Journal of Chemical Physics: All Topics

Relaxation of Voronoi shells in hydrated molecular ionic liquids

G. Neumayr, C. Schroder, and O. Steinhauser
The relaxation of solvation shells is studied following a twofold strategy based on a direct analysis of simulated data as well as on a solution of a Markovian master equation. In both cases solvation shells are constructed by Voronoi decomposition or equivalent Delaunay tessellation. The theoretica ... [J. Chem. Phys. 131, 174509 (2009)] published Fri Nov 6, 2009.

Improving replica exchange using driven scaling

Alexis J. Lee and Steven W. Rick
Replica exchange is a powerful simulation method in which simulations are run at a series of temperatures, with the highest temperature chosen so phase space can be sampled efficiently. In order for swaps to be accepted, the energy distributions of adjacent replicas must have some overlap. This can ... [J. Chem. Phys. 131, 174113 (2009)] published Fri Nov 6, 2009.

Dynamics of multidissociation paths of acetaldehyde photoexcited at 157 nm: Branching ratios, distributions of kinetic energy, and angular anisotropies of products

Shih-Huang Lee
After the photolysis of acetaldehyde (CHCHO) at 157.6 nm in a molecular-beam apparatus using photofragment translational spectroscopy and vacuum-ultraviolet photoionization to detect products, we observed 13 photofragments associated with six primary dissociation channels and secondary dissociation ... [J. Chem. Phys. 131, 174312 (2009)] published Fri Nov 6, 2009.

Hard repulsive barrier in hot adatom motion during dissociative adsorption of oxygen on Ag(100)

Ming-Feng Hsieh, Deng-Sung Lin, Heiko Gawronski, and Karina Morgenstern
Random pairing simulation and low temperature scanning tunneling microscopy (STM) are used to investigate the detailed O dissociative adsorption processes at 200 K for various coverages. The distribution of oxygen adatoms shows a strong repulsion between the adsorbates with a radius of ~0.8 nm. The ... [J. Chem. Phys. 131, 174709 (2009)] published Fri Nov 6, 2009.

Ab initio study of the excited singlet states of all-trans alpha,omega-diphenylpolyenes with one to seven polyene double bonds: Simulation of the spectral data within FranckCondon approximation

Wataru Mizukami, Yuki Kurashige, Masahiro Ehara, Takeshi Yanai, and Takao Itoh
Computational simulations of the electronic spectra with ab initio electronic structure calculations are presented for all-trans alpha,omega-diphenylpolyenes with the polyene double bond number (N) from 1 to 7. A direct comparison of the fluorescence spectra of diphenylpolyenes was made between the ... [J. Chem. Phys. 131, 174313 (2009)] published Fri Nov 6, 2009.

A relook at the compliance constants in redundant internal coordinates and some new insights

M. Vijay Madhav and S. Manogaran
The compliance constants, the inverse of the force constant matrix elements offer the advantage that any one of them could be calculated directly without the need to calculate the full Hessian. Here we show that such a direct calculation produces accurate results. Since the diagonal G and the compli ... [J. Chem. Phys. 131, 174112 (2009)] published Fri Nov 6, 2009.

Electronic states of CuPc chains on the Au(110) surface

F. Evangelista, A. Ruocco, R. Gotter, A. Cossaro, L. Floreano et al.
The electronic properties of Cu-phthalocyanine (CuPc) molecules flat lying along the channels of the Au(110) reconstructed surface have been investigated by means of ultraviolet and x-ray photoelectron spectroscopy. The ordered chains give rise to a highly ordered single-layer structure with a (5 x ... [J. Chem. Phys. 131, 174710 (2009)] published Fri Nov 6, 2009.

Connectivity effects in the segmental self- and cross-reorientation of unentangled polymer melts

A. Ottochian, D. Molin, A. Barbieri, and D. Leporini
The segmental (bond) rotational dynamics in a polymer melt of unentangled, linear bead-spring chains is studied by molecular dynamics simulations. To single out the connectivity effects, states with limited deviations from the Gaussian behavior of the linear displacement are considered. Both the sel ... [J. Chem. Phys. 131, 174902 (2009)] published Fri Nov 6, 2009.

Tribology of the lubricant quantized sliding state

Ivano Eligio Castelli, Rosario Capozza, Andrea Vanossi, Giuseppe E. Santoro, Nicola Manini et al.
In the framework of Langevin dynamics, we demonstrate clear evidence of the peculiar quantized sliding state, previously found in a simple one-dimensional boundary lubricated model [A. Vanossi et al., Phys. Rev. Lett. 97, 056101 (2006)], for a substantially less idealized two-dimensional description ... [J. Chem. Phys. 131, 174711 (2009)] published Fri Nov 6, 2009.

Phase diagram and structural properties of a simple model for one-patch particles

Achille Giacometti, Fred Lado, Julio Largo, Giorgio Pastore, and Francesco Sciortino
We study the thermodynamic and structural properties of a simple, one-patch fluid model using the reference hypernetted-chain (RHNC) integral equation and specialized Monte Carlo simulations. In this model, the interacting particles are hard spheres, each of which carries a single identical, arbitra ... [J. Chem. Phys. 131, 174114 (2009)] published Fri Nov 6, 2009.

Do the interfacial fluidities of cationic reverse micelles enhance with an increase in the water content?

K. S. Mali and G. B. Dutt
The role of cosurfactant and water on the interfacial fluidities of reverse micelles formed with the cationic surfactant, cetyltrimethylammonium bromide (CTAB) has been examined by measuring the fluorescence anisotropies of two structurally similar ionic solutes, rhodamine 110 and fluorescein. For t ... [J. Chem. Phys. 131, 174708 (2009)] published Fri Nov 6, 2009.

Density imbalances and free energy of lipid transfer in supported lipid bilayers

Chenyue Xing and Roland Faller
Supported lipid bilayers are an abundant research platform for understanding the behavior of real cell membranes as they allow for additional mechanical stability and at the same time have a fundamental structure approximating cell membranes. However, in computer simulations these systems have been ... [J. Chem. Phys. 131, 175104 (2009)] published Fri Nov 6, 2009.

Comprehensive study of sodium, copper, and silver clusters over a wide range of sizes 2<=N<=75

Masahiro Itoh, Vijay Kumar, Tadafumi Adschiri, and Yoshiyuki Kawazoe
The geometric and electronic structures of Na, Cu, and Ag metal clusters are systematically studied based on the density functional theory over a wide range of cluster sizes 2<=N<=75. A remarkable similarity is observed between the optimized geometric structures of alkali and noble metal clusters ov ... [J. Chem. Phys. 131, 174510 (2009)] published Fri Nov 6, 2009.

Thermal properties and Brillouin-scattering study of glass, crystal, and glacial states in n-butanol

Merzak Hassaine, Rafael J. Jimenez-Rioboo, Irina V. Sharapova, Oxana A. Korolyuk, Alexander I. Krivchikov et al.
We investigated through noncommercial calorimetry and elastoacoustic Brillouin experiments the phase diagram of n-butanol and measured the specific heat and the thermal conductivity in a wide low-temperature range for its three different states, namely, glass, crystal, and the so-called glacial stat ... [J. Chem. Phys. 131, 174508 (2009)] published Fri Nov 6, 2009.

