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21 May 2009

Volume 130, Issue 19, Articles (19xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 130, 194101 (2009); http://dx.doi.org/10.1063/1.3129843 (13 pages)

Eric Vanden-Eijnden and Maddalena Venturoli
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back to top Theoretical Methods and Algorithms

Markovian milestoning with Voronoi tessellations

Eric Vanden-Eijnden and Maddalena Venturoli

J. Chem. Phys. 130, 194101 (2009); http://dx.doi.org/10.1063/1.3129843 (13 pages) | Cited 18 times

Online Publication Date: 15 May 2009

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A new milestoning procedure using Voronoi tessellations is proposed. In the new procedure, the edges of Voronoi cells are used as milestones, and the necessary kinetic information about the transitions between the milestones is calculated by running molecular dynamics (MD) simulations restricted to these cells. Like the traditional milestoning technique, the new procedure offers a reduced description of the original dynamics and permits to efficiently compute the various quantities necessary in this description. However, unlike traditional milestoning, the new procedure does not require to reinitialize trajectories from the milestones, and thereby it avoids the approximation made in traditional milestoning that the distribution for reinitialization is the equilibrium one. In this paper we concentrate on Markovian milestoning, which we show to be valid under suitable assumptions, and we explain how to estimate the rate matrix of transitions between the milestones from data collected from the MD trajectories in the Voronoi cells. The rate matrix can then be used to compute mean first passage times between milestones and reaction rates. The procedure is first illustrated on test-case examples in two dimensions and then applied to study the kinetics of protein insertion into a lipid bilayer by means of a coarse-grained model.
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87.15.kt Protein-membrane interactions
82.20.Wt Computational modeling; simulation
82.20.Db Transition state theory and statistical theories of rate constants
82.20.Uv Stochastic theories of rate constants
87.15.ap Molecular dynamics simulation
87.15.R- Reactions and kinetics

Two-component relativistic density functional method for computing nonsingular complex linear response of molecules based on the zeroth order regular approximation

Ajitha Devarajan, Alexander Gaenko, and Jochen Autschbach

J. Chem. Phys. 130, 194102 (2009); http://dx.doi.org/10.1063/1.3123765 (13 pages) | Cited 7 times

Online Publication Date: 15 May 2009

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We report the implementation of a frequency-dependent two-component relativistic density functional theory method based on the zeroth order regular approximation (ZORA) for computations of complex linear response of molecules including spin-orbit coupling. The implementation is based on Slater-type atomic orbital basis functions and makes extensive use of density fitting techniques. The complex response is obtained by applying damping in the computations. The method is validated by computations of the real and imaginary part of the static and dynamic polarizability of group 12 atoms, of a number of heavy-atom diatomic molecules, of a range of two- and three-dimensional gold clusters, and of group 8 oxides and metallocenes. Simulated spectra—a plot of extinction coefficient as a function of frequency—obtained from the isotropic imaginary polarizability are compared to broadened spectra obtained from two-component ZORA excitation energies and oscillator strengths.
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31.30.jd Relativistic corrections due to negative-energy states or processes
31.15.E- Density-functional theory
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
36.40.Cg Electronic and magnetic properties of clusters

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies

Eric Vanden-Eijnden and Maddalena Venturoli

J. Chem. Phys. 130, 194103 (2009); http://dx.doi.org/10.1063/1.3130083 (17 pages) | Cited 18 times

Online Publication Date: 15 May 2009

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An improved and simplified version of the finite temperature string (FTS) method [ W. E, W. Ren, and E. Vanden-Eijnden, J. Phys. Chem. B 109, 6688 (2005) ] is proposed. Like the original approach, the new method is a scheme to calculate the principal curves associated with the Boltzmann–Gibbs probability distribution of the system, i.e., the curves which are such that their intersection with the hyperplanes perpendicular to themselves coincides with the expected position of the system in these planes (where perpendicular is understood with respect to the appropriate metric). Unlike more standard paths such as the minimum energy path or the minimum free energy path, the location of the principal curve depends on global features of the energy or the free energy landscapes and thereby may remain appropriate in situations where the landscape is rough on the thermal energy scale and/or entropic effects related to the width of the reaction channels matter. Instead of using constrained sampling in hyperplanes as in the original FTS, the new method calculates the principal curve via sampling in the Voronoi tessellation whose generating points are the discretization points along this curve. As shown here, this modification results in greater algorithmic simplicity. As a by-product, it also gives the free energy associated with the Voronoi tessellation. The new method can be applied both in the original Cartesian space of the system or in a set of collective variables. We illustrate FTS on test-case examples and apply it to the study of conformational transitions of the nitrogen regulatory protein C receiver domain using an elastic network model and to the isomerization of solvated alanine dipeptide.
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87.15.R- Reactions and kinetics
82.39.Rt Reactions in complex biological systems
82.30.Qt Isomerization and rearrangement
82.20.Fd Collision theories; trajectory models
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Wt Computational modeling; simulation

