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7 May 2009

Volume 130, Issue 17, Articles (17xxxx)

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J. Chem. Phys. 130, 174501 (2009); http://dx.doi.org/10.1063/1.3124187 (9 pages)

Saman Alavi, Robin Susilo, and John A. Ripmeester
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DNA origami impedance measurement at room temperature

Alfredo D. Bobadilla, Edson P. Bellido, Norma L. Rangel, Hong Zhong, Michael L. Norton, Alexander Sinitskii, and Jorge M. Seminario

J. Chem. Phys. 130, 171101 (2009); http://dx.doi.org/10.1063/1.3127362 (4 pages) | Cited 1 time

Online Publication Date: 1 May 2009

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The frequency response of triangular DNA origami is obtained at room temperature. The sample shows a high impedance at low frequencies, e.g., at zero frequency 20 GΩ, which decreases almost linearly with the logarithm of the frequency reaching a low and flat value at 100 kHz where the impedance turns from capacitive to resistive, concluding that DNA can be used for transmission of signals at frequencies larger than 100 kHz. It is also found that characteristics of DNA cannot be completely disentangled from the characteristics of the substrate on which it is deposited, making the design of molecular circuits more challenging than the design of circuits with present lumped devices; this is a natural feature at the nanoscale.
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87.14.gk DNA
85.65.+h Molecular electronic devices
84.37.+q Measurements in electric variables (including voltage, current, resistance, capacitance, inductance, impedance, and admittance, etc.)
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The work-Hamiltonian connection and the usefulness of the Jarzynski equality for free energy calculations

Eric N. Zimanyi and Robert J. Silbey

J. Chem. Phys. 130, 171102 (2009); http://dx.doi.org/10.1063/1.3132747 (3 pages) | Cited 3 times

Online Publication Date: 6 May 2009

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The connection between work and changes in the Hamiltonian for a system with a time-dependent Hamiltonian has recently been called into question, casting doubt on the usefulness of the Jarzynski equality for calculating free energy changes. In this paper, we discuss the relationship between two possible definitions of free energy and show how some recent disagreements regarding the applicability of the Jarzynski equality are the result of different authors' using different definitions of free energy. Finally, in light of the recently raised doubts, we explicitly demonstrate that it is indeed possible to obtain physically relevant free energy profiles from molecular pulling experiments by using the Jarzynski equality and the results of Hummer and Szabo.
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05.70.Ce Thermodynamic functions and equations of state
05.70.Ln Nonequilibrium and irreversible thermodynamics
05.20.-y Classical statistical mechanics
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back to top Theoretical Methods and Algorithms

Accurate interaction energies at density functional theory level by means of an efficient dispersion correction

Alisa Krishtal, Kenno Vanommeslaeghe, András Olasz, Tamás Veszprémi, Christian Van Alsenoy, and Paul Geerlings

J. Chem. Phys. 130, 174101 (2009); http://dx.doi.org/10.1063/1.3126248 (8 pages) | Cited 14 times

Online Publication Date: 1 May 2009

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This paper presents an approach for obtaining accurate interaction energies at the density functional theory level for systems where dispersion interactions are important. This approach combines Becke and Johnson’s [J. Chem. Phys. 127, 154108 (2007)] method for the evaluation of dispersion energy corrections and a Hirshfeld method for partitioning of molecular polarizability tensors into atomic contributions. Due to the availability of atomic polarizability tensors, the method is extended to incorporate anisotropic contributions, which prove to be important for complexes of lower symmetry. The method is validated for a set of 18 complexes, for which interaction energies were obtained with the B3LYP, PBE, and TPSS functionals combined with the aug-cc-pVTZ basis set and compared with the values obtained at the CCSD(T) level extrapolated to a complete basis set limit. It is shown that very good quality interaction energies can be obtained by the proposed method for each of the examined functionals, the overall performance of the TPSS functional being the best, which with a slope of 1.00 in the linear regression equation and a constant term of only 0.1 kcal/mol allows to obtain accurate interaction energies without any need of a damping function for complexes close to their exact equilibrium geometry.
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31.15.E- Density-functional theory
31.15.bw Coupled-cluster theory
32.30.-r Atomic spectra
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.15.Bh General molecular conformation and symmetry; stereochemistry

Comparison of second-order split operator and Chebyshev propagator in wave packet based state-to-state reactive scattering calculations