The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method

Dmitri G. Fedorov and Kazuo Kitaura (北浦和夫)
We have examined the role of the exchange in describing the electrostatic potential in the fragment molecular orbital method and showed that it should be included in the total Fock matrix to obtain an accurate one-electron spectrum; however, adding it to the Fock matrices of individual fragments and ... [J. Chem. Phys. 131, 171106 (2009)] published Fri Nov 6, 2009.

Experimental and theoretical investigations on the epitaxial growth of 4,4 stilbenedicarboxylic acid molecules on Au(111)

Yan Feng Zhang, Yong Yang, Yoshiyuki Kawazoe, and Tadahiro Komeda
We report on scanning tunneling microscope observations of the epitaxial growth of 4,4 stilbenedicarboxylic acid (SDA) molecules on Au(111), with the coverage ranges from submonolayer to one monolayer. The surface assembly evolves from one-dimensional molecular chains to striped islands and finally ... [J. Chem. Phys. 131, 174706 (2009)] published Thu Nov 5, 2009.

The Landau free energy of a melt of graft copolymers

M. A. Aliev and S. I. Kuchanov
New graphical algorithm is proposed to find vertex functions which are the coefficients of expansion of the Landau free energy of polydisperse multigraft copolymers whose macromolecules comprise an arbitrary number of types of side chains. This algorithm imposes no restriction on length distribution ... [J. Chem. Phys. 131, 174111 (2009)] published Thu Nov 5, 2009.

Femtosecond time resolved coherent anti-Stokes Raman spectroscopy of HN mixtures in the Dicke regime: Experiments and modeling of velocity effects

H. Tran, F. Chaussard, N. Le Cong, B. Lavorel, O. Faucher et al.
In this paper, we present measurements and modeling of femtosecond time resolved coherent anti-Stokes Raman spectroscopy (CARS) signal in HN mixtures at low densities. Three approaches have been used to model the CARS response. The first is the usual sum of Voigt profiles. In the second approach, th ... [J. Chem. Phys. 131, 174310 (2009)] published Thu Nov 5, 2009.

Hydrogen bonding in acetone clusters probed by near-edge x-ray absorption fine structure spectroscopy in the carbon and oxygen K-edge regions

Y. Tamenori, O. Takahashi, K. Yamashita, T. Yamaguchi, K. Okada et al.
Hydrogen bonding in acetone clusters was investigated using near-edge x-ray absorption fine structure (NEXAFS) spectroscopy and density functional theory calculations in the carbon and oxygen K-edge regions. The partial-ion-yield (PIY) curves of the cluster ions were measured as the NEXAFS spectra o ... [J. Chem. Phys. 131, 174311 (2009)] published Thu Nov 5, 2009.

Vibrational spectroscopy of neutral silicon clusters via far-IR-VUV two color ionization

Andre Fielicke, Jonathan T. Lyon, Marko Haertelt, Gerard Meijer, Pieterjan Claes et al.
Tunable far-infrared-vacuum-ultraviolet two color ionization is used to obtain vibrational spectra of neutral silicon clusters in the gas phase. Upon excitation with tunable infrared light prior to irradiation with UV photons we observe strong enhancements in the mass spectrometric signal of specifi ... [J. Chem. Phys. 131, 171105 (2009)] published Thu Nov 5, 2009.

The photodissociation of CHI in the red edge of the A-band: Comparison between slice imaging experiments and multisurface wave packet calculations

L. Rubio-Lago, A. Garcia-Vela, A. Arregui, G. A. Amaral, and L. Banares
The photodissociation of methyl iodide at different wavelengths in the red edge of the A-band (286333 nm) has been studied using a combination of slice imaging and resonance enhanced multiphoton ionization detection of the methyl fragment in the vibrational ground state (nu=0). The kinetic energy di ... [J. Chem. Phys. 131, 174309 (2009)] published Thu Nov 5, 2009.

Phase equilibria in DOPC/DPPC: Conversion from gel to subgel in two component mixtures

Miranda L. Schmidt, Latifa Ziani, Michelle Boudreau, and James H. Davis
Biological membranes contain a mixture of phospholipids with varying degrees of hydrocarbon chain unsaturation. Mixtures of long chain saturated and unsaturated lipids with cholesterol have attracted a lot of attention because of the formation of two coexisting fluid bilayer phases in such systems o ... [J. Chem. Phys. 131, 175103 (2009)] published Thu Nov 5, 2009.

Diffusion behavior in a liquid-liquid interfacial crystallization by molecular dynamics simulations

Akira Kitayama, Shinya Yamanaka, Kazunori Kadota, Atsuko Shimosaka, Yoshiyuki Shirakawa et al.
Interfacial crystallization, such as surface crystallization in solution (solid-liquid) and liquid-liquid crystallization, gives us an asymmetric reaction field and is a technique for morphology control of crystals. In the liquid-liquid crystallization, the concentration distribution of solute ions ... [J. Chem. Phys. 131, 174707 (2009)] published Thu Nov 5, 2009.

Adsorbate-induced absorption redshift in an organic-inorganic cluster conjugate: Electronic effects of surfactants and organic adsorbates on the lowest excited states of a methanethiol-CdSe conjugate

Christopher Liu, Sang-Yoon Chung, Sungyul Lee, Shimon Weiss, and Daniel Neuhauser
Bioconjugated CdSe quantum dots are promising reagents for bioimaging applications. Experimentally, the binding of a short peptide has been found to redshift the optical absorption of nanoclusters [J. Tsay et al., J. Phys. Chem. B 109, 1669 (2005)]. This study examines this issue by performing densi ... [J. Chem. Phys. 131, 174705 (2009)] published Thu Nov 5, 2009.

Molecular rotor dynamics influenced by the elastic modulus of polyethylene nanocomposites

Ah-Young Jee, Haneul Kwon, and Minyung Lee
We observed that the excited-state twisting motion of 3,3-diethyloxacarbocyanine in polymer nanocomposites (PNCs) depends strongly on the elastic modulus of medium. PNCs consist of low density polyethylene dispersed with surface-functionalized nanodiamonds with various alkyl groups. The mechanical p ... [J. Chem. Phys. 131, 171104 (2009)] published Thu Nov 5, 2009.

Cumulant decomposition of reduced density matrices, multireference normal ordering, and Wicks theorem: A spin-free approach

K. R. Shamasundar
We propose a spin-free approach to the cumulant decomposition of reduced density matrices of singlet and spin-rotation or SU(2) invariant ensemble of nonsinglet states as in [W. Kutzelnigg and D. Mukherjee, J. Chem. Phys. 110, 2800 (1999); 116, 4787 (2002)]. We provide a simple recursive procedure t ... [J. Chem. Phys. 131, 174109 (2009)] published Wed Nov 4, 2009.

Erratum: Interaction between silver nanowires and CO on a stepped platinum surface [J. Chem. Phys. 131, 064702 (2009)]

R. Streber, B. Trankenschuh, J. Schock, C. Papp, H.-P. Steinruck et al.
Abstract not available. [J. Chem. Phys. 131, 179901 (2009)] published Wed Nov 4, 2009.

