Journal of Chemical Physics: All Topics

Disparate product distributions observed in MoWO (x=03; y=39) reactions with DO and CO

David W. Rothgeb, Ekram Hossain, Jennifer E. Mann, and Caroline Chick Jarrold
Results of gas phase reactivity studies on group six transition metal suboxide clusters, MoO, MoWO, MoWO, and WO (MoWO, x=03; y=ca. 39) with both DO and CO are reported. Sequential oxidation for the more reduced species, MoWO+DO/CO-->MoWO+D/CO, and dissociative addition for certain species, MoWO+DO ... [J. Chem. Phys. 132, 064302 (2010)] published Tue Feb 9, 2010.

Parallel tempering Monte Carlo simulations of lysozyme orientation on charged surfaces

Yun Xie, Jian Zhou, and Shaoyi Jiang
In this work, the parallel tempering Monte Carlo (PTMC) algorithm is applied to accurately and efficiently identify the global-minimum-energy orientation of a protein adsorbed on a surface in a single simulation. When applying the PTMC method to simulate lysozyme orientation on charged surfaces, it ... [J. Chem. Phys. 132, 065101 (2010)] published Tue Feb 9, 2010.

Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories

John S. Perkyns, Gillian C. Lynch, Jesse J. Howard, and B. Montgomery Pettitt
Solvation forces dominate protein structure and dynamics. Integral equation theories allow a rapid and accurate evaluation of the effect of solvent around a complex solute, without the sampling issues associated with simulations of explicit solvent molecules. Advances in integral equation theories m ... [J. Chem. Phys. 132, 064106 (2010)] published Tue Feb 9, 2010.

Density functional theory study of the optical and electronic properties of oligomers based on phenyl-ethynyl units linked to triazole, thiadiazole, and oxadiazole rings to be used in molecular electronics

Andres Garzon, Jose M. Granadino-Roldan, Monica Moral, Gregorio Garcia, M. Paz Fernandez-Liencres et al.
In the present work, we have studied from a theoretical perspective the geometry and electronic properties of the series of related compounds 2,5-bis(phenylethynyl)-1,3,4-thiadiazole, 2,5-bis(phenylethynyl)-1,3,4-oxadiazole, and 2,5-bis(phenylethynyl)-1,2,4-triazole as candidates for electron-conduc ... [J. Chem. Phys. 132, 064901 (2010)] published Tue Feb 9, 2010.

A Chebychev propagator with iterative time ordering for explicitly time-dependent Hamiltonians

Mamadou Ndong, Hillel Tal-Ezer, Ronnie Kosloff, and Christiane P. Koch
A propagation method for time-dependent Schrodinger equations with an explicitly time-dependent Hamiltonian is developed where time ordering is achieved iteratively. The explicit time dependence of the time-dependent Schrodinger equation is rewritten as an inhomogeneous term. At each step of the ite ... [J. Chem. Phys. 132, 064105 (2010)] published Tue Feb 9, 2010.

Statistical model for small clusters transforming from one isomer to another

Xiao-Jing Han, Yin Wang, Zheng-Zhe Lin, Wenxian Zhang, Jun Zhuang et al.
Based on the fact that the kinetic energy of one atom in small cluster still obeys the Boltzmann distribution, a statistical model is developed to predict the time consumed by a small cluster transforming from one isomer to another and is tested by vast molecular dynamics simulations of C isomers tr ... [J. Chem. Phys. 132, 064103 (2010)] published Mon Feb 8, 2010.

Theoretical study for the reaction of CHCN with O(P)

Jingyu Sun, Yizhen Tang, Xiujuan Jia, Fang Wang, Hao Sun et al.
The low-lying triplet and singlet potential energy surfaces of the O(P)+CHCN reaction have been studied at the G3(MP2)//B3LYP/6-311+G(d,p) level. On the triplet surface, six kinds of pathways are revealed, namely, direct hydrogen abstraction, C-addition/elimination, N-addition/elimination, substitut ... [J. Chem. Phys. 132, 064301 (2010)] published Mon Feb 8, 2010.

On the linear response and scattering of an interacting molecule-metal system

David J. Masiello and George C. Schatz
A many-body Green's function approach to the microscopic theory of plasmon-enhanced spectroscopy is presented within the context of localized surface-plasmon resonance spectroscopy and applied to investigate the coupling between quantum-molecular and classical-plasmonic resonances in monolayer-coate ... [J. Chem. Phys. 132, 064102 (2010)] published Mon Feb 8, 2010.

Assessment of an analytical density matrix derived from a modified ColleSalvetti approach to the electron gas

Sebastien Ragot
The RagotCortona model of local correlation energy [S. Ragot and P. Cortona, J. Chem. Phys. 121, 7671 (2004)] revisits the initial approach of Colle and Salvetti [Theor. Chim. Acta 37, 329 (1975)] in order to reinstate the kinetic contribution T to the total correlation energy E. In this work, the o ... [J. Chem. Phys. 132, 064104 (2010)] published Mon Feb 8, 2010.

AQUASOL: An efficient solver for the dipolar PoissonBoltzmannLangevin equation

Patrice Koehl and Marc Delarue
The PoissonBoltzmann (PB) formalism is among the most popular approaches to modeling the solvation of molecules. It assumes a continuum model for water, leading to a dielectric permittivity that only depends on position in space. In contrast, the dipolar PoissonBoltzmannLangevin (DPBL) formalism rep ... [J. Chem. Phys. 132, 064101 (2010)] published Mon Feb 8, 2010.

Isomer identification and resolution in small gold clusters

Wei Huang, Rhitankar Pal, Lei-Ming Wang, Xiao Cheng Zeng, and Lai-Sheng Wang
A variety of experimental techniques are used to resolve energetically close isomers of Au and Au by combining photoelectron spectroscopy and ab initio calculations. Two structurally distinct isomers are confirmed to exist in the cluster beam for both clusters. Populations of the different isomers i ... [J. Chem. Phys. 132, 054305 (2010)] published Fri Feb 5, 2010.

