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21 May 2013

Volume 138, Issue 19, Articles (19xxxx)

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J. Chem. Phys. 138, 195101 (2013); http://dx.doi.org/10.1063/1.4803507 (11 pages)

Mu-Jie Huang, Raymond Kapral, Alexander S. Mikhailov, and Hsuan-Yi Chen
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Communication: Pressure fluctuations in isotropic solids and fluids

J. P. Wittmer, H. Xu, P. Polińska, F. Weysser, and J. Baschnagel

J. Chem. Phys. 138, 191101 (2013); http://dx.doi.org/10.1063/1.4807305 (3 pages)

Online Publication Date: 15 May 2013

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Comparing isotropic solids and fluids at either imposed volume or pressure, we investigate various correlations of the instantaneous pressure and its ideal and excess contributions. Focusing on the compression modulus K, it is emphasized that the stress fluctuation representation of the elastic moduli may be obtained directly (without a microscopic displacement field) by comparing the stress fluctuations in conjugated ensembles. This is made manifest by computing the Rowlinson stress fluctuation expression Krow of the compression modulus for NPT-ensembles. It is shown theoretically and numerically that Krow|P = Pid(2 − Pid/K) with Pid being the ideal pressure contribution.
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46.25.Cc Theoretical studies
62.10.+s Mechanical properties of liquids
02.60.-x Numerical approximation and analysis
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Communication: State-to-state photodissociation study by the two-color VUV-VUV laser pump-probe time-slice velocity-map-imaging-photoion method

Hong Gao, Yu Song, William M. Jackson, and C. Y. Ng

J. Chem. Phys. 138, 191102 (2013); http://dx.doi.org/10.1063/1.4807302 (4 pages)

Online Publication Date: 16 May 2013

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We demonstrate that combining two independently tunable vacuum ultraviolet (VUV) lasers and the time-slice velocity-map-imaging-photoion (VMI-PI) method allows the rovibronically state-selected photodissociation study of CO in the VUV region along with the state-selective detection of product C(3P0,1,2) using the VUV-UV (1+1′) resonance-enhanced photoionization and the VUV Rydberg autoionization methods. Both tunable VUV lasers are generated based on the two-photon resonance-enhanced four-wave mixing scheme using a pulsed rare gas jet as the nonlinear medium. The observed fine-structure distributions of product C(3PJ), J = 0, 1, and 2, are found to depend on the CO rovibronic state populated by VUV photoexcitation. The branching ratios for C(3P0) + O(3PJ): C(3P0) + O(1D2), C(3P1) + O(3PJ): C(3P1) + O(1D2), and C(3P2) + O(3PJ): C(3P2) + O(1D2), which were determined based on the time-slice VMI-PI measurements of C+ ions formed by J-state selective photoionization sampling of C(3P0,1,2), also reveal strong dependences on the spin-orbit state of C(3P0,1,2). By combining the measured branching ratios and fine-structure distributions of C(3P0,1,2), we have determined the correlated distributions of C(3P0,1,2) accompanying the formation of O(1D2) and O(3PJ) produced in the VUV photodissociation of CO. The success of this demonstration experiment shows that the VUV photodissociation pump-VUV photoionization probe method is promising for state-to-state photodissociation studies of many small molecules, which are relevant to planetary atmospheres as well as fundamental understanding of photodissociation dynamics.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
42.65.Jx Beam trapping, self-focusing and defocusing; self-phase modulation
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Pw Fine and hyperfine structure
33.20.Ni Vacuum ultraviolet spectra
33.80.Be Level crossing and optical pumping
33.80.Eh Autoionization, photoionization, and photodetachment
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back to top Theoretical Methods and Algorithms

Non-linear eigensolver-based alternative to traditional SCF methods

B. Gavin and E. Polizzi

J. Chem. Phys. 138, 194101 (2013); http://dx.doi.org/10.1063/1.4804419 (8 pages)

Online Publication Date: 15 May 2013

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The self-consistent procedure in electronic structure calculations is revisited using a highly efficient and robust algorithm for solving the non-linear eigenvector problem, i.e., H({ψ})ψ = Eψ. This new scheme is derived from a generalization of the FEAST eigenvalue algorithm to account for the non-linearity of the Hamiltonian with the occupied eigenvectors. Using a series of numerical examples and the density functional theory-Kohn/Sham model, it will be shown that our approach can outperform the traditional SCF mixing-scheme techniques by providing a higher converge rate, convergence to the correct solution regardless of the choice of the initial guess, and a significant reduction of the eigenvalue solve time in simulations.
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31.15.xr Self-consistent-field methods
31.15.E- Density-functional theory

Doubly electron-attached and doubly ionized equation-of-motion coupled-cluster methods with 4-particle–2-hole and 4-hole–2-particle excitations and their active-space extensions