The interaction of Al atoms with water molecules: A theoretical study

S. Alvarez-Barcia and J. R. Flores
The interaction of individual Al atoms with water molecules has been studied from the point of view of the energy by means of ab initio and DFT calculations in order to find the pathways for the generation of HAlOH(HO) or AlOH(HO)+H. The potential energy surface of the Al(HO) (n=03) systems has been ... [J. Chem. Phys. 131, 174307 (2009)] published Wed Nov 4, 2009.

Isofulminic acid, HONC: Ab initio theory and microwave spectroscopy

Mirjana Mladenovic, Marius Lewerenz, Michael C. McCarthy, and Patrick Thaddeus
Isofulminic acid, HONC, the most energetic stable isomer of isocyanic acid HNCO, higher in energy by 84 kcal/mol, has been detected spectroscopically by rotational spectroscopy supported by coupled cluster electronic structure calculations. The fundamental rotational transitions of the normal, carbo ... [J. Chem. Phys. 131, 174308 (2009)] published Wed Nov 4, 2009.

First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent

Veronica M. Sanchez, Mariela Sued, and Damian A. Scherlis
Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framewor ... [J. Chem. Phys. 131, 174108 (2009)] published Wed Nov 4, 2009.

Ca impurity in small mixed HeHe clusters

R. Guardiola, J. Navarro, D. Mateo, and M. Barranco
The structure of small mixed helium clusters doped with one calcium atom has been determined within the diffusion Monte Carlo framework. The results show that the calcium atom sits at the HeHe interface. This is in agreement with previous studies, both experimental and theoretical, performed for lar ... [J. Chem. Phys. 131, 174110 (2009)] published Wed Nov 4, 2009.

Neutron scattering study of the dynamics of a polymer melt under nanoscopic confinement

Margarita Krutyeva, Jaime Martin, Arantxa Arbe, Juan Colmenero, Carmen Mijangos et al.
Poly(ethylene oxide) confined in an anodic aluminum oxide solid matrix has been studied by different neutron scattering techniques in the momentum transfer (Q-vector) range 0.2<=Q=|Q-vector |<=1.9 A. The cylindrical pores of the matrix present a diameter (40 nm) much smaller than their length (150 ... [J. Chem. Phys. 131, 174901 (2009)] published Wed Nov 4, 2009.

Universal perturbative explicitly correlated basis set incompleteness correction

Martin Torheyden and Edward F. Valeev
Basis set incompleteness error for an arbitrary approximate electronic wave function is robustly reduced using a second-order perturbative correction into a basis of explicitly correlated, internally contracted geminal functions. The Hylleraas functional for the second-order energy correction is eva ... [J. Chem. Phys. 131, 171103 (2009)] published Wed Nov 4, 2009.

In situ high-pressure study of diborane by infrared spectroscopy

Yang Song, Chitra Murli, and Zhenxian Liu
As the simplest stable boron hydride in its condensed phase, diborane exhibits an interesting structural chemistry with uniquely bridged hydrogen bonds. Here we report the first room-temperature infrared (IR) absorption spectra of solid diborane compressed to pressures as high as 50 GPa using a diam ... [J. Chem. Phys. 131, 174506 (2009)] published Tue Nov 3, 2009.

A separable shadow Hamiltonian hybrid Monte Carlo method

Christopher R. Sweet, Scott S. Hampton, Robert D. Skeel, and Jesus A. Izaguirre
Hybrid Monte Carlo (HMC) is a rigorous sampling method that uses molecular dynamics (MD) as a global Monte Carlo move. The acceptance rate of HMC decays exponentially with system size. The shadow hybrid Monte Carlo (SHMC) was previously introduced to reduce this performance degradation by sampling i ... [J. Chem. Phys. 131, 174106 (2009)] published Tue Nov 3, 2009.

Comparison of the resonance-enhanced multiphoton ionization spectra of pyrrole and 2,5-dimethylpyrrole: Building toward an understanding of the electronic structure and photochemistry of porphyrins

Joseph M. Beames, Michael G. D. Nix, and Andrew J. Hudson
The photophysical properties of porphyrins have relevance for their use as light-activated drugs in cancer treatment and sensitizers in solid-state solar cells. However, the appearance of their UV-visible spectra is usually explained inadequately by qualitative molecular-orbital theories. We intend ... [J. Chem. Phys. 131, 174305 (2009)] published Tue Nov 3, 2009.

Fragmentation properties of three-membered heterocyclic molecules by partial ion yield spectroscopy: CHO and CHS

W. C. Stolte, I. Dumitriu, S.-W. Yu, G. Ohrwall, M. N. Piancastelli et al.
We investigated the photofragmentation properties of two three-membered ring heterocyclic molecules, CHO and CHS, by total and partial ion yield spectroscopy. Positive and negative ions have been collected as a function of photon energy around the C 1s and O 1s ionization thresholds in CHO, and arou ... [J. Chem. Phys. 131, 174306 (2009)] published Tue Nov 3, 2009.

Long-range corrected double-hybrid density functionals

Jeng-Da Chai and Martin Head-Gordon
We extend the range of applicability of our previous long-range corrected (LC) hybrid functional, omegaB97X [J.-D. Chai and M. Head-Gordon, J. Chem. Phys. 128, 084106 (2008)], with a nonlocal description of electron correlation, inspired by second-order MollerPlesset (many-body) perturbation theory. ... [J. Chem. Phys. 131, 174105 (2009)] published Tue Nov 3, 2009.

A soft-core GayBerne model for the simulation of liquid crystals by Hamiltonian replica exchange

Roberto Berardi, Claudio Zannoni, Juho S. Lintuvuori, and Mark R. Wilson
The GayBerne (GB) potential has proved highly successful in the simulation of liquid crystal phases, although it is fairly demanding in terms of resources for simulations of large (e.g., N>10) systems, as increasingly required in applications. Here, we introduce a soft-core GB model, which exhibits ... [J. Chem. Phys. 131, 174107 (2009)] published Tue Nov 3, 2009.

Dielectric discontinuity effects on the adsorption of a linear polyelectrolyte at the surface of a neutral nanoparticle

Marianne Seijo, Martin Pohl, Serge Ulrich, and Serge Stoll
The formation of complexes between nanoparticles and polyelectrolytes is a key process for the control of the reactivity of manufactured nanoparticles and rational design of core shell nanostructures. In this work, we investigate the influence of the nanoparticle dielectric constant on the adsorptio ... [J. Chem. Phys. 131, 174704 (2009)] published Tue Nov 3, 2009.

Vibrational circular dichroism signal enhancement using self-heterodyning with elliptically polarized laser pulses

Jan Helbing and Mathias Bonmarin
Vibrational circular dichroism (VCD) spectra were recorded using elliptically polarized ultrashort laser pulses, produced with the help of a photoelastic modulator. The short polarization axis of the elliptical light acts as a phase-locked local oscillator field, heterodyning the chiral signal gener ... [J. Chem. Phys. 131, 174507 (2009)] published Tue Nov 3, 2009.

Failure of the constrained equilibrium hypothesis in nucleation

Lawrence S. Bartell
The purpose of this investigation is to find whether solutions of the BeckerDoringTunitskii coupled differential equations can yield results closely paralleling those found in molecular dynamics (MD) simulations of freezing. What is investigated, in particular, is the validity of the constrained equ ... [J. Chem. Phys. 131, 174505 (2009)] published Tue Nov 3, 2009.