Zhigang Sun, Soo-Y. Lee, Hua Guo, and Dong H. Zhang

J. Chem. Phys. 130, 174102 (2009); http://dx.doi.org/10.1063/1.3126363 (11 pages) | Cited 9 times

Online Publication Date: 1 May 2009

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A detailed comparison of the time-dependent wave packet method using the split operator propagator and recently introduced Chebyshev real wave packet approach for calculating reactive scattering processes is reported. As examples, the state-to-state differential cross sections of the H+H′D(v0 = 0,j0 = 1)→H′D+H/H′H+D reaction, the state-to-state reaction probabilities of the 16O+35O2 (v0 = 0,j0 = 0)→17O+16O18O/18O+16O17O reaction, the H+O2→O+HO reaction, and the F+HD→HF+D reaction are calculated, using an efficient reactant-coordinate-based method on an L-shape grid which allows the extraction of the state-to-state information of the two product channels simultaneously. These four reactions have quite different dynamic characteristics and thus provide a comprehensive picture of the relative advantages of these two propagation methods for describing reactive scattering dynamics. The results indicate that the Chebyshev real wave packet method is typically more accurate, particularly for reactions dominated by long-lived resonances. However, the split operator approach is often more cost effective, making it a method of choice for fast reactions. In addition, our results demonstrate accuracy of the reactant-coordinate-based method for extracting state-to-state information.
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82.20.Rp State to state energy transfer
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Hf Product distribution

Refining the weighted stochastic simulation algorithm

Dan T. Gillespie, Min Roh, and Linda R. Petzold

J. Chem. Phys. 130, 174103 (2009); http://dx.doi.org/10.1063/1.3116791 (10 pages) | Cited 3 times

Online Publication Date: 6 May 2009

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The weighted stochastic simulation algorithm (wSSA) recently introduced by Kuwahara and Mura [ J. Chem. Phys. 129, 165101 (2008) ] is an innovative variation on the stochastic simulation algorithm (SSA). It enables one to estimate, with much less computational effort than was previously thought possible using a Monte Carlo simulation procedure, the probability that a specified event will occur in a chemically reacting system within a specified time when that probability is very small. This paper presents some procedural extensions to the wSSA that enhance its effectiveness in practical applications. The paper also attempts to clarify some theoretical issues connected with the wSSA, including its connection to first passage time theory and its relation to the SSA.
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82.20.Uv Stochastic theories of rate constants
02.50.Cw Probability theory
82.20.Wt Computational modeling; simulation

General treatment of paramagnetic relaxation enhancement associated with translational diffusion

D. Kruk and J. Kowalewski

J. Chem. Phys. 130, 174104 (2009); http://dx.doi.org/10.1063/1.3119635 (12 pages) | Cited 10 times

Online Publication Date: 6 May 2009

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A theory of nuclear spin relaxation in isotropic liquids for nuclear spins interacting with electron spins, residing in other molecules (the outer-sphere relaxation), is presented. The approach, valid outside of the Redfield limit for electron spin relaxation, is an extension of the Swedish slow motion theory [ Benetis et al., Mol. Phys. 48, 329 (1983) ; Nilsson and Kowalewski, J. Magn. Reson. 146, 345 (2000) ] for inner-sphere relaxation. It is demonstrated that the outer-sphere relaxation rate can be expressed as an integral of a product of a translational diffusion correlation function and a function analogous to the inner-sphere spectral density. A numerical implementation of the theory is described and applied to a large number of realistic parameter sets for S = 7/2 and S = 1, which may correspond to Gd(III) and Ni(II) systems. It is shown that the outer-sphere contribution is relevant and should be included into the analysis of nuclear magnetic relaxation dispersion relaxation profiles, especially for slow relative translational diffusion and fast molecular tumbling.
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76.60.Es Relaxation effects
66.10.C- Diffusion and thermal diffusion

Quasidiabatic states described by coupled-cluster theory

Takatoshi Ichino, Jürgen Gauss, and John F. Stanton

J. Chem. Phys. 130, 174105 (2009); http://dx.doi.org/10.1063/1.3127246 (16 pages) | Cited 9 times

Online Publication Date: 7 May 2009

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In an attempt to expand the utility of the model Hamiltonian technique developed by Köppel, Domcke, and Cederbaum (KDC) [Adv. Chem. Phys. 57, 59 (1984) ], an ansatz for quasidiabatic wave functions is introduced in the framework of equation-of-motion coupled-cluster (EOM-CC) theory. Based on the ansatz, the theory for the analytic first derivative of the off-diagonal element of the quasidiabatic potential matrix is developed by extending the theory for the analytic gradient of the EOM-CC energy. This analytic derivative is implemented for EOM-CCSD (singles and doubles approximation) calculations of radicals subject to pseudo-Jahn–Teller and Jahn–Teller interactions. Its applicability in construction of the KDC quasidiabatic model potential is discussed.
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31.15.bw Coupled-cluster theory
31.30.-i Corrections to electronic structure