Jun Shen and Piotr Piecuch

J. Chem. Phys. 138, 194102 (2013); http://dx.doi.org/10.1063/1.4803883 (16 pages)

Online Publication Date: 16 May 2013

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The full and active-space doubly electron-attached (DEA) and doubly ionized (DIP) equation-of-motion coupled-cluster (EOMCC) methods with up to 4-particle–2-hole (4p-2h) and 4-hole–2-particle (4h-2p) excitations are developed. By examining bond breaking in F2 and low-lying singlet and triplet states in the methylene, (HFH)−, and trimethylenemethane biradicals, we demonstrate that the DEA- and DIP-EOMCC methods with an active-space treatment of 4p-2h and 4h-2p excitations reproduce the results of the analogous full calculations at the small fraction of the computer effort, while improving the DEA/DIP-EOMCC theories truncated at 3p-1h/3h-1p excitations.
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34.80.Ht Dissociation and dissociative attachment
31.15.bw Coupled-cluster theory
33.15.Fm Bond strengths, dissociation energies
31.15.vj Electron correlation calculations for atoms and ions: excited states

Potential energy curves via double electron-attachment calculations: Dissociation of alkali metal dimers

Monika Musiał, Katarzyna Kowalska-Szojda, Dmitry I. Lyakh, and Rodney J. Bartlett

J. Chem. Phys. 138, 194103 (2013); http://dx.doi.org/10.1063/1.4804164 (8 pages)

Online Publication Date: 16 May 2013

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The recently developed method [M. Musiał, J. Chem. Phys. 136, 134111 (2012)10.1063/1.3700438] to study double electron attached states has been applied to the description of the ground and excited state potential energy curves of the alkali metal dimers. The method is based on the multireference coupled cluster scheme formulated within the Fock space formalism for the (2,0) sector. Due to the use of the efficient intermediate Hamiltonian formulation, the approach is free from the intruder states problem. The description of the neutral alkali metal dimers is accomplished via attaching two electrons to the corresponding doubly ionized system. This way is particularly advantageous when a closed shell molecule dissociates into open shell subunits while its doubly positive cation generates the closed shell fragments. In the current work, we generate the potential energy curves for the ground and multiple excited states of the Li2 and Na2 molecules. In all cases the potential energy curves are smooth for the entire range of interatomic distances (from the equilibrium point to the dissociation limit). Based on the calculated potential energy curves, we are able to compute spectroscopic parameters of the systems studied.
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34.80.Ht Dissociation and dissociative attachment
34.80.Lx Recombination, attachment, and positronium formation
31.15.bw Coupled-cluster theory
31.50.Bc Potential energy surfaces for ground electronic states
31.50.Df Potential energy surfaces for excited electronic states

Uncertainty quantification in MD simulations of concentration driven ionic flow through a silica nanopore. I. Sensitivity to physical parameters of the pore

F. Rizzi, R. E. Jones, B. J. Debusschere, and O. M. Knio

J. Chem. Phys. 138, 194104 (2013); http://dx.doi.org/10.1063/1.4804666 (19 pages)

Online Publication Date: 17 May 2013

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In this article, uncertainty quantification is applied to molecular dynamics (MD) simulations of concentration driven ionic flow through a silica nanopore. We consider a silica pore model connecting two reservoirs containing a solution of sodium (Na+) and chloride (Cl−) ions in water. An ad hoc concentration control algorithm is developed to simulate a concentration driven counter flow of ions through the pore, with the ionic flux being the main observable extracted from the MD system. We explore the sensitivity of the system to two physical parameters of the pore, namely, the pore diameter and the gating charge. First we conduct a quantitative analysis of the impact of the pore diameter on the ionic flux, and interpret the results in terms of the interplay between size effects and ion mobility. Second, we analyze the effect of gating charge by treating the charge density over the pore surface as an uncertain parameter in a forward propagation study. Polynomial chaos expansions and Bayesian inference are exploited to isolate the effect of intrinsic noise and quantify the impact of parametric uncertainty on the MD predictions. We highlight the challenges arising from the heterogeneous nature of the system, given the several components involved, and from the substantial effect of the intrinsic thermal noise.
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47.56.+r Flows through porous media
47.60.-i Flow phenomena in quasi-one-dimensional systems
47.52.+j Chaos in fluid dynamics
47.11.Mn Molecular dynamics methods
02.70.Ns Molecular dynamics and particle methods
02.50.Tt Inference methods

Uncertainty quantification in MD simulations of concentration driven ionic flow through a silica nanopore. II. Uncertain potential parameters