Publisher's Note: An interpretation of the anomalous Pi vibronic structure in the far-UV spectrum of CO [J. Chem. Phys. 132, 024311 (2010)]

H. Lefebvre-Brion, H. P. Liebermann, and G. J. Vazquez
Abstract not available. [J. Chem. Phys. 132, 059902 (2010)] published Fri Feb 5, 2010.

Translational and rotational friction on a colloidal rod near a wall

J. T. Padding and W. J. Briels
We present particulate simulation results for translational and rotational friction components of a shish-kebab model of a colloidal rod with aspect ratio (length over diameter) L/D=10 in the presence of a planar hard wall. Hydrodynamic interactions between rod and wall cause an overall enhancement ... [J. Chem. Phys. 132, 054511 (2010)] published Fri Feb 5, 2010.

Electric potential and bending rigidity of a wormlike particle in electrolyte solution

V. A. Andreev and A. I. Victorov
Using the linearized PoissonBoltzmann equation (LPB) we derive an asymptotic expansion for the electrostatic potential of charged torus immersed in solution of an electrolyte in the limit of high salinity and large major radius of the torus. The small parameter of this expansion is the ratio of the ... [J. Chem. Phys. 132, 054902 (2010)] published Fri Feb 5, 2010.

Critical behavior of interacting monomers adsorbed on one-dimensional channels arranged in a triangular cross-sectional structure: Mixed interactions along and across the channels

P. M. Pasinetti, F. Roma, J. L. Riccardo, and A. J. Ramirez-Pastor
Monte Carlo simulations and finite-size scaling analysis have been carried out to study the critical behavior in a submonolayer lattice-gas which mimics a nanoporous environment. In this model, the adsorbent is modeled as one-dimensional channels of equivalent adsorption sites arranged in a triangul ... [J. Chem. Phys. 132, 054111 (2010)] published Fri Feb 5, 2010.

Indistinguishability and interference in the coherent control of atomic and molecular processes

Jiangbin Gong and Paul Brumer
The subtle and fundamental issue of indistinguishability and interference between independent pathways to the same target state is examined in the context of coherent control of atomic and molecular processes, with emphasis placed on possible which-way information due to quantum entanglement establi ... [J. Chem. Phys. 132, 054306 (2010)] published Fri Feb 5, 2010.

Overcharging and charge reversal in the electrical double layer around the point of zero charge

G. Ivan Guerrero-Garcia, Enrique Gonzalez-Tovar, Martin Chavez-Paez, and Marcelo Lozada-Cassou
The ionic adsorption around a weakly charged spherical colloid, immersed in size-asymmetric 1:1 and 2:2 salts, is studied. We use the primitive model (PM) of an electrolyte to perform Monte Carlo simulations as well as theoretical calculations by means of the hypernetted chain/mean spherical approxi ... [J. Chem. Phys. 132, 054903 (2010)] published Fri Feb 5, 2010.

B3LYP calculations of cerium oxides

Jolla Kullgren, Christopher W. M. Castleton, Carsten Muller, David Munoz Ramo, and Kersti Hermansson
In this paper we evaluate the performance of density functional theory with the B3LYP functional for calculations on ceria (CeO) and cerium sesquioxide (CeO). We demonstrate that B3LYP is able to describe CeO and CeO reasonably well. When compared to other functionals, B3LYP performs slightly better ... [J. Chem. Phys. 132, 054110 (2010)] published Fri Feb 5, 2010.

Two-bath model for activated surface diffusion of interacting adsorbates

R. Martinez-Casado, A. S. Sanz, G. Rojas-Lorenzo, and S. Miret-Artes
The diffusion and low vibrational motions of adsorbates on surfaces can be well described by a purely stochastic model, the so-called interacting single adsorbate model, for low-moderate coverages (theta<~0.12). Within this model, the effects of thermal surface phonons and adsorbate-adsorbate collis ... [J. Chem. Phys. 132, 054704 (2010)] published Thu Feb 4, 2010.

Reinvestigation of the Rb (2)Pia Sigma band on helium nanodroplets

G. Aubock, M. Aymar, O. Dulieu, and W. E. Ernst
It is well known that alkali-metal molecules are preferentially observed in the weak van der Waals-bound high spin states by helium droplet isolation spectroscopy. In [F. R. Bruhl et al., J. Chem. Phys. 115, 10275 (2001)] the Rb (2)Pia Sigma band on He droplets was investigated by laser-induced fluo ... [J. Chem. Phys. 132, 054304 (2010)] published Thu Feb 4, 2010.

Radiation chemistry in ammonia-water ices

M. J. Loeffler, U. Raut, and R. A. Baragiola
We studied the effects of 100 keV proton irradiation on films of ammonia-water mixtures between 20 and 120 K. Irradiation destroys ammonia, leading to the formation and trapping of H, N, NO, and NO, the formation of cavities containing radiolytic gases, and ejection of molecules by sputtering. Using ... [J. Chem. Phys. 132, 054508 (2010)] published Thu Feb 4, 2010.

Proton disorder and the dielectric constant of type II clathrate hydrates

Steven W. Rick and David L. Freeman
Computational studies are presented examining the degree of proton disorder in argon and molecular hydrogen sII clathrate hydrates. Results are presented using a variety of model potentials for the dielectric constant, the proton order parameter, and the molecular volume for the clathrate systems. T ... [J. Chem. Phys. 132, 054509 (2010)] published Thu Feb 4, 2010.

