Journal of Chemical Physics: All Topics

Quasielastic and inelastic neutron scattering study of methyl group rotation in solid and liquid pentafluoroanisole and pentafluorotoluene

Christoph Smuda, Gerd Gemmecker, and Tobias Unruh
The rotational motion of the methyl group in pentafluoroanisole (PFA) and in pentafluorotoluene (PFT), respectively, was investigated by quasielastic neutron scattering (QENS). For solid PFA, the rotation can be described by a model for uniaxial rotational jumps between three equidistant sites on a ... [J. Chem. Phys. 128, 194502 (2008)] published Fri May 16, 2008.

Low-energy electron diffraction and induced damage in hydrated DNA

Thomas M. Orlando, Doogie Oh, Yanfeng Chen, and Alexandr B. Aleksandrov
Elastic scattering of 530 eV electrons within the B-DNA 5-CCGGCGCCGG-3 and A-DNA 5-CGCGAATTCGCG-3 DNA sequences is calculated using the separable representation of a free-space electron propagator and a curved wave multiple scattering formalism. The disorder brought about by the surrounding water a ... [J. Chem. Phys. 128, 195102 (2008)] published Fri May 16, 2008.

Time dependent quantum dynamics study of the Ne + H[sub 2][sup +](v = 0--4) --> NeH[sup +] + H proton transfer reaction

Jordi Mayneris, Jose Daniel Sierra, and Miguel Gonzalez
The Ne+H-->NeH+H proton transfer reaction was studied using the time dependent real wave packet quantum dynamics method at the helicity decoupling level, considering the H molecular ion in the (v=04, j=0) vibrorotational states and a wide collision energy interval. The calculated reaction probabilit ... [J. Chem. Phys. 128, 194307 (2008)] published Fri May 16, 2008.

Effects of pressure and temperature on the carrier transports in organic crystal: A first-principles study

L. J. Wang, Q. K. Li, and Z. Shuai
By employing density-functional theory coupled with HolsteinPeierls model, we investigate the pressure and temperature dependence of the hole and electron mobilities in naphthalene single crystal from atmospheric pressure up to 2.1 GPa (at room temperature) and from 5 to 296 K (at ambient pressu ... [J. Chem. Phys. 128, 194706 (2008)] published Fri May 16, 2008.

Electron impact ionization of size selected hydrogen clusters (H[sub 2])[sub N]: Ion fragment and neutral size distributions

Oleg Kornilov and J. Peter Toennies
Clusters consisting of normal H molecules, produced in a free jet expansion, are size selected by diffraction from a transmission nanograting prior to electron impact ionization. For each neutral cluster (H) (N=240), the relative intensities of the ion fragments H are measured with a mass spectromet ... [J. Chem. Phys. 128, 194306 (2008)] published Fri May 16, 2008.

Size- and charge-dependent geometric and electronic structures of Bi[sub n] (Bi[sub n][sup -]) clusters (n = 2--13) by first-principles simulations

Liming Gao, Pinglin Li, Heqiang Lu, S. F. Li, and Z. X. Guo
Neutral and negatively charged bismuth clusters, Bi and Bi (n=213), are investigated by first-principles simulations with the scalar-relativistic projector-augmented wave potential and the spin-polarized generalized gradient approximation. Both types of clusters show size-dependent odd-even oscillat ... [J. Chem. Phys. 128, 194304 (2008)] published Thu May 15, 2008.

Eckart axis conditions, Gauss' principle of least constraint, and the optimal superposition of molecular structures

Gerald R. Kneller
The relation of the Eckart axis conditions for polyatomic vibrating molecules to the problem of optimal superposition of molecular structures has been pointed out recently [J. Chem. Phys. 122, 224105 (2005)]. Here, it is shown that both problems are intimately related to Gauss' principle of least co ... [J. Chem. Phys. 128, 194101 (2008)] published Thu May 15, 2008.

Separation of long-range and short-range interactions in Rydberg states of diatomic molecules

Jeffrey J. Kay, Stephen L. Coy, Vladimir S. Petrovic, Bryan M. Wong, and Robert W. Field
Observation and analysis of the f([script-l]=3), g([script-l]=4), and h([script-l]=5) Rydberg series of CaF in the range 13<=n<=17 is presented. Simultaneous analysis of the f, g, and h Rydberg series of CaF, combined with significant improvements to the long-range model for nonpenetrating Rydberg s ... [J. Chem. Phys. 128, 194301 (2008)] published Thu May 15, 2008.

Electronic and magnetic properties of armchair and zigzag graphene nanoribbons

Frank J. Owens
The electronic properties, band gap, and ionization potential of zigzag and armchair graphene nanoribbons are calculated as a function of the number of carbon atoms in the ribbon employing density functional theory at the B3LYP/6-31G level. In armchair ribbons, the ionization potential and band gap ... [J. Chem. Phys. 128, 194701 (2008)] published Thu May 15, 2008.

Theoretical study of the dynamics of the H + CH[sub 4] and H + C[sub 2]H[sub 6] reactions using a specific-reaction-parameter semiempirical Hamiltonian

Joshua P. Layfield, Matthew D. Owens, and Diego Troya
We present a theoretical study of the reactions of hydrogen atoms with methane and ethane molecules and isotopomers. High-accuracy electronic-structure calculations have been carried out to characterize representative regions of the potential-energy surface (PES) of various reaction pathways, includ ... [J. Chem. Phys. 128, 194302 (2008)] published Thu May 15, 2008.

Energy difference space random walk to achieve fast free energy calculations

Donghong Min and Wei Yang
A method is proposed to efficiently obtain free energy differences. In the present algorithm, free energy calculations proceed by the realization of an energy difference space random walk. Thereby, this algorithm can greatly improve the sampling of the regions in phase space where target states over ... [J. Chem. Phys. 128, 191102 (2008)] published Thu May 15, 2008.

Comment on ``New method to analyze simulations of activated processes'' [J. Chem. Phys. [bold 126], 134103 (2007)]

Lawrence S. Bartell and David T. Wu
... [J. Chem. Phys. 128, 197101 (2008)] published Thu May 15, 2008.

Anomalous structural and mechanical properties of solids confined in quasi-one-dimensional strips

Debasish Chaudhuri and Surajit Sengupta
We show using computer simulations and mean field theory that a system of particles in two dimensions, when laterally confined by a pair of parallel hard walls within a quasi-one-dimensional channel, possesses several anomalous structural and mechanical properties not observed in the bulk. Depending ... [J. Chem. Phys. 128, 194702 (2008)] published Thu May 15, 2008.

Carbon nanotube motors driven by carbon nanotube

Yoshiteru Takagi, Tsuyoshi Uda, and Takahisa Ohno
We propose a new type of carbon nanotube (CNT) motor composed of a single-wall CNT (SWCNT) and a double-wall CNT (DWCNT), that are in mechanical contact. The rotational motion of our CNT motor is controllable by the translational motion of the SWCNT along the axis of the DWCNT. From molecular dynami ... [J. Chem. Phys. 128, 194704 (2008)] published Thu May 15, 2008.