TIGER2: An improved algorithm for temperature intervals with global exchange of replicas

Xianfeng Li, Robert A. Latour, and Steven J. Stuart

J. Chem. Phys. 130, 174106 (2009); http://dx.doi.org/10.1063/1.3129342 (9 pages) | Cited 6 times

Online Publication Date: 7 May 2009

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An empirical sampling method for molecular simulation based on “temperature intervals with global exchange of replicas” (TIGER2) has been developed to reduce the high demand for computational resources and the low computational efficiency of the conventional replica-exchange molecular dynamics (REMD) method. This new method overcomes the limitation of its previous version, called TIGER, which requires the assumption of constant heat capacity during quenching of replicas from elevated temperatures to the baseline temperature. The robustness of the TIGER2 method is examined by comparing it against a Metropolis Monte Carlo simulation for sampling the conformational distribution of a single butane molecule in vacuum, a REMD simulation for sampling the behavior of alanine dipeptide in explicit solvent, and REMD simulations for sampling the folding behavior of two peptides, (AAQAA)3 and chignolin, in implicit solvent. The agreement between the results from these conventional sampling methods and the TIGER2 simulations indicates that the TIGER2 algorithm is able to closely approximate a Boltzmann-weighted ensemble of states for these systems but without the limiting assumptions that were required for the original TIGER algorithm. TIGER2 is an efficient replica-exchange sampling method that enables the number of replicas that are used for a replica-exchange simulation to be substantially reduced compared to the conventional REMD method.
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31.15.xv Molecular dynamics and other numerical methods
87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.15.ap Molecular dynamics simulation
87.15.ak Monte Carlo simulations
33.15.Bh General molecular conformation and symmetry; stereochemistry

Nonadiabatic dynamics at metal surfaces: Independent-electron surface hopping

Neil Shenvi, Sharani Roy, and John C. Tully

J. Chem. Phys. 130, 174107 (2009); http://dx.doi.org/10.1063/1.3125436 (12 pages) | Cited 14 times

Online Publication Date: 7 May 2009

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Recent experiments have shown convincing evidence for nonadiabatic energy transfer from adsorbate degrees of freedom to surface electrons during the interaction of molecules with metal surfaces. In this paper, we propose an independent-electron surface hopping algorithm for the simulation of nonadiabatic gas-surface dynamics. The transfer of energy to electron-hole pair excitations of the metal is successfully captured by hops between electronic adiabats. The algorithm is able to account for the creation of multiple electron-hole pairs in the metal due to nonadiabatic transitions. Detailed simulations of the vibrational relaxation of nitric oxide on a gold surface, employing a multistate potential energy surface fit to density functional theory calculations, confirm that our algorithm can capture the underlying physics of the inelastic scattering process.
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68.43.-h Chemisorption/physisorption: adsorbates on surfaces
79.20.Rf Atomic, molecular, and ion beam impact and interactions with surfaces
34.35.+a Interactions of atoms and molecules with surfaces
34.50.Ez Rotational and vibrational energy transfer
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
68.43.Pq Adsorbate vibrations
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Full-dimensional ab initio potential energy surface and vibrational configuration interaction calculations for vinyl

Amit R. Sharma, Bastiaan J. Braams, Stuart Carter, Benjamin C. Shepler, and Joel M. Bowman

J. Chem. Phys. 130, 174301 (2009); http://dx.doi.org/10.1063/1.3120607 (9 pages) | Cited 10 times

Online Publication Date: 1 May 2009

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The potential energy landscape and two permutationally invariant, full-dimensional ab initio-based potential energy surfaces (PESs) for the doublet vinyl radical, C2H3, are described. The first of the two surfaces, denoted as PES/S, describes the equivalent CH2CH global minimum and the saddle point separating them, planar and nonplanar H-atom migration saddle points, a methylcarbyne local minimum that is due to a Jahn–Teller conical intersection, and the saddle point connecting it with the global minimum. The second PES, denoted PES/D, contains all stationary points of PES/S and in addition describes dissociation to C2H2+H fragments, including the saddle point to dissociation along a least-energy path. The surfaces are least-squares fits to electronic energies obtained with use of the spin-restricted coupled cluster singles and doubles with perturbative treatment of triples method and augmented correlation consistent polarized valence triple zeta basis sets, using permutationally invariant polynomials in “Morse variables” and a many-body expansion. PES/S is a fit to roughly 34 000 and PES/D to roughly 50 000 electronic structure energies. PES/S is used in full-dimensional, vibrational configuration interaction calculations of the vinyl zero-point energy and fundamental vibrational energies, which are compared to recent experiments.
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31.50.Bc Potential energy surfaces for ground electronic states
31.30.-i Corrections to electronic structure
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.bw Coupled-cluster theory
31.15.vq Electron correlation calculations for polyatomic molecules
02.60.Ed Interpolation; curve fitting