Exact ionization potentials from wavefunction asymptotics: The extended Koopmans’ theorem, revisited

Diederik Vanfleteren, Dimitri Van Neck, Paul W. Ayers, Robert C. Morrison, and Patrick Bultinck

J. Chem. Phys. 130, 194104 (2009); http://dx.doi.org/10.1063/1.3130044 (10 pages) | Cited 2 times

Online Publication Date: 18 May 2009

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A simple explanation is given for the exactness of the extended Koopmans’ theorem, (EKT) for computing the removal energy of any many-electron system to the lowest-energy ground state ion of a given symmetry. In particular, by removing the electron from a “removal orbital” of appropriate symmetry that is concentrated in the asymptotic region, one obtains the exact ionization potential and the exact Dyson orbital for the corresponding state of the ion. It is argued that the EKT is not restricted to many-electron systems but holds for any finite many-body system, provided that the interaction vanishes for increasing interparticle distance. A necessary and sufficient condition for the validity of the EKT for any state (not just the lowest-energy states of a given symmetry) in terms of the third-order reduced density matrix is stated and derived.
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31.15.xr Self-consistent-field methods
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
31.50.Bc Potential energy surfaces for ground electronic states

Preparation of many-body states for quantum simulation

Nicholas J. Ward, Ivan Kassal, and Alán Aspuru-Guzik

J. Chem. Phys. 130, 194105 (2009); http://dx.doi.org/10.1063/1.3115177 (9 pages) | Cited 4 times

Online Publication Date: 18 May 2009

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While quantum computers are capable of simulating many quantum systems efficiently, the simulation algorithms must begin with the preparation of an appropriate initial state. We present a method for generating physically relevant quantum states on a lattice in real space. In particular, the present algorithm is able to prepare general pure and mixed many-particle states of any number of particles. It relies on a procedure for converting from a second-quantized state to its first-quantized counterpart. The algorithm is efficient in that it operates in time that is polynomial in all the essential descriptors of the system, the number of particles, the resolution of the lattice, and the inverse of the maximum final error. This scaling holds under the assumption that the wave function to be prepared is bounded or its indefinite integral is known and that the Fock operator of the system is efficiently simulatable.
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03.67.Lx Quantum computation architectures and implementations
03.67.Ac Quantum algorithms, protocols, and simulations
03.65.Fd Algebraic methods
02.10.De Algebraic structures and number theory
05.50.+q Lattice theory and statistics (Ising, Potts, etc.)

Band structures built by the elongation method

Anna Pomogaeva, Michael Springborg, Bernard Kirtman, Feng Long Gu, and Yuriko Aoki

J. Chem. Phys. 130, 194106 (2009); http://dx.doi.org/10.1063/1.3131262 (8 pages) | Cited 7 times

Online Publication Date: 18 May 2009

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A recently proposed approach for extracting band structures from finite-cluster calculations is improved so that (avoided) band crossings can be handled and the problems related to so-called doublings and holes are reduced. In particular, we demonstrate how the method can be combined with the elongation method for the finite-system calculations and apply it to extracting band structures for polymers from oligomer calculations. As illustrations of the approach we discuss a chain of water molecules, polyacetylene, polyethylene, and a BN nanotube without and with an impurity.
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71.20.Rv Polymers and organic compounds

A study of cumulant approximations to n-electron valence multireference perturbation theory

Dominika Zgid, Debashree Ghosh, Eric Neuscamman, and Garnet Kin-Lic Chan

J. Chem. Phys. 130, 194107 (2009); http://dx.doi.org/10.1063/1.3132922 (11 pages) | Cited 10 times

Online Publication Date: 18 May 2009

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We investigate the possibility of reducing the complexity of multireference perturbation theory through cumulant based approximations to the high-order density matrices that appear in such theories. Our test cases show that while the cumulant approximated forms are degraded in accuracy relative to the parent theory and exhibit intruder state problems that must be carefully handled, they may provide a route to a simple estimation of dynamic correlation when the parent perturbation theory is infeasible. Nonetheless, further work is clearly needed on better approximations to the denominators in the perturbation theory.
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31.15.xp Perturbation theory
33.15.Dj Interatomic distances and angles

