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28 Dec 2006

Volume 125, Issue 24, Articles (24xxxx)

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Using the histogram test to quantify reaction coordinate error

Baron Peters

J. Chem. Phys. 125, 241101 (2006); http://dx.doi.org/10.1063/1.2409924 (4 pages) | Cited 13 times

Online Publication Date: 27 December 2006

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Many schemes for calculating reaction rates and free energy barriers require an accurate reaction coordinate, but it is difficult to quantify reaction coordinate accuracy for complex processes like protein folding and nucleation. The histogram test, based on estimated committor probabilities, is often used as a qualitative indicator for good reaction coordinates. This paper derives the mean and variance of the intrinsic committor distribution in terms of the mean and variance of the histogram of committor estimates. These convenient formulas enable the first quantitative calculations of reaction coordinate error for complex systems. An example shows that the approximate transition state surface from Peters’ and Trout’s reaction coordinate for nucleation in the Ising model gives a mean committor probability of 0.495 and a standard deviation of 0.042.
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82.20.Pm Rate constants, reaction cross sections, and activation energies
87.15.R- Reactions and kinetics
87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways

Relativistic effective core potential calculations of Hg and eka-Hg (E112) interactions with gold: Spin-orbit density functional theory modeling of Hg–Aun and E112–Aun systems

E. A. Rykova, A. Zaitsevskii, N. S. Mosyagin, T. A. Isaev, and A. V. Titov

J. Chem. Phys. 125, 241102 (2006); http://dx.doi.org/10.1063/1.2403850 (3 pages) | Cited 8 times

Online Publication Date: 27 December 2006

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Interactions of eka-Hg (E112) and Hg atoms with small gold clusters were studied in the frame of the relativistic effective core potential model using the density functional theory (DFT) approach incorporating spin-dependent (magnetic) interactions. The choice of the exchange-correlation functional was based on a comparison of the results of DFT and large-scale coupled cluster calculations for E112Au and HgAu at the scalar relativistic level. A close similarity between the E112Aun and HgAun equilibrium structures was observed. The E112 binding energies on Aun are typically smaller than those for Hg by ca. 25%–32% and the equilibrium E112-Au separations are always slightly larger than their Hg-Au counterparts.
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36.40.Mr Spectroscopy and geometrical structure of clusters
31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions
31.15.bw Coupled-cluster theory
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back to top Theoretical Methods and Algorithms

Analogies and differences between two ways to evaluate the global hardness

Miquel Torrent-Sucarrat and Paul Geerlings

J. Chem. Phys. 125, 244101 (2006); http://dx.doi.org/10.1063/1.2406072 (7 pages) | Cited 12 times

Online Publication Date: 22 December 2006

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The weight of the energetic components (electronic kinetic, electron-nucleus and electron-electron Coulombic, and correlation energies) of the ionization potential, electron affinity, chemical potential, and global hardness is evaluated and contrasted with the energetic components of the hardness kernel and the experimental values of these properties for 40 systems. The contrast of the hardness terms obtained from finite difference and hardness kernel gives some insight on the possible implications to differentiate the electronic energy with respect to the number electrons or the electron density.
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31.15.E- Density-functional theory
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy

Quantal cumulant dynamics: General theory

Yasuteru Shigeta, Hideaki Miyachi, and Kimihiko Hirao

J. Chem. Phys. 125, 244102 (2006); http://dx.doi.org/10.1063/1.2404677 (9 pages) | Cited 15 times

Online Publication Date: 22 December 2006

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The authors have derived coupled equations of motion of cumulants that consist of a symmetric-ordered product of the position and momentum fluctuation operators in one dimension. The key point is the utilization of a position shift operator acting on a potential operator, where the expectation value of the shift operator is evaluated using the cumulant expansion technique. In particular, the equations of motion of the second-order cumulant and the expectation values of the position and momentum operators are given. The resultant equations are expressed by those variables and a quantal potential that consists of an exponential function of the differential operators and the original potential. This procedure enables us to perform quantal (semiclassical) dynamics in one dimension. In contrast to a second-order quantized Hamilton dynamics by Prezhdo and Pereverzev which conserves the total energy only with an odd-order Taylor expansion of the potential [ J. Chem. Phys. 116, 4450 (2002) ; 117, 2995 (2002) ], the present quantal cumulant dynamics method exactly conserves the energy, even if a second-order approximation of the cumulants is adopted, because the present scheme does not truncate the given potential. The authors propose three schemes, (i) a truncation, (ii) a summation of derivatives, and (iii) a convolution method, for evaluating the quantal potentials for several types of potentials. The numerical results show that although the truncation method preserves the energy to some degree, the trajectory obtained gradually deviates from that of the summation scheme after 2000 steps. The phase space structure obtained by the truncation scheme is also different from that of the summation scheme in a strongly anharmonic region.
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82.20.Fd Collision theories; trajectory models
82.20.Ln Semiclassical theory of reactions and/or energy transfer
03.65.-w Quantum mechanics

Comparative study of perturbative methods for computing electron transfer tunneling matrix elements with a nonorthogonal basis set

Antonios Teklos and Spiros S. Skourtis

J. Chem. Phys. 125, 244103 (2006); http://dx.doi.org/10.1063/1.2403859 (9 pages) | Cited 6 times

Online Publication Date: 22 December 2006

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The authors consider the problem of computing tunneling matrix elements for bridge-mediated electron transfer reactions using the Löwdin [J. Math. Phys. 3, 969 (1962); J. Mol. Spectrosc. 13, 326 (1964) ] projection-iteration technique with a nonorthogonal basis set. They compare the convergence properties of two different Löwdin projections, one containing the overlap matrix S and the other containing the inverse S−1 in the projected Hamiltonian. It was suggested in the literature that the projected Hamiltonian with S−1 has better convergence properties compared to the projected Hamiltonian with S. The authors test this proposal using a simple analytical model, and ab initio Hartree-Fock calculations on different molecules with several types of basis sets. Their calculations show that, for Gaussian-type basis sets, the projected Hamiltonian containing S has the best convergence properties, especially for diffuse basis sets and in the strong coupling limit. The limit of diffuse basis sets is relevant to tunneling matrix element calculations involving excited states and anionic electron transfer.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.20.Db Transition state theory and statistical theories of rate constants

Determination of complex absorbing potentials from the electron self-energy

Thomas M. Henderson, Giorgos Fagas, Eoin Hyde, and James C. Greer

J. Chem. Phys. 125, 244104 (2006); http://dx.doi.org/10.1063/1.2406070 (10 pages) | Cited 6 times

Online Publication Date: 26 December 2006

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The electronic conductance of a molecule making contact to electrodes is determined by the coupling of discrete molecular states to the continuum electrode density of states. Interactions between bound states and continua can be modeled exactly by using the (energy-dependent) self-energy or approximately by using a complex potential. We discuss the relation between the two approaches and give a prescription for using the self-energy to construct an energy-independent, nonlocal, complex potential. We apply our scheme to studying single-electron transmission in an atomic chain, obtaining excellent agreement with the exact result. Our approach allows us to treat electron-reservoir couplings independent of single-electron energies, allowing for the definition of a one-body operator suitable for inclusion into correlated electron transport calculations.
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85.65.+h Molecular electronic devices

H/D isotope effect on porphine and porphycene molecules with multicomponent hybrid density functional theory

Taro Udagawa and Masanori Tachikawa

J. Chem. Phys. 125, 244105 (2006); http://dx.doi.org/10.1063/1.2403857 (9 pages) | Cited 16 times

Online Publication Date: 26 December 2006

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To analyze the H/D isotope effect on porphine and porphycene molecules including the protonic/deuteronic quantum nature and electron correlation efficiently, the authors have developed the new scheme of the multicomponent hybrid density functional theory [MC̱(HF+DFT)]. The optimized geometries of porphine, porphycene, and these deuterated isotopomers by our MC̱(HF+DFT) method are in good agreement with the experimental “high-symmetric” structures, contrary to the “low-symmetric” geometries optimized by pure multicomponent Hartree-Fock method. The optimized geometries for HD-porphine and HD-porphycene molecules, in which an inner hydrogen is replaced to a deuterium, are found to be low symmetric. Such drastic geometrical change induces the electronic polarization, and gives rise to the slight dipole moment values in these HD species. Their results clearly indicate that the difference of the nuclear quantum nature between inner proton and inner deuteron directly influences the molecular geometry and electronic structure.
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31.15.E- Density-functional theory
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.30.Gs Hyperfine interactions and isotope effects
31.15.vq Electron correlation calculations for polyatomic molecules
31.15.xr Self-consistent-field methods