Infrared spectra of SF6−⋅HCOOH⋅Arn (n = 0–2): Infrared triggered reaction and Ar-induced reactive inhibition

Holger Schneider, Kaito Takahashi, Rex T. Skodje, and J. Mathias Weber

J. Chem. Phys. 130, 174302 (2009); http://dx.doi.org/10.1063/1.3125960 (10 pages) | Cited 1 time

Online Publication Date: 1 May 2009

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We present the infrared spectra of SF6−⋅HCOOH⋅Arm (m = 0–2) complexes. We find that the binding motif involves a single hydrogen bond between the SF6− anion and the OH group of the formic acid, with the CH group weakly tethered to a neighboring F atom. Similar to the case of hydrated SF6−, the SF bond involved in the (OH–F) bond is significantly stretched and weakened by the attachment of the HCOOH ligand. The bare complex undergoes reaction upon infrared absorption in the CH/OH stretching region of the formic acid moiety, leading predominantly to the formation of SF4−+2HF+CO2. The reaction can be inhibited by attachment of two Ar atoms. We discuss a likely reaction mechanism in the framework of ab initio calculations, suggesting that reaction proceeds via tunneling through the potential barrier.
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82.80.Dx Analytical methods involving electronic spectroscopy
82.20.Db Transition state theory and statistical theories of rate constants
82.30.Nr Association, addition, insertion, cluster formation
78.30.Jw Organic compounds, polymers

Doppler widths in electron quasielastic scattering from molecular gases

R. Moreh and D. Nemirovsky

J. Chem. Phys. 130, 174303 (2009); http://dx.doi.org/10.1063/1.3125968 (5 pages) | Cited 6 times

Online Publication Date: 1 May 2009

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Recent quasielastic electron scattering experiments on some molecular gases at Ee ≥ 1.8 keV have shown that the scattering is from single isotopes of the atomic components of the gas. The scattered electron lines at definite angles are Doppler broadened by the instantaneous kinetic energy (KE) of the scattering atoms. We calculated the KE of the scattering atoms by accounting for translation, rotation, and all normal modes of vibrations of the molecule. The results reveal some large and fundamental differences from literature estimates.
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34.80.Bm Elastic scattering
33.20.Sn Rotational analysis
33.70.Jg Line and band widths, shapes, and shifts
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis

Infrared absorption of gaseous c-ClCOOH and t-ClCOOH recorded with a step-scan Fourier-transform spectrometer

Li-Kang Chu and Yuan-Pern Lee

J. Chem. Phys. 130, 174304 (2009); http://dx.doi.org/10.1063/1.3122722 (8 pages) | Cited 3 times

Online Publication Date: 4 May 2009

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Two conformers of ClCOOH were produced upon irradiation at 355 nm of a gaseous flowing mixture of Cl2, HCOOH, and N2. A step-scan Fourier-transform infrared spectrometer coupled with a multipass absorption cell was utilized to monitor the transient spectra of ClCOOH. Absorption bands with origins at 1808.0 and 1328.5 cm−1 are attributed to the C = O stretching and COH bending modes of t-ClCOOH, respectively; those at 1883.0 and 1284.9 cm−1 are assigned as the C = O stretching and COH bending modes of c-ClCOOH, respectively. These observed vibrational wavenumbers agree with corresponding values for t-ClCOOH and c-ClCOOH predicted with B3LYP/aug-cc-pVTZ density-functional theory and the observed rotational contours agree satisfactorily with simulated bands based on predicted rotational parameters. The observed relative intensities indicate that t-ClCOOH is more stable than c-ClCOOH by ∼ 3 kJ mol−1. A simple kinetic model is employed to account for the production and decay of ClCOOH.
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33.20.Ea Infrared spectra
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.E- Density-functional theory

