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28 Aug 2012

Volume 137, Issue 8, Articles (08xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 137, 084901 (2012); http://dx.doi.org/10.1063/1.4745480 (6 pages)

M. K. Glagolev, V. V. Vasilevskaya, and A. R. Khokhlov
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Perspective: Supercooled liquids and glasses

M. D. Ediger and Peter Harrowell

J. Chem. Phys. 137, 080901 (2012); http://dx.doi.org/10.1063/1.4747326 (15 pages) | Cited 17 times

Online Publication Date: 23 August 2012

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Supercooled liquids and glasses are important for current and developing technologies. Here we provide perspective on recent progress in this field. The interpretation of supercooled liquid and glass properties in terms of the potential energy landscape is discussed. We explore the connections between amorphous structure, high frequency motions, molecular motion, structural relaxation, stability against crystallization, and material properties. Recent developments that may lead to new materials or new applications of existing materials are described.
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61.43.Fs Glasses
81.30.Hd Constant-composition solid-solid phase transformations: polymorphic, massive, and order-disorder
64.70.K- Solid-solid transitions
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Communication: Thermal rectification in liquids by manipulating the solid-liquid interface

Sohail Murad and Ishwar K. Puri

J. Chem. Phys. 137, 081101 (2012); http://dx.doi.org/10.1063/1.4749288 (4 pages) | Cited 1 time

Online Publication Date: 31 August 2012

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Thermal rectification, the origin of which lies in modifying the thermal resistance in a nonlinear manner, could significantly improve the thermal management of a wide range of nano-devices (both electronic and thermoelectric), thereby improving their efficiencies. Since rectification requires a material to be inhomogeneous, it has been typically associated with solids. However, the structure of solids is relatively difficult to manipulate, which makes the tuning of thermal rectification devices challenging. Since liquids are more amenable to tuning, this could open up new applications for thermal rectification. We use molecular dynamics simulations to demonstrate thermal rectification using liquid water. This is accomplished by creating an inhomogeneous water phase, either by changing the morphology of the surface in contact with the liquid or by imposing an arbitrary external force, which in practice could be through an electric or magnetic field. Our system consists of a bulk fluid that is confined in a reservoir that is bounded by two walls, one hot and the other cold. The interfacial (Kapitza) thermal resistance at the solid-fluid interface and the density gradient of the bulk fluid both influence the magnitude of the thermal rectification. However, we find that the role of the interfacial resistance is more prominent than the application of an external force on the bulk fluid.
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73.40.Ei Rectification
61.20.Ja Computer simulation of liquid structure
66.25.+g Thermal conduction in nonmetallic liquids
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Variational approach for nonpolar solvation analysis

Zhan Chen, Shan Zhao, Jaehun Chun, Dennis G. Thomas, Nathan A. Baker, Peter W. Bates, and G. W. Wei

J. Chem. Phys. 137, 084101 (2012); http://dx.doi.org/10.1063/1.4745084 (9 pages) | Cited 1 time

Online Publication Date: 23 August 2012

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Solvation analysis is one of the most important tasks in chemical and biological modeling. Implicit solvent models are some of the most popular approaches. However, commonly used implicit solvent models rely on unphysical definitions of solvent-solute boundaries. Based on differential geometry, the present work defines the solvent-solute boundary via the variation of the nonpolar solvation free energy. The solvation free energy functional of the system is constructed based on a continuum description of the solvent and the discrete description of the solute, which are dynamically coupled by the solvent-solute boundaries via van der Waals interactions. The first variation of the energy functional gives rise to the governing Laplace-Beltrami equation. The present model predictions of the nonpolar solvation energies are in an excellent agreement with experimental data, which supports the validity of the proposed nonpolar solvation model.
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87.15.R- Reactions and kinetics
82.20.Yn Solvent effects on reactivity
82.30.-b Specific chemical reactions; reaction mechanisms

Exact dynamic properties of molecular motors

N. J. Boon and R. B. Hoyle

J. Chem. Phys. 137, 084102 (2012); http://dx.doi.org/10.1063/1.4746392 (15 pages)

Online Publication Date: 23 August 2012

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Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman [“A schematic method of deriving the rate laws of enzyme-catalyzed reactions,” J. Phys. Chem. 60, 1375–1378 (1956)]10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.
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87.15.H- Dynamics of biomolecules
87.15.K- Molecular interactions; membrane-protein interactions
87.15.R- Reactions and kinetics
87.16.Nn Motor proteins (myosin, kinesin dynein)
87.14.ej Enzymes
87.15.ap Molecular dynamics simulation