Parallel computation of coupled-cluster hyperpolarizabilities

Jeff R. Hammond and Karol Kowalski

J. Chem. Phys. 130, 194108 (2009); http://dx.doi.org/10.1063/1.3134744 (11 pages) | Cited 14 times

Online Publication Date: 18 May 2009

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Static hyperpolarizabilities of molecules (water, acetonitrile, chloroform, and para-nitroaniline) are calculated with large basis sets using coupled-cluster response theory and compared to four common density functional theory methods. These results reveal which methods and basis sets are appropriate for nonlinear optical studies for different types of molecules and provide a means for estimating errors from the quantum chemical approximation when including vibrational contributions or solvent effects at the QM/MM level. The largest calculation reported, which was for 72 electrons in 812 functions at C2v symmetry, took only a few hours on 256 nodes demonstrating that even larger calculations are quite feasible using modern supercomputers.
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31.15.bw Coupled-cluster theory
31.15.E- Density-functional theory
33.20.Tp Vibrational analysis
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.70.Jg Line and band widths, shapes, and shifts
33.15.Mt Rotation, vibration, and vibration-rotation constants

Magnetic anisotropy from density functional calculations. Comparison of different approaches: Mn12O12 acetate as a test case

Christoph van Wüllen

J. Chem. Phys. 130, 194109 (2009); http://dx.doi.org/10.1063/1.3134430 (14 pages) | Cited 10 times

Online Publication Date: 18 May 2009

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Magnetic anisotropy is the capability of a system in a triplet or higher spin state to store magnetic information. Although the source of the magnetic anisotropy is the zero-field splitting of the ground state of the system, there is a difference between these two quantities that has to be fully rationalized before one makes comparisons. This is especially important for small spins such as triplets, where the magnetic anisotropy energy is only half of the zero-field splitting. Density functional calculations of magnetic anisotropy energies correspond to a high-field limit where the spins are aligned by the external magnetic field. Data are presented for the well-studied molecular magnet Mn12O12 acetate. Both perturbative and self-consistent treatments, different quasirelativistic Hamiltonians (zeroth order regular approximation, Douglas–Kroll, effective core potentials) and exchange-correlation functionals are compared. It is shown that some effects usually considered minor, such as the inclusion of the exchange-correlation potential in the effective one-particle spin-orbit operator, lead to sizable differences when computing magnetic anisotropy energies. Higher-order contributions, that is, the difference between self-consistent and perturbative results, increase the magnetic anisotropy energy somewhat but do not introduce sizeable quartic terms or an in-plane anisotropy. In numerical experiments, on can switch off and on spin-orbit coupling at individual atomic sites. This procedure yields single-site contributions to the overall magnetic anisotropy energy that could be used as parameters in phenomenological spin Hamiltonians. If ferrimagnetic systems are treated with broken symmetry density functional methods where the Kohn–Sham reference function is not a spin eigenfunction, corrections are needed which depend on the size of the exchange couplings in the system and must therefore be evaluated case by case.
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75.30.Gw Magnetic anisotropy
75.50.Xx Molecular magnets
75.30.Et Exchange and superexchange interactions
75.40.Mg Numerical simulation studies
75.10.Dg Crystal-field theory and spin Hamiltonians

Nested variant of the method of moments of coupled cluster equations for vertical excitation energies and excited-state potential energy surfaces

Karol Kowalski

J. Chem. Phys. 130, 194110 (2009); http://dx.doi.org/10.1063/1.3132592 (12 pages) | Cited 8 times

Online Publication Date: 19 May 2009

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In this article we discuss the problem of proper balancing of the noniterative corrections to the ground- and excited-state energies obtained with approximate coupled cluster (CC) and equation-of-motion CC (EOMCC) approaches. It is demonstrated that for a class of excited states dominated by single excitations and for states with medium doubly excited component, the newly introduced nested variant of the method of moments of CC equations provides mathematically rigorous way of balancing the ground- and excited-state correlation effects. The resulting noniterative methodology accounting for the effect of triples is tested using its parallel implementation on the systems, for which iterative CC/EOMCC calculations with full inclusion of triply excited configurations or their most important subset are numerically feasible.
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31.15.bw Coupled-cluster theory
31.50.Df Potential energy surfaces for excited electronic states

Approximate normal mode analysis based on vibrational subsystem analysis with high accuracy and efficiency