F. Rizzi, R. E. Jones, B. J. Debusschere, and O. M. Knio

J. Chem. Phys. 138, 194105 (2013); http://dx.doi.org/10.1063/1.4804669 (16 pages)

Online Publication Date: 17 May 2013

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This article extends the uncertainty quantification analysis introduced in Paper I for molecular dynamics (MD) simulations of concentration driven ionic flow through a silica nanopore. Attention is now focused on characterizing, for a fixed pore diameter of D = 21 Å, the sensitivity of the system to the Lennard-Jones energy parameters, ɛNa+ and ɛCl−, defining the depth of the potential well for the two ions Na+ and Cl−, respectively. A forward propagation analysis is applied to map the uncertainty in these parameters to the MD predictions of the ionic fluxes. Polynomial chaos expansions and Bayesian inference are exploited to isolate the effect of the intrinsic noise, stemming from thermal fluctuations of the atoms, and properly quantify the impact of parametric uncertainty on the target MD predictions. A Bayes factor analysis is then used to determine the most suitable regression model to represent the MD noisy data. The study shows that the response surface of the Na+ conductance can be effectively inferred despite the substantial noise level, whereas the noise partially hides the underlying trend in the Cl− conductance data over the studied range. Finally, the dependence of the conductances on the uncertain potential parameters is analyzed in terms of correlations with key bulk transport coefficients, namely, viscosity and collective diffusivities, computed using Green-Kubo time correlations.
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47.56.+r Flows through porous media
66.20.Cy Theory and modeling of viscosity and rheological properties, including computer simulation
47.52.+j Chaos in fluid dynamics
05.20.Jj Statistical mechanics of classical fluids

Assessment of range-separated time-dependent density-functional theory for calculating C6 dispersion coefficients

Julien Toulouse, Elisa Rebolini, Tim Gould, John F. Dobson, Prasenjit Seal, and János G. Ángyán

J. Chem. Phys. 138, 194106 (2013); http://dx.doi.org/10.1063/1.4804981 (9 pages)

Online Publication Date: 21 May 2013

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We assess a variant of linear-response range-separated time-dependent density-functional theory (TDDFT), combining a long-range Hartree-Fock (HF) exchange kernel with a short-range adiabatic exchange-correlation kernel in the local-density approximation (LDA) for calculating isotropic C6 dispersion coefficients of homodimers of a number of closed-shell atoms and small molecules. This range-separated TDDFT tends to give underestimated C6 coefficients of small molecules with a mean absolute percentage error of about 5%, a slight improvement over standard TDDFT in the adiabatic LDA which tends to overestimate them with a mean absolute percentage error of 8%, but close to time-dependent Hartree-Fock which has a mean absolute percentage error of about 6%. These results thus show that introduction of long-range HF exchange in TDDFT has a small but beneficial impact on the values of C6 coefficients. It also confirms that the present variant of range-separated TDDFT is a reasonably accurate method even using only a LDA-type density functional and without adding an explicit treatment of long-range correlation.
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31.15.ee Time-dependent density functional theory
31.15.eg Exchange-correlation functionals (in current density functional theory)
31.15.xr Self-consistent-field methods

Discrete variable representation in electronic structure theory: Quadrature grids for least-squares tensor hypercontraction

Robert M. Parrish, Edward G. Hohenstein, Todd J. Martínez, and C. David Sherrill

J. Chem. Phys. 138, 194107 (2013); http://dx.doi.org/10.1063/1.4802773 (15 pages)

Online Publication Date: 21 May 2013

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We investigate the application of molecular quadratures obtained from either standard Becke-type grids or discrete variable representation (DVR) techniques to the recently developed least-squares tensor hypercontraction (LS-THC) representation of the electron repulsion integral (ERI) tensor. LS-THC uses least-squares fitting to renormalize a two-sided pseudospectral decomposition of the ERI, over a physical-space quadrature grid. While this procedure is technically applicable with any choice of grid, the best efficiency is obtained when the quadrature is tuned to accurately reproduce the overlap metric for quadratic products of the primary orbital basis. Properly selected Becke DFT grids can roughly attain this property. Additionally, we provide algorithms for adopting the DVR techniques of the dynamics community to produce two different classes of grids which approximately attain this property. The simplest algorithm is radial discrete variable representation (R-DVR), which diagonalizes the finite auxiliary-basis representation of the radial coordinate for each atom, and then combines Lebedev-Laikov spherical quadratures and Becke atomic partitioning to produce the full molecular quadrature grid. The other algorithm is full discrete variable representation (F-DVR), which uses approximate simultaneous diagonalization of the finite auxiliary-basis representation of the full position operator to produce non-direct-product quadrature grids. The qualitative features of all three grid classes are discussed, and then the relative efficiencies of these grids are compared in the context of LS-THC-DF-MP2. Coarse Becke grids are found to give essentially the same accuracy and efficiency as R-DVR grids; however, the latter are built from explicit knowledge of the basis set and may guide future development of atom-centered grids. F-DVR is found to provide reasonable accuracy with markedly fewer points than either Becke or R-DVR schemes.
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31.15.E- Density-functional theory
31.15.xp Perturbation theory

A generalized any-particle propagator theory: Prediction of proton affinities and acidity properties with the proton propagator

Manuel Díaz-Tinoco, Jonathan Romero, J. V. Ortiz, Andrés Reyes, and Roberto Flores-Moreno

