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7 Mar 2011

Volume 134, Issue 9, Articles (09xxxx)

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J. Chem. Phys. 134, 095101 (2011); http://dx.doi.org/10.1063/1.3541251 (18 pages)

Gaël De Paëpe, Józef R. Lewandowski, Antoine Loquet, Matt Eddy, Simon Megy, Anja Böckmann, and Robert G. Griffin
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Communication: Direct angle-resolved measurements of collision dynamics with electronically excited molecules: NO(A2Σ+) + Ar

Jeffrey J. Kay, Grant Paterson, Matthew L. Costen, Kevin E. Strecker, Kenneth G. McKendrick, and David W. Chandler

J. Chem. Phys. 134, 091101 (2011); http://dx.doi.org/10.1063/1.3563016 (3 pages) | Cited 2 times

Online Publication Date: 3 March 2011

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We report direct doubly differential (quantum state and angle-resolved) scattering measurements involving short-lived electronically excited molecules using crossed molecular beams. In our experiment, supersonic beams of nitric oxide and argon atoms collide at 90°. In the crossing region, NO molecules are excited to the A2Σ+state by a pulsed nanosecond laser, undergo rotationally inelastic collisions with Ar atoms, and are then detected 400 ns later (approximately twice the radiative lifetime of the A2Σ+state) by 1 + 1′ multiphoton ionization via the E2Σ+ state. The velocity distributions of the scattered molecules are recorded using velocity-mapped ion imaging. The resulting images provide a direct measurement of the state-to-state differential scattering cross sections. These results demonstrate that sufficient scattering events occur during the short lifetimes typical of molecular excited states (∼200 ns, in this case) to allow spectroscopically detected quantum-state-resolved measurements of products of excited-state collisions.
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34.50.Ez Rotational and vibrational energy transfer
33.80.Eh Autoionization, photoionization, and photodetachment
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
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Communication: CO oxidation by silver and gold cluster cations: Identification of different active oxygen species

Denisia M. Popolan and Thorsten M. Bernhardt

J. Chem. Phys. 134, 091102 (2011); http://dx.doi.org/10.1063/1.3563631 (3 pages) | Cited 4 times

Online Publication Date: 7 March 2011

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The oxidation of carbon monoxide with nitrous oxide on mass-selected Au 3+ and Ag 3+ clusters has been investigated under multicollision conditions in an octopole ion trap experiment. The comparative study reveals that for both gold and silver cations carbon dioxide is formed on the clusters. However, whereas in the case of Au 3+ the cluster itself acts as reactive species that facilitates the formation of CO2 from N2O and CO, for silver the oxidized clusters Ag3Ox+ (n = 1–3) are identified as active in the CO oxidation reaction. Thus, in the case of the silver cluster cations N2O is dissociated and one oxygen atom is suggested to directly react with CO, whereas a second kind of oxygen strongly bound to silver is acting as a substrate for the reaction.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
33.15.Fm Bond strengths, dissociation energies
37.10.Ty Ion trapping
36.40.Jn Reactivity of clusters
36.40.Wa Charged clusters
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Local ab initio methods for calculating optical band gaps in periodic systems. I. Periodic density fitted local configuration interaction singles method for polymers

Marco Lorenz, Denis Usvyat, and Martin Schütz

J. Chem. Phys. 134, 094101 (2011); http://dx.doi.org/10.1063/1.3554209 (14 pages) | Cited 4 times

Online Publication Date: 1 March 2011

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We present a density fitted local configuration interaction singles (CIS) method for calculating optical band gaps in 1D-periodic systems. The method is based on the Davidson diagonalization procedure, carried out in the reciprocal space. The one-electron part of the matrix–vector products is also evaluated in the reciprocal space, where the diagonality of the Fock matrix can be exploited. The contraction of the CIS vectors with the two electron integrals is performed in the direct space in the basis of localized occupied (Wannier) and virtual (projected atomic) orbitals. The direct space approach allows to utilize the sparsity of the integrals due to the local representation and locality of the exciton. The density fitting approximation employed for the two electron integrals reduces the nominal scaling with unit cell size to O(N4). Test calculations on a series of prototypical systems demonstrate that the method in its present stage can be used to calculate the excitonic band gaps of polymers with up to a few dozens of atoms in the cell. The computational cost depends on the locality of the exciton, but even relatively delocalized excitons occurring in the polybiphenyl in the parallel orientation, can be routinely treated with this method.
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71.20.Rv Polymers and organic compounds
71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)
71.35.-y Excitons and related phenomena
78.20.Ci Optical constants (including refractive index, complex dielectric constant, absorption, reflection and transmission coefficients, emissivity)