Towards a minimal stochastic model for a large class of diffusion-reactions on biological membranes

Michael W. Chevalier and Hana El-Samad

J. Chem. Phys. 137, 084103 (2012); http://dx.doi.org/10.1063/1.4746692 (15 pages)

Online Publication Date: 23 August 2012

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Diffusion of biological molecules on 2D biological membranes can play an important role in the behavior of stochastic biochemical reaction systems. Yet, we still lack a fundamental understanding of circumstances where explicit accounting of the diffusion and spatial coordinates of molecules is necessary. In this work, we illustrate how time-dependent, non-exponential reaction probabilities naturally arise when explicitly accounting for the diffusion of molecules. We use the analytical expression of these probabilities to derive a novel algorithm which, while ignoring the exact position of the molecules, can still accurately capture diffusion effects. We investigate the regions of validity of the algorithm and show that for most parameter regimes, it constitutes an accurate framework for studying these systems. We also document scenarios where large spatial fluctuation effects mandate explicit consideration of all the molecules and their positions. Taken together, our results derive a fundamental understanding of the role of diffusion and spatial fluctuations in these systems. Simultaneously, they provide a general computational methodology for analyzing a broad class of biological networks whose behavior is influenced by diffusion on membranes.
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87.15.Vv Diffusion
87.15.Ya Fluctuations
87.10.Mn Stochastic modeling
87.15.R- Reactions and kinetics
87.16.dj Dynamics and fluctuations
02.50.Cw Probability theory

Particle-swarm structure prediction on clusters

Jian Lv, Yanchao Wang, Li Zhu, and Yanming Ma

J. Chem. Phys. 137, 084104 (2012); http://dx.doi.org/10.1063/1.4746757 (8 pages) | Cited 9 times

Online Publication Date: 23 August 2012

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We have developed an efficient method for cluster structure prediction based on the generalization of particle swarm optimization (PSO). A local version of PSO algorithm was implemented to utilize a fine exploration of potential energy surface for a given non-periodic system. We have specifically devised a technique of so-called bond characterization matrix (BCM) to allow the proper measure on the structural similarity. The BCM technique was then employed to eliminate similar structures and define the desirable local search spaces. We find that the introduction of point group symmetries into generation of cluster structures enables structural diversity and apparently avoids the generation of liquid-like (or disordered) clusters for large systems, thus considerably improving the structural search efficiency. We have incorporated Metropolis criterion into our method to further enhance the structural evolution towards low-energy regimes of potential energy surfaces. Our method has been extensively benchmarked on Lennard-Jones clusters with different sizes up to 150 atoms and applied into prediction of new structures of medium-sized Lin (n = 20, 40, 58) clusters. High search efficiency was achieved, demonstrating the reliability of the current methodology and its promise as a major method on cluster structure prediction.
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36.40.Mr Spectroscopy and geometrical structure of clusters
02.60.Pn Numerical optimization
31.50.-x Potential energy surfaces
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions

Avoided crossings, conical intersections, and low-lying excited states with a single reference method: The restricted active space spin-flip configuration interaction approach

David Casanova

J. Chem. Phys. 137, 084105 (2012); http://dx.doi.org/10.1063/1.4747341 (10 pages) | Cited 2 times

Online Publication Date: 24 August 2012

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The restricted active space spin-flip CI (RASCI-SF) performance is tested in the electronic structure computation of the ground and the lowest electronically excited states in the presence of near-degeneracies. The feasibility of the method is demonstrated by analyzing the avoided crossing between the ionic and neutral singlet states of LiF along the molecular dissociation. The two potential energy surfaces (PESs) are explored by means of the energies of computed adiabatic and approximated diabatic states, dipole moments, and natural orbital electronic occupancies of both states. The RASCI-SF methodology is also used to study the ground and first excited singlet surface crossing involved in the double bond isomerization of ethylene, as a model case. The two-dimensional PESs of the ground (S0) and excited (S1) states are calculated for the complete configuration space of torsion and pyramidalization molecular distortions. The parameters that define the state energetics in the vicinity of the S0/S1 conical intersection region are compared to complete active space self-consistent field (CASSCF) results. These examples show that it is possible to describe strongly correlated electronic states using a single reference methodology without the need to expand the wavefunction to high levels of collective excitations. Finally, RASCI is also examined in the electronic structure characterization of the ground and 21Ag−, 11Bu+, 11Bu−, and 13Bu− states of all-trans polyenes with two to seven double bonds and beyond. Transition energies are compared to configuration interaction singles, time-dependent density functional theory (TDDFT), CASSCF, and its second-order perturbation correction calculations, and to experimental data. The capability of RASCI-SF to describe the nature and properties of each electronic state is discussed in detail. This example is also used to expose the properties of different truncations of the RASCI wavefunction and to show the possibility to use an excitation operator with any number of α-to-β electronic promotions.
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36.20.Kd Electronic structure and spectra
31.15.V- Electron correlation calculations for atoms, ions and molecules
33.15.Fm Bond strengths, dissociation energies
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.80.Be Level crossing and optical pumping
36.20.Hb Configuration (bonds, dimensions)