J. Chem. Phys. 138, 194108 (2013); http://dx.doi.org/10.1063/1.4805030 (10 pages)

Online Publication Date: 21 May 2013

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We have recently extended the electron propagator theory to the treatment of any type of particle using an Any-Particle Molecular Orbital (APMO) wavefunction as reference state. This approach, called APMO/PT, has been implemented in the LOWDIN code to calculate correlated binding energies, for any type of particle in molecular systems. In this work, we present the application of the APMO/PT approach to study proton detachment processes. We employed this method to calculate proton binding energies and proton affinities for a set of inorganic and organic molecules. Our results reveal that the second-order proton propagator (APMO/PP2) quantitatively reproduces experimental trends with an average deviation of less than 0.41 eV. We also estimated proton affinities with an average deviation of 0.14 eV and the proton hydration free energy using APMO/PP2 with a resulting value of −270.2 kcal/mol, in agreement with other results reported in the literature. Results presented in this work suggest that the APMO/PP2 approach is a promising tool for studying proton acid/base properties.
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31.15.xr Self-consistent-field methods
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy

Anharmonic state counts and partition functions for molecules via classical phase space integrals in curvilinear coordinates

Eugene Kamarchik and Ahren W. Jasper

J. Chem. Phys. 138, 194109 (2013); http://dx.doi.org/10.1063/1.4804420 (8 pages)

Online Publication Date: 21 May 2013

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An algorithm is presented for calculating fully anharmonic vibrational state counts, state densities, and partition functions for molecules using Monte Carlo integration of classical phase space. The algorithm includes numerical evaluations of the elements of the Jacobian and is general enough to allow for sampling in arbitrary curvilinear or rectilinear coordinate systems. Invariance to the choice of coordinate system is demonstrated for vibrational state densities of methane, where we find comparable sampling efficiency when using curvilinear z-matrix and rectilinear Cartesian normal mode coordinates. In agreement with past work, we find that anharmonicity increases the vibrational state density of methane by a factor of ∼2 at its dissociation threshold. For the vinyl radical, we find a significant (∼10×) improvement in sampling efficiency when using curvilinear z-matrix coordinates relative to Cartesian normal mode coordinates. We attribute this improved efficiency, in part, to a more natural curvilinear coordinate description of the double well associated with the H2C–C–H wagging motion. The anharmonicity correction for the vinyl radical state density is ∼1.4 at its dissociation threshold. Finally, we demonstrate that with trivial parallelizations of the Monte Carlo step, tractable calculations can be made for the vinyl radical using direct ab initio potential energy surface evaluations and a composite QCISD(T)/MP2 method.
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33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.xp Perturbation theory
31.50.-x Potential energy surfaces
back to top Atoms, Molecules, and Clusters

The structures of neutral transition metal doped silicon clusters, SinX (n = 6−9; X = V, Mn)

Pieterjan Claes, Vu Thi Ngan, Marko Haertelt, Jonathan T. Lyon, André Fielicke, Minh Tho Nguyen, Peter Lievens, and Ewald Janssens

J. Chem. Phys. 138, 194301 (2013); http://dx.doi.org/10.1063/1.4803871 (7 pages)

Online Publication Date: 15 May 2013

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We present a combined experimental and theoretical investigation of small neutral vanadium and manganese doped silicon clusters SinX (n = 6−9, X = V, Mn). These species are studied by infrared multiple photon dissociation and mass spectrometry. Structural identification is achieved by comparison of the experimental data with computed infrared spectra of low-lying isomers using density functional theory at the B3P86/6-311+G(d) level. The assigned structures of the neutral vanadium and manganese doped silicon clusters are compared with their cationic counterparts. In general, the neutral and cationic SinV0,+ and SinMn0,+ clusters have similar structures, although the position of the capping atoms depends for certain sizes on the charge state. The influence of the charge state on the electronic properties of the clusters is also investigated by analysis of the density of states, the shapes of the molecular orbitals, and NBO charge analysis of the dopant atom.
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36.40.Mr Spectroscopy and geometrical structure of clusters
36.40.Cg Electronic and magnetic properties of clusters
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
33.20.Ea Infrared spectra
33.15.Ta Mass spectra
33.80.Gj Diffuse spectra; predissociation, photodissociation

Water nanodroplets: Predictions of five model potentials

Sergey Kazachenko and Ajit J. Thakkar

J. Chem. Phys. 138, 194302 (2013); http://dx.doi.org/10.1063/1.4804399 (10 pages)

Online Publication Date: 15 May 2013

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Putative global minima for five intermolecular potential energy models are reported for water clusters (H2O)n with n ⩽ 55. The models studied include three empirical, pairwise-additive potential energy surfaces, TIP4P, TIP4P-Ew, and TIP4P/2005, which use fixed point charges and rigid monomers. The other two, TTM2.1-F and AMOEBA, are polarizable, include non-additive inductive effects, have flexible monomers, and were parametrized, at least partially, using ab initio data. The n = 51 cluster has the same structure and is exceptionally stable for all five potentials. A structured inner core can be seen in cage clusters with n > 37. Periplanar rings, branched rings, and coils are among the structural motifs of the inner core.
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36.40.Mr Spectroscopy and geometrical structure of clusters
61.46.Bc Structure of clusters (e.g., metcars; not fragments of crystals; free or loosely aggregated or loosely attached to a substrate)
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
31.50.-x Potential energy surfaces
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions

The ethyl radical in superfluid helium nanodroplets: Rovibrational spectroscopy and ab initio computations

Paul L. Raston, Jay Agarwal, Justin M. Turney, Henry F. Schaefer, III, and Gary E. Douberly

J. Chem. Phys. 138, 194303 (2013); http://dx.doi.org/10.1063/1.4804435 (13 pages)

Online Publication Date: 15 May 2013

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The ethyl radical has been isolated and spectroscopically characterized in 4He nanodroplets. The band origins of the five CH stretch fundamentals are shifted by < 2 cm−1 from those reported for the gas phase species [S. Davis, D. Uy, and D. J. Nesbitt, J. Chem. Phys. 112, 1823 (2000)10.1063/1.480746; T. Häber, A. C. Blair, D. J. Nesbitt, and M. D. Schuder, J. Chem. Phys. 124, 054316 (2006)10.1063/1.2140740]. The symmetric CH2 stretching band (v1) is rotationally resolved, revealing nuclear spin statistical weights predicted by G12 permutation-inversion group theory. A permanent electric dipole moment of 0.28 (2) D is obtained via the Stark spectrum of the v1 band. The four other CH stretch fundamental bands are significantly broadened in He droplets and lack rotational fine structure. This broadening is attributed to symmetry dependent vibration-to-vibration relaxation facilitated by the He droplet environment. In addition to the five fundamentals, three a1′ overtone/combination bands are observed, and each of these have resolved rotational substructure. These are assigned to the 2v12, v4 + v6, and 2v6 bands through comparisons to anharmonic frequency computations at the CCSD(T)/cc-pVTZ level of theory.
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31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
31.15.xh Group-theoretical methods
31.30.jp Electron electric dipole moment
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Sn Rotational analysis

A new ab initio based global HOOH(13A″) potential energy surface for the O(3P) + H2O(X1A1) ↔ OH(X2Π) + OH(X2Π) reaction

Jun Li and Hua Guo

J. Chem. Phys. 138, 194304 (2013); http://dx.doi.org/10.1063/1.4804418 (10 pages)

Online Publication Date: 16 May 2013

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An accurate global potential energy surface is developed for the title reaction by fitting more than 36 000 of ab initio points at the CCSD(T)/AVTZ level using the permutation invariant polynomial method. The canonical rate constants for both the forward and reverse directions of the title reaction are determined on the new potential energy surface and the agreement with experiment is satisfactory. In addition, the dynamics of the forward reaction is investigated with the quasi-classical trajectory method. It is found that this direct abstraction reaction has a backward bias in its product angular distribution, consistent with a direct rebound mechanism. The OH product newly formed by the reaction exhibits a bimodal rotational state distribution, due apparently to secondary collisions with the slowly recoiling spectator OH product.
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82.20.Kh Potential energy surfaces for chemical reactions
82.20.Fd Collision theories; trajectory models
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Pm Rate constants, reaction cross sections, and activation energies

Direct-dynamics VTST study of hydrogen or deuterium abstraction and C–C bond formation or dissociation in the reactions of CH3 + CH4, CH3 + CD4, CH3D + CD3, CH3CH3 + H, and CH3CD3 + D

Shapour Ramazani

J. Chem. Phys. 138, 194305 (2013); http://dx.doi.org/10.1063/1.4803862 (10 pages)

Online Publication Date: 20 May 2013

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Direct-dynamics variational transition-state theory calculations are studied at the MPWB1K/6-311++G(d,p) level for the four parts of reactions. The first part is hydrogen or deuterium abstraction in the reactions of CH3 + CH4, CH3 + CD4, and CH3D + CH3. The second part involves C–C bond formation in these reactions. The third one is the reactions of CH3CH3 + H and CH3CD3 + D to form of H2, HD, and D2. The last one is the dissociation of C–C bonds in the last group of reactions. The ground-state vibrational adiabatic potential is plotted for all channels. We have carried out direct-dynamics calculations of the rate constants, including multidimensional tunneling in the temperature range T = 200–2200 K. The results of CVT/μOMT rate constants were in good agreement with the experimental data which were available for some reactions. Small-curvature tunneling and Large-curvature tunneling with the LCG4 version were used to include the quantum effects in calculation of the rate constants. To try to find the region of formation and dissociation of bounds we have also reported the variations of harmonic vibrational frequencies along the reaction path. The thermally averaged transmission probability (P(E)exp (−ΔE/RT)) and representative tunneling energy at 298 K are reported for the reactions in which tunneling is important. We have calculated kinetic isotope effect which shows tunneling and vibrational contributions are noticeable to determine the rate constant. Nonlinear least-squares fitting is used to calculate rate constant expressions in the temperature range 200–2200 K. These expressions revealed that pre-exponential factor includes two parts; the first part is a constant number which is important at low temperatures while the second part is temperature dependent which is significant at high temperatures.
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82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.20.Db Transition state theory and statistical theories of rate constants
82.20.Hf Product distribution
82.20.Tr Kinetic isotope effects including muonium