Benchmark calculations for dissipative dynamics of a system coupled to an anharmonic bath with the multiconfiguration time-dependent Hartree method

S. López-López, R. Martinazzo, and M. Nest

J. Chem. Phys. 134, 094102 (2011); http://dx.doi.org/10.1063/1.3556940 (7 pages)

Online Publication Date: 1 March 2011

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In this paper, we present benchmark results for dissipative dynamics of a harmonic oscillator coupled to an anharmonic bath of Morse oscillators. The microscopic Hamiltonian has been chosen so that the anharmonicity can be adjusted as a free parameter, and its effect can be isolated. This leads to a temperature dependent spectral density of the bath, which is studied for ohmic and lorentzian cases. Also, we compare numerically exact multiconfiguration time-dependent Hartree results with approximate solutions using continuous configuration time-dependent self-consistent field and local coherent state approximation.
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03.65.Ge Solutions of wave equations: bound states

Transition-metal dioxides: A case for the intersite term in Hubbard-model functionals

Heather J. Kulik and Nicola Marzari

J. Chem. Phys. 134, 094103 (2011); http://dx.doi.org/10.1063/1.3559452 (8 pages) | Cited 2 times

Online Publication Date: 2 March 2011

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Triatomic transition-metal oxides in the “inserted dioxide” (O–M–O) structure represent one of the simplest examples of systems that undergo qualitative geometrical changes via subtle electronic-structure modulation. We consider here three transition-metal dioxide molecules (MO2 where M = Mn, Fe, or Co), for which the equilibrium structural (e.g., bent or linear geometry) and electronic (e.g., spin or symmetry) properties have been challenging to assign both theoretically and experimentally. Augmenting a standard density-functional theory (DFT) approach with a Hubbard term (DFT+U) occasionally overlocalizes the 3d manifold, leading to an incorrect bond elongation and, in turn, poor equilibrium geometries for MO2 molecules, while preserving good spin-state splittings. Proper description of both geometry and energetics for these molecules is recovered; however, through either calculating DFT+U relaxations at fixed M–O bond lengths or by inclusion of an intersite interaction term V that favors M(3d)–O(2p) interactions. In this latter case, both U and V are calculated fully from first-principles and are not fitting parameters. Finally, we identify an approach that more accurately determines the Hubbard U over a coordinate in which the covalent character of bonding varies.
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71.10.Fd Lattice fermion models (Hubbard model, etc.)
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
61.50.Lt Crystal binding; cohesive energy

Exponentially and pre-exponentially correlated Gaussians for atomic quantum calculations

Keeper L. Sharkey and Ludwik Adamowicz

J. Chem. Phys. 134, 094104 (2011); http://dx.doi.org/10.1063/1.3553177 (6 pages)

Online Publication Date: 2 March 2011

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Explicitly correlated, n-electron, one-center s Gaussian (ECG) functions that depend on the interelectron distances in the exponent are combined with s ECGs which also depend on the interelectron separations through pre-exponential rij2 multipliers. The pre-exponentially rij2-dependent ECGs are included in the basis to better describe the interelectron correlation and the interelectron cusps. The basis set is tested in the calculations of the ground state of the beryllium atom (9Be).
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03.65.-w Quantum mechanics

Transport, phase transitions, and wetting in micro/nanochannels: A phase field/DDFT approach

