Journal of Chemical Physics: All Topics

Erratum: Theoretical predictions of properties and gas-phase chromatography behaviour of bromides of group-5 elements Nb, Ta, and element 105, Db [J. Chem. Phys. 136, 034308 (2012)]

V. Pershina and J. Anton
Abstract not available. [J. Chem. Phys. 136, 069901 (2012)] published Fri Feb 10, 2012.

Kinetic pathways to peptide aggregation on surfaces: The effects of beta-sheet propensity and surface attraction

Alex Morriss-Andrews and Joan-Emma Shea
Mechanisms of peptide aggregation on hydrophobic surfaces are explored using molecular dynamics simulations with a coarse-grained peptide representation. Systems of peptides are studied with varying degrees of backbone rigidity (a measure of beta-sheet propensity) and degrees of attraction between t ... [J. Chem. Phys. 136, 065103 (2012)] published Fri Feb 10, 2012.

Calculations of nonlinear response properties using the intermediate state representation and the algebraic-diagrammatic construction polarization propagator approach: Two-photon absorption spectra

S. Knippenberg, D. R. Rehn, M. Wormit, J. H. Starcke, I. L. Rusakova et al.
An earlier proposed approach to molecular response functions based on the intermediate state representation (ISR) of polarization propagator and algebraic-diagrammatic construction (ADC) approximations is for the first time employed for calculations of nonlinear response properties. The two-photon a ... [J. Chem. Phys. 136, 064107 (2012)] published Fri Feb 10, 2012.

How to impose stick boundary conditions in coarse-grained hydrodynamics of Brownian colloids and semi-flexible fiber rheology

Robert D. Groot
Long-range hydrodynamics between colloidal particles or fibers is modelled by the fluid particle model. Two methods are considered to impose the fluid boundary conditions at colloidal surfaces. In the first method radial and transverse friction forces between particle and solvent are applied such th ... [J. Chem. Phys. 136, 064901 (2012)] published Fri Feb 10, 2012.

Mechanism of OH radical hydration: A comparative computational study of liquid and supercritical solvent

Dorota Swiatla-Wojcik and Joanna Szala-Bilnik
Flexible models of the radical and water molecules including short-range interaction of hydrogen atoms have been employed in molecular dynamic simulation to understand mechanism of OH hydration in aqueous systems of technological importance. A key role of H-bond connectivity patterns of water molecu ... [J. Chem. Phys. 136, 064510 (2012)] published Fri Feb 10, 2012.

New determination of the adiabatic ionization potential of the BaOH radical from laser photoionization-molecular beam experiments and ab initio calculations

Maximiliano Rossa, Ivan Cabanillas-Vidosa, Gustavo A. Pino, and Juan C. Ferrero
The adiabatic ionization potential of the BaOH radical, as generated in a laser vaporization-supersonic expansion source has been determined by laser photoionization experiments to be (4.55 0.03) eV. This value supports the three lowest out of seven previous experimental estimates, the former rangi ... [J. Chem. Phys. 136, 064303 (2012)] published Fri Feb 10, 2012.

Local structural models of complex oxygen- and hydroxyl-rich GaP/InP(001) surfaces

Brandon C. Wood, Tadashi Ogitsu, and Eric Schwegler
We perform density-functional theory calculations on model surfaces to investigate the interplay between the morphology, electronic structure, and chemistry of oxygen- and hydroxyl-rich surfaces of InP(001) and GaP(001). Four dominant local oxygen topologies are identified based on the coordination ... [J. Chem. Phys. 136, 064705 (2012)] published Fri Feb 10, 2012.

Absorption by DNA single strands of adenine isolated in vacuo: The role of multiple chromophores

Lisbeth Munksgaard Nielsen, Sara Ovad Pedersen, Maj-Britt Suhr Kirketerp, and Steen Brondsted Nielsen
The degree of electronic coupling between DNA bases is a topic being up for much debate. Here we report on the intrinsic electronic properties of isolated DNA strands in vacuo free of solvent, which is a good starting point for high-level excited states calculations. Action spectra of DNA single str ... [J. Chem. Phys. 136, 064302 (2012)] published Fri Feb 10, 2012.

Critical lines for an unequal size of molecules in a binary gas-liquid mixture around the van Laar point using the combination of the Tompa model and the van der Waals equation

Mustafa Gencaslan and Mustafa Keskin
We combine the modified Tompa model with the van der Waals equation to study critical lines for an unequal size of molecules in a binary gas-liquid mixture around the van Laar point. The van Laar point is coined by Meijer and it is the only point at which the mathematical double point curve is stabl ... [J. Chem. Phys. 136, 064106 (2012)] published Fri Feb 10, 2012.

Coherent control and time-dependent density functional theory: Towards creation of wave packets by ultrashort laser pulses

Shampa Raghunathan and Mathias Nest
Explicitly time-dependent density functional theory (TDDFT) is a formally exact theory, which can treat very large systems. However, in practice it is used almost exclusively in the adiabatic approximation and with standard ground state functionals. Therefore, if combined with coherent control theor ... [J. Chem. Phys. 136, 064104 (2012)] published Fri Feb 10, 2012.

Electronic states and the influence of oxygen addition on the optical absorption behaviour of manganese phthalocyanine

R. Friedrich, T. Hahn, J. Kortus, M. Fronk, F. Haidu et al.
The effects of electronic states and air exposure on the spectroscopic properties of manganese phthalocyanine (MnPc) have been examined. The observed features of the Q-band in the absorption spectra can be explained by intrinsic electronic properties of MnPc, i.e., the formation of singly charged mo ... [J. Chem. Phys. 136, 064704 (2012)] published Fri Feb 10, 2012.

Transient-time correlation function applied to mixed shear and elongational flows

Remco Hartkamp, Stefano Bernardi, and B. D. Todd
The transient-time correlation function (TTCF) method is used to calculate the nonlinear response of a homogeneous atomic fluid close to equilibrium. The TTCF response of the pressure tensor subjected to a time-independent planar mixed flow of shear and elongation is compared to directly averaged no ... [J. Chem. Phys. 136, 064105 (2012)] published Fri Feb 10, 2012.