Low-energy electron collisions with thiophene

R. F. da Costa, M. T. do N. Varella, M. A. P. Lima, and M. H. F. Bettega

J. Chem. Phys. 138, 194306 (2013); http://dx.doi.org/10.1063/1.4805107 (6 pages)

Online Publication Date: 20 May 2013

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We report on elastic integral, momentum transfer, and differential cross sections for collisions of low-energy electrons with thiophene molecules. The scattering calculations presented here used the Schwinger multichannel method and were carried out in the static-exchange and static-exchange plus polarization approximations for energies ranging from 0.5 eV to 6 eV. We found shape resonances related to the formation of two long-lived π* anion states. These resonant structures are centered at the energies of 1.00 eV (2.85 eV) and 2.82 eV (5.00 eV) in the static-exchange plus polarization (static-exchange) approximation and belong to the B1 and A2 symmetries of the C2v point group, respectively. Our results also suggest the existence of a σ* shape resonance in the B2 symmetry with a strong d-wave character, located at around 2.78 eV (5.50 eV) as obtained in the static-exchange plus polarization (static-exchange) calculation. It is worth to mention that the results obtained at the static-exchange plus polarization level of approximation for the two π* resonances are in good agreement with the electron transmission spectroscopy results of 1.15 eV and 2.63 eV measured by Modelli and Burrow [J. Phys. Chem. A 108, 5721 (2004)10.1021/jp048759a]. The existence of the σ* shape resonance is in agreement with the observations of Dezarnaud-Dandiney et al. [J. Phys. B 31, L497 (1998)10.1088/0953-4075/31/11/004] based on the electron transmission spectra of dimethyl(poly)sulphides. A comparison among the resonances of thiophene with those of pyrrole and furan is also performed and, altogether, the resonance spectra obtained for these molecules point out that electron attachment to π* molecular orbitals is a general feature displayed by these five-membered heterocyclic compounds.
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34.80.Bm Elastic scattering
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.-p Calculations and mathematical techniques in atomic and molecular physics
34.80.Lx Recombination, attachment, and positronium formation

Ab initio study of ground and excited states of 6Li40Ca and 6Li88Sr molecules

Geetha Gopakumar, Minori Abe, Masahiko Hada, and Masatoshi Kajita

J. Chem. Phys. 138, 194307 (2013); http://dx.doi.org/10.1063/1.4804622 (14 pages)

Online Publication Date: 21 May 2013

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We present quantum-chemical calculations for the ground and some low-lying excited states of isolated LiCa and LiSr molecules using multi-state complete active space second-order perturbation theory (MS-CASPT2). The potential energy curves (PECs) and their corresponding spectroscopic constants, obtained at the spin-free (SF) and spin-orbit (SO) levels, agree well with available experimental values. Our SO-MS-CASPT2 calculation at the atomic limit (R = 100 a.u.) with the largest basis set reproduces experimental atomic excitation energies within 3% for both LiCa and LiSr. In addition, permanent dipole moments and transition dipole moments at the SF level are also obtained. Rovibrational calculations of the ground and selected excited states, together with the spontaneous emission rates, demonstrate that the formation of ultracold LiCa and LiSr molecules in low-lying vibrational levels of the electronic ground state may be possible.
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31.15.ag Excitation energies and lifetimes; oscillator strengths
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
31.50.Bc Potential energy surfaces for ground electronic states
31.50.Df Potential energy surfaces for excited electronic states
31.15.xp Perturbation theory
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations

Theoretical prediction of rare gas inserted hydronium ions: HRgOH2+

Ayan Ghosh, Debashree Manna, and Tapan K. Ghanty

J. Chem. Phys. 138, 194308 (2013); http://dx.doi.org/10.1063/1.4804623 (8 pages)

Online Publication Date: 21 May 2013

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A possibility of existence of new species through insertion of a rare gas atom in hydronium ion resulting into HRgOH2+ cation (Rg = He, Ar, Kr, and Xe) has been explored by using various ab initio quantum chemical techniques. Structure, harmonic vibrational frequencies, stability, and charge distribution of HRgOH2+ species as obtained using density functional theory, second order Møller-Plesset perturbation theory, and coupled-cluster theory based methods are reported in this work. All the calculated results suggest that the HRgOH2+ species are stable enough with respect to all the dissociation channels, except the 2-body dissociation path (H3O+ + Rg). Nevertheless, this 2-body dissociation channel connected through the relevant transition state is associated with a finite barrier, which in turn would prevent the metastable species in transforming to global minimum products. The calculated values of topological properties within the framework of quantum theory of atoms-in-molecules are found to be consistent with the bond length values. Structural and energetic parameters clearly suggest that it might be possible to prepare and characterize the HRgOH2+ species (except HHeOH2+) using electron bombardment matrix isolation technique in a way similar to that of the preparation of (Rg2H)+ or mixed (RgHRg′)+ cations.
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82.30.Nr Association, addition, insertion, cluster formation
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.20.Db Transition state theory and statistical theories of rate constants
82.20.Ej Quantum theory of reaction cross section
33.15.Bh General molecular conformation and symmetry; stereochemistry