Walter Mickel, Laurent Joly, and Thierry Biben

J. Chem. Phys. 134, 094105 (2011); http://dx.doi.org/10.1063/1.3557061 (14 pages)

Online Publication Date: 2 March 2011

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While the flow of a liquid in a macroscopic channel is usually described using hydrodynamics with no-slip boundary conditions at the walls of the channel, transport phenomena in microchannels involve physics at many different scales due to the interplay between the micrometric section of the channel and the micro- or nanometric roughness of the boundaries. Roughness can have many different effects such as increasing the friction between the liquid and the walls (leading to the macroscopic no-slip boundary condition) or on the contrary reduce it thanks to the Wenzel–Cassie–Baxter wetting transition induced by capillarity. Here we detail a phase-field/dynamic density functional theory model able to account for the wetting transitions, the resulting friction between the wall and the fluid, and compressible hydrodynamics at high viscosity contrast.
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47.85.Np Fluidics
68.08.Bc Wetting
47.55.nb Capillary and thermocapillary flows
47.60.Dx Flows in ducts and channels

Fragmentation and reactivity in collisions of protonated diglycine with chemically modified perfluorinated alkylthiolate-self-assembled monolayer surfaces

George L. Barnes, Kelsey Young, Li Yang, and William L. Hase

J. Chem. Phys. 134, 094106 (2011); http://dx.doi.org/10.1063/1.3558736 (13 pages)

Online Publication Date: 3 March 2011

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Direct dynamics simulations are reported for quantum mechanical (QM)/molecular mechanical (MM) trajectories of N-protonated diglycine (gly2-H+) colliding with chemically modified perfluorinated octanethiolate self-assembled monolayer (SAM) surfaces. The RM1 semiempirical theory is used for the QM component of the trajectories. RM1 activation and reaction energies were compared with those determined from higher-level ab initio theories. Two chemical modifications are considered in which a head group (–COCl or –CHO) is substituted on the terminal carbon of a single chain of the SAM. These surfaces are designated as the COCl-SAM and CHO-SAM, respectively. Fragmentation, peptide reaction with the SAM, and covalent linkage of the peptide or its fragments with the SAM surface are observed. Peptide fragmentation via concerted CH2–CO bond breakage is the dominant pathway for both surfaces. HCl formation is the dominant species produced by reaction with the COCl-SAM, while for the CHO-SAM a concerted H-atom transfer from the CHO-SAM to the peptide combined with either a H-atom or radical transfer from the peptide to the surface to form singlet reaction products is the dominant pathway. A strong collision energy dependence is found for the probability of peptide fragmentation, its reactivity, and linkage with the SAM. Surface deposition, i.e., covalent linkage between the surface and the peptide, is compared to recent experimental observations of such bonding by Laskin and co-workers [Phys. Chem. Chem. Phys. 10, 1512 (2008)]. Qualitative differences in reactivity are seen between the COCl-SAM and CHO-SAM showing that chemical identity is important for surface reactivity. The probability of reactive surface deposition, which is most closely analogous to experimental observables, peaks at a value of around 20% for a collision energy of 50 eV.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.20.Bc State selected dynamics and product distribution
82.20.Fd Collision theories; trajectory models
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.30.Nr Association, addition, insertion, cluster formation

Ab initio interatomic decay widths of excited states by applying Stieltjes imaging to Lanczos pseudospectra

S. Kopelke, K. Gokhberg, V. Averbukh, F. Tarantelli, and L. S. Cederbaum

J. Chem. Phys. 134, 094107 (2011); http://dx.doi.org/10.1063/1.3558739 (11 pages) | Cited 1 time

Online Publication Date: 3 March 2011

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Electronically excited states of atoms and molecules in an environment may decay in interatomic processes by transferring excess energy to neighboring species and ionizing them. The corresponding interatomic decay width is the most important characteristic of the decay allowing to calculate its efficiency and the final states’ distribution. In this paper we present calculations of interatomic widths by the Fano–Stieltjes method applied to Lanczos pseudospectra, which has been previously shown to provide accurate autoionization widths in atoms and molecules. The use of Lanczos pseudospectra allows one to avoid the full diagonalization bottleneck and makes the method applicable to larger systems. We apply the present method to the calculation of interatomic decay widths in NeMg, NeAr and HCN·Mgn, n = 1, 2 clusters. The results are compared with widths obtained analytically and by other ab initio methods where available.
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36.40.-c Atomic and molecular clusters
31.50.Df Potential energy surfaces for excited electronic states
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
31.15.ag Excitation energies and lifetimes; oscillator strengths
33.80.Eh Autoionization, photoionization, and photodetachment

