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21 March 2008

Volume 128, Issue 11,  Articles (11xxxx)

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COMMUNICATIONS

An alternative near-neighbor definition of hydrogen bonding in water

A. D. Hammerich and V. Buch

J. Chem. Phys. 128, 111101 (2008) (4 pages)

Online Publication Date: 17 March 2008

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A definition of hydrogen bonding in water is proposed in which an H[centered ellipsis]O pair forms a hydrogen bond if (a) an oxygen atom is the nearest nonchemically bonded neighbor of a hydrogen atom; and (b) the hydrogen is the first or the second intermolecular near-neighbor of the oxygen. Unlike the commonly employed hydrogen-bond definitions, this definition does not depend on the choice of geometric or energetic cutoffs applied to continuous distributions of properties. With the present definition, the distribution of O[centered ellipsis]H bond lengths decays smoothly to zero in a physically reasonable range. After correction for the presence of intermittent hydrogen bonds, this definition appears to provide a more stable description of hydrogen bonds and coordination shells than the more conventional cutoff-based definition. “Partial” H bonds satisfying only one of the two bonding requirements serve as transition states in the H-bond network evolution.
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33.15.Dj, 34.20.Gj

Ruelle–Takens–Newhouse scenario in reaction-diffusion-convection system

Marcello Antonio Budroni, Marco Masia, Mauro Rustici, Nadia Marchettini, Vitaly Volpert, and Pier Carlo Cresto

J. Chem. Phys. 128, 111102 (2008) (4 pages)

Online Publication Date: 17 March 2008

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Direct numerical simulations of the transition process from periodic to chaotic dynamics are presented for two variable Oregonator-diffusion model coupled with convection. Numerical solutions to the corresponding reaction-diffusion-convection system of equations show that natural convection can change in a qualitative way, the evolution of concentration distribution, as compared with convectionless conditions. The numerical experiments reveal distinct bifurcations as the Grashof number is increased. A transition to chaos similar to Ruelle–Takens–Newhouse scenario is observed. Numerical results are in agreement with the experiments.
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44.25.+f, 47.27.te, 47.27.Cn, 47.70.Fw, 47.20.Ky

Influence of functional groups on charge transport in molecular junctions

D. J. Mowbray, G. Jones, and K. S. Thygesen

J. Chem. Phys. 128, 111103 (2008) (5 pages)

Online Publication Date: 18 March 2008

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Using density functional theory (DFT), we analyze the influence of five classes of functional groups, as exemplified by NO2, OCH3, CH3, CCl3, and I, on the transport properties of a 1,4-benzenedithiolate (BDT) and 1,4-benzenediamine (BDA) molecular junction with gold electrodes. Our analysis demonstrates how ideas from functional group chemistry may be used to engineer a molecule's transport properties, as was shown experimentally and using a semiempirical model for BDA [Nano Lett. 7, 502 (2007)]. In particular, we show that the qualitative change in conductance due to a given functional group can be predicted from its known electronic effect (whether it is sigma/pi donating/withdrawing). However, the influence of functional groups on a molecule's conductance is very weak, as was also found in the BDA experiments. The calculated DFT conductances for the BDA species are five times larger than the experimental values, but good agreement is obtained after correcting for self-interaction and image charge effects.
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85.65.+h
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ARTICLES

Theoretical Methods and Algorithms

Simple finite field nuclear relaxation method for calculating vibrational contribution to degenerate four-wave mixing

Bernard Kirtman and Josep M. Luis

J. Chem. Phys. 128, 114101 (2008) (4 pages)

Online Publication Date: 18 March 2008

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A simple extended finite field nuclear relaxation procedure for calculating vibrational contributions to degenerate four-wave mixing (also known as the intensity-dependent refractive index) is presented. As a by-product one also obtains the static vibrationally averaged linear polarizability, as well as the first and second hyperpolarizability. The methodology is validated by illustrative calculations on the water molecule. Further possible extensions are suggested.
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33.15.Mt, 33.20.Tp, 42.65.Hw, 33.15.Kr

Investigation of the benzene-dimer potential energy surface: DFT/CCSD(T) correction scheme

Ota Bludský, Miroslav Rubeš, Pavel Soldán, and Petr Nachtigall

J. Chem. Phys. 128, 114102 (2008) (8 pages)

Online Publication Date: 18 March 2008

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A novel method, designated as the density functional theory/coupled-cluster with single and double and perturbative triple excitation [DFT/CCSD(T)] correction scheme, was developed for precise calculations of weakly interacting sp2 hydrocarbon molecules and applied to the benzene dimer. The DFT/CCSD(T) interaction energies are in excellent agreement with the estimated CCSD(T)/complete basis set interaction energies. The tilted T-shaped structure having Cs symmetry was determined to be a global minimum on the benzene-dimer potential energy surface (PES), approximately 0.1  kcal/mol more stable than the parallel-displaced structure. A fully optimized set of ten stationary points on the benzene-dimer PES is proposed for the evaluation of the reliability of methods for the description of weakly interacting systems.
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31.15.E-, 31.50.-x, 31.15.bw, 31.15.xp, 33.15.Bh

Performance of the M06 family of exchange-correlation functionals for predicting magnetic coupling in organic and inorganic molecules

Rosendo Valero, Ramon Costa, Ibério de P. R. Moreira, Donald G. Truhlar, and Francesc Illas

J. Chem. Phys. 128, 114103 (2008) (8 pages)

Online Publication Date: 19 March 2008

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The performance of the M06 family of exchange-correlation potentials for describing the electronic structure and the Heisenberg magnetic coupling constant (J) is investigated using a set of representative open-shell systems involving two unpaired electrons. The set of molecular systems studied has well defined structures, and their magnetic coupling values are known experimentally. As a general trend, the M06 functional is about equally as accurate as B3LYP or PBE0. The performance of local functionals is important because of their economy and convenience for large-scale calculations; we find that M06-L local functional of the M06 family largely improves over the local spin density approximation and the generalized gradient approximation.
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31.15.eg

Calculation of free-energy differences and potentials of mean force by a multi-energy gap method

Huan-Xiang Zhou

J. Chem. Phys. 128, 114104 (2008) (8 pages)

Online Publication Date: 19 March 2008

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A method is proposed to significantly accelerate the convergence of free-energy calculations. It introduces a bias factor in Monte Carlo simulations or, equivalently, a bias force in molecular dynamics simulations. The bias factor targets the energy gap, i.e., the difference in energy function between two states, and is therefore specifically designed for calculating free-energy differences. The goal is to make the probability density of the energy gap as uniform as possible, thus allowing for its accurate determination. An iterative procedure, based on simulations at higher temperatures, is devised to obtain the bias factor. The same method naturally extends to the calculation of potentials of mean force. The generalized coordinate, for which the potential of mean force is to be calculated, now plays the role of the energy gap. Applications to model systems confirm the expected increase in accuracy of calculated free-energy differences and potentials of mean force.
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05.70.Ce, 02.50.Cw, 02.50.Ng

An analysis through order [h-bar]2 of a surface hopping expansion of the nonadiabatic wave function

Michael F. Herman and Yinghua Wu

J. Chem. Phys. 128, 114105 (2008) (11 pages)

Online Publication Date: 19 March 2008

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It is shown that a surface hopping expansion of the semiclassical wave function formally satisfies the time independent Schrödinger equation for many-state, multidimensional problems. This wave function includes terms involving hops between different adiabatic quantum states as well as momentum changes without change of state at each point along classical trajectories. The single-state momentum changes correct for the order [h-bar]2 errors due to the semiclassical approximation that are present even in single surface problems. A prescription is provided for the direction of this momentum change and the amplitude associated with it. The direction of the momentum change for energy conserving hops between adiabatic states is required to be in the direction of the nonadiabatic coupling vector. The magnitude of the posthop momentum in this direction is determined by the energy, but the sign is not. Hops with both signs of this momentum component are required in order for the wave function to formally satisfy the Schrödinger equation. Numerical results are presented which illustrate how the surface hopping expansion can be implemented and the accuracy that can be obtained.
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03.65.Ge, 03.65.Sq

Electron-nucleus cusp correction and forces in quantum Monte Carlo

Manolo C. Per, Salvy P. Russo, and Ian K. Snook

J. Chem. Phys. 128, 114106 (2008) (6 pages)

Online Publication Date: 19 March 2008

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A simple method is presented which ensures the electron-nucleus cusp condition is satisfied by the Slater-Jastrow wavefunctions commonly employed in quantum Monte Carlo simulations. The method is applied in variational energy calculations of the neon atom and a selection of molecules using both Gaussian and Slater basis sets. In addition, we discuss the relationship between the electron-nucleus cusps and the variance of forces, and investigate the sensitivity of forces to the quality of the cusps for various diatomic molecules.
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34.80.Bm, 02.70.Ss, 31.15.xt

Energy and energy gradient matrix elements with N-particle explicitly correlated complex Gaussian basis functions with L=1

Sergiy Bubin and Ludwik Adamowicz

J. Chem. Phys. 128, 114107 (2008) (15 pages)

Online Publication Date: 20 March 2008

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In this work we consider explicitly correlated complex Gaussian basis functions for expanding the wave function of an N-particle system with the L=1 total orbital angular momentum. We derive analytical expressions for various matrix elements with these basis functions including the overlap, kinetic energy, and potential energy (Coulomb interaction) matrix elements, as well as matrix elements of other quantities. The derivatives of the overlap, kinetic, and potential energy integrals with respect to the Gaussian exponential parameters are also derived and used to calculate the energy gradient. All the derivations are performed using the formalism of the matrix differential calculus that facilitates a way of expressing the integrals in an elegant matrix form, which is convenient for the theoretical analysis and the computer implementation. The new method is tested in calculations of two systems: the lowest P state of the beryllium atom and the bound P state of the positronium molecule (with the negative parity). Both calculations yielded new, lowest-to-date, variational upper bounds, while the number of basis functions used was significantly smaller than in previous studies. It was possible to accomplish this due to the use of the analytic energy gradient in the minimization of the variational energy.
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31.15.xt

Calculation of electric dipole (hyper)polarizabilities by long-range-correction scheme in density functional theory: A systematic assessment for polydiacetylene and polybutatriene oligomers

Bernard Kirtman, Sean Bonness, Alejandro Ramirez-Solis, Benoit Champagne, Hironori Matsumoto, and Hideo Sekino

J. Chem. Phys. 128, 114108 (2008) (5 pages)

Online Publication Date: 20 March 2008

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The long-range correction (LC) for treating electron exchange in density functional theory, combined with the Becke–Lee–Yang–Parr (BLYP) exchange-correlation functional, was used to determine (hyper)polarizabilities of polydiacetylene/polybutatriene oligomers. In comparison with coupled-cluster calculations including single and double excitations as well as a perturbative treatment of triple excitations, our values indicate that the tendency of conventional functionals to result in a catastrophic overshoot for these properties is alleviated but not eliminated. No clear-cut preference for LC-BLYP over Hartree–Fock values is obtained. This analysis is consistent with the calculations of Sekino et al. [J. Chem. Phys. 126, 014107 (2007)] on polyacetylene and molecular hydrogen oligomers. Thus, the performance of LC-BLYP with regard to (hyper)polarizabilities of quasilinear conjugated systems is now well characterized.
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33.15.Kr, 31.15.eg, 31.15.bw

Electronic excited-state energies from a linear response theory based on the ground-state two-electron reduced density matrix