Electronic contributions to infrared spectra of adsorbate molecules on metal surfaces: Ethene on Cu(1 1 1)

O. Skibbe, M. Binder, A. Otto, and A. Pucci
Already at coverages well below 1 ML copper ad-atoms on Cu(1 1 1) significantly modify infrared reflection-absorption spectra of ethene (CH) on Cu(1 1 1). Raman modes of the centrosymmetric molecule appear in the spectra. Their lines do not involve significant shifts of vibration frequencies as they ... [J. Chem. Phys. 128, 194703 (2008)] published Thu May 15, 2008.

Maximum Caliber: A variational approach applied to two-state dynamics

Gerhard Stock, Kingshuk Ghosh, and Ken A. Dill
We show how to apply a general theoretical approach to nonequilibrium statistical mechanics, called Maximum Caliber, originally suggested by E. T. Jaynes [Annu. Rev. Phys. Chem. 31, 579 (1980)], to a problem of two-state dynamics. Maximum Caliber is a variational principle for dynamics in the same s ... [J. Chem. Phys. 128, 194102 (2008)] published Thu May 15, 2008.

Subdiffusive dynamics of a liquid crystal in the isotropic phase

Luca De Gaetani, Giacomo Prampolini, and Alessandro Tani
The isotropic phase dynamics of a system of 4-n-hexyl-4-cyano-biphenyl (6CB) molecules has been studied by molecular dynamics computer simulations. We have explored the range of 275330 K keeping the system isotropic, although supercooled under its nematic transition temperature. The weak rototransl ... [J. Chem. Phys. 128, 194501 (2008)] published Thu May 15, 2008.

Coarse-grained lattice kinetic Monte Carlo simulation of systems of strongly interacting particles

Jianguo Dai, Warren D. Seider, and Talid Sinno
A general approach is presented for spatially coarse-graining lattice kinetic Monte Carlo (LKMC) simulations of systems containing strongly interacting particles. While previous work has relied on approximations that are valid in the limit of weak interactions, here we show that it is possible to co ... [J. Chem. Phys. 128, 194705 (2008)] published Thu May 15, 2008.

Topology of magnetic-field induced electron current density in the cubane molecule

Stefano Pelloni and Paolo Lazzeretti
A spatial model of the electronic current density induced in the cubane molecule by applying an external magnetic-field has been constructed employing quantum mechanical methods at the HartreeFock level of accuracy. The topological features of the current density vector field are described via a sta ... [J. Chem. Phys. 128, 194305 (2008)] published Thu May 15, 2008.

The NO + O[sub 3] reaction: A triple oxygen isotope perspective on the reaction dynamics and atmospheric implications for the transfer of the ozone isotope anomaly

J. Savarino, S. K. Bhattacharya, S. Morin, M. Baroni, and J.-F. Doussin
Atmospheric nitrate shows a large oxygen isotope anomaly (Delta O), characterized by an excess enrichment of O over O, similar to the ozone molecule. Modeling and observations assign this specific isotopic composition mainly to the photochemical steady state that exists in the atmosphere between oz ... [J. Chem. Phys. 128, 194303 (2008)] published Thu May 15, 2008.

Two scale generalized model of polypeptide chains

A. V. Badasyan, Sh. A. Tonoyan, A. V. Tsarukyan, Y. Sh. Mamasakhlisov, A. S. Benight et al.
The generalized model of polypeptide chains (GMPC) is expanded to simultaneously consider two types of interactions occurring over different scales. This new two scale GMPC is applied in several specific cases to examine: The combined influence of stacking or antistacking and hydrogen bonding, or sp ... [J. Chem. Phys. 128, 195101 (2008)] published Thu May 15, 2008.

UV-induced protonation of molecules adsorbed on ice surfaces at low temperature

Eui-Seong Moon, Chang-Woo Lee, Joon-Ki Kim, Seong-Chan Park, and Heon Kang
UV irradiation of ice films adsorbed with methylamine molecules induces protonation of the adsorbate molecules at low temperature (50130 K). The observation indicates that long-lived protonic defects are created in the ice film by UV light, and they transfer protons to the adsorbate molecules via t ... [J. Chem. Phys. 128, 191101 (2008)] published Thu May 15, 2008.

Micellar crystals in solution from molecular dynamics simulations

J. A. Anderson, C. D. Lorenz, and A. Travesset
Polymers with both soluble and insoluble blocks typically self-assemble into micelles, which are aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing concentration, these micelles often form gels that exhibit crys ... [J. Chem. Phys. 128, 184906 (2008)] published Wed May 14, 2008.

The potential energy curves of low-lying electronic states of S[sub 2]O

Huixian Han, Bingbing Suo, Zhenyi Jiang, Yubin Wang, and Zhenyi Wen
Potential energy curves (PECs) of the symmetric and asymmetric bent SO molecules are constructed using the configuration-based multireference second order perturbation theory and multireference configuration interaction with single and double excitations. Based on the PECs, the equilibrium structure ... [J. Chem. Phys. 128, 184312 (2008)] published Wed May 14, 2008.

Construction of a generalized gradient approximation by restoring the density-gradient expansion and enforcing a tight Lieb--Oxford bound

Yan Zhao and Donald G. Truhlar
Recently, a generalized gradient approximation (GGA) to the density functional, called PBEsol, was optimized (one parameter) against the jellium-surface exchange-correlation energies, and this, in conjunction with changing another parameter to restore the first-principles gradient expansion for exch ... [J. Chem. Phys. 128, 184109 (2008)] published Wed May 14, 2008.

A spline for your saddle

Rebecca Granot and Roi Baer
Pinpointing extrema on a multidimensional hypersurface is an important generic problem with a broad scope of application in statistical mechanics, biophysics, chemical reaction dynamics, and quantum chemistry. Local minima of the hypersurface correspond to metastable structures and are usually the m ... [J. Chem. Phys. 128, 184111 (2008)] published Wed May 14, 2008.

Thermodynamically consistent integral equation for soft repulsive spheres

Mauricio D. Carbajal-Tinoco
We present a new closure relation that is an extension of the thermodynamically consistent approximation of Rogers and Young [Phys. Rev. A 30, 999 (1984)]. In the proposed closure, we introduce a nonlinear term along with an additional thermodynamic consistency equation. We compare some thermodynami ... [J. Chem. Phys. 128, 184507 (2008)] published Wed May 14, 2008.

Analysis of charge transfer effects in molecular complexes based on absolutely localized molecular orbitals

Rustam Z. Khaliullin, Alexis T. Bell, and Martin Head-Gordon
A new method based on absolutely localized molecular orbitals (ALMOs) is proposed to measure the degree of intermolecular electron density delocalization (charge transfer) in molecular complexes. ALMO charge transfer analysis (CTA) enables separation of the forward and backward charge transfer compo ... [J. Chem. Phys. 128, 184112 (2008)] published Wed May 14, 2008.