Combining explicitly correlated R12 and Gaussian geminal electronic structure theories

Edward F. Valeev

J. Chem. Phys. 125, 244106 (2006); http://dx.doi.org/10.1063/1.2403852 (10 pages) | Cited 33 times

Online Publication Date: 26 December 2006

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Explicitly correlated R12 methods using a single short-range correlation factor (also known as F12 methods) have dramatically smaller basis set errors compared to the standard wave function counterparts, even when used with small basis sets. Correlations on several length scales, however, may not be described efficiently with one correlation factor. Here the authors explore a more general MP2-R12 method in which each electron pair uses a set of (contracted) Gaussian-type geminals (GTGs) with fixed exponents, whose coefficients are optimized linearly. The following features distinguish the current method from related explicitly correlated approaches published in the literature: (1) only two-electron integrals are needed, (2) the only approximations are the resolution of the identity and the generalized Brillouin condition, (3) only linear parameters are optimized, and (4) an arbitrary number of (non-)contracted GTGs can appear. The present method using only three GTGs and a double-zeta quality basis computed valence correlation energies for a set of 20 small molecules only 2.2% removed from the basis set limit. The average basis set error reduces to 1.2% using a near-complete set of seven GTGs with the double-zeta basis set. The conventional MP2 energies computed with much larger quadruple, quintuple, and sextuple basis sets all had larger average errors: 4.6%, 2.4%, and 1.5%, respectively. The new method compares well to the published MP2-R12 method using a single Slater-type geminal (STG) correlation factor. For example, the average basis set error in the absolute MP2-R12 energy obtained with the exp(−r12) correlation factor is 1.7%. Correlation contribution to atomization energies evaluated with the present method and with the STG-based method only required a double-zeta basis set to exceed the precision of the conventional sextuple-zeta result. The new method is shown to always be numerically stable if linear dependencies are removed from the two-particle basis and the zeroth-order Hamiltonian matrix is made positive definite.
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31.15.V- Electron correlation calculations for atoms, ions and molecules
33.15.Fm Bond strengths, dissociation energies
31.15.xp Perturbation theory

Quantum mechanical polarizable force field (QMPFF3): Refinement and validation of the dispersion interaction for aromatic carbon

A. G. Donchev, N. G. Galkin, L. B. Pereyaslavets, and V. I. Tarasov

J. Chem. Phys. 125, 244107 (2006); http://dx.doi.org/10.1063/1.2403855 (12 pages) | Cited 8 times

Online Publication Date: 26 December 2006

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The authors have recently introduced a general, polarizable force field QMPFF fitted solely to high-level quantum mechanical data for simulations of biomolecular systems. Here the authors demonstrate using an advanced version QMPFF3 how the problem of insufficient accuracy of the MP2-based training set for the aromatic carbon atom type can be effectively solved by a simple model correction using state-of-the-art CCSD(T) data. The approach demonstrates excellent transferability, which is confirmed for three phases of matter by accurate calculations of the second virial coefficient for benzene vapor and various properties of liquid benzene and polyaromatic hydrocarbon crystals.
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31.15.bw Coupled-cluster theory
31.15.xp Perturbation theory
51.30.+i Thermodynamic properties, equations of state
64.30.-t Equations of state of specific substances

Automatic integration of the reaction path using diagonally implicit Runge-Kutta methods

