: Configuration interaction in the space of ionized 1h and 2h1p determinants

Anna A. Golubeva, Piotr A. Pieniazek, and Anna I. Krylov

J. Chem. Phys. 130, 124113 (2009); http://dx.doi.org/10.1063/1.3098949 (10 pages) | Cited 6 times

Online Publication Date: 25 March 2009

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An implementation of gradient and energy calculations for configuration interaction variant of equation-of-motion coupled cluster with single and double substitutions for ionization potentials (EOM-IP-CCSD) is reported. The method (termed IP-CISD) treats the ground and excited doublet electronic states of an N-electron system as ionizing excitations from a closed-shell N+1-electron reference state. The method is naturally spin adapted, variational, and size intensive. The computational scaling is N5, in contrast with the N6 scaling of EOM-IP-CCSD. The performance and capabilities of the new approach are demonstrated by application to the uracil cation and water and benzene dimer cations by benchmarking IP-CISD against more accurate IP-CCSD. The equilibrium geometries, especially relative differences between different ionized states, are well reproduced. The average absolute errors and the standard deviations averaged for all bond lengths in all electronic states (58 values in total) are 0.014 and 0.007 Å, respectively. IP-CISD systematically underestimates intramolecular distances and overestimates intermolecular ones, because of the underlying uncorrelated Hartree–Fock reference wave function. The IP-CISD excitation energies of the cations are of a semiquantitative value only, showing maximum errors of 0.35 eV relative to EOM-IP-CCSD. Trends in properties such as dipole moments, transition dipoles, and charge distributions are well reproduced by IP-CISD.
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31.15.V- Electron correlation calculations for atoms, ions and molecules
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Dj Interatomic distances and angles
31.15.xr Self-consistent-field methods
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
31.15.bw Coupled-cluster theory

Numerical evaluation of electron repulsion integrals for pseudoatomic orbitals and their derivatives

Masayuki Toyoda and Taisuke Ozaki

J. Chem. Phys. 130, 124114 (2009); http://dx.doi.org/10.1063/1.3082269 (7 pages) | Cited 5 times

Online Publication Date: 25 March 2009

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A numerical method to calculate the four-center electron-repulsion integrals for strictly localized pseudoatomic orbital basis sets has been developed. Compared to the conventional Gaussian expansion method, this method has an advantage in the ease of combination with O(N) density functional calculations. Additional mathematical derivations are also presented including the analytic derivatives of the integrals with respect to atomic positions and spatial damping of the Coulomb interaction due to the screening effect. In the numerical test for a simple molecule, the convergence up to 10−5 hartree in energy is successfully obtained with a feasible cost of computation.
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31.15.xv Molecular dynamics and other numerical methods
02.30.Rz Integral equations
31.30.-i Corrections to electronic structure

The static-exchange electron-water pseudopotential, in conjunction with a polarizable water model: A new Hamiltonian for hydrated-electron simulations

Leif D. Jacobson, Christopher F. Williams, and John M. Herbert

J. Chem. Phys. 130, 124115 (2009); http://dx.doi.org/10.1063/1.3089425 (18 pages) | Cited 14 times

Online Publication Date: 25 March 2009

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Previously, Turi and Borgis [J. Chem. Phys. 117, 6186 (2002)] parametrized an electron-water interaction potential, intended for use in simulations of hydrated electrons, by considering H2O− in the “static exchange” (essentially, frozen-core Hartree–Fock) approximation, then applying an approximate Phillips–Kleinman procedure to construct a one-electron pseudopotential representing the electron-water interaction. To date, this pseudopotential has been used exclusively in conjunction with a simple point charge water model that is parametrized for bulk water and yields poor results for small, neutral water clusters. Here, we extend upon the work of Turi and Borgis by reparametrizing the electron-water pseudopotential for use with the AMOEBA water model, which performs well for neutral clusters. The result is a one-electron model Hamiltonian for (H2O)n−, in which the one-electron wave function polarizes the water molecules, and vice versa, in a fully self-consistent fashion. The new model is fully variational and analytic energy gradients are available. We have implemented the new model using a modified Davidson algorithm to compute eigenstates, with the unpaired electron represented on a real-space grid. Comparison to ab initio electronic structure calculations for (H2O)n− cluster isomers ranging from n = 2 to n = 35 reveals that the new model is significantly more accurate than the Turi–Borgis model, for both relative isomer energies and for vertical electron detachment energies. Electron-water polarization interactions are found to be much more significant for cavity states of the unpaired electron than for surface states.
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36.40.Cg Electronic and magnetic properties of clusters
36.40.Mr Spectroscopy and geometrical structure of clusters
31.15.A- Ab initio calculations
31.15.xr Self-consistent-field methods
34.20.Gj Intermolecular and atom-molecule potentials and forces
36.40.Wa Charged clusters