NO chemisorption dynamics on thick FePc and ttbu-FePc films

N. L. Tran, S. R. Bishop, T. J. Grassman, G. C. Poon, F. I. Bohrer, W. C. Trogler, and A. C. Kummel

J. Chem. Phys. 130, 174305 (2009); http://dx.doi.org/10.1063/1.3085808 (7 pages) | Cited 2 times

Online Publication Date: 6 May 2009

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The NO chemisorption dynamics on ordered multilayer iron phthalocyanine (FePc) and quasiamorphous multilayer tetra-t-butyl FePc (ttbu-FePc) films on a Au(111) substrate was investigated using the King and Wells reflection technique. The NO zero coverage or initial sticking probabilities (S0) were measured as a function of sample temperature (Ts) and beam energy (Ei). The experimental results for both films show a monotonic decrease in S0 with increasing Ts and Ei consistent with NO adsorption occurring via a multiple pathway precursor-mediated mechanism in which the adsorbate initially physisorbs to the FePc organics, diffuses, and chemisorbs to the Fe metal center. The saturation coverage is 3% for the multilayer FePc surface and only 2% for the multilayer ttbu-FePc surface consistent with NO chemisorption occurring only on the Fe metal, where NO chemisorbs to 100% of the surface Fe metal centers. The reduced saturation coverage in the ttbu-FePc film is attributed to fewer Fe metal centers in the less dense ttbu-FePc films. A comparison of NO sticking on a multilayer FePc/Au(111) film with NO sticking on a monolayer FePc/Au(111) film shows that S0 is greater on the multilayer FePc film for all Ts and Ei, consistent with an increase in collision inelasticity for NO/multilayer FePc/Au(111).
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68.43.Jk Diffusion of adsorbates, kinetics of coarsening and aggregation
66.30.Ny Chemical interdiffusion; diffusion barriers
68.55.-a Thin film structure and morphology

Determination of the ionization and dissociation energies of the hydrogen molecule

Jinjun Liu, Edcel J. Salumbides, Urs Hollenstein, Jeroen C. J. Koelemeij, Kjeld S. E. Eikema, Wim Ubachs, and Frédéric Merkt

J. Chem. Phys. 130, 174306 (2009); http://dx.doi.org/10.1063/1.3120443 (8 pages) | Cited 18 times

Online Publication Date: 6 May 2009

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The transition wave number from the EF 1Σg+(v = 0,N = 1) energy level of ortho-H2 to the 54p11(0) Rydberg state below the X+ 2Σg+(v+ = 0,N+ = 1) ground state of ortho-H2+ has been measured to be 25 209.997 56±(0.000 22)statistical±(0.000 07)systematic cm−1. Combining this result with previous experimental and theoretical results for other energy level intervals, the ionization and dissociation energies of the hydrogen molecule have been determined to be 124 417.491 13(37) and 36 118.069 62(37) cm−1, respectively, which represents a precision improvement over previous experimental and theoretical results by more than one order of magnitude. The new value of the ionization energy can be regarded as the most precise and accurate experimental result of this quantity, whereas the dissociation energy is a hybrid experimental-theoretical determination.
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33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
33.80.Gj Diffuse spectra; predissociation, photodissociation
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
31.50.Df Potential energy surfaces for excited electronic states

On the controversial nature of the 1 1Bu and 2 1Bu states of trans-stilbene: The n-electron valence state perturbation theory approach

Celestino Angeli, Roberto Improta, and Fabrizio Santoro

J. Chem. Phys. 130, 174307 (2009); http://dx.doi.org/10.1063/1.3131263 (6 pages) | Cited 1 time

Online Publication Date: 6 May 2009

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The nature of two lowest-energy states of Bu symmetry of trans-stilbene and the accurate calculation of their vertical excitation energy have been the subject of a controversy because time dependent density functional theory (TD-DFT) calculations, in agreement with experimental observations, have questioned the results obtained with multireference perturbation theory (MRPT) in the CASPT2 implementation. This paper aims to solve this controversy. By using a different version of MRPT, the n-electron valence state perturbation theory method, the description provided by TD-DFT is confirmed: the lowest Bu singlet state has a HOMO→LUMO nature and a large oscillator strength (HOMO refers to highest occupied molecular orbital and LUMO refers to lowest unoccupied molecular orbital), while the second Bu singlet state has a mixed HOMO−1→LUMO and HOMO→LUMO+1 nature, has an oscillator strength almost vanishing, and is located at 0.6–0.7 eV higher than the first excited state. The computed vertical excitation energy to the first state (3.8–4.0 eV) is in good agreement with the experimental value.
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31.15.ee Time-dependent density functional theory
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
31.15.xp Perturbation theory

Assignment of photoelectron spectra of (TiO2)n with n = 1–3

Yuzhen Liu, Yongbo Yuan, Zhoubin Wang, Kaiming Deng, Chuanyun Xiao, and Qunxiang Li