Accelerating self-consistent field convergence with the augmented RoothaanHall energy function

Xiangqian Hu and Weitao Yang
Based on Pulay's direct inversion iterative subspace (DIIS) approach, we present a method to accelerate self-consistent field (SCF) convergence. In this method, the quadratic augmented RoothaanHall (ARH) energy function, proposed recently by Host and co-workers [J. Chem. Phys. 129, 124106 (2008)], i ... [J. Chem. Phys. 132, 054109 (2010)] published Thu Feb 4, 2010.

The single donator-single acceptor hydrogen bonding structure in water probed by Raman spectroscopy

Qiang Sun
In this work, the Raman spectra of aqueous CE solutions are recorded and utilized to demonstrate the existence of single donator-single acceptor (DA) hydrogen bonding in water. From Raman OH stretching bands of aqueous CE solutions, the relative intensity of 3430 cm subband increases with CE concen ... [J. Chem. Phys. 132, 054507 (2010)] published Thu Feb 4, 2010.

A mean field approach for computing solid-liquid surface tension for nanoscale interfaces

Chi-cheng Chiu, R. J. K. Udayana Ranatunga, David Torres Flores, D. Vladimir Perez, Preston B. Moore et al.
The physical properties of a liquid in contact with a solid are largely determined by the solid-liquid surface tension. This is especially true for nanoscale systems with high surface area to volume ratios. While experimental techniques can only measure surface tension indirectly for nanoscale syste ... [J. Chem. Phys. 132, 054706 (2010)] published Thu Feb 4, 2010.

Methane dissociation and adsorption on Ni(111), Pt(111), Ni(100), Pt(100), and Pt(110)-(1 x 2): Energetic study

Sven Nave, Ashwani Kumar Tiwari, and Bret Jackson
We use density functional theory to examine 24 transition states for methane dissociation on five different metal surfaces. In our calculations, the nonlocal exchange-correlation effects are treated within the generalized gradient approximation using the PerdewBurkeErnzerhof functional. In all cases ... [J. Chem. Phys. 132, 054705 (2010)] published Thu Feb 4, 2010.

Generic behavior of the hydrodynamic function of charged colloidal suspensions

Jacek Gapinski, Adam Patkowski, and Gerhard Nagele
We discuss the generic behavior of the hydrodynamic function H(q) and diffusion function D(q) characterizing the short-time diffusion in suspensions of charge-stabilized colloidal spheres, by covering the whole fluid regime. Special focus is given to the behavior of these functions at the freezing t ... [J. Chem. Phys. 132, 054510 (2010)] published Thu Feb 4, 2010.

Correlation consistent basis sets for molecular core-valence effects with explicitly correlated wave functions: The atoms BNe and AlAr

J. Grant Hill, Shivnath Mazumder, and Kirk A. Peterson
Correlation consistent basis sets have been optimized for accurately describing core-core and core-valence correlation effects with explicitly correlated F12 methods. The new sets, denoted cc-pCVnZ-F12 (n=D, T, Q) and aug-cc-pCVnZ (n=D, T, Q, 5), were developed by augmenting the cc-pVnZ-F12 and aug- ... [J. Chem. Phys. 132, 054108 (2010)] published Thu Feb 4, 2010.

Reactions of ruthenium and rhodium atoms with carbon monoxide and dinitrogen mixtures: A combined experimental and theoretical study

Ling Jiang, Zhang-Hui Lu, and Qiang Xu
Laser-ablated Ru and Rh atoms react with CO and N mixture in excess neon to produce the carbonylmetal dinitrogen complexes, (NN)MCO (M=Ru,Rh; n=1,2) and NNRu(CO), as well as metal carbonyls and dinitrogen complexes. These carbonylmetal dinitrogen complexes are characterized using infrared spectrosc ... [J. Chem. Phys. 132, 054504 (2010)] published Wed Feb 3, 2010.

Carrier transport simulation in a model liquid crystalline system with the biaxial GayBerne potential

Masanao Goto, Hideo Takezoe, and Ken Ishikawa
In this paper, we performed carrier transport simulation to understand the unusual temperature dependence of the carrier mobility observed in nematic liquid crystals. For this purpose, we made a model liquid crystalline system consisting of biaxial GayBerne particles, and then we simulated hopping t ... [J. Chem. Phys. 132, 054506 (2010)] published Wed Feb 3, 2010.

Excited states of PbF: A four-component relativistic study

Shigeyoshi Yamamoto and Hiroshi Tatewaki
The electronic states of lead monofluoride (PbF) are studied from the (Pb 6s) (F 2p-pi) (F 2p-sigma) (Pb 6p-pi) X ground state up to the F state, using the four-component relativistic configuration interaction and Fock-space coupled-cluster singles and doubles methods. Difficulties arising from ... [J. Chem. Phys. 132, 054303 (2010)] published Wed Feb 3, 2010.

Retardation effects breaking long-range orientational ordering in dipolar fluids

Gunnar Karlstrom and Per Linse
A strongly coupled dipolar fluid confined in a sphere has been examined by Monte Carlo simulations using a modified distance-dependent pair interaction to emulate retardation effects. The effective dipole-dipole interaction and a property closely related to Kirkwood's g-factor have been analyzed for ... [J. Chem. Phys. 132, 054505 (2010)] published Wed Feb 3, 2010.

Theoretical study of the bonding in M-RG complexes and the transport of M through rare gas (M=Ca, Sr, and Ra; n=1 and 2; and RG=HeRn)

Adrian M. Gardner, Carolyn D. Withers, Timothy G. Wright, Kimberly I. Kaplan, Chivone Y. N. Chapman et al.
We present high level ab initio potential energy curves for the M-RG complexes, where n=1 and 2; RG=HeRn; and M=Ca, Sr, and Ra. Spectroscopic constants have been derived from these potentials and are compared with a wide range of experimental and previous theoretical data, and good agreement is gene ... [J. Chem. Phys. 132, 054302 (2010)] published Wed Feb 3, 2010.