Dynamics and efficiency of a self-propelled, diffusiophoretic swimmer

Benedikt Sabass and Udo Seifert
Active diffusiophoresisswimming through interaction with a self-generated, neutral, solute gradientis a paradigm for autonomous motion at the micrometer scale. We study this propulsion mechanism within a linear response theory. First, we consider several aspects relating to the dynamics of the swimm ... [J. Chem. Phys. 136, 064508 (2012)] published Thu Feb 9, 2012.

Communication: Angle-resolved thermal dissociative sticking of CH on Pt(111): Further indication that rotation is a spectator to the gas-surface reaction dynamics

J. K. Navin, S. B. Donald, D. G. Tinney, G. W. Cushing, and I. Harrison
Effusive molecular beam measurements of angle-resolved thermal dissociative sticking coefficients for CH impinging on a Pt(111) surface, at a temperature of 700 K, are reported and compared to theoretical predictions. The reactivity falls off steeply as the molecular angle of incidence increases awa ... [J. Chem. Phys. 136, 061101 (2012)] published Thu Feb 9, 2012.

Time-resolved simultaneous polarized and depolarized light scattering system with high sensitivity to optical anisotropy: Application to phase separation of an optically isotropic liquid mixture

Takehito Koyama and Hajime Tanaka
Depolarized light scattering is widely used to probe the spatial correlation of optical anisotropy in crystals, liquid crystals, and viscoelastic materials under stress, and a powerful means to study a non-equilibrium pattern evolution process of such a system. To follow the temporal change in the d ... [J. Chem. Phys. 136, 064509 (2012)] published Thu Feb 9, 2012.

Gas-phase structures of neutral silicon clusters

Marko Haertelt, Jonathan T. Lyon, Pieterjan Claes, Jorg de Haeck, Peter Lievens et al.
Vibrational spectra of neutral silicon clusters Si, in the size range of n = 610 and for n = 15, have been measured in the gas phase by two fundamentally different IR spectroscopic methods. Silicon clusters composed of 8, 9, and 15 atoms have been studied by IR multiple photon dissociation spectrosc ... [J. Chem. Phys. 136, 064301 (2012)] published Thu Feb 9, 2012.

Folding of small origamis

Jean Michel Arbona, Jean-Pierre Aime, and Juan Elezgaray
A model that preserves the known thermodynamic properties of double stranded DNA is introduced to study the formation of more complex DNA constructions, such as small origamis or Holliday junctions. We show that the thermodynamic behaviour of these complex DNA constructions is not only given by thei ... [J. Chem. Phys. 136, 065102 (2012)] published Thu Feb 9, 2012.

A neural network potential-energy surface for the water dimer based on environment-dependent atomic energies and charges

Tobias Morawietz, Vikas Sharma, and Jorg Behler
Understanding the unique properties of water still represents a significant challenge for theory and experiment. Computer simulations by molecular dynamics require a reliable description of the atomic interactions, and in recent decades countless water potentials have been reported in the literature ... [J. Chem. Phys. 136, 064103 (2012)] published Thu Feb 9, 2012.

Elucidation of spin echo small angle neutron scattering correlation functions through model studies

Chwen-Yang Shew and Wei-Ren Chen
Several single-modal Debye correlation functions to approximate part of the overall Debey correlation function of liquids are closely examined for elucidating their behavior in the corresponding spin echo small angle neutron scattering (SESANS) correlation functions. We find that the maximum length ... [J. Chem. Phys. 136, 064506 (2012)] published Wed Feb 8, 2012.

Analysis of time resolved femtosecond and femtosecond/picosecond coherent anti-Stokes Raman spectroscopy: Application to toluene and Rhodamine 6G

Kai Niu and Soo-Y. Lee
The third-order polarization for coherent anti-Stokes Raman scattering (CARS) from a pure state is described by 48 terms in perturbation theory, but only 4 terms satisfy the rotating wave approximation. They are represented by Feynman dual time-line diagrams and four-wave mixing energy level diagram ... [J. Chem. Phys. 136, 064504 (2012)] published Wed Feb 8, 2012.

Accurate thermochemistry from a parameterized coupled-cluster singles and doubles model and a local pair natural orbital based implementation for applications to larger systems

Lee M. J. Huntington, Andreas Hansen, Frank Neese, and Marcel Nooijen
We have recently introduced a parameterized coupled-cluster singles and doubles model (pCCSD(alpha, beta)) that consists of a bivariate parameterization of the CCSD equations and is inspired by the coupled electron pair approximations. In our previous work, it was demonstrated that the pCCSD(1, 1) m ... [J. Chem. Phys. 136, 064101 (2012)] published Wed Feb 8, 2012.

Structure and properties of metal-exchanged zeolites studied using gradient-corrected and hybrid functionals. III. Energetics and vibrational spectroscopy of adsorbates

Florian Goltl and Jurgen Hafner
The influence of the exchange-correlation functional (semilocal gradient corrected or hybrid functional) on density-functional studies of the adsorption of CO and NO in Cu- and Co-exchanged chabazite has been investigated, extending the studies of the structural and electronic properties of these ma ... [J. Chem. Phys. 136, 064503 (2012)] published Wed Feb 8, 2012.

Activation of water on the TiO (110) surface: The case of Ti adatoms

Meng Miao, Yingchun Liu, Qi Wang, Tao Wu, Liping Huang et al.
Using first-principles calculations we have studied the reactions of water over Ti adatoms on the (110) surface of rutile TiO. Our results provide fundamental insights into the microscopic mechanisms that drive this reaction at the atomic level and assess the possibility of using this system to acti ... [J. Chem. Phys. 136, 064703 (2012)] published Wed Feb 8, 2012.

First principles analysis of the initial oxidation of Si(001) and Si(111) surfaces terminated with H and CH

Huashan Li, Zhibin Lin, Zhigang Wu, and Mark T. Lusk
Transition state analyses have been carried out within a density functional theory setting to explain and quantify the distinctly different ways in which hydrogen and methyl terminations serve to protect silicon surfaces from the earliest onset of oxidation. We find that oxidation occurs via direct ... [J. Chem. Phys. 136, 064507 (2012)] published Wed Feb 8, 2012.