Single-molecule stochastic times in a reversible bimolecular reaction

Peter Keller and Angelo Valleriani

J. Chem. Phys. 137, 084106 (2012); http://dx.doi.org/10.1063/1.4747337 (7 pages) | Cited 1 time

Online Publication Date: 27 August 2012

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In this work, we consider the reversible reaction between reactants of species A and B to form the product C. We consider this reaction as a prototype of many pseudobiomolecular reactions in biology, such as for instance molecular motors. We derive the exact probability density for the stochastic waiting time that a molecule of species A needs until the reaction with a molecule of species B takes place. We perform this computation taking fully into account the stochastic fluctuations in the number of molecules of species B. We show that at low numbers of participating molecules, the exact probability density differs from the exponential density derived by assuming the law of mass action. Finally, we discuss the condition of detailed balance in the exact stochastic and in the approximate treatment.
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87.15.R- Reactions and kinetics
02.50.Cw Probability theory
02.50.Ey Stochastic processes
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
82.20.Uv Stochastic theories of rate constants

NMR shielding tensors for density fitted local second-order Møller-Plesset perturbation theory using gauge including atomic orbitals

Stefan Loibl and Martin Schütz

J. Chem. Phys. 137, 084107 (2012); http://dx.doi.org/10.1063/1.4744102 (15 pages) | Cited 1 time

Online Publication Date: 27 August 2012

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An efficient method for the calculation of nuclear magnetic resonance (NMR) shielding tensors is presented, which treats electron correlation at the level of second-order Møller-Plesset perturbation theory. It uses spatially localized functions to span occupied and virtual molecular orbital spaces, respectively, which are expanded in a basis of gauge including atomic orbitals (GIAOs or London atomic orbitals). Doubly excited determinants are restricted to local subsets of the virtual space and pair energies with an interorbital distance beyond a certain threshold are omitted. Furthermore, density fitting is employed to factorize the electron repulsion integrals. Ordinary Gaussians are employed as fitting functions. It is shown that the errors in the resulting NMR shielding constant, introduced (i) by the local approximation and (ii) by density fitting, are very small or even negligible. The capabilities of the new program are demonstrated by calculations on some extended molecular systems, such as the cyclobutane pyrimidine dimer photolesion with adjacent nucleobases in the native intrahelical DNA double strand (ATTA sequence). Systems of that size were not accessible to correlated ab initio calculations of NMR spectra before. The presented method thus opens the door to new and interesting applications in this area.
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87.15.M- Spectra of biomolecules
36.20.Kd Electronic structure and spectra
31.15.vq Electron correlation calculations for polyatomic molecules
31.15.xp Perturbation theory
87.14.gk DNA
87.15.ad Analytical theories

Analytic calculation of second-order electric response properties with the normalized elimination of the small component (NESC) method

Wenli Zou, Michael Filatov, and Dieter Cremer

J. Chem. Phys. 137, 084108 (2012); http://dx.doi.org/10.1063/1.4747335 (9 pages) | Cited 1 time

Online Publication Date: 28 August 2012

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Analytic second derivatives of the relativistic energy for the calculation of electric response properties are derived utilizing the normalized elimination of the small component (NESC) method. Explicit formulas are given for electric static dipole polarizabilities and infrared intensities by starting at the NESC representation of electric dipole moments. The analytic derivatives are implemented in an existing NESC program and applied to calculate dipole moments, polarizabilities, and the infrared spectra of gold- and mercury-containing molecules as well as some actinide molecules. Comparison with experiment reveals the accuracy of NESC second order electric response properties.
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33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.20.Ea Infrared spectra
31.15.X- Alternative approaches