Accurate freezing and melting equations for the Lennard-Jones system

Sergey A. Khrapak and Gregor E. Morfill

J. Chem. Phys. 134, 094108 (2011); http://dx.doi.org/10.1063/1.3561698 (3 pages) | Cited 3 times

Online Publication Date: 3 March 2011

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Analyzing three approximate methods to locate liquid–solid coexistence in simple systems, an observation is made that all of them predict the same functional dependence of the temperature on density at freezing and melting of the conventional Lennard-Jones (LJ) system. The emerging equations can be written as T = Aρ4+Bρ2 in normalized units. We suggest to determine the values of the coefficients A at freezing and melting from the high-temperature limit, governed by the inverse 12th power repulsive potential. The coefficients B can be determined from the triple point parameters of the LJ fluid. This produces freezing and melting equations which are exact in the high-temperature limit and at the triple point and show remarkably good agreement with numerical simulation data in the intermediate region.
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64.70.dj Melting of specific substances
64.70.dm General theory of the solid-liquid transition
64.60.fd General theory of critical region behavior

The effect of electron interactions on the universal properties of systems with optimized off-resonant intrinsic hyperpolarizability

David S. Watkins and Mark G. Kuzyk

J. Chem. Phys. 134, 094109 (2011); http://dx.doi.org/10.1063/1.3560031 (10 pages)

Online Publication Date: 3 March 2011

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Because of the potentially large number of important applications of nonlinear optics, researchers have expended a great deal of effort to optimize the second-order molecular nonlinear-optical response, called the hyperpolarizability. The focus of our present studies is the intrinsic hyperpolarizability, which is a scale-invariant quantity that removes the effects of simple scaling, thus being the relevant quantity for comparing molecules of varying sizes. Past theoretical studies have focused on structural properties that optimize the intrinsic hyperpolarizability, which have characterized the structure of the quantum system based on the potential energy function, placement of nuclei, geometry, and the effects of external electric and magnetic fields. Those previous studies focused on single-electron models under the influence of an average potential. In the present studies, we generalize our calculations to two-electron systems and include electron interactions. As with the single-electron studies, universal properties are found that are common to all systems—be they molecules, nanoparticles, or quantum gases—when the hyperpolarizability is near the fundamental limit.
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31.15.-p Calculations and mathematical techniques in atomic and molecular physics
31.10.+z Theory of electronic structure, electronic transitions, and chemical binding

Determination of molecular vibrational state energies using the ab initio semiclassical initial value representation: Application to formaldehyde

Stephanie Y. Y. Wong, David M. Benoit, Marius Lewerenz, Alex Brown, and Pierre-Nicholas Roy

J. Chem. Phys. 134, 094110 (2011); http://dx.doi.org/10.1063/1.3553179 (10 pages) | Cited 2 times

Online Publication Date: 3 March 2011

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We have demonstrated the use of ab initio molecular dynamics (AIMD) trajectories to compute the vibrational energy levels of molecular systems in the context of the semiclassical initial value representation (SC-IVR). A relatively low level of electronic structure theory (HF/3-21G) was used in this proof-of-principle study. Formaldehyde was used as a test case for the determination of accurate excited vibrational states. The AIMD-SC-IVR vibrational energies have been compared to those from curvilinear and rectilinear vibrational self-consistent field/vibrational configuration interaction with perturbation selected interactions-second-order perturbation theory (VSCF/VCIPSI-PT2) and correlation-corrected vibrational self-consistent field (cc-VSCF) methods. The survival amplitudes were obtained from selecting different reference wavefunctions using only a single set of molecular dynamics trajectories. We conclude that our approach is a further step in making the SC-IVR method a practical tool for first-principles quantum dynamics simulations.
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31.15.xv Molecular dynamics and other numerical methods
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.xr Self-consistent-field methods

On the relation between orbital-localization and self-interaction errors in the density functional theory treatment of organic semiconductors