Selective probe of the morphology and local vibrations at carbon nanoasperities

Toshihiko Fujimori (藤森&#x 5229;彦), Koki Urita (瓜田&#x 5E78;幾), David Tomanek, Tomonori Ohba (大場&#x 53CB;則), Isamu Moriguchi (森口&#x 52C7;) et al.
We introduce a way to selectively probe local vibration modes at nanostructured asperities such as tips of carbon nanohorns. Our observations benefit from signal amplification in surface-enhanced Raman scattering (SERS) at sites near a silver surface. We observe nanohorn tip vibration modes in the r ... [J. Chem. Phys. 136, 064505 (2012)] published Wed Feb 8, 2012.

Structure and properties of metal-exchanged zeolites studied using gradient-corrected and hybrid functionals. II. Electronic structure and photoluminescence spectra

Florian Goltl and Jurgen Hafner
The influence of the choice of the exchange-correlation functional (semilocal gradient corrected or hybrid functionals) on the electronic properties of metal-exchanged zeolites has been investigated for Cu- and Co-exchanged chabazite. The admixture of exact exchange in hybrid functionals increases t ... [J. Chem. Phys. 136, 064502 (2012)] published Wed Feb 8, 2012.

Mesoscopic analysis of Gibbs' criterion for sessile nanodroplets on trapezoidal substrates

F. Dutka, M. Napiorkowski, and S. Dietrich
By taking into account precursor films accompanying nanodroplets on trapezoidal substrates we show that on a mesoscopic level of description one does not observe the phenomenon of liquid-gas-substrate contact line pinning at substrate edges. This phenomenon is present in a macroscopic description an ... [J. Chem. Phys. 136, 064702 (2012)] published Wed Feb 8, 2012.

The role of surface defects in multi-exciton generation of lead selenide and silicon semiconductor quantum dots

Heather M. Jaeger, Sean Fischer, and Oleg V. Prezhdo
Multi-exciton generation (MEG), the creation of more than one electron-hole pair per photon absorbed, occurs for excitation energies greater than twice the bandgap (E). Imperfections on the surface of quantum dots, in the form of atomic vacancies or incomplete surface passivation, lead to less than ... [J. Chem. Phys. 136, 064701 (2012)] published Wed Feb 8, 2012.

The role of structure in the nonlinear mechanics of cross-linked semiflexible polymer networks

Nicholas Agung Kurniawan, Soren Enemark, and Raj Rajagopalan
The microstructural basis of the characteristic nonlinear mechanics of biopolymer networks remains unclear. We present a 3D network model of realistic, cross-linked semiflexible fibers to study strain-stiffening and the effect of fiber volume-occupancy. We identify two structural parameters, namely, ... [J. Chem. Phys. 136, 065101 (2012)] published Wed Feb 8, 2012.

Structure and properties of metal-exchanged zeolites studied using gradient-corrected and hybrid functionals. I. Structure and energetics

Florian Goltl and Jurgen Hafner
The structural and energetic properties of purely siliceous, proton-, and Cu- and Co-exchanged chabazite have been studied using periodic density-functional (DFT) calculations with both conventional gradient-corrected exchange-correlation functionals and hybrid functionals mixing exact (i.e., Hartre ... [J. Chem. Phys. 136, 064501 (2012)] published Wed Feb 8, 2012.

Revised self-consistent continuum solvation in electronic-structure calculations

Oliviero Andreussi, Ismaila Dabo, and Nicola Marzari
The solvation model proposed by Fattebert and Gygi [J. Comput. Chem. 23, 662 (2002)] and Scherlis et al. [J. Chem. Phys. 124, 074103 (2006)] is reformulated, overcoming some of the numerical limitations encountered and extending its range of applicability. We first recast the problem in terms of ind ... [J. Chem. Phys. 136, 064102 (2012)] published Wed Feb 8, 2012.

A model for codependent reversible/irreversible growth processes

Sagi Eppel
A model for codependent growth that combines reversible and irreversible bond formation is developed. The system is composed of two processes: A reversible process which is fast but does not lead to a stable growth by itself, while the irreversible process is stable but is too slow to occur by itsel ... [J. Chem. Phys. 136, 054705 (2012)] published Tue Feb 7, 2012.

Ultrafast resonance-enhanced multiphoton ionization in the azabenzenes: Pyridine, pyridazine, pyrimidine, and pyrazine

Timothy D. Scarborough, David B. Foote, and Cornelis J. G. J. Uiterwaal
We report on the ultrafast photoionization of pyridine, pyridazine, pyrimidine, and pyrazine. These four molecules represent a systematic series of perturbations into the structure of a benzene ring which explores the substitution of a CH entity with a nitrogen atom, creating a heterocyclic structur ... [J. Chem. Phys. 136, 054309 (2012)] published Tue Feb 7, 2012.

Quadrupole-bound anions: Efficacy of positive versus negative quadrupole moments

W. R. Garrett
A pseudopotential method is utilized to study the critical stability of model anions formed by long-range quadrupolar molecular potentials. Results indicate that critical quadrupole moments of simple point-charge triads do not serve well as predictors of real quadrupole-bound anions of systems with ... [J. Chem. Phys. 136, 054116 (2012)] published Tue Feb 7, 2012.

Search for a small hole in a cavity wall by intermittent bulk and surface diffusion

Alexander M. Berezhkovskii and Alexander V. Barzykin
We study the search of a small round hole in the wall of a spherical cavity by a diffusing particle, which can reversibly bind to the cavity wall and diffuse on the surface being in the bound state. There are two channels for the particle first passage to the hole, through the bulk, and through the ... [J. Chem. Phys. 136, 054115 (2012)] published Tue Feb 7, 2012.

Cold collisions of complex polyatomic molecules

Zhiying Li and Eric J. Heller
We introduce a method for classical trajectory calculations to simulate collisions between atoms and large rigid asymmetric-top molecules. We investigate the formation of molecule-helium complexes in buffer-gas cooling experiments at a temperature of 6.5 K for molecules as large as naphthalene. Our ... [J. Chem. Phys. 136, 054306 (2012)] published Mon Feb 6, 2012.