Local hardness equalization: Exploiting the ambiguity

Paul W. Ayers and Robert G. Parr
In the density-functional theory of chemical reactivity, the local hardness is known to be an ambiguous concept. The mathematical structure associated with this problematic situation is elaborated and three common definitions for the local hardness are critically examined: the frontier local hardnes ... [J. Chem. Phys. 128, 184108 (2008)] published Wed May 14, 2008.

Gibbs ensemble Monte Carlo simulation of adsorption for model surfactant solution in confined slit pores

Lili Liu, Xiaoning Yang, and Zhijun Xu
An isobaric-isothermal Gibbs ensemble Monte Carlo simulation has been carried out to study the adsorption of a model surfactant/solvent mixture in slit nanopores. The adsorption isotherms, the density distributions, and the configuration snapshots were simulated to illustrate the adsorption and self ... [J. Chem. Phys. 128, 184712 (2008)] published Wed May 14, 2008.

Solution of the Percus-Yevick equation for hard disks

M. Adda-Bedia, E. Katzav, and D. Vella
The authors solve the Percus-Yevick equation in two dimensions by reducing it to a set of simple integral equations. They numerically obtain both the pair correlation function and the equation of state for a hard disk fluid and find good agreement with available Monte Carlo results. The present meth ... [J. Chem. Phys. 128, 184508 (2008)] published Wed May 14, 2008.

Deuteron NMR relaxation, spectra, and evidence for the order-disorder phase transition in (ND[sub 4])[sub 2]PtCl[sub 6]

A. Birczynski, E. E. Ylinen, M. Punkkinen, M. Prager, A. M. Szymocha et al.
Deuteron NMR relaxation and spectra were studied at the resonance frequency of 46 MHz in polycrystalline (ND)PtCl between 3005 K. The relaxation rate maximum near 50 K is about 53% smaller than the calculated maximum related to 120 degrees rotations about the threefold symmetry axes of the ammon ... [J. Chem. Phys. 128, 184510 (2008)] published Wed May 14, 2008.

Complex-time velocity autocorrelation functions for Lennard-Jones fluids with quantum pair-product propagators

Jeb Kegerreis, Akira Nakayama, and Nancy Makri
We use the pair-product approximation to the complex-time quantum mechanical propagator to obtain accurate quantum mechanical results for the symmetrized velocity autocorrelation function of a Lennard-Jones fluid at two points on the thermodynamic phase diagram. A variety of tests are performed to d ... [J. Chem. Phys. 128, 184509 (2008)] published Wed May 14, 2008.

Single-sweep methods for free energy calculations

Luca Maragliano and Eric Vanden-Eijnden
A simple, efficient, and accurate method is proposed to map multidimensional free energy landscapes. The method combines the temperature-accelerated molecular dynamics (TAMD) proposed in [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006)] with a variational reconstruction method ... [J. Chem. Phys. 128, 184110 (2008)] published Wed May 14, 2008.

Electronic and structural investigations of gold clusters doped with copper: Au[sub n - 1]Cu[sup -] (n = 13--19)

Shahab Zorriasatein, Kavita Joshi, and D. G. Kanhere
We have obtained the ground state and the equilibrium geometries of Au and AuCu in the size range of n=1319. We have used first principles density functional theory within plane wave and Gaussian basis set methods. For each of the cluster we have obtained at least 100 distinct isomers. The anions of ... [J. Chem. Phys. 128, 184314 (2008)] published Wed May 14, 2008.

Theory of resonance energy transfer involving nanocrystals: The role of high multipoles

Roi Baer and Eran Rabani
A theory for the fluorescence resonance energy transfer (FRET) between a pair of semiconducting nanocrystal quantum dots is developed. Two types of donor-acceptor couplings for the FRET rate are described: dipole-dipole (d-d) and the dipole-quadrupole (d-q) couplings. The theory builds on a simple e ... [J. Chem. Phys. 128, 184710 (2008)] published Wed May 14, 2008.

Conformational study of jet-cooled L-phenylglycine

Hyung Min Kim, Kyu Young Han, Juyeon Park, Seong Keun Kim, and Zee Hwan Kim
We investigated the conformational structures of L-phenylglycine in the gas phase by photoionization and double resonance spectroscopy techniques as well as high-level ab initio calculations. The UV-UV and IR-UV double resonance spectroscopy suggested that there exists only one conformer that has a ... [J. Chem. Phys. 128, 184313 (2008)] published Wed May 14, 2008.

Theory of laser enhancement of ultracold reactions: The fermion-boson population transfer by adiabatic passage of [sup 6]Li+[sup 6]Li[sup 7]Li(T[sub r] = 1 mK) -->[sup 6]Li[sup 6]Li+[sup 7]Li(T[sub p] = 1 mK)

Xuan Li and Gregory A. Parker
We present a new theory of population transfer by adiabatic passage. This theory relates laser catalysis to adiabatic passage, enhancing chemical reactions with the freedom to choose the translational energies of the reactants and products separately. The process, A+BC<-->ABC(v)<-->AB+C, involves tw ... [J. Chem. Phys. 128, 184113 (2008)] published Wed May 14, 2008.

Density functional theory of inhomogeneous liquids. II. A fundamental measure approach

James F. Lutsko
Previously, it has been shown that the direct correlation function for a LennardJones fluid could be modeled by a sum of that for hard-spheres, a mean-field tail, and a simple linear correction in the core region constructed so as to reproduce the (known) bulk equation of state of the fluid [Lutsko, ... [J. Chem. Phys. 128, 184711 (2008)] published Wed May 14, 2008.

Ab initio based polarizable force field parametrization

Marco Masia
Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics si ... [J. Chem. Phys. 128, 184107 (2008)] published Wed May 14, 2008.

Single particle and pair dynamics in water--formic acid mixtures containing ionic and neutral solutes: Nonideality in dynamical properties

Rini Gupta and Amalendu Chandra
A series of molecular dynamics simulations of waterformic acid mixtures containing either an ionic solute or a neutral hydrophobic solute has been performed to study the extent of nonideality in the dynamics of these solutes for varying composition of the mixtures. The diffusion coefficients of the ... [J. Chem. Phys. 128, 184506 (2008)] published Tue May 13, 2008.

Insights from first principles molecular dynamics studies toward infrared multiple-photon and single-photon action spectroscopy: Case study of the proton-bound dimethyl ether dimer

Xiaohu Li, David T. Moore, and Srinivasan S. Iyengar
We have used finite temperature ab initio molecular dynamics simulations in conjunction with computation of critical quantum nuclear effects to probe the differences between single-photon argon tagged action spectral results and infrared multiple-photon dissociation experiments for a proton bound mo ... [J. Chem. Phys. 128, 184308 (2008)] published Tue May 13, 2008.

Structures and electronic properties of small FeB[sub n] (n = 1--10) clusters

Zhi Yang and Shi-Jie Xiong
The geometries, stabilities, electronic properties, and magnetism of FeB clusters up to n=10 are systematically studied with density functional theory. We find that our optimized structures of FeB, FeB, FeB, and FeB clusters are more stable than those proposed in previous literature. The results sho ... [J. Chem. Phys. 128, 184310 (2008)] published Tue May 13, 2008.

