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28 Apr 2009

Volume 130, Issue 16, Articles (16xxxx)

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J. Chem. Phys. 130, 164901 (2009); http://dx.doi.org/10.1063/1.3119311 (10 pages)

Xiaofei Xu and Dapeng Cao
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Theory of competitive adsorption-nucleation in polypeptide-mediated biomineralization

M. Muthukumar

J. Chem. Phys. 130, 161101 (2009); http://dx.doi.org/10.1063/1.3126582 (5 pages) | Cited 1 time

Online Publication Date: 27 April 2009

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The process of biomineralization occurs in various natural organisms with astonishing ease by the interplay between polymers and mineralization but eludes a fundamental understanding. In addressing how specific polymers direct selection of mineral morphologies and their growth kinetics, we present a new model based on a competition between adsorption of polymers onto selective interfaces and nucleation growth of minerals. The model is couched in the context of zinc oxide, crystallized from solutions containing polypeptides, where systematic experimental data are available. Adsorption of the polymer onto certain crystallographic planes leads to poisoning of the surfaces, and as a result these surfaces are arrested from further growth. By this mechanism, originally disfavored growth sectors are promoted to grow by suppressing the initial faster growing sectors. Our theory predicts the relative growth rates of different sectors altered by selective adsorption of polymers. Theoretical prediction of the dependence of the aspect ratio on polypeptide concentration is in agreement with experimental results, providing credence to the applicability of adsorption-nucleation models to polymer-mediated biomineralization.
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87.15.N- Properties of solutions of macromolecules
87.15.K- Molecular interactions; membrane-protein interactions
81.10.Aj Theory and models of crystal growth; physics and chemistry of crystal growth, crystal morphology, and orientation
68.43.Mn Adsorption kinetics
61.66.Fn Inorganic compounds
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Net transport due to noise-induced internal reciprocating motion

Yurii A. Makhnovskii, Viktor M. Rozenbaum, Dah-Yen Yang, and Sheng Hsien Lin

J. Chem. Phys. 130, 164101 (2009); http://dx.doi.org/10.1063/1.3116790 (10 pages)

Online Publication Date: 22 April 2009

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We consider a system of two coupled Brownian particles fluctuating between two states. The fluctuations are produced by both equilibrium thermal and external nonthermal noise, the transition rates depending on the interparticle distance. An externally induced modulation of the transition rates acts on the internal degree of freedom (the interparticle distance) and generates reciprocating motion along this coordinate. The system moves unidirectionally due to rectification of the internal motion by asymmetric friction fluctuations and thus operates as a dimeric motor that converts input energy into net movement. The properties of the motor are primarily determined by the properties of the reciprocating engine, represented by the interparticle distance dynamics. Two main mechanisms are recognized by which the engine operates: energetic and informational. In the physically important cases where only one of the motion-inducing mechanisms is operative, exact solutions can be found for the model with linearly coupled particles. We focus on the informational mechanism, in which thermal noise is involved as a vital component and the reciprocating velocity exhibits a rich behavior as a function of the model parameters. An efficient rectification method for the reciprocating motion is also discussed.
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87.14.-g Biomolecules: types
05.40.Ca Noise
87.10.-e General theory and mathematical aspects
87.16.-b Subcellular structure and processes
05.40.Jc Brownian motion

Coverage of dynamic correlation effects by density functional theory functionals: Density-based analysis for neon

K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski

J. Chem. Phys. 130, 164102 (2009); http://dx.doi.org/10.1063/1.3116157 (9 pages) | Cited 3 times

Online Publication Date: 22 April 2009

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The problem of linking the dynamic electron correlation effects defined in traditional ab initio methods [or wave function theories (WFTs)] with the structure of the individual density functional theory (DFT) exchange and correlation functionals has been analyzed for the Ne atom, for which nondynamic correlation effects play a negligible role. A density-based approach directly hinged on difference radial-density (DRD) distributions defined with respect the Hartree–Fock radial density has been employed for analyzing the impact of dynamic correlation effects on the density. Attention has been paid to the elimination of basis-set incompleteness errors. The DRD distributions calculated by several ab initio methods have been compared to their DFT counterparts generated for representatives of several generations of broadly used exchange-correlation functionals and for the recently developed orbital-dependent OEP2 exchange-correlation functional [ Bartlett et al., J. Chem. Phys. 122, 034104 (2005) ]. For the local, generalized-gradient, and hybrid functionals it has been found that the dynamic correlation effects are to a large extend accounted for by densities resulting from exchange-only calculations. Additional calculations with self-interaction corrected exchange potentials indicate that this finding cannot be explained as an artifact caused by the self-interaction error. It has been demonstrated that the VWN5 and LYP correlation functionals do not represent any substantial dynamical correlation effects on the electron density, whereas these effects are well represented by the orbital-dependent OEP2 correlation functional. Critical comparison of the present results with their counterparts reported in literature has been made. Some attention has been paid to demonstrating the differences between the energy- and density-based perspectives. They indicate the usefulness of density-based criteria for developing new exchange-correlation functionals.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
31.15.A- Ab initio calculations
31.15.xr Self-consistent-field methods

