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28 December 2006

Volume 125, Issue 24,  Articles (24xxxx)

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COMMUNICATIONS

Using the histogram test to quantify reaction coordinate error

Baron Peters

J. Chem. Phys. 125, 241101 (2006) (4 pages)

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, 87.15.Rn, 87.15.Cc

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) (3 pages)

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, 31.30.Jv, 31.15.Dv
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ARTICLES

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) (7 pages)

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.Ew, 33.15.Ry

Quantal cumulant dynamics: General theory

Yasuteru Shigeta, Hideaki Miyachi, and Kimihiko Hirao

J. Chem. Phys. 125, 244102 (2006) (9 pages)

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, 82.20.Ln, 03.65.-w

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) (9 pages)

Online Publication Date: 22 December 2006

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See Also: Erratum

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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, 82.20.Db

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) (10 pages)

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

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) (9 pages)

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 [MC[underaccent underbar [below] (HF+DFT)]. The optimized geometries of porphine, porphycene, and these deuterated isotopomers by our MC[underaccent underbar [below] (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.Ew, 33.15.Bh, 31.30.Gs, 31.25.Qm, 31.15.Ne

Combining explicitly correlated R12 and Gaussian geminal electronic structure theories

Edward F. Valeev

J. Chem. Phys. 125, 244106 (2006) (10 pages)

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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31.25.-v, 33.15.Fm, 31.15.Md

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) (12 pages)

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.Dv, 31.15.Md, 51.30.+i, 64.30.+t

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

Steven K. Burger and Weitao Yang

J. Chem. Phys. 125, 244108 (2006) (12 pages)

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, 82.20.Kh, 82.30.-b

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) (8 pages)

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.Ar, 31.15.Pf, 31.25.Eb

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) (7 pages)

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, 33.15.Mt, 31.15.Ne, 31.15.Ar, 31.50.-x

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) (17 pages)

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-MRCCSD[script T]). The results seem quite encouraging in comparison with the experimental values. The controversial 2Pi 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.Dv, 33.15.Ry

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

Photoelectron imaging of I<sub>2</sub><sup>-</sup> 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) (6 pages)

Online Publication Date: 28 December 2006

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We report the anion photoelectron spectrum of I<sub>2</sub><sup>-</sup> 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  1Sigma<sub>g</sub><sup>+</sup>(0<sub>g</sub><sup>+</sup>), A[prime]  3Piu(2u), A  3Piu(1u), and B  3Piu(0<sub>u</sub><sup>+</sup>) electronic states as well as bands resulting from transitions to the repulsive regions of several I2 electronic states: the B[prime]  3Piu(0<sub>u</sub><sup>-</sup>), B[double-prime]  1Piu(1u), 3Pig(2g), a  3Pig(1g), 3Pig(0<sub>g</sub><sup>-</sup>), and C  3Sigma<sub>u</sub><sup>+</sup>(1u) states. We simulate the photoelectron spectrum using literature parameters for the I<sub>2</sub><sup>-</sup> 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: 3Pig(0<sub>g</sub><sup>-</sup>), 1Pig3(1g), 1  3Sigma<sub>g</sub><sup>-</sup>3(0<sub>g</sub><sup>+</sup>), and the 1Sigma<sub>g</sub><sup>-</sup>3(0<sub>u</sub><sup>-</sup>) 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  3Piu(0<sub>u</sub><sup>+</sup>) state.
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33.60.-q, 31.50.Df, 33.80.Eh

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) (7 pages)

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 pi* 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 pi* 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.Gg, 87.15.Kg, 87.15.Aa

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) (11 pages)

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.Jv, 31.15.Ew, 02.70.Dh

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

Andreas D. Koutselos

J. Chem. Phys. 125, 244304 (2006) (8 pages)

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 O<sub>2</sub><sup>+</sup> 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, 31.15.Ar

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) (8 pages)

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, 61.20.Gy, 64.75.+g

Excess-entropy-based anomalies for a waterlike fluid

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

J. Chem. Phys. 125, 244502 (2006) (8 pages)

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.Cb, 66.60.+a, 66.20.+d, 65.20.+w

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) (9 pages)

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, 78.30.Ly, 78.35.+c, 81.40.Jj, 62.20.Dc, 78.20.Hp

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) (7 pages)