Conformational properties of macromolecular pyramoids and their potential use as nano-containers

M. Kosmas and P. Efthymiopoulos
We study the macroscopic behavior of a pyramid-like nano-construct made of linear macromolecular chains. The average mean square end-to-end distances of the six edges of the pyramoid are evaluated by means of the Gaussian chain model and are found smaller than those of free chains because of archite ... [J. Chem. Phys. 136, 054905 (2012)] published Mon Feb 6, 2012.

Formation of dodecagonal quasicrystals in two-dimensional systems of patchy particles

Marjolein N. van der Linden, Jonathan P. K. Doye, and Ard A. Louis
The behaviour of two-dimensional patchy particles with five and seven regularly arranged patches is investigated by computer simulation. For higher pressures and wider patch widths, hexagonal crystals have the lowest enthalpy, whereas at lower pressures and for narrower patches, lower density crysta ... [J. Chem. Phys. 136, 054904 (2012)] published Mon Feb 6, 2012.

Methyl group rotation, H spin-lattice relaxation in an organic solid, and the analysis of nonexponential relaxation

Peter A. Beckmann and Evan Schneider
We report H spin-lattice relaxation measurements in polycrystalline 4,4-dimethoxybiphenyl at temperatures between 80 and 300 K at NMR frequencies of omega/2pi = 8.50, 22.5, and 53.0 MHz. The data are interpreted in terms of the simplest possible Bloch-Wangsness-Redfield methyl group hopping model. D ... [J. Chem. Phys. 136, 054508 (2012)] published Mon Feb 6, 2012.

Effects of particles on stability of flow-induced precursors

Peng-Wei Zhu, Andrew W. Phillips, and Graham Edward
The effect of two colorant particles with different surface geometries on the stability of shear-induced precursors in isotactic polypropylene was studied after the cessation of shear flow at 140 degrees C. In the absence of particles, the shear-induced precursors survived for at least 100 s after ... [J. Chem. Phys. 136, 054903 (2012)] published Mon Feb 6, 2012.

Correlated intermolecular coupling fluctuations in photosynthetic complexes

Sebastiaan M. Vlaming and Robert J. Silbey
The functioning and efficiency of natural photosynthetic complexes is strongly influenced by their embedding in a noisy protein environment, which can even serve to enhance the transport efficiency. Interactions with the environment induce fluctuations of the transition energies and couplings betwee ... [J. Chem. Phys. 136, 055102 (2012)] published Mon Feb 6, 2012.

Mobility matrix of a spherical particle translating and rotating in a viscous fluid confined in a spherical cell, and the rate of escape from the cell

B. U. Felderhof and A. Sellier
The mobility matrix of a spherical particle moving in a spherical cavity, filled with a viscous incompressible fluid, and with no-slip boundary condition at the wall of the cavity, is evaluated from the Oseen tensor for the cavity by the method used by Lorentz for a particle near a planar wall. For ... [J. Chem. Phys. 136, 054703 (2012)] published Mon Feb 6, 2012.

Nonadiabatic dynamics of O(D) + N(XSigma)-->O(P) + N(XSigma) on three coupled potential surfaces: Symmetry, Coriolis, spin-orbit, and Renner-Teller effects

Paolo Defazio, Pablo Gamallo, and Carlo Petrongolo
We present the spin-orbit (SO) and Renner-Teller (RT) quantum dynamics of the spin-forbidden quenching O(D) + N(XSigma)-->O(P) + N(XSigma) on the NO X-tildeA, aA, and b-tildeA coupled PESs. We use the permutation-inversion symmetry, propagate coupled-channel (CC) real wavepackets, and compute initia ... [J. Chem. Phys. 136, 054308 (2012)] published Mon Feb 6, 2012.

Surface area controlled heterogeneous nucleation

Brian Steer, Boris Gorbunov, Jonathan Rowles, and David Green
Heterogeneous nucleation of liquid from a gas phase on nanoparticles has been studied under various saturation ratios and nuclei size. The probability of liquid droplet nucleation, especially at a low degree of deviation from equilibrium, was measured for both atmospheric aerosol particles and engin ... [J. Chem. Phys. 136, 054704 (2012)] published Mon Feb 6, 2012.

The electronic spectrum of the C-CH radical

Dongfeng Zhao (赵东锋), Harold Linnartz, and Wim Ubachs
The electronic gas-phase absorption spectrum of the bent carbon-chain radical, HCCHCH with C symmetry, is recorded in the 595 nm region by cavity ring-down spectroscopy through an expanding hydrogen plasma. An unambiguous spectroscopic identification becomes possible from a systematic deuterium labe ... [J. Chem. Phys. 136, 054307 (2012)] published Mon Feb 6, 2012.

Exploring the competition between localization and delocalization of the neutral soliton defect in polyenyl chains with the orbital optimized second order opposite spin method

Westin Kurlancheek, Rohini Lochan, Keith Lawler, and Martin Head-Gordon
Theory and implementation of the analytical nuclear gradient is presented for orbital optimized scaled opposite-spin perturbation theory (O2). Evaluation of the O2 analytical gradient scales with the 4th power of molecular size, like the O2 energy. Since the O2 method permits optimization of the orb ... [J. Chem. Phys. 136, 054113 (2012)] published Mon Feb 6, 2012.

Stochastic mapping of the Michaelis-Menten mechanism

Eva Doka and Gabor Lente
The Michaelis-Menten mechanism is an extremely important tool for understanding enzyme-catalyzed transformation of substrates into final products. In this work, a computationally viable, full stochastic description of the Michaelis-Menten kinetic scheme is introduced based on a stochastic equivalent ... [J. Chem. Phys. 136, 054111 (2012)] published Mon Feb 6, 2012.

Quasi-variational coupled cluster theory

James B. Robinson and Peter J. Knowles
We extend our previous work on the construction of new approximations of the variational coupled cluster method. By combining several linked pair functional transformations in such a way as to give appropriately balanced infinite-order contributions, in order to approximate well at all orders, we f ... [J. Chem. Phys. 136, 054114 (2012)] published Mon Feb 6, 2012.