Jeffrey Hafner and Wenjun Zheng

J. Chem. Phys. 130, 194111 (2009); http://dx.doi.org/10.1063/1.3141022 (7 pages) | Cited 5 times

Online Publication Date: 20 May 2009

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Normal mode analysis (NMA) has been proven valuable in modeling slow conformational dynamics of biomolecular structures beyond the reach of direct molecular simulations. However, it remains computationally expensive to directly solve normal modes for large biomolecular systems. In this study, we have evaluated the accuracy and efficiency of two approximate NMA protocols—one based on our recently proposed vibrational subsystem analysis (VSA), the other based on the rotation translation block (RTB), in comparison with standard NMA that directly solves a full Hessian matrix. By properly accounting for flexibility within blocks of residues or atoms based on a subsystem-environment partition, VSA-based NMA has attained a much higher accuracy than RTB and much lower computing cost than standard NMA. Therefore, VSA enables accurate and efficient calculations of normal modes from all-atom or coarse-grained potential functions, which promise to improve conformational sampling driven by low-frequency normal modes.
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87.15.hp Conformational changes
87.15.ap Molecular dynamics simulation

Enhanced sampling in generalized ensemble with large gap of sampling parameter: Case study in temperature space random walk

Cheng Zhang and Jianpeng Ma

J. Chem. Phys. 130, 194112 (2009); http://dx.doi.org/10.1063/1.3139192 (6 pages) | Cited 4 times

Online Publication Date: 20 May 2009

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We present an efficient sampling method for computing a partition function and accelerating configuration sampling. The method performs a random walk in the λ space, with λ being any thermodynamic variable that characterizes a canonical ensemble such as the reciprocal temperature β or any variable that the Hamiltonian depends on. The partition function is determined by minimizing the difference of the thermal conjugates of λ (the energy in the case of λ = β), defined as the difference between the value from the dynamically updated derivatives of the partition function and the value directly measured from simulation. Higher-order derivatives of the partition function are included to enhance the Brownian motion in the λ space. The method is much less sensitive to the system size, and to the size of λ window than other methods. On the two dimensional Ising model, it is shown that the method asymptotically converges the partition function, and the error of the logarithm of the partition function is much smaller than the algorithm using the Wang–Landau recursive scheme. The method is also applied to off-lattice model proteins, the AB models, in which cases many low energy states are found in different models.
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05.40.Fb Random walks and Levy flights
05.40.Jc Brownian motion
05.50.+q Lattice theory and statistics (Ising, Potts, etc.)
02.50.-r Probability theory, stochastic processes, and statistics

Statistical mechanical theory for non-equilibrium systems. IX. Stochastic molecular dynamics

Phil Attard

J. Chem. Phys. 130, 194113 (2009); http://dx.doi.org/10.1063/1.3138762 (10 pages) | Cited 4 times

Online Publication Date: 20 May 2009

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The general form for the probability density and for the transition probability of a nonequilibrium system is given. Maximization of the latter gives a generalized fluctuation-dissipation theorem by providing a molecular basis for Langevin’s friction force that avoids continuum hydrodynamics. The result shows that the friction coefficient must be proportional to the variance of the stochastic equations of motion. Setting the variance to zero but keeping the friction coefficient nonzero reduces the theory to a Hoover thermostat without explicit constraint, although such a limit violates the physical requirement of proportionality between the dissipation and the fluctuation. A stochastic molecular dynamics algorithm is developed for both equilibrium and nonequilibrium systems, which is tested for steady heat flow and for a time-varying, driven Brownian particle.
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05.70.Ln Nonequilibrium and irreversible thermodynamics
05.20.-y Classical statistical mechanics
05.10.Gg Stochastic analysis methods (Fokker-Planck, Langevin, etc.)
05.40.-a Fluctuation phenomena, random processes, noise, and Brownian motion
02.50.Ey Stochastic processes

On the accurate calculation of polarizabilities and second hyperpolarizabilities of polyacetylene oligomer chains using the CAM-B3LYP density functional

Peter A. Limacher, Kurt V. Mikkelsen, and Hans Peter Lüthi

J. Chem. Phys. 130, 194114 (2009); http://dx.doi.org/10.1063/1.3139023 (7 pages) | Cited 30 times

Online Publication Date: 21 May 2009

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The polarizability and second hyperpolarizability of polyacetylene oligomer chains of increasing size up to C24H26 were investigated by means of the Coulomb-attenuating method (CAM-B3LYP) using response theory. It was found that this long-range corrected density functional removes to large parts the overestimation observed for standard methods and in many cases provides results close to those of coupled cluster calculations. A direct comparison to experimentally observed dynamic hyperpolarizabilities is made to estimate the accuracy of the method. A basis set study revealed a noticeable contribution of diffuse orbitals to the hyperpolarizability also for larger oligomers. Furthermore, CAM-B3LYP is also confirmed to provide molecular geometries close to experimentally observed structures, especially for longer chain lengths.
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33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
36.20.Fz Constitution (chains and sequences)
31.15.E- Density-functional theory