Loren Greenman and David A. Mazziotti

J. Chem. Phys. 128, 114109 (2008) (7 pages)

Online Publication Date: 20 March 2008

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Ground-state two-particle reduced density matrices (2-RDMs) are used to calculate excited-state energy spectra. Solving the Schrödinger equation for excited states dominated by single excitations from the ground-state wavefunction requires the ground-state 2- and 3-RDMs. The excited states, however, can be obtained without a knowledge of the ground-state 3-RDM by two methods: (i) cumulant expansion methods which build the 3-RDM from the 2-RDM, and (ii) double commutator methods which eliminate the 3-RDM. Previous work [Mazziotti, Phys. Rev. A 68, 052501 (2003)] examined the accuracy of excited states extracted from ground-state 2-RDMs, which were calculated by full configuration interaction or the variational 2-RDM method. In this work we employ (i) advances in semidefinite programming to treat the excited states of water and hydrogen fluoride and chains of hydrogen atoms, and (ii) the addition of partial three-particle N-representability conditions to compute more accurate ground-state 2-RDMs. With the hydrogen chains we examine the metal-to-insulator transition as measured by the band gap (the difference between the ground-state and the first excited-state energies), which is difficult for excited-state methods to capture.
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71.30.+h, 71.15.Qe, 71.15.Ap

Concurrent triple-scale simulation of molecular liquids

Rafael Delgado-Buscalioni, Kurt Kremer, and Matej Praprotnik

J. Chem. Phys. 128, 114110 (2008) (9 pages)

Online Publication Date: 20 March 2008

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We present a triple-scale simulation of a molecular liquid, in which the atomistic, coarse-grained, and continuum descriptions of the liquid are concurrently coupled. The presented multiscale approach, which covers the length scales ranging from the micro- to macroscale, is a combination of two dual-scale models: a particle-based adaptive resolution scheme (AdResS), which couples the atomic and mesoscopic scales, and a hybrid continuum-molecular dynamics scheme (HybridMD). The combined AdResS-HybridMD scheme successfully sorts out the problem of large molecule insertion in the hybrid particle-continuum simulations of molecular liquids. The combined model is shown to correctly describe the hydrodynamics within a hybrid particle-continuum framework. The presented approach opens up the possibility to perform efficient grand-canonical molecular dynamics simulations of truly open molecular liquid systems.
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61.20.Ja

High-accuracy extrapolated ab initio thermochemistry. III. Additional improvements and overview

Michael E. Harding, Juana Vázquez, Branko Ruscic, Angela K. Wilson, Jürgen Gauss, and John F. Stanton

J. Chem. Phys. 128, 114111 (2008) (15 pages)

Online Publication Date: 21 March 2008

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Effects of increased basis-set size as well as a correlated treatment of the diagonal Born-Oppenheimer approximation are studied within the context of the high-accuracy extrapolated ab initio thermochemistry (HEAT) theoretical model chemistry. It is found that the addition of these ostensible improvements does little to increase the overall accuracy of HEAT for the determination of molecular atomization energies. Fortuitous cancellation of high-level effects is shown to give the overall HEAT strategy an accuracy that is, in fact, higher than most of its individual components. In addition, the issue of core-valence electron correlation separation is explored; it is found that approximate additive treatments of the two effects have limitations that are significant in the realm of <1  kJ  mol−1 theoretical thermochemistry.
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31.15.A-, 31.15.V-, 82.60.-s

Directionally negative friction: A method for enhanced sampling of rare event kinetics

James MacFadyen, Jeff Wereszczynski, and Ioan Andricioaei

J. Chem. Phys. 128, 114112 (2008) (9 pages)

Online Publication Date: 21 March 2008

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A method exploiting the properties of an artificial (nonphysical) Langevin dynamics with a negative frictional coefficient along a suitable manifold and positive friction in the perpendicular directions is presented for the enhanced calculation of time-correlation functions for rare event problems. Exact time-correlation functions that describe the kinetics of the transitions for the all-positive, physical system can be calculated by reweighting the generated trajectories according to stochastic path integral treatment involving a functional weight based on an Onsager–Machlup action functional. The method is tested on a prototypical multidimensional model system featuring the main elements of conformational space characteristic of complex condensed matter systems. Using the present method, accurate estimates of rate constants require at least three order of magnitudes fewer trajectories than regular Langevin dynamics. The method is particularly useful in calculating kinetic properties in the context of multidimensional energy landscapes that are characteristic of complex systems such as proteins and nucleic acids.
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82.20.Wt, 82.20.Uv

Dynamics of molecules in strong oscillating electric fields using time-dependent Hartree–Fock theory

Henk Eshuis, Gabriel G. Balint-Kurti, and Frederick R. Manby

J. Chem. Phys. 128, 114113 (2008) (6 pages)

Online Publication Date: 21 March 2008

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Restricted and unrestricted forms of time-dependent Hartree–Fock theory have been implemented and used to study the electronic dynamics of ethene, benzene, and the formaldehyde cation subjected to both weak and strong oscillating electric fields. Absorption spectra and frequency-dependent polarizabilities are calculated via the instantaneous dipole moment and its derivative. In the weak field limit the computed excitation energies agree very well with those obtained using linearized time-dependent Hartree–Fock theory, which is valid only in the low-field perturbation limit. For strong fields the spectra show higher-order excitations, and a shift in the position of the excitations, which is due to the nonadiabatic response of the molecules to the field. For open-shell systems in the presence of strong oscillating electric fields, unrestricted time-dependent Hartree–Fock theory predicts the value of S2 to vary strongly with time.
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31.15.xr, 33.15.Kr, 33.20.-t

Global fitting without a global model: Regularization based on the continuity of the evolution of parameter distributions

Jason T. Giurleo and David S. Talaga

J. Chem. Phys. 128, 114114 (2008) (18 pages)

Online Publication Date: 21 March 2008

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We introduce a new approach to global data fitting based on a regularization condition that invokes continuity in the global data coordinate. Stabilization of the data fitting procedure comes from probabilistic constraint of the global solution to physically reasonable behavior rather than to specific models of the system behavior. This method is applicable to the fitting of many types of spectroscopic data including dynamic light scattering, time-correlated single-photon counting (TCSPC), and circular dichroism. We compare our method to traditional approaches to fitting an inverse Laplace transform by examining the evolution of multiple lifetime components in synthetic TCSPC data. The global regularizer recovers features in the data that are not apparent from traditional fitting. We show how our approach allows one to start from an essentially model-free fit and progress to a specific model by moving from probabilistic to deterministic constraints in both Laplace transformed and nontransformed coordinates.
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78.20.Fm, 78.35.+c

Electron-electron cusp condition and asymptotic behavior for the Pauli potential in pair density functional theory

Á. Nagy and C. Amovilli

J. Chem. Phys. 128, 114115 (2008) (4 pages)

Online Publication Date: 21 March 2008

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In the ground state, the pair density n can be determined by solving a single auxiliary equation of a two-particle problem. Electron-electron cusp condition and asymptotic behavior for the Pauli potential of the effective potential of the two-particle equation are presented.
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31.15.E-, 31.15.ve

The three-dimensional nonadiabatic dynamics calculation of DH<sub>2</sub><sup>+</sup> and HD<sub>2</sub><sup>+</sup> systems by using the trajectory surface hopping method based on the Zhu–Nakamura theory

Bin Li and Ke-Li Han

J. Chem. Phys. 128, 114116 (2008) (7 pages)

Online Publication Date: 21 March 2008

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A theoretical investigation on the nonadiabatic processes of the full three-dimensional D++H2 and H++D2 reaction systems has been performed by using trajectory surface hopping (TSH) method based on the Zhu–Nakamura (ZN) theory. This ZN-TSH method refers to not only classically allowed hops but also classically forbidden hops. The potential energy surface constructed by Kamisaka et al. is employed in the calculation. A new iterative method is proposed to yield the two-dimensional seam surface from the topography of the adiabatic potential surfaces, in which the inconvenience of directly solving the first-order partial differential equation is avoided. The cross sections of these two systems are calculated for three competing channels of the reactive charge transfer, the nonreactive charge transfer, and the reactive noncharge transfer, for ground rovibrational state of H2 or D2. Also, this study provides reaction probabilities of these three processes for the total angular momentum J=0 and ground initial vibrational state of H2 or D2. The calculated results from ZN-TSH method are in good agreement with the exact quantum calculations and the experimental measurements.
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82.30.Fi, 82.20.Kh, 82.20.Fd

First-principles calculations of magnetic circular dichroism spectra

Dmitry Ganyushin and Frank Neese

J. Chem. Phys. 128, 114117 (2008) (13 pages)

Online Publication Date: 21 March 2008

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An elaborate approach for the prediction of magnetic circular dichroism (MCD) spectra in the framework of highly correlated multiconfigurational ab initio methods is presented. The MCD transitions are computed by the explicit treatment of spin-orbit coupled (SOC) and spin-spin coupled (SSC) N-electron states. These states are obtained from the diagonalization of the SOC and SSC operators along with the spin and orbital Zeeman operators in the basis of a preselected number of roots of the spin-free Hamiltonian. Therefore, zero-field splittings due to the SOC and SSC interactions along with the magnetic field splittings are explicitly accounted for in the ground as well as the excited states. This makes it possible to calculate simultaneously all MCD A, B, and C terms even beyond the linear response limit. The SOC is computed using a multicenter mean-field approximation to the Breit–Pauli Hamiltonian. Two-electron SSC terms are included in the treatment without further approximations. The MCD transition intensities are subjected to numerical orientational averaging in order to treat the most commonly encountered case of randomly oriented molecules. The simulated MCD spectra for the OH, NH, and CH radicals as well as for [Fe(CN)6]3− are in good agreement with the experimental spectra. In the former case, the significant effects of the inert gas matrices in which the experimental spectra were obtained were modeled in a phenomenological way.
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78.20.Ls, 71.70.Ej

Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

CCSD calculations on C14, C18, and C22 carbon clusters

Sundaram Arulmozhiraja and Takahisa Ohno

J. Chem. Phys. 128, 114301 (2008) (9 pages)

Online Publication Date: 17 March 2008

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The structure and energetics of the ring isomers of C4n+2 (n=3–5) carbon clusters were studied by using coupled-cluster singles and doubles excitation theory to overcome the vast differences existing in the literature. The results obtained in the present study clearly indicate that C14, C18, and C22 carbon rings have bond-length and bond-angle alternated acetylenic minimum energy structures. Contrarily, density functional theory calculations were unable to predict these acetylenic-type structures and they ended up with the cumulenic structures. It is found from the coupled-cluster studies that the lowest-energy ring isomer for the first two members of C4n+2 series is a bond-angle alternated cumulenic D(2n+1)h symmetry structure while the same for the remaining members is a bond-length and bond-angle alternated C(2n+1)h symmetry structure. In C4n+2 carbon rings, Peierls-type distortion, transformation from bond-angle alternated to bond-length alternated minimum energy structures, occurs at C14 carbon ring.
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36.40.Mr, 31.15.bw, 31.15.es, 33.15.Dj

Oscillator strengths and line widths of dipole-allowed transitions in 14N2 between 89.7 and 93.5  nm

G. Stark, B. R. Lewis, A. N. Heays, K. Yoshino, P. L. Smith, and K. Ito

J. Chem. Phys. 128, 114302 (2008) (10 pages)

Online Publication Date: 17 March 2008

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Line oscillator strengths in the 20 electric dipole-allowed bands of 14N2 in the 89.7–93.5  nm (111480–106950  cm−1) region are reported from photoabsorption measurements at an instrumental resolution of ~6  mÅ (0.7  cm−1) full width at half maximum. The absorption spectrum comprises transitions to vibrational levels of the 3psigmau  c<sub>4</sub><sup>[prime]</sup>  1Sigma<sub>u</sub><sup>+</sup>, 3ppiu  c3  1Piu, and 3ssigmag  o3  1Piu Rydberg states and of the b[prime]  1Sigma<sub>u</sub><sup>+</sup> and b  1Piu valence states. The J dependences of band f values derived from the experimental line f values are reported as polynomials in J[prime](J[prime]+1) and are extrapolated to J[prime]=0 in order to facilitate comparisons with results of coupled Schrödinger-equation calculations. Most bands in this study are characterized by a strong J dependence of the band f values and display anomalous P-, Q-, and R-branch intensity patterns. Predissociation line widths, which are reported for 11 bands, also exhibit strong J dependences. The f value and line width patterns can inform current efforts to develop comprehensive spectroscopic models that incorporate rotational effects and predissociation mechanisms, and they are critical for the construction of realistic atmospheric radiative-transfer models.
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33.70.Ca, 33.70.Jg, 33.20.Tp, 33.80.Rv, 33.80.Gj