The multi-configuration electron-nuclear dynamics method applied to LiH

Inga S. Ulusoy and Mathias Nest
The multi-configuration electron-nuclear dynamics (MCEND) method is a nonadiabatic quantum dynamics approach to the description of molecular processes. MCEND is a combination of the multi-configuration time-dependent Hartree (MCTDH) method for atoms and its antisymmetrized equivalent MCTDHF for elec ... [J. Chem. Phys. 136, 054112 (2012)] published Mon Feb 6, 2012.

The sign problem and population dynamics in the full configuration interaction quantum Monte Carlo method

J. S. Spencer, N. S. Blunt, and W. M.C. Foulkes
The recently proposed full configuration interaction quantum Monte Carlo method allows access to essentially exact ground-state energies of systems of interacting fermions substantially larger than previously tractable without knowledge of the nodal structure of the ground-state wave function. We in ... [J. Chem. Phys. 136, 054110 (2012)] published Mon Feb 6, 2012.

Trajectory-guided configuration interaction simulations of multidimensional quantum dynamics

Scott Habershon
We propose an approach to modelling multidimensional quantum systems which uses direct-dynamics trajectories to guide wavefunction propagation. First, trajectory simulations are used to generate a sample of dynamically relevant configurations on the potential energy surface (PES). Second, the sample ... [J. Chem. Phys. 136, 054109 (2012)] published Mon Feb 6, 2012.

Nonadiabatic excited-state molecular dynamics: Numerical tests of convergence and parameters

Tammie Nelson, Sebastian Fernandez-Alberti, Vladimir Chernyak, Adrian E. Roitberg, and Sergei Tretiak
Nonadiabatic molecular dynamics simulations, involving multiple Born-Oppenheimer potential energy surfaces, often require a large number of independent trajectories in order to achieve the desired convergence of the results, and simulation relies on different parameters that should be tested and com ... [J. Chem. Phys. 136, 054108 (2012)] published Fri Feb 3, 2012.

When does the non-variational nature of second-order Moller-Plesset energies manifest itself? All-electron correlation energies for open-shell atoms from K to Br

Shane P. McCarthy and Ajit J. Thakkar
All-electron correlation energies E are not very well known for open-shell atoms with more than 18 electrons. The complete basis-set (CBS) limits of second-order Moller-Plesset (MP2) perturbation theory energies are obtained for open-shell atoms by computations in large basis sets combined with a kn ... [J. Chem. Phys. 136, 054107 (2012)] published Fri Feb 3, 2012.

Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol

Jane R. Allison, Sereina Riniker, and Wilfred F. van Gunsteren
The time- and length-scale accessible to molecular dynamics simulations of biomolecular systems using atomic-level (AL) models is most limited by the calculation of the solvent-solvent interactions, which comprise the majority of the interactions and yet are seldom of specific interest. Coarse-grain ... [J. Chem. Phys. 136, 054505 (2012)] published Fri Feb 3, 2012.

Effect of dimensionality on the continuum percolation of overlapping hyperspheres and hypercubes

S. Torquato
We show analytically that the [0, 1], [1, 1], and [2, 1] Pade approximants of the mean cluster number S for both overlapping hyperspheres and overlapping oriented hypercubes are upper bounds on this quantity in any Euclidean dimension d. These results lead to lower bounds on the percolation threshol ... [J. Chem. Phys. 136, 054106 (2012)] published Fri Feb 3, 2012.

Competing effects of rare gas atoms in matrix isolation spectroscopy: A case study of vibrational shift of BeO in Xe and Ar matrices

Akira Nakayama, Keisuke Niimi, Yuriko Ono, and Tetsuya Taketsugu
We investigate the vibrational shift of beryllium oxide (BeO) in Xe matrix as well as in Ar matrix environments by mixed quantum-classical simulation and examine the origin of spectral shift in details. BeO is known to form strong chemical complex with single rare gas atom, and it is predicted from ... [J. Chem. Phys. 136, 054506 (2012)] published Fri Feb 3, 2012.

Structurally determined directionality identifies the boundary between mobile and immobile domains in a disordered material

Vanessa K. de Souza and Peter Harrowell
The structure and available degrees of freedom of an amorphous configuration can determine the location of dynamic heterogeneities. In the same way, these features can also determine the directionality of the particle motion. In this paper we propose that directionality can be attributed to those pa ... [J. Chem. Phys. 136, 054507 (2012)] published Fri Feb 3, 2012.

Angle-resolved metastable fragment yields spectra of N and CO in K-edge excitation energy region

Tatsuo Gejo, Takashi Tamura, Kenji Honma, Eiji Shigemasa, Yasumasa Hikosaka et al.
Angle-resolved metastable fragments yields spectra have been measured in the N 1s ionization region of the N and C 1s ionization region of CO. These spectra are compared with zero kinetic energy electron and photoelectron spectra. It has been shown that an isotropic metastable fragments yields spect ... [J. Chem. Phys. 136, 054201 (2012)] published Fri Feb 3, 2012.

Dispersion-corrected density functional theory calculations of the molecular binding of n-alkanes on Pd(111) and PdO(101)

Abbin Antony, Can Hakanoglu, Aravind Asthagiri, and Jason F. Weaver
We investigated the molecular binding of n-alkanes on Pd(111) and PdO(101) using conventional density functional theory (DFT) and the dispersion-corrected DFT-D3 method. In agreement with experimental findings, DFT-D3 predicts that the n-alkane desorption energies scale linearly with the molecule ch ... [J. Chem. Phys. 136, 054702 (2012)] published Fri Feb 3, 2012.

Iterative diagonalization in the state-averaged multi-configurational time-dependent Hartree approach: Excited state tunneling splittings in malonaldehyde

Thorsten Hammer and Uwe Manthe
An iterative block Lanczos-type diagonalization scheme utilizing the state-averaged multi-configurational time-dependent Hartree (MCTDH) approach is introduced. Combining propagation in real and imaginary time and using a set of initial seed wavefunctions corresponding to excitations via the differe ... [J. Chem. Phys. 136, 054105 (2012)] published Fri Feb 3, 2012.

Finite-difference time-domain simulation of light induced charge dynamics in silver nanoparticles

Zixuan Hu, Mark A. Ratner, and Tamar Seideman
We use a finite-difference time-domain (FDTD) approach to describe and control light-induced charge dynamics via two constructs consisting of nanoscale silver cylinders. The charge dynamics is found to be significantly different from the energy dynamics intensively studied in the past in similar sys ... [J. Chem. Phys. 136, 054504 (2012)] published Thu Feb 2, 2012.