Self-assembly of nanocomponents into composite structures: Derivation and simulation of Langevin equations

S. Pankavich, Z. Shreif, Y. Miao, and P. Ortoleva

J. Chem. Phys. 130, 194115 (2009); http://dx.doi.org/10.1063/1.3134683 (10 pages) | Cited 4 times

Online Publication Date: 21 May 2009

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The kinetics of the self-assembly of nanocomponents into a virus, nanocapsule, or other composite structure is analyzed via a multiscale approach. The objective is to achieve predictability and to preserve key atomic-scale features that underlie the formation and stability of the composite structures. We start with an all-atom description, the Liouville equation, and the order parameters characterizing nanoscale features of the system. An equation of Smoluchowski type for the stochastic dynamics of the order parameters is derived from the Liouville equation via a multiscale perturbation technique. The self-assembly of composite structures from nanocomponents with internal atomic structure is analyzed and growth rates are derived. Applications include the assembly of a viral capsid from capsomers, a ribosome from its major subunits, and composite materials from fibers and nanoparticles. Our approach overcomes errors in other coarse-graining methods, which neglect the influence of the nanoscale configuration on the atomistic fluctuations. We account for the effect of order parameters on the statistics of the atomistic fluctuations, which contribute to the entropic and average forces driving order parameter evolution. This approach enables an efficient algorithm for computer simulation of self-assembly, whereas other methods severely limit the timestep due to the separation of diffusional and complexing characteristic times. Given that our approach does not require recalibration with each new application, it provides a way to estimate assembly rates and thereby facilitate the discovery of self-assembly pathways and kinetic dead-end structures.
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81.16.Dn Self-assembly
87.90.+y Other topics in biological and medical physics (restricted to new topics in section 87)
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Photodissociation dynamics of Ar2+ and Ar3+ excited by 527 nm photons

V. Lepère, Y. J. Picard, M. Barat, J. A. Fayeton, B. Lucas, and K. Béroff

J. Chem. Phys. 130, 194301 (2009); http://dx.doi.org/10.1063/1.3130974 (7 pages) | Cited 3 times

Online Publication Date: 18 May 2009

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The photofragmentation dynamics of Ar2+ and Ar3+ clusters has been investigated at a 527 nm wavelength (2.35 eV) using a setup that allows simultaneous detection of the ionic and neutral fragments in a coincidence experiment. Measurement of positions and times of flight enables in principle a complete description of the fragmentation dynamics. The photofragmentation dynamics of Ar3+ clusters is similar to that of Ar2+ with, in addition, the ejection of a third fragment that can be neutral or ionized via a resonant electron capture. This is attributed to the triangular geometry of the Ar3+ ion.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
36.40.Vz Optical properties of clusters
36.40.Qv Stability and fragmentation of clusters
36.40.Mr Spectroscopy and geometrical structure of clusters
34.70.+e Charge transfer

