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22 Oct 2005

Volume 123, Issue 16, Articles (16xxxx)

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Size-dependent structures of NanIn−1+ cluster ions with a methanol adsorbate: A combined study by photodissociation spectroscopy and density-functional theory calculation

Fuminori Misaizu, Mamoru Tsuruta, Hironori Tsunoyama, Ari Furuya, Koichi Ohno, and Masami Lintuluoto

J. Chem. Phys. 123, 161101 (2005); http://dx.doi.org/10.1063/1.2102909 (4 pages)

Online Publication Date: 24 October 2005

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Methanol adsorption sites on NanIn−1+ ions were investigated. Photoexcitation to charge-transfer states of NanIn−1+ (methanol) predominantly produces two fragment ions: Nan−1In−2+ (methanol) (neutral NaI loss) and Nan−1In−2+ (neutral NaI and methanol loss), without forming NanIn−1+ (methanol loss). The relative intensities of these fragments are correlated with the geometries and binding energies.
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36.40.Mr Spectroscopy and geometrical structure of clusters
82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
82.50.-m Photochemistry
36.40.Wa Charged clusters
68.43.Mn Adsorption kinetics
61.46.-w Structure of nanoscale materials
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions

Electronic excited-state mixing in NeCl2

Ramón Hernández-Lamoneda and Kenneth C. Janda

J. Chem. Phys. 123, 161102 (2005); http://dx.doi.org/10.1063/1.2120507 (4 pages) | Cited 7 times

Online Publication Date: 24 October 2005

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Ab initio calculations that explicitly include spin-orbit interactions are reported for the NeCl2 system of electronic states. A surprising curve crossing is observed for the C2v, T-shaped geometry. Away from the C2v geometry, the states mix, as expected. On the basis of these new results we propose a new mechanism for electronic energy transfer from highly vibrationally excited levels of the B electronic state of the chlorine molecule. It is proposed that as long as vibrational predissociation of NeCl2 proceeds by direct coupling of the initial state to the continuum states the Ne atom does not sample geometries that efficiently quench the Cl2 B electronic state. However, when the vibrational dynamics changes to the intramolecular vibrational relaxation regime the Ne atom becomes quite effective at coupling the Cl2 B math state with a math state.
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31.15.A- Ab initio calculations
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.80.Gj Diffuse spectra; predissociation, photodissociation

Exchange-correlation functional with broad accuracy for metallic and nonmetallic compounds, kinetics, and noncovalent interactions

Yan Zhao, Nathan E. Schultz, and D. G. Truhlar

J. Chem. Phys. 123, 161103 (2005); http://dx.doi.org/10.1063/1.2126975 (4 pages) | Cited 149 times

Online Publication Date: 24 October 2005

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By incorporating kinetic-energy density in a balanced way in the exchange and correlational functionals and removing self-correlation effects, we have designed a density functional that is broadly applicable to organometallic, inorganometallic, and nonmetallic bonding, thermochemistry, thermochemical kinetics, and noncovalent interactions as well as satisfying the uniform electron gas limit. The average error is reduced by a factor of 1.3 compared with the best previously available functionals, but even more significantly, we find a functional that has a high accuracy for all four categories of interaction.
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31.15.E- Density-functional theory
82.20.Sb Correlation function theory of rate constants and its applications
82.60.Cx Enthalpies of combustion, reaction, and formation

Oxygen adsorption at anionic free and supported Au clusters

L. M. Molina and B. Hammer

J. Chem. Phys. 123, 161104 (2005); http://dx.doi.org/10.1063/1.2110195 (5 pages) | Cited 31 times

Online Publication Date: 24 October 2005

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The structure, stability, and O2 adsorption properties of anionic Aun (n = 1–11) clusters either free or supported at defected MgO(100) surfaces are investigated using density-functional theory. O2 adsorption is strong whenever unpaired electrons are present, except for at some small, supported, planar, high-band-gap clusters. These clusters have the unpaired electrons pinned by the Madelung potential of the support. Larger clusters (starting at Au7–Au8) become three dimensional and metallic. This ensures that while one cluster orbital is pinned to the defect, another orbital at comparable energy can undergo depletion, thus binding O2 with charge transfer.
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61.46.-w Structure of nanoscale materials
68.43.De Statistical mechanics of adsorbates
68.43.Fg Adsorbate structure (binding sites, geometry)
68.43.Hn Structure of assemblies of adsorbates (two- and three-dimensional clustering)
68.43.Mn Adsorption kinetics

