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14 April 2008

Volume 128, Issue 14,  Articles (14xxxx)

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ARTICLES

Theoretical Methods and Algorithms

A sparse matrix based full-configuration interaction algorithm

Zoltán Rolik, Ágnes Szabados, and Péter R. Surján

J. Chem. Phys. 128, 144101 (2008) (11 pages)

Online Publication Date: 8 April 2008

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We present an algorithm related to the full-configuration interaction (FCI) method that makes complete use of the sparse nature of the coefficient vector representing the many-electron wave function in a determinantal basis. Main achievements of the presented sparse FCI (SFCI) algorithm are (i) development of an iteration procedure that avoids the storage of FCI size vectors; (ii) development of an efficient algorithm to evaluate the effect of the Hamiltonian when both the initial and the product vectors are sparse. As a result of point (i) large disk operations can be skipped which otherwise may be a bottleneck of the procedure. At point (ii) we progress by adopting the implementation of the linear transformation by Olsen et al. [J. Chem Phys. 89, 2185 (1988)] for the sparse case, getting the algorithm applicable to larger systems and faster at the same time. The error of a SFCI calculation depends only on the dropout thresholds for the sparse vectors, and can be tuned by controlling the amount of system memory passed to the procedure. The algorithm permits to perform FCI calculations on single node workstations for systems previously accessible only by supercomputers.
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03.65.Ge

Single switch surface hopping for molecular dynamics with transitions

Clotilde Fermanian Kammerer and Caroline Lasser

J. Chem. Phys. 128, 144102 (2008) (9 pages)

Online Publication Date: 8 April 2008

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A trajectory surface hopping algorithm is proposed, which stems from a mathematically rigorous analysis of propagation through conical intersections of potential energy surfaces. Since nonadiabatic transitions are only performed when a classical trajectory attains one of its local minimal surface gaps, the algorithm is called single switch surface hopping. Numerical experiments for a two mode Jahn–Teller system are presented, which illustrate the asymptotic justification of the method as well as its good performance in the physically relevant parameter range.
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03.65.Fd, 03.65.Ta, 03.65.Sq

The electron affinity of gallium nitride (GaN) and digallium nitride (GaNGa): The importance of the basis set superposition error in strongly bound systems

Demeter Tzeli and Athanassios A. Tsekouras

J. Chem. Phys. 128, 144103 (2008) (7 pages)

Online Publication Date: 8 April 2008

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The electron affinity of GaN and Ga2N as well as the geometries and the dissociation energies of the ground states of gallium nitrides GaN, GaN−, Ga2N, and Ga2N− were systematically studied by employing the coupled cluster method, RCCSD(T), in conjunction with a series of basis sets, (aug-)cc-pVxZ(-PP), x=D, T, Q, and 5 and cc-pwCVxZ(-PP), x=D, T, and Q. The calculated dissociation energy and the electron affinity of GaN are 2.12 and 1.84  eV, respectively, and those of Ga2N are 6.31 and 2.53  eV. The last value is in excellent agreement with a recent experimental value for the electron affinity of Ga2N of 2.506±0.008  eV. For such quality in the results to be achieved, the Ga 3d electrons had to be included in the correlation space. Moreover, when a basis set is used, which has not been developed for the number of the electrons which are correlated in a calculation, the quantities calculated need to be corrected for the basis set superposition error.
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33.15.Ry, 33.15.Bh, 31.15.bw

Improved transition path sampling methods for simulation of rare events

Manan Chopra, Rohit Malshe, Allam S. Reddy, and J. J. de Pablo

J. Chem. Phys. 128, 144104 (2008) (5 pages)

Online Publication Date: 9 April 2008

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The free energy surfaces of a wide variety of systems encountered in physics, chemistry, and biology are characterized by the existence of deep minima separated by numerous barriers. One of the central aims of recent research in computational chemistry and physics has been to determine how transitions occur between deep local minima on rugged free energy landscapes, and transition path sampling (TPS) Monte-Carlo methods have emerged as an effective means for numerical investigation of such transitions. Many of the shortcomings of TPS-like approaches generally stem from their high computational demands. Two new algorithms are presented in this work that improve the efficiency of TPS simulations. The first algorithm uses biased shooting moves to render the sampling of reactive trajectories more efficient. The second algorithm is shown to substantially improve the accuracy of the transition state ensemble by introducing a subset of local transition path simulations in the transition state. The system considered in this work consists of a two-dimensional rough energy surface that is representative of numerous systems encountered in applications. When taken together, these algorithms provide gains in efficiency of over two orders of magnitude when compared to traditional TPS simulations.
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82.20.Db, 82.20.Fd, 82.20.Wt, 82.60.-s

Application of magnetically perturbed time-dependent density functional theory to magnetic circular dichroism: Calculation of [script B] terms

Michael Seth, Mykhaylo Krykunov, Tom Ziegler, Jochen Autschbach, and Arup Banerjee

J. Chem. Phys. 128, 144105 (2008) (17 pages)

Online Publication Date: 9 April 2008

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Magnetically perturbed time-dependent density functional theory is applied to the calculation of the magnetic circular dichroism (MCD) [script B] terms of closed shell molecules. Two approaches to evaluating [script B] term parameters are described: a sum-over-states–type approach and an approach based on the direct solution of the matrix equations. The advantages and disadvantages and technical challenges of each approach are described. The interpretation of the parameters in terms of ground and excited state perturbations are discussed. Several applications of the methodology are described. Calculations of the MCD of ethene are used to compare the sum-over-states and direct solution approaches and to illustrate the potential for analysis. The other applications involving azabenzes, sulfur-nitrogen heterocycles and quinone molecules are compared with experiment and other theoretical calculations. For the most part, all important features of the observed spectra are reproduced.
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33.55.+b, 33.57.+c, 31.15.ee, 31.15.xp

Correlation regions within a localized molecular orbital approach

Ricardo A. Mata, Hans-Joachim Werner, and Martin Schütz

J. Chem. Phys. 128, 144106 (2008) (8 pages)

Online Publication Date: 9 April 2008

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A hybrid scheme for the computation of reaction energies in large molecular systems is proposed. The approach is based on localized orbitals and allows for the treatment of different parts of a molecule at different computational levels. The localized orbitals are assigned to regions, and then different local correlation methods, such as local MP2 or local CCSD(T), can be applied to different regions. In contrast to previous hybrid schemes, the molecule does not have to be split into parts and, therefore, it is not necessary to saturate dangling bonds using link atoms. For fixed region sizes, the cost of the high-level calculation becomes independent of the molecular size, and it is demonstrated that [script O](1) scaling can be achieved. Illustrative applications are presented and the convergence of the results with respect to the size of the regions is investigated for reaction energies, barrier heights, and weakly bound complexes.
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82.20.Pm, 82.20.Wt, 31.15.xp, 31.15.bw, 31.15.V-

Dispersion energy from density-fitted density susceptibilities of singles and doubles coupled cluster theory

Tatiana Korona and Bogumil Jeziorski

J. Chem. Phys. 128, 144107 (2008) (10 pages)

Online Publication Date: 10 April 2008

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A new method of calculation of the second-order dispersion energy is proposed. It is based on the Longuet-Higgins formula [Faraday Discuss. Chem. Soc. 40, 7 (1965)], which describes the dispersion interaction in terms of frequency-dependent density susceptibilities of monomers. In this study, the density susceptibilities are obtained from the coupled cluster theory at the singles and doubles level. Density fitting is applied in order to reduce the computational effort for the evaluation of density susceptibilities. It is shown that density fitting improves the scaling of the computational resources with molecular size by one order of magnitude without affecting the accuracy of the resulting dispersion energy. Numerical results are presented for several van der Waals molecules to illustrate the performance of the new approach.
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31.15.bw, 31.15.E-

Intramolecular basis set superposition error effects on the planarity of benzene and other aromatic molecules: A solution to the problem

David Asturiol, Miquel Duran, and Pedro Salvador

J. Chem. Phys. 128, 144108 (2008) (5 pages)

Online Publication Date: 10 April 2008

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Recently, the surprising result that ab initio calculations on benzene and other planar arenes at correlated MP2, MP3, configuration interaction with singles and doubles (CISD), and coupled cluster with singles and doubles levels of theory using standard Pople's basis sets yield nonplanar minima has been reported. The planar optimized structures turn out to be transition states presenting one or more large imaginary frequencies, whereas single-determinant-based methods lead to the expected planar minima and no imaginary frequencies. It has been suggested that such anomalous behavior can be originated by two-electron basis set incompleteness error. In this work, we show that the reported pitfalls can be interpreted in terms of intramolecular basis set superposition error (BSSE) effects, mostly between the C–H moieties constituting the arenes. We have carried out counterpoise-corrected optimizations and frequency calculations at the Hartree–Fock, B3LYP, MP2, and CISD levels of theory with several basis sets for a number of arenes. In all cases, correcting for intramolecular BSSE fixes the anomalous behavior of the correlated methods, whereas no significant differences are observed in the single-determinant case. Consequently, all systems studied are planar at all levels of theory. The effect of different intramolecular fragment definitions and the particular case of charged species, namely, cyclopentadienyl and indenyl anions, respectively, are also discussed.
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31.15.am, 31.15.V-, 33.15.Bh

Multiconfiguration optimized effective potential method for a density-functional treatment of static correlation

Martin Weimer, Fabio Della Sala, and Andreas Görling

J. Chem. Phys. 128, 144109 (2008) (18 pages)

Online Publication Date: 10 April 2008

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An approach to treat static correlation within a density-functional framework is presented. To that end, a multiconfiguration optimized effective potential (MCOEP) method is derived. In contrast to standard multiconfiguration self-consistent field (MCSCF) methods and previous combinations of MCSCF procedures with density-functional theory, the MCOEP method yields well-defined physically meaningful orbital and eigenvalue spectra. In addition to the electronic ground state also excited electronic states can be described. The MCOEP method is implemented invoking the localized Hartree–Fock approximation, leading to a multiconfiguration localized Hartree–Fock approach. Applications of the new method to the dissociation of the hydrogen molecule and the isomerization of ethene and cyclobutadiene show that it is capable of describing situations that are characterized by strong static correlation
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31.15.E-, 31.15.xr, 82.30.Lp

Origin and control of superlinear polarizability scaling in chemical potential equalization methods

G. Lee Warren, Joseph E. Davis, and Sandeep Patel

J. Chem. Phys. 128, 144110 (2008) (14 pages)

Online Publication Date: 10 April 2008

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Many common chemical potential equalization (µEq) methods are known to suffer from a superlinear scaling of the polarizability with increasing molecular size that interferes with model transferability and prevents the straightforward application of these methods to large, biochemically relevant molecules. In the present work, we systematically investigate the origins of this scaling and the mechanisms whereby some existing methods successfully temper the scaling. We demonstrate several types of topological charge constraints distinct from the usual single molecular charge constraint that can successfully achieve linear polarizability scaling in atomic charge based equilibration models. We find the use of recently employed charge conservation constraints tied to small molecular units to be an effective and practical approach for modulating the polarizability scaling in atomic µEq schemes. We also analyze the scaling behavior of several µEq schemes in the bond representation and derive closed-form expressions for the polarizability scaling in a linear atomic chain model; for a single molecular charge constraint these expressions demonstrate a cubic dependence of the polarizability on molecular size compared with linear scaling obtainable in the case of the atom-atom charge transfer (AACT) and split-charge equilibration (SQE) schemes. Application of our results to the trans N-alkane series reveals that in certain situations, the AACT and SQE schemes can become unstable due to an indefinite Hessian matrix. Consequently, we discuss sufficient criteria for ensuring stability within these schemes.
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87.15.R-, 33.15.Kr