Electronic currents and Born-Oppenheimer molecular dynamics

Serguei Patchkovskii

J. Chem. Phys. 137, 084109 (2012); http://dx.doi.org/10.1063/1.4747540 (9 pages) | Cited 1 time

Online Publication Date: 28 August 2012

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Born-Oppenheimer variable separation is the mainstay of studies of chemical reactivity and dynamics. A long-standing problem of this ansatz is the absence of electronic currents in a system undergoing dynamics. I analyze the physical origin of the “missing” electronic currents in Born-Oppenheimer wavefunctions. By examining the problem within the multi-state Born-Huang ansatz, I demonstrate that electronic currents arise from the first-order non-adiabatic coupling to electronically excited states. I derive two expressions for the electronic currents induced by nuclear motion. The sum-over-the-states formula, identical to the result of “complete adiabatic” treatment of Nafie [J. Chem. Phys. 79, 4950 (1983)]10.1063/1.445588 leads to a transparent and intuitive physical picture of the induced currents, but is unsuitable for practical implementation in all but the simplest systems. The equivalent expression in terms of the electronic energy derivatives is straightforward to implement numerically. I present first applications of this approach to small systems of potential chemical interest.
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31.15.xv Molecular dynamics and other numerical methods
31.50.Df Potential energy surfaces for excited electronic states
71.15.Pd Molecular dynamics calculations (Car-Parrinello) and other numerical simulations
82.20.Gk Electronically non-adiabatic reactions
82.20.Rp State to state energy transfer

Population and coherence dynamics in light harvesting complex II (LH2)

Shu-Hao Yeh, Jing Zhu, and Sabre Kais

J. Chem. Phys. 137, 084110 (2012); http://dx.doi.org/10.1063/1.4747622 (9 pages)

Online Publication Date: 28 August 2012

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The electronic excitation population and coherence dynamics in the chromophores of the photosynthetic light harvesting complex 2 (LH2) B850 ring from purple bacteria (Rhodopseudomonas acidophila) have been studied theoretically at both physiological and cryogenic temperatures. Similar to the well-studied Fenna-Matthews-Olson (FMO) protein, oscillations of the excitation population and coherence in the site basis are observed in LH2 by using a scaled hierarchical equation of motion approach. However, this oscillation time (300 fs) is much shorter compared to the FMO protein (650 fs) at cryogenic temperature. Both environment and high temperature are found to enhance the propagation speed of the exciton wave packet yet they shorten the coherence time and suppress the oscillation amplitude of coherence and the population. Our calculations show that a long-lived coherence between chromophore electronic excited states can exist in such a noisy biological environment.
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87.15.H- Dynamics of biomolecules
87.14.E- Proteins
87.15.Pc Electronic and electrical properties
42.25.Kb Coherence

Validation of the reaction thermodynamics associated with NaSc(BH4)4 from first-principles calculations: Detecting metastable paths and identifying the minimum free energy path

Ki Chul Kim

J. Chem. Phys. 137, 084111 (2012); http://dx.doi.org/10.1063/1.4748262 (9 pages) | Cited 1 time

Online Publication Date: 29 August 2012

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A critical drawback with first-principles thermodynamic calculations is the absence of the vibrational and entropic contributions to the prediction of reaction mechanisms, which could conclusively show that the predicted reaction mechanism might be not the most stable reaction path. This study focused on providing an answer to this problem by examining possible metastable paths for five reactant mixtures whose reaction mechanisms were previously predicted using first-principles thermodynamic calculations. The aim of this study was to find a minimum free energy path among all the possible paths of each reactant mixture. This effort provided the clear conclusion that the original reaction paths predicted from first-principles thermodynamic calculations were the most stable reaction paths at an appropriate H2 pressure range for all cases. An additional examination associated with density functional theory uncertainty suggests how the ambiguity of reaction mechanisms predicted based on thermodynamic calculations should be understood and dealt with.
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82.60.Cx Enthalpies of combustion, reaction, and formation
82.20.-w Chemical kinetics and dynamics
88.30.R- Hydrogen storage

Vibronic coupling in asymmetric bichromophores: Theory and application to diphenylmethane