J. Chem. Phys. 130, 174308 (2009); http://dx.doi.org/10.1063/1.3126776 (6 pages) | Cited 4 times

Online Publication Date: 6 May 2009

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This paper reports a comprehensive study of (TiO2)n (n = 1–3) clusters on their structures, vertical electron affinities (VEA) and adiabatic electron affinities (AEA), and excited states that are further correlated with experimental photoelectron spectra (PES). Local density functional and time-dependent density functional methods (TTDFT) with 6–31G(d) basis set are used. For (TiO2)n with n = 1 and 3, the ground-state geometries are found to have C2v and Cs structures, respectively, in both neutral and anionic charge states. For neutral (TiO2)2, the most stable structure corresponds to a C2h conformation. For anionic (TiO2)2−, two isomers with C2h and C2v symmetries are identified to be nearly isoenergetic. This conclusion is supported by reoptimization at CCSD/6–31G(d) level and single-point calculation at CCSD(T)/6-311+G(d) level. Hence, they are competitive candidates for the ground-state structure of (TiO2)2−. For TiO2 and (TiO2)3, the calculated VEA and AEA values agree well with the experimental data. For (TiO2)2, the VEA and AEA obtained with the C2v structure agree well with the experimental data while those with the C2h structure do not. The subsequent assignment of PES indicates that it is the C2v isomer of (TiO2)2− that represents the structure from which the photoexcitation in experimental PES takes place. TDDFT is used to determine the excited states of (TiO2)n (n = 1–3) and the calculated excitation energies are in good agreement with PES experiment.
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79.60.-i Photoemission and photoelectron spectra
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.20.Ps Other inorganic compounds
61.46.Bc Structure of clusters (e.g., metcars; not fragments of crystals; free or loosely aggregated or loosely attached to a substrate)

Kinetic nucleation model for free expanding water condensation plume simulations

Zheng Li, Jiaqiang Zhong, Deborah A. Levin, and Barbara J. Garrison

J. Chem. Phys. 130, 174309 (2009); http://dx.doi.org/10.1063/1.3129804 (10 pages) | Cited 5 times

Online Publication Date: 7 May 2009

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Recent direct simulation Monte Carlo (DSMC) simulations of homogeneous condensation in free expansion water plumes [ Z. Li, J. Zhong, D. A. Levin, and B. Garrison, AIAA J. 47, 1241 (2009) ] show that the nucleation rate is a key factor for accurately modeling condensation phenomenon. In this work, we use molecular dynamics (MD) simulations of a free expansion to explore the microscopic mechanisms of water dimer formation and develop collision models required by DSMC. Bimolecular and termolecular dimer cluster formation mechanisms are considered and the former is found to be the main mechanism in expanding flows to vacuum. MD simulations between two water molecules using the simple point charge intermolecular potential were performed to predict the bimolecular dimer formation probability and the probability was found to decrease with collision energy. The formation probabilities and postcollisional velocity and energy distributions were then integrated into DSMC simulations of a free expansion of an orifice condensation plume with different chamber stagnation temperatures and pressures. The dimer mole fraction was found to increase with distance from the orifice and become constant after a distance of about two orifice diameters. Similar to experiment, the terminal dimer mole fraction was found to decrease with chamber stagnation temperatures and increase linearly with chamber stagnation pressures which is consistent with a bimolecular nucleation mechanism.
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64.70.fm Thermodynamics studies of evaporation and condensation
47.40.-x Compressible flows; shock waves
47.11.Mn Molecular dynamics methods
64.60.qe General theory and computer simulations of nucleation

A combining rule calculation of the ground state van der Waals potentials of the mercury rare-gas complexes

X. W. Sheng, P. Li, and K. T. Tang

J. Chem. Phys. 130, 174310 (2009); http://dx.doi.org/10.1063/1.3126779 (9 pages) | Cited 11 times

Online Publication Date: 7 May 2009

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The ground state van der Waals potentials of the Hg–RG (RG = He,Ne,Ar,Kr,Xe) systems are generated by the Tang–Toennies potential model. The parameters of the model are calculated from the potentials of the homonuclear mercury and rare-gas dimers with combining rules. The predicted spectroscopic parameters for these mercury rare-gas complexes are in good agreement with available experimental values, except for Hg–He. In the repulsive and potential well regions, the predicted potential energy curves agree with the available experimental hybrid potentials, but they differ in the long range part of the potential. On the other hand, the present potentials are in agreement with the ab initio CCSD(T) calculations in the long range part of the potential, but there are some differences in the short repulsive regions. According to the present theory, the reduced potential curves of these five systems, including Hg–He, are almost identical to each other. This reduced potential curve can also describe, within a few percent, the five reduced potentials obtained from the ab initio CCSD(T) calculations. These reduced potentials have a potential bowl that is wider than that of the rare-gas dimers, but narrower than the mercury dimer.
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34.20.Cf Interatomic potentials and forces
31.15.A- Ab initio calculations
31.50.-x Potential energy surfaces
31.15.bw Coupled-cluster theory