Energy relaxation versus spectral diffusion of the OH-stretching vibration of HOD in liquid-to-supercritical deuterated water

Dirk Schwarzer, Jörg Lindner, and Peter Vöhringer

J. Chem. Phys. 123, 161105 (2005); http://dx.doi.org/10.1063/1.2110087 (4 pages) | Cited 9 times

Online Publication Date: 25 October 2005

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The dynamics of vibrational energy relaxation (VER) of the OH-stretching vibration of HOD in liquid-to-supercritical heavy water is studied as a function of temperature and solvent density by femtosecond mid-infrared spectroscopy. Using the dielectric constant of the fluid both, the OH-stretching absorption frequency and the VER rate, can be correlated phenomenologically with the average hydrogen-bond connectivity within the random D2O network. This correlation enables the identification of thermodynamic conditions under which spectral diffusion due to hydrogen-bond breakage/formation is much faster than VER.
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61.25.Em Molecular liquids
78.30.C- Liquids
65.20.-w Thermal properties of liquids
77.22.Ch Permittivity (dielectric function)
77.84.Nh Liquids, emulsions, and suspensions; liquid crystals
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back to top Theoretical Methods and Algorithms

Molecular dynamics in the isothermal-isobaric ensemble: The requirement of a “shell” molecule. I. Theory and phase-space analysis

Mark J. Uline and David S. Corti

J. Chem. Phys. 123, 164101 (2005); http://dx.doi.org/10.1063/1.2064512 (14 pages) | Cited 4 times

Online Publication Date: 21 October 2005

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Current constant pressure molecular-dynamics (MD) algorithms are not consistent with the recent reformulation of the isothermal-isobaric (NpT) ensemble. The NpT ensemble partition function requires the use of a “shell” molecule to identify uniquely the volume of the system, thereby avoiding the redundant counting of configurations [e.g., G. J. M. Koper and H. Reiss, J. Phys. Chem. 100, 422 (1996) ; D. S. Corti, Phys. Rev. E, 64, 016128 (2001) ]. So far, only the NpT Monte Carlo method has been updated to allow the system volume to be defined by a shell particle [ D. S. Corti, Mol. Phys. 100, 1887 (2002) ]. A shell particle has yet to be incorporated into MD simulations. The proper modification of the NpT MD algorithm is therefore the subject of this paper. Unlike Andersen’s method [ H. C. Andersen, J. Chem. Phys. 72, 2384 (1980) ] where a piston of unknown mass serves to control the response time of volume fluctuations, the newly proposed equations of motion impose a constant external pressure via the introduction of a shell particle of known mass. Hence, the system itself sets the time scales for pressure and volume fluctuations. The new algorithm is subject to a number of fundamentally rigorous tests to ensure that the equations of motion sample phase space correctly. We also show that the Hoover NpT algorithm [ W. G. Hoover, Phys. Rev. A. 31, 1695 (1985) ; 34, 2499 (1986) ] does sample phase correctly, but only when periodic boundary conditions are employed.
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65.40.G- Other thermodynamical quantities
61.43.Bn Structural modeling: serial-addition models, computer simulation
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion

Molecular dynamics in the isothermal-isobaric ensemble: The requirement of a “shell” molecule. II. Simulation results