Finding important anharmonic terms in the sixth-order potential energy function by the scaled hypersphere search method: An application to vibrational analyses of molecules and clusters

Satoshi Maeda, Yu Watanabe, and Koichi Ohno

J. Chem. Phys. 128, 144111 (2008) (11 pages)

Online Publication Date: 11 April 2008

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A fitting method of the sixth-order potential energy function is proposed, where ab initio potential energy data for the fitting are sampled in directions containing maximal anharmonic downward distortions detected by the scaled hypersphere search (SHS) method. This technique has been applied to H2O, HCHO, HCOOH, C2H4, CH3OH, CH3CHO, CH3NH2, B2H6, (H2O)2, and (H2O)3, where, without using the symmetry, 176, 904, 1432, 2992, 2520, 2760, 3608, 6232, 768, and 1456 times single-point energy calculations, respectively, were required for obtaining anharmonic terms. Experimental IR peak positions of not only fundamentals but also overtones and combinations in the excitation energy range of 1000–4000  cm−1 could be reproduced very accurately by the post-vibrational self-consistent field theory employing potential functions obtained by the present SHS based polynomial fitting method.
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34.20.-b, 31.15.A-, 33.15.Mt, 33.20.Tp, 33.20.Ea, 31.15.xr

Improved supermolecular second order Møller–Plesset intermolecular interaction energies using time-dependent density functional response theory

Andreas Heßelmann

J. Chem. Phys. 128, 144112 (2008) (9 pages)

Online Publication Date: 11 April 2008

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The supermolecular second order Møller-Plesset (MP2) intermolecular interaction energy is corrected by employing time-dependent density functional (TDDFT) response theory. This is done by replacing the uncoupled second order dispersion contribution contained in the supermolecular MP2 energy with the coupled dispersion energy obtained from the TDDFT approach. Preliminary results for the rare gas dimers He2, Ne2, and Ar2 and a few structures of the (HF)2 and (H2O)2 dimers show that the conventional MP2 interaction energies are considerably improved by this procedure if compared to coupled cluster singles doubles with perturbative triples [CCSD(T)] interaction energies. However, the quality of the interaction energies obtained in this way strongly depends on the exchange-correlation potential employed in the monomer calculations: It is shown that an exact exchange-only potential surprisingly often performs better than an asymptotically corrected hybrid exchange-correlation potential. Therefore the method proposed in this work is similar to the method by Cybulski and Lytle [J. Chem. Phys., 127, 141102 (2007)] which corrects the supermolecular MP2 energies with a scaled dispersion energy from time-dependent Hartree–Fock. The results in this work are also compared to the combination of density functional theory and intermolecular perturbation theory.
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34.20.Gj, 31.15.ee, 31.15.eg, 33.15.Bh, 31.15.xr

Semiempirical evaluation of post-Hartree–Fock diagonal-Born–Oppenheimer corrections for organic molecules

José R. Mohallem

J. Chem. Phys. 128, 144113 (2008) (4 pages)

Online Publication Date: 11 April 2008

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Recent post-Hartree–Fock calculations of the diagonal-Born-Oppenheimer correction empirically show that it behaves quite similar to atomic nuclear mass corrections. An almost constant contribution per electron is identified, which converges with system size for specific series of organic molecules. This feature permits pocket-calculator evaluation of the corrections within thermochemical accuracy (10−1  mhartree or kcal/mol).
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31.15.xr

Quantum theory of (femtosecond) time-resolved stimulated Raman scattering

Zhigang Sun, J. Lu, Dong H. Zhang, and Soo-Y. Lee

J. Chem. Phys. 128, 144114 (2008) (13 pages)

Online Publication Date: 11 April 2008

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We present a complete perturbation theory of stimulated Raman scattering (SRS), which includes the new experimental technique of femtosecond stimulated Raman scattering (FSRS), where a picosecond Raman pump pulse and a femtosecond probe pulse simultaneously act on a stationary or nonstationary vibrational state. It is shown that eight terms in perturbation theory are required to account for SRS, with observation along the probe pulse direction, and they can be grouped into four nonlinear processes which are labeled as stimulated Raman scattering or inverse Raman scattering (IRS): SRS(I), SRS(II), IRS(I), and IRS(II). Previous FSRS theories have used only the SRS(I) process or only the “resonance Raman scattering” term in SRS(I). Each process can be represented by an overlap between a wave packet in the initial electronic state and a wave packet in the excited Raman electronic state. Calculations were performed with Gaussian Raman pump and probe pulses on displaced harmonic potentials to illustrate various features of FSRS, such as high time and frequency resolution; Raman gain for the Stokes line, Raman loss for the anti-Stokes line, and absence of the Rayleigh line in off-resonance FSRS from a stationary or decaying v=0 state; dispersive line shapes in resonance FSRS; and the possibility of observing vibrational wave packet motion with off-resonance FSRS.
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42.65.Dr, 42.65.Re, 33.15.Mt, 33.80.Rv, 33.70.Jg

Obtaining the two-body density matrix in the density matrix renormalization group method

Dominika Zgid and Marcel Nooijen

J. Chem. Phys. 128, 144115 (2008) (13 pages)

Online Publication Date: 11 April 2008

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We present an approach that allows to produce the two-body density matrix during the density matrix renormalization group (DMRG) run without an additional increase in the current disk and memory requirements. The computational cost of producing the two-body density matrix is proportional to O(M3k2+M2k4). The method is based on the assumption that different elements of the two-body density matrix can be calculated during different steps of a sweep. Hence, it is desirable that the wave function at the convergence does not change during a sweep. We discuss the theoretical structure of the wave function ansatz used in DMRG, concluding that during the one-site DMRG procedure, the energy and the wave function are converging monotonically at every step of the sweep. Thus, the one-site algorithm provides an opportunity to obtain the two-body density matrix free from the N-representability problem. We explain the problem of local minima that may be encountered in the DMRG calculations. We discuss theoretically why and when the one- and two-site DMRG procedures may get stuck in a metastable solution, and we list practical solutions helping the minimization to avoid the local minima.
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31.15.E-, 02.20.-a

The density matrix renormalization group self-consistent field method: Orbital optimization with the density matrix renormalization group method in the active space

Dominika Zgid and Marcel Nooijen

J. Chem. Phys. 128, 144116 (2008) (11 pages)

Online Publication Date: 11 April 2008

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We present the density matrix renormalization group self-consistent field (DMRG-SCF) approach that is analogous to the complete active space self-consisted field (CASSCF) method but instead of using for the description of the active space the full configuration interaction (FCI) method, the DMRG-SCF uses the density matrix renormalization group (DMRG) method. The DMRG-SCF approach, similarly to CASSCF, properly describes the multiconfigurational character of the wave function but avoids the exponential scaling of the FCI method and replaces it with a polynomial scaling. Hence, calculations for a larger number of orbitals and electrons in the active space are possible since the DMRG method provides an efficient tool to automatically select from the full Hilbert space the many-body contracted basis states that are the most important for the description of the wave function.
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31.15.E-, 31.15.xr, 31.15.am

Orbital optimization in the density matrix renormalization group, with applications to polyenes and beta-carotene

Debashree Ghosh, Johannes Hachmann, Takeshi Yanai, and Garnet Kin-Lic Chan

J. Chem. Phys. 128, 144117 (2008) (14 pages)

Online Publication Date: 11 April 2008

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In previous work we have shown that the density matrix renormalization group (DMRG) enables near-exact calculations in active spaces much larger than are possible with traditional complete active space algorithms. Here, we implement orbital optimization with the DMRG to further allow the self-consistent improvement of the active orbitals, as is done in the complete active space self-consistent field (CASSCF) method. We use our resulting DMRG-CASSCF method to study the low-lying excited states of the all-trans polyenes up to C24H26 as well as beta-carotene, correlating with near-exact accuracy the optimized complete pi-valence space with up to 24 active electrons and orbitals, and analyze our results in the light of the recent discovery from resonance Raman experiments of new optically dark states in the spectrum.
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31.15.xr, 33.80.Rv

Partially linearized, fully size-extensive, and reduced multireference coupled-cluster methods. I. Formalism and mutual relationship

Xiangzhu Li and Josef Paldus

J. Chem. Phys. 128, 144118 (2008) (11 pages)

Online Publication Date: 11 April 2008

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We describe a fully size-extensive alternative of the reduced multireference (RMR) coupled-cluster (CC) method with singles (S) and doubles (D) that generates a subset of higher-than-pair cluster amplitudes, using linearized CC equations from the full CC chain, projected onto the corresponding higher-than-doubly excited configurations. This approach is referred to as partially linearized (pl) MR CCSD method and characterized by the acronym plMR CCSD. In contrast to a similar CCSDT-1 method [Y. S. Lee et al., J. Chem. Phys. 81, 5906 (1984)] this approach also considers higher than triples (currently up to hexuples), while focusing only on a small subset of such amplitudes, referred to as the primary ones. These amplitudes are selected using similar criteria as in RMR CCSD. An extension considering secondary triples via the standard (T)-type corrections, resulting in the plMR CCSD(T) method, is also considered. The relationship of RMR and plMR CCSD and CCSD(T) approaches is discussed, and their performance and characteristics are the subject of the subsequent Part II of this paper.
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31.15.bw

Partially linearized, fully size-extensive, and reduced multireference coupled-cluster methods. II. Applications and performance

Xiangzhu Li and Josef Paldus

J. Chem. Phys. 128, 144119 (2008) (13 pages)

Online Publication Date: 11 April 2008

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The partially linearized (pl), fully size-extensive multireference (MR) coupled-cluster (CC) method, fully accounting for singles (S) and doubles (D) and approximately for a subset of primary higher than doubles, referred to as plMR CCSD, as well as its plMR CCSD(T) version corrected for secondary triples, as described in Part I of this paper [X. Li and J. Paldus, J. Chem. Phys. 128, 144118 (2008)], are applied to the problem of bond breaking in the HF, F2, H2O, and N2 molecules, as well as to the H4 model, using basis sets of a DZ or a cc-pVDZ quality that enable a comparison with the full configuration interaction (FCI) exact energies for a given ab initio model. A comparison of the performance of the plMR CCSD/CCSD(T) approaches with those of the reduced MR (RMR) CCSD/CCSD(T) methods, as well as with the standard single reference (SR) CCSD and CCSD(T) methods, is made in each case. For the H4 model and N2 we also compare our results with the completely renormalized (CR) CC(2,3) method [P. Piecuch and M. Wloch, J. Chem. Phys. 123, 224105 (2005)]. An important role of a proper choice of the model space for the MR-type methods is also addressed. The advantages and shortcomings of all these methods are pointed out and discussed, as well as their size-extensivity characteristics, in which case we distinguish supersystems involving noninteracting SR and MR subsystems from those involving only MR-type subsystems. Although the plMR-type approaches render fully size-extensive results, while the RMR CCSD may slightly violate this property, the latter method yields invariably superior results to the plMR CCSD ones and is more easy to apply in highly demanding cases, such as the triple-bond breaking in the nitrogen molecule.
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36.20.Hb, 31.15.A-