Bifurcation of no-return transition states in many-body chemical reactions

Chun-Biu Li, Mikito Toda, and Tamiki Komatsuzaki

J. Chem. Phys. 130, 124116 (2009); http://dx.doi.org/10.1063/1.3079819 (7 pages) | Cited 8 times

Online Publication Date: 26 March 2009

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A new method is presented to study bifurcation of no-return transition states (TSs) at potential saddles for systems of many degrees of freedom (dof). The method enables us to investigate analytically when and how the no-return TS bifurcates. Our method reveals a new aspect of bifurcation for systems of many dof, i.e., the action variables of the bath dof play a role of control parameters as long as they remain approximately conserved. As an illustrative example, we demonstrate our new method by using a three atomic exchange reaction. The bifurcation of no-return TSs gives rise to a short-lived intermediate state at the saddle, which results in the overestimation of the reaction rate. Hence, the understanding of the bifurcation of the no-return TS is crucial to capture the complexity in kinetics and dynamics of the reactions. The definability of no-return TSs in many-body chemical reactions is also addressed under the occurrence of bifurcation above the reaction threshold.
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82.40.Bj Oscillations, chaos, and bifurcations
82.20.Db Transition state theory and statistical theories of rate constants

Phase-space surface hopping: Nonadiabatic dynamics in a superadiabatic basis

Neil Shenvi

J. Chem. Phys. 130, 124117 (2009); http://dx.doi.org/10.1063/1.3098321 (10 pages) | Cited 4 times

Online Publication Date: 26 March 2009

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In this paper, we construct a phase-space surface hopping algorithm for use in systems that exhibit strong nonadiabatic coupling. The algorithm is derived from a representation of the electronic basis which is a function of the nuclear phase-space coordinates rather than the nuclear position coordinates. This phase-space adiabatic basis can be understood in the context of Berry’s superadiabatic basis formalism as the first-order superadiabatic correction to the conventional position-space adiabatic basis. This superadiabatic representation leads to nuclear dynamics described not by Newton’s equations of motion but by generalized Hamilton’s equations of motion. The phase-space surface hopping algorithm captures physical effects that cannot be described by traditional algorithms. For a simple model problem, we show that phase-space surface hopping is more accurate than position-space surface hopping, especially when the nonadiabatic coupling is strong.
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82.20.Kh Potential energy surfaces for chemical reactions

Coupled cluster and density functional studies on geometries and energies of excited C2v states of ozone

Friedrich Grein

J. Chem. Phys. 130, 124118 (2009); http://dx.doi.org/10.1063/1.3099609 (9 pages) | Cited 8 times

Online Publication Date: 26 March 2009

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The performance of single-determinant methods for finding geometries and energies of excited states is tested on the ozone molecule. Geometries for low-lying singlet and triplet states of ozone were optimized by CCSD(T) and density functional theory (DFT) (with BPW91 functional) methods. DFT geometries were found to lie close to CCSD(T) values. Most CCSD(T) and DFT geometries and energies are in good agreement with available experimental and recent high-level theoretical values, with deviations lying within 0.02 Å, 2°, and 0.3 eV. An exception is the 1 1B2 state, having a larger deviation of bond distance and energy. A multiconfigurational treatment is required for this state. DFT geometry optimizations and calculations of vibrational frequencies were extended to higher states, covering over 30 excited states of ozone, with adiabatic excitation energies up to about 6 eV. Calculated harmonic frequencies showed several states, including 1 1B2, to be saddle points. Multireference configuration interaction (MRCI) bending potentials for first and second singlet and triplet states were used in verifying the CCSD(T) and DFT geometries and for locating additional minima. For first states, DFT bending potentials are compared with MRCI potentials. As a criterion for the quality of single-determinant geometries and energies of excited states, comparison of their vertical excitation energies with MRCI or time-dependent DFT values is recommended.
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31.15.bw Coupled-cluster theory
31.15.V- Electron correlation calculations for atoms, ions and molecules
33.20.Tp Vibrational analysis
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Dj Interatomic distances and angles
31.15.E- Density-functional theory

Rate constants calculation with a simple mixed quantum/classical implementation of the flux-flux correlation function method

