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28 Feb 2007

Volume 126, Issue 8, Articles (08xxxx)

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Four-component relativistic theory for nuclear magnetic shielding constants: The orbital decomposition approach

Yunlong Xiao, Daoling Peng, and Wenjian Liu

J. Chem. Phys. 126, 081101 (2007); http://dx.doi.org/10.1063/1.2565724 (4 pages) | Cited 23 times

Online Publication Date: 27 February 2007

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The authors present a scheme to simplify four-component relativistic calculations of nuclear magnetic shielding constants. The central idea is to decompose each first order orbital into two terms, one is magnetically balanced and directly leads to the diamagnetic term, and the other is, to leading order of relativity, kinetically balanced and can therefore simply be represented in the basis of unperturbed positive energy states. As a matrix formulation, the present approach is far simpler than other operator theories. Combined with the Dirac-Kohn-Sham ansatz, the nuclear magnetic shielding constants for the Kr, Xe, and Rn atoms as well as the HBr and HI molecules are calculated, and the results compare favorably with those of other schemes.
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31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions
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back to top Theoretical Methods and Algorithms

Multinomial tau-leaping method for stochastic kinetic simulations

Michel F. Pettigrew and Haluk Resat

J. Chem. Phys. 126, 084101 (2007); http://dx.doi.org/10.1063/1.2432326 (15 pages) | Cited 15 times

Online Publication Date: 22 February 2007

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We introduce the multinomial tau-leaping (MτL) method for general reaction networks with multichannel reactant dependencies. The MτL method is an extension of the binomial tau-leaping method where efficiency is improved in several ways. First, τ-leaping steps are determined simply and efficiently using a priori information and Poisson distribution-based estimates of expectation values for reaction numbers over a tentative τ-leaping step. Second, networks are partitioned into closed groups of reactions and corresponding reactants in which no group reactant set is found in any other group. Third, product formation is factored into upper-bound estimation of the number of times a particular reaction occurs. Together, these features allow larger time steps where the numbers of reactions occurring simultaneously in a multichannel manner are estimated accurately using a multinomial distribution. Furthermore, we develop a simple procedure that places a specific upper bound on the total reaction number to ensure non-negativity of species populations over a single multiple-reaction step. Using two disparate test case problems involving cellular processes—epidermal growth factor receptor signaling and a lactose operon model—we show that the τ-leaping based methods such as the MτL algorithm can significantly reduce the number of simulation steps thus increasing the numerical efficiency over the exact stochastic simulation algorithm by orders of magnitude.
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82.20.Uv Stochastic theories of rate constants
82.20.Hf Product distribution
87.15.R- Reactions and kinetics
87.17.Aa Modeling, computer simulation of cell processes

Optimization of quantum Monte Carlo wave functions by energy minimization

Julien Toulouse and C. J. Umrigar

J. Chem. Phys. 126, 084102 (2007); http://dx.doi.org/10.1063/1.2437215 (16 pages) | Cited 39 times

Online Publication Date: 22 February 2007

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We study three wave function optimization methods based on energy minimization in a variational Monte Carlo framework: the Newton, linear, and perturbative methods. In the Newton method, the parameter variations are calculated from the energy gradient and Hessian, using a reduced variance statistical estimator for the latter. In the linear method, the parameter variations are found by diagonalizing a nonsymmetric estimator of the Hamiltonian matrix in the space spanned by the wave function and its derivatives with respect to the parameters, making use of a strong zero-variance principle. In the less computationally expensive perturbative method, the parameter variations are calculated by approximately solving the generalized eigenvalue equation of the linear method by a nonorthogonal perturbation theory. These general methods are illustrated here by the optimization of wave functions consisting of a Jastrow factor multiplied by an expansion in configuration state functions (CSFs) for the C2 molecule, including both valence and core electrons in the calculation. The Newton and linear methods are very efficient for the optimization of the Jastrow, CSF, and orbital parameters. The perturbative method is a good alternative for the optimization of just the CSF and orbital parameters. Although the optimization is performed at the variational Monte Carlo level, we observe for the C2 molecule studied here, and for other systems we have studied, that as more parameters in the trial wave functions are optimized, the diffusion Monte Carlo total energy improves monotonically, implying that the nodal hypersurface also improves monotonically.
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31.15.xt Variational techniques
31.15.xp Perturbation theory

Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles

Hisashi Okumura, Satoru G. Itoh, and Yuko Okamoto

J. Chem. Phys. 126, 084103 (2007); http://dx.doi.org/10.1063/1.2434972 (17 pages) | Cited 15 times

Online Publication Date: 26 February 2007

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The authors propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isobaric-isothermal ensembles. They also present a symplectic algorithm in the constant normal pressure and lateral surface area ensemble and that combined with the Parrinello-Rahman algorithm. Employing the symplectic integrators for MD algorithms, there is a conserved quantity which is close to Hamiltonian. Therefore, they can perform a MD simulation more stably than by conventional nonsymplectic algorithms. They applied this algorithm to a TIP3P pure water system at 300 K and compared the time evolution of the Hamiltonian with those by the nonsymplectic algorithms. They found that the Hamiltonian was conserved well by the symplectic algorithm even for a time step of 4 fs. This time step is longer than typical values of 0.5–2 fs which are used by the conventional nonsymplectic algorithms.
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61.20.Ja Computer simulation of liquid structure
31.15.-p Calculations and mathematical techniques in atomic and molecular physics

Symmetry-adapted-cluster/symmetry-adapted-cluster configuration interaction methodology extended to giant molecular systems: Ring molecular crystals

Hiroshi Nakatsuji, Tomoo Miyahara, and Ryoichi Fukuda

J. Chem. Phys. 126, 084104 (2007); http://dx.doi.org/10.1063/1.2464113 (18 pages) | Cited 14 times

Online Publication Date: 27 February 2007

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The symmetry adapted cluster (SAC)/symmetry adapted cluster configuration interaction (SAC-CI) methodology for the ground, excited, ionized, and electron-attached states of molecules was extended to giant molecular systems. The size extensivity of energy and the size intensivity of excitation energy are very important for doing quantitative chemical studies of giant molecular systems and are designed to be satisfied in the present giant SAC/SAC-CI method. The first extension was made to giant molecular crystals composed of the same molecular species. The reference wave function was defined by introducing monomer-localized canonical molecular orbitals (ml-CMO’s), which were obtained from the Hartree-Fock orbitals of a tetramer or a larger oligomer within the electrostatic field of the other part of the crystal. In the SAC/SAC-CI calculations, all the necessary integrals were obtained after the integral transformation with the ml-CMO’s of the neighboring dimer. Only singles and doubles excitations within each neighboring dimer were considered as linked operators, and perturbation selection was done to choose only important operators. Almost all the important unlinked terms generated from the selected linked operators were included: the unlinked terms are important for keeping size extensivity and size intensivity. Some test calculations were carried out for the ring crystals of up to 10 000-mer, confirming the size extensivity and size intensivity of the calculated results and the efficiency of the giant method in comparison with the standard method available in GAUSSIAN 03. Then, the method was applied to the ring crystals of ethylene and water 50-mers, and formaldehyde 50-, 100-, and 500-mers. The potential energy curves of the ground state and the polarization and electron-transfer-type excited states were calculated for the intermonomer distances of 2.8–100 Å. Several interesting behaviors were reported, showing the potentiality of the present giant SAC/SAC-CI method for molecular engineering.
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31.15.vq Electron correlation calculations for polyatomic molecules
31.15.xr Self-consistent-field methods
31.50.Df Potential energy surfaces for excited electronic states
33.15.Bh General molecular conformation and symmetry; stereochemistry
34.80.Lx Recombination, attachment, and positronium formation

Calculation of highly excited vibrational states using a Richardson-Leja-Davidson scheme

Hans O. Karlsson

J. Chem. Phys. 126, 084105 (2007); http://dx.doi.org/10.1063/1.2646409 (7 pages) | Cited 2 times

Online Publication Date: 28 February 2007

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An efficient computational scheme for calculating highly excited vibrational eigenstates is proposed, combining a Richardson-Leja spectral filter with a novel version of the Davidson method [J. Comput. Phys. 17, 87 (1975) ]. Highly excited eigenstates of the Rb2 and H2O molecules are computed to test and verify the method. On the average less than 2.5 outer recursions per eigenstate are needed. For each outer Davidson recursion, less than 20 inner filter recursions per eigenstate are needed on the average.
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31.15.xv Molecular dynamics and other numerical methods
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis

On the use of local diffusion models for path ensemble averaging in potential of mean force computations