Mark J. Uline and David S. Corti

J. Chem. Phys. 123, 164102 (2005); http://dx.doi.org/10.1063/1.2064547 (16 pages) | Cited 3 times

Online Publication Date: 21 October 2005

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The results of a series of constant pressure and temperature molecular-dynamics (MD) simulation studies based on the rigorous shell particle formulation of the isothermal-isobaric (NpT) ensemble are presented. These MD simulations validate the newly proposed constant pressure equations of motion in which a “shell” particle is used to define uniquely the volume of the system [ M. J. Uline and D. S. Corti, J. Chem. Phys. (to be published), preceding paper ]. Ensemble averages obtained with the new MD NpT algorithm match the ensemble averages obtained using the previously derived shell particle Monte Carlo NpT method [ D. S. Corti, Mol. Phys. 100, 1887 (2002) ]. In addition, we also verify that the Hoover NpT MD algorithm [ W. G. Hoover, Phys. Rev. A 31, 1695 (1985); 34, 2499 (1986) ] generates the correct ensemble averages, though only when periodic boundary conditions are employed. The extension of the shell particle MD algorithm to multicomponent systems is also discussed, in which we show for equilibrium properties that the identity of the shell particle is completely arbitrary when periodic boundary conditions are applied. Self-diffusion coefficients determined with the shell particle equations of motion are also identical to those obtained in other ensembles. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the effects of the shell particle on the dynamics of the system. Overall, the shell particle MD algorithm is an effective simulation method for studying systems exposed to a constant external pressure and may provide an advantage over other existing constant pressure approaches when developing nonequilibrium MD methods.
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65.40.G- Other thermodynamical quantities
61.43.Bn Structural modeling: serial-addition models, computer simulation
66.30.-h Diffusion in solids
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion

Direct evaluation of multicomponent phase equilibria using flat-histogram methods

Jeffrey R. Errington and Vincent K. Shen

J. Chem. Phys. 123, 164103 (2005); http://dx.doi.org/10.1063/1.2064628 (9 pages) | Cited 15 times

Online Publication Date: 21 October 2005

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We present a method for directly locating density-driven phase transitions in multicomponent systems. Phase coexistence conditions are determined through manipulation of a total density probability distribution evaluated over a density range that includes both coexisting phases. Saturation quantities are determined through appropriate averaging of density-dependent mean values of a given property of interest. We discuss how to implement the method in both the grand-canonical and isothermal-isobaric semigrand ensembles. Calculations can be conducted using any of the recently introduced flat-histogram techniques. Here, we combine the general algorithm with a transition-matrix approach to produce an efficient self-adaptive technique for determining multicomponent phase equilibrium properties. To assess the performance of the new method, we generate phase diagrams for a number of binary and ternary Lennard-Jones mixtures.
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64.60.-i General studies of phase transitions
61.20.Gy Theory and models of liquid structure

Efficient treatment of the Hartree interaction in the relativistic Kohn-Sham problem

Alexei V. Matveev, Sonjoy Majumder, and Notker Rösch

J. Chem. Phys. 123, 164104 (2005); http://dx.doi.org/10.1063/1.2079907 (8 pages) | Cited 5 times

Online Publication Date: 25 October 2005

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We elaborate the two-component Douglas-Kroll reduction of the Dirac-Kohn-Sham problem of relativistic density-functional theory as introduced by Matveev and Rösch [J. Chem. Phys. 118, 3997 (2003) ]. That method retains corrections to the Coulomb self-interaction (or Hartree) term of the energy functional that are due to the picture change. Using analytic expressions for the matrix elements, one is able to abandon the resolution of the identity approach for a crucial step of the relativistic transformation. Thus, a major source of uncertainties of the method is eliminated because basis sets no longer have to be extended by functions of higher angular momentum, previously required to ensure kinetic balance. This approach also relies on the electron charge-density fitting scheme via an auxiliary basis set. An efficient approximate implementation results if one restricts the relativistic transformation to the spherically symmetric atom-centered auxiliary functions. It provides accurate results while simplifying greatly the expressions for the matrix elements of the relativistically transformed operators and significantly reducing the computational effort. We demonstrate the performance of the method for the fine structure of one-electron levels of the Hg atom, the g-tensor shifts of NO2, and the properties of the diatomic molecules Bi2, Pb2, PbO, and TlH.
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31.15.E- Density-functional theory
31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions
33.15.Pw Fine and hyperfine structure