Vacuum-UV negative photoion spectroscopy of CF3Cl, CF3Br, and CF3I

M. J. Simpson, R. P. Tuckett, K. F. Dunn, C. A. Hunniford, and C. J. Latimer

J. Chem. Phys. 130, 194302 (2009); http://dx.doi.org/10.1063/1.3137103 (11 pages) | Cited 10 times

Online Publication Date: 19 May 2009

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Using synchrotron radiation, negative ions are detected by mass spectrometry following vacuum-UV photoexcitation of trifluorochloromethane (CF3Cl), trifluorobromomethane (CF3Br), and trifluoroiodomethane (CF3I). The anions F−, X−, F2−, FX−, CF−, CF2−, and CF3− are observed from all three molecules, where X = Cl, Br, or I, and their ion yields recorded in the range of 8–35 eV. With the exception of Br− and I−, the anions observed show a linear dependence of signal with pressure, showing that they arise from unimolecular ion-pair dissociation. Dissociative electron attachment, following photoionization of CF3Br and CF3I as the source of low-energy electrons, is shown to dominate the observed Br− and I− signals, respectively. Cross sections for ion-pair formation are put onto an absolute scale by calibrating the signal strengths with those of F− from both SF6 and CF4. These anion cross sections are normalized to vacuum-UV absorption cross sections, where available, and the resulting quantum yields are reported. Anion appearance energies are used to calculate upper limits to 298 K bond dissociation energies for Do(CF3−X), which are consistent with literature values. We report new data for Do(CF2I+–F) ≤ 2.7±0.2 eV and ΔfH298o(CF2I+) ≤ (598±22) kJ mol−1. No ion-pair formation is observed below the ionization energy of the parent molecule for CF3Cl and CF3Br, and only weak signals (in both I− and F−) are detected for CF3I. These observations suggest that neutral photodissociation is the dominant exit channel to Rydberg state photoexcitation at these lower energies.
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33.80.Eh Autoionization, photoionization, and photodetachment
34.80.Ht Dissociation and dissociative attachment
33.80.Gj Diffuse spectra; predissociation, photodissociation
33.60.+q Photoelectron spectra
33.15.Ta Mass spectra
33.20.Ni Vacuum ultraviolet spectra

Time-dependent wave packet and quasiclassical trajectory study of the C(3P)+OH(X 2Π)→CO(X 1Σ+)+H(2S) reaction at the state-to-state level

Niyazi Bulut, Alexandre Zanchet, Pascal Honvault, Béatrice Bussery-Honvault, and Luis Bañares

J. Chem. Phys. 130, 194303 (2009); http://dx.doi.org/10.1063/1.3125956 (9 pages) | Cited 7 times

Online Publication Date: 19 May 2009

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The first calculations of state-to-state reaction probabilities and product state-resolved integral cross sections at selected collision energies (0.05, 0.1, 0.5, and 1.0 eV) for the title reaction on the ab initio potential energy surface of [Zanchet et al. J. Phys. Chem. A 110, 12017 (2006)] with the OH reagent in selected rovibrational states (v = 0–2, j = 0–5) have been carried out by means of the real wave packet (RWP) and quasiclassical trajectory (QCT) methods. State-selected total reaction probabilities have been calculated for total angular momentum J = 0 in a broad range of collision energies. Integral cross sections and state-specific rate coefficients have been obtained from the corresponding J = 0 RWP reaction probabilities for initially selected rovibrational states by means of a capture model. The calculated RWP and QCT state-selected rate coefficients are practically temperature independent. Both RWP and QCT reaction probabilities, integral cross sections, and rate coefficients are almost independent of the initial rotational excitation. The RWP results are found to be in an overall good agreement with the corresponding QCT results. The present results have been compared with earlier wave packet calculations carried out on the same potential energy surface.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Fd Collision theories; trajectory models
82.20.Rp State to state energy transfer
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Kh Potential energy surfaces for chemical reactions

High-resolution spectroscopy of weak and short-lived bands of the S1 1B3u←S0 1Ag transition of naphthalene

Kazuto Yoshida, Yosuke Semba, Shunji Kasahara, Takaya Yamanaka, and Masaaki Baba

J. Chem. Phys. 130, 194304 (2009); http://dx.doi.org/10.1063/1.3122039 (6 pages) | Cited 6 times

Online Publication Date: 19 May 2009

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Rotationally resolved high-resolution spectra and fluorescence decay curves have been observed for weak and short-lived vibronic bands of the S1 1B3u←S0 1Ag transition of naphthalene. Fluorescence lifetime of the vibronic band with an excess energy of 1390 cm−1 (000+1390 cm−1 band) is remarkably shorter than that of other bands. Zeeman splitting of rotational lines is very small, so that the main radiationless process is not intersystem crossing to the triplet state but internal conversion to the ground state. The lifetime is thought to be governed by the strength of vibronic coupling between vibrational levels of the S0 and S1 states. As for the 000+2570 cm−1 band, energy shifts were found in only a few rotational levels although the excess energy was higher than the threshold of intramolecular vibrational redistribution. We conclude that all of the rotational levels are mixed with other vibrational levels. The 000+3068 cm−1 band spectrum is fairly complicated with numerous rotational lines, which is attributed to strong vibronic coupling with the S2 1B2u state.
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33.50.Dq Fluorescence and phosphorescence spectra
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Sn Rotational analysis
33.20.Tp Vibrational analysis

Theoretical study of Ban+–RG (RG = rare gas) complexes and transport of Ban+ through RG (n = 1,2; RG = He–Rn)