Christopher P. Calderon

J. Chem. Phys. 126, 084106 (2007); http://dx.doi.org/10.1063/1.2567098 (11 pages) | Cited 10 times

Online Publication Date: 28 February 2007

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We use a constant velocity steered molecular dynamics (SMD) simulation of the stretching of deca-alanine in vacuum to demonstrate a technique that can be used to create a surrogate processes approximation (SPA) using the time series that come out of SMD simulations. In this article, the surrogate processes are constructed by first estimating a sequence of local parametric diffusion models along a SMD trajectory and then a single global model is constructed by piecing the local models together through smoothing splines (estimation is made computationally feasible by likelihood function approximations). The SPAs are then “bootstrapped” in order to obtain a plausible range of work values associated with a particular SMD realization. This information is then used to assist in estimating a potential of mean force constructed by appealing to the Jarzynski equality. When this procedure is repeated for a small number of SMD paths, it is shown that the global models appear to come from a single family of closely related diffusion processes. Possible techniques for exploiting this observation are also briefly discussed. The findings of this paper have potential relevance to computationally expensive computer simulations and experimental works involving optical tweezers where it is difficult to collect a large number of samples, but possible to sample accurately and frequently in time.
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87.15.H- Dynamics of biomolecules
87.15.Vv Diffusion

The effective local potential method: Implementation for molecules and relation to approximate optimized effective potential techniques

Artur F. Izmaylov, Viktor N. Staroverov, Gustavo E. Scuseria, Ernest R. Davidson, Gabriel Stoltz, and Eric Cancès

J. Chem. Phys. 126, 084107 (2007); http://dx.doi.org/10.1063/1.2434784 (9 pages) | Cited 20 times

Online Publication Date: 28 February 2007

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We have recently formulated a new approach, named the effective local potential (ELP) method, for calculating local exchange-correlation potentials for orbital-dependent functionals based on minimizing the variance of the difference between a given nonlocal potential and its desired local counterpart [ V. N. Staroverov et al., J. Chem. Phys. 125, 081104 (2006) ]. Here we show that under a mildly simplifying assumption of frozen molecular orbitals, the equation defining the ELP has a unique analytic solution which is identical with the expression arising in the localized Hartree-Fock (LHF) and common energy denominator approximations (CEDA) to the optimized effective potential. The ELP procedure differs from the CEDA and LHF in that it yields the target potential as an expansion in auxiliary basis functions. We report extensive calculations of atomic and molecular properties using the frozen-orbital ELP method and its iterative generalization to prove that ELP results agree with the corresponding LHF and CEDA values, as they should. Finally, we make the case for extending the iterative frozen-orbital ELP method to full orbital relaxation.
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31.15.xr Self-consistent-field methods

Gaussian-4 theory

Larry A. Curtiss, Paul C. Redfern, and Krishnan Raghavachari

J. Chem. Phys. 126, 084108 (2007); http://dx.doi.org/10.1063/1.2436888 (12 pages) | Cited 165 times

Online Publication Date: 28 February 2007

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The Gaussian-4 theory (G4 theory) for the calculation of energies of compounds containing first- (Li–F), second- (Na–Cl), and third-row main group (K, Ca, and Ga–Kr) atoms is presented. This theoretical procedure is the fourth in the Gaussian-n series of quantum chemical methods based on a sequence of single point energy calculations. The G4 theory modifies the Gaussian-3 (G3) theory in five ways. First, an extrapolation procedure is used to obtain the Hartree-Fock limit for inclusion in the total energy calculation. Second, the d-polarization sets are increased to 3d on the first-row atoms and to 4d on the second-row atoms, with reoptimization of the exponents for the latter. Third, the QCISD(T) method is replaced by the CCSD(T) method for the highest level of correlation treatment. Fourth, optimized geometries and zero-point energies are obtained with the B3LYP density functional. Fifth, two new higher level corrections are added to account for deficiencies in the energy calculations. The new method is assessed on the 454 experimental energies in the G3/05 test set [ L. A. Curtiss, P. C. Redfern, and K. Raghavachari, J. Chem. Phys. 123, 124107 (2005) ], and the average absolute deviation from experiment shows significant improvement from 1.13 kcal/mol (G3 theory) to 0.83 kcal/mol (G4 theory). The largest improvement is found for 79 nonhydrogen systems (2.10 kcal/mol for G3 versus 1.13 kcal/mol for G4). The contributions of the new features to this improvement are analyzed and the performance on different types of energies is discussed.
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31.15.xr Self-consistent-field methods
31.15.bw Coupled-cluster theory
31.15.E- Density-functional theory
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Dynamics of dissociative recombination versus electron ejection in single rovibronic resonances of BH