Electronic polarizability and Judd--Ofelt parameters of Nd[sup 3+] and Er[sup 3+] ions in transparent crystallized glasses with nonlinear optical Ba[sub 2]TiSi[sub 2]O[sub 8] nanocrystals

N. Maruyama, T. Honma, and T. Komatsu
Transparent crystallized glasses consisting of nonlinear optical BaTiSiO nanocrystals are prepared in EuO-, NdO-, and ErO-doped 40BaO20TiO40SiO glasses by a conventional heat treatment method in order to clarify the optical properties of rare-earth (RE) ions in nanocrystals. The electronic polarizab ... [J. Chem. Phys. 128, 184706 (2008)] published Tue May 13, 2008.

Theoretical and experimental studies of collision-induced electronic energy transfer from v = 0--3 of the E(0[sub g][sup +]) ion-pair state of Br[sub 2]: Collisions with He and Ar

J. Matthew Hutchison, Robin R. O'Hern, Thomas A. Stephenson, Yury V. Suleimanov, and Alexei A. Buchachenko
Collisions of Br, prepared in the E(0) ion-pair (IP) electronic state, with He or Ar result in electronic energy transfer to the D, D, and beta IP states. These events have been examined in experimental and theoretical investigations. Experimentally, analysis of the wavelength resolved emission spec ... [J. Chem. Phys. 128, 184311 (2008)] published Tue May 13, 2008.

Hartree--Fock calculations with linearly scaling memory usage

Elias Rudberg, Emanuel H. Rubensson, and Pawel Salek
We present an implementation of a set of algorithms for performing HartreeFock calculations with resource requirements in terms of both time and memory directly proportional to the system size. In particular, a way of directly computing the HartreeFock exchange matrix in sparse form is described whi ... [J. Chem. Phys. 128, 184106 (2008)] published Tue May 13, 2008.

Minimum energy pathways of brittle and ductile deformation/fracture processes

Dirk Zahn
An alternative approach to exploring deformation and fracture processes from molecular dynamics simulations is presented. The underlying concept is based on the transition path sampling scheme which was proven powerful for unprejudiced mechanistic analyses of rare reaction events and phase transitio ... [J. Chem. Phys. 128, 184707 (2008)] published Tue May 13, 2008.

Interface electronic states and molecular structure of a triarylamine based hole conductor on rutile TiO[sub 2](110)

E. M. J. Johansson, M. Odelius, P. G. Karlsson, H. Siegbahn, A. Sandell et al.
The molecular and electronic surface structure of a triarylamine based hole-conductor (HC) molecule evaporated onto rutile TiO(110) single crystal is investigated by means of synchrotron light based photoelectron spectroscopy and x-ray absorption spectroscopy in combination with calculations based o ... [J. Chem. Phys. 128, 184709 (2008)] published Tue May 13, 2008.

Gamma-point lattice free energy estimates from O(1) force calculations

Johannes Voss and Tejs Vegge
We present a new method for estimating the vibrational free energy of crystal (and molecular) structures employing only a single force calculation, for a particularly displaced configuration, in addition to the calculation of the ground state configuration. This displacement vector is the sum of the ... [J. Chem. Phys. 128, 184708 (2008)] published Tue May 13, 2008.

H/D isotope effect of methyl internal rotation for acetaldehyde in ground state as calculated from a multicomponent molecular orbital method

Takayoshi Ishimoto, Yasuyuki Ishihara, Hiroyuki Teramae, Masaaki Baba, and Umpei Nagashima
We have analyzed the differences in the methyl internal rotation induced by the H/D isotope effect for acetaldehyde (CHCHO) and deuterated acetaldehyde (CDCDO) in ground state by means of the multicomponent molecular orbital (MC[underaccent underbar [below] MO) method, which directly accounts for t ... [J. Chem. Phys. 128, 184309 (2008)] published Tue May 13, 2008.

The range of ambient radius for an active bubble in sonoluminescence and sonochemical reactions

Kyuichi Yasui, Toru Tuziuti, Judy Lee, Teruyuki Kozuka, Atsuya Towata et al.
Numerical simulations of nonequilibrium chemical reactions inside an air bubble in liquid water irradiated by ultrasound have been performed for various ambient bubble radii. The intensity of sonoluminescence (SL) has also been calculated taking into account electron-atom bremsstrahlung, radiative a ... [J. Chem. Phys. 128, 184705 (2008)] published Tue May 13, 2008.

Entropy of polydisperse chains: Solution on the Bethe lattice

Minos A. Neto and Jurgen F. Stilck
We consider the entropy of polydisperse chains placed on a lattice. In particular, we study a model for equilibrium polymerization, where the polydispersivity is determined by two activities, for internal and endpoint monomers of a chain. We solve the problem exactly on a Bethe lattice with arbitrar ... [J. Chem. Phys. 128, 184904 (2008)] published Tue May 13, 2008.

Molecular dynamics simulations on the local order of liquid and amorphous ZnTe

Jose Pedro Rino, Denilson Borges, Rita C. Mota, and Mauricio A. P. Silva
Molecular dynamics studies of structural and dynamical correlations of molten and vitreous states under several conditions of density and temperature were performed. We use an effective recently proposed interatomic potential, consisting of two- and three-body covalent interactions which has success ... [J. Chem. Phys. 128, 184704 (2008)] published Tue May 13, 2008.

Optimal control design of NMR and dynamic nuclear polarization experiments using monotonically convergent algorithms

Ivan I. Maximov, Zdenek Tosner, and Niels Chr. Nielsen
Optimal control theory has recently been introduced to nuclear magnetic resonance (NMR) spectroscopy as a means to systematically design and optimize pulse sequences for liquid- and solid-state applications. This has so far primarily involved numerical optimization using gradient-based methods, whic ... [J. Chem. Phys. 128, 184505 (2008)] published Tue May 13, 2008.

Rheological complexity in simple chain models

Taylor C. Dotson, Julieanne V. Heffernan, Joanne Budzien, Keenan T. Dotson, Francisco Avila et al.
Dynamical properties of short freely jointed and freely rotating chains are studied using molecular dynamics simulations. These results are combined with those of previous studies, and the degree of rheological complexity of the two models is assessed. New results are based on an improved analysis p ... [J. Chem. Phys. 128, 184905 (2008)] published Tue May 13, 2008.

Mode excitation Monte Carlo simulations of mesoscopically large membranes

Oded Farago
Solvent-free coarse grained models represent one of the most promising approaches for molecular simulations of mesoscopically large membranes. In these models, the size of the simulated membrane is limited by the slow relaxation time of the longest bending mode. Here, we present a Monte Carlo algori ... [J. Chem. Phys. 128, 184105 (2008)] published Tue May 13, 2008.