The longitudinal optic-like mode in molten alkali halides: A molecular dynamics approximation to inelastic x-ray scattering experiments

O. Alcaraz and J. Trullas
The contribution of the long-wavelength fluctuations in the particle number, mass, and charge densities to the inelastic x-ray scattering dynamical structure factor for molten NaI and other molten alkali halides is accurately analyzed in the high frequencies region of the longitudinal optic-like mod ... [J. Chem. Phys. 132, 054503 (2010)] published Tue Feb 2, 2010.

Method and basis set dependence of anharmonic ground state nuclear wave functions and zero-point energies: Application to SSSH

Stephen J. Kolmann and Meredith J. T. Jordan
One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy sur ... [J. Chem. Phys. 132, 054105 (2010)] published Tue Feb 2, 2010.

The weighted ensemble path sampling method is statistically exact for a broad class of stochastic processes and binning procedures

Bin W. Zhang, David Jasnow, and Daniel M. Zuckerman
The weighted ensemble method, introduced by Huber and Kim [Biophys. J. 70, 97 (1996)], is one of a handful of rigorous approaches to path sampling of rare events. Expanding earlier discussions, we show that the technique is statistically exact for a wide class of Markovian and non-Markovian dynamics ... [J. Chem. Phys. 132, 054107 (2010)] published Tue Feb 2, 2010.

Hyperfine interaction and Stark effect in the b Pi-X [summation](0,0) band of copper monofluoride, CuF

Fang Wang and Timothy C. Steimle
The low-rotational levels of the b Pi-X [summation](0,0) band of copper monofluoride, CuF, were recorded field free and in the presence of a static electric field. The field-free spectrum was analyzed to produce a refined set of fine and hyperfine parameters for the b Pi(v=0) state. The permanent el ... [J. Chem. Phys. 132, 054301 (2010)] published Tue Feb 2, 2010.

Short-time Fourier transform analysis of real-time time-dependent HartreeFock and time-dependent density functional theory calculations with Gaussian basis functions

Tomoko Akama and Hiromi Nakai
We propose a novel analysis of real-time (RT) time-dependent HartreeFock and time-dependent density functional theory (TDHF/TDDFT) calculations using a short-time Fourier transform (STFT) technique. RT-TDHF/TDDFT calculations of model dimers were carried out and analyzed using the STFT technique, in ... [J. Chem. Phys. 132, 054104 (2010)] published Tue Feb 2, 2010.

Circumstantial evidence in support of bivelocity hydrodynamic theory for mixtures

Howard Brenner
Based upon findings with respect to the viability of the expression j=rhoD[del]v-hat hypothesized to represent the constitutive equation for the diffusive volume flux in ideal binary mixtures (rho=mass density, v-hat =1/rho=specific volume, and D=volume diffusion coefficient), implicit evidence is o ... [J. Chem. Phys. 132, 054106 (2010)] published Tue Feb 2, 2010.

Simulation of pseudopolyrotaxane formation and orientational order between pseudopolyrotaxanes

Naohito Urakami, Junko Imada, and Takashi Yamamoto
We have performed Brownian dynamics simulations in order to investigate the formation of a pseudopolyrotaxane (PPRX) with cyclodextrins (CDs) and a polymer chain and the development of orientational order between PPRXs. The coarse-grained model is used to model the CDs and the polymer chain. In our ... [J. Chem. Phys. 132, 054901 (2010)] published Tue Feb 2, 2010.

Modeling the solid-liquid phase transition in saturated triglycerides

David A. Pink, Charles B. Hanna, Christophe Sandt, Adam J. MacDonald, Ronald MacEachern et al.
We investigated theoretically two competing published scenarios for the melting transition of the triglyceride trilaurin (TL): those of (1) Corkery et al. [Langmuir 23, 7241 (2007)], in which the average state of each TL molecule in the liquid phase is a discotic Y conformer whose three chains are d ... [J. Chem. Phys. 132, 054502 (2010)] published Tue Feb 2, 2010.

Communications: Infrared spectroscopy of gas phase CH ions: The cyclopropenyl and propargyl cations

Allen M. Ricks, Gary E. Douberly, Paul v. R. Schleyer, and Michael A. Duncan
CH ions produced with a pulsed discharge source and cooled in a supersonic beam are studied with infrared laser photodissociation spectroscopy in the 8004000 cm region using the rare gas tagging method. Vibrational bands in the CH stretching and fingerprint regions confirm the presence of both the ... [J. Chem. Phys. 132, 051101 (2010)] published Tue Feb 2, 2010.

Publisher's Note: Accurate description of phase diagram of clathrate hydrates at the molecular level [J. Chem. Phys. 131, 244510 (2009)]

Rodion V. Belosludov, Oleg S. Subbotin, Hiroshi Mizuseki, Yoshiyuki Kawazoe, and Vladimir R. Belosludov
Abstract not available. [J. Chem. Phys. 132, 059901 (2010)] published Mon Feb 1, 2010.

Variational geminal-augmented multireference self-consistent field theory: Two-electron systems

Sergey A. Varganov and Todd J. Martinez
We introduce a geminal-augmented multiconfigurational self-consistent field method for describing electron correlation effects. The approach is based on variational optimization of a MCSCF-type wave function augmented by a single geminal. This wave function is able to account for some dynamic correl ... [J. Chem. Phys. 132, 054103 (2010)] published Mon Feb 1, 2010.

First-principles study of ultrathin (2 x 2) Gd nanowires encapsulated in carbon nanotubes

Jae-Hyeon Parq, Jaejun Yu, and Gunn Kim
Using density-functional calculations, we investigate the structural and magnetic properties of ultrathin Gd and Gd-carbide nanowires (NWs) encapsulated in narrow carbon nanotubes (CNTs). The equilibrium geometry of an encapsulated (2 x 2) Gd-NW is markedly different from that of bulk Gd crystals. T ... [J. Chem. Phys. 132, 054701 (2010)] published Mon Feb 1, 2010.