Adaptive biasing force method for scalar and vector free energy calculations

Eric Darve, David Rodríguez-Gómez, and Andrew Pohorille

J. Chem. Phys. 128, 144120 (2008) (13 pages)

Online Publication Date: 11 April 2008

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In free energy calculations based on thermodynamic integration, it is necessary to compute the derivatives of the free energy as a function of one (scalar case) or several (vector case) order parameters. We derive in a compact way a general formulation for evaluating these derivatives as the average of a mean force acting on the order parameters, which involves first derivatives with respect to both Cartesian coordinates and time. This is in contrast with the previously derived formulas, which require first and second derivatives of the order parameter with respect to Cartesian coordinates. As illustrated in a concrete example, the main advantage of this new formulation is the simplicity of its use, especially for complicated order parameters. It is also straightforward to implement in a molecular dynamics code, as can be seen from the pseudocode given at the end. We further discuss how the approach based on time derivatives can be combined with the adaptive biasing force method, an enhanced sampling technique that rapidly yields uniform sampling of the order parameters, and by doing so greatly improves the efficiency of free energy calculations. Using the backbone dihedral angles Phi and Psi in N-acetylalanyl-N[prime]-methylamide as a numerical example, we present a technique to reconstruct the free energy from its derivatives, a calculation that presents some difficulties in the vector case because of the statistical errors affecting the derivatives.
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05.70.Ce, 02.70.Ns

Hamiltonian replica exchange molecular dynamics using soft-core interactions

Jozef Hritz and Chris Oostenbrink

J. Chem. Phys. 128, 144121 (2008) (10 pages)

Online Publication Date: 14 April 2008

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To overcome the problem of insufficient conformational sampling within biomolecular simulations, we have developed a novel Hamiltonian replica exchange molecular dynamics (H-REMD) scheme that uses soft-core interactions between those parts of the system that contribute most to high energy barriers. The advantage of this approach over other H-REMD schemes is the possibility to use a relatively small number of replicas with locally larger differences between the individual Hamiltonians. Because soft-core potentials are almost the same as regular ones at longer distances, most of the interactions between atoms of perturbed parts will only be slightly changed. Rather, the strong repulsion between atoms that are close in space, which in many cases results in high energy barriers, is weakened within higher replicas of our proposed scheme. In addition to the soft-core interactions, we proposed to include multiple replicas using the same Hamiltonian/level of softness. We have tested the new protocol on the GTP and 8-Br-GTP molecules, which are known to have high energy barriers between the anti and syn conformation of the base with respect to the sugar moiety. During two 25  ns MD simulations of both systems the transition from the more stable to the less stable (but still experimentally observed) conformation is not seen at all. Also temperature REMD over 50 replicas for 1  ns did not show any transition at room temperature. On the other hand, more than 20 of such transitions are observed in H-REMD using six replicas (at three different Hamiltonians) during 6.8  ns per replica for GTP and 12 replicas (at six different Hamiltonians) during 8.7  ns per replica for 8-Br-GTP. The large increase in sampling efficiency was obtained from an optimized H-REMD scheme involving soft-core potentials, with multiple simulations using the same level of softness. The optimization of the scheme was performed by fast mimicking [J. Hritz and C. Oostenbrink, J. Chem. Phys. 127, 204104 (2007)].
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87.15.ap, 87.15.B-, 87.15.hg, 87.15.hp

Toward accurate thermochemical models for transition metals: G3Large basis sets for atoms Sc–Zn

Nicholas J. Mayhall, Krishnan Raghavachari, Paul C. Redfern, Larry A. Curtiss, and Vitaly Rassolov

J. Chem. Phys. 128, 144122 (2008) (9 pages)

Online Publication Date: 14 April 2008

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An augmented valence triple-zeta basis set, referred to as G3Large, is reported for the first-row transition metal elements Sc through Zn. The basis set is constructed in a manner similar to the G3Large basis set developed previously for other elements (H–Ar, K, Ca, Ga–Kr) and used as a key component in Gaussian-3 theory. It is based on a contraction of a set of 15s13p5d Gaussian primitives to 8s7p3d, and also includes sets of f and g polarization functions, diffuse spd functions, and core df polarization functions. The basis set is evaluated with triples-augmented coupled cluster [CCSD(T)] and Brueckner orbital [BD(T)] methods for a small test set involving energies of atoms, atomic ions, and diatomic hydrides. It performs well for the low-lying s-->d excitation energies of atoms, atomic ionization energies, and the dissociation energies of the diatomic hydrides. The Brueckner orbital-based BD(T) method performs substantially better than Hartree–Fock–based CCSD(T) for molecules such as NiH, where the starting unrestricted Hartree–Fock wavefunction suffers from a high degree of spin contamination. Comparison with available data for geometries of transition metal hydrides also shows good agreement. A smaller basis set without core polarization functions, G3MP2Large, is also defined.
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31.15.bw, 33.15.Ry, 31.15.xr, 32.10.Hq

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

Computed lifetimes of metastable states of the NO2+ dication

R. Baková, J. Fišer, T. Šedivcová-Uhlíková, and V. Špirko

J. Chem. Phys. 128, 144301 (2008) (7 pages)

Online Publication Date: 8 April 2008

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Based on the ab initio potential energy, spin-orbit coupling, electronic transition dipole moment, and radial nonadiabatic coupling functions, the energy level positions, lifetimes, and radiative transition probabilities (Einstein A coefficients) have been determined for the lowest electronic states of NO2+ using the log-amplitude-phase, stabilization, and complex-scaling methods. The calculated characteristics are in reasonable agreement to the available experimental data, thus, evidencing the reliability of the theoretical predictions for the characteristics unobserved to date. With the exception of the v<=2 vibrational states of the B  2Sigma+ electronic state, the calculated radiative lifetimes of the excited electronic states are longer than their predissociation lifetimes, hence, accounting for the failure of the attempts which have been made so far to observe any emission from the latter states.
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31.15.aj, 33.70.Ca, 33.15.Mt, 33.20.Tp, 33.80.Gj, 31.50.Df

Quantum dynamics study of the K+HF(v=0–2,j=0)-->KF+H reaction and comparison with quasiclassical trajectory results

Jordi Mayneris, Rodrigo Martínez, Jordi Hernando, Stephen K. Gray, and Miguel González

J. Chem. Phys. 128, 144302 (2008) (7 pages)

Online Publication Date: 8 April 2008

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Extensive quantum real wave packet calculations within the helicity decoupling approximation are used to analyze the influence of the HF vibrational excitation on the K+HF(v=0–2,j=0)-->KF+H reaction. Quantum reaction probabilities P and reaction cross sections sigma are compared with corresponding quasiclassical trajectory (QCT) results. Disregarding threshold regions for v=0 and 1 (v=2 has no threshold), both approaches lead to remarkably similar results, particularly for sigma, validating the use of the QCT method for this system. When moving from v=0 to v=1 there is a large increase in P and sigma, as expected for a late barrier system. For v=2 the reaction becomes exoergic and P[approximate]0.95 (with the exception of large total angular momenta where centrifugal barriers play a role). While substantial vibrational enhancement of the reactivity is thus seen, it is still quite less than that inferred from experimental data in the intermediate and high collision energy ranges. The origin of this discrepancy is unclear.
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82.30.Hk, 82.20.Pm, 82.20.Ej, 82.20.Fd

Excitation levels and magic numbers of small parahydrogen clusters (N<=40)

Rafael Guardiola and Jesús Navarro

J. Chem. Phys. 128, 144303 (2008) (7 pages)

Online Publication Date: 9 April 2008

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The excitation energies of parahydrogen clusters have been systematically calculated by the diffusion Monte Carlo technique in steps of 1  molecule from 3  to  40  molecules. These clusters possess a very rich spectra, with angular momentum excitations arriving up to L=13 for the heavier ones. No regular pattern can be guessed in terms of the angular momenta and the size of the cluster. Clusters with N=13 and 36 are characterized by a peak in the chemical potential and a large energy gap of the first excited level, which indicate the magical character of these clusters. From the calculated excitation energies, the partition function has been obtained, thus allowing for an estimate of thermal effects. An enhanced production is predicted for cluster sizes of N=13, 31, and 36, which is in agreement with the experiment.
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36.40.Mr, 33.80.Rv

Potential energy curve for isomerization of N2H2 and C2H4 using the improved virtual orbital multireference Møller–Plesset perturbation theory

Rajat K. Chaudhuri, Karl F. Freed, Sudip Chattopadhyay, and Uttam Sinha Mahapatra

J. Chem. Phys. 128, 144304 (2008) (10 pages)

Online Publication Date: 9 April 2008

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Multireference Møller–Plesset (MRMP) perturbation theory [K. Hirao, Chem. Phys. Lett. 190, 374 (1992)] is modified to use improved virtual orbitals (IVOs) and is applied to study ground state potential energy curves for isomerization and dissociation of the N2H2 and C2H4 molecules. In contrast to traditional MRMP or multistate multiconfiguration quasidegenerate perturbation theory where the reference functions are obtained from (often difficult to converge) state averaged multiconfiguration self-consistent field methods, our reference functions are represented in terms of computationally efficient IVOs. For convenience in comparisons with other methods, a first order complete active space configuration interaction (CASCI) calculation with the IVOs is followed by the use of the IVOs in MRMP to incorporate residual electron correlation effects. The potential energy curves calculated from the IVO-MRMP method are compared with computations using state-of-the-art coupled cluster singles and doubles (CCSD) methods and variants thereof to assess the efficacy of the IVO-MRMP scheme. The present study clearly demonstrates that unlike the CCSD and its variants, the IVO-MRMP approach provides smooth and reliable ground state potential energy curves for isomerization of these systems. Although the rigorously size-extensive completely renormalized CC theory with noniterative triples corrections (CR-CC(2,3)) likewise provides relatively smooth curves, the CR-CC(2,3) calculations overestimate the cis-trans barrier height for N2H2. The ground state spectroscopic constants predicted by the IVO-CASCI method agree well with experiment and with other highly correlated ab initio methods.
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82.30.Qt, 82.20.Kh, 82.30.Lp

Theoretical studies on the bonding and thermodynamic properties of GenSim (m+n=5) clusters: The precursors of germanium/silicon nanomaterials