An efficient generalized polyelectron population analysis in orbital spaces: The hole-expansion methodology

P. Karafiloglou

J. Chem. Phys. 130, 164103 (2009); http://dx.doi.org/10.1063/1.3116083 (13 pages) | Cited 4 times

Online Publication Date: 22 April 2009

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We present relations leading to an efficient generalized population analysis in orbital spaces of usual delocalized molecular orbital wave functions. Besides the calculation of the diagonal elements of the reduced density matrices of any order, one can also calculate efficiently the probabilities (or, in general, the weights) of various occupation schemes of local electronic structures, by using generalized density operators referring to both electrons and electron holes. Within this population analysis, correlated molecular orbital wave functions can be used, and there are no restrictions to the number of the analyzed electrons and electron holes. It is based on the hole-expansion methodology, according to which a given electronic population is expanded in terms involving only electron holes, which as shown, can be calculated very efficiently; usual difficulties arising from the necessity to handle extremely large local determinantal basis sets are avoided, without introducing approximations. Although an emphasis is given for populations in the basis of orthogonal orbital spaces (providing probabilities), the case of nonorthogonal ones is also considered in order to show the connection of the generalized populations and the traditional weights obtained from valence-bond wave functions. Physically meaningful populations can be obtained by using natural orbitals, such as the natural atomic orbitals (NAOs) (orthogonal orbitals) or the pre-NAO’s (nonorthogonal orbitals); numerical applications for pyrrole molecule are presented in the basis of these natural orbitals.
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31.15.E- Density-functional theory
31.15.xw Valence bond calculations
31.15.xr Self-consistent-field methods

Optimal sampling efficiency in Monte Carlo simulation with an approximate potential

Joshua D. Coe, Thomas D. Sewell, and M. Sam Shaw

J. Chem. Phys. 130, 164104 (2009); http://dx.doi.org/10.1063/1.3116788 (12 pages) | Cited 5 times

Online Publication Date: 22 April 2009

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Building on the work of Iftimie et al. [J. Chem. Phys. 113, 4852 (2000) ] and Gelb [J. Chem. Phys. 118, 7747 (2003) ], Boltzmann sampling of an approximate potential (the “reference” system) is used to build a Markov chain in the isothermal-isobaric ensemble. At the end points of the chain, the energy is evaluated at a more accurate level (the “full” system) and a composite move encompassing all of the intervening steps is accepted on the basis of a modified Metropolis criterion. For reference system chains of sufficient length, consecutive full energies are statistically decorrelated and thus far fewer are required to build ensemble averages with a given variance. Without modifying the original algorithm, however, the maximum reference chain length is too short to decorrelate full configurations without dramatically lowering the acceptance probability of the composite move. This difficulty stems from the fact that the reference and full potentials sample different statistical distributions. By manipulating the thermodynamic variables characterizing the reference system (pressure and temperature, in this case), we maximize the average acceptance probability of composite moves, lengthening significantly the random walk between consecutive full energy evaluations. In this manner, the number of full energy evaluations needed to precisely characterize equilibrium properties is dramatically reduced. The method is applied to a model fluid, but implications for sampling high-dimensional systems with ab initio or density functional theory potentials are discussed.
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02.50.Ng Distribution theory and Monte Carlo studies
02.50.Ga Markov processes
82.60.Hc Chemical equilibria and equilibrium constants

Bottlenecks to vibrational energy flow in carbonyl sulfide: Structures and mechanisms