Nonequilibrium Fock space for the electron transport problem

D. S. Kosov
Based on the formalism of thermofield dynamics we propose a concept of nonequilibrium Fock space and nonequilibrium quasiparticles for quantum many-body system in nonequilibrium steady state. We develop a general theory as well as demonstrate the utility of the approach on the example of electron tr ... [J. Chem. Phys. 131, 171102 (2009)] published Tue Nov 3, 2009.

Nonproduct quadrature grids for solving the vibrational Schrodinger equation

Gustavo Avila and Tucker Carrington, Jr.
The size of the quadrature grid required to compute potential matrix elements impedes solution of the vibrational Schrodinger equation if the potential does not have a simple form. This quadrature grid-size problem can make computing (ro)vibrational spectra impossible even if the size of the basis u ... [J. Chem. Phys. 131, 174103 (2009)] published Mon Nov 2, 2009.

On the kinetics of the Al+Cl reaction: Cluster degradation in consecutive steps

Matthias Olzmann, Ralf Burgert, and Hansgeorg Schnockel
The kinetics of the reaction system initiated by the Al+Cl reaction was experimentally studied in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The Al clusters were produced by laser desorption/ionization of LiAlH, then transferred into the ICR cell, cooled by collisions wi ... [J. Chem. Phys. 131, 174304 (2009)] published Mon Nov 2, 2009.

Monodisperse self-assembly in a model with protein-like interactions

Alex W. Wilber, Jonathan P. K. Doye, Ard A. Louis, and Anna C. F. Lewis
We study the self-assembly behavior of patchy particles with proteinlike interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the thermodynamics and dynamics of self-assembly as a function of the parame ... [J. Chem. Phys. 131, 175102 (2009)] published Mon Nov 2, 2009.

Valence ionization spectra of group six metal hexacarbonyls studied by the symmetry-adapted cluster-configuration interaction method

Ryoichi Fukuda, Seigo Hayaki, and Hiroshi Nakatsuji
The valence ionization spectra up to 20 eV of group six metal carbonyls, chromium hexacarbonyl, molybdenum hexacarbonyl, and tungsten hexacarbonyl were studied by the symmetry-adapted cluster-configuration interaction (SAC-CI) method. The assignments of the spectra are given based on reliable SAC-CI ... [J. Chem. Phys. 131, 174303 (2009)] published Mon Nov 2, 2009.

Geometry and stability of CuN (n=16) and CuN (n=15) clusters

Jian-Ning Ding, Ning-Yi Yuan, Feng Li, Gu-Qiao Ding, Zhi-Gang Chen et al.
The gradient-corrected density functional calculation is applied to search the lowest-energy configurations of CuN (n=16) clusters and the calculation indicated that CuN cluster is the most stable one. Based on the result, we further investigate the equilibrium geometries and stabilities of the CuN ... [J. Chem. Phys. 131, 174102 (2009)] published Mon Nov 2, 2009.

On the difference between the transition properties calculated with linear response- and equation of motion-CCSD approaches

Marco Caricato, Gary W. Trucks, and Michael J. Frisch
In this work, we quantitatively investigate the difference between the linear response (LR) and the equation of motion (EOM) coupled cluster (CC) approaches in the calculation of transition properties, namely, dipole and oscillator strengths, for the most widely used truncated CC wave function, whic ... [J. Chem. Phys. 131, 174104 (2009)] published Mon Nov 2, 2009.

Bulk viscosity universality and scaling function near the binary liquid consolute point

Jayanta K. Bhattacharjee, Ireneusz Iwanowski, and Udo Kaatze
The hydrodynamical equations and the notion of a frequency dependent complex specific heat near the critical point of binary liquids are used to obtain an expression for the low-frequency bulk viscosity. In this way the interrelations between different theoretical models, treating the critical sound ... [J. Chem. Phys. 131, 174502 (2009)] published Mon Nov 2, 2009.

Photodissociation cross sections of ClOOCl at 248.4 and 266 nm

Chien-Yu Lien, Wei-Yen Lin, Hsueh-Ying Chen, Wen-Tsung Huang, Bing Jin et al.
This study utilized a mass-resolved detection of ClOOCl to determine its photodissociation cross section, which is the product of the absorption cross section and dissociation quantum yield. An effusive molecular beam of ClOOCl was generated and its photodissociation probability was determined throu ... [J. Chem. Phys. 131, 174301 (2009)] published Mon Nov 2, 2009.

Block correlated coupled cluster method with the complete active-space self-consistent-field reference function: Applications for low-lying electronic excited states

Jun Shen and Shuhua Li
Block correlated coupled cluster (BCCC) method with the complete active-space (CAS) self-consistent-field reference function (CAS-BCCC) has been applied to investigate the vertical excitation energies of low-lying valence excited states in a number of medium-sized organic molecules, including unsatu ... [J. Chem. Phys. 131, 174101 (2009)] published Mon Nov 2, 2009.

Self-assembly of monodisperse clusters: Dependence on target geometry

Alex W. Wilber, Jonathan P. K. Doye, and Ard A. Louis
We apply a simple model system of patchy particles to study monodisperse self-assembly using the Platonic solids as target structures. We find marked differences between the assembly behaviors of the different systems. Tetrahedra, octahedral, and icosahedra assemble easily, while cubes are more chal ... [J. Chem. Phys. 131, 175101 (2009)] published Mon Nov 2, 2009.

Coadsorption of CO and NO on the CuO(111) surface: A periodic density functional theory study

Bao-Zhen Sun, Wen-Kai Chen, and Yi-Jun Xu
Coadsorption of carbon monoxide (CO) and nitric oxide (NO) on the CuO(111) surface was studied using periodic density functional theory calculations. It is interesting to find that CO+NO on CuO(111) could react to form adsorbed NCO surface species. Coadsorption of CO and NO could give rise to the fo ... [J. Chem. Phys. 131, 174503 (2009)] published Mon Nov 2, 2009.

The isotropic-nematic interface with an oblique anchoring condition

S. M. Kamil, A. K. Bhattacharjee, R. Adhikari, and Gautam I. Menon
We present numerical and analytic results for uniaxial and biaxial orders at the isotropic-nematic interface within GinzburgLandaude Gennes theory. We study the case where an oblique anchoring condition is imposed asymptotically on the nematic side of the interface, reproducing results of previous w ... [J. Chem. Phys. 131, 174701 (2009)] published Mon Nov 2, 2009.

Solid-liquid equilibria and triple points of n-6 Lennard-Jones fluids

Alauddin Ahmed and Richard J. Sadus
Molecular dynamics simulations are reported for the solid-liquid coexistence properties of n-6 Lennard-Jones fluids, where n=12, 11, 10, 9, 8, and 7. The complete phase behavior for these systems has been obtained by combining these data with vapor-liquid simulations. The influence of n on the solid ... [J. Chem. Phys. 131, 174504 (2009)] published Mon Nov 2, 2009.

Optimal excitation of Na nuclear spins in the presence of residual quadrupolar coupling and quadrupolar relaxation

Jae-Seung Lee, Ravinder R. Regatte, and Alexej Jerschow
Optimal control theory is applied for designing pulse sequences to optimally excite a spin-3/2 system with residual quadrupolar coupling in the presence of quadrupolar relaxation. A homogeneous form of the master equation is constructed to simulate the dynamics of the spin system, and a general opti ... [J. Chem. Phys. 131, 174501 (2009)] published Mon Nov 2, 2009.