Water clusters adsorbed on polycyclic aromatic hydrocarbons: Energetics and conformational dynamics

Aude Simon and Fernand Spiegelman

J. Chem. Phys. 138, 194309 (2013); http://dx.doi.org/10.1063/1.4805015 (13 pages)

Online Publication Date: 21 May 2013

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In this work, we present some classical molecular dynamics (MD) simulations and finite temperature infrared (IR) spectra of water clusters adsorbed on coronene (C24H12), a compact polycyclic aromatic hydrocarbon (PAH). The potential energy surface is obtained within the self-consistent-charge density-functional based tight-binding approach with modifications insuring the correct description of water-water and water-PAH interactions. This scheme is benchmarked for the minimal energy structures of (C24H12)(H2O)n (n = 3–10) against density-functional theory (DFT) calculations and for the low-energy isomers of (H2O)6 and (C6H6)(H2O)3 against correlated wavefunction and DFT calculations. A detailed study of the low energy isomers of (C24H12)(H2O)3, 6 complexes is then provided. On-the-fly Born-Oppenheimer MD simulations are performed in the temperature T range 10–350 K for (C24H12)(H2O)n (n = 3–7) complexes. The description of the evolution of the systems with T is provided with emphasis on (C24H12)(H2O)n (n = 3,6). For T in the range 50–150 K, isomerisation processes are observed and when T increases, a solid-to-liquid phase-change like behavior is shown. The desorption of one water molecule is frequently observed at 300 K. The isomerisation processes are evidenced on the finite temperature IR spectra and the results are presented for (C24H12)(H2O)n (n = 3,6). A signature for the edge-coordination of the water cluster on the PAH is also proposed.
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36.40.Mr Spectroscopy and geometrical structure of clusters
36.40.Sx Diffusion and dynamics of clusters
68.43.-h Chemisorption/physisorption: adsorbates on surfaces
68.43.Mn Adsorption kinetics
31.15.aq Strongly correlated electron systems: generalized tight-binding method
31.15.E- Density-functional theory
31.50.-x Potential energy surfaces
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
33.20.Ea Infrared spectra

Vibrational overtone spectroscopy and intramolecular dynamics of C–H stretches in pyrrole

Alexander Portnov, Michael Epshtein, Salman Rosenwaks, and Ilana Bar

J. Chem. Phys. 138, 194310 (2013); http://dx.doi.org/10.1063/1.4804540 (6 pages)

Online Publication Date: 21 May 2013

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Room-temperature photoacoustic spectra and jet-cooled action spectra of the regions of the first and second C–H stretch overtones of pyrrole were measured with the goal of gaining new insight on the vibrational patterns and the intramolecular energy flow out of the initially excited vibrational states. The rotational cooling of the action spectra helped in observing hitherto unresolved features, assisting determination of the existing multiple bands and their positions in each region. These bands were analyzed by building vibrational Hamiltonian matrices related to a simplified joint local-mode/normal-mode (LM/NM) model, accounting for two types of C–H stretches and their Fermi resonances with the CCH deformation modes. The diagonalization of the LM/NM vibrational Hamiltonians and the fitting of the eigenvalues to the band positions revealed model parameters, enabling assignment of the observed bands. The time dependences of the survival probabilities of the C–H stretches in the region of the first and second overtones, deduced from the vibrational Hamiltonian, show quantum beats due to the couplings to the deformations and decays driven by weaker interactions to the bath states. The C–H stretches, although somewhat lower in energy, show stronger coupling than the N–H stretches.
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33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Sn Rotational analysis
33.20.Tp Vibrational analysis
back to top Liquids, Glasses, and Crystals

Structure of kaolinite and influence of stacking faults: Reconciling theory and experiment using inelastic neutron scattering analysis

Claire E. White, Gordon J. Kearley, John L. Provis, and Daniel P. Riley

J. Chem. Phys. 138, 194501 (2013); http://dx.doi.org/10.1063/1.4804306 (7 pages)

Online Publication Date: 15 May 2013

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The structure of kaolinite at the atomic level, including the effect of stacking faults, is investigated using inelastic neutron scattering (INS) spectroscopy and density functional theory (DFT) calculations. The vibrational dynamics of the standard crystal structure of kaolinite, calculated using DFT (VASP) with normal mode analysis, gives good agreement with the experimental INS data except for distinct discrepancies, especially for the low frequency modes (200 – 400 cm−1). By generating several types of stacking faults (shifts in the a,b plane for one kaolinite layer relative to the adjacent layer), it is seen that these low frequency modes are affected, specifically through the emergence of longer hydrogen bonds (O–H⋯O) in one of the models corresponding to a stacking fault of −0.3151a − 0.3151b. The small residual disagreement between observed and calculated INS is assigned to quantum effects (which are not taken into account in the DFT calculations), in the form of translational tunneling of the proton in the hydrogen bonds, which lead to a softening of the low frequency modes. DFT-based molecular dynamics simulations show that anharmonicity does not play an important role in the structural dynamics of kaolinite.
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61.72.Nn Stacking faults and other planar or extended defects
82.30.Rs Hydrogen bonding, hydrophilic effects
61.50.Lt Crystal binding; cohesive energy
63.20.dh Fitted theory