Photofragment translational spectroscopy of propargyl radicals at 248  nm

Scott J. Goncher, David T. Moore, Niels E. Sveum, and Daniel M. Neumark

J. Chem. Phys. 128, 114303 (2008) (8 pages)

Online Publication Date: 17 March 2008

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The photodissociation of propargyl radical, C3H3, and its perdeuterated isotopolog was investigated using photofragment translational spectroscopy. Propargyl radicals were produced by 193  nm photolysis of allene entrained in a molecular beam expansion and then photodissociated at 248  nm. Photofragment time-of-flight spectra were measured at a series of laboratory angles using electron impact ionization coupled to a mass spectrometer. Data for ion masses corresponding to C3H2+, C3H+, C3+, and the analogous deuterated species show that both H and H2 loss occur. The translational energy distributions for these processes have average values <ET>=5.7 and 15.3  kcal/mol, respectively, and are consistent with dissociation on the ground state following internal conversion, with no exit barrier for H loss but a tight transition state for H2 loss. Our translational energy distribution for H atom loss is similar to that in a previous work on propargyl in which the H atom, rather than the heavy fragment, was detected. The branching ratio for H loss/H2 loss was determined to be 97.6/2.4±1.2, in good agreement with previous calculations.
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82.50.Hp, 82.30.Cf, 82.80.Dx

Vibrational effects on the reaction of NO2+ with C2H2: Effects of bending and bending angular momentum

Jason M. Boyle, Brady W. Uselman, Jianbo Liu, and Scott L. Anderson

J. Chem. Phys. 128, 114304 (2008) (12 pages)

Online Publication Date: 18 March 2008

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NO2+ in six different vibrational states was reacted with C2H2 over the center-of-mass energy range from 0.03  to  3.3  eV. The reaction, forming NO++C2H2O and NO+C2H2O+, shows a bimodal dependence on collision energy (Ecol). At low Ecol, the reaction is quite inefficient (<2%) despite this being a barrierless, exoergic reaction, and is strongly inhibited by Ecol. For Ecol>~0.5  eV, a second mechanism turns on, with an efficiency reaching ~27% for Ecol>3  eV. The two reaction channels have nearly identical dependence on Ecol and NO2+ vibrational state, and identical recoil dynamics, leading to the conclusion that they represent a single reaction path throughout most of the collision. All modes of NO2+ vibrational excitation enhance both channels at all Ecol, however, the effects of bend (010) and bend overtone (0200) excitation are particularly strong (factor of 4). In contrast, the asymmetric stretch (001), which intuition suggests should be coupled to the reaction coordinate, leads to only a factor of ~2 enhancement, as does the symmetric stretch (100). Perhaps the most surprising effect is that of the bending angular momentum, which strongly suppress reaction, even though both the energy and angular momentum involved are tiny compared to the collision energy and angular momentum. The results are interpreted in light of ab initio and Rice-Ramsperger-Kassel-Marcus calculations.
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82.30.Cf, 82.20.Fd

Rovibrational spectroscopy and intramolecular dynamics of 1,2-trans-d2-ethene in the first C[Single Bond]H stretch overtone region

Amir Zwielly, Alexander Portnov, Chen Levi, Salman Rosenwaks, and Ilana Bar

J. Chem. Phys. 128, 114305 (2008) (6 pages)

Online Publication Date: 18 March 2008

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The first overtone region of the C[Single Bond]H stretching vibration of 1,2-trans-d2-ethene (HDC[Double Bond]CDH) was monitored via jet-cooled action spectroscopy and room temperature photoacoustic spectroscopy. The spectra include a strong band, which we assigned as the nu1+nu9 C[Single Bond]H stretch vibration, and five additional bands related to transitions to coupled states. The spectral features were modeled in terms of a six-state deperturbation analysis, revealing the energies of the zero-order states and the relatively strong couplings between the initially excited nu1+nu9 state and the doorway states. Considering these energies and the fundamental frequencies of 1,2-trans-d2-ethene and presuming that only low-order resonances are involved in the couplings enabled the assignment of the states. The analysis also allowed obtaining insight on energy flow and to find out that the energy oscillations between the C[Single Bond]H stretch state and the doorway states occur on a subpicosecond time scale.
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33.15.Mt, 33.20.Vq

A time-dependent quantum dynamics investigation of the guanine-cytosine system: A six-dimensional model

Giovanni Villani

J. Chem. Phys. 128, 114306 (2008) (8 pages)

Online Publication Date: 18 March 2008

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The dynamics of the guanine-cytosine base pair has been studied in the time-dependent quantum approach. A six-dimensional model involving the nonlinear three hydrogen bridges has been utilized. The modifications induced in the hydrogen transfer from a base to the other by the explicit inclusion of the out-of-plane hydrogen atom position in the three bridges have been evidenced and the consequences on stacking interaction and base pair opening are considered. The relevance of these aspects in biological properties has been suggested.
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87.15.ag, 87.14.gk, 87.10.-e

High resolution and low-temperature photoelectron spectroscopy of an oxygen-linked fullerene dimer dianion: C120O2−

Xue-Bin Wang, Katerina Matheis, Ilya N. Ioffe, Alexey A. Goryunkov, Jie Yang, Manfred M. Kappes, and Lai-Sheng Wang

J. Chem. Phys. 128, 114307 (2008) (6 pages)

Online Publication Date: 18 March 2008

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C120O comprises two C60 cages linked by a furan ring and is formed by reactions of C60O and C60. We have produced doubly charged anions of this fullerene dimer (C120O2−) and studied its electronic structure and stability using photoelectron spectroscopy and theoretical calculations. High resolution and vibrationally resolved photoelectron spectra were obtained at 70  K and at several photon energies. The second electron affinity of C120O was measured to be 1.02±0.03  eV and the intramolecular Coulomb repulsion was estimated to be about 0.8  eV in C120O2− on the basis of the observed repulsive Coulomb barrier. A low-lying excited state (2B1) was also observed for C120O− at 0.09  eV above the ground state (2A1). The C120O2− dianion can be viewed as a single electron on each C60 ball very weakly coupled. Theoretical calculations showed that the singlet and triplet states of C120O2− are nearly degenerate and can both be present in the experiment. The computed electron binding energies and excitation energies, as well as Franck–Condon factors, are used to help interpret the photoelectron spectra. A C–C bond-cleaved isomer, C60–O–C602−, was also observed with a higher electron binding energy of 1.54  eV.
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33.60.+q, 33.15.Ry, 33.15.Mt, 33.20.Tp, 33.70.Ca

Quantum Monte Carlo calculations of the potential energy curve of the helium dimer

R. Springall, M. C. Per, S. P. Russo, and I. K. Snook

J. Chem. Phys. 128, 114308 (2008) (4 pages)

Online Publication Date: 19 March 2008

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We report results of two quantum Monte Carlo methods—variational Monte Carlo and diffusion Monte Carlo—on the potential energy curve of the helium dimer. In contrast to previous quantum Monte Carlo calculations on this system, we have employed trial wave functions of the Slater-Jastrow form and used the fixed node approximation for the fermion nodal surface. We find both methods to be in excellent agreement with the best theoretical results at short range. In addition, the diffusion Monte Carlo results give very good agreement across the whole potential energy curve, while the Slater-Jastrow wave function fails to bind the dimer at all.
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31.50.-x, 31.15.-p

Eliminating spin contamination in auxiliary-field quantum Monte Carlo: Realistic potential energy curve of F2

Wirawan Purwanto, W. A. Al-Saidi, Henry Krakauer, and Shiwei Zhang

J. Chem. Phys. 128, 114309 (2008) (7 pages)

Online Publication Date: 19 March 2008

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The use of an approximate reference state wave function |Phir> in electronic many-body methods can break the spin symmetry of Born–Oppenheimer spin-independent Hamiltonians. This can result in significant errors, especially when bonds are stretched or broken. A simple spin-projection method is introduced for auxiliary-field quantum Monte Carlo (AFQMC) calculations, which yields spin-contamination-free results, even with a spin-contaminated |Phir>. The method is applied to the difficult F2 molecule, which is unbound within unrestricted Hartree–Fock (UHF). With a UHF |Phir>, spin contamination causes large systematic errors and long equilibration times in AFQMC in the intermediate, bond-breaking region. The spin-projection method eliminates these problems and delivers an accurate potential energy curve from equilibrium to the dissociation limit using the UHF |Phir>. Realistic potential energy curves are obtained with a cc-pVQZ basis. The calculated spectroscopic constants are in excellent agreement with experiment.
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31.50.-x, 31.15.xr, 33.15.Fm, 33.15.Mt

Infrared spectra of (HCOOH)2 and (DCOOH)2 in rare gas matrices: A comparative study with gas phase spectra

Fumiyuki Ito

J. Chem. Phys. 128, 114310 (2008) (12 pages)

Online Publication Date: 19 March 2008

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Infrared absorption spectra of (HCOOH)2 and (DCOOH)2 in solid argon, krypton, and xenon matrices have been measured and each fundamental band has been assigned. Spectra in Ar and Kr matrices showed notable splitting in contrast to those in Xe, which suggests a difference in structure of the trapping sites. A comparison with the reported jet-cooled spectra has shown that vibrational structures of the spectra of (HCOOH)2 and (DCOOH)2 in the O[Single Bond]H stretching region are preserved in the matrices. On the other hand, the C[Single Bond]O stretching band of (HCOOH)2 shows a drastic change upon matrix isolation, wherein the Fermi-triad feature observed in gas phase [F. Ito, Chem. Phys. Lett. 447, 202 (2007)] could not be identified. No substantial change of the vibrational structure has been found for matrix-isolated (DCOOH)2. The differences of the vibrational structures in the matrix-isolation spectra and in the jet-cooled spectra have been qualitatively accounted for using the idea of anharmonic couplings among “matrix-shifted harmonic states.”
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33.15.Mt, 33.20.Tp, 33.20.Ea

Core localization and sigma* delocalization in the O 1s core-excited sulfur dioxide molecule

Andreas Lindgren, Nobuhiro Kosugi, Mathieu Gisselbrecht, Antti Kivimäki, Florian Burmeister, Arnaldo Naves de Brito, and Stacey L. Sorensen

J. Chem. Phys. 128, 114311 (2008) (10 pages)

Online Publication Date: 19 March 2008

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Electron-ion-ion coincidence measurements of sulfur dioxide at discrete resonances near the O 1s ionization edge are reported. The spectra are analyzed using a model based upon molecular symmetry and on the geometry of the molecule. We find clear evidence for molecular alignment that can be ascribed to symmetry properties of the ground and core-excited states. Configuration interaction (CI) calculations indicate geometry changes in accord with the measured spectra. For the SO2 molecule, however, we find that the localized core hole does not produce measurable evidence for valence localization, since the transition dipole moment is not parallel to a breaking sigma* O–S bond, in contrast to the case of ozone. The dissociation behavior based upon the CI calculations using symmetry-broken orbitals while fixing a localized core-hole site is found to be nearly equivalent to that using symmetry-adapted orbitals. This implies that the core-localization effect is not strong enough to localize the sigma* valence orbital.
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33.15.Bh, 33.80.Gj, 82.50.-m, 31.15.vq, 33.15.Kr

Electronically excited states and visible region photodissociation spectroscopy of Aum+·Arn clusters (m=7–9): Molecular dimensionality transition?