Pawel Wielgus, Szczepan Roszak, D. Majumdar, Julia Saloni, and Jerzy Leszczynski

J. Chem. Phys. 128, 144305 (2008) (10 pages)

Online Publication Date: 10 April 2008

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Theoretical studies on the GenSim clusters have been carried out using advanced ab initio approaches. The lowest energy isomers were determined for the clusters with compositions n+m=2–5. All possible isomers arising due to permutations of Ge and Si atoms were investigated. The L-shaped structure for the trimers, tetragonal with diagonal bond for tetramers, and a trigonal bipyramid for pentamers represent the energy optimized ground state geometries. The bonding analyses revealed that the trimers and tetramers are stabilized through multicenter pi bonding. In pentamers, this stabilizing factor is eliminated due to the further cluster growth. The ionization of clusters does not change their geometrical characteristics. The agreement of the calculated ionization and atomization energies with those obtained from the mass spectrometric studies (through estimated appearance potential) validated the reported structures of the clusters. The bonding properties of these species are discussed using their molecular orbital characteristics and analysis of natural bond orbital population data.
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61.46.Bc, 65.80.+n, 73.22.-f, 71.15.-m

Observation of the 5p Rydberg states of sulfur difluoride radical by resonance-enhanced multiphoton ionization spectroscopy

Qun Zhang, Xiaoguo Zhou, Quanxin Li, Shuqin Yu, and Xingxiao Ma

J. Chem. Phys. 128, 144306 (2008) (5 pages)

Online Publication Date: 10 April 2008

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Sulfur difluoride radicals in their ground state have been produced by a “laser-free” pulsed dc discharge of the SF6/Ar gas mixtures in a supersonic molecular beam and detected by mass-selective resonance-enhanced multilphoton ionization (REMPI) spectroscopy in the wavelength range of 408–420  nm. Analyses of the (3+1) REMPI excitation spectrum have enabled identification of three hitherto unknown Rydberg states of this radical. Following the Rydberg state labeling in our previous work [see J. Phys. Chem. A 102, 7233 (1998)], these we label the K-tilde(5p1) [nu0-0=71  837  cm−1, omega<sub>1</sub><sup>[prime]</sup>(a1  sym  str)=915  cm−1], L-tilde(5p2) [nu0-0=72  134  cm−1, omega<sub>1</sub><sup>[prime]</sup>(a1  sym  str)=912  cm−1], and M-tilde(5p3) [nu0-0=72  336  cm−1, omega<sub>1</sub><sup>[prime]</sup>(a1  sym  str)=926  cm−1] Rydberg states, respectively. [Origins, relative to the lowest vibrational level of the X-tilde   1A1 ground state, and vibrational frequencies of the symmetric S–F stretching mode are suggested by the numbers in brackets.] Photofragmentation process of SF<sub>2</sub><sup>+</sup>-->SF++F that relates to the REMPI spectrum was discussed.
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33.80.Rv, 33.80.Eh, 33.15.Mt, 33.20.Tp, 33.80.Gj

Structures of MAu16− (M=Ag, Li, Na, and K): How far is the endohedral doping?

Wei Fa and Jinming Dong

J. Chem. Phys. 128, 144307 (2008) (4 pages)

Online Publication Date: 10 April 2008

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The structural and electronic properties of MAu16− (M=Ag, Li, Na, and K) have been studied by the scalar relativistic all-electron density-functional calculations, in which particular attention is paid to the stability of the endohedral Au16− cage doped by different dopant atoms. It is found that only the smaller atoms, such as Cu, Li, and Na, can be stably encapsulated in the Au16− cage, while the addition of the larger Ag or K atom prefers to locate in the surface or outside of the cage, which is inconsistent with the previous hypothesis that the Au16− cage could act as a container to hold an arbitrary heterometal atom. The stable endohedral Li@Au16− and Na@Au16− have a large energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital gap, indicating that they are chemically stable and may be used as potential building blocks for designing cluster-assembled materials.
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31.15.E-, 36.40.Cg, 36.40.Mr, 31.15.bw

Ab initio investigation of the electronic structure and bonding of BH, BH−, and HBBH molecules

Evangelos Miliordos and Aristides Mavridis

J. Chem. Phys. 128, 144308 (2008) (15 pages)

Online Publication Date: 11 April 2008

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By correlating all electrons and employing core-tuned correlation consistent basis sets of quintuple-zeta quality, we applied multireference and coupled-cluster methods to study 32 electronic states of the diatomic BH molecule, two bound states of BH−, and three states of the linear HBBH molecule. We have constructed full potential energy curves and profiles, reporting binding energies, geometries, spectroscopic parameters, dipole moments, and energy separations, whereas our numerical results are in excellent agreement with available experimental numbers. We are trying as well to interpret the binding modes of a large number of the examined states. 18 states of BH are of Rydberg character, with the BH− anion revealing similar structural characteristics to the isoelectronic CH species. The first three states of HBBH X-tilde   3Sigma<sub>g</sub><sup>-</sup>, ã  1Deltag, and b-tilde   1Sigma<sub>g</sub><sup>+</sup> diabatically correlate to two a  3Pi BH fragments, they are similar to the states b  3Sigma<sub>g</sub><sup>-</sup>, B  1Deltag, and B[prime]  1Sigma<sub>g</sub><sup>+</sup> of the isoelectronic molecule C2, however, their ordering follows that of the first three states of the O2 molecule.
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31.15.A-, 31.15.bw, 31.50.-x, 33.15.Ry, 33.15.Bh, 31.15.vn

An ab initio study based on a finite nucleus model for isotope fractionation in the U(III)–U(IV) exchange reaction system

Minori Abe, Tatsuya Suzuki, Yasuhiko Fujii, and Masahiko Hada

J. Chem. Phys. 128, 144309 (2008) (6 pages)

Online Publication Date: 11 April 2008

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Isotope fractionation in the U(III)–U(IV) reaction system was investigated by a series of atomic relativistic ab initio calculations using the multiconfigurational Dirac–Coulomb Hartree–Fock method. To evaluate the nuclear volume effect on the fractionation, the Fermi statistical distribution function was adopted for nuclear charge density. The isotope fractionation coefficient epsilon resulting from the nuclear volume difference was evaluated from the total electronic energies of U3+ and U4+, based on the theoretical equation proposed by Bigeleisen [J. Am. Chem. Soc. 118, 3676 (1996)]. The calculated fractionation coefficient epsilon in the present work for the isotopic pair 235U and 238U at 293  K is 0.0031, which is quite close to the experimentally observed value of 0.0027. Discussion is extended to the nuclear volume effects on isotopic fractionations in the Pu(III)–Pu(IV) and Eu(II)–Eu(III) exchange systems.
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32.10.Bi, 31.15.A-

The role of the excited electronic states in the C++H2O reaction

Jesús R. Flores and Adán B. González

J. Chem. Phys. 128, 144310 (2008) (11 pages)

Online Publication Date: 14 April 2008

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The electronic excited states of the [COH2]+ system have been studied in order to establish their role in the dynamics of the C++H2O-->[COH]++H reaction, which is a prototypical ion-molecule reaction. The most relevant minima and saddle points of the lowest excited state have been determined and energy profiles for the lowest excited doublet and quartet electronic states have been computed along the fragmentation and isomerization coordinates. Also, nonadiabatic coupling strengths between the ground and the first excited state have been computed where they can be large. Our analysis suggests that the first excited state could play an important role in the generation of the formyl isomer, which has been detected in crossed beam experiments [D. M. Sonnenfroh et al., J. Chem. Phys. 83, 3985 (1985)], but could not be explained in quasiclassical trajectory computations [Y. Ishikawa et al., Chem. Phys. Lett. 370, 490 (2003); J. R. Flores, J. Chem. Phys. 125, 164309 (2006)].
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34.50.Gb, 33.80.Rv, 82.30.Qt, 82.50.-m

Recoil excitation of vibrational structure in the carbon 1s photoelectron spectrum of CF4

T. Darrah Thomas, Edwin Kukk, Rami Sankari, Hironobu Fukuzawa, Georg Prümper, Kiyoshi Ueda, Ralph Püttner, James Harries, Yusuke Tamenori, Takahiro Tanaka, Masamitsu Hoshino, and Hiroshi Tanaka

J. Chem. Phys. 128, 144311 (2008) (10 pages)

Online Publication Date: 14 April 2008

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The carbon 1s photoelectron spectrum of CF4 measured at photon energies from 330  to  1500  eV shows significant contributions from nonsymmetric vibrational modes. These increase linearly as the photon energy increases. The excitation of these modes, which is not predicted in the usual Franck–Condon point of view, arises from the recoil momentum imparted to the carbon atom in the ionization process. A theory is presented for quantitative prediction of the recoil effect; the predictions of this theory are in agreement to the measurements. The experiments also yield the vibrational frequencies of the symmetric and asymmetric stretching modes in core-ionized CF4, the change in CF bond length upon ionization, −0.61  pm, and the Lorentzian linewidth of the carbon 1s hole, 67  meV.
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33.15.Mt, 33.20.Tp, 33.60.+q, 33.80.Eh, 33.70.Ca, 31.15.-p

The permanent electric dipole moment of calcium monodeuteride

Jinhai Chen and Timothy C. Steimle

J. Chem. Phys. 128, 144312 (2008) (6 pages)

Online Publication Date: 14 April 2008

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The sub-Doppler laser induced fluorescence spectra of numerous branch features in the B  2Sigma+−X  2Sigma+(0,0) band of calcium monodeuteride were recorded field-free and in the presence of a static electric field of up to 7  kV/cm. The field-free spectra were analyzed to produce an improved set of fine structure parameters for the B  2Sigma+(v=0) state. The observed electric field induced splittings and shifts were analyzed to produce permanent electric dipole moments of 2.57(3) and 2.51(3)  D for B  2Sigma+(v=0) and X  2Sigma+(v=0) states, respectively. The permanent electric dipole moment for the X  2Sigma+(v=0) state of CaH is estimated to be 2.53(3)  D.
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33.50.Dq, 33.15.Pw, 33.15.Mt, 33.20.Tp, 33.80.Rv, 33.70.Jg

The photodissociation of the water dimer in the A-tilde band: A twelve-dimensional quasiclassical study

G. Avila, G. J. Kroes, and M. C. van Hemert

J. Chem. Phys. 128, 144313 (2008) (21 pages)

Online Publication Date: 14 April 2008

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The quasiclassical absorption spectrum of the water dimer in the A-tilde band was calculated taking into account motion in all degrees of freedom of the system. The ab initio excited state potentials employed were interpolated by the modified Shepard interpolation method using QMRCI energies and state-averaged MCSCF gradients and Hessians. The ground state vibrational wavefunction was variationally calculated using an adiabatic separation between the high and low frequency normal modes of the system. The calculated spectrum of water dimer shows a clear blueshift with respect to the monomer, but also a small red tail, in agreement with the prediction by Harvey et al. [J. Chem. Phys. 109, 8747 (1998)]. Previous three-dimensional model studies of the photodissociation of the water dimer by Valenzano et al. [J. Chem. Phys. 123, 034303 (2005)] did not show this red tail. A thorough analysis of the dependence of the spectrum on the modes coupled explicitly in the calculation of the spectrum shows that the red tail is due to coupling between the intramolecular stretch vibrations on different monomers.
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33.80.Gj, 31.15.A-, 31.15.xr, 33.15.Mt, 33.20.Tp, 33.70.Jg