Intermolecular interactions and the thermodynamic properties of supercritical fluids

Tesfaye M. Yigzawe and Richard J. Sadus

J. Chem. Phys. 138, 194502 (2013); http://dx.doi.org/10.1063/1.4803855 (11 pages)

Online Publication Date: 16 May 2013

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The role of different contributions to intermolecular interactions on the thermodynamic properties of supercritical fluids is investigated. Molecular dynamics simulation results are reported for the energy, pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound of fluids interacting via both the Lennard-Jones and Weeks-Chandler-Andersen potentials. These properties were obtained for a wide range of temperatures, pressures, and densities. For each thermodynamic property, an excess value is determined to distinguish between attraction and repulsion. It is found that the contributions of intermolecular interactions have varying effects depending on the thermodynamic property. The maxima exhibited by the isochoric and isobaric heat capacities, isothermal compressibilities, and thermal expansion coefficient are attributed to interactions in the Lennard-Jones well. Repulsion is required to obtain physically realistic speeds of sound and both repulsion and attraction are necessary to observe a Joule-Thomson inversion curve. Significantly, both maxima and minima are observed for the isobaric and isochoric heat capacities of the supercritical Lennard-Jones fluid. It is postulated that the loci of these maxima and minima converge to a common point via the same power law relationship as the phase coexistence curve with an exponent of β = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids.
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61.43.Bn Structural modeling: serial-addition models, computer simulation
64.70.-p Specific phase transitions
81.30.-t Phase diagrams and microstructures developed by solidification and solid-solid phase transformations
65.40.De Thermal expansion; thermomechanical effects
65.40.Ba Heat capacity
back to top Surfaces, Interfaces, and Materials

Elementary steps of the catalytic NOx reduction with NH3: Cluster studies on adsorbate diffusion and dehydrogenation at vanadium oxide substrate

M. Gruber and K. Hermann

J. Chem. Phys. 138, 194701 (2013); http://dx.doi.org/10.1063/1.4804160 (11 pages)

Online Publication Date: 15 May 2013

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We discuss the details of important steps of the selective catalytic reduction (SCR) of NOx at model V2O5(010) substrate. First, diffusion processes at the substrate surface are considered where hydrogen and ammonium, NH4, are used as examples. Hydrogen diffusion, a prerequisite for water formation involving substrate oxygen, is described by diffusion paths between adjacent surface oxygen sites. Corresponding energy barriers are determined mainly by the flexibility and the amount of distortion of the oxygen atoms which participate in the O–H–O bridge formation at the transition state. Further, diffusion of sub-surface oxygen to fill surface oxygen vacancies of the V2O5(010) substrate has been considered and results in reactive surface sites which have not been discussed so far. NH4 diffusion at the V2O5(010) surface can be described as a combined tumbling and rotation process characterized by quite low diffusion barriers which make the adsorbate rather mobile. Finally, hydrogenation and dehydrogenation of different NHx species at the V2O5(010) substrate surface are studied where special emphasis is given to the influence of surface reduction simulated locally by oxygen vacancies. The results confirm experimental findings of the presence of both NH2 and NH4 species after ammonia adsorption at the V2O5(010) surface.
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82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
68.43.Jk Diffusion of adsorbates, kinetics of coarsening and aggregation
68.43.-h Chemisorption/physisorption: adsorbates on surfaces
68.43.Mn Adsorption kinetics
68.47.Gh Oxide surfaces

Density functional theory study of the organic functionalization of hydrogenated silicene

Pamela Rubio-Pereda and Noboru Takeuchi

J. Chem. Phys. 138, 194702 (2013); http://dx.doi.org/10.1063/1.4804545 (7 pages)

Online Publication Date: 16 May 2013

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Silicene, the silicon analogous of graphene, is a newly synthesized two-dimensional nanomaterial, with unique features and promising potential applications. In this paper we present density functional theory calculations of the organic functionalization of hydrogenated silicene with acetylene, ethylene, and styrene. The results are compared with previous works of the adsorption on H-Si[111]. For styrene, binding energies for the intermediate and final states as well as the energy barrier for hydrogen abstraction are rather similar for the two systems. On the other hand, results for acetylene and ethylene are surprisingly different in H-silicene: the abstraction barrier is much smaller in H-silicene than in H-Si[111]. These differences can be understood by the different electrostatic potentials due to the presence of the H atoms at the bottom of the silicene bilayer that allows the delocalization of the spin density at the reaction intermediate state.
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68.43.Mn Adsorption kinetics
71.15.Nc Total energy and cohesive energy calculations
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
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