Ultrafast ring opening in 1,3-cyclohexadiene investigated by simplex-based spectral unmixing

J. L. White, J. Kim, V. S. Petrovic, and P. H. Bucksbaum
We use spectral unmixing to determine the number of transient photoproducts and to track their evolution following the photo-excitation of 1,3-cyclohexadiene (CHD) to form 1,3,5-hexatriene (HT) in the gas phase. The ring opening is initiated with a 266 nm ultraviolet laser pulse and probed via fragm ... [J. Chem. Phys. 136, 054303 (2012)] published Thu Feb 2, 2012.

Coupled-cluster, Moller Plesset (MP2), density fitted local MP2, and density functional theory examination of the energetic and structural features of hydrophobic solvation: Water and pentane

Yasaman Ghadar and Aurora E. Clark
The interaction potentials between immiscible polar and non-polar solvents are a major driving force behind the formation of liquid:liquid interfaces. In this work, the interaction energy of waterpentane dimer has been determined using coupled-cluster theory with single double (triple) excitations [ ... [J. Chem. Phys. 136, 054305 (2012)] published Thu Feb 2, 2012.

Fitting properties from density functional theory based molecular dynamics simulations to parameterize a rigid water force field

Jonas Sala, Elvira Guardia, Jordi Marti, Daniel Spangberg, and Marco Masia
In the quest towards coarse-grained potentials and new water models, we present an extension of the force matching technique to parameterize an all-atom force field for rigid water. The methodology presented here allows to improve the matching procedure by first optimizing the weighting exponents pr ... [J. Chem. Phys. 136, 054103 (2012)] published Thu Feb 2, 2012.

Photoluminescence spectroscopy of pure pentacene, perfluoropentacene, and mixed thin films

F. Anger, J. O. Osso, U. Heinemeyer, K. Broch, R. Scholz et al.
We report detailed temperature dependent photoluminescence (PL) spectra of pentacene (PEN), perfluoropentacene (PFP), and PEN:PFP mixed thin films grown on SiO. PEN and PFP are particularly suitable for this study, since they are structurally compatible for good intermixing and form a model donor/ac ... [J. Chem. Phys. 136, 054701 (2012)] published Thu Feb 2, 2012.

Dressed adiabatic and diabatic potentials to study conical intersections for F + H

Anita Das, Tapas Sahoo, Debasis Mukhopadhyay, Satrajit Adhikari, and Michael Baer
We follow a suggestion by Lipoff and Herschbach [Mol. Phys. 108, 1133 (2010)] and compare dressed and bare adiabatic potentials to get insight regarding the low-energy dynamics (e.g., cold reaction) taking place in molecular systems. In this particular case, we are interested to study the effect of ... [J. Chem. Phys. 136, 054104 (2012)] published Thu Feb 2, 2012.

Nuclear signatures on the molecular harmonic emission and the attosecond pulse generation

Liqiang Feng and Tianshu Chu
In this paper, we theoretically investigate the nuclear signatures effects, i.e., the initial vibrational state and the isotopic effects on the generations of the molecular high-order harmonics and the attosecond pulses when the model H/D ions are exposed to a 5 fs/800 nm chirp pulse. The numerical ... [J. Chem. Phys. 136, 054102 (2012)] published Thu Feb 2, 2012.

Investigation of intermolecular interactions in perylene films on Au(111) by infrared spectroscopy

Li Ding, Philip Schulz, Azadeh Farahzadi, Kostiantyn V. Shportko, and Matthias Wuttig
Intermolecular interactions in crystalline perylene films on Au(111) have been investigated by Fourier transform infrared spectroscopy. Dimer modes of vibrations are observed in the crystalline film, in contrast to the monomer modes found for isolated perylene molecules. These dimers are formed via ... [J. Chem. Phys. 136, 054503 (2012)] published Thu Feb 2, 2012.

Dynamics of H + CO at E = 30 eV

Christopher Stopera, Buddhadev Maiti, Thomas V. Grimes, Patrick M. McLaurin, and Jorge A. Morales
The astrophysically relevant system H + CO (v = 0) --> H + CO (v) at E = 30 eV is studied with the simplest-level electron nuclear dynamics (SLEND) method. This investigation follows previous successful SLEND studies of H + H and H + N at E = 30 eV [J. Morales, A. Diz, E. Deumens, and Y. Ohrn, J. Ch ... [J. Chem. Phys. 136, 054304 (2012)] published Thu Feb 2, 2012.

Effect of the range of repulsions on the existence of a stable liquid phase

Ryan J. Larsen and Charles F. Zukoski
Experimental and theoretical results have established that the range of the attraction plays a critical role in determining whether a particle system exhibits a stable liquid phase. Changes to the range of the repulsions can similarly affect the existence of a stable liquid phase; however, these eff ... [J. Chem. Phys. 136, 054901 (2012)] published Wed Feb 1, 2012.

Low energy collisions of CN(XSigma) with He in magnetic fields

Eryin Feng, Xi Shao, Chunhua Yu, Chunyan Sun, and Wuying Huang
A theoretical investigation of the HeCN(Sigma) complex is presented. We perform ab initio calculations of the interaction potential energy surface and carry out accurate calculations of bound energy levels of the complex including the molecular fine structure. We find the potential has a shallow min ... [J. Chem. Phys. 136, 054302 (2012)] published Wed Feb 1, 2012.

Cage occupancies in the high pressure structure H methane hydrate: A neutron diffraction study

C. A. Tulk, D. D. Klug, A. M. dos Santos, G. Karotis, M. Guthrie et al.
A neutron diffraction study was performed on the CD : DO structure H clathrate hydrate to refine its CD fractional cage occupancies. Samples of ice VII and hexagonal (sH) methane hydrate were produced in a ParisEdinburgh press and in situ neutron diffraction data collected. The data were analyzed wi ... [J. Chem. Phys. 136, 054502 (2012)] published Wed Feb 1, 2012.