Quantum mechanical study of vibrational energy transfer in Ar–O3 collisions: Influence of symmetry

M. V. Ivanov, S. Yu. Grebenshchikov, and R. Schinke

J. Chem. Phys. 130, 174311 (2009); http://dx.doi.org/10.1063/1.3126247 (10 pages) | Cited 5 times

Online Publication Date: 7 May 2009

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The vibrational energy transfer in Ar–O3 collisions is investigated within the breathing sphere approximation. Ozone wave functions are calculated with a simplified potential energy surface and used in the close coupling scattering equations. Inelastic transition probabilities are determined for all bound states of O3. Energy transfer is studied in one asymmetric, 16O16O18O, and two symmetric isotopomers, 16O16O16O and 16O18O16O. Two measures of the energy transfer are considered: Microcanonical deactivation for a fixed collision energy and thermal vibrational relaxation described by the master equation at a fixed temperature. In either case, the energy transfer is symmetry independent near the dissociation threshold and the sensitivity to symmetry grows as the ozone energy decreases.
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34.50.Ez Rotational and vibrational energy transfer
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
31.50.-x Potential energy surfaces

Two- and three-photon absorption of organic ionic pyrylium based materials

Prakash Chandra Jha, Yi Luo, Ioannis Polyzos, Peter Persephonis, and Hans Ågren

J. Chem. Phys. 130, 174312 (2009); http://dx.doi.org/10.1063/1.3123742 (7 pages)

Online Publication Date: 7 May 2009

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Pyrylium dyes having the same basic chemical structure, differing only to a specific substituent, have been used as novel materials for multiphoton three-dimensional data storage. Electronic absorption spectra, two-photon and three-photon absorption properties of this class of pyrylium dyes, have been studied theoretically and compared to experimental results. The effects of the counteranion, the surrounding solvent, and electron releasing and electron withdrawing groups in specific positions of the basic structure have been explored in detail. It is argued that on grounds of the quality of experimental spectroscopic agreement, the computed two- and three-photon data may be used in pulse propagation simulations of three-dimensional recording in optical memories.
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33.15.Bh General molecular conformation and symmetry; stereochemistry
31.70.Dk Environmental and solvent effects
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
42.79.Vb Optical storage systems, optical disks

H3+ as a trap for noble gases-3: Multiple trapping of neon, argon, and krypton in XnH3+ (n = 1–3)

F. Pauzat, Y. Ellinger, J. Pilmé, and O. Mousis

J. Chem. Phys. 130, 174313 (2009); http://dx.doi.org/10.1063/1.3126777 (15 pages) | Cited 2 times

Online Publication Date: 7 May 2009

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Recent studies on the formation of XH3+ noble gas complexes have shown strategic implications for the composition of the atmospheres of the giant planets as well as for the composition of comets. One crucial factor in the astrophysical process is the relative abundances of the noble gases versus H3+. It is the context in which the possibility for clustering with more than one noble gas (XnH3+ up to n = 3) has been investigated for noble gases X ranging from neon to krypton. In order to assert our results, a variety of methods have been used including ab initio coupled cluster CCSD and CCSD(T), MP2, and density functional BH&HLYP levels of theory. All complexes with one, two, and three noble gases are found to be stable in the Ne, Ar, and Kr families. These stable structures are planar with the noble gases attached to the apices of the H3+ triangle. The binding energy of the nth atom, defined as the XnH3+→Xn−1H3++X reaction energy, increases slightly with n varying from 1 to 3 in the neon series, while it decreases in the argon series and shows a minimum for n = 2 in the krypton series. The origin of this phenomenon is to be found in the variations in the respective vibrational energies. A topological analysis of the electron localization function shows the importance of the charge transfer from the noble gases toward H3+ as a driving force in the bonding along the series. It is also consistent with the increase in the atomic polarizabilities from neon to krypton. Rotational constants and harmonic frequencies are reported in order to provide a body of data to be used for the detection in laboratory prior to space observations. This study strongly suggests that the noble gases could be sequestered even in an environment where the H3+ abundance is small.
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31.15.A- Ab initio calculations
31.15.E- Density-functional theory
31.15.bw Coupled-cluster theory
34.70.+e Charge transfer
37.10.-x Atom, molecule, and ion cooling methods

Photolysis of n-butyl nitrite and isoamyl nitrite at 355 nm: A time-resolved Fourier transform infrared emission spectroscopy and ab initio study