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, 61.20.Gy, 87.14.Ee, 87.15.Cc, 87.15.Nn

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) (9 pages)

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

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

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

J. Chem. Phys. 125, 244506 (2006) (10 pages)

Online Publication Date: 27 December 2006

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The ionic liquids BMIM+I−, BMIM+BF<sub>4</sub><sup>-</sup>, and BMIM+PF<sub>6</sub><sup>-</sup> 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 g<sub>00</sub><sup>110</sup>(r) and g<sub>00</sub><sup>101</sup>(r) are the first distance dependent coefficients of the pairwise orientational distribution function g(rij,Omega1,Omega2,Omega12). 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 Gkappa(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 G<sub>k</sub><sup>[infinity]</sup> 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 epsilon(omega=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 epsilon(omega=0) is observed.
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61.20.Ja, 77.22.Ch, 61.25.Em

Vibrational energy relaxation of azide in water

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

J. Chem. Phys. 125, 244507 (2006) (8 pages)

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, 61.20.-p

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) (16 pages)

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, 61.25.Em, 78.30.Cp

Nuclear spin relaxation of sodium cations in bacteriophage Pf1 solutions

D. N. Sobieski, N. R. Krueger, S. Vyas, and M. P. Augustine

J. Chem. Phys. 125, 244509 (2006) (15 pages)

Online Publication Date: 29 December 2006

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The nuclear magnetic resonance (NMR) spectra for the I=3/2 23Na cation dissolved into filamentous bacteriophage Pf1 solutions display line splittings and relaxation times consistent with an interaction between the 23Na nuclear quadrupole moment and the electric field gradient produced by the negatively charged Pf1 particles. The 23Na NMR line splittings and relaxation rates corresponding to magnetization recovery and single, double, and triple quantum coherence decays are measured in Pf1 solutions and compared to theoretical values. The deviation of the observed dc spectral density J(0) from the equal first harmonic J(omega0) and second harmonic J(2omega0) values as J(omega0)=J(2omega0)[not-equal]J(0) in these solutions suggests that ion migration in the electric field gradient of the Pf1 particles produces an anisotropic relaxation mechanism. Correlation functions and thus spectral densities for this process are calculated from solutions to the Fokker-Planck equation for radial motion in an electric potential and used to estimate measured relaxation rates. Appropriate electric potentials are generated from the solutions to the Poisson-Boltzmann equation for a charged Pf1 particle in aqueous phase, functions that lead to theoretical estimates of NMR line splittings consistent with experimental observations.
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87.15.Mi, 87.15.Nn, 82.56.Na, 82.56.Pp

Are recent water models obtained by fitting diffraction data consistent with infrared/Raman and x-ray absorption spectra?

Mikael Leetmaa, Mathias Ljungberg, Hirohito Ogasawara, Michael Odelius, Lars-Åke Näslund, Anders Nilsson, and Lars G. M. Pettersson

J. Chem. Phys. 125, 244510 (2006) (12 pages)

Online Publication Date: 29 December 2006

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X-ray absorption (XA) spectra have been computed based on water structures obtained from a recent fit to x-ray and neutron diffraction data using models ranging from symmetrical to asymmetrical local coordination of the water molecules [A. K. Soper, J. Phys.: Condens. Matter 17, S3273 (2005)]. It is found that both the obtained symmetric and asymmetric structural models of water give similar looking XA spectra, which do not match the experiment. The fitted models both contain unphysical structures that are allowed by the diffraction data, where, e.g., hydrogen-hydrogen interactions may occur. A modification to the asymmetric model, in which the non-hydrogen-bonded OH intramolecular distance is allowed to become shorter while the bonded OH distance becomes longer, improves the situation somewhat, but the overall agreement is still unsatisfactory. The electric field (E-field) distributions and infrared (IR) spectra are also calculated using two established theoretical approaches, which, however, show significant discrepancies in their predictions for the asymmetric structural models. Both approaches predict the Raman spectrum of the symmetric model fitted to the diffraction data to be significantly blueshifted compared to experiment. At the moment no water model exists that can equally well describe IR/Raman, x-ray absorption spectroscopy, and diffraction data.
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61.25.Em, 78.30.Cp

Aging correlation functions of the interrupted fractional Fokker-Planck propagator