Prediction of metastable metal-rare gas fluorides: FMRgF (M=Be and Mg; Rg=Ar, Kr and Xe)

T. Jayasekharan and T. K. Ghanty

J. Chem. Phys. 128, 144314 (2008) (10 pages)

Online Publication Date: 14 April 2008

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The structure, stability, charge redistribution, bonding, and harmonic vibrational frequencies of rare gas containing group II-A fluorides with the general formula FMRgF (where M=Be and Mg; Rg=Ar, Kr, and Xe) have been investigated using second order Møller–Plesset perturbation theory, density functional theory, and coupled cluster theory [CCSD(T)] methods. The species, FMRgF show a quasilinear structure at the minima and a bent structure at the transition state. The predicted species are unstable with respect to the two-body dissociation channel, leading to the global minima (MF2+Rg) on the singlet potential energy surface. However, with respect to other two-body dissociation channel (FM+RgF), they are found to be stable and have high positive energies on the same surface. The computed binding energy for the two-body dissociation channels are 94.0, 164.7, and 199.7  kJ  mol−1 for FBeArF, FBeKrF, FBeXeF, respectively, at CCSD(T) method. The corresponding energy values are 83.4, 130.7, and 180.1  kJ  mol−1 for FMgArF, FMgKrF, and FMgXeF, respectively, at the same level of theory. With respect to the three-body dissociation (FM+Rg+F) channel as well as dissociation into atomic constituent, they are also found to be stable and have high positive energies. The dissociation of the predicted species typically proceeds via MRgF bending mode at the transition state. The computed barrier heights for the transition states are 11.4, 32.2, and 57.6  kJ  mol−1 for FBeArF, FBeKrF, and FBeXeF, respectively, at the CCSD(T) method. The corresponding barrier heights for the Mg containing species are 2.1, 9.2, and 32.1  kJ  mol−1 along the series Ar[Single Bond]Kr[Single Bond]Xe, respectively. The M[Single Bond]Rg bond energies of the FMRgF species is significantly higher than the corresponding bond energies of the M+[Single Bond]Rg species (~53 and ~15  kJ  mol−1 for Be+[Single Bond]Ar and Mg+[Single Bond]Ar, respectively). The computed energy diagram as well as the geometrical parameters along with the AIM results suggest that the species are metastable with partial covalent character in the M[Single Bond]Rg bonding. Thus, it may be possible to prepare and to characterize these species using low temperature matrix isolation technique.
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33.20.Tp, 33.15.Mt, 31.15.bw, 31.15.E-, 33.15.Bh, 31.50.-x

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

A hybrid explicit/implicit solvation method for first-principle molecular dynamics simulations

Giuseppe Brancato, Nadia Rega, and Vincenzo Barone

J. Chem. Phys. 128, 144501 (2008) (10 pages)

Online Publication Date: 9 April 2008

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In this work, we present a hybrid explicit/implicit solvation model, well suited for first-principles molecular dynamics simulations of solute-solvent systems. An effective procedure is presented that allows to reliably model a solute with a few explicit solvation shells, ensuring solvent bulk behavior at the boundary with the continuum. Such an approach is integrated with high-level ab initio methods using localized basis functions to perform first-principles or mixed quantum mechanics/molecular mechanics simulations within the extended-Lagrangian formalism. A careful validation of the model along with illustrative applications to solutions of acetone and glycine radical are presented, considering two solvents of different polarity, namely, water and chloroform. Results show that the present model describes dynamical and solvent effects with an accuracy at least comparable to that of conventional approaches based on periodic boundary conditions.
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61.20.Ja, 82.30.-b

Proton transfer in a polar solvent from ring polymer reaction rate theory

Rosana Collepardo-Guevara, Ian R. Craig, and David E. Manolopoulos

J. Chem. Phys. 128, 144502 (2008) (13 pages)

Online Publication Date: 9 April 2008

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We have used the ring polymer molecular dynamics method to study the Azzouz–Borgis model for proton transfer between phenol (AH) and trimethylamine (B) in liquid methyl chloride. When the A–H distance is used as the reaction coordinate, the ring polymer trajectories are found to exhibit multiple recrossings of the transition state dividing surface and to give a rate coefficient that is smaller than the quantum transition state theory value by an order of magnitude. This is to be expected on kinematic grounds for a heavy-light-heavy reaction when the light atom transfer coordinate is used as the reaction coordinate, and it clearly precludes the use of transition state theory with this reaction coordinate. As has been shown previously for this problem, a solvent polarization coordinate defined in terms of the expectation value of the proton transfer distance in the ground adiabatic quantum state provides a better reaction coordinate with less recrossing. These results are discussed in light of the wide body of earlier theoretical work on the Azzouz–Borgis model and the considerable range of previously reported values for its proton and deuteron transfer rate coefficients.
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82.20.Db, 82.20.Pm, 82.30.Hk

Nature of metal–nonmetal transition in metal–ammonia solutions. II. From uniform metallic state to inhomogeneous electronic microstructure

Gennady N. Chuev and Pascal Quémerais

J. Chem. Phys. 128, 144503 (2008) (12 pages)

Online Publication Date: 10 April 2008

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Applying semianalytical models of nonideal plasma, we evaluate the behavior of the metallic phase in metal–ammonia solutions (MAS). This behavior is mainly controlled by the degenerate electron gas, which remains stable down to 5 MPM due to high solvent polarizability and strong dielectric screening of solvated ions. Comparing the behavior of the metallic state with those of localized solvated electrons, we have estimated the miscibility gap Deltan for various alkali metals and found Deltan(Na)>Deltan(K). It is rather narrow in Rb−NH3 and does not occur in Cs−NH3 solutions, which is in full agreement with the experiments. The case of Li is discussed separately. The difference calculated in the excess free energies of the metallic and nonmetallic phases is in the order of kBT, yielding a thermally fluctuating mixed state at intermediate metal concentrations. It results in a continuous metal–nonmetal (MNM) transition above the consolute point Tc and a phase separation below Tc. We propose a criterion for the MNM transition which may be attributed to the line of the maximum of compressibility above Tc. This line crosses the spinodal one at the critical temperature. Finally, we assert that a new electronic phase similar to microemulsion should also arise between the spinodal and the binodal lines.
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71.30.+h, 64.75.-g, 65.40.G-

Theoretical and numerical study of the phase diagram of patchy colloids: Ordered and disordered patch arrangements

Emanuela Bianchi, Piero Tartaglia, Emanuela Zaccarelli, and Francesco Sciortino

J. Chem. Phys. 128, 144504 (2008) (10 pages)

Online Publication Date: 10 April 2008

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We report theoretical and numerical evaluations of the phase diagram for a model of patchy particles. Specifically, we study hard spheres whose surface is decorated by a small number f of identical sites (“sticky spots”) interacting via a short-ranged square-well attraction. We theoretically evaluate, solving the Wertheim theory, the location of the critical point and the gas-liquid coexistence line for several values of f and compare them to the results of Gibbs and grand canonical Monte Carlo simulations. We study both ordered and disordered arrangements of the sites on the hard-sphere surface and confirm that patchiness has a strong effect on the phase diagram: the gas-liquid coexistence region in the temperature-density plane is significantly reduced as f decreases. We also theoretically evaluate the locus of specific heat maxima and the percolation line.
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82.70.Dd, 61.20.Ja

Thermodynamics and dynamics of a monoatomic glass former. Constant pressure and constant volume behavior

Vitaliy Kapko, Dmitry V. Matyushov, and C. Austen Angell

J. Chem. Phys. 128, 144505 (2008) (12 pages)

Online Publication Date: 10 April 2008

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We report constant-volume and constant-pressure simulations of the thermodynamic and dynamic properties of the low-temperature liquid and crystalline phases of the modified Stillinger–Weber (SW) model. We have found an approximately linear temperature increase of the effective Gaussian width of the distribution of inherent structures. This effect comes from non-Gaussianity of the landscape and is consistent with the predictions of the Gaussian excitations model representing the thermodynamics of the configurational manifold as an ensemble of excitations, each carrying an excitation entropy. The SW model provides us with both the configurational and excess entropies, with the difference mostly attributed to vibrational anharmonicity. We therefore can address the distinction between the excess thermodynamic quantities, often used to interpret experiments, and configurational thermodynamics used to describe the dynamics in the Adam–Gibbs (AG) equation. However we are limited computationally to work at temperatures above the “crossover” temperature at which the breakdown in the Adam–Gibbs relation has been identified in laboratory studies. We find a new break in the slope of the constant pressure AG plot (in the same sense but at much higher temperature than with laboratory data) when the excess entropy is used in the AG equation. This break, which we associate with anharmonic vibrational effects, is not seen when the configurational entropy is used. The simulation diffusivity data are equally well fitted by the AG equation and by a new equation, derived within the Gaussian excitations model, that emphasizes enthalpy over entropy as the thermodynamic control variable for transport in viscous liquids. We show that the modified SW model has close links to the behavior observed for bulk metallic glasses, both in its diffusional and in its thermodynamic properties.
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65.60.+a, 61.43.Fs, 63.50.Lm, 66.30.hh

Optically controlled resonance energy transfer: Mechanism and configuration for all-optical switching

David S. Bradshaw and David L. Andrews

J. Chem. Phys. 128, 144506 (2008) (11 pages)

Online Publication Date: 10 April 2008

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In a molecular system of energy donors and acceptors, resonance energy transfer is the primary mechanism by means of which electronic energy is redistributed between molecules, following the excitation of a donor. Given a suitable geometric configuration it is possible to completely inhibit this energy transfer in such a way that it can only be activated by application of an off-resonant laser beam: this is the principle of optically controlled resonance energy transfer, the basis for an all-optical switch. This paper begins with an investigation of optically controlled energy transfer between a single donor and acceptor molecule, identifying the symmetry and structural constraints and analyzing in detail the dependence on molecular energy level positioning. Spatially correlated donor and acceptor arrays with linear, square, and hexagonally structured arrangements are then assessed as potential configurations for all-optical switching. Built on quantum electrodynamical principles the concept of transfer fidelity, a parameter quantifying the efficiency of energy transportation, is introduced and defined. Results are explored by employing numerical simulations and graphical analysis. Finally, a discussion focuses on the advantages of such energy transfer based processes over all-optical switching of other proposed forms.
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33.80.-b, 34.70.+e

Vibrational dynamics and structural investigation of 2,2[prime]-dipyridylketone using Raman, IR and UV-visible spectroscopy aided by ab initio and density functional theory calculation

Pinaky Sett, Tumpa Mishra, Joydeep Chowdhury, Manas Ghosh, Subrato Chattopadhyay, Susil Kumar Sarkar, and Prabal Kumar Mallick

J. Chem. Phys. 128, 144507 (2008) (13 pages)

Online Publication Date: 14 April 2008

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Detailed investigation on the vibrational and electronic spectra has been carried out in order to study various properties of 2,2[prime]-dipyridylketone molecule in its ground and excited electronic states. To get insight into the structural and symmetry features of the molecule, Raman excitation profiles of several normal modes have been analyzed. The polarized Raman spectra in different environments along with their IR counterpart have been critically surveyed and different normal modes have been assigned. The knowledge in regard to the positions of different excited electronic states has been acquired from the study of electronic absorption spectra. All the experimental observations have been substantiated and corroborated theoretically by the quantum chemical calculation. Possibility of exciton splitting of the 1La band has been explored both from theoretical and experimental points of view.
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33.20.Tp, 33.20.Fb, 33.20.Lg, 33.20.Kf, 33.15.Bh, 31.15.A-