Ben Nebgen, Frank Lee Emmert, III, and Lyudmila V. Slipchenko

J. Chem. Phys. 137, 084112 (2012); http://dx.doi.org/10.1063/1.4747336 (12 pages) | Cited 3 times

Online Publication Date: 30 August 2012

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The theory for modeling vibronic interactions in bichromophores was introduced in sixties by Witkowski and Moffitt [J. Chem. Phys. 33, 872 (1960)10.1063/1.1731278] and extended by Fulton and Gouterman [J. Chem. Phys. 35, 1059 (1961)10.1063/1.1701181]. The present work describes extension of this vibronic model to describe bichromophores with broken vibrational symmetry such as partly deuterated molecules. Additionally, the model is extended to include inter-chromophore vibrational modes. The model can treat multiple vibrational modes by employing Lanczos diagonalization procedure of sparse matrices. The developed vibronic model is applied to simulation of vibronic spectra of flexible bichromophore diphenylmethane and compared to high-resolution experimental spectra [J. A. Stearns, N. R. Pillsbury, K. O. Douglass, C. W. Müller, T. S. Zwier, and D. F. Plusquellic, J. Chem. Phys. 129, 224305 (2008)10.1063/1.3028543].
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33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.15.X- Alternative approaches
33.20.Tp Vibrational analysis

Dynamics of a Holstein polaron with off-diagonal coupling

Yang Zhao, Bin Luo, Yuyu Zhang, and Jun Ye

J. Chem. Phys. 137, 084113 (2012); http://dx.doi.org/10.1063/1.4748140 (10 pages) | Cited 2 times

Online Publication Date: 31 August 2012

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Dynamics of a one-dimensional Holstein polaron with off-diagonal exciton-phonon coupling is studied by employing the Dirac-Frenkel time-dependent variational principle. The trial state used is the Davydov D2 Ansatz with two sets of variational parameters, one for each constituting particle in the linearly coupled exciton-phonon system. Validity of the approach is carefully checked by quantifying how faithfully the trial state follows the Schrödinger equation. A close examination of variational outputs reveals fine details of polaron dynamics and intricacies of dynamic exciton-phonon correlations. In the absence of diagonal coupling, the change in the polaron effective mass hinges on the sign of the transfer integral due to the antisymmetric nature of the off-diagonal coupling. The role of the off-diagonal coupling switches from being an agent of transport at moderate coupling strengths to that of localization at large coupling strengths. Increasing the phonon bandwidth leads to a reduced polaron effective mass at the zone center and an overall lowering of the polaron band.
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71.38.-k Polarons and electron-phonon interactions
71.35.-y Excitons and related phenomena
63.20.kk Phonon interactions with other quasiparticles

Relating normal vibrational modes to local vibrational modes with the help of an adiabatic connection scheme

Wenli Zou, Robert Kalescky, Elfi Kraka, and Dieter Cremer

J. Chem. Phys. 137, 084114 (2012); http://dx.doi.org/10.1063/1.4747339 (11 pages) | Cited 5 times

Online Publication Date: 31 August 2012

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Information on the electronic structure of a molecule and its chemical bonds is encoded in the molecular normal vibrational modes. However, normal vibrational modes result from a coupling of local vibrational modes, which means that only the latter can provide detailed insight into bonding and other structural features. In this work, it is proven that the adiabatic internal coordinate vibrational modes of Konkoli and Cremer [Int. J. Quantum Chem. 67, 29 (1998)]10.1002/(SICI)1097-461X(1998)67:1<29::AID-QUA3>3.0.CO;2-0 represent a unique set of local modes that is directly related to the normal vibrational modes. The missing link between these two sets of modes are the compliance constants of Decius, which turn out to be the reciprocals of the local mode force constants of Konkoli and Cremer. Using the compliance constants matrix, the local mode frequencies of any molecule can be converted into its normal mode frequencies with the help of an adiabatic connection scheme that defines the coupling of the local modes in terms of coupling frequencies and reveals how avoided crossings between the local modes lead to changes in the character of the normal modes.
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31.15.-p Calculations and mathematical techniques in atomic and molecular physics
33.15.Fm Bond strengths, dissociation energies
33.20.Tp Vibrational analysis

Multibody local approximation: Application to conformational entropy calculations on biomolecules

Ernesto Suárez and Dimas Suárez

J. Chem. Phys. 137, 084115 (2012); http://dx.doi.org/10.1063/1.4748104 (11 pages) | Cited 1 time

Online Publication Date: 31 August 2012

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Multibody type expansions like mutual information expansions are widely used for computing or analyzing properties of large composite systems. The power of such expansions stems from their generality. Their weaknesses, however, are the large computational cost of including high order terms due to the combinatorial explosion and the fact that truncation errors do not decrease strictly with the expansion order. Herein, we take advantage of the redundancy of multibody expansions in order to derive an efficient reformulation that captures implicitly all-order correlation effects within a given cutoff, avoiding the combinatory explosion. This approach, which is cutoff dependent rather than order dependent, keeps the generality of the original expansions and simultaneously mitigates their limitations provided that a reasonable cutoff can be used. An application of particular interest can be the computation of the conformational entropy of flexible peptide molecules from molecular dynamics trajectories. By combining the multibody local estimations of conformational entropy with average values of the rigid-rotor and harmonic-oscillator entropic contributions, we obtain by far a tighter upper bound of the absolute entropy than the one obtained by the broadly used quasi-harmonic method.
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87.15.ap Molecular dynamics simulation
87.14.ef Peptides
87.15.hp Conformational changes
87.64.Aa Computer simulation
back to top Atoms, Molecules, and Clusters