First-principles study of methane dehydrogenation on a bimetallic Cu/Ni(111) surface

Wei An, X. C. Zeng, and C. Heath Turner
We present density-functional theory calculations of the dehydrogenation of methane and CH (x=13) on a Cu/Ni(111) surface, where Cu atoms are substituted on the Ni surface at a coverage of (1/4) monolayer. As compared to the results on other metal surfaces, including Ni(111), a similar activation me ... [J. Chem. Phys. 131, 174702 (2009)] published Mon Nov 2, 2009.

Structure and optical properties of core-shell bimetallic AgNi clusters: Comparison with pure silver and nickel clusters

M. Harb, F. Rabilloud, and D. Simon
We present the structural, electronic, and optical properties of bimetallic AgNi (n<=7) clusters investigated in the framework of the density functional theory (DFT) (DFT and time-dependent DFT). The structure of AgNi clusters is found to be governed essentially by the formation of a Ni-core surroun ... [J. Chem. Phys. 131, 174302 (2009)] published Mon Nov 2, 2009.

Calculation of hydrogen storage capacity of metal-organic and covalent-organic frameworks by spillover

Mayur Suri, Matthew Dornfeld, and Eric Ganz
We have used accurate ab initio quantum chemistry calculations together with a simple model to study the hydrogen storage capacity of metal-organic and covalent-organic frameworks by spillover. Recent experiments by Tsao et al. [J. Am. Chem. Soc. 131, 1404 (2009)] {based on an earlier work by Li and ... [J. Chem. Phys. 131, 174703 (2009)] published Mon Nov 2, 2009.

A least-constraint principle for population dynamics and reaction kinetics: Modeling entropy-controlled chemical hypercycles

Denis Horvath and Gerald R. Kneller
In this paper, we investigate the treatment of constraints in rate equations describing the temporal evolution of biological populations or chemical reactions. We present a formulation for arbitrary holonomic and linear nonholonomic constraints which ensures the positivity of the dynamical variables ... [J. Chem. Phys. 131, 171101 (2009)] published Mon Nov 2, 2009.

Low-lying electronic states of CHNO via photoelectron imaging of the nitromethane anion

Daniel J. Goebbert, Kostyantyn Pichugin, and Andrei Sanov
Negative-ion photoelectron imaging at 532, 392, 355, and 266 nm is used to assign several low-lying electronic states of neutral nitromethane CHNO at the geometry corresponding to the anion equilibrium. The observed neutral states include (in the order of increasing binding energy) the X A ground st ... [J. Chem. Phys. 131, 164308 (2009)] published Fri Oct 30, 2009.

Time-dependent multiconfiguration theory for describing molecular dynamics in diatomic-like molecules

Tsuyoshi Kato and Kaoru Yamanouchi
We extend the multiconfiguration time-dependent HartreeFock (MCTDHF) theory, which is originally developed for the investigation of electronic dynamics in atoms and molecules within the clamped nuclear model, for describing molecular dynamics in diatomic-like molecular systems which are composed of ... [J. Chem. Phys. 131, 164118 (2009)] published Fri Oct 30, 2009.

Correction to the ClausiusMosotti equation: The dielectric constant of nonpolar fluids from Monte Carlo simulations

Monika Valisko and Dezső Boda
We examine the dielectric constant of nonpolar fluids by direct Monte Carlo simulations on the basis of the polarizable hard sphere (PHS) model, where the spheres carry molecular polarizabilities. Point dipoles are induced in the spheres partly by an external electric field and partly by other molec ... [J. Chem. Phys. 131, 164120 (2009)] published Fri Oct 30, 2009.

Transition state analysis of solid-solid transformations in nanocrystals

Michael Grunwald and Christoph Dellago
A systematic simulation methodology is introduced for the accurate determination of experimentally measurable quantities characterizing solid-solid phase transformations under pressure. The atomistic mechanisms of nucleation and growth in a structural transformation of pressurized CdSe nanocrystals ... [J. Chem. Phys. 131, 164116 (2009)] published Fri Oct 30, 2009.

Fluctuation-induced spreading of size distribution in condensation kinetics

V. G. Dubrovskii
One of the major results of condensation theory is the time independence of the size distribution shape (in terms of a certain invariant size) at the stage of regular growth of particles. This property follows directly from the simplified Zeldovich equation in the continuous form, where the fluctuat ... [J. Chem. Phys. 131, 164514 (2009)] published Fri Oct 30, 2009.

Photodissociation of phosgene: Theoretical evidence for the ultrafast and synchronous concerted three-body process

Qiu Fang, Feng Zhang, Lin Shen, Wei-Hai Fang, and Yi Luo
The potential energy surfaces for ClCO dissociation into CO+Cl+Cl in the lowest two electronic singlet states (S and S) have been determined by the complete active space self-consistent field, coupled-cluster method with single and double excitations (CCSD), and equation-of-motion CCSD calculations, ... [J. Chem. Phys. 131, 164306 (2009)] published Fri Oct 30, 2009.

Local behavior of the first-order gradient correction to the ThomasFermi kinetic energy functional

David Garcia-Aldea, T. Martin-Blas, and J. E. Alvarellos
The first-order gradient correction to the ThomasFermi functional proposed by Haq et al. [Chem. Phys. Lett. 111, 79 (1984)] has been tested by evaluating both the total kinetic energy and the local kinetic energy density. For the kinetic energy density, we have evaluated its deviation from the exact ... [J. Chem. Phys. 131, 164117 (2009)] published Fri Oct 30, 2009.

Direct determination of the Tolman length from the bulk pressures of liquid drops via molecular dynamics simulations

Alan E. van Giessen and Edgar M. Blokhuis
An expression for the difference in pressure between a liquid drop in equilibrium with its vapor Deltap=pp is derived from previous expressions for the components of the IrvingKirkwood pressure tensor. This expression, as well as the bulk values of the pressure tensor, is then evaluated via molecula ... [J. Chem. Phys. 131, 164705 (2009)] published Fri Oct 30, 2009.

Atomic-resolution imaging of size-selected platinum clusters on TiO(110) surfaces

Noritake Isomura, Xingyang Wu, and Yoshihide Watanabe
Size-selected Pt (n=4,710,15) clusters were deposited on TiO(110)(1 x 1) surfaces and imaged at atomic resolution using an ultrahigh-vacuum scanning tunneling microscope with a carbon nanotube tip. Clusters smaller than Pt lay flat on the surface with a planar structure and a planar-to-three-dimensi ... [J. Chem. Phys. 131, 164707 (2009)] published Fri Oct 30, 2009.

State-resolved manipulations of optical gain in semiconductor quantum dots: Size universality, gain tailoring, and surface effects

Ryan R. Cooney, Samuel L. Sewall, D. M. Sagar, and Patanjali Kambhampati
Optical gain in strongly confined colloidal semiconductor quantum dots is measured using state resolved pump/probe spectroscopy. Though size tunable optical amplification has been previously reported for these materials, the influence of confinement enhanced multiexcitonic interactions has limited p ... [J. Chem. Phys. 131, 164706 (2009)] published Fri Oct 30, 2009.