A mode-coupling theory treatment of the transport coefficients of the Lennard–Jones fluid

S. A. Egorov

J. Chem. Phys. 128, 144508 (2008) (7 pages)

Online Publication Date: 14 April 2008

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We apply mode-coupling theory to study shear viscosity and self-diffusion coefficient of the Lennard–Jones fluid throughout the entire fluid region of the phase diagram. Theoretical results are compared with the extensive simulation data and good agreement is found. In addition, theory is compared to the experimental data on the transport coefficients of inert gas fluids.
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66.20.Cy, 66.10.C-, 61.20.Ja, 61.20.Gy

Scaling law of stable single cells in density fingering of chemical fronts

Tamara Tóth, Dezsö Horváth, and Ágota Tóth

J. Chem. Phys. 128, 144509 (2008) (4 pages)

Online Publication Date: 14 April 2008

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See Also: Erratum

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Stable single fingers evolving in a thin layer of hydrodynamically unstable reactive solution are investigated in moderately wide Hele–Shaw cells. The mixing length associated with the final pattern is shown to be proportional to the width of the container. The scaling law, which is best illustrated by the overlay of temporal average front profiles, is demonstrated for two chemical compositions and boundaries of different thermal conductances. The observed single finger is found to be independent of the orientation of the reaction vessel for a wide range of tilt angles.
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82.30.Cf, 82.65.+r, 82.20.Hf, 47.15.gp

Polarized pump-probe measurements of electronic motion via a conical intersection

Darcie A. Farrow, Wei Qian, Eric R. Smith, Allison A. Ferro, and David M. Jonas

J. Chem. Phys. 128, 144510 (2008) (22 pages)

Online Publication Date: 14 April 2008

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Polarized femtosecond pump-probe spectroscopy is used to observe electronic wavepacket motion for vibrational wavepackets centered on a conical intersection. After excitation of a doubly degenerate electronic state in a square symmetric silicon naphthalocyanine molecule, electronic motions cause a ~100  fs drop in the polarization anisotropy that can be quantitatively predicted from vibrational quantum beat modulations of the pump-probe signal. Vibrational symmetries are determined from the polarization anisotropy of the vibrational quantum beats. The polarization anisotropy of the totally symmetric vibrational quantum beats shows that the electronic wavepackets equilibrate via the conical intersection within ~200  fs. The relationship used to predict the initial electronic polarization anisotropy decay from the asymmetric vibrational quantum beat amplitudes indicates that the initial width of the vibrational wavepacket determines the initial speed of electronic wavepacket motion. For chemically reactive conical intersections, which can have 1000 times greater stabilization energies than the one observed here, the same theory predicts electronic equilibration within 2  fs. Such electronic movements would be the fastest known chemical processes.
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33.15.Mt, 33.20.Tp, 33.80.Rv

Test of the consistency of various linearized semiclassical initial value time correlation functions in application to inelastic neutron scattering from liquid para-hydrogen

Jian Liu and William H. Miller

J. Chem. Phys. 128, 144511 (2008) (15 pages)

Online Publication Date: 14 April 2008

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The linearized approximation to the semiclassical initial value representation (LSC-IVR) is used to calculate time correlation functions relevant to the incoherent dynamic structure factor for inelastic neutron scattering from liquid para-hydrogen at 14 K. Various time correlations functions were used which, if evaluated exactly, would give identical results, but they do not because the LSC-IVR is approximate. Some of the correlation functions involve only linear operators, and others involve nonlinear operators. The consistency of the results obtained with the various time correlation functions thus provides a useful test of the accuracy of the LSC-IVR approximation and its ability to treat correlation functions involving both linear and nonlinear operators in realistic anharmonic systems. The good agreement of the results obtained from different correlation functions, their excellent behavior in the spectral moment tests based on the exact moment constraints, and their semiquantitative agreement with the inelastic neutron scattering experimental data all suggest that the LSC-IVR is indeed a good short-time approximation for quantum mechanical correlation functions.
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61.25.-f, 61.05.fg, 61.20.Gy

Thermal history effects and methyl tunneling dynamics in a supramolecular complex of calixarene and para-xylene

K. S. Panesar, A. J. Horsewill, F. Cuda, M. Carravetta, S. Mamone, A. Danquigny, M. C. Grossel, and M. H. Levitt

J. Chem. Phys. 128, 144512 (2008) (8 pages)

Online Publication Date: 14 April 2008

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The low-temperature structure and dynamics of guest molecules of p-xylene incorporated in the isopropyl-calix[4] arene(2:1) p-xylene complex have been investigated by solid state nuclear magnetic resonance (NMR). Using one-dimensional 1H-decoupled 13C cross-polarization magic-angle-spinning (MAS) NMR and two-dimensional 1H–13C correlation spectroscopy, a full assignment of the 13C and 1H chemical shifts has been made. Using 1H NMR relaxometry, the effects of thermal history on the structure of the system have been investigated. Rapidly cooled samples have 1H spin-lattice relaxation times T1, which at low temperature (T<60  K) are typically two orders of magnitude faster than those observed in annealed samples which have been cooled slowly over many hours. In both forms, the low-temperature relaxation is driven by the dynamics of the weakly hindered methyl rotors of the p-xylene guest. The substantial difference in T1 is attributed in the rapidly cooled sample to disorder in the structure of the complex leading to a wide distribution of correlation times and methyl barrier heights. A comparison of the linewidths and splittings in the high resolution 13C MAS spectra of the two forms provides structural insight into the nature of the disorder. Using 1H field-cycling NMR relaxometry, the methyl dynamics of the p-xylene guest in the annealed sample have been fully characterized. The B-field dependence of the 1H T1 maps out the spectral density from which the correlation times are directly measured. The methyl barrier heights are determined from an analysis of the temperature dependence.
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76.60.Cq, 76.60.Es

Surfaces, Interfaces, and Materials

Combining density functional theory and cluster expansion methods to predict H2 permeance through Pd-based binary alloy membranes

Lymarie Semidey-Flecha and David S. Sholl

J. Chem. Phys. 128, 144701 (2008) (10 pages)

Online Publication Date: 8 April 2008

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First-principles calculations offer a useful complement to experimental approaches for characterizing hydrogen permeance through dense metal membranes. A challenge in applying these methods to disordered alloys is to make quantitative predictions for the net solubility and diffusivity of interstitial H based on the spatially local information that can be obtained from first-principles calculations. In this study, we used a combination of density functional theory calculations and a cluster expansion method to describe interstitial H in alloys of composition Pd96M4, where M=Ag, Cu, and Rh. The cluster expansion approach highlights the shortcomings of simple lattice models that have been used in the past to study similar systems. We use Sieverts' law to calculate H solubility and a kinetic Monte Carlo scheme to find the diffusivity of H in PdAg, PdCu, and PdRh alloys at a temperature range of 400<=T<=1200  K. From these results, we are able to predict the permeability of hydrogen through membranes made from these Pd-based binary alloys.
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64.75.Bc, 61.72.jj, 66.30.Lw, 89.30.Aa

New algorithm in the basin hopping Monte Carlo to find the global minimum structure of unary and binary metallic nanoclusters

Hyoung Gyu Kim, Si Kyung Choi, and Hyuck Mo Lee

J. Chem. Phys. 128, 144702 (2008) (4 pages)

Online Publication Date: 9 April 2008

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The basin-hopping Monte Carlo algorithm was modified to more effectively determine a global minimum structure in pure and binary metallic nanoclusters. For a pure metallic Ag55 nanocluster, the newly developed quadratic basin-hopping Monte Carlo algorithm is 3.8 times more efficient than the standard basin-hopping Monte Carlo algorithm. For a bimetallic Ag42Pd13 nanocluster, the new algorithm succeeds in finding the global minimum structure by 18.3% even though the standard basin-hopping Monte Carlo algorithm fails to achieve it.
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61.46.Bc, 61.43.Bn, 36.40.Mr

The effect of the surface of SnO2 nanoribbons on their luminescence using x-ray absorption and luminescence spectroscopy

X. T. Zhou, J. G. Zhou, M. W. Murphy, J. Y. P. Ko, F. Heigl, T. Regier, R. I. R. Blyth, and T. K. Sham

J. Chem. Phys. 128, 144703 (2008) (5 pages)

Online Publication Date: 9 April 2008

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X-ray excited optical luminescence (XEOL) and x-ray absorption near-edge structure in total electron, x-ray fluorescence, and photoluminescence yields at Sn M5,4-, O K-, and Sn K-edges have been used to study the luminescence from SnO2 nanoribbons. The effect of the surface on the luminescence from SnO2 nanoribbons was studied by preferential excitation of the ions in the near-surface region and at the normal lattice positions, respectively. No noticeable change of luminescence from SnO2 nanoribbons was observed if the Sn ions in the near-surface region were excited selectively, while the luminescence intensity changes markedly when Sn or O ions at the normal lattice positions were excited across the corresponding edges. Based on the experimental results, we show that the luminescence from SnO2 nanoribbons is dominated by energy transfer from the excitation of the whole SnO2 lattice to the surface states. Surface site specificity is not observable due to its low concentration and weak absorption coefficient although the surface plays an important role in the emission as a luminescence center. The energy transfer and site specificity of the XEOL or the lack of the site specificity from a single-phase sample is discussed.
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78.55.Hx, 78.70.Dm, 78.70.En, 78.67.Bf, 78.20.Ci, 73.20.At

Hydrogen storage in pure and Li-doped carbon nanopores: Combined effects of concavity and doping

I. Cabria, M. J. López, and J. A. Alonso

J. Chem. Phys. 128, 144704 (2008) (8 pages)

Online Publication Date: 9 April 2008

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Density functional calculations are reported for the adsorption of molecular hydrogen on carbon nanopores. Two models for the pores have been considered: (i) The inner walls of (7,7) carbon nanotubes and (ii) the highly curved inner surface of nanotubes capped on one end. The effect of Li doping is investigated in all cases. The hydrogen physisorption energies increase due to the concavity effect inside the clean nanotubes and on the bottom of the capped nanotubes. Li doping also enhances the physisorption energies. The sum of those two effects leads to an increase by a factor of almost 3 with respect to the physisorption in the outer wall of undoped nanotubes and in flat graphene. Application of a quantum-thermodynamical model to clean cylindrical pores of diameter 9.5  Å, the diameter of the (7,7) tube, indicates that cylindrical pores of this size can store enough hydrogen to reach the volumetric and gravimetric goals of the Department of Energy at 77  K and low pressures, although not at 300  K. The results are useful to explain the experiments on porous carbons. Optimizations of the pore size, concavity, and doping appear as promising alternatives for achieving the goals at room temperature.
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84.60.-h, 68.43.Mn, 61.43.Gt, 61.72.up