James B. Witkoskie and Jianshu Cao

J. Chem. Phys. 125, 244511 (2006) (5 pages)

Online Publication Date: 29 December 2006

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The authors explore aging in a general semi-Markov process with arbitrary waiting time distributions and discuss the role of trapping phenomenon in glasses in determining the waiting time distributions. In certain limits, they obtain a two-time propagator for the fractional Fokker-Planck equation through coordination, but one can generalize the construction to incorporate cutoffs in the aging of the system, i.e., the interrupted aging. The construction allows the incorporation of cutoffs in the aging of the system, and the exploration of signatures of aging effects in systems that eventually achieve equilibrium. Cutoffs in aging effects are illustrated for interrupted fractional diffusion in a harmonic potential and for the on-time probability of a quantum dot system.
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81.40.Cd, 61.43.Fs, 66.30.-h

Time scales and pathways of vibrational energy relaxation in liquid CHBr3 and CDBr3

Sai G. Ramesh and Edwin L. Sibert, III

J. Chem. Phys. 125, 244512 (2006) (8 pages)

Online Publication Date: 29 December 2006

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Molecular dynamics simulations are used in conjunction with Landau-Teller, fluctuating Landau-Teller, and time-dependent perturbation theories to investigate energy flow out of various vibrational states of liquid CHBr3 and CDBr3. The CH stretch overtone is found to relax with a time scale of about 1  ps compared to the 50  ps rate for the fundamental. The relaxation pathways and rates for the CD stretch decay in CDBr3 are computed in order to understand the changes arising from deuteration. While the computed relaxation rate agrees well with experiments, the pathway is found to be more complex than anticipated. In addition to the above channels for CH(D) stretch relaxation that involve only the hindered translations and rotations of the solvent, routes involving off-resonant and resonant excitations of solvent vibrational modes are also examined. Finally, the decay of energy from low frequency states to near-lying solute states and solvent vibrations are studied.
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61.20.Ja, 61.20.Lc, 63.50.+x

Relaxation of the CH stretch in liquid CHBr3: Solvent effects and decay rates using classical nonequilibrium simulations

Sai G. Ramesh and Edwin L. Sibert, III

J. Chem. Phys. 125, 244513 (2006) (9 pages)

Online Publication Date: 29 December 2006

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This article addresses two questions regarding the decay of the CH stretch in liquid CHBr3. The first is whether the initial steps of the relaxation primarily involve energy redistribution within the excited molecule alone. Gas phase quantum mechanical and classical calculations are performed to examine the role of the solvent in this process. At the fundamental excitation level, it is found that CH stretch decay is, in fact, strongly solvent driven. The second question is on the applicability of a fully classical approach to the calculation of CH stretch condensed phase decay rates. To this end, nonequilibrium molecular dynamics simulations are performed. The results are compared with quantum mechanical rates computed previously. The two methods are found to be in fair agreement with each other. However, care must be exercised in the interpretation of the classical results.
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61.20.Ja, 63.50.+x

Surfaces, Interfaces, and Materials

Current rectification by asymmetric molecules: An ab initio study

Yan-hong Zhou, Xiao-hong Zheng, Ying Xu, and Zhao Yang Zeng

J. Chem. Phys. 125, 244701 (2006) (5 pages)

Online Publication Date: 22 December 2006

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Current rectification effect in an asymmetric molecule HCOO–C6H4–(CH2)n sandwiched between two aluminum electrodes has been studied using an ab initio nonequilibrium Green's function method. The conductance of the system decreases exponentially with the increasing number n of CH2. The phenomenon of current rectification is observed such that a very small current appears at negative bias and a sharp negative differential resistance at a critical positive bias when n>=2. The rectification effect arises from the asymmetric structure of the molecule and the molecule-electrode couplings. A significant rectification ratio of ~38 can be achieved when n=5.
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73.40.Ei, 73.40.Ns, 71.15.-m

Fitting a free-form scattering length density profile to reflectivity data using temperature-proportional quenching

Charles F. Laub and Tonya L. Kuhl

J. Chem. Phys. 125, 244702 (2006) (8 pages)

Online Publication Date: 27 December 2006

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A technique for fitting a free-form scattering length density profile to reflectivity data via least-squares minimization is presented. The approach combines aspects of simulated annealing with a parametrized representation of the scattering length density profile. The ability of the algorithm to accurately recover the scattering length density profile from arbitrary initial parameter values is demonstrated for simulated and experimental data.
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61.10.Eq, 61.12.Bt