Alexia N. Gloess, Holger Schneider, J. Mathias Weber, and Manfred M. Kappes

J. Chem. Phys. 128, 114312 (2008) (9 pages)

Online Publication Date: 19 March 2008

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Photodissociation spectra were determined for Aum+·Arn (m=7; n=0–3 and m=8,9; n=0,1) in the photon energy range of 2.14–3.02  eV. Experimental data were compared with predictions of dipole allowed transitions using time-dependent density functional theory (TDDFT) as applied to cluster structures from both DFT (B3-LYP functional) and ab initio calculations at the MP2 level. Argon adduct formation does not significantly perturb the bare metal cluster core structure, but it does change the metal cluster spectrum for highly symmetric cluster structures. The photodissociation spectra are consistent with a transition from planar to three-dimensional gold cluster core geometries between m=7 and m=8 for both n=0 and 1. TDDFT predictions for favored isomers describe experimental absorption features to within ±0.25  eV. We also discuss size-dependent trends in TDDFT transition energies for the lowest energy two- and three-dimensional structures of Aum+(m=3–9).
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33.80.Gj, 31.15.ee, 31.15.A-, 31.15.xp, 36.40.Mr

Orbit-orbit relativistic corrections to the pure vibrational non-Born-Oppenheimer energies of H2

Monika Stanke, Dariusz Kedziera, Sergiy Bubin, Marcin Molski, and Ludwik Adamowicz

J. Chem. Phys. 128, 114313 (2008) (15 pages)

Online Publication Date: 20 March 2008

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We report the derivation of the orbit-orbit relativistic correction for calculating pure vibrational states of diatomic molecular systems with sigma electrons within the framework that does not assume the Born-Oppenheimer (BO) approximation. The correction is calculated as the expectation value of the orbit-orbit interaction operator with the non-BO wave function expressed in terms of explicitly correlated Gaussian functions multiplied by even powers of the internuclear distance. With that we can now calculate the complete relativistic correction of the order of alpha2 (where alpha=1/c). The new algorithm is applied to determine the full set of the rotationless vibrational levels and the corresponding transition frequencies of the H2 molecule. The results are compared with the previous calculations, as well as with the frequencies obtained from the experimental spectra. The comparison shows the need to include corrections higher than second order in alpha to further improve the agreement between the theory and the experiment.
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31.30.J-, 31.15.aj, 33.15.Mt

A velocity map ion imaging study of difluorobenzene-water complexes: Binding energies and recoil distributions

Susan M. Bellm, Rebecca J. Moulds, Matthew P. van Leeuwen, and Warren D. Lawrance

J. Chem. Phys. 128, 114314 (2008) (7 pages)

Online Publication Date: 20 March 2008

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The binding energies of the p-, m-, and o-difluorobenzene-H2O complexes have been measured by velocity map ion imaging to be 922±10, 945±10, and 891±4  cm−1, respectively. The lack of variation provides circumstantial evidence for water binding to the three isomers via the same interaction, viz. an in-plane O–H[centered ellipsis]F hydrogen bond to one of the fluorine atoms on the ring, with a second, weaker interaction of the water O atom with an ortho hydrogen, as determined previously for the p-difluorobenzene-H2O complex [Kang et al., J. Phys. Chem. A 109, 767 (2005)]. The ground state binding energies for the difluorobenzene-H2O complexes are ~5%–11% larger than that for benzene-H2O, where binding occurs to the pi electrons out-of-plane. However, in the S1 state the binding energies of the o- and p-difluorobenzene-H2O complexes are smaller than the benzene-H2O value, raising an interesting question about whether the geometry at the global energy minimum remains in-plane in the excited electronic states of these two complexes. Recoil energy distributions for dissociation of p-difluorobenzene-H2O have been measured from the [overline 3[sup 1]], [overline 5[sup 2]], and [overline 3[sup 1]5[sup 1]] levels of the excited electronic state. These levels are 490, 880, and 1304  cm−1, respectively, above the dissociation threshold. Within the experimental uncertainty, the recoil energy distributions are the same for dissociation from these three states, with average recoil energies of ~100  cm−1. These recoil energies are 60% larger than was observed for the dissociation of p-difluorobenzene-Ar, which is a substantially smaller increase than the 400% seen in a comparable study of dissociation within the triplet state for pyrazine-Ar, -H2O complexes. The majority of the available energy is partitioned into vibration and rotation of the fragments.
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33.15.Ry, 33.15.Mt, 33.20.Tp, 33.20.Sn, 33.15.Bh, 33.15.Fm

A density-functional study of the possibility of noncollinear magnetism in small Mn clusters using SIESTA and the generalized gradient approximation to exchange and correlation

R. C. Longo, M. M. G. Alemany, J. Ferrer, A. Vega, and L. J. Gallego

J. Chem. Phys. 128, 114315 (2008) (5 pages)

Online Publication Date: 20 March 2008

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We investigated the possibility of noncollinear magnetism in small Mnn clusters (n=2–6) using the density-functional method SIESTA with the generalized gradient approximation (GGA) to exchange and correlation. The lowest-energy states identified were collinear, with the atomic spin magnetic moments pointing in the same direction, for Mn2 and Mn3, and noncollinear for Mn4, Mn5 and, most decidedly, Mn6. These SIESTA/GGA results, which are compared with those of an earlier SIESTA study that used the local spin density approximation, are qualitatively in keeping with the result obtained by VASP/GGA calculations.
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36.40.Cg, 33.15.Kr, 31.15.eg

The double Renner effect in the X-tilde   2A[double-prime] and à 2A[prime] electronic states of HO2

Vladlen V. Melnikov, Tina Erica Odaka, Per Jensen, and Tsuneo Hirano

J. Chem. Phys. 128, 114316 (2008) (10 pages)

Online Publication Date: 21 March 2008

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A theoretical investigation of the X-tilde   2A[double-prime] and à 2A[prime] electronic states of the HO2 radical is reported. Both electronic states have nonlinear equilibrium geometries and they correlate with a 2Pi state at linear geometries so that they exhibit the Renner effect. In highly excited bending states, there is tunneling between two equivalent minima (with geometries where the H nucleus is bound to one, or the other, of the two O nuclei), and the two linear geometries H–O–O and O–O–H become accessible to the molecule. Thus, HO2 affords an example of the so-called double Renner effect. Three-dimensional potential energy surfaces for the X-tilde   2A[double-prime] and à 2A[prime] electronic states of HO2 have been calculated ab initio and the global potential energy surfaces for the states have been constructed. These surfaces have been used, in conjunction with the computer program DR [Odaka et al., J. Mol. Structure 795, 14 (2006); Odaka et al., J. Chem. Phys. 126, 094301 (2007)], for calculating HO2 rovibronic energies in the “double-Renner”-degenerate electronic states X-tilde   2A[double-prime] and à 2A[prime]. The results of the ab initio calculations, the rovibronic energies obtained, and analyses of the wavefunctions for selected states are presented.
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33.20.Wr, 33.15.Bh, 31.50.Df, 31.15.ae

Gerade-ungerade symmetry breaking in HD: Bound states supported by the I[prime]  1Pig outer potential well

T. P. Grozdanov and R. McCarroll

J. Chem. Phys. 128, 114317 (2008) (9 pages)

Online Publication Date: 21 March 2008

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Gerade-ungerade symmetry breaking in HD for the bound states supported by the shallow outer I[prime]  1Pig potential is studied theoretically. By clarifying the asymptotic behavior of the relevant nonadiabatic couplings among the stats correlating to the n=2 dissociation limit, simple two-state (for f-parity) and three-state (for e-parity) approximations are formulated. They reproduce binding energies in very good agreement with recent spectroscopic measurements. Comparisons with the calculations based on a single model potential are presented and the dependence of the results on the used ab initio Born-Oppenheimer (clamped nuclei) potentials is discussed.
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33.15.Fm, 33.15.Ry, 31.15.ap

Nonempirical statistical theory for molecular evaporation from nonrigid clusters

Mikiya Fujii and Kazuo Takatsuka

J. Chem. Phys. 128, 114318 (2008) (15 pages)

Online Publication Date: 21 March 2008

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We propose a nonempirical statistical theory to give the reaction rate and the kinetic energy distribution of fragments for molecular evaporation from highly nonrigid atomic and van der Waals clusters. To quantify the theory, an efficient and accurate method to evaluate the absolute value of classical density of states (the Thomas–Fermi density in phase space) and the flux at the so-called dividing surface is critically important, and we have devised such an efficient method. The theory and associated methods are verified by numerical comparison with the corresponding molecular dynamics simulation through the study of Ar2 evaporation from Ar8 cluster, in which evaporation is strongly coupled with structural isomerization dynamics. It turns out that the nonempirical statistical theory gives quite an accurate reaction rate. We also study the kinetic energy release (KER) arising from these evaporations and its Boltzmann-like distribution both for atomic and diatomic evaporations. This provides a general relation between the KER and temperature of the fragments.
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31.15.bt, 36.40.Cg, 34.20.Gj, 82.30.Qt

State of the art theoretical study and comparison to experiment for the phenol[centered ellipsis]argon complex

Jiří Černý, Xin Tong, Pavel Hobza, and Klaus Müller-Dethlefs

J. Chem. Phys. 128, 114319 (2008) (6 pages)

Online Publication Date: 21 March 2008

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The phenol[centered ellipsis]argon complex was studied by means of various high level ab initio quantum mechanics methods and high resolution threshold ionization spectroscopy. The structure and stabilization energy of different conformers were determined. Stabilization energy of van der Waals bonded and H-bonded PhOH[centered ellipsis]Ar complex determined at CCSD(T) complete basis set (CBS) level for CP-RI-MP2/cc-pVTZ/Ar aug-cc-pVTZ geometries amount to 434 and 285  cm−1. The CCSD(T)/CBS were constructed either as a sum of MP2/CBS interaction energy and CCSD(T) correction term [difference between CCSD(T) and MP2 correlation energies determined with medium basis set] or directly from CCSD(T)/aug-cc-pVDZ and aug-cc-pVTZ energies. Both schemes provide very similar values. Harmonic vibrational analysis revealed that the H-bonded structure does not represent energy minimum but first order transition structure. The respective imaginary vibrational mode (16  cm−1) connects two possible argon locations—above and below the phenol aromatic ring. Including the DeltaZPVE, we obtained stabilization enthalpy at 0  K of 389  cm−1. This value is marginally higher (25–35  cm−1, 0.07–0.10  kcal/mol) than the experimental value. The determination of DeltaZPVE constitutes the most significant error and possible improvements should come from more accurate evaluation of the (nonharmonic) vibrational frequencies.
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31.15.A-, 31.15.bw, 33.15.Mt, 33.20.Tp, 33.15.Bh

Dipole and quadrupole moment functions of the hydrogen halides HF, HCl, HBr, and HI: A Hirshfeld interpretation

James F. Harrison

J. Chem. Phys. 128, 114320 (2008) (12 pages)

Online Publication Date: 21 March 2008

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The dipole and quadrupole moment functions of the hydrogen halides are calculated using a large polarized basis and correlated wavefunctions and compared to experiment and previous calculations. These functions are analyzed in terms of local moments constructed using the Hirshfeld method. The dipole moment is the sum of the functions qHR+µH and µX with qH being the charge on the hydrogen atom, R the internuclear separation, µH and µX the atomic dipoles on the hydrogen and halogen atoms. We find that qHR+µH is always positive and has a maximum at bond lengths larger than the equilibrium. In HF, µF is slightly positive at the maximum in qHR+µH and has little effect on the resultant maximum in the dipole moment function (DMF). µCl, µBr, and µI, on the other hand, are increasingly more negative at the maximum of qHR+µH and have a profound effect on the width of the maximum of the resulting DMF, successively broadening it and completely eliminating it at HI. The quadrupole moment function (QMF) (with the halogen as origin) is given by Theta(HX)=Theta<sub>HX</sub><sup>proto</sup>+deltaThetaX+deltaThetaH+2µHR+qHR2, where Theta<sub>HX</sub><sup>proto</sup> is the quadrupole moment of the separated atoms (the halogen in this instance) and deltaThetaX+deltaThetaH the change in the in situ quadrupole moments of the halogen and hydrogen atoms. The maximum in the QMF and its slope at equilibrium are determined essentially by 2µHR+qHR2, which is known once the DMF is known. deltaThetaX+deltaThetaH is always negative while Theta<sub>HX</sub><sup>proto</sup> is positive, so one can approximate the molecular quadrupole moment to within 10% as Theta(HX)>Theta<sub>HX</sub><sup>proto</sup>+2µHR+qHR2.
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33.15.Kr, 33.15.Dj

Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Absorption and emission lineshapes and solvation dynamics of NO in supercritical Ar

Christopher N. Tiftickjian and S. A. Egorov

J. Chem. Phys. 128, 114501 (2008) (7 pages)

Online Publication Date: 17 March 2008

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We perform a theoretical study of electronic spectroscopy of dilute NO in supercritical Ar fluid. Absorption and emission lineshapes for the A2Sigma+<--X2Pi Rydberg transition of NO in argon have been previously measured and simulated, which yielded results for the NO/Ar ground- and excited-state pair potentials [Larrégaray et al., Chem. Phys. 308, 13 (2005)]. Using these potentials, we have performed molecular dynamics simulations and theoretical statistical mechanical calculations of absorption and emission lineshapes and nonequilibrium solvation correlation functions for a wide range of solvent densities and temperatures. Theory was shown to be in good agreement with simulation. Linear response treatment of solvation dynamics was shown to break down at near-critical temperature due to dramatic change in the solute-solvent microstructure upon solute excitation to the Rydberg state and the concomitant increase of the solute size.
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61.20.Ja, 82.30.Nr

Nuclear spin conversion of methane in solid parahydrogen

Yuki Miyamoto, Mizuho Fushitani, Daisuke Ando, and Takamasa Momose

J. Chem. Phys. 128, 114502 (2008) (10 pages)

Online Publication Date: 17 March 2008

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The nuclear spin conversion of CH4 and CD4 isolated in solid parahydrogen was investigated by high resolution Fourier transform infrared spectroscopy. From the analysis of the temporal changes of rovibrational absorption spectra, the nuclear spin conversion rates associated with the rotational relaxation from the J=1 state to the J=0 state for both species were determined at temperatures between 1 and 6  K. The conversion rate of CD4 was found to be 2–100 times faster than that of CH4 in this temperature range. The faster conversion in CD4 is attributed to the quadrupole interaction of D atoms in CD4, while the conversion in CH4 takes place mainly through the nuclear spin–nuclear spin interaction. The conversion rates depend on crystal temperature strongly above 3.5  K for CH4 and above 2  K for CD4, while the rates were almost constant below these temperatures. The temperature dependence indicates that the one-phonon process is dominant at low temperatures, while two-phonon processes become important at higher temperatures as a cause of the nuclear spin conversion.
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67.80.dk, 78.30.Jw, 76.60.Gv, 71.70.Jp

A microscopic view of substitution reactions solvated by ionic liquids

Guilherme M. Arantes and Mauro C. C. Ribeiro

J. Chem. Phys. 128, 114503 (2008) (9 pages)

Online Publication Date: 18 March 2008

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The solvation effect of the ionic liquid 1-N-butyl-3-methylimidazolium hexafluorophosphate on nucleophilic substitution reactions of halides toward the aliphatic carbon of methyl p-nitrobenzenesulfonate (pNBS) was investigated by computer simulations. The calculations were performed by using a hybrid quantum-mechanical/molecular-mechanical (QM/MM) methodology. A semiempirical Hamiltonian was first parametrized on the basis of comparison with ab initio calculations for Cl− and Br− reaction with pNBS at gas phase. In condensed phase, free energy profiles were obtained for both reactions. The calculated reaction barriers are in agreement with experiment. The structure of species solvated by the ionic liquid was followed along the reaction progress from the reagents, through the transition state, to the final products. The simulations indicate that this substitution reaction in the ionic liquid is slower than in nonpolar molecular solvents proper to significant stabilization of the halide anion by the ionic liquid in comparison with the transition state with delocalized charge. Solute-solvent interactions in the first solvation shell contain several hydrogen bonds that are formed or broken in response to charge density variation along the reaction coordinate. The detailed structural analysis can be used to rationalize the design of new ionic liquids with tailored solvation properties.
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82.30.Hk, 82.20.Db, 82.20.Hf, 82.20.Wt, 82.20.Yn

Thermodynamics of adiabatic cross polarization

Jae-Seung Lee and A. K. Khitrin

J. Chem. Phys. 128, 114504 (2008) (7 pages)

Online Publication Date: 19 March 2008

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Using a spin-temperature approach, we describe a scheme of adiabatic cross polarization, based on demagnetization/remagnetization, when the Zeeman order of abundant nuclei in the laboratory frame is first adiabatically converted into the dipolar order, and then, into the Zeeman order of rare nuclei. The scheme, implemented with two low-power frequency-sweeping pulses, is very efficient for static samples and can significantly increase polarization of rare nuclei, compared to the conventional Hartmann–Hahn cross polarization. The experimental examples are presented for a solid, liquid crystal, and small molecules in a liquid-crystalline solvent.
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75.60.Ej, 71.70.Ej, 61.30.-v

Effect of noise on chemical waves in three-dimensional reaction-diffusion systems with gradient

Xiaochuan Lu, Chunyan Wang, Chun Qiao, Yabi Wu, Qi Ouyang, and Hongli Wang

J. Chem. Phys. 128, 114505 (2008) (5 pages)

Online Publication Date: 19 March 2008

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The effect of noise on chemical waves in a quasi-three-dimensional reaction-diffusion medium with a gradient in the third dimension is studied using the FitzHugh–Nagumo model [R. FitzHugh, Biophysics J. 1, 445 (1961)]. Numerical simulations reveal that noise of appropriate intensity can postpone the onset of turbulence and stabilize the three-dimensional (3D) waves which would otherwise undergo the gradient-induced collapse. It is also found that the 3D waves can be interrupted by incident irregularities when the noise is not too strong; it can be induced into complete turbulence when the noise is strong enough. A mathematical analysis is given based on the dependence of the oscillation frequency on the control parameter. It agrees qualitatively with our numerical findings.
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05.40.Ca, 82.20.-w, 47.27.-i

Stimulated echoes and two-dimensional nuclear magnetic resonance spectra for solids with simple line shapes

Burkhard Geil, Gregor Diezemann, and Roland Böhmer

J. Chem. Phys. 128, 114506 (2008) (12 pages)

Online Publication Date: 20 March 2008

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Nuclear magnetic resonance (NMR) experiments on ion conductors often yield rather unstructured spectra, which are hard to interpret if the relation between the actual translational motion of the mobile species and the changes of the NMR frequencies is not known. In order to facilitate a general analysis of experiments on solids with such spectra, different models for the stochastic evolution of the NMR frequencies are considered. The treated models involve random frequency jumps, diffusive evolutions, or approximately fixed frequency jumps. Two-dimensional nuclear magnetic resonance spectra as well as stimulated-echo functions for the study of slow and ultraslow translational dynamics are calculated for Gaussian equilibrium line shapes. The results are compared with corresponding ones from rotational models and with experimental data.
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76.60.Lz, 66.30.Dn

Self-consistent Ornstein–Zernike approximation for the Yukawa fluid with improved direct correlation function

A. Reiner and J. S. Høye

J. Chem. Phys. 128, 114507 (2008) (7 pages)

Online Publication Date: 20 March 2008

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Thermodynamic consistency of the mean spherical approximation as well as the self-consistent Ornstein–Zernike approximation (SCOZA) with the virial route to thermodynamics is analyzed in terms of renormalized gamma-ordering. For continuum fluids, this suggests the addition of a short-ranged contribution to the usual SCOZA direct correlation function, and the shift of the adjustable parameter from the potential term to this new term. The range of this contribution is fixed by imposing consistency with the virial route at the critical point. Comparison of the results of our theory for the hard-core Yukawa potential with the simulation data show very good agreement for cases where the liquid-vapor transition is stable or not too far into the metastable region with respect to the solid state. In the latter case for extremely short-ranged interactions discrepancies arise.
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61.20.Gy, 65.20.De, 64.60.F-, 64.70.F-

Sound velocity dispersion in room temperature ionic liquids studied using the transient grating method

M. Fukuda, M. Terazima, and Y. Kimura

J. Chem. Phys. 128, 114508 (2008) (8 pages)

Online Publication Date: 21 March 2008

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Sound velocity is determined by the transient grating method in a range from 106  to  1010  Hz in three room temperature ionic liquids, 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide, 1-butyl-3-methylimidazolium hexafluorophosphate, and N,N,N-trimethyl-N-propylammonium bis(trifluoromethanesulfonyl)imide. In all room temperature ionic liquids studied, the sound velocity increased with increasing frequency. The cause of this change is posited to be structural relaxation in the room temperature ionic liquids. Frequency dependence of the sound velocity is not reproduced by a simple Debye relaxation model. The sound velocity dispersion relation in 1-butyl-3-methylimidazolium hexafluorophosphate matches a Cole–Davidson function with parameters determined by a dielectric relaxation [C. Daguenet et al., J. Phys. Chem. B 110, 12682 (2006)], indicating that structural and reorientational relaxations are strongly coupled. Conversely, the sound velocity dispersions of the other two ionic liquids measured do not match those measured for dielectric relaxation, implying that structural relaxation is much faster than the reorientational relaxation. This difference is discussed in relation to the motilities of anions and cations.
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61.25.Em, 62.60.+v, 77.22.Gm

Statistical mechanical theory for steady state systems. VIII. General theory for a Brownian particle driven by a time- and space-varying force

Phil Attard and Angus Gray–Weale

J. Chem. Phys. 128, 114509 (2008) (16 pages)

Online Publication Date: 21 March 2008

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A Brownian particle subject to a time- and space-varying force is studied with the second entropy theory for nonequilibrium statistical mechanics. A fluctuation expression is obtained for the second entropy of the path, and this is maximized to obtain the most likely path of the particle. Two approaches are used, one based on the velocity correlation function and one based on the position correlation function. The approaches are a perturbation about the free particle result and are exact for weak external forces. They provide a particularly simple way of including memory effects in time-varying driven diffusion. The theories are tested against computer simulation data for a Brownian particle trapped in an oscillating parabolic well. They accurately predict the phase lag and amplitude as a function of drive frequency, and they account quantitatively for the memory effects that are important at high frequencies and that are missing in the simplest Langevin equation.
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05.20.-y, 05.40.Jc, 05.70.Ce, 02.30.Hq, 05.60.-k

The global phase behavior of the two-component systems with intracomponent association: Flory approach

M. V. Belousov, M. V. Tamm, and I. Ya. Erukhimovich

J. Chem. Phys. 128, 114510 (2008) (11 pages)

Online Publication Date: 21 March 2008

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Within the Flory approach we study the phase diagrams of two-component fluids, the molecules of each component AfA, BfB bearing fA (fB) functional groups capable of forming thermoreversible A–A and B–B bonds. We develop a general procedure to classify these diagrams depending on the values of four governing parameters—entropies and normalized energies of A–A and B–B bonds, and give full topological classification of phase diagrams with fA,B>=3. We show that these phase diagrams can have immiscibility loops and up to four critical points.
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65.20.-w, 64.75.Bc, 64.60.F-, 61.25.Em