Min Ji, Junfeng Zhen, Qun Zhang, and Yang Chen

J. Chem. Phys. 130, 174314 (2009); http://dx.doi.org/10.1063/1.3129806 (5 pages) | Cited 3 times

Online Publication Date: 7 May 2009

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We report on the photodissociation dynamics study of n-butyl nitrite and isoamyl nitrite by means of time-resolved Fourier transform infrared (TR-FTIR) emission spectroscopy. The obtained TR-FTIR emission spectra of the nascent NO fragments produced in the 355 nm laser photolysis of the two alkyl nitrite species showed an almost identical rotational temperature and vibrational distributions of NO. In addition, a close resemblance between the two species was also found in the measured temporal profiles of the IR emission of NO and the recorded UV absorption spectra. The experimental results are consistent with our ab initio calculations using the time-dependent density functional theory at the B3LYP/6-311G(d,p) level, which indicate that the substitution of one of the two γ-H atoms in n-C4H9ONO with a methyl group to form (CH3)2C3H5ONO has only a minor effect on the photodissociation dynamics of the two molecules.
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82.50.Bc Processes caused by infrared radiation
82.20.Db Transition state theory and statistical theories of rate constants
82.80.Gk Analytical methods involving vibrational spectroscopy
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Linking microscopic guest properties to macroscopic observables in clathrate hydrates: Guest-host hydrogen bonding

Saman Alavi, Robin Susilo, and John A. Ripmeester

J. Chem. Phys. 130, 174501 (2009); http://dx.doi.org/10.1063/1.3124187 (9 pages) | Cited 24 times

Online Publication Date: 1 May 2009

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Molecular dynamics simulations are used to compare microscopic structures and guest dynamics to macroscopic properties in structure II clathrate hydrates with cyclopentane, tetrahydrofuran (THF), 1,3-dioxolane, tetrahydropyran (THP), and p-dioxane as guests. Significant differences are observed between structural parameters and rotational dynamics for the different guests. The simulations show the formation of guest-host hydrogen bonds between the ether oxygen atoms of THF and THP and the cage water hydrogen atoms of the clathrate but the absence of similar hydrogen bonds in the clathrate hydrates of the other guests on the time scale of the calculations. This guest-host hydrogen bonding leads to the formation of Bjerrum L-defects in the clathrate water lattice where two adjacent water molecules have no covalently bonded hydrogen atom between them. Unlike Bjerrum defects of ice lattices, these guest-induced L-defects are not accompanied by the formation of a D-defect at an adjacent site in the water lattice. At the simulation temperature of 200 K, the guest-water hydrogen bonds in the THF clathrate are short lived (lifetime less than 1 ps) but in the THP they are longer lived (a minimum of 100 ps). A van’t Hoff plot for the probability of defect formation in THF as a function of temperature gives an activation barrier of ∼ 8.3 kJ/mol for guest-host defect formation in the THF clathrate. The consequences of the defect formation on the thermal expansivity, isothermal compressibility, dipole-dipole correlation function, and mechanical stability of the clathrate are discussed.
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61.50.Lt Crystal binding; cohesive energy
65.40.De Thermal expansion; thermomechanical effects
62.20.F- Deformation and plasticity
81.40.Lm Deformation, plasticity, and creep

Energetic recoils in UO2 simulated using five different potentials

Ram Devanathan, Jianguo Yu, and William J. Weber

J. Chem. Phys. 130, 174502 (2009); http://dx.doi.org/10.1063/1.3125967 (9 pages) | Cited 7 times

Online Publication Date: 1 May 2009

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This report presents the results of classical molecular dynamics simulations of the diffuse premelting transition, melting, and defect production by 1 keV U recoils in UO2 using five different rigid ion potentials. The experimentally observed premelting transition occurred for all five cases. For all the potentials studied, dynamic defect annealing is highly effective and is accompanied by replacement events on the anion sublattice. The primary damage state after ∼ 15 ps consists of isolated Frenkel pairs and interstitial and vacancy clusters of various sizes. The average displacement energy varies from ∼ 28 to ∼ 83 eV and the number of Frenkel pairs is different by a factor of 3 depending on the choice of potential. The size and spatial distribution of vacancy and interstitial clusters is drastically different for the potentials studied. The results provide statistics of defect production. They point to a pressing need to determine defect formation, migration, and binding energies in UO2 from first principles and to develop reliable potentials based on this data for simulating microstructural evolution in nuclear fuel under operating conditions.
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61.72.Cc Kinetics of defect formation and annealing
61.43.Bn Structural modeling: serial-addition models, computer simulation
28.52.Fa Materials
61.72.jd Vacancies
61.72.jj Interstitials
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