Fluids in porous media. I. A hard sponge model

S. L. Zhao, W. Dong, and Q. H. Liu

J. Chem. Phys. 125, 244703 (2006) (16 pages)

Online Publication Date: 27 December 2006

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The morphology of many porous materials is spongelike. Despite the abundance of such materials, simple models which allow for a theoretical description of these materials are still lacking. Here, we propose a hard sponge model which is made by digging spherical cavities in a solid continuum. We found an analytical expression for describing the interaction potential between fluid particles and the spongelike porous matrix. The diagrammatic expansions of different correlation functions are derived as well as that of grand potential. We derived also the Ornstein-Zernike (OZ) equations for this model. In contrast to Madden-Glandt model of random porous media [W. G. Madden and E. D. Glandt, J. Stat. Phys. 51, 537 (1988)], the OZ equations for a fluid confined in our hard sponge model have some similarity to the OZ equations of a three-component fluid mixture. We show also how the replica method can be extended to study our sponge model and that the same OZ equations can be derived also from the extended replica method.
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61.43.Gt, 68.43.Mn

Hopping times of two hard disks diffusing in a channel

K. K. Mon and J. K. Percus

J. Chem. Phys. 125, 244704 (2006) (5 pages)

Online Publication Date: 27 December 2006

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A finite difference method was used to solve numerically the multidimensional diffusion equation describing the time evolution of two hard disks diffusing in a narrow hard channel. The authors extract an estimate for the average time tauhop needed for the disks to hop pass each other. For narrow channels near the hopping threshold, tauhop diverges and is consistent with the scaling prediction of the transition state theory. This provides a much-needed rigorous benchmark to test an approximate solution to the diffusion problem.
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66.10.Cb, 61.20.Ja

Diffusion-limited binding to a site on the wall of a membrane channel

Leonardo Dagdug and Alexander M. Berezhkovskii

J. Chem. Phys. 125, 244705 (2006) (7 pages)

Online Publication Date: 27 December 2006

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The authors develop a theory of diffusion-controlled reactions with a site located on the wall of a cylindrical membrane channel that connects two reservoirs containing diffusing particles which are trapped by the site at the first contact. An expression for the Laplace transform of the rate coefficient, k(t), is derived assuming that the size of the site is small compared to the channel radius. The expression is used to find the stationary value of the rate coefficient, k([infinity]), as a function of the length and radius of the channel, the radius of the site, and its position inside the channel (distances from the two ends of the channel) as well as the particle diffusion constants in the bulk and in the channel. Their derivation is based on the one-dimensional description of the particle motion in the channel, which is generalized to include binding to the site into consideration. The validity of the approximate one-dimensional description of diffusion and binding was checked by three-dimensional Brownian dynamics simulations. They found that the one-dimensional description works reasonably well when the size of the site does not exceed 0.2 of the channel radius.
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82.20.Pm

Towards atomic site-selective sensitivity in tip-enhanced Raman spectroscopy

Norihiko Hayazawa, Hiroyuki Watanabe, Yuika Saito, and Satoshi Kawata

J. Chem. Phys. 125, 244706 (2006) (7 pages)

Online Publication Date: 28 December 2006

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Depending on each nitrogen atom of adenine molecule to which a silver atom of a metallic tip approaches, tip-enhanced near-field Raman spectroscopy may show a potential to achieve atomic site-selective detection sensitivity. Molecular vibrational calculations show that silver atoms and adenine molecule create several isomers generating specific vibrational modes of each isomer that are shifted or not observable in isolated adenine molecule itself. Here, the authors observe the specific vibrational modes and spectral shifts of isomers experimentally and are in good agreement with their calculations.
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33.20.Fb, 33.20.Tp, 33.15.Mt, 33.15.Bh, 33.70.Jg

New approach to the kinetics of heterogeneous unary nucleation on liquid aerosols of a binary solution