R. Paškauskas, C. Chandre, and T. Uzer

J. Chem. Phys. 130, 164105 (2009); http://dx.doi.org/10.1063/1.3103219 (11 pages) | Cited 1 time

Online Publication Date: 22 April 2009

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Finding the causes for the nonstatistical vibrational energy relaxation in the planar carbonyl sulfide (OCS) molecule is a longstanding problem in chemical physics: Not only is the relaxation incomplete long past the predicted statistical relaxation time but it also consists of a sequence of abrupt transitions between long-lived regions of localized energy modes. We report on the phase space bottlenecks responsible for this slow and uneven vibrational energy flow in this Hamiltonian system with three degrees of freedom. They belong to a particular class of two-dimensional invariant tori which are organized around elliptic periodic orbits. We relate the trapping and transition mechanisms with the linear stability of these structures.
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34.10.+x General theories and models of atomic and molecular collisions and interactions (including statistical theories, transition state, stochastic and trajectory models, etc.)
82.20.Db Transition state theory and statistical theories of rate constants
82.20.Nk Classical theories of reactions and/or energy transfer

Approximated electron repulsion integrals: Cholesky decomposition versus resolution of the identity methods

Florian Weigend, Marco Kattannek, and Reinhart Ahlrichs

J. Chem. Phys. 130, 164106 (2009); http://dx.doi.org/10.1063/1.3116103 (8 pages) | Cited 26 times

Online Publication Date: 22 April 2009

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We compare two procedures to gain efficiency by approximating two-electron integrals in molecular electronic structure calculations. The first one is based on a Cholesky decomposition (CD) of two-electron integrals, the second one on the use of preoptimized auxiliary or fitting basis sets employed in a “resolution of the identity” (RI) technique. We present and test auxiliary bases for approximating the Coulomb term, which further improves accuracy over previously proposed fitting bases. It is shown that RI methods lead to insignificant errors only, which are partly comparable to or even better than that of CD treatments; but RI procedures are superior in speed. CD methods have certain advantages, however, particularly for extended basis sets.
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31.15.xr Self-consistent-field methods
31.15.xp Perturbation theory
31.15.E- Density-functional theory

Dissociation aided and side chain sampling enhanced Hamiltonian replica exchange

Yuguang Mu

J. Chem. Phys. 130, 164107 (2009); http://dx.doi.org/10.1063/1.3120483 (8 pages) | Cited 4 times

Online Publication Date: 23 April 2009

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A new application of Hamiltonian replica exchange method is suggested: The potential energy function is adjusted in such a way that repulsive forces between atoms of solute are reinforced. This dissociation action helps the system to escape from the local minima on the free energy landscape. Compared with other Hamiltonian replica exchange methods in which the potential energy between solute atoms and between solute and solvent atoms was reduced, and compared with the temperature replica exchange method, the new scheme displays superior ability to overcome large free energy barrier in a model system. For protein simulation, the side chain conformation sampling turns out to be an issue and an enhancement method is introduced. Combining the dissociation aided method with the specific side chain sampling technique is proven to be a help to explore the complex energy landscape of protein, which is demonstrated by three independent ab initio folding simulations on the trpzip2 peptide.
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82.20.Wt Computational modeling; simulation
87.15.rs Dissociation
82.37.Rs Single molecule manipulation of proteins and other biological molecules
34.20.Gj Intermolecular and atom-molecule potentials and forces

Energy-consistent pseudopotentials and correlation consistent basis sets for the 5d elements Hf–Pt

Detlev Figgen, Kirk A. Peterson, Michael Dolg, and Hermann Stoll

J. Chem. Phys. 130, 164108 (2009); http://dx.doi.org/10.1063/1.3119665 (12 pages) | Cited 47 times

Online Publication Date: 23 April 2009

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New relativistic energy-consistent pseudopotentials have been generated for the 5d transition metals Hf–Pt. The adjustment was done in numerical two-component multiconfiguration Hartree–Fock calculations, using atomic valence-energy spectra from four-component multiconfiguration Dirac–Hartree–Fock calculations as reference data. The resulting two-component pseudopotentials replace the [Kr]4d104f14 cores of the 5d transition metals and can easily be split into a scalar-relativistic and a spin-orbit part. They reproduce the all-electron reference energy data with deviations of ∼ 0.01 eV for configurational averages and ∼ 0.05 eV for individual relativistic states. Full series of correlation consistent basis sets from double to quintuple-zeta have also been developed in this work for use with the new pseudopotentials. In addition, all-electron triple-zeta quality correlation consistent basis sets are also reported in order to provide calibration for the pseudopotential treatment. The accuracy of both the pseudopotentials and basis sets are assessed in extensive coupled cluster benchmark calculations of atomic ionization potentials, electron affinities, and selected excitation energies of all the 5d metal atoms, including the effects of spin-orbit coupling.
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31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions
31.15.xr Self-consistent-field methods
32.50.+d Fluorescence, phosphorescence (including quenching)
31.15.bw Coupled-cluster theory