Steven K. Burger and Weitao Yang

J. Chem. Phys. 125, 244108 (2006); http://dx.doi.org/10.1063/1.2402166 (12 pages) | Cited 5 times

Online Publication Date: 27 December 2006

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The diagonally implicit Runge-Kutta framework is shown to be a general form for constructing stable, efficient steepest descent reaction path integrators, of any order. With this framework tolerance driven, adaptive step-size methods can be constructed by embedding methods to obtain error estimates of each step without additional computational cost. There are many embedded and nonembedded, diagonally implicit Runge-Kutta methods available from the numerical analysis literature and these are reviewed for orders two, three, and four. New embedded methods are also developed which are tailored to the application of reaction path following. All integrators are summarized and compared for three systems: the Müller-Brown [Theor. Chem. Acta 53, 75 (1979)] potential and two gas phase chemical reactions. The results show that many of the methods are capable of integrating efficiently while reliably keeping the error bound within the desired tolerance. This allows the reaction path to be determined through automatic integration by only specifying the desired accuracy and transition state.
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82.20.Db Transition state theory and statistical theories of rate constants
82.20.Kh Potential energy surfaces for chemical reactions
82.30.-b Specific chemical reactions; reaction mechanisms

Simple Hamiltonians which exhibit drastic failures by variational determination of the two-particle reduced density matrix with some well known N-representability conditions

Maho Nakata, Bastiaan J. Braams, Mituhiro Fukuda, Jerome K. Percus, Makoto Yamashita, and Zhengji Zhao

J. Chem. Phys. 125, 244109 (2006); http://dx.doi.org/10.1063/1.2406073 (8 pages) | Cited 4 times

Online Publication Date: 27 December 2006

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Calculations on small molecular systems indicate that the variational approach employing the two-particle reduced density matrix (2-RDM) as the basic unknown and applying the P, Q, G, T1, and T2 representability conditions provides an accuracy that is competitive with the best standard ab initio methods of quantum chemistry. However, in this paper we consider a simple class of Hamiltonians for which an exact ground state wave function can be written as a single Slater determinant and yet the same 2-RDM approach gives a drastically nonrepresentable result. This shows the need for stronger representability conditions than the mentioned ones.
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31.15.A- Ab initio calculations
31.15.xt Variational techniques
31.15.ve Electron correlation calculations for atoms and ions: ground state

Efficient correlation-corrected vibrational self-consistent field computation of OH-stretch frequencies using a low-scaling algorithm

David M. Benoit

J. Chem. Phys. 125, 244110 (2006); http://dx.doi.org/10.1063/1.2423006 (7 pages) | Cited 21 times

Online Publication Date: 27 December 2006

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The authors present a new computational scheme to perform accurate and fast direct correlation-corrected vibrational self-consistent field (CC-VSCF) computations for a selected number of vibrational modes, which is aimed at predicting a few vibrations in large molecular systems. The method is based on a systematic selection of vibrational mode-mode coupling terms, leading to the direct ab initio construction of a sparse potential energy surface. The computational scaling of the CC-VSCF computation on the generated surface is then further reduced by using a screening procedure for the correlation-correction contributions. The proposed method is applied to the computation of the OH-stretch frequency of five aliphatic alcohols. The authors investigate the influence of different pseudopotential and all-electron basis sets on the quality of the correlated potential energy surfaces computed and on the OH-stretch frequencies calculated for each surface. With the help of these test systems, the authors show that their method offers a computational scaling that is two orders of magnitude lower than a standard CC-VSCF method and that it is of equal accuracy.
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33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.xr Self-consistent-field methods
31.15.A- Ab initio calculations
31.50.-x Potential energy surfaces

Explicitly intruder-free valence-universal multireference coupled cluster theory as applied to ionization spectroscopy