Constrained-pairing mean-field theory. II. Exact treatment of dissociations to nondegenerate orbitals

Gustavo E. Scuseria and Takashi Tsuchimochi
Our recently proposed constrained-pairing mean-field theory (CPMFT) is here extended to deal with dissociation of electron pairs to nondegenerate orbitals. To achieve this goal, we introduce the concept of asymptotic constraints. This extended CPMFT model can exactly dissociate polyatomic molecules ... [J. Chem. Phys. 131, 164119 (2009)] published Fri Oct 30, 2009.

Solid-solid phase transition in hard ellipsoids

M. Radu, P. Pfleiderer, and T. Schilling
We present a computer simulation study of the crystalline phases of hard ellipsoids of revolution. A previous study [P. Pfleiderer and T. Schilling, Phys. Rev. E 75, 020402 (2007)]. showed that for aspect ratios a/b>=3 the previously suggested stretched-fcc phase [D. Frenkel and B. Mulder, Mol. Phys ... [J. Chem. Phys. 131, 164513 (2009)] published Fri Oct 30, 2009.

The van der Waals coefficients between carbon nanostructures and small molecules: A time-dependent density functional theory study

C. Kamal, T. K. Ghanty, Arup Banerjee, and Aparna Chakrabarti
We employ all-electron ab initio time-dependent density functional theory based method to calculate the long-range dipole-dipole dispersion coefficient, namely, the van der Waals (vdW) coefficient (C) between fullerenes and finite-length carbon nanotubes as well as between these structures and diffe ... [J. Chem. Phys. 131, 164708 (2009)] published Fri Oct 30, 2009.

Site-specific behavior in de-excitation spectra of FSiCHCHSi(CH) in the Si 1s excitation region

I. H. Suzuki, A. Nitta, H. Fukuzawa, K. Ueda, O. Takahashi et al.
Excitation (total ion yield) and de-excitation (resonant photoemission) spectra have been measured in the Si 1s photoexcitation region of the FSiCHCHSi(CH) molecule using monochromatized undulator radiation. Theoretical calculations within the framework of density functional theory have reproduced t ... [J. Chem. Phys. 131, 164309 (2009)] published Fri Oct 30, 2009.

Low ionization potentials of binuclear superalkali BLi

Jing Tong, Ying Li, Di Wu, Zhi-Ru Li, and Xu-Ri Huang
A new type of binuclear superalkali BLi and its corresponding cation BLi were theoretically predicted based on the density functional theory calculations. BLi was found to have six minimum energy structures corresponding to five cation states exhibiting superalkali nature. The global minima of BLi a ... [J. Chem. Phys. 131, 164307 (2009)] published Fri Oct 30, 2009.

Estimating the viscoelastic moduli of a complex fluid from observation of Brownian motion

B. U. Felderhof
A procedure is proposed to estimate the viscoelastic properties of a complex fluid from the behavior of the velocity autocorrelation function of a suspended Brownian particle in a limited range of time. The procedure is tested for a model complex fluid with given frequency-dependent shear viscosity. ... [J. Chem. Phys. 131, 164904 (2009)] published Thu Oct 29, 2009.

Implicit and explicit solvent models for the simulation of a single polymer chain in solution: Lattice Boltzmann versus Brownian dynamics

Tri T. Pham, Ulf D. Schiller, J. Ravi Prakash, and Burkhard Dunweg
We present a comparative study of two computer simulation methods to obtain static and dynamic properties of dilute polymer solutions. The first approach is a recently established hybrid algorithm based on dissipative coupling between molecular dynamics and lattice Boltzmann (LB), while the second i ... [J. Chem. Phys. 131, 164114 (2009)] published Thu Oct 29, 2009.

Calculation of semiclassical free energy differences along nonequilibrium classical trajectories

M. F. Gelin and D. S. Kosov
We have derived several relations, which allow the evaluation of the system free energy changes in the leading order in [h-bar] along classically generated trajectories. The results are formulated in terms of purely classical Hamiltonians and trajectories, so that semiclassical partition functions c ... [J. Chem. Phys. 131, 164510 (2009)] published Thu Oct 29, 2009.

Erratum: First-principles local density approximation+U and generalized gradient approximation+U study of plutonium oxides [J. Chem. Phys. 128, 084705 (2008)]

Bo Sun, Ping Zhang, and Xian-Geng Zhao
Abstract not available. [J. Chem. Phys. 131, 169903 (2009)] published Thu Oct 29, 2009.

Ultrafast energy relaxation and anisotropy decay of the librational motion in liquid water: A molecular dynamics study

Takuma Yagasaki, Junichi Ono, and Shinji Saito
We theoretically investigate intermolecular motions in liquid water in terms of third-order infrared (IR) spectroscopy. We calculate two-dimensional (2D) IR spectra, pump-probe signals, and three-pulse stimulated photon echo signals from the combination of equilibrium and nonequilibrium molecular dy ... [J. Chem. Phys. 131, 164511 (2009)] published Thu Oct 29, 2009.

The stiffness of a fully stretched polyethylene chain: A Raman jet spectroscopy extrapolation

Tobias N. Wassermann, Jonas Thelemann, Philipp Zielke, and Martin A. Suhm
Linear alkanes with n=516 C-atoms are partially relaxed into their stretched all-trans conformation by supersonic jet expansion. Their longitudinal acoustic modes are identified by spontaneous Raman scattering and deperturbed from transverse bending mode components and Fermi resonance with combinati ... [J. Chem. Phys. 131, 161108 (2009)] published Thu Oct 29, 2009.

Erratum: Electronic spectra of the linear polyyne cations HCH (n=28): An ab initio study [J. Chem. Phys. 131, 144307 (2009)]

Jinglai Zhang, Xugeng Guo, and Zexing Cao
Abstract not available. [J. Chem. Phys. 131, 169904 (2009)] published Thu Oct 29, 2009.

Transformations of the distribution of nuclei formed in a nucleation pulse: Interface-limited growth

Vitaly A. Shneidman
A typical nucleation-growth process is considered: a system is quenched into a supersaturated state with a small critical radius r and is allowed to nucleate during a finite time interval t, after which the supersaturation is abruptly reduced to a fixed value with a larger critical radius r. The siz ... [J. Chem. Phys. 131, 164115 (2009)] published Thu Oct 29, 2009.

Rheology and phase behavior of dense casein micelle dispersions

A. Bouchoux, B. Debbou, G. Gesan-Guiziou, M.-H. Famelart, J.-L. Doublier et al.
Casein micelle dispersions have been concentrated through osmotic stress and examined through rheological experiments. In conditions where the casein micelles are separated from each other, i.e., below random-close packing, the dispersions have exactly the flow and dynamic properties of the polydisp ... [J. Chem. Phys. 131, 165106 (2009)] published Thu Oct 29, 2009.

Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations

Hongxing Lei, Zhi-Xiang Wang, Chun Wu, and Yong Duan
Successful ab initio folding of proteins with both alpha-helix and beta-sheet requires a delicate balance among a variety of forces in the simulation model, which may explain that the successful folding of any alpha/beta proteins to within experimental error has yet to be reported. Here we demonstra ... [J. Chem. Phys. 131, 165105 (2009)] published Thu Oct 29, 2009.