Fluid epitaxialization effect on velocity dependence of dynamic contact angle in molecular scale

Takahiro Ito, Yosuke Hirata, and Yutaka Kukita
Molecular dynamics simulations were used to investigate the effect of epitaxial ordering of the fluid molecules on the microscopic dynamic contact angle. The simulations were performed in a Couette-flow-like geometry where two immiscible fluids were confined between two parallel walls moving in oppo ... [J. Chem. Phys. 132, 054702 (2010)] published Mon Feb 1, 2010.

Relativistic quantum Monte Carlo method using zeroth-order regular approximation Hamiltonian

Yutaka Nakatsuka, Takahito Nakajima, Maho Nakata, and Kimihiko Hirao
We propose a new relativistic treatment in the quantum Monte Carlo (QMC) technique using the zeroth-order regular approximation (ZORA) Hamiltonian. The novel ZORA local energy is derived, and its availability is examined with some variational Monte Carlo calculations. We optimize the wave functions ... [J. Chem. Phys. 132, 054102 (2010)] published Mon Feb 1, 2010.

Anomalous nonlinear response of glassy liquids: General arguments and a mode-coupling approach

Marco Tarzia, Giulio Biroli, Alexandre Lefevre, and Jean-Philippe Bouchaud
We study theoretically the nonlinear response properties of glass formers. We establish several general results, which together with the assumption of time-temperature superposition, lead to a relation between the nonlinear response and the derivative of the linear response with respect to temperatu ... [J. Chem. Phys. 132, 054501 (2010)] published Mon Feb 1, 2010.

Spin filter effect of manganese phthalocyanine contacted with single-walled carbon nanotube electrodes

Xin Shen, Lili Sun, Enrico Benassi, Ziyong Shen, Xingyu Zhao et al.
We present a theoretical study of the spin transport through a manganese phthalocyanine (MnPc) molecule sandwiched between two semi-infinite armchair single-walled carbon nanotube (SWCNT) electrodes. Ab initio modeling is performed by combing the nonequilibrium Green's function formalism with spin d ... [J. Chem. Phys. 132, 054703 (2010)] published Mon Feb 1, 2010.

Interpolation schemes for peptide rearrangements

Marianne S. Bauer, Birgit Strodel, Szilard N. Fejer, Elena F. Koslover, and David J. Wales
A variety of methods (in total seven) comprising different combinations of internal and Cartesian coordinates are tested for interpolation and alignment in connection attempts for polypeptide rearrangements. We consider Cartesian coordinates, the internal coordinates used in CHARMM, and natural inte ... [J. Chem. Phys. 132, 054101 (2010)] published Mon Feb 1, 2010.

FokkerPlanck analysis of separation dependent potentials and diffusion coefficients in simulated microscopy experiments

Daniel J. Beltran-Villegas, Ray M. Sehgal, Dimitrios Maroudas, David M. Ford, and Michael A. Bevan
Total internal reflection microscopy (TIRM) and video microscopy (VM) are methods for nonintrusively measuring weak colloidal interactions important to many existing and emerging applications. Existing analyses of TIRM measured single particle trajectories can be used to extract particle-surface pot ... [J. Chem. Phys. 132, 044707 (2010)] published Fri Jan 29, 2010.

Brownian particles in an external field: Asymptotic distribution functions and mean square displacement

Leonardo Ferrari
A simple procedure is proposed by which the long-time form of the distribution of large (or heavy) ions in a fluid, in a time-varying electric field, is obtained as asymptotic solution of the FokkerPlanck (or KleinKramers) equation. In this way, it is shown that, when the initial ion distribution is ... [J. Chem. Phys. 132, 044907 (2010)] published Fri Jan 29, 2010.

An investigation of collisional processes in a Dicke narrowed transition of water vapor in the 7.8 [mu]m spectral region by frequency down-chirped quantum cascade laser spectroscopy

Nicola Tasinato, Geoffrey Duxbury, Nigel Langford, and Kenneth G. Hay
Information about intermolecular potentials is usually obtained through the analysis of the absorption line shapes recorded in the frequency domain. This approach is also adopted to study the effects of motional narrowing and speed dependence of the pressure broadening coefficients. On the other han ... [J. Chem. Phys. 132, 044316 (2010)] published Fri Jan 29, 2010.

A Monte Carlo algorithm for computing spin echo small angle neutron scattering correlation functions in real space: Hard sphere liquids

Chwen-Yang Shew and Wei-Ren Chen
A Monte Carlo algorithm is developed to compute the autocorrelation function of liquids and the corresponding spatial correlation function from spin echo small angle neutron scattering (SESANS) spectra. The accuracy of the simulation algorithm is tested with isolated hard spheres and single dumbbell ... [J. Chem. Phys. 132, 044906 (2010)] published Fri Jan 29, 2010.

Communications: Comparison of activation barriers for the JohariGoldstein and alpha relaxations and its implications

Martin Goldstein
The range of activation barrier heights for the JohariGoldstein (JG) relaxation in glasses is shown to overlap the range for the main (alpha) relaxation, but to be on the average somewhat lower. This suggests the JG relaxation, like the alpha, involve transitions between megabasins in the energy lan ... [J. Chem. Phys. 132, 041104 (2010)] published Fri Jan 29, 2010.

An intrinsic formation mechanism for midgap electronic states in semiconductor glasses

Andriy Zhugayevych and Vassiliy Lubchenko
We argue that semiconducting quenched liquids and frozen glasses may exhibit a set of peculiar electronic states of topological origin. These states reside at strained regions arising during structural reconfigurations between distinct aperiodic states intrinsic to quenched melts. The strained regio ... [J. Chem. Phys. 132, 044508 (2010)] published Thu Jan 28, 2010.