Sudip Chattopadhyay, Asish Mitra, and Dhiman Sinha

J. Chem. Phys. 125, 244111 (2006); http://dx.doi.org/10.1063/1.2403858 (17 pages) | Cited 5 times

Online Publication Date: 28 December 2006

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Although it is quite promising to compute the spectroscopic energies [say, ionization potential (IP)] via the traditional valence-universal multireference coupled cluster (VUMRCC) method based on the description of the complete model space being seriously plagued by the perennial intruder state problem, the eigenvalue independent partitioning (EIP) based VUMRCC (coined as EIP-MRCC) method is quite effective to predict the spectroscopic energies in an intruder-free manner. Hence, the EIP-MRCC method is suitable for generating both the principal IPs and the satellite IPs of the inner-valence region. An EIP strategy converts the nonlinear VUMRCC equations for M(m,n) dimensional model space of m hole and n particle to a non-Hermitian eigenproblem of larger dimension whose M(m,n) roots are only physically meaningful. To increase the quality of the computed energy differences in the sense of chemical accuracy and to locate the correct position of it in the spectrum, the inclusion of higher-body cluster operators on top of all the standard singles-doubles is not the only pivotal issue, the effect of the size of the basis set is also equally important. This paper illustrates these issues by calculating the principal and satellite IPs of HF and HCl molecules using various basis sets (viz., Dunning's cc-pVDZ, cc-pVTZ, and cc-pVQZ) via EIP-MRCC method with full inclusion of triples (abbreviated as EIP-MRCCSDT). The results seem quite encouraging in comparison with the experimental values. The controversial math satellite at 28.67 eV of HCl of Svensson et al. [J. Chem. Phys. 89, 7193 (1988) ] is also reported.
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31.15.bw Coupled-cluster theory
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Photoelectron imaging of I2− at 5.826 eV

Bradley F. Parsons, Sean M. Sheehan, Kathryn E. Kautzman, Terry A. Yen, and Daniel M. Neumark

J. Chem. Phys. 125, 244301 (2006); http://dx.doi.org/10.1063/1.2363990 (6 pages) | Cited 6 times

Online Publication Date: 28 December 2006

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We report the anion photoelectron spectrum of I2− taken at 5.826 eV detachment energy using velocity mapped imaging. The photoelectron spectrum exhibits bands resulting from transitions to the bound regions of the X math(0g+), A′ math(2u), A math(1u), and B math(0u+) electronic states as well as bands resulting from transitions to the repulsive regions of several I2 electronic states: the B′ math(0u−), B″ math(1u), math(2g), a math(1g), math(0g−), and C math(1u) states. We simulate the photoelectron spectrum using literature parameters for the I2− and I2 ground and excited states. The photoelectron spectrum includes bands resulting from transitions to several high-lying excited states of I2 that have not been seen experimentally: math(0g−), math3(1g), 1 math3(0g+), and the math3(0u−) states of I2. Finally, the photoelectron spectrum at 5.826 eV allows for the correction of a previous misassignment for the vertical detachment energy of the I2 B math(0u+) state.
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33.60.+q Photoelectron spectra
31.50.Df Potential energy surfaces for excited electronic states
33.80.Eh Autoionization, photoionization, and photodetachment

Interaction of low-energy electrons with the purine bases, nucleosides, and nucleotides of DNA

Carl Winstead and Vincent McKoy

J. Chem. Phys. 125, 244302 (2006); http://dx.doi.org/10.1063/1.2424456 (7 pages) | Cited 21 times

Online Publication Date: 28 December 2006

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The authors report results from computational studies of the interaction of low-energy electrons with the purine bases of DNA, adenine and guanine, as well as with the associated nucleosides, deoxyadenosine and deoxyguanosine, and the nucleotide deoxyadenosine monophosphate. Their calculations focus on the characterization of the π* shape resonances associated with the bases and also provide general information on the scattering of slow electrons by these targets. Results are obtained for adenine and guanine both with and without inclusion of polarization effects, and the resonance energy shifts observed due to polarization are used to predict π* resonance energies in associated nucleosides and nucleotides, for which static-exchange calculations were carried out. They observe slight shifts between the resonance energies in the isolated bases and those in the nucleosides.
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87.14.G- Nucleic acids
87.15.K- Molecular interactions; membrane-protein interactions
87.15.A- Theory, modeling, and computer simulation

Relativistic density functional calculations using two-spinor minimax finite-element method and linear combination of atomic orbitals for ZnO, CdO, HgO, UubO and Cu2, Ag2, Au2, Rg2

O. Kullie, H. Zhang, J. Kolb, and D. Kolb

J. Chem. Phys. 125, 244303 (2006); http://dx.doi.org/10.1063/1.2409288 (11 pages) | Cited 6 times

Online Publication Date: 29 December 2006

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In previous work the authors have presented a highly accurate two-spinor fully relativistic solution of the two-center Coulomb problem utilizing the finite-element method (FEM) and furthermore developed a relativistic minimax two-spinor linear combination of atomic orbitals (LCAO). In the present paper the authors present Dirac-Fock-Slater (DFS-) density functional calculations for two-atomic molecules up to super heavy systems using the fully nonlinear minimax FEM and the minimax LCAO in its linearized approximation (linear approximation to relativistic minimax). The FEM gives highly accurate benchmark results for the DFS functional. Especially considering molecules with up to super heavy atoms such as UubO and Rg2, the authors found that LCAO fails to give the correct systematic trends. The accurate FEM results shed a new light on the quality of the DFS-density functional.
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31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions
31.15.E- Density-functional theory
02.70.Dh Finite-element and Galerkin methods