Maureen F. McGuirk, Larry A. Viehland, Edmond P. F. Lee, W. H. Breckenridge, Carolyn D. Withers, Adrian M. Gardner, Richard J. Plowright, and Timothy G. Wright

J. Chem. Phys. 130, 194305 (2009); http://dx.doi.org/10.1063/1.3132543 (9 pages) | Cited 10 times

Online Publication Date: 19 May 2009

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We present high-level ab initio potential energy curves for barium cations and dications interacting with RG atoms (RG = rare gas). These potentials are employed to derive spectroscopic parameters for the Ba+–RG and Ba2+–RG complexes, and also to derive the transport coefficients for Ba+ and Ba2+ moving through a bath of the rare gas. The results are compared to the limited experimental data, which generally show reasonable agreement. We identify a large change in binding energy going from Ba+–He and Ba+–Ne to Ba+–Ar, which is not present in Ba2+–RG, and show that this is due to significant dispersion interactions in Ba+–RG.
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31.50.-x Potential energy surfaces
31.15.ac High-precision calculations for few-electron (or few-body) atomic systems
34.20.Gj Intermolecular and atom-molecule potentials and forces
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy

Vibrational energy transfer in O2(v = 2–8)–O2(v = 0) collisions

Ramesh D. Sharma and Judith A. Welsh

J. Chem. Phys. 130, 194306 (2009); http://dx.doi.org/10.1063/1.3132588 (8 pages)

Online Publication Date: 20 May 2009

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Starting with multipolar-multipolar interaction for intermolecular potential we have carried out a calculation of rate coefficients for transfer of one quantum of vibrational energy upon impact of O2(2 ≤ v ≤ 8) with O2(v = 0) as a function of temperature (150 K ≤ T ≤ 450 K). The equations for energy transfer, in the second order of perturbation theory, mediated by isotropic and anisotropic dispersion interactions, are derived. None of the parameters appearing in the calculation were adjusted to obtain agreement with the experimentally measured rate coefficients. The results of the calculation are compared with experimentally measured room temperature rate coefficients of the disappearance of O2(v) upon collision with O2(v = 0). The agreement is found to be good for the disappearance of O2(v = 3) and O2(v = 5). For O2(v = 2) the calculation gives a larger rate coefficient than the measured value, while for O2(v = 4) it gives a smaller value than obtained by measurement. For O2(v = 8) it agrees with one measurement and gives a value smaller than another measurement and a calculation.
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34.50.Ez Rotational and vibrational energy transfer
34.20.Gj Intermolecular and atom-molecule potentials and forces

Valence and inner-valence shell dissociative photoionization of CO in the 26–33 eV range. I. Ion-electron kinetic energy correlation and laboratory frame photoemission

M. Lebech, J. C. Houver, and D. Dowek

J. Chem. Phys. 130, 194307 (2009); http://dx.doi.org/10.1063/1.3125223 (8 pages) | Cited 1 time

Online Publication Date: 21 May 2009

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The (VA+, Ve, math) vector correlation method, combining imaging and time-of-flight resolved electron-ion coincidence techniques, is used to probe dissociative photoionization (DPI) of CO induced by vacuum ultra violet linearly or circularly polarized synchrotron radiation in the 26–33 eV photon excitation energy range. It provides original information about both the photoionization dynamics of the CO molecule and the dissociation dynamics of the CO+ molecular ions. The explored region corresponds to valence and inner-valence CO+ ionic states, which involve doubly or multiply excited electronic configurations. In this paper I we identify up to 17 DPI reaction pathways by the position of the intermediate CO+ molecular states in the Franck–Condon region and the (C++O) or (O++C) dissociation limits to which they correlate. For these processes we report the laboratory frame βC+/O+ and βe asymmetry parameters as well as the relative branching ratios in selected binding energy bands. The I(χ,θe,φe) molecular frame photoelectron angular distributions for selected PI processes will be reported in a companion paper II and compared with multichannel Schwinger configuration interaction ab initio calculations of these observables.
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33.80.Eh Autoionization, photoionization, and photodetachment
33.80.Gj Diffuse spectra; predissociation, photodissociation
33.60.+q Photoelectron spectra
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
31.15.vn Electron correlation calculations for diatomic molecules
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Mirror symmetry and vibrational structure in optical spectra of chlorophyll a