The weak covalent bond in NgAuF (Ng=Ar, Kr, Xe): A challenge for subsystem density functional theory

S. Maya Beyhan, Andreas W. Gotz, Christoph R. Jacob, and Lucas Visscher
We have assessed the accuracy of a representative set of currently available approximate kinetic-energy functionals used within the frozen-density embedding scheme for the NgAuF (Ng=Ar, Kr, Xe) molecules, which we partitioned into a Ng and a AuF subsystem. Although it is weak, there is a covalent in ... [J. Chem. Phys. 132, 044114 (2010)] published Thu Jan 28, 2010.

Nonadiabatic couplings in the collisional removal of O(b Sigma,v) by O

F. Dayou, M. I. Hernandez, J. Campos-Martinez, and R. Hernandez-Lamoneda
The effect of nonadiabatic couplings on the collisional removal of O(b Sigma,v) by O(X Sigma, v=0) is investigated. Two-dimensional adiabatic and quasidiabatic potential energy surfaces for the excited dimer states and the corresponding nonadiabatic radial couplings have been computed by means of a ... [J. Chem. Phys. 132, 044313 (2010)] published Thu Jan 28, 2010.

Interactions of graphene sheets deduced from properties of polycyclic aromatic hydrocarbons

Rafal Podeszwa
Intermolecular interactions of coronene dimer were studied with symmetry-adapted perturbation theory based on the density functional theory description of the monomers [SAPT(DFT)]. The most stable stacked structure was found to have the interaction energy of 17.45 kcal/mol, slightly lower than the s ... [J. Chem. Phys. 132, 044704 (2010)] published Thu Jan 28, 2010.

Optical to ultraviolet spectra of sandwiches of benzene and transition metal atoms: Time dependent density functional theory and many-body calculations

J. I. Martinez, J. M. Garcia-Lastra, M. J. Lopez, and J. A. Alonso
The optical spectra of sandwich clusters formed by transition metal atoms (titanium, vanadium, and chromium) intercalated between parallel benzene molecules have been studied by time-dependent density functional theory (TDDFT) and many-body perturbation theory. Sandwiches with different number of la ... [J. Chem. Phys. 132, 044314 (2010)] published Thu Jan 28, 2010.

Enhancement and de-enhancement effects in vibrational resonance Raman optical activity

Sandra Luber, Johannes Neugebauer, and Markus Reiher
In this study, we investigate interference between several excited electronic states in resonance enhanced vibrational Raman optical activity (RROA) spectra. A gradient FranckCondon model for the excited-state potential energy surface is applied in order to include vibronic effects in the descriptio ... [J. Chem. Phys. 132, 044113 (2010)] published Thu Jan 28, 2010.

Impact of ligands on CO adsorption in metal-organic frameworks: First principles study of the interaction of CO with functionalized benzenes. II. Effect of polar and acidic substituents

Antonio Torrisi, Caroline Mellot-Draznieks, and Robert G. Bell
Intermolecular interactions between the CO molecule and a range of functionalized aromatic molecules have been investigated using density functional theory. The work is directed toward the design of linker molecules which could form part of new metal-organic framework materials with enhanced affinit ... [J. Chem. Phys. 132, 044705 (2010)] published Thu Jan 28, 2010.

Nucleation theory with delayed interactions: An application to the early stages of the receptor-mediated adhesion/fusion kinetics of lipid vesicles

Antonio Raudino and Martina Pannuzzo
A semiquantitative theory aimed to describe the adhesion kinetics between soft objects, such as living cells or vesicles, has been developed. When rigid bodies are considered, the adhesion kinetics is successfully described by the classical Derjaguin, Landau, Verwey, and Overbeek (DLVO) picture, whe ... [J. Chem. Phys. 132, 045103 (2010)] published Thu Jan 28, 2010.

CO-promoted formation of the alkali-oxygen bond on Ni(111)

A. Politano, A. R. Marino, and G. Chiarello
High-resolution electron energy loss spectroscopy was used to study the coadsorption of alkali metals (Na, K) and oxygen on clean and CO-modified Ni(111) surfaces. We unambiguously show that on an alkali-precovered surface, the alkali-O bond was not formed upon O exposure. On the contrary, the alkal ... [J. Chem. Phys. 132, 044706 (2010)] published Thu Jan 28, 2010.

Halogen and hydrogen bonding to the Br atom in complexes of FBr

Sean A. C. McDowell
A computational study predicts a number of stable, unusual halogen- and hydrogen-bonded complexes involving FBr, NCH, and FH. Starting from the linear halogen-bonded FBr[centered ellipsis]NCH dimer, increasingly more stable complexes are obtained by the successive hydrogen bonding of one to three FH ... [J. Chem. Phys. 132, 044312 (2010)] published Thu Jan 28, 2010.

Dynamical heterogeneity in lattice glass models

Richard K. Darst, David R. Reichman, and Giulio Biroli
In this paper, we consider in detail the properties of dynamical heterogeneity in lattice glass models (LGMs). LGMs are lattice models whose dynamical rules are based on thermodynamic, as opposed to purely kinetic, considerations. We devise a LGM that is not prone to crystallization and displays pro ... [J. Chem. Phys. 132, 044510 (2010)] published Thu Jan 28, 2010.

Erratum: Classical theory for the in-plane scattering of atoms from corrugated surfaces: Application to the ArAg(111) system [J. Chem. Phys. 130, 194710 (2009)]

Eli Pollak and Salvador Miret-Artes
Abstract not available. [J. Chem. Phys. 132, 049901 (2010)] published Thu Jan 28, 2010.