Mixed quantum-classical molecular dynamics simulation of vibrational relaxation of ions in an electrostatic field

Andreas D. Koutselos

J. Chem. Phys. 125, 244304 (2006); http://dx.doi.org/10.1063/1.2424457 (8 pages) | Cited 3 times

Online Publication Date: 29 December 2006

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The vibrational relaxation of ions in low-density gases under the action of an electrostatic field is reproduced through a molecular dynamics simulation method. The vibration is treated though quantum mechanics and the remaining degrees of freedom are considered classical. The procedure is tested through comparison against analytic results for a two-dimensional quantum model and by studying energy exchange during binary ion-atom collisions. Finally, the method has been applied successfully to the calculation of the mobility and the vibrational relaxation rate of O2+ in Kr as a function of the mean collision energy using a model interaction potential that reproduces the potential minimum of a previously known ab initio potential surface. The calculation of the steady mean vibrational motion of the ions in (flow) drift tubes seems straightforward, though at the expense of large amounts of computer time.
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34.50.Ez Rotational and vibrational energy transfer
31.15.A- Ab initio calculations
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Nonlinear effects on solvation dynamics in simple mixtures

Shuhei Murata and Akira Yoshimori

J. Chem. Phys. 125, 244501 (2006); http://dx.doi.org/10.1063/1.2409713 (8 pages) | Cited 2 times

Online Publication Date: 22 December 2006

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The authors applied the time dependent density functional method (TDDFM) and a linear model to solvation dynamics in simple binary solvents. Changing the solute-solvent interactions at t = 0, the authors calculated the time evolution of density fields for solvent particles after the change (t>0) by the TDDFM and linear model. First, the authors changed the interaction of only one component of solvents. In this case, the TDDFM showed that the solvation time decreased monotonically with a mole fraction of the solvent strongly interacting with the solute. The monotonical decreases agreed with experimental results, while the linear model did not reproduce these results. The authors also calculated the solvation time by changing the interaction of both components. The calculation showed that the mole fraction dependence had the peak. The TDDFM presented a much higher peak than the linear model. The difference between the TDDFM and the linear model was caused by a nonlinear effect on an exchange process of solvent particles.
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82.30.Nr Association, addition, insertion, cluster formation
61.20.Gy Theory and models of liquid structure
64.75.-g Phase equilibria

Excess-entropy-based anomalies for a waterlike fluid

Jeffrey R. Errington, Thomas M. Truskett, and Jeetain Mittal

J. Chem. Phys. 125, 244502 (2006); http://dx.doi.org/10.1063/1.2409932 (8 pages) | Cited 57 times

Online Publication Date: 22 December 2006

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See Also: Erratum

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Many thermodynamic and dynamic properties of water display unusual behavior at low enough temperatures. In a recent study, Yan et al. [Phys. Rev. Lett. 95, 130604 (2005) ] identified a spherically symmetric two-scale potential that displays many of the same anomalous properties as water. More specifically, for select parametrizations of the potential, one finds that the regions where isothermal compression anomalously (i) decreases the fluid’s structural order, (ii) increases its translational self-diffusivity, and (iii) increases its entropy form nested domes in the temperature-density plane. These property relationships are similar to those found for more realistic models of water. In this work, the authors provide evidence that suggests that the anomalous regions specified above can all be linked through knowledge of the excess entropy. Specifically, the authors show how entropy scaling relationships developed by Rosenfeld [Phys. Rev. A 15, 2545 (1977) ] can be used to describe the region of diffusivity anomalies and to predict the state conditions for which anomalous viscosity and thermal conductivity behavior might be found.
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66.10.C- Diffusion and thermal diffusion
66.25.+g Thermal conduction in nonmetallic liquids
66.20.-d Viscosity of liquids; diffusive momentum transport
65.20.-w Thermal properties of liquids