On the accuracy of one-component pseudopotential spin-orbit calculations

Emmanuel Fromager, Lucas Visscher, Laurent Maron, and Christian Teichteil

J. Chem. Phys. 123, 164105 (2005); http://dx.doi.org/10.1063/1.2072927 (10 pages) | Cited 3 times

Online Publication Date: 25 October 2005

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Improvements on current one-component extraction procedures of spin-orbit pseudopotentials are investigated for high accuracy computation of spin-orbit coupling energies. By means of the perturbation-theory formalism we first show that spin-orbit pseudopotentials, extracted at the one-component self-consistent-field level from a reference all-electron Dirac-Coulomb or Dirac-Coulomb-Breit calculation, include valence spin-orbit polarization and relaxation effects. As a consequence the use of these pseudopotentials in uncontracted spin-orbit configuration interaction (CI) with singles from the reference ground-state configuration gives rise to double counting of these spin-orbit effects. Two new methods that avoid such double counting have been investigated. The first, so-called “explicit” method, calculates explicitly, by means of a four-component spin-orbit CI, the double-counted spin-orbit effects and removes them from the pseudopotentials. Due to the nonadditivity of the core and valence spin-orbit effects as well as the so-called “pseudovariational collapse,” this method is shown to be cumbersome. In the second “implicit” method the spin-orbit pseudopotential is extracted at the spin-orbit polarized and relaxed level by means of a single-excitation spin-orbit CI calculation. Atomic tests on iodine demonstrate the ability of the latter method to solve the double-counting problem.
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31.15.xp Perturbation theory
31.15.xr Self-consistent-field methods
31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions

New constraints upon the electron-electron repulsion energy functional of the one-electron reduced density matrix

Jerzy Cioslowski

J. Chem. Phys. 123, 164106 (2005); http://dx.doi.org/10.1063/1.2074527 (4 pages) | Cited 7 times

Online Publication Date: 26 October 2005

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Three strict constraints upon the electron-electron repulsion energy functional of the one-electron reduced density matrix (the 1-matrix) are obtained by combining its invariance and stationary properties with the extended Koopmans’ theorem. The constraints relate the quantities derived from the functional pertaining to an N-electron system with those of its (N−1)-electron congener. Together with the N-representability requirement for the 1-matrix of the congener, identities involving the electron-electron repulsion energies of the two systems and their derivatives with respect to the 1-matrices seriously narrow down the choices for potential approximate density-matrix functionals. This fact is well illustrated in the case of two-electron systems, where the validity of the new constraints is confirmed and found to originate from a nontrivial cancellation among different terms. Thus, the constraints provide a new tool for the construction and testing of new functionals that complements the previously known conditions such as the reproduction of the homogeneous gas energies and momentum distributions, convexity, and the N-representability of the associated 2-matrices.
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31.15.E- Density-functional theory
31.15.V- Electron correlation calculations for atoms, ions and molecules

Fast evaluation of polarizable forces

Wei Wang and Robert D. Skeel

J. Chem. Phys. 123, 164107 (2005); http://dx.doi.org/10.1063/1.2056544 (12 pages) | Cited 2 times

Online Publication Date: 26 October 2005

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Polarizability is considered to be the single most significant development in the next generation of force fields for biomolecular simulations. However, the self-consistent computation of induced atomic dipoles in a polarizable force field is expensive due to the cost of solving a large dense linear system at each step of a simulation. This article introduces methods that reduce the cost of computing the electrostatic energy and force of a polarizable model from about 7.5 times the cost of computing those of a nonpolarizable model to less than twice the cost. This is probably sufficient for the routine use of polarizable forces in biomolecular simulations. The reduction in computing time is achieved by an efficient implementation of the particle-mesh Ewald method, an accurate and robust predictor based on least-squares fitting, and non-stationary iterative methods whose fast convergence is accelerated by a simple preconditioner. Furthermore, with these methods, the self-consistent approach with a larger timestep is shown to be faster than the extended Lagrangian approach. The use of dipole moments from previous timesteps to calculate an accurate initial guess for iterative methods leads to an energy drift, which can be made acceptably small. The use of a zero initial guess does not lead to perceptible energy drift if a reasonably strict convergence criterion for the iteration is imposed.
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31.15.-p Calculations and mathematical techniques in atomic and molecular physics
61.20.Ja Computer simulation of liquid structure

Improvement of semiempirical response properties with charge-dependent response density