Statistical analysis of time resolved single molecule fluorescence data without time binning

G. Hinze and T. Basche
We depict two algorithms to calculate correlation functions from two different time resolved single molecule fluorescence experiments without the need of time binning. Our first procedure allows to calculate the reduced linear dichroism from polarization resolved fluorescence data. Since we process ... [J. Chem. Phys. 132, 044509 (2010)] published Thu Jan 28, 2010.

Spectroscopic measurements of SO line parameters in the 9.2 [mu]m atmospheric region and theoretical determination of self-broadening coefficients

Nicola Tasinato, Andrea Pietropolli Charmet, Paolo Stoppa, Santi Giorgianni, and Giovanni Buffa
Sulfur dioxide is still the subject of numerous spectroscopic studies since it plays an active role in the chemistry of Earth's atmosphere and it is a molecule of proven astrophysical importance. In the present work we have determined the self-broadening and integrated absorption coefficients for se ... [J. Chem. Phys. 132, 044315 (2010)] published Thu Jan 28, 2010.

Communications: Survival of the fittest: Accelerating convergence in full configuration-interaction quantum Monte Carlo

Deidre Cleland, George H. Booth, and Ali Alavi
We provide a very simple adaptation of our recently published quantum Monte Carlo algorithm in full configuration-interaction (Slater determinant) spaces which dramatically reduces the number of walkers required to achieve convergence. A survival criterion is imposed for newly spawned walkers. We de ... [J. Chem. Phys. 132, 041103 (2010)] published Thu Jan 28, 2010.

Coupling of twist and writhe in short DNA loops

Shlomi Medalion, Shay M. Rappaport, and Yitzhak Rabin
While bending and twist can be treated as independent degrees of freedom for linear DNA molecules, the loop closure constraint introduces a coupling between these variables in circular DNA. We performed Monte Carlo simulations of wormlike rods with both bending and twist rigidity in order to study t ... [J. Chem. Phys. 132, 045101 (2010)] published Wed Jan 27, 2010.

Crossed-beam studies of electron transfer to oriented trichloronitromethane, CClNO, molecules

Peter W. Harland and Philip R. Brooks
Fast potassium atoms donate an electron to CClNO molecules to form K ions and the negative ions O, Cl, NO, CCl, CClNO, CClNO, and CClNO. Threshold energies are measured for these ions and electron affinities for CClNO, CClNO, and CClNO are estimated to be 2.35, 2.35, and 1.89 eV (0.6 eV), respective ... [J. Chem. Phys. 132, 044307 (2010)] published Wed Jan 27, 2010.

On the Cholesky decomposition for electron propagator methods: General aspects and application on C

Victor P. Vysotskiy and Lorenz S. Cederbaum
To treat the electronic structure of large molecules by electron propagator methods we developed a parallel computer program called P-RICDSigma. The program exploits the sparsity of the two-electron integral matrix by using Cholesky decomposition techniques. The advantage of these techniques is that ... [J. Chem. Phys. 132, 044110 (2010)] published Wed Jan 27, 2010.

Universal correction for the BeckeJohnson exchange potential

E. Rasanen, S. Pittalis, and C. R. Proetto
The BeckeJohnson exchange potential [A. D. Becke and E. R. Johnson, J. Chem. Phys. 124, 221101 (2006)] has been successfully used in electronic structure calculations within density-functional theory. However, in its original form, the potential may dramatically fail in systems with non-Coulombic ex ... [J. Chem. Phys. 132, 044112 (2010)] published Wed Jan 27, 2010.

A quasiclassical trajectory study of the OH+SO reaction: The role of rotational energy

M. Y. Ballester, Y. Orozco-Gonzalez, J. D. Garrido, and H. F. Dos Santos
A full dimensional quasiclassical trajectory study of the OH+SO reaction is presented with the aim of investigating the role of the reactants rotational energy in the reactivity. Different energetic combinations with one and both reactants rotationally excited are studied. A passive method is used t ... [J. Chem. Phys. 132, 044310 (2010)] published Wed Jan 27, 2010.

Photodissociation of ozone in the Hartley band: Potential energy surfaces, nonadiabatic couplings, and singlet/triplet branching ratio

R. Schinke and G. C. McBane
The lowest five A states of ozone, involved in the photodissociation with UV light, are analyzed on the basis of multireference configuration interaction electronic structure calculations with emphasis on the various avoided crossings in different regions of coordinate space. Global diabatic potenti ... [J. Chem. Phys. 132, 044305 (2010)] published Wed Jan 27, 2010.

A first-principles study of weakly bound molecules using exact exchange and the random phase approximation

Huy-Viet Nguyen and Giulia Galli
We present a study of the binding energy (BE) curves of rare gas and alkaline-earth dimers using an energy functional that includes exact exchange (EXX) and correlation energies within the random phase approximation (RPA). Our results for the equilibrium positions and long range behavior of the pote ... [J. Chem. Phys. 132, 044109 (2010)] published Wed Jan 27, 2010.

Phase diagram of colloid-rod system

S. K. Lai and Xuhui Xiao
The semigrand ensemble theory [H. N. W. Lekkerkerker, W. C. K. Poon, P. N. Pusey, A. Stroobants, and P. B. Warren, Europhys. Lett. 20, 559 (1992)] in conjunction with the fundamental measure density functional theory [V. B. Warshavsky and X. Song, Phys. Rev. E 69, 061113 (2004)] are used to construc ... [J. Chem. Phys. 132, 044905 (2010)] published Wed Jan 27, 2010.

Temperature dependence of the fine-structure resolved rate coefficients for collisions of O(XSigma) with He

Francois Lique
Rotational excitation of the O(XSigma) with He is investigated. The calculations are based on the potential energy surface of Groenenboom and Struniewicz [J. Chem. Phys. 113, 9562 (2000)]. Close coupling calculations of the collisional excitation cross sections of the fine-structure levels of O by H ... [J. Chem. Phys. 132, 044311 (2010)] published Wed Jan 27, 2010.