Heat capacity, Raman, and Brillouin scattering studies of M2O–MgO–WO3–P2O5 glasses (M = K,Rb)

M. Maczka, J. Hanuza, J. Baran, A. Hushur, and S. Kojima

J. Chem. Phys. 125, 244503 (2006); http://dx.doi.org/10.1063/1.2403127 (9 pages) | Cited 1 time

Online Publication Date: 26 December 2006

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The authors report the results of temperature-dependent Brillouin scattering from both transverse and longitudinal acoustic waves, heat capacity studies as well as room temperature Raman scattering studies on M2O–MgO–WO3–P2O5 glasses (M = K,Rb). These results were used to obtain information about structure and various properties of the studied glasses such as fragility, elastic moduli, ratio of photoelastic constants, and elastic anharmonicity. They have found that both glasses have similar properties but replacement of K+ ions by Rb+ ions in the glass network leads to decrease of elastic parameters and P44 photoelastic constant due to increase of fragility. Based on Brillouin spectroscopy they show that a linear correlation between longitudinal and shear elastic moduli holds over a large temperature range. This result supports the literature data that the Cauchy-type relation represents a general rule for amorphous solids. An analysis of the Boson peak revealed that the form of the frequency distribution of the excess density of states is in agreement with the Euclidean random matrix theory. The reason of the observed shift of the maximum frequency of the Boson peak when K+ ions are substituted for Rb+ ions is also briefly discussed.
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65.60.+a Thermal properties of amorphous solids and glasses: heat capacity, thermal expansion, etc.
78.35.+c Brillouin and Rayleigh scattering; other light scattering
81.40.Jj Elasticity and anelasticity, stress-strain relations
62.20.D- Elasticity
78.20.hb Piezo-optical, elasto-optical, acousto-optical, and photoelastic effects

Changes in thermodynamic quantities upon contact of two solutes in solvent under isochoric and isobaric conditions

Masahiro Kinoshita, Yuichi Harano, and Ryo Akiyama

J. Chem. Phys. 125, 244504 (2006); http://dx.doi.org/10.1063/1.2403873 (7 pages) | Cited 15 times

Online Publication Date: 27 December 2006

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The changes in excess thermodynamic quantities upon the contact of two solutes immersed in a solvent are analyzed using the radial-symmetric and three-dimensional versions of the integral equation theory. A simple model mimicking a solute in water is employed. The solute-solute interaction energy is not included in the calculations. Under the isochoric condition, the solute contact always leads to a positive entropy change irrespective of the solute solvophobicity or solvophilicity. The energy change is negative for solvophobic solutes while it is positive for solvophilic ones. Under the isobaric condition, the contact of solvophobic solutes results in system-volume compression but that of solvophilic ones gives rise to expansion. Effects of the compression and expansion on the changes in enthalpy and entropy are enlarged with rising temperature. When the solute solvophobicity is sufficiently high, the entropy change (multiplied by the absolute temperature) can become negative due to the compression, except at low temperatures with the result of an even larger, negative enthalpy change. The expansion in the case of solvophilic solutes leads to a large, positive entropy change accompanied by an even larger, positive enthalpy change. The changes in enthalpy and entropy are strongly dependent on the temperature. However, the changes in enthalpy and entropy are largely cancelled out and the temperature dependency of the free-energy change is much weaker. The authors also discuss possible relevance to the enthalpy-entropy compensation experimentally known for a variety of physicochemical processes in aqueous solution such as protein folding.
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65.20.-w Thermal properties of liquids
61.20.Gy Theory and models of liquid structure
87.14.E- Proteins
87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.15.N- Properties of solutions of macromolecules

Contact effects on electronic transport in donor-bridge-acceptor complexes interacting with a thermal bath