Juliana Palma

J. Chem. Phys. 130, 124119 (2009); http://dx.doi.org/10.1063/1.3097134 (7 pages) | Cited 2 times

Online Publication Date: 27 March 2009

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A simple mixed quantum/classical (mixed-Q/C) implementation of the flux-flux correlation function method has been applied to evaluate rate constants for a two-dimensional model system. The model consists of an Eckart barrier resembling the collinear H+H2 reaction, linearly coupled to a harmonic oscillator. Results are presented for a broad range of parameters for temperatures between 140 and 300 K. It is found that the mixed-Q/C method gives fairly accurate results as long as the reaction does not involve too many recrossings. This suggests that the methodology could be extended to treat direct polyatomic reactions in gas phase.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Sb Correlation function theory of rate constants and its applications
82.20.Db Transition state theory and statistical theories of rate constants

Charge asymmetry in pure vibrational states of the HD molecule

Sergiy Bubin, Filip Leonarski, Monika Stanke, and Ludwik Adamowicz

J. Chem. Phys. 130, 124120 (2009); http://dx.doi.org/10.1063/1.3094047 (6 pages) | Cited 6 times

Online Publication Date: 27 March 2009

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Very accurate variational calculations of all rotationless states (also called pure vibrational states) of the HD molecule have been performed within the framework that does not assume the Born–Oppenheimer (BO) approximation. The non-BO wave functions of the states describing the internal motion of the proton, the deuteron, and the two electrons were expanded in terms of one-center explicitly correlated Gaussian functions multiplied by even powers of the internuclear distance. Up to 6000 functions were used for each state. Both linear and nonlinear parameters of the wave functions of all 18 states were optimized with a procedure that employs the analytical gradient of the energy with respect to the nonlinear parameters of the Gaussians. These wave functions were used to calculate expectation values of the interparticle distances and some other related quantities. The results allow elucidation of the charge asymmetry in HD as a function of the vibrational excitation.
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33.20.Tp Vibrational analysis
31.15.xt Variational techniques

Calibration of 119Sn isomer shift using ab initio wave function methods

Reshmi Kurian and Michael Filatov

J. Chem. Phys. 130, 124121 (2009); http://dx.doi.org/10.1063/1.3094259 (8 pages) | Cited 8 times

Online Publication Date: 31 March 2009

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The isomer shift for the 23.87 keV M1 resonant transition in the 119Sn nucleus is calibrated with the help of ab initio calculations. The calibration constant α(119Sn) obtained from Hartree–Fock (HF) calculations (αHF(119Sn) = (0.081±0.002)a0−3 mm/s) and from second-order Møller–Plesset (MP2) calculations (αMP2(119Sn) = (0.091±0.002)a0−3 mm/s) are in good agreement with the previously obtained values. The importance of a proper treatment of electron correlation effects is demonstrated on the basis of a statistical analysis of the results of the calibration. The approach used in the calibration is applied to study the 119Sn isomer shift in CaSnO3 perovskite under pressure. Comparison with the experimental results for the pressure range of 0–36 GPa shows that the current methodology is capable of describing tiny variations of isomer shift with reasonable accuracy.
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76.80.+y Mössbauer effect; other γ-ray spectroscopy
71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)
71.20.-b Electron density of states and band structure of crystalline solids
71.45.Gm Exchange, correlation, dielectric and magnetic response functions, plasmons

Parallel implementation of the equation-of-motion coupled-cluster singles and doubles method and application for radical adducts of cytosine

Tomasz Kuś, Victor F. Lotrich, and Rodney J. Bartlett

J. Chem. Phys. 130, 124122 (2009); http://dx.doi.org/10.1063/1.3091293 (7 pages) | Cited 10 times

Online Publication Date: 31 March 2009

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The equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) method has been implemented into the massively parallel ACES III program using two alternative strategies: (1) storing the entire EOM Hamiltonian matrix prior to diagonalization and (2) recomputing the four-virtual part of the matrix from integrals in a direct mode. The second is found to be far more efficient. EOM-CC shows virtually ideal scaling from 32 to 256 processors. With basis sets as large as 552 functions, the program was applied to determine vertical excitation energies for five cytosine radical adducts of –OH and –H at three sites C5, C6, and N3. These radicals are considered to play an important role in radiation induced DNA damage. The excitation energy spectrum shows two distinct patterns for the lowest transitions distinguishing the C6–OH, C6–H, and N3–H adducts from the C5–OH and C5–H. The results indicate that the two lowest transitions of the C6–OH isomer should contribute to the experimentally observed absorption maximum at 2.88 eV, while the third and fourth transitions of C6–OH and the two lowest transitions of C5–OH contribute to the 3.65 eV absorption maximum. We also report the CCSD with noniterative triples correction [CCSD(T)] relative energies of the C5–OH and C6–OH adducts using 1000 processors.
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87.15.ag Quantum calculations
87.14.gk DNA
31.15.bw Coupled-cluster theory
02.60.Dc Numerical linear algebra
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