C. Ricardo Viteri, Andrew T. Gilkison, and Edward R. Grant

J. Chem. Phys. 126, 084301 (2007); http://dx.doi.org/10.1063/1.2484107 (6 pages) | Cited 1 time

Online Publication Date: 22 February 2007

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Optical-optical-optical triple resonance spectroscopy isolates transitions to vibrationless Rydberg states of BH with principal quantum numbers from n = 7 to 50. Corresponding resonances appear in the excitation spectrum of excited boron atoms produced by the dissociative relaxation of these states. The decay to neutral products occurs on a nanosecond time scale. Yet, corresponding resonances show Fano coupling widths that approach 1 cm−1. Above threshold, spontaneous ionization dominates, but line shapes match for resonances with the same electron orbital quantum numbers built on v+ = 0 and v+ = 1 cores. This striking feature-for-feature similarity in predissociation and autoionization line shapes affirms that inelastic electron-cation scattering pathways leading to electron ejection and dissociative recombination proceed through a common continuum.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
33.40.+f Multiple resonances (including double and higher-order resonance processes, such as double nuclear magnetic resonance, electron double resonance, and microwave optical double resonance)
34.80.Lx Recombination, attachment, and positronium formation
33.70.Jg Line and band widths, shapes, and shifts
33.80.Eh Autoionization, photoionization, and photodetachment
34.80.Ht Dissociation and dissociative attachment

Oscillator strengths and radiative lifetimes for C2: Swan, Ballik-Ramsay, Phillips, and d 3Πg←c 3Σu+ systems

Damian L. Kokkin, George B. Bacskay, and Timothy W. Schmidt

J. Chem. Phys. 126, 084302 (2007); http://dx.doi.org/10.1063/1.2436879 (11 pages) | Cited 20 times

Online Publication Date: 22 February 2007

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High level ab initio calculations, using multireference configuration interaction (MRCI) techniques, have been carried out to investigate the spectroscopic properties of the singlet A 1Πu←X 1Σg+ Phillips, the triplet d 3Πg←a 3Σu Swan, the b 3Σg−←a 3Πu Ballik-Ramsay, and the d 3Πg←c 3Σu+ transitions of C2. The MRCI expansions are based on full-valence complete active space self-consistent-field reference states and utilize the aug-cc-pV6Z basis set to resolve valence electron correlation. Core and core-valence correlations and scalar relativistic energy corrections were also incorporated in the computed potential energy surfaces. Nonadiabatic and spin-orbit effects were explored and found to be of negligible importance in the calculations. Harmonic frequencies and rotational constants are typically within 0.1% of experiment. The calculated radiative lifetimes compare very well with the available experimental data. Oscillator strengths are reported for all systems: fv′v″, where 0 ⩽ v ⩽ 5.
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33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
31.15.A- Ab initio calculations
31.15.xr Self-consistent-field methods
31.50.Gh Surface crossings, non-adiabatic couplings
31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions
33.15.Mt Rotation, vibration, and vibration-rotation constants

Accurate quantum calculations of the reaction rates for H/D+CH4

Rob van Harrevelt, Gunnar Nyman, and Uwe Manthe

J. Chem. Phys. 126, 084303 (2007); http://dx.doi.org/10.1063/1.2464102 (6 pages) | Cited 20 times

Online Publication Date: 22 February 2007

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In previous work [ T. Wu, H. J. Werner, and U. Manthe, Science 306, 2227 (2004) ], accurate quantum reaction rate calculations of the rate constant for the H+CH4→CH3+H2 reaction have been presented. Both the electronic structure calculations and the nuclear dynamics calculations are converged with respect to the basis sets employed. In this paper, the authors apply the same methodology to an isotopic variant of this reaction: D+CH4→CH3+HD. Accurate rate constants are presented for temperatures between 250 and 400 K. For temperatures between 400 and 800 K, they use a harmonic extrapolation to obtain approximate rate constants for H/D+CH4. The calculations suggest that the experimentally reported rate constants for D+CH4 are about a factor of 10–20 too high. For H+CH4, more accurate experiments are available and agreement is much better: the difference is less than a factor of 2.6. The kinetic isotope effect for the H/D+CH4 reactions is studied and compared with experiment and transition state theory (TST) calculations. Harmonic TST was found to provide a good description of the kinetic isotope effect.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Ej Quantum theory of reaction cross section
82.20.Tr Kinetic isotope effects including muonium
82.20.Db Transition state theory and statistical theories of rate constants
82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)