Roie Volkovich and Uri Peskin

J. Chem. Phys. 125, 244505 (2006); http://dx.doi.org/10.1063/1.2401611 (9 pages) | Cited 7 times

Online Publication Date: 27 December 2006

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A model for electron transfer in donor-bridge-acceptor complexes with electronic coupling to nuclear bridge modes is studied using the Redfield formulation. We demonstrate that the transport mechanism through the molecular bridge is controlled by the location of the electronic-nuclear coupling term along the bridge. As the electronic-nuclear coupling term is shifted from the donor/acceptor-bridge contact sites into the bridge, the mechanism changes from kinetic transport (incoherent, thermally activated, and bridge-length independent) to coherent tunneling oscillations. This study joins earlier works aiming to explore the factors which control the mechanism of electronic transport through molecular bridges and molecular wires.
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85.65.+h Molecular electronic devices

Simulation studies of ionic liquids: Orientational correlations and static dielectric properties

C. Schröder, T. Rudas, and O. Steinhauser

J. Chem. Phys. 125, 244506 (2006); http://dx.doi.org/10.1063/1.2404674 (10 pages) | Cited 34 times

Online Publication Date: 27 December 2006

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The ionic liquids BMIM+I−, BMIM+BF4−, and BMIM+PF6− were simulated by means of the molecular dynamics method over a time period of more than 100 ns. Besides the common structural analysis, e.g., radial distribution functions and three dimensional occupancy plots, a more sophisticated orientational analysis was performed. The angular correlation functions g00110(r) and g00101(r) are the first distance dependent coefficients of the pairwise orientational distribution function g(rij,Ω1,Ω2,Ω12). These functions help to interpret the three dimensional plot and reveal interesting insights into the local structure of the analyzed ionic liquids. Furthermore, the collective network of ionic liquids can be characterized by the Kirkwood factor Gκ(r) [ J. Chem. Phys. 7, 911 (1939) ]. The short-range behavior (r<10 Å) of this factor may be suitable to predict the water miscibility of the ionic liquid. The long-range limit of Gk∞ is below 1 which demonstrates the strongly coupled nature of the ionic liquid networks. In addition, this factor relates the orientational structure and the dielectric properties of the ionic liquids. The static dielectric constant ϵ(ω = 0) for the simulated system is 8.9–9.5. Since in ionic liquids the very same molecule contributes to the total dipole moment as well as carries a net charge, a small, but significant contribution of the cross term between the total dipole moment and the electric current to ϵ(ω = 0) is observed.
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61.20.Ja Computer simulation of liquid structure
77.22.Ch Permittivity (dielectric function)
61.25.Em Molecular liquids

Vibrational energy relaxation of azide in water

Shuzhou Li, J. R. Schmidt, and J. L. Skinner

J. Chem. Phys. 125, 244507 (2006); http://dx.doi.org/10.1063/1.2408421 (8 pages) | Cited 11 times

Online Publication Date: 27 December 2006

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Vibrational lifetimes of the asymmetric stretch fundamental of azide anion in normal and heavy water have been measured experimentally, with results in the range of a few picoseconds. This is an interesting problem for theoretical study because of the competition between intramolecular (relaxation to the other excited vibrational states of azide) and purely intermolecular (relaxation to azide’s ground vibrational state) pathways. In addition it is important to understand the origin of the solvent isotope effect. Building on the seminal work of Morita and Kato [J. Chem. Phys. 109, 5511 (1998)] , the authors develop a simple model based on a two-dimensional description of the azide stretching vibrations. A novel aspect of their theory is the use of an “on-the-fly” optimized quantum mechanical/molecular mechanical approach to calculate the system-bath coupling. Their theoretical lifetimes are in good agreement with experiment for azide in both normal and heavy water. They find that the predominant relaxation pathway is intramolecular. The solvent isotope effect arises from the different librational frequencies in normal and heavy water.
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63.50.-x Vibrational states in disordered systems
61.20.-p Structure of liquids

Phenol-benzene complexation dynamics: Quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy

Kijeong Kwac, Chewook Lee, Yousung Jung, Jaebeom Han, Kyungwon Kwak, Junrong Zheng, M. D. Fayer, and Minhaeng Cho

J. Chem. Phys. 125, 244508 (2006); http://dx.doi.org/10.1063/1.2403132 (16 pages) | Cited 16 times

Online Publication Date: 28 December 2006

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Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol’s first solvent shell.
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61.20.Ja Computer simulation of liquid structure
61.25.Em Molecular liquids
78.30.C- Liquids
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