Probing interactions between core-electron transitions by ultrafast two-dimensional x-ray coherent correlation spectroscopy

Igor V. Schweigert and Shaul Mukamel
Two-dimensional x-ray correlation spectra (2DXCS) obtained by varying two delay periods in a time-resolved coherent all-x-ray four-wave-mixing measurement are simulated for the N 1s and O 1s transitions of aminophenol. The necessary valence and core-excited states are calculated using singly and dou ... [J. Chem. Phys. 128, 184307 (2008)] published Mon May 12, 2008.

A molecular view of heterogeneous catalysis

Claus Hviid Christensen and Jens K. Norskov
The establishment of a molecular view of heterogeneous catalysis has been hampered for a number of reasons. There are, however, recent developments, which show that we are now on the way towards reaching a molecular-scale picture of the way solids work as catalysts. By a combination of new theoretic ... [J. Chem. Phys. 128, 182503 (2008)] published Mon May 12, 2008.

Modeling doped and defective oxides in catalysis with density functional theory methods: Room for improvements

Gianfranco Pacchioni
Due to the well-known problem of the self-interaction, standard density functional theory (DFT) methods tend to produce delocalized holes and electrons in defective oxide materials even when there is ample experimental evidence of a strong localization. For late transition metal compounds or rare ea ... [J. Chem. Phys. 128, 182505 (2008)] published Mon May 12, 2008.

Non-Faradaic electrochemical activation of catalysis

Costas G. Vayenas and Costas G. Koutsodontis
The use of fuel cells for carrying out oxidation reactions with cogeneration of electrical power and chemicals led, upon cofeeding oxygen and fuel at the anode, to the discovery of the effect of non-Faradaic electrochemical modification of catalytic activity or electrochemical promotion of catalysis ... [J. Chem. Phys. 128, 182506 (2008)] published Mon May 12, 2008.

Heterogeneous catalysis: Enigmas, illusions, challenges, realities, and emergent strategies of design

John Meurig Thomas
Predominantly this article deals with the question of how to design new solid catalysts for a variety of industrial and laboratory-orientated purposes. A generally applicable strategy, illustrated by numerous examples, is made possible based on the use of nanoporous materials on to the (high-area) i ... [J. Chem. Phys. 128, 182502 (2008)] published Mon May 12, 2008.

Evolution of the surface science of catalysis from single crystals to metal nanoparticles under pressure

Gabor A. Somorjai and Jeong Y. Park
Vacuum studies of metal single crystal surfaces using electron and molecular beam scattering revealed that the surface atoms relocate when the surface is clean (reconstruction) and when it is covered by adsorbates (adsorbate-induced restructuring). It was also discovered that atomic steps and other ... [J. Chem. Phys. 128, 182504 (2008)] published Mon May 12, 2008.

Advanced synthesis for advancing heterogeneous catalysis

Peter C. Stair
There are tremendous needs and opportunities for the understanding and application of heterogeneous catalysis in the solution of vexing technological problems. Nanoscale, catalytically active phases, particularly metal nanoparticles and metal oxide clusters, supported on high surface area oxides (su ... [J. Chem. Phys. 128, 182507 (2008)] published Mon May 12, 2008.

Preface to Special Topic: A Survey of Some New Developments in Heterogeneous Catalysis

H. Metiu
This special topic section on heterogeneous catalysis contains essays on fast-evolving topics by several leading scientists in the field. In this preface, I outline those issues, raised in the special topic articles, that seemed most interesting to me. I selected those aspects that should be of grea ... [J. Chem. Phys. 128, 182501 (2008)] published Mon May 12, 2008.

Negative Poisson's ratios in siliceous zeolite MFI-silicalite

Carmen Sanchez-Valle, Zoe A. D. Lethbridge, Stanislav V. Sinogeikin, Jennifer J. Williams, Richard I. Walton et al.
Brillouin scattering measurements of the single-crystal elastic properties of the as-made zeolite silicalite |(CH)NF|[SiO]-MFI provides the first experimental evidence for on-axis negative Poisson's ratios (auxeticity) in a synthetic zeolite structure. MFI laterally contracts when compressed and lat ... [J. Chem. Phys. 128, 184503 (2008)] published Fri May 9, 2008.

Tests of Monte Carlo perturbation theory for the free energy of liquid copper

C. W. Greeff
Monte Carlo perturbation theory, in which terms in the thermodynamic perturbation series are evaluated by Monte Carlo averaging, has potentially large advantages in efficiency for calculating free energies of liquids from ab initio potential surfaces. In order to test the accuracy of perturbation th ... [J. Chem. Phys. 128, 184104 (2008)] published Fri May 9, 2008.

Vibrational overtone initiated unimolecular dissociation of HOCH[sub 2]OOH and HOCD[sub 2]OOH: Evidence for mode selective behavior

Jamie Matthews, Juliane L. Fry, Coleen M. Roehl, Paul O. Wennberg, and Amitabha Sinha
The vibrational overtone induced unimolecular dissociation of HMHP (HOCHOOH) and HMHP-d (HOCDOOH) into OH and HOCHO (HOCDO) fragments is investigated in the region of the 4nu and 5nu bands. The unimolecular dissociation rates in the threshold region, corresponding to the 4nu band, exhibit measurable ... [J. Chem. Phys. 128, 184306 (2008)] published Fri May 9, 2008.

Confinement free energy of flexible polyelectrolytes in spherical cavities

Rajeev Kumar and M. Muthukumar
A weakly charged flexible polyelectrolyte chain in a neutral spherical cavity is analyzed by using self-consistent field theory within an explicit solvent model. Assuming the radial symmetry for the system, it is found that the confinement of the chain leads to creation of a charge density wave alon ... [J. Chem. Phys. 128, 184902 (2008)] published Fri May 9, 2008.

Effectively doubling the magnetic field in spin-(1/2)--spin-1, HSQC, HDQC, coupled HSQC, and coupled HDQC in solution NMR

S. Chandra Shekar, Jonathan M. Backer, and Mark E. Girvin
Pulse sequences for spin-(1/2)spin-1 pair heteronuclear single quantum correlation (HSQC), heteronuclear double quantum correlation (HDQC), and coupled-HSQC, and coupled-HDQC NMR spectroscopies are outlined, and experimental realization for a CH pair is demonstrated in solution state. In both the co ... [J. Chem. Phys. 128, 184501 (2008)] published Fri May 9, 2008.

Benchmark calculations for reduced density-matrix functional theory

N. N. Lathiotakis and Miguel A. L. Marques
Reduced density-matrix functional theory (RDMFT) is a promising alternative approach to the problem of electron correlation. Like standard density functional theory, it contains an unknown exchange-correlation functional, for which several approximations have been proposed in the last years. In this ... [J. Chem. Phys. 128, 184103 (2008)] published Fri May 9, 2008.

Interchain coupling effects on dynamics of photoexcitations in conjugated polymers

Y. Meng, B. Di, X. J. Liu, Z. An, and C. Q. Wu
Within an extended SuSchriefferHeeger model including interchain interactions and the extended Hubbard model, the dynamical relaxation of photoexcitations in two coupled conjugated polymer chains is investigated by using a nonadiabatic evolution method. Initially, one of the two chains is photoexcit ... [J. Chem. Phys. 128, 184903 (2008)] published Fri May 9, 2008.

Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory

Yoshiteru Yonetani, Yutaka Maruyama, Fumio Hirata, and Hidetoshi Kono
Because proteins and DNA interact with each other and with various small molecules in the presence of water molecules, we cannot ignore their hydration when discussing their structural and energetic properties. Although high-resolution crystal structure analyses have given us a view of tightly bound ... [J. Chem. Phys. 128, 185102 (2008)] published Fri May 9, 2008.

A new class of silicon-carbon clusters: A full study of the hydrogenated Si[sub n]C[sub 2]H[sub 2], n = 3,4,5, clusters in comparison with their isoelectronic carboranes C[sub 2]B[sub n]H[sub n + 2]

Aristides D. Zdetsis
The structural and electronic characteristics of the SiCH, n=3,4,5, clusters are studied by ab initio calculations based on coupled cluster and density functional theory using the hybrid B3LYP functional. It is demonstrated that all three clusters are structurally and electronically homologous to th ... [J. Chem. Phys. 128, 184305 (2008)] published Fri May 9, 2008.

Melting mechanism of monolayers adsorbed in cylindrical pores: The influence of the pore wall roughness

B. Kuchta, L. Firlej, R. Denoyel, S. Rols, M. R. Johnson et al.
We have analyzed the mechanism of melting of molecular layers adsorbed in porous materials with cylindrical pores and rough pore walls. The working example studied here is a monolayer of methane molecules adsorbed in MCM-41 pore of diameter 2R=4 nm. Both experimental (neutron scattering) and simula ... [J. Chem. Phys. 128, 184703 (2008)] published Fri May 9, 2008.

Infrared absorption line shapes in the classical limit: A comparison of the classical dipole and fluctuating frequency approximations

J. R. Schmidt and S. A. Corcelli
Infrared spectroscopy is a versatile technique for probing the structure and dynamics of condensed-phase systems. Simulating infrared absorption spectra with molecular dynamics (MD) offers a powerful means to establish a molecular-level interpretation of experimental results, as well as a basis for ... [J. Chem. Phys. 128, 184504 (2008)] published Fri May 9, 2008.

Damping of sound waves in the terahertz range and strength of the boson peak

Livia E. Bove, C. Petrillo, A. Fontana, and A. P. Sokolov
By applying a new two-step line-shape analysis to inelastic neutron and x-ray scattering spectra of glassy systems, we were able to resolve the acoustic excitations from the low-frequency excess modes and to accurately estimate the damping of sound waves in the terahertz frequency range. Using this ... [J. Chem. Phys. 128, 184502 (2008)] published Fri May 9, 2008.

Time-dependent multiconfiguration theory for electronic dynamics of molecules in intense laser fields: A description in terms of numerical orbital functions

Tsuyoshi Kato and Hirohiko Kono
The equations of motion (EOMs) for spin orbitals in the coordinate representation are derived within the framework of the time-dependent multiconfiguration theory developed for electronic dynamics of molecules in intense laser fields. We then tailor the EOMs for diatomic (or linear) molecules to app ... [J. Chem. Phys. 128, 184102 (2008)] published Fri May 9, 2008.

Neutron scattering investigation of a diluted blend of poly(ethylene oxide) in polyethersulfone

A.-C. Genix, A. Arbe, S. Arrese-Igor, J. Colmenero, D. Richter et al.
By using quasielastic neutron scattering (QENS) with isotopic labeling we have investigated the component dynamics in a miscible blend of polyethersulfone (PES) and poly(ethylene oxide) (PEO) with 75% content in weight of PES. Due to the large difference in the glass-transition temperatures, T's, of ... [J. Chem. Phys. 128, 184901 (2008)] published Thu May 8, 2008.

Dynamics of the F[sub 2] reaction with the simplest pi-bonding molecule

Yu-Ju Lu, Tingxian Xie, Jing-Wen Fang, Hua-Chieh Shao, and Jim J. Lin
The reaction of F+CH has been investigated with crossed molecular beam experiments and high level ab initio calculations. For a wide range of collision energies up to 11 kcal/mol, only one reaction channel could be observed in the gas phase. The primary products of this channel were identified as F ... [J. Chem. Phys. 128, 184302 (2008)] published Thu May 8, 2008.

Nonadiabatic transitions between lambda-doubling states in the capture of a diatomic molecule by an ion

M. Auzinsh, E. I. Dashevskaya, I. Litvin, E. E. Nikitin, and J. Troe
The low-energy capture of a dipolar diatomic molecule in an adiabatically isolated electronic state with a good quantum number Omega (Hund's coupling case a) by an ion occurs adiabatically with respect to rotational transitions of the diatom. However, the capture dynamics may be nonadiabatic with re ... [J. Chem. Phys. 128, 184304 (2008)] published Thu May 8, 2008.

Ultrafast transformation of graphite to diamond: An ab initio study of graphite under shock compression

Christopher J. Mundy, Alessandro Curioni, Nir Goldman, I.-F. Will Kuo, Evan J. Reed et al.
We report herein ab initio molecular dynamics simulations of graphite under shock compression in conjunction with the multiscale shock technique. Our simulations reveal that a novel short-lived layered diamond intermediate is formed within a few hundred of femtoseconds upon shock loading at a shock ... [J. Chem. Phys. 128, 184701 (2008)] published Thu May 8, 2008.

Phase, shape, and architecture of SF[sub 6] and SF[sub 6]/CO[sub 2] aerosol particles: Infrared spectra and modeling of vibrational excitons

George Firanescu, David Luckhaus, and Ruth Signorell
Information on the phase, shape, and architecture of pure SF and mixed SF/CO aerosol particles is extracted from experimental infrared spectra by comparison with predictions from quantum mechanical exciton calculations. The radius of the particles lies around 50 nm. The following extensions to our ... [J. Chem. Phys. 128, 184301 (2008)] published Thu May 8, 2008.

Adiabatic and nonadiabatic dynamics in the CH[sub 3](CD[sub 3]) + HCl reaction

Bertrand Retail, Julie K. Pearce, Stuart J. Greaves, Rebecca A. Rose, and Andrew J. Orr-Ewing
The scattering dynamics leading to the formation of Cl (P) and Cl (P) products of the CH+HCl reaction (at a mean collision energy =22.3 kcal mol) and the Cl (P) products of the CD+HCl reaction (at =19.4 kcal mol) have been investigated by using photodissociation of CHI and CDI as sources of tran ... [J. Chem. Phys. 128, 184303 (2008)] published Thu May 8, 2008.

Density functional study on the structural and thermodynamic properties of aqueous DNA-electrolyte solution in the framework of cell model

Ke Wang, Yang-Xin Yu, and Guang-Hua Gao
A density functional theory (DFT) in the framework of cell model is proposed to calculate the structural and thermodynamic properties of aqueous DNA-electrolyte solution with finite DNA concentrations. The hard-sphere contribution to the excess Helmholtz energy functional is derived from the modifie ... [J. Chem. Phys. 128, 185101 (2008)] published Thu May 8, 2008.