Gas phase spectra of all-benzenoid polycyclic aromatic hydrocarbons: Triphenylene

Damian L. Kokkin, Neil J. Reilly, Tyler P. Troy, Klaas Nauta, and Timothy W. Schmidt

J. Chem. Phys. 126, 084304 (2007); http://dx.doi.org/10.1063/1.2484344 (7 pages) | Cited 4 times

Online Publication Date: 22 February 2007

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The jet-cooled laser-induced fluorescence and dispersed fluorescence spectra of the S1(A1′)←S0(A1′) transition of triphenylene are reported. The spectra exhibit false origins of e′ symmetry which are modeled by performing calculations of Herzberg-Teller coupling using time-dependent density functional theory. It is found that this level of theory reproduces the main features of the observed spectra. The oscillator strength of the strongest band is calculated to be f = 7×10−4. From a combination of theory and the observed upper state lifetime of 41 ns, an estimate of the fluorescence yield is made of ΦF = 0.084, in agreement with previous studies in the condensed phase.
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33.50.Dq Fluorescence and phosphorescence spectra
31.15.E- Density-functional theory
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors

Interacting resonances in the F+H2 reaction revisited: Complex terms, Riemann surfaces, and angular distributions

D. Sokolovski, S. K. Sen, V. Aquilanti, S. Cavalli, and D. De Fazio

J. Chem. Phys. 126, 084305 (2007); http://dx.doi.org/10.1063/1.2432120 (11 pages) | Cited 18 times

Online Publication Date: 22 February 2007

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We study the effect of overlapping resonances on the angular distributions of the reaction F+H2(v = 0,j = 0)→HF(v = 2,j = 0)+H in the collision energy range from 5 to 65 meV, i.e., under the reaction barrier. Reactive scattering calculations were performed using the hyperquantization algorithm on the potential energy surface of Stark and Werner [J. Chem. Phys. 104, 6515 (1996)]. The positions of the Regge and complex energy poles are obtained by Padé reconstruction of the scattering matrix element. The Sturmian theory is invoked to relate the Regge and complex energy terms. For two interacting resonances, a two-sheet Riemann surface is contracted and inverted. The semiclassical complex angular momentum analysis is used to decompose the scattering amplitude into the direct and resonance contributions.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Db Transition state theory and statistical theories of rate constants

Ground state structures and photoelectron spectroscopy of [Com(coronene)]− complexes

Anil K. Kandalam, Boggavarapu Kiran, Puru Jena, Xiang Li, Andrej Grubisic, and Kit H. Bowen

J. Chem. Phys. 126, 084306 (2007); http://dx.doi.org/10.1063/1.2437202 (9 pages) | Cited 6 times

Online Publication Date: 23 February 2007

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A synergistic approach involving theory and experiment has been used to study the structure and properties of neutral and negatively charged cobalt-coronene [Com(coronene)] complexes. The calculations are based on density functional theory with generalized gradient approximation for exchange and correlation potential, while the experiments are carried out using photoelectron spectroscopy of mass selected anions. The authors show that the geometries of neutral and anionic Co(coronene) and Co2(coronene) are different from those of the corresponding iron-coronene complexes and that both the Co atom and the dimer prefer to occupy η2-bridge binding sites. However, the magnetic coupling between the Co atoms remains ferromagnetic as it is between iron atoms supported on a coronene molecule. The accuracy of the theoretical results is established by comparing the calculated vertical detachment energies, and adiabatic electron affinities with their experimental data.
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36.40.Mr Spectroscopy and geometrical structure of clusters
31.15.E- Density-functional theory
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.60.+q Photoelectron spectra
36.40.Cg Electronic and magnetic properties of clusters
36.40.Wa Charged clusters

Femtosecond dynamics of Cu(CD3OD)