T. Körzdörfer

J. Chem. Phys. 134, 094111 (2011); http://dx.doi.org/10.1063/1.3556979 (9 pages) | Cited 3 times

Online Publication Date: 3 March 2011

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It is commonly argued that the self-interaction error (SIE) inherent in semilocal density functionals is related to the degree of the electronic localization. Yet at the same time there exists a latent ambiguity in the definitions of the terms “localization” and “self-interaction,” which ultimately prevents a clear and readily accessible quantification of this relationship. This problem is particularly pressing for organic semiconductor molecules, in which delocalized molecular orbitals typically alternate with localized ones, thus leading to major distortions in the eigenvalue spectra. This paper discusses the relation between localization and SIEs in organic semiconductors in detail. Its findings provide further insights into the SIE in the orbital energies and yield a new perspective on the failure of self-interaction corrections that identify delocalized orbital densities with electrons.
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71.15.Mb Density functional theory, local density approximation, gradient and other corrections

Coarse-graining errors and numerical optimization using a relative entropy framework

Aviel Chaimovich and M. Scott Shell

J. Chem. Phys. 134, 094112 (2011); http://dx.doi.org/10.1063/1.3557038 (15 pages) | Cited 3 times

Online Publication Date: 3 March 2011

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The ability to generate accurate coarse-grained models from reference fully atomic (or otherwise “first-principles”) ones has become an important component in modeling the behavior of complex molecular systems with large length and time scales. We recently proposed a novel coarse-graining approach based upon variational minimization of a configuration-space functional called the relative entropy, Srel, that measures the information lost upon coarse-graining. Here, we develop a broad theoretical framework for this methodology and numerical strategies for its use in practical coarse-graining settings. In particular, we show that the relative entropy offers tight control over the errors due to coarse-graining in arbitrary microscopic properties, and suggests a systematic approach to reducing them. We also describe fundamental connections between this optimization methodology and other coarse-graining strategies like inverse Monte Carlo, force matching, energy matching, and variational mean-field theory. We suggest several new numerical approaches to its minimization that provide new coarse-graining strategies. Finally, we demonstrate the application of these theoretical considerations and algorithms to a simple, instructive system and characterize convergence and errors within the relative entropy framework.
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31.15.xt Variational techniques
05.70.Ce Thermodynamic functions and equations of state
02.70.Uu Applications of Monte Carlo methods

Inversion of two-dimensional potentials from frequency-resolved spectroscopic data

Xuan Li and Moshe Shapiro

J. Chem. Phys. 134, 094113 (2011); http://dx.doi.org/10.1063/1.3561494 (4 pages) | Cited 4 times

Online Publication Date: 4 March 2011

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We report the first successful reconstruction of two-dimensional potential energy surfaces (PES) using the magnitudes and positions of a set of frequency-resolved fluorescence (or absorption) lines. The inversion proceeds by first extracting the phases of the transition-dipole matrix elements, yielding, together with the (ground) PES to (from) which emission (absorption) occurs, a point by point reconstruction of the two-dimensional excited state PES. The inversion procedure is highly accurate even for PES with multiple minima and many missing lines, with typical RMS errors <0.002 cm−1 in the classically allowed region and <0.018 cm−1 in the classically forbidden region.
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31.50.Df Potential energy surfaces for excited electronic states
33.70.Jg Line and band widths, shapes, and shifts
33.50.Dq Fluorescence and phosphorescence spectra

Langevin–Bloch equations for a spin bath

Arnab Ghosh, Sudarson Sekhar Sinha, and Deb Shankar Ray

J. Chem. Phys. 134, 094114 (2011); http://dx.doi.org/10.1063/1.3556706 (7 pages)

Online Publication Date: 7 March 2011

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We derive the Bloch equations for a two-level system coupled to a spin bath of infinitely many two-level atoms to examine phase and energy relaxation of an optically excited system. We show that increasing temperature assists coherence. This is reflected in a number of anomalous features of relaxation of the system, e.g., decrease of integrated absorption coefficient with temperature, nonlinear variation of linewidth with incident power. We also predict that thermally induced coherence may result in anomalous narrowing of linewidth, reminiscent (but distinct) of “motional narrowing” of spectral line. The theoretical results are discussed in the light of absorption–emission experiments on single quantum dots.
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32.70.Jz Line shapes, widths, and shifts
31.15.-p Calculations and mathematical techniques in atomic and molecular physics
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Dynamical mean-field theory from a quantum chemical perspective