Self-assembled monolayer of alkanephosphoric acid on nanotextured Ti

Sylvain Clair, Fabio Variola, Mykola Kondratenko, Pawel Jedrzejowski, Antonio Nanci, Federico Rosei, and Dmitrii F. Perepichka

J. Chem. Phys. 128, 144705 (2008) (6 pages)

Online Publication Date: 9 April 2008

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Surface modification of titanium and its alloys is of great importance for their practical application as biomedical implants. We have studied and compared assembly of dodecylphosphoric acid on commercial polished and on nanostructured titanium disks. The latter were produced by chemical etching that created nanoscale pits of typical size of about 20  nm. Enhanced hydrophobicity and high molecular density were obtained after functionalization of the nanotextured substrate. Aging tests showed a lifetime of the organic films of about one month in phosphate buffer. The samples were characterized by means of infrared spectroscopy, contact angle measurements, ellipsometry, and atomic force and scanning tunneling microscopies.
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68.47.Pe, 68.35.bd, 81.40.Cd, 78.30.Jw, 81.65.Cf

Ion condensation on charged patterned surfaces

Yuri S. Velichko, Francisco J. Solis, and Monica Olvera de la Cruz

J. Chem. Phys. 128, 144706 (2008) (9 pages)

Online Publication Date: 10 April 2008

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We study ion condensation on a patterned surface with stripes of alternating charge. The competition between adsorbed ion-ion and adsorbed ion-surface interactions leads to the formation of different strongly correlated structures of condensed ions in the low-temperature limit (LTL). We consider two types of arrangements which have lowest energy in the LTL: (1) ions adsorbed onto the stripe center lines and (2) arrays of dipoles at the interfaces between charged domains. We determine the preferred arrangement as a function of surface charge density, the chemical potential of the ions in the surrounding medium, and the geometric parameters of the system. We determine the conditions for the appearance of more complex ionic patterns by considering simple perturbations of the stripe-centered and dipolar array structures.
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79.20.Rf, 68.43.-h, 82.60.-s

The structure and energetics of (GaAs)n, (GaAs)<sub>n</sub><sup>-</sup>, and (GaAs)<sub>n</sub><sup>+</sup> (n=2–15)

G. L. Gutsev, E. Johnson, M. D. Mochena, and C. W. Bauschlicher, Jr.

J. Chem. Phys. 128, 144707 (2008) (9 pages)

Online Publication Date: 14 April 2008

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Electronic and geometrical structures of neutral, negatively, and positively charged (GaAs)n clusters are computed using density functional theory with generalized gradient approximation. All-electron computations are performed on (GaAs)2–(GaAs)9 while effective core potentials (ECPs) are used for (GaAs)9–(GaAs)15. Calibration calculations on GaAs and (GaAs)9 species support the use of the ECP for the larger clusters. The ground-state geometries of (GaAs)<sub>n</sub><sup>-</sup> and/or (GaAs)<sub>n</sub><sup>+</sup> are different from the corresponding neutral ground-state geometry, except for n=7, 9, 12, 14, and 15, where the neutral and ions have similar structures. Beginning with n=6, all atoms are three coordinate, except for (GaAs)<sub>10</sub><sup>+</sup> and (GaAs)<sub>13</sub><sup>+</sup>. For the larger species, there is a competition between fullerenes built from hexagons and rhombi and geometrical configurations where Ga–Ga and As–As bonds are formed, which results in the formation of pentagons. As expected, the static polarizability varies in the order of anion>neutral>cation, but the values are rather similar for all three charge states. The thermodynamic stability for the loss of GaAs is reported.
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71.20.Nr, 71.15.Mb, 65.40.-b

Pressure effects on CrCl63− embedded in cubic Cs2NaMCl6 (M=Sc,Y) lattices: Study through periodic and cluster calculations

J. M. García-Lastra, M. Moreno, and M. T. Barriuso

J. Chem. Phys. 128, 144708 (2008) (11 pages)

Online Publication Date: 14 April 2008

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The structural, elastic, vibrational, and optical properties of cubic elpasolites Cs2NaMCl6 (M=Sc,Y) containing CrCl63− complexes have been investigated by means of both periodic and cluster calculations as a function of pressure in the framework of density functional theory. Aside from calculating the host lattice bulk modulus BH and the local modulus B1 associated with the CrCl63−, complex particular attention is paid to the pressure dependence of Huang–Rhys factors, Sa and Se (related to local a1g and eg modes), and the Stokes shift associated with the first electronic excited state 4T2g (t2g2eg) of CrCl63−. The present calculations provide a big difference between BH=231  kbars and B1=676  kbars derived for Cs2NaScCl6:Cr3+ at zero pressure which plays a key role for a right interpretation of pressure effects on vibration frequencies and optical parameters due to CrCl63−. The significant decrease of Huang–Rhys factors, Sa and Se, due to the pressure observed experimentally is well accounted for by the present work which supports that [partial-derivative]Sa/[partial-derivative]P is determined by the Grüneisen constant gammaa of the a1g local mode (whose frequency is nua) and the dependence of 10Dq on the metal-ligand distance. At the same time, the present results point out that the Stokes shift would be little pressure dependent in the range of 0–50  kbars. Accordingly the Ham effect in the 4T2g (t2g2eg) state of CrCl63− in the cubic elpasolites would also happen for a pressure up to 50  kbars but the spin-orbit constant would increase with respect to that at zero pressure. From the analysis carried out in this work it is also concluded that the figures dnua/dP=0.55  cm−1/kbar and dSa/dP=−7.2×10−3  kbar−1 extracted from the complex emission band of Cs2NaScCl6:Cr3+ are hardly compatible. This fact underlines the usefulness of ab initio calculations for helping in the analysis of complex experimental findings. Finally, as the CrCl63− unit is found to be to a good extent elastically decoupled from the rest of the elpasolite lattice, a model is shown to lead to an approximate relation between the pressure derivative of the local modulus and the Grüneisen constant gammaa.
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62.50.-p, 62.20.de, 63.70.+h, 78.20.Hp, 71.15.Mb

Characterization of enantiospecific chemisorption on chiral Cu surfaces vicinal to Cu(111) and Cu(100) using density functional theory

Bhawna Bhatia and David S. Sholl

J. Chem. Phys. 128, 144709 (2008) (9 pages)

Online Publication Date: 14 April 2008

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Surfaces of simple fcc metals such as Cu with nonzero and unequal Miller indices are intrinsically chiral. Density functional theory (DFT) calculations are a useful way to study the enantiospecific adsorption of small chiral molecules on these chiral metal surfaces. We report DFT calculations of seven chiral molecules on several structurally distinct chiral Cu surfaces. These surfaces include two surfaces with (111)-oriented terraces and one with (100)-oriented terraces. Calculations are also described on a surface that was modified to mimic the surface structures that typically appear on real metal surfaces following thermally driven fluctuations in step edges. Our results provide initial information on how variation in the surface structure of intrinsically chiral metal surfaces can affect the enantiospecific adsorption of small molecules on these surfaces.
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68.35.B-, 68.43.Fg

Cage and tube structures of medium-sized zinc oxide clusters (ZnO)n (n=24, 28, 36, and 48)

Baolin Wang, Xiaoqiu Wang, Guibin Chen, Shigeru Nagase, and Jijun Zhao

J. Chem. Phys. 128, 144710 (2008) (6 pages)

Online Publication Date: 14 April 2008

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Following our recent work which revealed that the lowest-energy structures of (ZnO)n (n=9–18) follow cage and tube structural growth patterns with stacks of small subunits of (ZnO)2 and (ZnO)3 [Wang et al., J. Phys. Chem. C 111, 4956 (2007)], we have extended the search for the most stable structures to some larger clusters, i.e., (ZnO)n (n=24, 28, 36, and 48) by using gradient-corrected density-functional theory (DFT). A number of starting configurations belonging to different structural motifs were generated from handmade constructions with chemical intuition and then optimized via DFT calculations. Within the size range studied, cage and tube structures were found to be the most preferred structural motifs for the (ZnO)n clusters.
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71.15.Mb, 73.22.-f, 61.46.Bc

Extracting maximum information from polarized surface vibrational spectra: Application to etched, H-terminated Si(110) surfaces

Ian T. Clark, Brandon S. Aldinger, Ankush Gupta, and Melissa A. Hines

J. Chem. Phys. 128, 144711 (2008) (9 pages)

Online Publication Date: 14 April 2008

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A general method to maximize the information extracted from polarized surface absorption spectra is developed and applied to the study of etched Si(110) surfaces. In essence, this technique transforms spectra from the experimental reference frame, which is defined by the direction of the surface electric field during irradiation by s- and p-polarized light, into a more appropriate Cartesian reference frame defined by the surface normal and the plane of incidence. If the Cartesian reference frame is aligned with high symmetry directions of the system, significant spectral simplification can result. This analysis relies on the well-known boundary conditions on interfacial electric fields and is independent of any adsorbate screening or the effective dielectric constant of the adsorbate layer. The validity of this analysis is demonstrated on the spectra of NH4F-etched, H-terminated Si(110). The transition dipole moments of the symmetric and antisymmetric Si[Single Bond]H stretch modes associated with flat terraces are polarized along the [110] and [001] directions, respectively. Two additional modes with transition dipoles polarized along the [001] and [1[overline 1]0] directions are assigned to defect species associated with microfaceting and other surface roughness. Data taken in two different experimental geometries are shown to be in excellent quantitative agreement, confirming the validity of the technique. Additionally, the measured adsorbate layer dielectric constant is in good agreement with previously reported values for hydrogen-terminated silicon surfaces.
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78.30.Am, 81.65.Cf, 68.35.B-, 68.47.Fg, 77.22.Ch

Polymers and Complex Systems

Conformational behavior of polymers adsorbed on nanotubes

Inna Gurevitch and Simcha Srebnik

J. Chem. Phys. 128, 144901 (2008) (8 pages)

Online Publication Date: 9 April 2008

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The importance of hydrophobic interactions in determining polymer adsorption and wrapping of carbon nanotubes is still under debate. In this work, we concentrate on the effect of short-ranged weakly attractive hydrophobic interactions between polymers and nanotubes (modeled as an infinitely long and smooth cylindrical surface), neglecting all other interactions apart for chain flexibility. Using coarse-grained Monte Carlo simulation of such simplified systems, we find that uniform adsorption and wrapping of the nanotube occur for all degrees of chain flexibility for tubes with sufficiently large outer radii. However, the adsorbed conformations depend on chain stiffness, ranging from randomly adsorbed conformations of the flexible chain to perfect helical or multihelical conformations (in the case of more concentrated solutions) of the rigid chains. Adsorption appears to occur in a sequential manner, wrapping the nanotube nearly one monomer at a time from the point of contact. Once adsorbed, the chains travel on the surface of the cylinder, retaining their helical conformations for the semiflexible and rigid chains. Our findings may provide additional insight to experimentally observed ordered polymer wrapping of carbon nanotubes.
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68.43.-h, 61.48.De