Wilhelmy plate artifacts in elastic monolayers

T. A. Witten, Jin Wang, L. Pocivavsek, and K. Y. C. Lee
A recent article [L. Pocivavsek et al., Soft Matter4, 2019 (2008)] by some of us pointed out difficulties in interpreting Wilhelmy plate measurements on elastic Langmuir monolayers that support anisotropic stress. Using a simplified geometry it showed conditions in which the Wilhelmy plate measures ... [J. Chem. Phys. 132, 046102 (2010)] published Wed Jan 27, 2010.

Molecular dynamics study of congruent melting of the equimolar ionic liquid-benzene inclusion crystal [emim][NTf]CH

M. H. Kowsari, Saman Alavi, Mahmud Ashrafizaadeh, and Bijan Najafi
We use molecular dynamics simulations to study the structure, dynamics, and details of the mechanism of congruent melting of the equimolar mixture of 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl) imide with benzene, [emim][NTf]CH. Changes in the molecular arrangement, radial distribution ... [J. Chem. Phys. 132, 044507 (2010)] published Wed Jan 27, 2010.

The effect of hydrogen bonding on the diffusion of water in n-alkanes and n-alcohols measured with a novel single microdroplet method

Jonathan T. Su, P. Brent Duncan, Amit Momaya, Arimatti Jutila, and David Needham
While the StokesEinstein (SE) equation predicts that the diffusion coefficient of a solute will be inversely proportional to the viscosity of the solvent, this relation is commonly known to fail for solutes, which are the same size or smaller than the solvent. Multiple researchers have reported that ... [J. Chem. Phys. 132, 044506 (2010)] published Wed Jan 27, 2010.

First-principles analysis of the CN bond scission of methylamine on Mo-based model catalysts

Cun-Qin Lv, Jun Li, Shu-Xia Tao, Kai-Cheng Ling, and Gui-Chang Wang
The CN bond breaking of methylamine on clean, carbon (nitrogen, oxygen)-modified Mo(100) [denoted as Mo(100) and Mo(100)C(N,O), respectively], MoC(100), MoN(100), and Pt(100) surfaces has been investigated by the first-principles density functional theory (DFT) calculations. The results show that th ... [J. Chem. Phys. 132, 044111 (2010)] published Wed Jan 27, 2010.

Experimental and theoretical study of the reaction of POCl with O

Ioannis S. K. Kerkines, Keiji Morokuma, Nedialka Iordanova, and A. A. Viggiano
The oxidation of the trichlorooxyphosphorus anion (POCl), which takes place in combustion flames, has been examined experimentally at a variety of temperatures and theoretically via ab initio and density functional methods. The reaction was examined in a turbulent ion flow tube and kinetics was meas ... [J. Chem. Phys. 132, 044309 (2010)] published Wed Jan 27, 2010.

Protection by organic ions against DNA damage induced by low energy electrons

A. Dumont, Y. Zheng, D. Hunting, and L. Sanche
It is well known that electrons below 15 eV induce strand breaks in DNA essentially via the formation of transient anions which decay by dissociative electron attachment (DEA) or into dissociative electronics states. The present article reports the results of a study on the influence of organic ions ... [J. Chem. Phys. 132, 045102 (2010)] published Wed Jan 27, 2010.

A transferable coarse-grained potential to study the structure of confined, supercritical Lennard-Jones fluids

T. Sanghi and N. R. Aluru
In this paper, we develop a transferable coarse-grained interatomic potential to study the structure of simple (spherical and nonpolar) Lennard-Jones (LJ) fluids confined at supercritical temperatures. The potential is used in empirical potential based quasicontinuum theory, [A. V. Raghunathan et al ... [J. Chem. Phys. 132, 044703 (2010)] published Wed Jan 27, 2010.

Triplet states of cyclopropenylidene and its isomers

Qunyan Wu, Qianyi Cheng, Yukio Yamaguchi, Qianshu Li, and Henry F. Schaefer, III
The unique importance of the cyclopropenylidene molecule conveys significance to its low-lying isomers. Eleven low-lying electronic triplet stationary points as well as the two lowest singlet structures of CH have been systematically investigated. This research used coupled cluster (CC) methods with ... [J. Chem. Phys. 132, 044308 (2010)] published Wed Jan 27, 2010.

Fluorescence of the perylene radical cation and an inaccessible D/D conical intersection: An MMVB, RASSCF, and TD-DFT computational study

Andrei M. Tokmachev, Martial Boggio-Pasqua, David Mendive-Tapia, Michael J. Bearpark, and Michael A. Robb
The photophysics of the perylene radical cation (Pe) was studied using the molecular mechanics-valence bond (MMVB) hybrid force field. Potential energy surfaces of the first three electronic states were investigated. Geometry optimizations of critical pointsincluding conical intersections between th ... [J. Chem. Phys. 132, 044306 (2010)] published Wed Jan 27, 2010.

Topological interactions between ring polymers: Implications for chromatin loops

Manfred Bohn and Dieter W. Heermann
Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The detailed topological and entropic forces between loops still rema ... [J. Chem. Phys. 132, 044904 (2010)] published Wed Jan 27, 2010.

Ewald-type formulas for Gaussian-basis Bloch states in one-dimensionally periodic systems

Joseph G. Fripiat, Joseph Delhalle, Isabelle Flamant, and Frank E. Harris
Expressions for integrals involving general Gaussian (s, p, d, …) basis Bloch functions are presented. Applying the Poisson transformation and the Ewald-type partitioning scheme, all lattice sums appearing in these expressions lead to fast convergence in both direct and Fourier spaces. Numeri ... [J. Chem. Phys. 132, 044108 (2010)] published Wed Jan 27, 2010.