Dominika Zgid and Garnet Kin-Lic Chan

J. Chem. Phys. 134, 094115 (2011); http://dx.doi.org/10.1063/1.3556707 (14 pages) | Cited 2 times

Online Publication Date: 7 March 2011

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We investigate the dynamical mean-field theory (DMFT) from a quantum chemical perspective. Dynamical mean-field theory offers a formalism to extend quantum chemical methods for finite systems to infinite periodic problems within a local correlation approximation. In addition, quantum chemical techniques can be used to construct new ab initio Hamiltonians and impurity solvers for DMFT. Here, we explore some ways in which these things may be achieved. First, we present an informal overview of dynamical mean-field theory to connect to quantum chemical language. Next, we describe an implementation of dynamical mean-field theory where we start from an ab initio Hartree–Fock Hamiltonian that avoids double counting issues present in many applications of DMFT. We then explore the use of the configuration interaction hierarchy in DMFT as an approximate solver for the impurity problem. We also investigate some numerical issues of convergence within DMFT. Our studies are carried out in the context of the cubic hydrogen model, a simple but challenging test for correlation methods. Finally, we finish with some conclusions for future directions.
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31.15.A- Ab initio calculations
31.15.xr Self-consistent-field methods
31.15.V- Electron correlation calculations for atoms, ions and molecules

Laser-induced breathing modes in metallic nanoparticles: A symmetric molecular dynamics study

Ming-Yaw Ng and Yia-Chung Chang

J. Chem. Phys. 134, 094116 (2011); http://dx.doi.org/10.1063/1.3563803 (10 pages)

Online Publication Date: 7 March 2011

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A highly efficient simulation method based on molecular dynamics and group theory is adopted to investigate the laser-induced breathing oscillation of gold and silver nanospheres. Nanoparticles with size ranging from 5.8 to 46.2 nm are discussed. The effect due to laser-induced heating is modeled by a symmetric sudden expansion of the nanospheres by increasing the interatomic distances. A long-range empirical potential model which is capable of describing the phonon dispersion curves of noble metals in the full frequency range is established. Group theory is fully exploited to increase the computation efficiency, and the oscillation behavior of nanospheres of over 3 × 106 atoms can be simulated efficiently. Oscillation frequencies of nanospheres are obtained by calculating the Fourier transform of the velocity autocorrelation function. The breathing modes of nanospheres are identified as the excitation of A1g modes with in-phase radial displacement of atoms in the nanospheres. The resulting oscillation spectra are in very good agreement with experimental data.
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63.22.-m Phonons or vibrational states in low-dimensional structures and nanoscale materials
61.80.Ba Ultraviolet, visible, and infrared radiation effects (including laser radiation)
63.20.D- Phonon states and bands, normal modes, and phonon dispersion

Complex wave patterns in an effective reaction–diffusion model for chemical reactions in microemulsions

Sergio Alonso, Karin John, and Markus Bär

J. Chem. Phys. 134, 094117 (2011); http://dx.doi.org/10.1063/1.3559154 (7 pages)

Online Publication Date: 7 March 2011

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An effective medium theory is employed to derive a simple qualitative model of a pattern forming chemical reaction in a microemulsion. This spatially heterogeneous system is composed of water nanodroplets randomly distributed in oil. While some steps of the reaction are performed only inside the droplets, the transport through the extended medium occurs by diffusion of intermediate chemical reactants as well as by collisions of the droplets. We start to model the system with heterogeneous reaction–diffusion equations and then derive an equivalent effective spatially homogeneous reaction–diffusion model by using earlier results on homogenization in heterogeneous reaction–diffusion systems [S.Alonso, M.Bär, and R.Kapral, J. Chem. Phys. 134, 214102 (2009)]. We study the linear stability of the spatially homogeneous state in the resulting effective model and obtain a phase diagram of pattern formation, that is qualitatively similar to earlier experimental results for the Belousov–Zhabotinsky reaction in an aerosol OT (AOT)-water-in-oil microemulsion [V.K.Vanag and I.R.Epstein, Phys. Rev. Lett. 87, 228301 (2001)]. Moreover, we reproduce many patterns that have been observed in experiments with the Belousov–Zhabotinsky reaction in an AOT oil-in-water microemulsion by direct numerical simulations.
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82.40.Ck Pattern formation in reactions with diffusion, flow and heat transfer
82.20.Fd Collision theories; trajectory models
82.70.Kj Emulsions and suspensions
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An efficient, fragment-based electronic structure method for molecular systems: Self-consistent polarization with perturbative two-body exchange and dispersion