Surfaces, Interfaces, and Materials

Kinetics of docking in postnucleation stages of self-assembly

Roberto A. Garza-López, Philippe Bouchard, Gregoire Nicolis, Mike Sleutel, Jack Brzezinski, and John J. Kozak

J. Chem. Phys. 128, 114701 (2008) (13 pages)

Online Publication Date: 17 March 2008

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In a previous study, the early stages of self-assembly in nanophase materials were explored by coupling a kinetic mean-field analysis with a lattice-based stochastic theory [J. J. Kozak et al., J. Chem. Phys. 126, 154701 (2007)]. Recent experimental results on the postnucleation stages of zeolite assembly and protein crystallite formation have suggested a new study, presented here, in which the docking of a platelet on the existing surface of a structured crystallite is similarly investigated. A model is designed which allows the quantification of factors affecting docking efficiency; principal among these is the structure of the template itself, which here is assumed to be either unstructured or bifurcated into terraces and edges/ledges. Going beyond our earlier study (in which diffusion was restricted to d=2 dimensions), the diffusion space here is enlarged to consider both d=2 and d=3 dimensional flows. By expanding the external diffusion space systematically, we are able to document the consequences (as regards docking efficiency) of diffusive flows in the near neighborhood of a developing crystallite versus surface-only processes. Particularly in regimes where the barriers to surface diffusion are high, and/or the probability of desorption significant, we find that d=3 dimensional processes (leading to a “direct hit”) can compete kinetically with surface-only mediated processes. Although the crystallite model studied here is simple, it can be diffeomorphically distorted into a manifold of possible geometries; in analogy with the classical theory of corresponding states, we argue that the familial relationship among these structures suggests that the generic results obtained provide a qualitatively correct description of the kinetics of docking on structured surfaces.
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81.16.Dn, 68.43.Jk, 68.43.Nr, 82.20.Db

Size extensivity of the direct optimized effective potential method

Tim Heaton-Burgess, Aron J. Cohen, Weitao Yang, and Ernest R. Davidson

J. Chem. Phys. 128, 114702 (2008) (8 pages)

Online Publication Date: 17 March 2008

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We investigate the size extensivity of the direct optimized effective potential procedure of Yang and Wu [Phys. Rev. Lett. 89, 143002 (2002)]. The choice of reference potential within the finite basis construction of the local Kohn–Sham potential can lead to a method that is not size extensive. Such a situation is encountered when one employs the Fermi–Amaldi potential, which is often used to enforce the correct asymptotic behavior of the exact exchange-correlation potential. The size extensivity error with the Fermi–Amaldi reference potential is shown to behave linearly with the number of electrons in the limit of an infinite number of well separated monomers. In practice, the error tends to be rather small and rapidly approaches the limiting linear behavior. Moreover, with a flexible enough potential basis set, the error can be decreased significantly. We also consider one possible reference potential, constructed from the van Leeuwen–Baerends potential, which provides a size extensive implementation while also enforcing the correct asymptotic behavior.
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31.15.eg

Orange-red luminescence from Cu doped CdS nanophosphor prepared using mixed Langmuir–Blodgett multilayers

P. Mandal, S. S. Talwar, S. S. Major, and R. S. Srinivasa

J. Chem. Phys. 128, 114703 (2008) (7 pages)

Online Publication Date: 17 March 2008

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Cu doped CdS nanophosphors were fabricated through Langmuir–Blodgett route for the first time. Precursors mixed Langmuir–Blodgett multilayers of cadmium arachidate–copper arachidate were used to grow doped sulfide nanoparticles within the organic matrix through postdeposition treatment with H2S gas. Changes in composition and layered structure of precursor multilayers were studied using Fourier transform infrared and x-ray reflection. Uptake of Cu in the multilayers was analyzed by inductively coupled plasma atomic emission spectroscopy measurements. Unannealed H2S exposed multilayers containing CdS nanoparticles show strong surface state emission centeredat ~570  nm, whereas Cu doped CdS nanoparticles show orange-red luminescence. Photoluminescence (PL) spectra of annealed-Cu doped CdS nanoparticles show distinct Cu-related emission compared to annealed-undoped CdS nanoparticles. Power dependent PL measurements of annealed samples show that an efficient carrier recombination takes place at T2 level of Cu++. The carrier relaxation from the excitonic states to T2 level results in the strong orange-red luminescence.
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78.55.Et, 78.67.Bf, 81.07.Bc, 81.05.Dz, 73.21.Ac, 73.63.Bd

Quantum studies of light particle trapping, sticking, and desorption on metal and graphite surfaces

Zuleika Medina and Bret Jackson

J. Chem. Phys. 128, 114704 (2008) (9 pages)

Online Publication Date: 17 March 2008

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A quantum mechanical formalism capable of describing the scattering, trapping, sticking, and desorption of an atom from a moving corrugated surface is presented. While the instantaneous particle-bath interaction is assumed to be weak, the particle and the bath can exchange energy over long periods of time. We have explored the trapping desorption and trapping-relaxation-sticking of He on Cu(110) and of H on graphite(0001). Higher substrate temperatures generally lead to increased trapping, but a higher desorption rate eventually leads to less, or zero sticking, at long times. In both cases, we observe that trapping in diffraction-mediated selective adsorption resonances can enhance sticking at low incident energies. While trapped in the resonance, the atom can relax toward the ground state of the gas-substrate attractive well. If the binding energy is larger than the amount of energy in the atom's motion parallel to the surface, it remains stuck at long times, at sufficiently low temperatures. We find sticking probabilities on the order of 1% at very low energies for both systems. In the vicinity of a selective adsorption resonance, this sticking can increase by several percent, depending on the size of the corrugation.
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68.43.Nr, 68.43.Mn, 79.20.Rf

Magnetic properties and quantum phase transitions of purely organic molecule-based ferrimagnets based on Green's function theory

Hua-Hua Fu, Kai-Lun Yao, and Zu-Li Liu

J. Chem. Phys. 128, 114705 (2008) (8 pages)

Online Publication Date: 17 March 2008

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Magnetic properties of a Heisenberg diamondlike spin chain model for purely organic molecule-based ferrimagnets are investigated by means of the many-body Green's function method within random phase approximation. The molecule-based ferrimagnet is composed of S=1 biradical and S=1/2 monoradical molecules alternating with intermolecular antiferromagnetic (AF) interactions, and the S=1 site is composed of two S=1/2 spins by a finite intramolecular ferromagnetic (F) interaction. The numerical results reveal that occurrence of ferrimagnetic spin alignments along the chain is determined by the intermolecular AF interactions. Owing to the very small intermolecular AF interactions, the curves of the product of magnetic susceptibility and temperature (chiT) against temperature display as a round peak at low temperatures, and the ferrimagnetic phase transition could only be detected at ultralow temperatures in practical organic compounds. Temperature- and magnetic-field-induced magnetic phase transitions are discussed, which are consistent with the experimental findings. The lower spatial symmetry of intermolecular interactions makes it easy to form spin pairs with a singlet (S=0) ground state along the chain and to reduce Curie temperature. The formations of molecular dimers and trimers along the chain have contributions to bring about F alignments with effective S=1/2 magnetic supramolecules and to enhance Curie temperature. In addition, the experimental data of the magnetic susceptibility measurements for a molecule-based ferrimagnet are also fairly compared with our theoretical results.
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75.50.Gg, 75.30.Kz, 73.43.Nq, 75.30.Cr, 75.10.Jm, 75.40.-s

Core level shifts of undercoordinated Pt atoms

Laura Bianchettin, Alessandro Baraldi, Stefano de Gironcoli, Erik Vesselli, Silvano Lizzit, Luca Petaccia, Giovanni Comelli, and Renzo Rosei

J. Chem. Phys. 128, 114706 (2008) (6 pages)

Online Publication Date: 18 March 2008

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We present the results of high-energy resolution core level photoelectron spectroscopy experiments paralleled by density functional theory calculations to investigate the electronic structure of highly undercoordinated Pt atoms adsorbed on Pt(111) and its correlation with chemical activity. Pt4f7/2 core level binding energies corresponding to atoms in different configurations are shown to be very sensitive not only to the local atomic coordination number but also to the interatomic bond lengths. Our results are rationalized by introducing an indicator, the effective coordination, which includes both contributions. The calculated energy center of the valence 5d-band density of states, which is a well known depicter of the surface chemical reactivity, shows a noteworthy correlation with the Pt4f7/2 core level shifts and with the effective coordination.
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68.43.-h, 79.60.Bm, 71.15.Mb, 73.20.At

Liquid-solid coexistence via the metadynamics approach

Santi Prestipino and Paolo V. Giaquinta

J. Chem. Phys. 128, 114707 (2008) (5 pages)

Online Publication Date: 18 March 2008

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The metadynamics method, recently proposed by Laio and Parrinello as a general tool to map multidimensional free-energy landscapes [A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 99, 12562 (2002)], has been exploited with the aim of illustrating the properties of generalized thermodynamic potentials across a discontinuous phase transition. Virtues and limitations of the method are discussed in the exemplifying case of the freezing of a Lennard-Jones fluid in two dimensions.
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05.20.Jj, 61.20.Ja

Estimation of the liquid-vapor spinodal from interfacial properties obtained from molecular dynamics and lattice Boltzmann simulations

A. R. Imre, G. Mayer, G. Házi, R. Rozas, and T. Kraska

J. Chem. Phys. 128, 114708 (2008) (11 pages)

Online Publication Date: 19 March 2008

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Interfacial pressure and density profiles are calculated from molecular dynamics and lattice Boltzmann simulations of a liquid film in equilibrium with its vapor. The set of local values of tangential pressure and density along an interface exhibits a van der Waals-type loop; starting from the stable vapor bulk phase one passes through metastable and unstable states to the stable liquid bulk phase. The minimum and maximum values of the profile of tangential pressure are related to the liquid and vapor spinodal states, respectively. The spinodal pressures turn out to be linearly related to the extreme values of the tangential pressure in the interface. The comparison with equations of state shows good agreement with the simulation results of the spinodals. In addition the properties of the metastable region are obtained. Based on this investigation a method is proposed for the estimation of the liquid spinodal from experimentally obtained interfacial properties. Estimations for water and helium are presented.
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68.15.+e, 64.70.F-, 64.30.-t, 61.20.Ja, 64.60.My

New insight brought by density functional theory on the chemical state of alaninol on Cu(100): Energetics and interpretation of x-ray photoelectron spectroscopy data

S. Irrera and D. Costa

J. Chem. Phys. 128, 114709 (2008) (10 pages)

Online Publication Date: 19 March 2008

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In recent years, an increasing interest has been focused on the adsorption of molecules on surfaces due to the importance of technologies based on the interaction of organic systems with metals and oxides for biosensors, catalysis, and molecularly imprinted polymer technology. A particularly attractive area is the study of chiral surfaces, as these can act as heterogeneous catalysts and sensors in the stereochemical industrial processes. This work reports on an ab initio simulation of chemisorption of the D-alaninol on Cu (100). This system has been investigated systematically by using the Vienna ab initio simulation Package (VASP) which performs density functional theory (DFT) calculations in periodic boundary conditions. Molecular dynamics at 300  K is performed to explore all the possible geometries, finally, optimized at 0  K to obtain the adsorption modes. C 1s, O 1s, and N 1s, core level shift (CLS) calculations of those adsorption modes have been evaluated and compared with x-ray photoelectron spectroscopy experimental data. Energetic and CLS indicate that both chemical functions, the NH2 and the dehydrogenated hydroxyl, are involved in the bonding to the surface at low coverage. Atomic hydrogen coadsorbs in a fourfold hollow site. An atomistic thermodynamics approach suggests that at room temperature under UHV conditions, coadsorbed hydrogen has recombined as H2 and desorbed from the surface.
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68.43.Bc, 79.60.Dp, 82.65.+r

First principles studies for formation mechanism and properties of ethylene molecule adsorbing on diamond (100) surface