Margus Rätsep, Juha Linnanto, and Arvi Freiberg

J. Chem. Phys. 130, 194501 (2009); http://dx.doi.org/10.1063/1.3125183 (11 pages) | Cited 11 times

Online Publication Date: 15 May 2009

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The absorption and fluorescence emission spectra of chlorophyll a in different organic solvents where the central Mg atom is either penta- or hexacoordinated have been studied using conventional and selective spectroscopy methods at ambient and cryogenic temperatures. A breakdown of the basic model mirror-symmetry rule in relation to the lowest-energy Qy transitions was observed due to Franck–Condon and Hertzberg–Teller interactions. Detailed vibrational structure in the ground electronic state, virtually independent of the Mg coordination state, was revealed by hole-burning fluorescence line-narrowing technique. The total Huang–Rhys factor associated with the linear vibronic coupling strength of the solvent collective vibrations and the local chlorophyll a intramolecular vibrations is equal to 0.53±0.07 in fluorescence and to 0.39±0.05 in absorption. The electron-phonon coupling part was also found to depend on the excitation wavelength within the inhomogeneously broadened absorption origin band, its average value being Sph ≈ 0.38. All these numbers qualify for the weak vibronic coupling. A comparison of the conjugate Qy absorption and fluorescence emission spectra as well as the temperature dependence of the absorption spectra allowed unambiguous locating of the still controversial Qx absorption band position for penta- and hexacoordinated chlorophyll a species. The basic experimental findings have been qualitatively supported by semiempirical quantum chemical calculations.
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63.50.-x Vibrational states in disordered systems
78.55.Bq Liquids
78.30.C- Liquids

Microhydration effects on a model SN2 reaction in a nonpolar solvent

Katherine V. Nelson and Ilan Benjamin

J. Chem. Phys. 130, 194502 (2009); http://dx.doi.org/10.1063/1.3138902 (9 pages)

Online Publication Date: 15 May 2009

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Using a recently developed empirical valence bond model for the nucleophilic substitution reaction (SN2) in solution, we examine microhydration effects on the benchmark Cl−+CH3Cl reaction in liquid chloroform. Specifically, the effect of the hydration of the reactive system by one to five water molecules on the reaction-free energy profile and the rate constant is examined. We find that the activation-free energy is highly sensitive to the number of water molecules hydrating the nucleophile, increasing the barrier by about 4 kcal/mol by the first water molecule. With five water molecules, the barrier height is 10 kcal/mol larger than the barrier in bulk chloroform and only 3 kcal/mol below the barrier in bulk water. A number of properties vary monotonically with the number of water molecules, including the rate of change in the system’s electronic structure and the solvent stabilization of the transition state. These and other properties are a rapidly varying function of the reaction coordinate. Deviation from transition state theory due to barrier recrossing is not large and falls between the behavior in bulk water and bulk chloroform.
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82.30.Nr Association, addition, insertion, cluster formation
82.30.Rs Hydrogen bonding, hydrophilic effects
82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.20.Db Transition state theory and statistical theories of rate constants
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Yn Solvent effects on reactivity
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.60.-s Chemical thermodynamics

On the collective network of ionic liquid/water mixtures. III. Structural analysis of ionic liquids on the basis of Voronoi decomposition

C. Schröder, G. Neumayr, and O. Steinhauser

J. Chem. Phys. 130, 194503 (2009); http://dx.doi.org/10.1063/1.3127782 (11 pages) | Cited 12 times

Online Publication Date: 18 May 2009

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Three different mixtures of 1-butyl-3-methyl-imidazolium tetrafluoroborate with water have been studied by means of molecular dynamics simulations. Based on the classical Lopes–Padua force field trajectories of approximately 60 ns were computed. This is the third part of a series concerning the collective network of 1-butyl-3-methyl-imidazolium tetrafluoroborate/water mixtures. The first part [ C. Schröder et al., J. Chem. Phys. 127, 234503 (2007) ] dealt with the orientational structure and static dielectric constants. The second part [ C. Schröder et al., J. Chem. Phys. 129, 184501 (2008) ] was focused on the decomposition of the dielectric spectrum of these mixtures. In this work the focus lies on the characterization of the neighborhood of ionic liquids by means of the Voronoi decomposition. The Voronoi algorithm is a rational tool to uniquely decompose the space around a reference molecule without using any empirical parameters. Thus, neighborhood relations, direct and indirect ones, can be extracted and were used in combination with g-coefficients. These coefficients represent the generalization of the traditional radial distribution function in order to include the mutual positioning and orientation of anisotropic molecules. Furthermore, the Voronoi method provides, as a by-product, the mutual coordination numbers of molecular species.
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61.25.Em Molecular liquids
61.20.Ja Computer simulation of liquid structure
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