Leif D. Jacobson and John M. Herbert

J. Chem. Phys. 134, 094118 (2011); http://dx.doi.org/10.1063/1.3560026 (17 pages) | Cited 6 times

Online Publication Date: 7 March 2011

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We report a fragment-based electronic structure method, intended for the study of clusters and molecular liquids, that incorporates electronic polarization (induction) in a self-consistent fashion but treats intermolecular exchange and dispersion interactions perturbatively, as post-self-consistent field corrections, using a form of pairwise symmetry-adapted perturbation theory. The computational cost of the method scales quadratically as a function of the number of fragments (monomers), but could be made to scale linearly by exploiting distance-dependent thresholds. Extensive benchmark calculations are reported using the S22 database of high-level ab initio binding energies for dimers, and we find that average errors can be reduced to <1 kcal/mol with a suitable choice of basis set. Comparison to ab initio benchmarks for water clusters as large as (H2O)20 demonstrates that the method recovers ≳90% of the binding energy in these systems, at a tiny fraction of the computational cost. As such, this approach represents a promising path toward accurate, systematically improvable, and parameter-free simulation of molecular liquids.
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36.40.Cg Electronic and magnetic properties of clusters
61.25.Em Molecular liquids
31.15.xr Self-consistent-field methods
31.15.A- Ab initio calculations
34.20.Gj Intermolecular and atom-molecule potentials and forces

Overlapping fragments method for electronic structure calculation of large systems

Nenad Vukmirović and Lin-Wang Wang

J. Chem. Phys. 134, 094119 (2011); http://dx.doi.org/10.1063/1.3560956 (8 pages)

Online Publication Date: 7 March 2011

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We present a method for the calculation of the electronic structure of systems that contain tens of thousands of atoms. The method is based on the division of the system into mutually overlapping fragments and the representation of the single-particle Hamiltonian in the basis of eigenstates of these fragments. In practice, for the range of the system size that we studied (up to tens of thousands of atoms), the dominant part of the calculation scales linearly with the size of the system when all the states within a fixed energy interval are required. The method is highly suitable for making good use of parallel computing architectures. We illustrate the method by applying it to diagonalize the single-particle Hamiltonian obtained using the density functional theory based charge patching method in the case of amorphous alkane and polythiophene polymers.
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31.15.E- Density-functional theory
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Use of modified smooth exterior scaling method as an absorbing potential and its application

Dhruba J. Kalita and Ashish K. Gupta

J. Chem. Phys. 134, 094301 (2011); http://dx.doi.org/10.1063/1.3558737 (6 pages) | Cited 1 time

Online Publication Date: 1 March 2011

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Here, we propose a new complex path to achieve better absorption during the propagation of a wavepacket. In the proposed modified smooth exterior scaling (SES) method, scaling function, θ(x), has been chosen as a real function rather than complex (as used in a conventional smooth exterior scaling method). It greatly reduces the artificial reflections from the boundary edges. This modified SES method is applied to study the multiphoton dissociation of H2+ in intense laser field. The resonance states are calculated accurately.
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82.50.Pt Multiphoton processes
32.80.Wr Other multiphoton processes

High-level direct-dynamics variational transition state theory calculations including multidimensional tunneling of the thermal rate constants, branching ratios, and kinetic isotope effects of the hydrogen abstraction reactions from methanol by atomic hydrogen