Hao Jin, Ying Dai, Run Long, Meng Guo, Baibiao Huang, and Ruiqin Zhang

J. Chem. Phys. 128, 114710 (2008) (6 pages)

Online Publication Date: 20 March 2008

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We employed density functional theory within the generalized gradient approximation to investigate the diamond (100) surface, with hydrogen and ethylene terminations. The radical chain reaction is investigated by slab models, and two possible adsorption ways are found according to our calculations. In addition, the electron affinity of H-terminated diamond is also calculated, which indicates that the existence of negative electron affinity of H–C (100) surface provides a necessary condition for initiating radical chain reaction. Our results also imply that ethylene molecules can form strong C–C covalent bonds with diamond surface, which make it more resistant against degradation processes. Furthermore, according to the analysis of electronic structures, we have found localized gap state above the valence band, which is mainly contributed by the interaction between diamond surface and ethylene molecule and can weaken the surface conductivity of the adsorbed diamond.
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82.30.Cf, 68.43.Mn, 82.65.+r, 73.20.At, 73.25.+i

Nanomicrointerface to read molecular potentials into current-voltage based electronics

Norma L. Rangel and Jorge M. Seminario

J. Chem. Phys. 128, 114711 (2008) (9 pages)

Online Publication Date: 20 March 2008

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Molecular potentials are unreadable and unaddressable by any present technology. It is known that the proper assembly of molecules can implement an entire numerical processing system based on digital or even analogical computation. In turn, the outputs of this molecular processing unit need to be amplified in order to be useful. We have developed a nanomicrointerface to read information encoded in molecular level potentials and to amplify this signal to microelectronic levels. The amplification is performed by making the output molecular potential slightly twist the torsional angle between two rings of a pyridazine, 3,6-bis(phenylethynyl) (aza-OPE) molecule, requiring only fractions of kcal/mol energies. In addition, even if the signal from the molecular potentials is not enough to turn the ring or even if the angles are the same for different combinations of outputs, still the current output yields results that resemble the device as a field effect transistor, providing the possibility to reduce channel lengths to the range of just 1 or 2  nm. The slight change in the torsional angle yields readable changes in the current through the aza-OPE biased by an external applied voltage. Using ab initio methods, we computationally demonstrate the amplification of molecular potential signals into currents that can be read by standard circuits.
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85.65.+h

Single-file diffusion through inhomogeneous nanopores

Tusar Bandyopadhyay

J. Chem. Phys. 128, 114712 (2008) (6 pages)

Online Publication Date: 20 March 2008

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Strict one-dimensional diffusion, due to geometrical confinement in a nanopore, of an assembly of particles forbids overtaking by each other, giving rise to single-file diffusion (SFD). Smooth carbon nanotube is the epitome of SFD. However, natural nanoporous materials are far from smooth; morphologically, the nanopores' inner surface may provide an inhomogeneous environment for diffusion to occur, giving rise to subnormal diffusion even for an isolated particle diffusing through this fractal landscape. The realm of fractional diffusion (FD) falls under this paradigm. In order to understand the characteristics of SFD through inhomogeneous nanopores, here, we introduce a fractional SFD (FSFD) formalism that deals with a combination of these two phenomena, namely, SFD of particles, each of which are moving subdiffusively in one dimension. For an infinite system, we obtain the mean square displacement (MSD) of the combined entity and our analysis is based on FD equation for particles moving in concert where the single-file correlation is established through reflection principle. For a finite system, we calculate the transport probabilities based on continuous time random walk model. While both the diffusion mechanisms (SFD and FD) acting separately are responsible for slow dynamics at long times, their combined effect leads to ultraslow diffusion. For example, while the long time asymptote of MSD of SFD scales as sqrt(t), that for FSFD is sqrt(t[sup alpha]), where alpha is the measure of the extent of inhomogeneity. These findings, which are believed to occur in a natural inhomogeneous nanopore, is also important for design and fabrication of nanofluidic devices through which the fluid delivery can be engineered.
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61.43.Gt, 66.30.Pa, 66.30.Dn, 61.46.Fg

A unified theory for charge-carrier transport in organic crystals

Yuan-Chung Cheng and Robert J. Silbey

J. Chem. Phys. 128, 114713 (2008) (18 pages)

Online Publication Date: 20 March 2008

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To characterize the crossover from bandlike transport to hopping transport in molecular crystals, we study a microscopic model that treats electron-phonon interactions explicitly. A finite-temperature variational method combining Merrifield's transformation with Bogoliubov's theorem is developed to obtain the optimal basis for an interacting electron-phonon system, which is then used to calculate the bandlike and hopping mobilities for charge carriers. Our calculations on the one dimensional (1D) Holstein model at T=0  K and finite temperatures show that the variational basis gives results that compared favorably to other analytical methods. We also study the structures of polaron states at a broad range of parameters including different temperatures. Furthermore, we calculate the bandlike and hopping mobilities of the 1D Holstein model in different parameters and show that our theory predicts universal power-law decay at low temperatures and an almost temperature independent behavior at higher temperatures, in agreement with experimental observations. In addition, we show that as the temperature increases, hopping transport can become dominant even before the polaron state changes its character. Thus, our result indicates that the self-trapping transition studied in conventional polaron theories does not necessarily correspond to the bandlike to hopping transition in the transport properties in organic molecular crystals. Finally, a comparison of our 1D results with experiments on ultrapure naphthalene crystals suggests that the theory can describe the charge-carrier mobilities quantitatively across the whole experimental temperature range.
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72.20.Ee, 71.38.-k, 63.20.kd, 73.61.Ph, 72.80.Le

Benchmark density functional theory calculations for nanoscale conductance

M. Strange, I. S. Kristensen, K. S. Thygesen, and K. W. Jacobsen

J. Chem. Phys. 128, 114714 (2008) (8 pages)

Online Publication Date: 20 March 2008

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We present a set of benchmark calculations for the Kohn-Sham elastic transmission function of five representative single-molecule junctions. The transmission functions are calculated using two different density functional theory methods, namely an ultrasoft pseudopotential plane-wave code in combination with maximally localized Wannier functions and the norm-conserving pseudopotential code SIESTA which applies an atomic orbital basis set. All calculations have been converged with respect to the supercell size and the number of k|| points in the surface plane. For all systems we find that the SIESTA transmission functions converge toward the plane-wave result as the SIESTA basis is enlarged. Overall, we find that an atomic basis with double zeta and polarization is sufficient (and in some cases, even necessary) to ensure quantitative agreement with the plane-wave calculation. We observe a systematic downshift of the SIESTA transmission functions relative to the plane-wave results. The effect diminishes as the atomic orbital basis is enlarged; however, the convergence can be rather slow.
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73.63.Rt, 71.15.Mb, 71.15.Dx

Femtosecond time-resolved electronic sum-frequency generation spectroscopy: A new method to investigate ultrafast dynamics at liquid interfaces

Kentaro Sekiguchi, Shoichi Yamaguchi, and Tahei Tahara

J. Chem. Phys. 128, 114715 (2008) (8 pages)

Online Publication Date: 21 March 2008

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We developed a new surface-selective time-resolved nonlinear spectroscopy, femtosecond time-resolved electronic sum-frequency generation (TR-ESFG) spectroscopy, to investigate ultrafast dynamics of molecules at liquid interfaces. Its advantage over conventional time-resolved second harmonic generation spectroscopy is that it can provide spectral information, which is realized by the multiplex detection of the transient electronic sum-frequency signal using a broadband white light continuum and a multichannel detector. We studied the photochemical dynamics of rhodamine 800 (R800) at the air/water interface with the TR-ESFG spectroscopy, and discussed the ultrafast dynamics of the molecule as thoroughly as we do for the bulk molecules with conventional transient absorption spectroscopy. We found that the relaxation dynamics of photoexcited R800 at the air/water interface exhibited three characteristic time constants of 0.32  ps, 6.4  ps, and 0.85  ns. The 0.32  ps time constant was ascribed to the lifetime of dimeric R800 in the lowest excited singlet (S1) state (S1 dimer) that is directly generated by photoexcitation. The S1 dimer dissociates to a monomer in the S1 state (S1 monomer) and a monomer in the ground state with this time constant. This lifetime of the S1 dimer was ten times shorter than the corresponding lifetime in a bulk aqueous solution. The 6.4  ps and 0.85  ns components were ascribed to the decay of the S1 monomer (as well as the recovery of the dimer in the ground state). For the 6.4  ps time constant, there is no corresponding component in the dynamics in bulk water, and it is ascribed to an interface-specific deactivation process. The 0.85  ns time constant was ascribed to the intrinsic lifetime of the S1 monomer at the air/water interface, which is almost the same as the lifetime in bulk water. The present study clearly shows the feasibility and high potential of the TR-ESFG spectroscopy to investigate ultrafast dynamics at the interface.
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33.70.Ca, 82.53.Uv, 33.80.Gj, 33.80.Rv, 31.70.Dk

Mean-field density-functional model of a second-order wetting transition

K. Koga and B. Widom

J. Chem. Phys. 128, 114716 (2008) (8 pages)

Online Publication Date: 21 March 2008

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First- and second-order wetting transitions are contrasted. A mean-field density-functional model that leads to a second-order transition is introduced. The way in which it differs from an earlier, otherwise similar model in which the transition is first order is noted. The interfacial and line tensions in the model are obtained numerically and their behavior on approach to the transition is determined. The spatial variation of the model's densities in the neighborhood of the contact line near the wetting transition is also found and seen to be characteristically different at a second-order transition from what it is at a first-order transition. The results for the line tension and for the spatial variation of the densities are in accord with those from an earlier interface-displacement model of the same phenomena.
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68.03.Cd, 68.08.Bc

Adsorption dynamics of water on Pt{110}−(1×2)

Fathima R. Laffir, Vittorio Fiorin, and David A. King

J. Chem. Phys. 128, 114717 (2008) (9 pages)

Online Publication Date: 21 March 2008

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The dynamics of H2O adsorption on Pt{110}−(1×2) is studied using supersonic molecular beam and temperature programed desorption techniques. The sticking probabilities are measured using the King and Wells method at a surface temperature of 165  K. The absolute initial sticking probability s0 of H2O is 0.54±0.03 for an incident kinetic energy of 27  kJ/mol. However, an unusual molecular beam flux dependence on s0 is also found. At low water coverage (theta<1), the sticking probability is independent of coverage due either to diffusion in an extrinsic precursor state formed above bilayer islands or to incorporation into the islands. We define theta=1 as the water coverage when the dissociative sticking probability of D2 on a surface predosed with water has dropped to zero. The slow falling H2O sticking probability at theta>1 results from compression of the bilayer and the formation of multilayers. Temperature programed desorption of water shows fractional order kinetics consistent with hydrogen-bonded islands on the surface. A remarkable dependence of the initial sticking probability on the translational (1–27  kJ/mol) and internal energies of water is observed: s0 is found to be essentially a step function of translational energy, increasing fivefold at a threshold energy of 5  kJ/mol. The threshold migrates to higher energies with increasing nozzle temperature (300–700  K). We conclude that both rotational state and rotational alignment of the water molecules in the seeded supersonic expansion are implicated in dictating the adsorption process.
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68.43.Mn, 68.43.Vx, 66.30.Fq

Polymers and Complex Systems

Mesoscopic dynamics of inhomogeneous polymers based on variable cell shape dynamic self-consistent field theory