Overtone vibrational spectroscopy in H2-H2O complexes: A combined high level theoretical ab initio, dynamical and experimental study

Michael P. Ziemkiewicz, Christian Pluetzer, David J. Nesbitt, Yohann Scribano, Alexandre Faure, and Ad van der Avoird

J. Chem. Phys. 137, 084301 (2012); http://dx.doi.org/10.1063/1.4732581 (15 pages) | Cited 6 times

Online Publication Date: 22 August 2012

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First results are reported on overtone (vOH = 2 ← 0) spectroscopy of weakly bound H2-H2O complexes in a slit supersonic jet, based on a novel combination of (i) vibrationally mediated predissociation of H2-H2O, followed by (ii) UV photodissociation of the resulting H2O, and (iii) UV laser induced fluorescence on the nascent OH radical. In addition, intermolecular dynamical calculations are performed in full 5D on the recent ab initio intermolecular potential of Valiron et al. [J. Chem. Phys. 129, 134306 (2008)10.1063/1.2988314] in order to further elucidate the identity of the infrared transitions detected. Excellent agreement is achieved between experimental and theoretical spectral predictions for the most strongly bound van der Waals complex consisting of ortho (I = 1) H2 and ortho (I = 1) H2O (oH2-oH2O). Specifically, two distinct bands are seen in the oH2-oH2O spectrum, corresponding to internal rotor states in the upper vibrational manifold of Σ and Π rotational character. However, none of the three other possible nuclear spin modifications (pH2-oH2O, pH2-pH2O, or oH2-pH2O) are observed above current signal to noise level, which for the pH2 complexes is argued to arise from displacement by oH2 in the expansion mixture to preferentially form the more strongly bound species. Direct measurement of oH2-oH2O vibrational predissociation in the time domain reveals lifetimes of 15(2) ns and <5(2) ns for the Σ and Π states, respectively. Theoretical calculations permit the results to be interpreted in terms of near resonant energy levels and intermolecular alignment of the H2 and H2O wavefunctions, providing insight into predissociation dynamical pathways from these metastable levels.
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33.20.Tp Vibrational analysis
33.80.Gj Diffuse spectra; predissociation, photodissociation
34.20.Gj Intermolecular and atom-molecule potentials and forces
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Ea Infrared spectra

Effects of classical nonlinear resonances in grazing diatom-surface collisions

Antonia Ruiz and José P. Palao

J. Chem. Phys. 137, 084302 (2012); http://dx.doi.org/10.1063/1.4746689 (12 pages)

Online Publication Date: 22 August 2012

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Energy transfer between vibrational, rotational, and translational degrees of freedom of a molecule during a collision process is enhanced when the classical frequencies associated with the initial state are in the proximity of nonlinear resonance conditions. We present an analysis of the classical resonant effects in the collisions of light diatoms with periodic surfaces, and discuss the initial conditions in which these effects can be observed. In particular, we find that for grazing incidence and resonant initial values of the classical frequencies, corresponding to specific vibro-rotational molecular states and translational energies, an efficient energy transfer between the intramolecular vibro-rotational degrees of freedom and the translational degree of freedom along a symmetry direction on the surface can be found. This efficient energy transfer manifests itself in the emergence of specific peaks in the molecular diffraction patterns. The predictions of the resonance analysis are contrasted with the results of classical trajectory calculations obtained in a diatom-rigid surface collision model.
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34.35.+a Interactions of atoms and molecules with surfaces
33.15.Mt Rotation, vibration, and vibration-rotation constants

The J = 2 ortho levels of the v = 0 to 6 np singlet Rydberg series of molecular hydrogen revisited