Open-shell molecular electronic states from the parametric two-electron reduced-density-matrix method

A. Eugene DePrince, III and David A. Mazziotti

J. Chem. Phys. 130, 164109 (2009); http://dx.doi.org/10.1063/1.3116789 (7 pages) | Cited 5 times

Online Publication Date: 23 April 2009

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The parametric variational two-electron reduced-density-matrix (2-RDM) method, developed from an analysis of positivity (N-representability) constraints on the 2-RDM, is extended to treat both closed- and open-shell molecules in singlet, doublet, and triplet spin states. The parametric 2-RDM method can be viewed as using N-representability conditions to modify the 2-RDM from a configuration interaction singles-doubles wave function to make the energy size extensive while keeping the 2-RDM approximately N-representable [ J. Kollmar, Chem. Phys. 125, 084108 (2006) ; A. E. DePrince and D. A. Mazziotti, Phys. Rev. A 76, 049903 (2007) ]. Vertical excitation energies between triplet and singlet states are computed in a polarized valence triple-zeta basis set. In comparison to traditional single-reference wave function methods, the parametric 2-RDM method recovers a larger percentage of the multireference correlation in the singlet excited states, which improves the accuracy of the vertical excitation energies. Furthermore, we show that molecular geometry optimization within the parametric 2-RDM method can be efficiently performed through a Hellmann–Feynman-like relation for the energy gradient with respect to nuclear coordinates. Both the open-shell extension and the energy-gradient relation are applied to computing relative energies and barrier heights for the isomerization reaction HCN+↔HNC+. The computed 2-RDMs very nearly satisfy well known, necessary N-representability conditions.
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31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
33.15.Bh General molecular conformation and symmetry; stereochemistry

Intracule functional models. IV. Basis set effects

Jason K. Pearson, Deborah L. Crittenden, and Peter M. W. Gill

J. Chem. Phys. 130, 164110 (2009); http://dx.doi.org/10.1063/1.3122422 (7 pages) | Cited 11 times

Online Publication Date: 24 April 2009

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We have calculated position and dot intracules for a series of atomic and molecular systems, starting from an unrestricted Hartree–Fock wave function, expanded using the STO-3G, 6–31G, 6–311G, 6-311++G, 6-311++G(d,p), 6-311++G(3d,3p), and 6-311++G(3df,3pd) basis sets as well as the nonpolarized part of Dunning’s cc-pV5Z basis. We find that the basis set effects on the intracules are small and that correlation energies from the dot intracule ansatz are remarkably insensitive to the basis set quality. Mean absolute errors in correlation energies across the G1 data set agree to within 2 mEh for all basis sets tested.
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31.15.xr Self-consistent-field methods
31.15.E- Density-functional theory

Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

Xiancheng Zeng, Hao Hu, Xiangqian Hu, and Weitao Yang

J. Chem. Phys. 130, 164111 (2009); http://dx.doi.org/10.1063/1.3120605 (8 pages) | Cited 3 times

Online Publication Date: 24 April 2009

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A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids “on-the-fly” QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.60.Cx Enthalpies of combustion, reaction, and formation
82.39.Jn Charge (electron, proton) transfer in biological systems
82.39.Rt Reactions in complex biological systems
87.15.ap Molecular dynamics simulation
87.15.R- Reactions and kinetics

Exploring the capabilities of quantum optimal dynamic discrimination

Vincent Beltrani, Pritha Ghosh, and Herschel Rabitz

J. Chem. Phys. 130, 164112 (2009); http://dx.doi.org/10.1063/1.3114679 (12 pages) | Cited 4 times

Online Publication Date: 27 April 2009

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Optimal dynamic discrimination (ODD) uses closed-loop learning control techniques to discriminate between similar quantum systems. ODD achieves discrimination by employing a shaped control (laser) pulse to simultaneously exploit the unique quantum dynamics particular to each system, even when they are quite similar. In this work, ODD is viewed in the context of multiobjective optimization, where the competing objectives are the degree of similarity of the quantum systems and the level of controlled discrimination that can be achieved. To facilitate this study, the D-MORPH gradient algorithm is extended to handle multiple quantum systems and multiple objectives. This work explores the trade-off between laser resources (e.g., the length of the pulse, fluence, etc.) and ODD’s ability to discriminate between similar systems. A mechanism analysis is performed to identify the dominant pathways utilized to achieve discrimination between similar systems.
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03.65.Ta Foundations of quantum mechanics; measurement theory
02.60.Pn Numerical optimization
02.50.-r Probability theory, stochastic processes, and statistics