Rubén Meana-Pañeda, Donald G. Truhlar, and Antonio Fernández-Ramos

J. Chem. Phys. 134, 094302 (2011); http://dx.doi.org/10.1063/1.3555763 (14 pages) | Cited 3 times

Online Publication Date: 2 March 2011

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We report a detailed theoretical study of the hydrogen abstraction reaction from methanol by atomic hydrogen. The study includes the analysis of thermal rate constants, branching ratios, and kinetic isotope effects. Specifically, we have performed high-level computations at the MC3BB level together with direct dynamics calculations by canonical variational transition state theory (CVT) with the microcanonically optimized multidimensional tunneling (μOMT) transmission coefficient (CVT/μOMT) to study both the CH3OH + H → CH2OH + H2 (R1) reaction and the CH3OH + H → CH3O + H2 (R2) reaction. The CVT/μOMT calculations show that reaction R1 dominates in the whole range 298 ≤ T(K) ≤ 2500 and that anharmonic effects on the torsional mode about the C–O bond are important, mainly at high temperatures. The activation energy for the total reaction sum of R1 and R2 reactions changes substantially with temperature and, therefore, the use of straight-line Arrhenius plots is not valid. We recommend the use of new expressions for the total R1 + R2 reaction and for the R1 and R2 individual reactions.
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82.20.Tr Kinetic isotope effects including muonium
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Wt Computational modeling; simulation

Thermodynamic driving force for diffusion: Comparison between theory and simulation

Jessica R. Whitman, Gregory L. Aranovich, and Marc D. Donohue

J. Chem. Phys. 134, 094303 (2011); http://dx.doi.org/10.1063/1.3558782 (7 pages) | Cited 1 time

Online Publication Date: 2 March 2011

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In previous work, lattice density functional theory equations have been recast into differential form to determine a property whose gradient is universally proportional to the diffusive flux. For color counter diffusion, this property appears as the impingement rate onto vacancies and molecules of a species whose density gradient can be influenced by diffusion. Therefore, the impingement rate of a diffusing molecule depends on the mobility of its surroundings. In order to determine the validity of this finding, molecular dynamics simulations of color counter diffusion were performed in which the mobility of the solvent was varied to determine if the flux of the diffusing species responded to the change when all other factors, such as density gradient, available volume, and temperature are held constant.
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66.10.C- Diffusion and thermal diffusion
61.20.Ja Computer simulation of liquid structure

Infrared absorption of CH3OSO detected with time-resolved Fourier-transform spectroscopy

Jin-Dah Chen and Yuan-Pern Lee

J. Chem. Phys. 134, 094304 (2011); http://dx.doi.org/10.1063/1.3556817 (12 pages) | Cited 4 times

Online Publication Date: 2 March 2011

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A step-scan Fourier-transform spectrometer coupled with a multipass absorption cell was employed to detect temporally resolved infrared absorption spectra of CH3OSO produced upon irradiation of a flowing gaseous mixture of CH3OS(O)Cl in N2 or CO2 at 248 nm. Two intense transient features with origins near 1152 and 994 cm−1 are assigned to syn-CH3OSO; the former is attributed to overlapping bands at 1154 ± 3 and 1151 ± 3 cm−1, assigned to the S=O stretching mixed with CH3 rocking (ν8) and the S=O stretching mixed with CH3 wagging (ν9) modes, respectively, and the latter to the C−O stretching (ν10) mode at 994 ± 6 cm−1. Two weak bands at 2991 ± 6 and 2956 ± 3 cm−1 are assigned as the CH3 antisymmetric stretching (ν2) and symmetric stretching (ν3) modes, respectively. Observed vibrational transition wavenumbers agree satisfactorily with those predicted with quantum-chemical calculations at level B3P86/aug-cc-pVTZ. Based on rotational parameters predicted at that level, the simulated rotational contours of these bands agree satisfactorily with experimental results. The simulation indicates that the S=O stretching mode of anti-CH3OSO near 1164 cm−1 likely makes a small contribution to the observed band near 1152 cm−1. A simple kinetic model of self-reaction is employed to account for the decay of CH3OSO and yields a second-order rate coefficient k = (4 ± 2)×10−10 cm3 molecule−1 s−1.
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33.20.Ea Infrared spectra
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis
33.20.Sn Rotational analysis
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