M. Glass-Maujean, H. Schmoranzer, I. Haar, A. Knie, P. Reiss, and A. Ehresmann

J. Chem. Phys. 137, 084303 (2012); http://dx.doi.org/10.1063/1.4742311 (10 pages) | Cited 1 time

Online Publication Date: 23 August 2012

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The energies of the J = 2 ortho levels of the v = 0 to 6 Rydberg np singlet series of molecular hydrogen with absolute intensities of the R(1) and P(3) absorption lines were measured by a high-resolution synchrotron radiation experiment and calculated through a full ab initio multi-channel quantum defect approach.
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31.50.Df Potential energy surfaces for excited electronic states
31.15.ae Electronic structure and bonding characteristics

A generalised 17-state vibronic-coupling Hamiltonian model for ethylene

Joaquim Jornet-Somoza, Benjamin Lasorne, Michael A. Robb, Hans-Dieter Meyer, David Lauvergnat, and Fabien Gatti

J. Chem. Phys. 137, 084304 (2012); http://dx.doi.org/10.1063/1.4745861 (16 pages) | Cited 3 times

Online Publication Date: 23 August 2012

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In a previous work [B. Lasorne, M. A. Robb, H.-D. Meyer, and F. Gatti, “The electronic excited states of ethylene with large-amplitude deformations: A dynamical symmetry group investigation,” Chem. Phys. 377, 30–45 (2010)10.1016/j.chemphys.2010.08.011; B. Lasorne, M. A. Robb, H.-D. Meyer, and F. Gatti, Chem. Phys. 382, 132 (2011) (Erratum)]10.1016/j.chemphys.2011.01.004, we investigated the electronic structure of ethylene (ethene, C2H4) in terms of 17 dominant configurations selected at the multiconfiguration self-consistent field level of theory. These were shown to be sufficient to recover most of the static electron correlation among the first valence and Rydberg states at all geometries. We also devised a strategy to build a 17-quasidiabatic-state matrix representation of the electronic Hamiltonian for curvilinear coordinates using dynamical symmetry. Here, we present fitted surfaces in the form of a generalised vibronic-coupling Hamiltonian model for two nuclear coordinates, CC bond stretching and torsion. Dynamic electron correlation is included into the electronic structure to improve the energetics of the Rydberg states at the multireference configuration interaction level of theory. The chemical interpretation of the adiabatic states of interest does not change qualitatively, which validates our choice of underlying quasidiabatic states in the model. The absorption spectrum is calculated with quantum dynamics and partially assigned. This first two-dimensional model shows a surprisingly good agreement with the experimental spectrum.
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33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.15.vq Electron correlation calculations for polyatomic molecules
33.15.Fm Bond strengths, dissociation energies
33.20.Tp Vibrational analysis

Intermolecular vibrations of fluorobenzene-Ar up to 130 cm−1 in the ground electronic state

Jason R. Gascooke, Ula N. Alexander, and Warren D. Lawrance

J. Chem. Phys. 137, 084305 (2012); http://dx.doi.org/10.1063/1.4746688 (11 pages) | Cited 2 times

Online Publication Date: 24 August 2012

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Sixteen intermolecular vibrational levels of the S0 state of the fluorobenzene-Ar van der Waals complex have been observed using dispersed fluorescence. The levels range up to ∼130 cm−1 in vibrational energy. The vibrational energies have been modelled using a complete set of harmonic and quartic anharmonic constants and a cubic anharmonic coupling between the stretch and long axis bend overtone that becomes near ubiquitous at higher energies. The constants predict the observed band positions with a root mean square deviation of 0.04 cm−1. The set of vibrational levels predicted by the constants, which includes unobserved bands, has been compared with the predictions of ab initio calculations, which include all vibrational levels up to 70–75 cm−1. There are small differences in energy, particularly above 60 cm−1, however, the main differences are in the assignments and are largely due to the limitations of assigning the ab initio wavefunctions to a simple stretch, bend, or combination when the states are mixed by the cubic anharmonic coupling. The availability of these experimental data presents an opportunity to extend ab initio calculations to higher vibrational energies to provide an assessment of the accuracy of the calculated potential surface away from the minimum. The intermolecular modes of the fluorobenzene-Ar2 trimer complex have also been investigated by dispersed fluorescence. The dominant structure is a pair of bands with a ∼35 cm−1 displacement from the origin band. Based on the set of vibrational modes calculated from the fluorobenzene-Ar frequencies, they are assigned to a Fermi resonance between the symmetric stretch and symmetric short axis bend overtone. The analysis of this resonance provides a measurement of the coupling strength between the stretch and short axis bend overtone in the dimer, an interaction that is not directly observed. The coupling matrix elements determined for the fluorobenzene-Ar stretch-long axis bend overtone and stretch-short axis bend overtone couplings are remarkably similar (3.8 cm−1 cf. 3.2 cm−1). Several weak features seen in the fluorobenzene-Ar2 spectrum have also been assigned.
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34.50.Ez Rotational and vibrational energy transfer
31.15.A- Ab initio calculations
31.50.Bc Potential energy surfaces for ground electronic states
33.20.Tp Vibrational analysis
33.50.Dq Fluorescence and phosphorescence spectra
34.20.Gj Intermolecular and atom-molecule potentials and forces