Local and global properties of mixtures in one-dimensional systems. II. Exact results for the KirkwoodBuff integrals

Arieh Ben-Naim and Andres Santos
The KirkwoodBuff integrals for two-component mixtures in one-dimensional systems are calculated directly. The results are applied to square-well particles and found to agree with those obtained by the inversion of the KirkwoodBuff theory of solutions. ... [J. Chem. Phys. 131, 164512 (2009)] published Thu Oct 29, 2009.

Observation of buried water molecules in phospholipid membranes by surface sum-frequency generation spectroscopy

Maria Sovago, Erik Vartiainen, and Mischa Bonn
We investigate the structure and orientation of water molecules at the water-lipid interface, using vibrational sum-frequency generation in conjunction with a maximum entropy phase retrieval method. We find that interfacial water molecules have an orientation opposite to that predicted by electrosta ... [J. Chem. Phys. 131, 161107 (2009)] published Thu Oct 29, 2009.

Nondielectric long-range solvation of polar liquids in cubic symmetry

Joakim Stenhammar, Per Linse, and Gunnar Karlstrom
Long-range solvation properties of strongly coupled dipolar systems simulated using the Ewald and reaction field methods are assessed by using electric fluctuation formulas for a dielectric medium. Some components of the fluctuating electric multipole moments are suppressed, whereas other components ... [J. Chem. Phys. 131, 164507 (2009)] published Wed Oct 28, 2009.

Density-based energy decomposition analysis for intermolecular interactions with variationally determined intermediate state energies

Qin Wu, Paul W. Ayers, and Yingkai Zhang
The first purely density-based energy decomposition analysis (EDA) for intermolecular binding is developed within the density functional theory. The most important feature of this scheme is to variationally determine the frozen density energy, based on a constrained search formalism and implemented ... [J. Chem. Phys. 131, 164112 (2009)] published Wed Oct 28, 2009.

The CrD cation complex: Accurate experimental dissociation energy, intermolecular bond length, and vibrational parameters

V. Dryza and E. J. Bieske
The infrared spectrum of the T-shaped CrD complex is measured over the 27422820 cm range by detecting Cr photofragments. The main band, due to the DD stretch excitation, is shifted at 215 cm to lower energy from the Q transition of the free D molecule and displays clearly resolved rovibrational tr ... [J. Chem. Phys. 131, 164303 (2009)] published Wed Oct 28, 2009.

Near-field investigations of nanoshell cylinder dimers

Katja Hoflich, Ulrich Gosele, and Silke Christiansen
Metallic nanoparticles are known to exhibit strong particle size dependent localized surface plasmon resonances due to their specific optical response described via the complex dielectric function. Using the two-dimensional finite element method, the near-field behavior of core-shell nanocylinder di ... [J. Chem. Phys. 131, 164704 (2009)] published Wed Oct 28, 2009.

Spectroscopic study of the B Pi state of KH

Ang-Yu Lee (李昂諭) and Wei-Tzou Luh (陸維作)
The B Pi excited electronic state of KH has been observed for the first time by a pulsed fluorescence excitation spectroscopic technique. We have found only one vibrational level, in which seven e-parity and seven f-parity sublevels are identified. The Dunham-type coefficients A, A, and A and the me ... [J. Chem. Phys. 131, 164304 (2009)] published Wed Oct 28, 2009.

Effective interaction between large colloidal particles immersed in a bidisperse suspension of short-ranged attractive colloids

A. Jamnik
The effective force between two large hard spheres mimicking lyophobic colloids (solute) immersed in an asymmetric two-component mixture of smaller particles (solvents), interacting via Baxter's sticky hard sphere (SHS) potential, was studied using integral equation theory and Monte Carlo simulation ... [J. Chem. Phys. 131, 164111 (2009)] published Wed Oct 28, 2009.

Colloidal permeability of liquid membranes consisting of hard particles by nonequilibrium simulations

Maria J. Ariza and Antonio M. Puertas
A novel particulate membrane, comprised of a confined fluid of colloidal hard spheres, is presented and studied by means of simulations. Using a fluid of smaller hard spheres as feed, the transport properties of the membrane are studied as a function of the volume fractions of both the feed solution ... [J. Chem. Phys. 131, 164903 (2009)] published Wed Oct 28, 2009.

Size, shape, and flexibility of proteins and DNA

Nidhi Rawat and Parbati Biswas
Size, shape, and flexibility are the important topological parameters which characterize the functional specificity and different types of interactions in proteins and DNA. The size of proteins and DNA, often measured by the radius of gyration (R), are determined from the coordinates of their respec ... [J. Chem. Phys. 131, 165104 (2009)] published Wed Oct 28, 2009.

Analytic second derivatives in closed-shell coupled-cluster theory with spin-orbit coupling

Fan Wang and Jurgen Gauss
The theory for geometrical second derivatives of the energy is outlined for the recently suggested two-component coupled-cluster approach using relativistic effective core potentials with spin-orbit coupling included in the post-HartreeFock treatment [F. Wang, J. Gauss, and C. van Wullen, J. Chem. P ... [J. Chem. Phys. 131, 164113 (2009)] published Wed Oct 28, 2009.

Quantum dynamical effects in liquid water: A semiclassical study on the diffusion and the infrared absorption spectrum

Jian Liu, William H. Miller, Francesco Paesani, Wei Zhang, and David A. Case
The important role of liquid water in many areas of science from chemistry, physics, biology, geology to climate research, etc., has motivated numerous theoretical studies of its structure and dynamics. The significance of quantum effects on the properties of water, however, has not yet been fully r ... [J. Chem. Phys. 131, 164509 (2009)] published Wed Oct 28, 2009.

Diffractive optics based three-pulse photon echo peak shift studies of spectral diffusion in polar liquids: Evidence for long lived frequency correlations

Sohyun Park (박소현) and Taiha Joo (주태하)
We report a three-pulse photon echo peak shift (3PEPS) apparatus adopting a diffractive beam splitter to generate triplets of femtosecond pulses with tilted wave front, which enhances the overlap over the entire aperture in a noncollinear geometry while preserving femtosecond pulse duration. The app ... [J. Chem. Phys. 131, 164508 (2009)] published Wed Oct 28, 2009.

Theoretical study on effects of hydrogen bonding on the ring stretching modes of pyridine

An Yong Li, Hong Bo Ji, and Li Juan Cao
Pyridine generally acts as the proton acceptors in the hydrogen bonding interaction by using its lone pair n(N) or pi-electrons. Some previous research indicated that for the N-type H-bond, the ring breathing mode v, the N-para-C stretching mode v and the meta-CC stretching mode v of pyridine showed ... [J. Chem. Phys. 131, 164305 (2009)] published Wed Oct 28, 2009.

A pseudospectral method for optimal control of open quantum systems

Jr-Shin Li, Justin Ruths, and Dionisis Stefanatos
In this paper, we present a unified computational method based on pseudospectral approximations for the design of optimal pulse sequences in open quantum systems. The proposed method transforms the problem of optimal pulse design, which is formulated as a continuous-time optimal control problem, to ... [J. Chem. Phys. 131, 164110 (2009)] published Wed Oct 28, 2009.

A diffusional bimolecular propensity function

Daniel T. Gillespie
We derive an explicit formula for the propensity function (stochastic reaction rate) of a generic bimolecular chemical reaction in which the reactant molecules move about by diffusion, as solute molecules in a bath of much smaller and more numerous solvent molecules. Our derivation assumes that the ... [J. Chem. Phys. 131, 164109 (2009)] published Tue Oct 27, 2009.