Chiral nanopatterned surfaces as versatile enantiospecific adsorbents: A Monte Carlo model

Pawel Szabelski
This paper deals with the application of the Monte Carlo simulation method for modeling of adsorption of chiral molecules on a planar surface patterned with active binding sites. The enantiomers are assumed to be rigid chains composed of four identical segments, each occupying one binding site. The ... [J. Chem. Phys. 128, 184702 (2008)] published Thu May 8, 2008.

Accurate time propagation for the Schr[o-umlaut]dinger equation with an explicitly time-dependent Hamiltonian

Katharina Kormann, Sverker Holmgren, and Hans O. Karlsson
Several different numerical propagation techniques for explicitly time-dependent Hamiltonians are discussed and compared, with the focus on models of pump-probe experiments. The quality of the rotating wave approximation is analyzed analytically, and we point out under which circumstances the modeli ... [J. Chem. Phys. 128, 184101 (2008)] published Thu May 8, 2008.

Where there is a valley, there is a peak: Study of ion size and image effects on nanoelectroosmotic pumping

Yu Liu and Jun Yang
With the advent of nanotechnology, nano-electro-osmosis flow (nano-EOF) has shown great promise in the next generation of lab-on-a-chip systems such as attoliter or picoliter syringes or pipettors. In order to optimize the design of such systems and to precisely control analysis processes, it is imp ... [J. Chem. Phys. 128, 174708 (2008)] published Wed May 7, 2008.

Multiple free energies from a single simulation: Extending enveloping distribution sampling to nonoverlapping phase-space distributions

Clara D. Christ and Wilfred F. van Gunsteren
A recently proposed method to obtain free energy differences for multiple end states from a single simulation of a reference state which was called enveloping distribution sampling (EDS) [J. Chem. Phys. 126, 184110 (2007)] is expanded to situations where the end state configuration space densities d ... [J. Chem. Phys. 128, 174112 (2008)] published Wed May 7, 2008.

Perturbative theory and modeling of electronic-resonance-enhanced coherent anti-Stokes Raman scattering spectroscopy of nitric oxide

Joel P. Kuehner, Sameer V. Naik, Waruna D. Kulatilaka, Ning Chai, Normand M. Laurendeau et al.
A theory is developed for three-laser electronic-resonance-enhanced (ERE) coherent anti-Stokes Raman scattering (CARS) spectroscopy of nitric oxide (NO). A vibrational Q-branch Raman polarization is excited in the NO molecule by the frequency difference between visible Raman pump and Stokes beams. A ... [J. Chem. Phys. 128, 174308 (2008)] published Wed May 7, 2008.

Structure and function of window glass and Pyrex

J. C. Phillips and R. Kerner
Window glass is a ternary mixture, while Pyrex (after window glass, the most common form of commercial glass) is a quaternary. Here, we investigate the chemical, physical, and mathematical factors that determine the compositions of these optimized glasses. Previously, we succeeded in deriving exactl ... [J. Chem. Phys. 128, 174506 (2008)] published Wed May 7, 2008.

A new method to calculate Franck--Condon factors of multidimensional harmonic oscillators including the Duschinsky effect

Jia-Lin Chang
Calculations of FranckCondon factors are crucial for interpreting vibronic spectra of molecules and studying nonradiative processes. We have developed a new method for calculating FranckCondon factors of multidimensional harmonic oscillators including the Duschinsky effect. Closed-form formulas of t ... [J. Chem. Phys. 128, 174111 (2008)] published Wed May 7, 2008.

A comparative study of the Si + O[sub 2] --> SiO + O reaction dynamics from quasiclassical trajectory and statistical based methods

Fabrice Dayou, Pascal Larregaray, Laurent Bonnet, Jean-Claude Rayez, Pedro Nilo Arenas et al.
The dynamics of the singlet channel of the Si+O-->SiO+O reaction is investigated by means of quasiclassical trajectory (QCT) calculations and two statistical based methods, the statistical quantum method (SQM) and a semiclassical version of phase space theory (PST). The dynamics calculations have be ... [J. Chem. Phys. 128, 174307 (2008)] published Wed May 7, 2008.

Kinetic Monte Carlo studies of hydrogen abstraction from graphite

H. M. Cuppen and L. Hornekaer
We present Monte Carlo simulations on EleyRideal abstraction reactions of atomic hydrogen chemisorbed on graphite. The results are obtained via a hybrid approach where energy barriers derived from density functional theory calculations are used as input to Monte Carlo simulations. By comparing with ... [J. Chem. Phys. 128, 174707 (2008)] published Wed May 7, 2008.

Spatial symmetry holes in many-electron atoms and molecules

Toshikatsu Koga and Masahiro Sekiya
When a many-electron system has a spatial symmetry, it is shown that there exist spatial symmetry holes, which imply that two or more electrons are prohibited from being at certain spatial positions simultaneously. Inversion holes, rotation holes, and reflection holes, which result from inversion, t ... [J. Chem. Phys. 128, 174110 (2008)] published Wed May 7, 2008.

1/f spectrum and memory function analysis of solvation dynamics in a room-temperature ionic liquid

Daun Jeong, M. Y. Choi, YounJoon Jung, and Hyung J. Kim
To understand the nonexponential relaxation associated with solvation dynamics in the ionic liquid 1-ethyl-3-methylimidazolium hexafluorophosphate, we study power spectra of the fluctuating FranckCondon energy gap of a diatomic probe solute via molecular dynamics simulations. Results show 1/f depend ... [J. Chem. Phys. 128, 174504 (2008)] published Tue May 6, 2008.

A suitable model for emeraldine salt

Adrian Varela-Alvarez and Jose A. Sordo
A new mechanism for the formation of doped polyaniline is presented. Besides providing suitable structural and spectroscopic parameters, the new mechanism allows for the rationalization of the experimentally observed equilibrium between polaron and bipolaron defects in emeraldine salt. The magnetic ... [J. Chem. Phys. 128, 174706 (2008)] published Tue May 6, 2008.

Unexpected molecular weight dependence of shish-kebab structure in the oriented linear low density polyethylene/high density polyethylene blends

Si Liang, Ke Wang, Changyu Tang, Qin Zhang, Rongni Du et al.
In this study, highly oriented shish-kebab structure was achieved via imposing oscillatory shear on the melts of linear low density polyethylene (LLDPE)/high density polyethylene (HDPE) blends during the packing stage of injection molding. To investigate the effect of molecular weight of HDPE on the ... [J. Chem. Phys. 128, 174902 (2008)] published Tue May 6, 2008.

Parametric polarization pulse shaping demonstrated for optimal control of NaK

Stefan M. Weber, Mateusz Plewicki, Fabian Weise, and Albrecht Lindinger
We present a routine for calculating and producing customized/parametric femtosecond laser pulses for investigating molecular processes involving the polarization. It is applied on the ionization of NaK molecules by feedback-loop optimization using the recently introduced double-pass serial setup th ... [J. Chem. Phys. 128, 174306 (2008)] published Tue May 6, 2008.