Synchrotron far infrared spectroscopy of the ground, ν5, and ν15 states of thiirane

Michael K. Bane, Christopher D. Thompson, Dominique R. T. Appadoo, and Don McNaughton

J. Chem. Phys. 137, 084306 (2012); http://dx.doi.org/10.1063/1.4747191 (6 pages)

Online Publication Date: 27 August 2012

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The high-resolution (0.001 cm−1) spectrum of thiirane has been recorded at the far-infrared beamline at the Australian synchrotron between 760‑400 cm−1 and 170‑10 cm−1. Ro-vibrational transitions of the highly Coriolis coupled ν5 (628.1 cm−1) and ν15 (669.7 cm−1) fundamentals, as well as pure rotational far-IR transitions have been assigned, and rotational, centrifugal distortion, and Coriolis interaction parameters determined. ν15 gains the vast majority of its intensity from an interesting Coriolis intensity stealing mechanism, which is also outlined.
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33.20.Ea Infrared spectra
33.15.Mt Rotation, vibration, and vibration-rotation constants

Ionization and Coulomb explosion of small group 10 transition metal oxide clusters in strong light fields

Matt W. Ross and A. W. Castleman, Jr.

J. Chem. Phys. 137, 084307 (2012); http://dx.doi.org/10.1063/1.4748139 (7 pages) | Cited 4 times

Online Publication Date: 28 August 2012

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The ionization properties of small group 10 metal oxide clusters are explored using ultrafast pulses centered at 624 nm. Maximum atomic charge states resulting from Coulomb explosion were observed to be Ni3+, Pd3+, Pt5+, and O2+ species with similar ionization potentials ∼30–35 eV. Ion signal as a function of laser intensity of each charge state of Ni, Pd, Pt, and O resulting from Coulomb explosion was mapped and compared to that predicted from semi-classical tunneling theory using sequential ionization potentials to quantify observed enhancements in ionization. The saturation intensity (Isat) of each charge state is measured and compared to previous studies on group 5 transition metal oxides. The atomic charge states of nickel showed a large enhancement in ionization compared to palladium and platinum, reflective of the differing bonding properties of each metal with oxygen. Results indicate that nickel oxide clusters undergo a greater extent of ionization enhancement as a result of multiple ionization mechanisms. The ionization enhancement behavior of each metal oxide species is explored herein.
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36.40.Jn Reactivity of clusters
33.80.Gj Diffuse spectra; predissociation, photodissociation
42.65.Re Ultrafast processes; optical pulse generation and pulse compression
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Fm Bond strengths, dissociation energies
33.80.Eh Autoionization, photoionization, and photodetachment

The electronic spectrum of CUONg4 (Ng = Ne, Ar, Kr, Xe): New insights in the interaction of the CUO molecule with noble gas matrices

Paweł Tecmer, Henk van Lingen, André Severo Pereira Gomes, and Lucas Visscher

J. Chem. Phys. 137, 084308 (2012); http://dx.doi.org/10.1063/1.4742765 (12 pages) | Cited 3 times

Online Publication Date: 28 August 2012

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The electronic spectrum of the CUO molecule was investigated with the IHFSCC-SD (intermediate Hamiltonian Fock-space coupled cluster with singles and doubles) method and with TD-DFT (time-dependent density functional theory) employing the PBE and PBE0 exchange–correlation functionals. The importance of both spin–orbit coupling and correlation effects on the low-lying excited-states of this molecule are analyzed and discussed. Noble gas matrix effects on the energy ordering and vibrational frequencies of the lowest electronic states of the CUO molecule were investigated with density functional theory (DFT) and TD-DFT in a supermolecular as well as a frozen density embedding (FDE) subsystem approach. This data is used to test the suitability of the FDE approach to model the influence of different matrices on the vertical electronic transitions of this molecule. The most suitable potential was chosen to perform relativistic wave function theory in density functional theory calculations to study the vertical electronic spectra of the CUO and CUONg4 with the IHFSCC-SD method.
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31.15.bw Coupled-cluster theory
31.15.ee Time-dependent density functional theory
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
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