Timothy J. Giese and Darrin M. York

J. Chem. Phys. 123, 164108 (2005); http://dx.doi.org/10.1063/1.2080007 (9 pages) | Cited 16 times

Online Publication Date: 26 October 2005

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The present work outlines a new method for treatment of charge-dependent polarizability in semiempirical quantum models for use in combined quantum-mechanical/molecular mechanical simulations of biological reactions. The method addresses a major shortcoming in the performance of conventional semiempirical models for these simulations that is tied to the use of a localized minimal atomic-orbital basis set. The present approach has the advantages that it uses a density basis that retains a set of linear-response equations, does not increase the atomic-orbital basis, and avoids the problem of artificial charge transfer and scaling of the polarizability seen in related models that allow atomic charges to fluctuate. The model introduces four new atom-based parameters and has been tested with the modified neglect of differential overlap d-orbital Hamiltonian against 1132 molecules and ions and shown to decrease the dipole moment and polarizability errors by factors of 2 and 10, respectively, with respect to density-functional results. The method performs impressively for a variety of charge states (from 2+ to 2−), and offers a potentially powerful extension in the design of next generation semiempirical quantum models for accurate simulations of highly charged biological reactions.
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87.15.R- Reactions and kinetics
87.15.A- Theory, modeling, and computer simulation

Coarse-grained free-energy-functional treatment of quasistatic multiscale processes in heterogeneous materials

H. Zhou, R. Feng, D. J. Diestler, and X. C. Zeng

J. Chem. Phys. 123, 164109 (2005); http://dx.doi.org/10.1063/1.2064607 (4 pages) | Cited 3 times

Online Publication Date: 27 October 2005

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A new treatment of quasistatic (reversible) multiscale processes in heterogeneous materials at nonzero temperature is presented. The system is coarse grained by means of a finite-element mesh. The coarse-grained free-energy functional (of the positions of the nodes of the mesh) appropriate to the thermodynamic-state variables controlled in the relevant process is minimized. Tests of the new procedure on a Lennard-Jonesium crystal yield thermomechanical properties in good agreement with the “exact” atomistic results.
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65.40.G- Other thermodynamical quantities

About the calculation of exchange coupling constants using density-functional theory: The role of the self-interaction error

Eliseo Ruiz, Santiago Alvarez, Joan Cano, and Víctor Polo

J. Chem. Phys. 123, 164110 (2005); http://dx.doi.org/10.1063/1.2085171 (7 pages) | Cited 98 times

Online Publication Date: 27 October 2005

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The effect of the correction of the self-interaction error on the calculation of exchange coupling constants with methods based on density-functional theory has been tested in simple model systems. The inclusion of the self-interaction correction cancels the nondynamical correlation energy contributions simulated by the commonly used functionals. Hence, such correction should be important in the accurate determination of exchange coupling constants. We have also tested several recent functionals to calculate exchange coupling constants in transition-metal complexes, such as meta-GGA functionals or new formulations of hybrid functionals. The influence of the basis set and of the use of pseudopotentials on the calculated J values has also been evaluated for a Fe(III) dinuclear complex in which the paramagnetic centers bear several unpaired electrons.
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71.45.Gm Exchange, correlation, dielectric and magnetic response functions, plasmons
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
75.20.Ck Nonmetals

A theoretical study of molecular conduction. II. A Hartree-Fock approach to transmission probability

Tomomi Shimazaki, Hitoshi Maruyama, Yoshihiro Asai, and Koichi Yamashita

J. Chem. Phys. 123, 164111 (2005); http://dx.doi.org/10.1063/1.2074127 (10 pages) | Cited 11 times

Online Publication Date: 27 October 2005

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In this paper, we discuss molecular conductivity based on Green’s function methods. In our calculations, we adopted the self-energy formalism to accommodate semi-infinite electrodes connected to a molecule, and the self-energy was obtained from the surface Green’s function of the electrodes. We adopted the formalism of the surface Green’s function derived by Sanvito et al. [Phys. Rev. B 59, 11936 (1999) ] and Krstic et al. [Phys. Rev. B 66, 205319 (2002) ], and although their formalisms for the surface Green’s function were different, we were able to demonstrate that these formalisms are mathematically identical. We analyzed the electron transmission probability by using the spectrum expression of Green’s function, instead of using the inverse matrix of the effective Hamiltonian that includes an isolated molecule and the electrodes. Finally, we calculated the transmission probability of benzenedithiol based on the Hartree-Fock method and analyzed the disappearance of the transmission probability due to the orbital interference.
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71.20.Rv Polymers and organic compounds
71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)
82.45.Fk Electrodes
82.45.Wx Polymers and organic materials in electrochemistry