Nonadiabatic corrections to rovibrational levels of H2

Krzysztof Pachucki and Jacek Komasa

J. Chem. Phys. 130, 164113 (2009); http://dx.doi.org/10.1063/1.3114680 (11 pages) | Cited 23 times

Online Publication Date: 27 April 2009

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The leading nonadiabatic corrections to rovibrational levels of a diatomic molecule are expressed in terms of three functions of internuclear distance: corrections to the adiabatic potential, the effective nuclear mass, and the effective moment of inertia. The resulting radial Schrödinger equation for nuclear motion is solved numerically yielding accurate nonadiabatic energies for all rovibrational levels of the H2 molecule. Results for states with J ≤ 10 are in excellent agreement with previous calculations by Wolniewicz, and for states with J>10 are new.
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31.50.Gh Surface crossings, non-adiabatic couplings
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.A- Ab initio calculations

Recovering four-component solutions by the inverse transformation of the infinite-order two-component wave functions

Maria Barysz, Łukasz Mentel, and Jerzy Leszczyński

J. Chem. Phys. 130, 164114 (2009); http://dx.doi.org/10.1063/1.3119714 (8 pages) | Cited 6 times

Online Publication Date: 28 April 2009

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The two-component Hamiltonian of the infinite-order two-component (IOTC) theory is obtained by a unitary block-diagonalizing transformation of the Dirac–Hamiltonian. Once the IOTC spin orbitals are calculated, they can be back transformed into four-component solutions. The transformed four component solutions are then used to evaluate different moments of the electron density distribution. This formally exact method may, however, suffer from certain approximations involved in its numerical implementation. As shown by the present study, with sufficiently large basis set of Gaussian functions, the Dirac values of these moments are fully recovered in spite of using the approximate identity resolution into eigenvectors of the p2 operator.
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03.65.Pm Relativistic wave equations
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
02.10.Ud Linear algebra

Approximating quantum many-body intermolecular interactions in molecular clusters using classical polarizable force fields

Gregory J. O. Beran

J. Chem. Phys. 130, 164115 (2009); http://dx.doi.org/10.1063/1.3121323 (9 pages) | Cited 12 times

Online Publication Date: 29 April 2009

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Many-body intermolecular interaction expansions provide a promising avenue for the efficient quantum mechanical treatment of molecular clusters and condensed-phase systems, but the computationally expensive three-body and higher terms are often nontrivial. When polar molecules are involved, these many-body terms are typically dominated by electrostatic induction effects, which can be approximated relatively easily. We demonstrate an accurate and inexpensive hybrid quantum/classical model in which one- and two-body interactions are computed quantum mechanically, while the many-body induction effects are approximated with a simple classical polarizable force field. Whereas typical hybrid quantum/classical models partition a system spatially into distinct quantum and classical regions, the model demonstrated here partitions based on the order in the many-body interaction series. This enables a spatially homogeneous treatment of the entire system, which could prove advantageous in studying a wide range of condensed-phase molecular systems.
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61.46.Bc Structure of clusters (e.g., metcars; not fragments of crystals; free or loosely aggregated or loosely attached to a substrate)
71.15.Nc Total energy and cohesive energy calculations
71.15.Mb Density functional theory, local density approximation, gradient and other corrections

Analysis and classification of symmetry breaking in linear ABA-type triatomics

Xiangzhu Li and Josef Paldus

J. Chem. Phys. 130, 164116 (2009); http://dx.doi.org/10.1063/1.3125005 (12 pages) | Cited 3 times

Online Publication Date: 29 April 2009

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The symmetry of the nuclear framework of polyatomic molecules is qualitatively lowered by small changes in their geometry. This may lead to a dramatic change in the nature of their Hartree–Fock (HF) solutions and to a singular behavior of the corresponding potential energy surfaces (PESs), which may persist even at the correlated level if based on these HF references. We examine a general shape of the restricted HF (RHF) and open-shell RHF PESs for the linear triatomic molecules of the ABA type in the vicinity of the symmetric D2h geometries and the role played by the spin-restricted (singlet or doublet) stability of the corresponding HF solutions. This enabled us to classify the character of these surfaces into three basic types depending on the nature of the cut of the PES along the asymmetric stretching mode coordinate. We also examine the implications of the type of these nodes on the PES obtained at the post-HF correlated CCSD(T) level as well as on the determination of the vibrational frequencies for both the symmetric and asymmetric stretching modes. When using either the numerical differentiation of the PES or the solution of the Schrödinger equation for the nuclear motion for this purpose, it is shown that either method yields very good results for the symmetric mode frequencies, while the former approach may yield highly erroneous values for the asymmetric mode frequencies depending on the type of the HF PES at the equilibrium geometry in which case the latter approach still provides us with reasonably good results.
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31.50.-x Potential energy surfaces
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.xr Self-consistent-field methods
31.15.bw Coupled-cluster theory
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis

Bubble merging in breathing DNA as a vicious walker problem in opposite potentials

Jonas Nyvold Pedersen, Mikael Sonne Hansen, Tomáš Novotný, Tobias Ambjörnsson, and Ralf Metzler

J. Chem. Phys. 130, 164117 (2009); http://dx.doi.org/10.1063/1.3117922 (21 pages) | Cited 2 times

Online Publication Date: 30 April 2009

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We investigate the coalescence of two DNA bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker–Planck approach, the characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behavior, while at high temperatures, the bubble corners perform drift diffusion toward coalescence. In the calculations, we map the bubble dynamics on the problem of two vicious walkers in opposite potentials. We also present a discrete master equation approach to the bubble coalescence problem. Numerical evaluation and stochastic simulation of the master equation show excellent agreement with the results from the continuum approach. Given that the coalesced state is thermodynamically stabilized against a state where only one or a few of the base pairs of the barrier region are re-established, it appears likely that this type of setup could be useful for the quantitative investigation of thermodynamic DNA stability data as well as the rate constants involved in the unzipping and zipping dynamics of DNA in single molecule fluorescence experiments.
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87.15.H- Dynamics of biomolecules
87.15.Vv Diffusion
87.15.mq Luminescence
87.15.Zg Phase transitions
87.15.A- Theory, modeling, and computer simulation
87.15.B- Structure of biomolecules

Microcanonical rates, gap times, and phase space dividing surfaces

Gregory S. Ezra, Holger Waalkens, and Stephen Wiggins

J. Chem. Phys. 130, 164118 (2009); http://dx.doi.org/10.1063/1.3119365 (15 pages) | Cited 8 times

Online Publication Date: 30 April 2009

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The general approach to classical unimolecular reaction rates due to Thiele is revisited in light of recent advances in the phase space formulation of transition state theory for multidimensional systems. Key concepts, such as the phase space dividing surface separating reactants from products, the average gap time, and the volume of phase space associated with reactive trajectories, are both rigorously defined and readily computed within the phase space approach. We analyze in detail the gap time distribution and associated reactant lifetime distribution for the isomerization reaction HCN⇌CNH, previously studied using the methods of phase space transition state theory. Both algebraic (power law) and exponential decay regimes have been identified. Statistical estimates of the isomerization rate are compared with the numerically determined decay rate. Correcting the RRKM estimate to account for the measure of the reactant phase space region occupied by trapped trajectories results in a drastic overestimate of the isomerization rate. Compensating but as yet not fully understood trapping mechanisms in the reactant region serve to slow the escape rate sufficiently that the uncorrected RRKM estimate turns out to be reasonably accurate, at least at the particular energy studied. Examination of the decay properties of subensembles of trajectories that exit the HCN well through either of two available symmetry related product channels shows that the complete trajectory ensemble effectively attains the full symmetry of the system phase space on a short time scale t≲0.5 ps, after which the product branching ratio is 1:1, the “statistical” value. At intermediate times, this statistical product ratio is accompanied by nonexponential (nonstatistical) decay. We point out close parallels between the dynamical behavior inferred from the gap time distribution for HCN and nonstatistical behavior recently identified in reactions of some organic molecules.
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82.30.Qt Isomerization and rearrangement
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Db Transition state theory and statistical theories of rate constants
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Fine structure and hyperfine perturbations in the pure rotational spectrum of the VCl radical in its X 5Δr state