Multiparticle collision dynamics modeling of viscoelastic fluids

Yu-Guo Tao, Ingo O. Götze, and Gerhard Gompper

J. Chem. Phys. 128, 144902 (2008) (12 pages)

Online Publication Date: 9 April 2008

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In order to investigate the rheological properties of viscoelastic fluids by mesoscopic hydrodynamics methods, we develop a multiparticle collision (MPC) dynamics model for a fluid of harmonic dumbbells. The algorithm consists of alternating streaming and collision steps. The advantage of the harmonic interactions is that the integration of the equations of motion in the streaming step can be performed analytically. Therefore, the algorithm is computationally as efficient as the original MPC algorithm for Newtonian fluids. The collision step is the same as in the original MPC method. All particles are confined between two solid walls moving oppositely, so that both steady and oscillatory shear flows can be investigated. Attractive wall potentials are applied to obtain a nearly uniform density everywhere in the simulation box. We find that both in steady and oscillatory shear flows, a boundary layer develops near the wall, with a higher velocity gradient than in the bulk. The thickness of this layer is proportional to the average dumbbell size. We determine the zero-shear viscosities as a function of the spring constant of the dumbbells and the mean free path. For very high shear rates, a very weak “shear thickening” behavior is observed. Moreover, storage and loss moduli are calculated in oscillatory shear, which show that the viscoelastic properties at low and moderate frequencies are consistent with a Maxwell fluid behavior. We compare our results with a kinetic theory of dumbbells in solution, and generally find good agreement.
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47.57.Qk, 47.15.Cb, 47.20.-k

Dissipative particle dynamics simulation of depletion layer and polymer migration in micro- and nanochannels for dilute polymer solutions

Dmitry A. Fedosov, George Em Karniadakis, and Bruce Caswell

J. Chem. Phys. 128, 144903 (2008) (14 pages)

Online Publication Date: 14 April 2008

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The flows of dilute polymer solutions in micro- and nanoscale channels are of both fundamental and practical importance in variety of applications in which the channel gap is of the same order as the size of the suspended particles or macromolecules. In such systems depletion layers are observed near solid-fluid interfaces, even in equilibrium, and the imposition of flow results in further cross-stream migration of the particles. In this work we employ dissipative particle dynamics to study depletion and migration in dilute polymer solutions in channels several times larger than the radius of gyration (Rg) of bead-spring chains. We compare depletion layers for different chain models and levels of chain representation, solvent quality, and relative wall-solvent-polymer interactions. By suitable scaling the simulated depletion layers compare well with the asymptotic lattice theory solution of depletion near a repulsive wall. In Poiseuille flow, polymer migration across the streamlines increases with the Peclet and the Reynolds number until the center-of-mass distribution develops two symmetric off-center peaks which identify the preferred chain positions across the channel. These appear to be governed by the balance of wall-chain repulsive interactions and an off-center driving force of the type known as the Segre–Silberberg effect.
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47.60.Dx, 68.08.-p, 47.11.-j

Biological Molecules, Biopolymers, and Biological Systems

Normal mode partitioning of Langevin dynamics for biomolecules

Christopher R. Sweet, Paula Petrone, Vijay S. Pande, and Jesús A. Izaguirre

J. Chem. Phys. 128, 145101 (2008) (13 pages)

Online Publication Date: 8 April 2008

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We propose a novel normal mode multiple time stepping Langevin dynamics integrator called NML. The aim is to approximate the kinetics or thermodynamics of a biomolecule by a reduced model based on a normal mode decomposition of the dynamical space. Our basis set uses the eigenvectors of a mass reweighted Hessian matrix calculated with a biomolecular force field. This particular choice has the advantage of an ordering according to the eigenvalues, which have a physical meaning of being the square of the mode frequency. Low frequency eigenvalues correspond to more collective motions, whereas the highest frequency eigenvalues are the limiting factor for the stability of the integrator. In NML, the higher frequency modes are overdamped and relaxed near their energy minimum while respecting the subspace of low frequency dynamical modes. Our numerical results confirm that both sampling and rates are conserved for an implicitly solvated alanine dipeptide model, with only 30% of the modes propagated, when compared to the full model. For implicitly solvated systems, NML gives a twofold improvement in efficiency over plain Langevin dynamics for sampling a small 22 atom (alanine dipeptide) model and in excess of an order of magnitude for sampling an 882 atom (bovine pancreatic trypsin inhibitor) model, with good scaling with system size subject to the number of modes propagated. NML has been implemented in the open source software PROTOMOL.
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87.15.Cc, 87.15.ap

Protein dynamics from a NMR perspective: Networks of coupled rotators and fractional Brownian dynamics

Vania Calandrini, Daniel Abergel, and Gerald R. Kneller

J. Chem. Phys. 128, 145102 (2008) (8 pages)

Online Publication Date: 10 April 2008

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Nuclear magnetic resonance (NMR) has proven to be the most valuable tool for investigating internal dynamics of proteins. In this perspective, the interpretation of NMR relaxation data eventually relies on a model of the motions. In this article, we propose to compare two radically different approaches that aim at describing internal dynamics in proteins. It is shown that the correlation functions predicted by a network of coupled rotators can be interpreted in terms of a heuristic approach based on fractional Brownian dynamics for each of the vectors in the network. Our results are interpreted in terms of the probability distributions of relaxation modes in both processes, the median of which turns out to be the relevant quantity for the comparison of both models.
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87.14.E-, 87.15.H-, 87.64.kj

Approximating nonequilibrium processes using a collection of surrogate diffusion models

Christopher P. Calderon and Riccardo Chelli

J. Chem. Phys. 128, 145103 (2008) (10 pages)

Online Publication Date: 11 April 2008

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The surrogate process approximation (SPA) is applied to model the nonequilibrium dynamics of a reaction coordinate (RC) associated with the unfolding and refolding processes of a deca-alanine peptide at 300  K. The RC dynamics, which correspond to the evolution of the end-to-end distance of the polypeptide, are produced by steered molecular dynamics (SMD) simulations and approximated using overdamped diffusion models. We show that the collection of (estimated) SPA models contain structural information “orthogonal” to the RC monitored in this study. Functional data analysis ideas are used to correlate functions associated with the fitted SPA models with the work done on the system in SMD simulations. It is demonstrated that the shape of the nonequilibrium work distributions for the unfolding and refolding processes of deca-alanine can be predicted with functional data analysis ideas using a relatively small number of simulated SMD paths for calibrating the SPA diffusion models.
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82.37.Np, 36.20.Ey, 36.20.Hb

Efficient chain moves for Monte Carlo simulations of a wormlike DNA model: Excluded volume, supercoils, site juxtapositions, knots, and comparisons with random-flight and lattice models

Zhirong Liu and Hue Sun Chan

J. Chem. Phys. 128, 145104 (2008) (31 pages)

Online Publication Date: 11 April 2008

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See Also: Erratum

Show Abstract
We develop two classes of Monte Carlo moves for efficient sampling of wormlike DNA chains that can have significant degrees of supercoiling, a conformational feature that is key to many aspects of biological function including replication, transcription, and recombination. One class of moves entails reversing the coordinates of a segment of the chain along one, two, or three axes of an appropriately chosen local frame of reference. These transformations may be viewed as a generalization, to the continuum, of the Madras–Orlitsky–Shepp algorithm for cubic lattices. Another class of moves, termed T±2, allows for interconversions between chains with different lengths by adding or subtracting two beads (monomer units) to or from the chain. Length-changing moves are generally useful for conformational sampling with a given site juxtaposition, as has been shown in previous lattice studies. Here, the continuum T±2 moves are designed to enhance their acceptance rate in supercoiled conformations. We apply these moves to a wormlike model in which excluded volume is accounted for by a bond-bond repulsion term. The computed autocorrelation functions for the relaxation of bond length, bond angle, writhe, and branch number indicate that the new moves lead to significantly more efficient sampling than conventional bead displacements and crankshaft rotations. A close correspondence is found in the equilibrium ensemble between the map of writhe computed for pair of chain segments and the map of site juxtapositions or self-contacts. To evaluate the more coarse-grained freely jointed chain (random-flight) and cubic lattice models that are commonly used in DNA investigations, twisting (torsional) potentials are introduced into these models. Conformational properties for a given superhelical density sigma may then be sampled by computing the writhe and using White's formula to relate the degree of twisting to writhe and sigma. Extensive comparisons of contact patterns and knot probabilities of the more coarse-grained models with the wormlike model show that the behaviors of the random-flight model are similar to that of DNA molecules in a solution environment with high ionic strengths, whereas the behaviors of the cubic lattice model with excluded volume are akin to that of DNA molecules under low ionic strengths.
Show PACS
87.14.gk, 87.15.ak
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LETTERS TO THE EDITOR

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Comment on “Markovian approximation in a coarse-grained description of atomic systems” [J. Chem. Phys. 125, 204101 (2006)]

David Cubero

J. Chem. Phys. 128, 147101 (2008) (2 pages)

Online Publication Date: 10 April 2008

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The authors concluded that the coarse-graining dynamics of a one-dimensional chain of oscillators interacting through Lennard–Jones potentials is Markovian, in contrast with the situation observed for harmonic lattices. However, with the help of a novel equation that relates the correlation of forces and momenta, I show that this conclusion is drawn from an incorrect analysis of the simulation data.
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02.50.Ga, 61.20.Gy
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Response to “Comment on `Markovian approximation in a coarse-grained description of atomic systems' ” [J. Chem. Phys. 128, 147101 (2008)]

Carmen Hijón, Mar Serrano, and Pep Español

J. Chem. Phys. 128, 147102 (2008) (3 pages)

Online Publication Date: 10 April 2008

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We show within the Mori theory of projection operators that the Green-Kubo formula using microscopic rather than projected forces is only valid if the description is Markovian. Therefore, the only way to assess whether a description is Markovian is through examining the predictions of the theory under the Markovian assumption. Although, in principle, the blob description for a unidimensional chain is non-Markovian, in practice the Markovian approximation describes reasonably well the coarse dynamics of the chain.
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02.50.Ga

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Publisher's Note: “Reference interaction site model and molecular dynamics study of structure and thermodynamics of methanol” [J. Chem. Phys. 127, 224501 (2007)]

D. Costa, G. Munaó, F. Saija, and C. Caccamo

J. Chem. Phys. 128, 149901 (2008) (1 page)

Online Publication Date: 10 April 2008

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61.66.Hq, 65.40.G-, 99.10.Fg
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Publisher's Note: “Mean field kinetic theory for a lattice gas model of fluids confined in porous materials” [J. Chem. Phys. 128, 084701 (2008)]

Peter A. Monson

J. Chem. Phys. 128, 149902 (2008) (1 page)

Online Publication Date: 10 April 2008

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99.10.Fg
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Erratum: “In situ high-pressure x-ray diffraction study of H2O ice VII” [J. Chem. Phys. 128, 064510 (2008)]

Maddury Somayazulu, Jinfu Shu, Chang-sheng Zha, Alexander F. Goncharov, Oliver Tschauner, Ho-kwang Mao, and Russell J. Hemley

J. Chem. Phys. 128, 149903 (2008) (1 page)

Online Publication Date: 14 April 2008

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62.50.-p, 99.10.Cd

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