Yuri Djikaev and Eli Ruckenstein

J. Chem. Phys. 125, 244707 (2006) (9 pages)

Online Publication Date: 28 December 2006

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The formation of a droplet on a hygroscopic center may occur either in a barrierless way via Köhler activation or via nucleation by overcoming a free energy barrier. Unlike the former, the latter mechanism of this process has been studied very little and only in the framework of the classical nucleation theory based on the capillarity approximation whereby a nucleating droplet behaves like a bulk liquid. In this paper the authors apply another approach to the kinetics of heterogeneous nucleation on liquid binary aerosols, based on a first passage time analysis which avoids the concept of surface tension for tiny droplets involved in nucleation. Liquid aerosols of a binary solution containing a nonvolatile solute are considered. In addition to modeling aerosols formed through the deliquescence of solid soluble particles, the considered aerosols constitute a rough model of “processed” marine aerosols. The theoretical results are illustrated by numerical calculations for the condensation of water vapor on binary aqueous aerosols with nonvolatile nondissociating solute molecules using Lennard-Jones potentials for the molecular interactions.
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64.70.Fx, 64.60.Qb, 82.70.Rr

Polymers, Biopolymers, and Complex Systems

Determination of rotary diffusivity of poly(n-propyl isocyanate) by molecular dynamics

M. Laso, N. Jimeno, L. M. Muneta, and M. Müller

J. Chem. Phys. 125, 244901 (2006) (7 pages)

Online Publication Date: 26 December 2006

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The rotational dynamics of a nondilute solution of the rodlike polymer poly(n-propyl isocyanate) (PPIC) has been studied on an atomistic model by means of a large-scale classical molecular dynamics investigation. The rotary diffusivity of PPIC in toluene solution has been determined from the Einsteinian diffusion regime of the end-to-end vector on the surface of the unit sphere and has been found to be Dr=10.5×105(±2.7)  s−1, which falls in the range of the experimental data available. A comparison of molecular dynamics predictions with theoretical and perturbation expansion predictions has also been performed.
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61.25.Hq, 61.20.Ja, 66.10.-x

Unified model of association-induced lower critical solution temperature phase separation and its application to solutions of telechelic poly(ethylene oxide) and of telechelic poly(N-isopropylacrylamide) in water

Yukinori Okada, Fumihiko Tanaka, Piotr Kujawa, and Françoise M. Winnik

J. Chem. Phys. 125, 244902 (2006) (11 pages)

Online Publication Date: 26 December 2006

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The authors present a model describing the coexistence of hydrophobic association and phase separation with lower critical solution temperature (LCST) in aqueous solutions of polymers carrying short hydrophobic chains at both chain ends (telechelic associating polymers). The LCST of these solutions is found to decrease along the sol/gel transition curve as a result of both end-chain association (association-induced phase separation) and direct hydrophobic interaction of the end chains with water. The authors relate the magnitude of the LCST decrease to a hydration cooperativity parameter sigma. The LCST decreases substantially (~100  K) in the case of random hydration (sigma=1), whereas only a small shift (~5–10  K) occurs in the case of cooperative hydration (sigma=0.3). The molecular weight dependence of the LCST drop is studied in detail in each case. The results are compared with experimental observations of the cloud points of telechelic poly(ethylene oxide) solutions, in which random hydration predominates, and of telechelic poly(N-isopropylacrylamide) solutions, in which cooperative hydration prevails.
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64.75.+g, 82.30.Nr, 82.70.Gg, 61.25.Hq, 61.20.Qg
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LETTERS TO THE EDITOR

Comments

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Comment on “Legendre-transform functionals for spin-density-functional theory” [J. Chem. Phys. 124, 224108 (2006)]

A. Holas and R. Balawender

J. Chem. Phys. 125, 247101 (2006) (2 pages)

Online Publication Date: 26 December 2006

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In this Comment the authors propose an alternative formulation of the starting point to the analysis performed in the commented paper [P. W. Ayers and W. Yang, J. Chem. Phys.124, 224108 (2006)]. An important role of the z component of the vector of the total spin angular momentum operator for the considered many-electron system is indicated. The authors believe their approach to be mathematically cleaner and conceptually easier than the original treatment.
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31.15.Ew

Errata

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Erratum: “Screened hybrid density functionals applied to solids” [J. Chem. Phys. 124, 154709 (2006)]

J. Paier, M. Marsman, K. Hummer, G. Kresse, I. C. Gerber, and J. G. Ángyán

J. Chem. Phys. 125, 249901 (2006) (2 pages)

Online Publication Date: 22 December 2006

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99.10.Cd, 71.15.Mb, 71.45.Gm, 71.70.Gm

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