Non-equilibrium umbrella sampling applied to force spectroscopy of soft matter

Y. X. Gao, G. M. Wang, D. R. M. Williams, Stephen R. Williams, Denis J. Evans et al.
Physical systems often respond on a timescale which is longer than that of the measurement. This is particularly true in soft matter where direct experimental measurement, for example in force spectroscopy, drives the soft system out of equilibrium and provides a non-equilibrium measure. Here we dem ... [J. Chem. Phys. 136, 054902 (2012)] published Wed Feb 1, 2012.

Combined depletion and electrostatic forces in polymer-induced membrane adhesion: A theoretical model

Antonio Raudino, Martina Pannuzzo, and Mikko Karttunen
We develop a semi-quantitative analytical theory to describe adhesion between two identical planar charged surfaces embedded in a polymer-containing electrolyte solution. Polymer chains are uncharged and differ from the solvent by their lower dielectric permittivity. The solution mimics physiologica ... [J. Chem. Phys. 136, 055101 (2012)] published Wed Feb 1, 2012.

Free energy landscapes for homogeneous nucleation of ice for a monatomic water model

Aleks Reinhardt and Jonathan P. K. Doye
We simulate the homogeneous nucleation of ice from supercooled liquid water at 220 K in the isobaric-isothermal ensemble using the MW monatomic water potential. Monte Carlo simulations using umbrella sampling are performed in order to determine the nucleation free energy barrier. We find the Gibbs e ... [J. Chem. Phys. 136, 054501 (2012)] published Wed Feb 1, 2012.

Quantum locality and equilibrium properties in low-temperature parahydrogen: A multiscale simulation study

R. Potestio and L. Delle Site
Parahydrogen is the spin-zero singlet state of molecular hydrogen, which at low temperature (between 14 and 25 K) is in a fluid state. A classical treatment of the system leads to unphysical freezing, and the inclusion of quantum delocalization of the molecule is then required to obtain a realistic ... [J. Chem. Phys. 136, 054101 (2012)] published Wed Feb 1, 2012.

Mg impurity in helium droplets

J. Navarro, D. Mateo, M. Barranco, and A. Sarsa
Within the diffusion Monte Carlo approach, we have determined the structure of isotopically pure and mixed helium droplets doped with one magnesium atom. For pure He clusters, our results confirm those of Mella et al. [J. Chem. Phys. 123, 054328 (2005)] that the impurity experiences a transition fro ... [J. Chem. Phys. 136, 054301 (2012)] published Wed Feb 1, 2012.

Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA

David A. Sivak and Phillip L. Geissler
The wormlike chain model of DNA bending accurately reproduces single-molecule force-extension profiles of long (kilobase) chains. These bending statistics over large scales do not, however, establish a unique microscopic model for elasticity at the 110 basepair (bp) scale, which holds particular int ... [J. Chem. Phys. 136, 045102 (2012)] published Tue Jan 31, 2012.

Dynamics of fibers in a wide microchannel

Agnieszka M. Slowicka, Maria L. Ekiel-Jezewska, Krzysztof Sadlej, and Eligiusz Wajnryb
Dynamics of single flexible non-Brownian fibers, tumbling in a Poiseuille flow between two parallel solid plane walls, is studied with the use of the HYDROMULTIPOLE numerical code, based on the multipole expansion of the Stokes equations, corrected for lubrication. Fibers, which are closer to a wall ... [J. Chem. Phys. 136, 044904 (2012)] published Tue Jan 31, 2012.

Solution-phase photochemistry of a [FeFe]hydrogenase model compound: Evidence of photoinduced isomerisation

Rafal Kania, Pim W. J. M. Frederix, Joseph A. Wright, Rein V. Ulijn, Christopher J. Pickett et al.
The solution-phase photochemistry of the [FeFe] hydrogenase subsite model ([mu]-S(CH)S)Fe(CO)(PMe) has been studied using ultrafast time-resolved infrared spectroscopy supported by density functional theory calculations. In three different solvents, n-heptane, methanol, and acetonitrile, relaxation ... [J. Chem. Phys. 136, 044521 (2012)] published Tue Jan 31, 2012.

Melting and superheating of sI methane hydrate: Molecular dynamics study

Grigory S. Smirnov and Vladimir V. Stegailov
Melting and decay of the superheated sI methane structure are studied using molecular dynamics simulation. The melting curve is calculated by the direct coexistence simulations in a wide range of pressures up to 5000 bar for the SPC/E, TIP4P/2005 and TIP4P/Ice water models and the united-atom model ... [J. Chem. Phys. 136, 044523 (2012)] published Tue Jan 31, 2012.

Parallel density matrix propagation in spin dynamics simulations

Luke J. Edwards and Ilya Kuprov
Several methods for density matrix propagation in parallel computing environments are proposed and evaluated. It is demonstrated that the large communication overhead associated with each propagation step (two-sided multiplication of the density matrix by an exponential propagator and its conjugate) ... [J. Chem. Phys. 136, 044108 (2012)] published Tue Jan 31, 2012.

A laser-induced fluorescence study of the jet-cooled nitrous oxide cation (NO)

Mohammed A. Gharaibeh and Dennis J. Clouthier
Laser-induced fluorescence and wavelength resolved emission spectra of the A Sigma X-tilde Pi electronic transition of the jet-cooled nitrous oxide cation have been recorded. The ions were produced in a pulsed electric discharge at the exit of a supersonic expansion using a precursor mixture of NO ... [J. Chem. Phys. 136, 044318 (2012)] published Tue Jan 31, 2012.

High energy transmission of AlO doped with light transition metals

C. Schuster, J. Klimke, and U. Schwingenschlogl
The transmission of transparent colored ceramics based on AlO doped with light transition metals is measured in the visible and infrared range. To clarify the role of the dopands we perform ab initiocalculations. We discuss the electronic structure and present optical spectra obtained in the indepen ... [J. Chem. Phys. 136, 044522 (2012)] published Tue Jan 31, 2012.

Low-energy rotational inelastic collisions of H + CO system

T. J. Dhilip Kumar and Sanjay Kumar
The quantum mechanical state-to-state rotational excitation cross sections have been computed using the ab initio ground electronic state potential energy surface of the system [M. Mladenovic and S. Schmatz, J. Chem. Phys. 109, 4456 (1998)] computed at coupled-cluster single and double and triple pe ... [J. Chem. Phys. 136, 044317 (2012)] published Tue Jan 31, 2012.