Efficient method for the calculation of time- and frequency-resolved four-wave mixing signals and its application to photon-echo spectroscopy

Maxim F. Gelin, Dassia Egorova, and Wolfgang Domcke

J. Chem. Phys. 123, 164112 (2005); http://dx.doi.org/10.1063/1.2062188 (11 pages) | Cited 25 times

Online Publication Date: 27 October 2005

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An efficient method has been developed for the calculation of third-order time- and frequency-resolved optical signals. To obtain the general four-wave mixing signal, seven auxiliary density matrices have to be propagated in time. For the special cases of two-pulse photon-echo and transient-grating signals, two or three density matrices, respectively, are required. The method is limited to weak laser fields (it is thus valid within the third-order perturbation theory) but allows for any pulse durations and automatically accounts for pulse-overlap effects. To illustrate the method, we present the explicit derivation of the three-pulse photon-echo signal. Any other third-order optical signal can be calculated in the same manner. As an example, two- and three-pulse photon-echo and transient-grating signals for a weakly damped displaced harmonic oscillator have been calculated.
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42.65.Jx Beam trapping, self-focusing and defocusing; self-phase modulation
42.50.Md Optical transient phenomena: quantum beats, photon echo, free-induction decay, dephasings and revivals, optical nutation, and self-induced transparency

Theoretical studies on magnetic circular dichroism by the finite perturbation method with relativistic corrections

Y. Honda, M. Hada, M. Ehara, H. Nakatsuji, and J. Michl

J. Chem. Phys. 123, 164113 (2005); http://dx.doi.org/10.1063/1.2080027 (9 pages) | Cited 10 times

Online Publication Date: 27 October 2005

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A theoretical method for calculating magnetic circular dichroism (MCD) of molecules is presented. We examined the numerical accuracy and the stability of the finite perturbation (FP) method and the sum-over-state (SOS) perturbation method. The relativistic effects are shown to be important for the MCD spectra of molecules containing heavy elements. Calculations using the FP and the SOS methods were carried out for ethylene, para- and ortho-benzoquinone, showing that the FP method is superior to the SOS method, as expected. The relativistic effect was examined using the second-order Douglas-Kroll Hamiltonians for the halogen molecules F2, Cl2, Br2, and I2. The Faraday terms of I2 and Br2 were strongly affected by the relativistic effects, while the effect was negligible for Cl2 and F2.
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33.55.+b Optical activity and dichroism
31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions
31.15.xp Perturbation theory

A regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical–molecular-mechanical calculations

P. K. Biswas and V. Gogonea

J. Chem. Phys. 123, 164114 (2005); http://dx.doi.org/10.1063/1.2064907 (9 pages) | Cited 11 times

Online Publication Date: 27 October 2005

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We describe a regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical (QM)–molecular-mechanical (MM) calculations. To remedy the nonphysical QM/MM Coulomb interaction at short distances arising from a point electrostatic potential (ESP) charge of the MM atom and also to accommodate the effect of polarized MM atom in the coupling Hamiltonian, we propose a partial-wave expansion of the ESP charge and describe the effect of a s-wave expansion, extended over the covalent radius rc, of the MM atom. The resulting potential describes that, at short distances, large scale cancellation of Coulomb interaction arises intrinsically from the localized expansion of the MM point charge and the potential self-consistently reduces to 1/rc at zero distance providing a renormalization to the Coulomb energy near interatomic separations. Employing this renormalized Hamiltonian, we developed an interface between the Car-Parrinello molecular-dynamics program and the classical molecular-dynamics simulation program Groningen machine for chemical simulations. With this hybrid code we performed QM/MM calculations on water dimer, imidazole carbon monoxide (CO) complex, and imidazole-heme-CO complex with CO interacting with another imidazole. The QM/MM results are in excellent agreement with experimental data for the geometry of these complexes and other computational data found in literature.
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31.15.xv Molecular dynamics and other numerical methods
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions

On the origins of approximations for stochastic chemical kinetics

Eric L. Haseltine and James B. Rawlings

J. Chem. Phys. 123, 164115 (2005); http://dx.doi.org/10.1063/1.2062048 (16 pages) | Cited 13 times

Online Publication Date: 27 October 2005

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This paper considers the derivation of approximations for stochastic chemical kinetics governed by the discrete master equation. Here, the concepts of (1) partitioning on the basis of fast and slow reactions as opposed to fast and slow species and (2) conditional probability densities are used to derive approximate, partitioned master equations, which are Markovian in nature, from the original master equation. Under different conditions dictated by relaxation time arguments, such approximations give rise to both the equilibrium and hybrid (deterministic or Langevin equations coupled with discrete stochastic simulation) approximations previously reported. In addition, the derivation points out several weaknesses in previous justifications of both the hybrid and equilibrium systems and demonstrates the connection between the original and approximate master equations. Two simple examples illustrate situations in which these two approximate methods are applicable and demonstrate the two methods’ efficiencies.
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82.20.Uv Stochastic theories of rate constants
82.30.-b Specific chemical reactions; reaction mechanisms

Efficient exact exchange approximations in density-functional theory

A. Heßelmann and F. R. Manby

J. Chem. Phys. 123, 164116 (2005); http://dx.doi.org/10.1063/1.2072887 (11 pages) | Cited 12 times

Online Publication Date: 27 October 2005

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Two approaches to approximate the Slater potential component of local exact exchange of density-functional theory are investigated. The first approach employs density fitting of the electrostatic potential integrals over two occupied orbitals and the other approach approximates the “exact” Slater potential with the potential derived from the Becke-Roussel [Phys. Rev. A. 39, 3761 (1989) ] model of the exchange hole. In both cases significant time savings can be achieved for larger systems compared to the calculation of the numerical Slater potential. It is then analyzed how well the orbitals obtained from the various total exchange potentials reproduce Hartree-Fock energies and molecular properties. A large range of atoms and small molecules has been utilized, including the three DNA bases adenine, thymine, and cytosine.
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36.20.Kd Electronic structure and spectra
31.15.E- Density-functional theory
31.15.xr Self-consistent-field methods
87.14.G- Nucleic acids
87.15.A- Theory, modeling, and computer simulation
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Accidental vibrational degeneracy in vibrational excited states observed with ultrafast two-dimensional IR vibrational echo spectroscopy

Junrong Zheng, Kyungwon Kwak, Tobias Steinel, John Asbury, Xin Chen, Jia Xie, and M. D. Fayer

J. Chem. Phys. 123, 164301 (2005); http://dx.doi.org/10.1063/1.2071967 (7 pages) | Cited 4 times

Online Publication Date: 21 October 2005

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The coupling between the OD stretch v = 2 level and benzene-ring modes in 2-methoxyphenol-OD (hydroxyl H replaced by D) is observed with ultrafast two-dimensional (2D) IR vibrational echo spectroscopy. Because of this coupling, the 1-2 transition peak in the 2D spectrum is split into a doublet with peaks of approximately equal amplitudes. Several molecules and solvents were used to study this phenomenon. Near-IR (NIR) spectroscopy measurements and density-functional theory calculations (B3LYP/6-31+G(d,p) level) were also applied. Experimental results and calculations show that the OD stretch 1-2 transition is coupled to a combination band related to the benzene-ring motions. A simple quantum-mechanical model indicates that the combination band has a frequency of 5172 and 5176.5 cm−1 in CCl4 and hexane, respectively. The transition between this combination band and the ground state is too weak to detect by NIR. The transition between this band and the OD stretch first excited state is also so weak that most of the intensity of the doublet comes from the oscillator strength produced by coupling to the OD stretch. The model gives the coupling strengths as 6.5 and 7 cm−1 in CCl4 and hexane, respectively.
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33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Ea Infrared spectra
31.15.E- Density-functional theory
33.70.Fd Absolute and relative line and band intensities
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors

Ab initio study of the reaction of H2 with an AuPt3 cluster

O. Olvera-Neria, A. Cruz, H. Luna-García, A. Anguiano-García, E. Poulain, and S. Castillo

J. Chem. Phys. 123, 164302 (2005); http://dx.doi.org/10.1063/1.2079887 (6 pages) | Cited 2 times

Online Publication Date: 21 October 2005

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The study of the interaction of a pyramidal tetramer of AuPt3 with H2 is carried out by means of Hartree-Fock self-consistent field (SCF) calculations using relativistic effective core potentials and multiconfigurational SCF plus multireference variational and perturbational on second-order Möller-Plesset configuration interaction calculations. The AuPt3–H2 interaction was carried out in Cs symmetry. The three lowest electronic states X math, A math, and a math of the bare cluster were considered in order to study this interaction. The AuPt3+H2 reaction by a Pt vertex shows that AuPt3 cluster in the three lowest-lying electronic states can spontaneously capture and dissociate the H2 molecule. While, by the AuPt2 face side, the AuPt3 cluster only in the A math electronic state can capture and dissociate the H2 molecule after surmounting a small energy barrier. For the Au vertex, this cluster in the three electronic states can also spontaneously capture and dissociate the H2 molecule. On the other hand, by the Pt3 face side, the AuPt3 cluster is able to capture and dissociate the H2 molecule after surmounting energy barriers, where the AuPt3 (X math and math)–H2 adsorption are slightly activated.
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82.20.Db Transition state theory and statistical theories of rate constants
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Hf Product distribution
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)

Structures and stability of medium-sized silicon clusters. III. Reexamination of motif transition in growth pattern from Si15 to Si20

Soohaeng Yoo and X. C. Zeng

J. Chem. Phys. 123, 164303 (2005); http://dx.doi.org/10.1063/1.2043127 (6 pages) | Cited 17 times

Online Publication Date: 24 October 2005

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It has been established from experiments that stable medium-sized ionic clusters Si15–Si20 are prolate in shape. Density-functional theories (DFTs) also predict that nearly all low-lying neutral clusters in this size range are prolate in shape. Moreover, most of them are built onto two generic structural motifs, either the tricapped-trigonal-prism (TTP) Si9 motif or the six/six Si6/Si6 (sixfold-puckered hexagonal ring Si6 plus six-atom tetragonal bipyramid Si6) motif. However, it appears that the exact location of the TTP-to-six/six motif transition is dependent on the functional (e.g., PBE or BLYP) used in the DFT calculations. Here, we present total-energy calculations for two series of clusters (one series containing six/six motif and the other containing the TTP motif) in the size range of Si16–Si20. The calculations were based on all-electron DFT methods with a medium [6-311G (2d)] and a large (cc-pVTZ) basis sets, as well as coupled-cluster single and double substitutions (including triple excitations) [CCSD(T)] method with a modest (cc-pVDZ) basis set. In the DFT calculations, two popular hybrid density functionals, the B3LYP and PBE1PBE, were selected. It is found that the B3LYP total-energy calculations slightly favor the six/six motif, whereas the PBE1PBE calculations slightly favor the TTP motif. The CCSD(T) total-energy calculations, however, show that isomers based on the six/six motif are energetically slightly favorable in the size range of Si16-Si20. Hence, the TTP-to-six/six motif transition is more likely to occur at Si16.
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36.40.Ei Phase transitions in clusters
31.15.E- Density-functional theory
31.15.bw Coupled-cluster theory

Water-ketones hydrogen bonding: The rotational spectrum of cyclobutanone-water

Sonia Melandri, Assimo Maris, B. Michela Giuliano, and Walther Caminati

J. Chem. Phys. 123, 164304 (2005); http://dx.doi.org/10.1063/1.2078767 (6 pages) | Cited 8 times

Online Publication Date: 24 October 2005

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The hydrogen-bonded complex cyclobutanone-water has been studied by Fourier-transform molecular-beam microwave spectroscopy in the frequency range of 6–18.5 GHz. The rotational spectra of ten isotopomers have been assigned and measured. Five of them have been obtained from different isotopic species (or configurations) of water (H2O, D2O, DOH, HOD, and H2 math). The remaining five correspond to the four singly substituted math and to the math species of cyclobutanone, observed in natural abundance. For all species the inertial defect is in the range from −10.44 to −10.50 uÅ2, showing that the cyclobutanone frame is effectively planar and that the water molecule is coplanar to this frame. The hydrogen bond, almost linear, is formed between a water proton and one of the lone pairs of the cyclobutanone oxygen.
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33.20.Bx Radio-frequency and microwave spectra
33.20.Sn Rotational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Fm Bond strengths, dissociation energies
31.30.Gs Hyperfine interactions and isotope effects
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