Folding simulations of gramicidin A into the beta-helix conformations: Simulated annealing molecular dynamics study

Takaharu Mori and Yuko Okamoto
Gramicidin A is a linear hydrophobic 15-residue peptide which consists of alternating D- and L-amino acids and forms a unique tertiary structure, called the beta-helix, to act as a cation-selective ion channel in the natural conditions. In order to investigate the intrinsic ability of the gramicidin ... [J. Chem. Phys. 131, 165103 (2009)] published Tue Oct 27, 2009.

Computing the viscosity of supercooled liquids. II. Silica and strong-fragile crossover behavior

Akihiro Kushima, Xi Lin, Ju Li, Xiaofeng Qian, Jacob Eapen et al.
A recently developed atomistic method capable of calculating the fragile (non-Arrhenius) temperature behavior of highly viscous liquids is further tested by studying a model of SiO, a glass former well known for its Arrhenius temperature behavior (strong). The method predicts an Arrhenius temperatur ... [J. Chem. Phys. 131, 164505 (2009)] published Tue Oct 27, 2009.

Liquid polymorphism, order-disorder transitions and anomalous behavior: A Monte Carlo study of the BellLavis model for water

Carlos E. Fiore, Marcia M. Szortyka, Marcia C. Barbosa, and Vera B. Henriques
The BellLavis model for liquid water is investigated through numerical simulations. The lattice-gas model on a triangular lattice presents orientational states and is known to present a highly bonded low density phase and a loosely bonded high density phase. We show that the model liquid-liquid tran ... [J. Chem. Phys. 131, 164506 (2009)] published Tue Oct 27, 2009.

Spatial updating in the great grand canonical ensemble

G. Orkoulas and Daniel P. Noon
In spatial updating grand canonical Monte Carlo, particle transfers are implemented by examining the local environment around a point in space. In the present work, these algorithms are extended to very high densities by allowing the volume to fluctuate, thus forming a great grand canonical ensemble ... [J. Chem. Phys. 131, 161106 (2009)] published Tue Oct 27, 2009.

Theoretical studies of UO(OH)(HO), UO(OH)(HO), NpO(OH)(HO), and PuO(OH)(HO) (n<=21) complexes in aqueous solution

Zhiji Cao and K. Balasubramanian
Extensive ab initio calculations have been carried out to study equilibrium structures, vibrational frequencies, and the nature of chemical bonds of hydrated UO(OH), UO(OH), NpO(OH), and PuO(OH) complexes that contain up to 21 water molecules both in first and second hydration spheres in both aqueou ... [J. Chem. Phys. 131, 164504 (2009)] published Tue Oct 27, 2009.

Error and efficiency of replica exchange molecular dynamics simulations

Edina Rosta and Gerhard Hummer
We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the ... [J. Chem. Phys. 131, 165102 (2009)] published Tue Oct 27, 2009.

Ubiquitous T-shaped isomers of OCS-hydrocarbon van der Waals complexes

J. Norooz Oliaee, M. Dehghany, Mahin Afshari, N. Moazzen-Ahmadi, and A. R. W. McKellar
Many weakly bound OCS-hydrocarbon complexes exhibit a relatively simple rotation-vibration band, characteristic of a T-shaped structure, which is redshifted (by 512 cm) from the OCS monomer nu frequency. Spectra of OCS with seven chain and ring hydrocarbons are described here. They allow a straight ... [J. Chem. Phys. 131, 161105 (2009)] published Tue Oct 27, 2009.

Wavepacket approach to the cumulative reaction probability within the flux operator formalism

Sophya Garashchuk and Tijo Vazhappilly
Expressions for the singular flux operator eigenfunctions and eigenvalues are given in terms of the Dirac delta-function representable as a localized Gaussian wavepacket. This functional form enables computation of the cumulative reaction probability N(E) from the wavepacket time-correlation functio ... [J. Chem. Phys. 131, 164108 (2009)] published Mon Oct 26, 2009.

Erratum: Uncertainties in scaling factors for ab initio vibrational zero-point energies [J. Chem. Phys. 130, 114102 (2009)]

Karl K. Irikura, Russell D. Johnson, III, Raghu N. Kacker, and Rudiger Kessel
Abstract not available. [J. Chem. Phys. 131, 169902 (2009)] published Mon Oct 26, 2009.

Kinetics of collision-induced reactions between hard-sphere reactants

Ji-Hyun Kim, Sangyun Lee, Jinuk Lee, and Sangyoub Lee
We investigate the reaction kinetics of hard-sphere reactants that undergo reaction upon collision. When the reaction probability at a given collision is unity, the Noyes rate theory provides an exact expression of the rate coefficient. For the general case with the reaction probability less than un ... [J. Chem. Phys. 131, 164503 (2009)] published Mon Oct 26, 2009.

Coulomb repulsion effect in two-electron nonadiabatic tunneling through a one-level redox molecule

Alexander M. Kuznetsov, Igor G. Medvedev, and Jens Ulstrup
We investigated Coulomb repulsion effects in nonadiabatic (diabatic) two-electron tunneling through a redox molecule with a single electronic level in a symmetric electrochemical contact under ambient conditions, i.e., room temperature and condensed matter environment. The electrochemical contact is ... [J. Chem. Phys. 131, 164703 (2009)] published Mon Oct 26, 2009.

Grand potential in thermodynamics of solid bodies and surfaces

A. I. Rusanov, A. K. Shchekin, and D. V. Tatyanenko
Using the chemical potential of a solid in a dissolved state or the corresponding component of the chemical potential tensor at equilibrium with the solution, a new concept of grand thermodynamic potential for solids has been suggested. This allows generalizing the definition of Gibbs' quantity sigm ... [J. Chem. Phys. 131, 161104 (2009)] published Mon Oct 26, 2009.

Molecular alignment using coherent resonant excitation: A new proposal for stereodynamic control of chemical reactions

Nandini Mukherjee
For the mode-selective control of chemical reaction, we present a new approach of molecular alignment using coherent resonant interaction with low intensity midinfrared optical pulses. Under coherent excitation, the alignment of vibrationally excited molecules becomes a function of the optical pulse ... [J. Chem. Phys. 131, 164302 (2009)] published Mon Oct 26, 2009.

KirkwoodBuff theory of molecular and protein association, aggregation, and cellular crowding

Moon Bae Gee and Paul E. Smith
An analysis of the effect of a cosolvent on the association of a solute in solution using the KirkwoodBuff theory of solutions is presented. The approach builds on the previous results of Ben-Naim by extending the range of applicability to include any number of components at finite concentrations in ... [J. Chem. Phys. 131, 165101 (2009)] published Mon Oct 26, 2009.

Hydrophobic effects on multivalent-salt-induced self-condensation of DNA

Tomonari Sumi, Chiaki Suzuki, and Hideo Sekino
Hydrophobic effects on multivalent-salt-induced self-condensation of a single polyelectrolyte chain such as DNA are investigated through a multiscale coarse-grained simulation based on density functional theory. We show that the water-mediated hydrophobic effect that was enhanced by hydration of mul ... [J. Chem. Phys. 131, 161103 (2009)] published Mon Oct 26, 2009.