Xuan Li, Ping Tang, Hongdong Zhang, Feng Qiu, and Yuliang Yang

J. Chem. Phys. 128, 114901 (2008) (11 pages)

Online Publication Date: 17 March 2008

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In this paper, we combine variable cell shape method with dynamic self-consistent field theory and extend to study structure and dynamics under shear for triblock copolymer melts. Due to shear, the calculation cell shape is variable and no longer orthogonal. Pseudospectral method is employed to solve the diffusion equation for chain propagator on the nonorthogonal coordinate and the shear periodical condition can be easily designed in terms of the variable cell shape method. By using this strategy, the shear induced morphology evolution is investigated for topologically complex polymeric systems such as linear and star triblock copolymers; the morphology of linear ABC triblock copolymers is more shear sensitive than that of star triblocks. In particular, once the chain propagator is obtained, the microscopic elastic stress and spatial stress distribution can be derived and thus the dynamic mechanical property can be calculated under shear. By imitating the dynamic storage modulus G[prime] corresponding to any given morphology in the oscillatory shear measurements, we explore the relationship between the morphology and the storage modulus G[prime] and extend to study the mechanism of phase separation dynamics as well as order-disorder transition (ODT) for linear and star triblock copolymers. The results show that the chain architecture can be easily distinguished by investigating the ODT, though the systems such as AB symmetric diblock and ABA triblock copolymers by coupling AB precursors almost exhibit similar microstructures. In addition, the storage modulus G[prime] and loss modulus G[double-prime] can be simultaneously determined in frequency sweeps of oscillatory shear measurements and the dependence of the moduli on phase separated patterns and the chain topology is investigated. The simulation findings are in qualitatively agreement with the experimental results.
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61.25.hk, 61.20.Gy, 66.10.C-, 62.10.+s, 64.60.Cn

Universal properties of mechanisms from two-state trajectories

O. Flomenbom and R. J. Silbey

J. Chem. Phys. 128, 114902 (2008) (13 pages)

Online Publication Date: 18 March 2008

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Finding the underlying mechanism from the statistical properties of an experimental two-state trajectory generated from dynamics in a complex on-off multisubstate kinetic scheme (KS) is the aim of many experiments. Since the data explicitly shows only transitions between substates of different states, information about the KS is lost, resulting in equivalence of KSs, i.e., the occurrence of different KSs that lead to the same data, in a statistical sense. In order to deal with this phenomenon, a canonical (unique) form of reduced dimensions (RD) is built from the data. RD forms are on-off networks with connections only between substates of different states, where the connections usually have nonexponential waiting time probability density functions. In this paper, we give a list of (about 50) relationships between properties of the data, the topology of reduced dimension forms, and features of KSs. Many of these relationships involve symmetries in RD forms, KSs, and the data and irreversible transitions in KSs. These relationships are useful both in theoretical analysis of on-off KSs and in the analysis of the data.
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87.15.Cc, 87.15.A-, 87.15.R-

The rate constant of polymer reversal inside a pore

Lei Huang and Dmitrii E. Makarov

J. Chem. Phys. 128, 114903 (2008) (9 pages)

Online Publication Date: 19 March 2008

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Translocation of biopolymers through pores is implicated in many biological phenomena. Confinement within a pore often breaks ergodicity on experimental and/or biological time scales by creating large entropic barriers to conformational rearrangements of the chain. Here, we study one example of such hindered rearrangement, in which the chain reverses its direction inside a long pore. Our goal is twofold. First, we study the dependence of the time scale of polymer reversal on the pore size and on the polymer length. Second, we examine the ability of simple one-dimensional theories to quantitatively describe a transition in a system with a complex energy landscape by comparing them with the exact rate constant obtained using brute-force simulations and the forward flux sampling method. We find that one-dimensional transition state theory (TST) using the polymer extension along the pore axis as the reaction coordinate adequately accounts for the exponentially strong dependence of the reversal rate constant on the pore radius r and the polymer length N, while the transmission factor, i.e., the ratio of the exact rate and the TST approximation, has a much weaker power law r and N dependence. We have further attempted to estimate the transmission factor from Kramer's theory, which assumes the reaction coordinate dynamics to be governed by a Langevin equation. However, such an approximation was found to be inadequate. Finally, we examine the scaling behavior of the reversal rate constant with N and r and show that finite size effects are important even for chains with N up to several hundreds.
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87.15.A-, 87.15.B-, 87.15.hp, 87.15.R-, 82.20.Pm

Force balance of particles trapped at fluid interfaces

Alvaro Domínguez, Martin Oettel, and S. Dietrich

J. Chem. Phys. 128, 114904 (2008) (12 pages)

Online Publication Date: 20 March 2008

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We study the effective forces acting between colloidal particles trapped at a fluid interface which itself is exposed to a pressure field. To this end, we apply what we call the “force approach,” which relies solely on the condition of mechanical equilibrium and turns to be in a certain sense less restrictive than the more frequently used “energy approach,” which is based on the minimization of a free energy functional. The goals are (i) to elucidate the advantages and disadvantages of the force approach as compared to the energy approach, and (ii) to disentangle which features of the interfacial deformation and of the capillary-induced forces between the particles follow from the gross feature of mechanical equilibrium alone, as opposed to features which depend on the details of, e.g., the interaction of the interface with the particles or the boundaries of the system. First, we derive a general stress-tensor formulation of the forces at the interface. On that basis we work out a useful analogy with two-dimensional electrostatics in the particular case of small deformations of the interface relative to its flat configuration. We apply this analogy in order to compute the asymptotic decay of the effective force between particles trapped at a fluid interface, extending the validity of the previous results and revealing the advantages and limitations of the force approach compared to the energy approach. It follows the application of the force approach to the case of deformations of a nonflat interface. In this context, we first compute the deformation of a spherical droplet due to the electric field of a charged particle trapped at its surface and conclude that the interparticle capillary force is unlikely to explain certain recent experimental observations within such a configuration. We finally discuss the application of our approach to a generally curved interface and show as an illustrative example that a nonspherical particle deposited on an interface forming a minimal surface is pulled to regions of larger curvature.
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82.70.Dd, 68.05.-n

Biological Molecules, Biopolymers, and Biological Systems

Electronic couplings and on-site energies for hole transfer in DNA: Systematic quantum mechanical/molecular dynamic study

Alexander A. Voityuk

J. Chem. Phys. 128, 115101 (2008) (5 pages)

Online Publication Date: 17 March 2008

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The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the pi stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15  ns MD trajectories for several DNA oligomers, we calculate the average coupling squares <V2> and the energies of basepair triplets XG+Y and XA+Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1  ps are considered. The three-state generalized Mulliken–Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B-DNA structure and show that in several important cases the couplings calculated for the idealized B-DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ~0.07  eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The XG+Y are by 0.5  eV more stable than XA+Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA.
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87.15.hg, 87.15.R-, 87.15.ap

Two-dimensional fluorescence resonance energy transfer as a probe for protein folding: A theoretical study

Christina L. Ting and Dmitrii E. Makarov

J. Chem. Phys. 128, 115102 (2008) (13 pages)

Online Publication Date: 17 March 2008

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We describe a two-dimensional (2D), four-color fluorescence resonance energy transfer (FRET) scheme, in which the conformational dynamics of a protein is followed by simultaneously observing the FRET signal from two different donor-acceptor pairs. For a general class of models that assume Markovian conformational dynamics, we relate the properties of the emission correlation functions to the rates of elementary kinetic steps in the model. We further use a toy folding model that treats proteins as chains with breakable cross-links to examine the relationship between the cooperativity of folding and FRET data and to establish what additional information about the folding dynamics can be gleaned from 2D, as opposed to one-dimensional FRET experiments. We finally discuss the potential advantages of the four-color FRET over the three-color FRET technique.
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87.15.hm, 87.15.hp, 87.15.B-, 87.14.E-, 87.15.A-, 36.20.Fz

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations

Yuqing Deng and Benoît Roux

J. Chem. Phys. 128, 115103 (2008) (8 pages)

Online Publication Date: 18 March 2008

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The binding of a ligand to a receptor is often associated with the displacement of a number of bound water molecules. When the binding site is exposed to the bulk region, this process may be sampled adequately by standard unbiased molecular dynamics trajectories. However, when the binding site is deeply buried and the exchange of water molecules with the bulk region may be difficult to sample, the convergence and accuracy in free energy perturbation (FEP) calculations can be severely compromised. These problems are further compounded when a reduced system including only the region surrounding the binding site is simulated. To address these issues, we couple molecular dynamics (MD) with grand canonical Monte Carlo (GCMC) simulations to allow the number of water to fluctuate during an alchemical FEP calculation. The atoms in a spherical inner region around the binding pocket are treated explicitly while the influence of the outer region is approximated using the generalized solvent boundary potential (GSBP). At each step during thermodynamic integration, the number of water in the inner region is equilibrated with GCMC and energy data generated with MD is collected. Free energy calculations on camphor binding to a deeply buried pocket in cytochrome P450cam, which causes about seven water molecules to be expelled, are used to test the method. It concluded that solvation free energy calculations with the GCMC/MD method can greatly improve the accuracy of the computed binding free energy compared to simulations with fixed number of water.
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65.20.-w, 61.20.Ja

Zinc cysteine active sites of metalloproteins: A density functional theory and x-ray absorption fine structure study

Nicholas Dimakis, Mohammed Junaid Farooqi, Emily Sofia Garza, and Grant Bunker

J. Chem. Phys. 128, 115104 (2008) (9 pages)

Online Publication Date: 18 March 2008

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Density functional theory (DFT) and x-ray absorption fine structure (XAFS) spectroscopy are complementary tools for the biophysical study of active sites in metalloproteins. DFT is used to compute XAFS multiple scattering Debye Waller factors, which are then employed in genetic algorithm-based fitting process to obtain a global fit to the XAFS in the space of fitting parameters. Zn-Cys sites, which serve important functions as transcriptional switches in Zn finger proteins and matrix metalloproteinases, previously have proven intractable by this method; here these limitations are removed. In this work we evaluate optimal DFT nonlocal functionals and basis sets for determining optimal geometries and vibrational densities of states of mixed ligation Zn(His)4−n(Cys)n sites. Theoretical results are compared to experimental XAFS measurements and Raman spectra from the literature and tabulated for use.
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87.15.B-, 87.15.A-, 87.15.M-

Molecular simulation of protein dynamics in nanopores. I. Stability and folding

Leili Javidpour, M. Reza Rahimi Tabar, and Muhammad Sahimi

J. Chem. Phys. 128, 115105 (2008) (15 pages)

Online Publication Date: 19 March 2008

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Discontinuous molecular dynamics simulations, together with the protein intermediate resolution model, an intermediate-resolution model of proteins, are used to carry out several microsecond-long simulations and study folding transition and stability of alpha-de novo–designed proteins in slit nanopores. Both attractive and repulsive interaction potentials between the proteins and the pore walls are considered. Near the folding temperature Tf and in the presence of the attractive potential, the proteins undergo a repeating sequence of folding/partially folding/unfolding transitions, with Tf decreasing with decreasing pore sizes. The unfolded states may even be completely adsorbed on the pore's walls with a negative potential energy. In such pores the energetic effects dominate the entropic effects. As a result, the unfolded state is stabilized, with a folding temperature Tf which is lower than its value in the bulk and that, compared with the bulk, the folding rate decreases. The opposite is true in the presence of a repulsive interaction potential between the proteins and the walls. Moreover, for short proteins in very tight pores with attractive walls, there exists an unfolded state with only one alpha-helical hydrogen bond and an energy nearly equal to that of the folded state. The proteins have, however, high entropies, implying that they cannot fold onto their native structure, whereas in the presence of repulsive walls the proteins do attain their native structure. There is a pronounced asymmetry between the two termini of the protein with respect to their interaction with the pore walls. The effect of a variety of factors, including the pore size and the proteins' length, as well as the temperature, is studied in detail.
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87.15.ap, 87.14.E-, 87.15.hm, 61.46.-w

Allovalency revisited: An analysis of multisite phosphorylation and substrate rebinding

Jason W. Locasale

J. Chem. Phys. 128, 115106 (2008) (10 pages)

Online Publication Date: 21 March 2008

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