Jack Barbera, Samantha Horvath, Vladimir Dribinski, Anne B. McCoy, and W. Carl Lineberger

J. Chem. Phys. 126, 084307 (2007); http://dx.doi.org/10.1063/1.2464103 (10 pages) | Cited 2 times

Online Publication Date: 27 February 2007

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We report the femtosecond nuclear dynamics of Cu(CD3OD) van der Waals clusters, investigated using photodetachment-photoionization spectroscopy. Photodetachment of an electron from Cu−(CD3OD) with a 150 fs, 398 nm laser pulse produces a vibrationally excited neutral complex that undergoes ligand reorientation and dissociation. The dynamics of Cu(CD3OD) on the neutral surface is interrogated by delayed femtosecond resonant two-photon ionization. Analysis of the resulting time-dependent signals indicates that the nascent Cu(CD3OD) complex dissociates on two distinct time scales of 3 and 30 ps. To understand the origins of the observed time scales, complimentary studies were performed. These included measurement of the photoelectron spectrum of Cu−(CD3OD) as well as a series of calculations of the structure and the electronic and vibrational energies of the anion and neutral complexes. Based on the comparisons of the experimental and calculated results for Cu(CD3OD) with those obtained from earlier studies of Cu(H2O), we conclude that the 3 ps time scale reflects the energy transfer from the rotation of CD3OD in the complex to the dissociation coordinate, while the 30 ps time scale reflects the energy transfer from the excited methyl torsion states to the dissociation coordinate.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
33.80.Eh Autoionization, photoionization, and photodetachment
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis

Dissociative wave packets and dynamic resonances

David Cardoza, Brett J. Pearson, and Thomas Weinacht

J. Chem. Phys. 126, 084308 (2007); http://dx.doi.org/10.1063/1.2437198 (6 pages) | Cited 7 times

Online Publication Date: 28 February 2007

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The authors examine the role of dynamic resonances in laser driven molecular fragmentation. The yields of molecular fragments can undergo dramatic changes as an impulsively excited dissociative wave packet passes through a dynamic resonance. The authors compare three different kinds of dynamic resonances in a series of molecular families and highlight the possibility of characterizing the dissociative wave function as it crosses the resonance location.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
31.15.-p Calculations and mathematical techniques in atomic and molecular physics

Fragmentation of methyl chloride studied by partial positive and negative ion-yield spectroscopy

D. Céolin, M. N. Piancastelli, R. Guillemin, W. C. Stolte, S.-W. Yu, O. Hemmers, and D. W. Lindle

J. Chem. Phys. 126, 084309 (2007); http://dx.doi.org/10.1063/1.2464093 (8 pages) | Cited 12 times

Online Publication Date: 28 February 2007

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The authors present partial-ion-yield experiments on the methyl chloride molecule excited in the vicinity of the Cl2p and C1s inner shells. A large number of fragments, cations produced by dissociation or recombination processes, as well as anionic species, have been detected. Although the spectra exhibit different intensity distributions depending on the core-excited atom, general observations include strong site-selective fragmentation along the C–Cl bond axis and a strong intensity dependence of transitions involving Rydberg series on fragment size.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
34.80.Lx Recombination, attachment, and positronium formation
33.15.Fm Bond strengths, dissociation energies

Predissociation of Bi2 A(0u+), v′ = 21–39

Michael W. Dolezal and Glen P. Perram

J. Chem. Phys. 126, 084310 (2007); http://dx.doi.org/10.1063/1.2567342 (6 pages) | Cited 1 time

Online Publication Date: 28 February 2007

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Collisionless lifetimes for Bi2 A(0u+), v′ = 20–39, J′ ⩽ 105 have been measured using pulsed laser induced fluorescence techniques to investigate the effects of predissociation. The observed predissociation rates, Γ = kpd(v′)J(J+1), are quite rapid, ranging from kpd = 1.53×102 s−1 for v′ = 21 to 1.5×105 s−1 for v′ = 39. The dense Bi2(A→X) spectrum required both traditional lifetime measurements and synthetic spectrum fits to laser excitation spectra to determine the full range of observed rates. A single, repulsive potential responsible for the observed A-state predissociation could not be identified to adequately describe the vibrational dependence of the predissociation rates.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
33.50.Dq Fluorescence and phosphorescence spectra
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Ionization induced relaxation in solvation structure: A comparison between Na(H2O)n and Na(NH3)n