D. T. Halfen, L. M. Ziurys, and John M. Brown

J. Chem. Phys. 130, 164301 (2009); http://dx.doi.org/10.1063/1.3108538 (10 pages)

Online Publication Date: 22 April 2009

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The pure rotational spectrum of the VCl radical in its 5Δr ground state has been recorded in the range 236–417 GHz using millimeter/submillimeter direct absorption techniques. This species was created in an ac discharge of VCl4 and argon. Ten rotational transitions of V35Cl were measured in all five Ω ladders; an additional nine transitions of the Ω = 1 spin state were recorded in order to evaluate the 51V hyperfine structure. Hyperfine interactions associated with the 35Cl nucleus were not resolved, consistent with the ionic structure of the molecule. Because of extensive perturbations caused by the low-lying A 5Πr excited state, the rotational spectrum of the ground state has been found to be quite irregular. The four lowest Ω ladders exhibit unusually large lambda-doubling interactions, with the Ω = 1 component showing the largest splitting, over 2 GHz in magnitude. The Ω = 1 transitions are also shifted to higher frequency relative to the other spin components. In addition, the hyperfine structure varies widely between the Ω ladders, and an avoided crossing is observed in two transitions of both the Ω = 1e and 2e components. The data have been analyzed with a case (c) Hamiltonian, and effective rotational, lambda-doubling, and hyperfine constants have been determined for V35Cl. Higher-order parity-dependent magnetic hyperfine terms dΔ2 and dΔ3 were required in the analysis, derived from perturbation theory, in addition to the usual dΔ parameter. The local perturbations evident in these spectra indicate that the A 5Πr excited state lies within the spin-orbit manifold of the ground state, well below the predicted value of 517 cm−1. Mixing of the A 5Πr and X 5Δr states apparently causes both local and global perturbations in the ground state spectrum.
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33.20.Bx Radio-frequency and microwave spectra
31.15.xp Perturbation theory
33.80.Be Level crossing and optical pumping
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Pw Fine and hyperfine structure

H3++H2 isotopic system at low temperatures: Microcanonical model and experimental study

Edouard Hugo, Oskar Asvany, and Stephan Schlemmer

J. Chem. Phys. 130, 164302 (2009); http://dx.doi.org/10.1063/1.3089422 (21 pages) | Cited 24 times

Online Publication Date: 22 April 2009

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State-to-state thermal rate coefficients for reactions of all H3++H2 isotopic variants are derived and compared to new experimental data. The theoretical data are also sought for astrochemical modeling of cold environments (<50 K). The rates are calculated on the basis of a microcanonical approach using the Langevin model and the conservation laws of mass, energy, angular momentum, and nuclear spin. Full scrambling of all five nuclei during the collision is assumed for the calculations and alternatively partial dynamical restrictions are considered. The ergodic principle of the collision is employed in two limiting cases, neglecting (weak ergodic limit) or accounting for explicit degeneracies of the reaction mechanisms (strong ergodic limit). The resulting sets of rate coefficients are shown to be consistent with the detailed balance and thermodynamical equilibrium constants. Rate coefficients, k(T), for the deuteration chain of H3+ with HD as well as H2D+/H3+ equilibrium ratios have been measured in a variable temperature 22-pole ion trap. In particular, the D2H++HD→D3++H2 rate coefficient indicates a change in reaction mechanism when going to higher temperatures. The good overall agreement between experiment and theory encourages the use of the theoretical predictions for astrophysical modeling.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.60.Hc Chemical equilibria and equilibrium constants
82.20.Hf Product distribution
95.30.Ft Molecular and chemical processes and interactions

Pure rotational spectra of the CCCF radical

Takashi Yoshikawa, Yoshihiro Sumiyoshi, and Yasuki Endo

J. Chem. Phys. 130, 164303 (2009); http://dx.doi.org/10.1063/1.3120444 (5 pages) | Cited 2 times

Online Publication Date: 22 April 2009

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Pure rotational transitions of a new carbon-chain radical CCCF in a supersonic jet have been observed for the first time using a Fourier-transform microwave spectrometer with a pulsed-discharge nozzle. The radical was produced by a pulsed electric discharge in a C2H2 and CF4 mixture diluted to 0.1% and 0.1% with Ne, respectively. Rotational transitions with spin and hyperfine splittings have been observed in the region from 9.1 GHz for NKaKc = 101−000 to 27.3 GHz for NKaKc = 303−202. The rotational constant, the spin-rotation interaction constant, and the hyperfine coupling constants due to the F nucleus have been precisely determined from the least-squares analysis, yielding math = 4555.8043(44), γeff = −7.105(16), bF,eff = 368(19), and ceff = −284.832(61) MHz. The determined molecular constants were compared with those obtained from high-level ab initio calculations and concluded that the CCCF radical has a bent ground state math2A′.
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33.20.Bx Radio-frequency and microwave spectra
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.A- Ab initio calculations

Structures and reactions of methanol molecules on cobalt cluster ions studied by infrared photodissociation spectroscopy

Shinichi Hirabayashi, Ryuji Okawa, Masahiko Ichihashi, Yoshiyuki Kawazoe, and Tamotsu Kondow