A theoretical study of the CXN radicals (X = F, Cl, Br): The effect of halogen substitution on structure, isomerization, and energetics

Cristina Puzzarini
Structural isomers of the CXN radicals, where X = F, Cl, and Br, have been investigated at high level of theory, i.e., using the coupled-cluster method in conjunction with correlation-consistent basis sets ranging in size from triple- to sextuple-zeta. Extrapolation to the complete basis-set limit a ... [J. Chem. Phys. 136, 044316 (2012)] published Tue Jan 31, 2012.

Infrared absorption by collisional HHe complexes at temperatures up to 9000 K and frequencies from 0 to 20 000 cm

Martin Abel, Lothar Frommhold, Xiaoping Li, and Katharine L. C. Hunt
Quantum chemical methods have been used elsewhere to obtain the potential energy surface (PES) and the induced dipole surface (IDS) of HHe collisional complexes at eight different HH bond distances, fifteen atom-molecule separations, and 19 angular orientations each [X. Li, A. Mandal, E. Miliordos, ... [J. Chem. Phys. 136, 044319 (2012)] published Tue Jan 31, 2012.

Interaction-induced dipoles of hydrogen molecules colliding with helium atoms: A new ab initio dipole surface for high-temperature applications

Xiaoping Li, Anirban Mandal, Evangelos Miliordos, and Katharine L. C. Hunt
We report new ab initio results for the interaction-induced dipole moments Delta[mu] of hydrogen molecules colliding with helium atoms. These results are needed in order to calculate collision-induced absorption spectra at high temperatures; applications include modeling the radiative profiles of ve ... [J. Chem. Phys. 136, 044320 (2012)] published Tue Jan 31, 2012.

Robust interpolation between weak- and strong-correlation regimes of quantum systems

Jerzy Cioslowski
A robust interpolation between the weak- and strong-correlation regimes of quantum systems is presented. It affords approximants to the function E(omega) describing the dependence of the total energy (or other observable) on the coupling parameter omega that measures the correlation strength. The ap ... [J. Chem. Phys. 136, 044109 (2012)] published Tue Jan 31, 2012.

Transport properties of the rough hard sphere fluid

Olga Kravchenko and Mark Thachuk
Results are presented of a systematic study of the transport properties of the rough hard sphere fluid. The rough hard sphere fluid is a simple model consisting of spherical particles that exchange linear and angular momenta, and energy upon collision. This allows a study of the sole effect of parti ... [J. Chem. Phys. 136, 044520 (2012)] published Mon Jan 30, 2012.

Growth of a Pt film on non-reduced ceria: A density functional theory study

David Loffreda and Francoise Delbecq
The growth of platinum on non-reduced CeO (111) surface is studied by means of calculations based on the density functional theory. Particles of increasing size are formed on the oxide surface by incorporating the platinum atoms one by one until multilayer films are obtained. The main conclusion is ... [J. Chem. Phys. 136, 044705 (2012)] published Mon Jan 30, 2012.

Product angular distributions in the ultraviolet photodissociation of NO

George C. McBane and Reinhard Schinke
The angular distribution of products from the ultraviolet photodissociation of nitrous oxide yielding O(D) and N(X Sigma) was investigated using classical trajectory calculations. The calculations modeled absorption only to the 2 A electronic state but used surface-hopping techniques to model nonad ... [J. Chem. Phys. 136, 044314 (2012)] published Mon Jan 30, 2012.

Coherently controlled molecular junctions

Uri Peskin and Michael Galperin
Within a generic model, we discuss the possibility of coherent control of charge fluxes in unbiased molecular junctions. The control is induced by resonances between the Rabi frequency due to a pumping laser field and internal characteristic frequencies of pre-designed molecular donor-bridge-accepto ... [J. Chem. Phys. 136, 044107 (2012)] published Mon Jan 30, 2012.

The electric double layer structure around charged spherical interfaces

Zhenwei Yao, Mark J. Bowick, and Xu Ma
We derive a formally simple approximate analytical solution to the Poisson-Boltzmann equation for the spherical system via a geometric mapping. Its regime of applicability in the parameter space of the spherical radius and the surface potential is determined, and its superiority over the linearized ... [J. Chem. Phys. 136, 044106 (2012)] published Mon Jan 30, 2012.

Semiclassical glory analyses in the time domain for the H + D(v = 0, j = 0) --> HD(v = 3, j = 0) + D reaction

Xiao Shan and J. N. L. Connor
We make the first application of semiclassical (SC) techniques to the plane-wavepacket formulation of time-domain (T-domain) scattering. The angular scattering of the state-to-state reaction, H + D(v = 0, j = 0) --> HD(v = 3, j = 0) + D, is analysed, where v and j are vibrational and rotational quan ... [J. Chem. Phys. 136, 044315 (2012)] published Mon Jan 30, 2012.

Tungsten monocarbide, WC: Pure rotational spectrum and C hyperfine interaction

Fang Wang and Timothy C. Steimle
The J = 1 --> 2 pure rotational transitions in the XDelta(v = 0) state of WC and WC were recorded using a pump/probe microwave optical double resonance (PPMODR) technique and analyzed to give fine structure parameters. The field-free [17.6]2<-- XDelta (1, 0) bands of the WC isotopologues were record ... [J. Chem. Phys. 136, 044312 (2012)] published Mon Jan 30, 2012.

New view of the ICN A continuum using photoelectron spectroscopy of ICN

Elisa M. Miller, Leonid Sheps, Yu-Ju Lu, Amanda S. Case, Anne B. McCoy et al.
Negative-ion photoelectron spectroscopy of ICN (X-tilde Sigma) reveals transitions to the ground electronic state (X-tilde Sigma) of ICN as well as the first five excited states (Pi, Pi, Pi, Pi, and Pi) that make up the ICN A continuum. By starting from the equilibrium geometry of the anion, photo ... [J. Chem. Phys. 136, 044313 (2012)] published Mon Jan 30, 2012.