On the nature of the high-frequency relaxation in a molecular glass former: A joint study of glycerol by field cycling NMR, dielectric spectroscopy, and light scattering

C. Gainaru, O. Lips, A. Troshagina, R. Kahlau, A. Brodin et al.
Fast field cycling H NMR relaxometry is applied to determine the dispersion of spin-lattice relaxation time T(omega) of the glass former glycerol in broad temperature (75360 K) and frequency (10 kHz30 MHz) ranges. The relaxation data are analyzed in terms of a susceptibility chi(omega)[proportion ... [J. Chem. Phys. 128, 174505 (2008)] published Tue May 6, 2008.

A new magic titanium-doped gold cluster and orientation dependent cluster-cluster interaction

Ming-Xing Chen and X. H. Yan
The stability and structures of titanium-doped gold clusters AuTi (n=216) are studied by the relativistic all-electron density-functional calculations. The most stable structures for AuTi clusters with n=27 are found to be planar. A structural transition of AuTi clusters from two-dimensional to thre ... [J. Chem. Phys. 128, 174305 (2008)] published Tue May 6, 2008.

Adsorption of water molecules inside a Au nanotube: A molecular dynamics study

Meng-Hsiung Weng, Wen-Jay Lee, Shin-Pon Ju, Chien-Hsiang Chao, Nan-Kai Hsieh et al.
A molecular dynamics simulation of water molecules through a Au nanotube with a diameter of 20 A at bulk densities 0.8, 1, and 1.2 g/cm has been carried out. The water molecules inside a nanoscale tube, unlike those inside a bulk tube, have a confined effect. The interaction energy of the Au nanot ... [J. Chem. Phys. 128, 174705 (2008)] published Mon May 5, 2008.

Excited states and photodissociation of hydroxymethyl hydroperoxide

Wolfgang Eisfeld and Joseph S. Francisco
The structure of hydroxymethyl hydroperoxide (HOCHOOH) (HMHP) has been examined using coupled cluster and multireference configuration interaction methods to study the excited states and probable photodissociation products. The results are compared to experiments. The vertical excitation energies fo ... [J. Chem. Phys. 128, 174304 (2008)] published Mon May 5, 2008.

Waterlike dynamic anomalies in a liquid described by a core-softened potential

S. A. Egorov
We present a theoretical study of transport properties of a liquid comprised of particles interacting via isotropic core-softened potential. Shear viscosity and self-diffusion coefficient are computed on the basis of the mode-coupling theory, with required structural input obtained from thermodynami ... [J. Chem. Phys. 128, 174503 (2008)] published Mon May 5, 2008.

Reversible folding simulation by hybrid Hamiltonian replica exchange

Weixin Xu, Tingfeng Lai, Ye Yang, and Yuguang Mu
Reversible foldings of a beta-hairpin peptide, chignolin, by recently invented hybrid Hamiltonian replica exchange molecular dynamics simulations based on PoissonBoltzmann model in explicit water are demonstrated. Initiated from extended structures the peptide folded and unfolded a couple of times i ... [J. Chem. Phys. 128, 175105 (2008)] published Mon May 5, 2008.

Effect of flexibility on surface tension and coexisting densities of water

Jorge Lopez-Lemus, Gustavo A. Chapela, and Jose Alejandre
Molecular dynamics simulations of pure water at the liquid-vapor interface are performed using direct simulation of interfaces in a liquid slab geometry. The effect of intramolecular flexibility on coexisting densities and surface tension is analyzed. The dipole moment profile across the liquid-vapo ... [J. Chem. Phys. 128, 174703 (2008)] published Mon May 5, 2008.

A constant entropy increase model for the selection of parallel tempering ensembles

Dubravko Sabo, Markus Meuwly, David L. Freeman, and J. D. Doll
The present paper explores a simple approach to the question of parallel tempering temperature selection. We argue that to optimize the performance of parallel tempering it is reasonable to require that the increase in entropy between successive temperatures be uniform over the entire ensemble. An e ... [J. Chem. Phys. 128, 174109 (2008)] published Mon May 5, 2008.

Computation of interior eigenvalues in electronic structure calculations facilitated by density matrix purification

Emanuel H. Rubensson and Sara Zahedi
Density matrix purification, is in this work, used to facilitate the computation of eigenpairs around the highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO, respectively) in electronic structure calculations. The ability of purification to give large separation between eig ... [J. Chem. Phys. 128, 176101 (2008)] published Mon May 5, 2008.

Exp6-polar thermodynamics of dense supercritical water

Sorin Bastea and Laurence E. Fried
We introduce a simple polar fluid model for the thermodynamics of dense supercritical water based on a Buckingham (exp-6) core and point dipole representation of the water molecule. The proposed exp6-polar thermodynamics, which is based on ideas originally applied to dipolar hard spheres, performs v ... [J. Chem. Phys. 128, 174502 (2008)] published Mon May 5, 2008.

Direct folding studies of various alpha and beta strands using replica exchange molecular dynamics simulation

Eunae Kim, Soonmin Jang, and Youngshang Pak
Previously we presented an all-atom force field with a generalized Born solvation model (param99MOD5/GBSA) for a more balanced description of alpha/beta propensities. We performed direct folding simulations on alpha helices (PDB code 2I9M and 1WN8), beta hairpins (15beta peptide and PDB code 1E0Q), ... [J. Chem. Phys. 128, 175104 (2008)] published Mon May 5, 2008.

Flexible chain molecules in the marginal and concentrated regimes: Universal static scaling laws and cross-over predictions

Manuel Laso and Nikos Ch. Karayiannis
We present predictions for the static scaling exponents and for the cross-over polymer volumetric fractions in the marginal and concentrated solution regimes. Corrections for finite chain length are made. Predictions are based on an analysis of correlated fluctuations in density and chain length, in ... [J. Chem. Phys. 128, 174901 (2008)] published Mon May 5, 2008.

Adsorption and electron-induced polymerization of methyl methacrylate on Ru(10[overline 1]0)

M. N. Hedhili, B. V. Yakshinskiy, R. Wasielewski, A. Ciszewski, and T. E. Madey
The adsorption and electron irradiation of methyl methacrylate (MMA) on a Ru(10[overline 1]0) surface have been studied using x-ray photoelectron spectroscopy (XPS), temperature programmed desorption (TPD), and low energy ion scattering. TPD analysis indicates that a monolayer of MMA chemisorbs and ... [J. Chem. Phys. 128, 174704 (2008)] published Mon May 5, 2008.

Unbiased computation of transition times by pathway recombination

J. Kuipers and G. T. Barkema
In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance, nucleation, protein folding, and chemical reactions. For these systems, direct simulation of phase space trajectories does not e ... [J. Chem. Phys. 128, 174108 (2008)] published Mon May 5, 2008.