J. Chem. Phys. 130, 164304 (2009); http://dx.doi.org/10.1063/1.3121503 (7 pages) | Cited 5 times

Online Publication Date: 22 April 2009

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Structures of methanol molecules chemisorbed on cobalt cluster ions, Con+ (n = 2–6), were investigated by infrared photodissociation (IR-PD) spectroscopy in the wavenumber range of 3400–4000 cm−1. All the IR-PD spectra measured exhibit an intense peak in the region of the OH stretching vibration. In the IR-PD spectra of Co2+(CH3OH)2,3 and Co3+(CH3OH)3, weak peaks were observed additionally in the vicinity of 3000 cm−1, being assignable to the CH stretching vibration. The comparison of the experimental results with the calculated ones leads us to conclude that (1) molecularly chemisorbed species, Con+(CH3OH)m (m = 1–3), and dissociatively chemisorbed species, Con+(CH3OH)m−1(CH3)(OH), are dominant and (2) the methanol dehydrogenation proceeds via an intermediate, Con+(CH3)(OH).
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36.40.Mr Spectroscopy and geometrical structure of clusters
33.20.Tp Vibrational analysis
33.20.Ea Infrared spectra
33.80.Gj Diffuse spectra; predissociation, photodissociation

Nitrous oxide dimer: An ab initio coupled-cluster study of isomers, interconversions, and infrared fundamental bands, and experimental observation of a new fundamental for the polar isomer

G. M. Berner, A. L. L. East, Mahin Afshari, M. Dehghany, N. Moazzen-Ahmadi, and A. R. W. McKellar

J. Chem. Phys. 130, 164305 (2009); http://dx.doi.org/10.1063/1.3121224 (8 pages) | Cited 11 times

Online Publication Date: 23 April 2009

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Improved quantum chemistry (coupled-cluster) results are presented for spectroscopic parameters and the potential energy surface for the N2O dimer. The calculations produce three isomer structures, of which the two lowest energy forms are those observed experimentally: a nonpolar C2h-symmetry planar slipped-antiparallel geometry (with inward-located O atoms) and a higher-energy polar Cs-symmetry planar slipped-parallel geometry. Harmonic vibrational frequencies and infrared intensities for these isomers are calculated. The low-frequency intermolecular vibrational mode predictions should be useful for future spectroscopic searches, and there is good agreement in the one case where an experimental value is available. The frequency shifts for the high-frequency intramolecular stretching vibrations, relative to the monomer, were calculated and used to help locate a new infrared band of the polar isomer, which corresponds to the weaker out-of-phase combination of the ν1 antisymmetric stretch of the individual monomers. The new band was observed in the region of the monomer ν1 fundamental for both (14N2O)2 and (15N2O)2 using a tunable infrared diode laser to probe a pulsed supersonic jet expansion, and results are presented.
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31.15.ae Electronic structure and bonding characteristics
31.15.bw Coupled-cluster theory
33.70.Fd Absolute and relative line and band intensities
33.20.Ea Infrared spectra
33.20.Tp Vibrational analysis
31.50.Bc Potential energy surfaces for ground electronic states
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)

Theoretical study of proton tunneling in the excited state of tropolone

Marek J. Wójcik, Łukasz Boda, and Marek Boczar

J. Chem. Phys. 130, 164306 (2009); http://dx.doi.org/10.1063/1.3115721 (5 pages)

Online Publication Date: 23 April 2009

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Ab initio CIS/6-311++G(d,p) calculations of geometry and vibrational frequencies have been carried out in the math state of tropolone. The grids of potential energy surfaces along the coordinates of high frequency tunneling vibration and the low-frequency coupled vibration have been calculated. Two-dimensional model potentials, formed from symmetric mode coupling potential and squeezed double well potential, have been fitted to the calculated potential energy surfaces and used to analyze proton dynamics. The tunneling splittings for different vibrationally excited states have been calculated and compared with the available experimental data. The model potential energy surfaces, based on the CIS/6-311++G(d,p) calculations, give good estimation of the tunneling energy splittings in the vibrationally ground and excited states of tropolone and explain monotonic decrease in tunneling splittings with the excitation of low-frequency out-of-plane modes and increase in the tunneling splittings with the excitation of low-frequency planar modes.
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31.15.A- Ab initio calculations
31.50.Df Potential energy surfaces for excited electronic states
31.15.vq Electron correlation calculations for polyatomic molecules
33.15.Bh General molecular conformation and symmetry; stereochemistry
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