Bing Gao and Zhi-Feng Liu

J. Chem. Phys. 126, 084501 (2007); http://dx.doi.org/10.1063/1.2464109 (11 pages) | Cited 18 times

Online Publication Date: 22 February 2007

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The constant ionization potential for hydrated sodium clusters Na(H2O)n just beyond n = 4, as observed in photoionization experiments, has long been a puzzle in violation of the well-known (n+1)−1/3 rule that governs the gradual transition in properties from clusters to the bulk. Based on first principles calculations, a link is identified between this puzzle and an important process in solution: the reorganization of the solvation structure after the removal of a charged particle. Na(H2O)n is a prototypical system with a solvated electron coexisting with a solvated sodium ion, and the cluster structure is determined by a balance among three factors: solute-solvent (Na+–H2O), solvent-solvent (H2O–H2O), and electron-solvent (OH{e}HO) interactions. Upon the removal of an electron by photoionization, extensive structural reorganization is induced to reorient OH{e}HO features in the neutral Na(H2O)n for better Na+–H2O and H2O–H2O interactions in the cationic Na+(H2O)n. The large amount of energy released, often reaching 1 eV or more, indicates that experimentally measured ion signals actually come from autoionization via vertical excitation to high Rydberg states below the vertical ionization potential, which induces extensive structural reorganization and the loss of a few solvent molecules. It provides a coherent explanation for all the peculiar features in the ionization experiments, not only for Na(H2O)n but also for Li(H2O)n and Cs(H2O)n. In addition, the contrast between Na(H2O)n and Na(NH3)n experiments is accounted for by the much smaller relaxation energy for Na(NH3)n, for which the structures and energetics are also elucidated.
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33.80.Eh Autoionization, photoionization, and photodetachment
36.40.-c Atomic and molecular clusters
31.15.E- Density-functional theory
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy

Anomalous nonlinear dielectric and Kerr effect relaxation steady state responses in superimposed ac and dc electric fields

William T. Coffey, Yuri P. Kalmykov, and Sergey V. Titov

J. Chem. Phys. 126, 084502 (2007); http://dx.doi.org/10.1063/1.2463694 (6 pages)

Online Publication Date: 22 February 2007

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It is shown how the rotational diffusion model of polar molecules (which may be described in microscopic fashion as the diffusion limit of a discrete time random walk on the surface of the unit sphere) may be extended to anomalous nonlinear dielectric relaxation and the dynamic Kerr effect by using a fractional kinetic equation. This fractional kinetic equation (obtained via a generalization of the noninertial kinetic equation of conventional rotational diffusion to fractional kinetics to include anomalous relaxation) is solved using matrix continued fractions yielding the complex nonlinear dielectric susceptibility and the Kerr function of an assembly of rigid dipolar particles acted on by external superimposed dc E0 and ac E1(t) = E1 cos ωt electric fields of arbitrary strengths. In the weak field limit, analytic equations for nonlinear response functions are also derived.
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77.22.Gm Dielectric loss and relaxation
78.20.Jq Electro-optical effects

Vibrational dynamics and stability of the high-pressure chain and ring phases in S and Se

Olga Degtyareva, Eduardo R. Hernández, Jorge Serrano, Maddury Somayazulu, Ho-kwang Mao, Eugene Gregoryanz, and Russell J. Hemley

J. Chem. Phys. 126, 084503 (2007); http://dx.doi.org/10.1063/1.2433944 (11 pages) | Cited 5 times

Online Publication Date: 22 February 2007

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The high-pressure phases of group-VI elements sulfur and selenium in their spiral chain and ring structures are examined by in situ Raman and x-ray diffraction techniques combined with first principles electronic structure calculations. The S-II, S-III, Se-I, and Se-VII having spiral chain structures and S-VI with a molecular six-member ring structure are studied in a wide P-T range. The square spiral chain structure of S-III and Se-VII is characterized by seven Raman modes that harden with increasing pressure. The calculations reproduce the observed frequencies and allow the authors to make the mode assignment. The “p-S” and “hplt” phases of sulfur reported by previous Raman studies are identified as S-II and S-III with the triangular and square spiral chain structures, respectively. The phase relations obtained by the x-ray and Raman measurements show that the high-pressure high-temperature phases of sulfur, observed by x-ray, can be induced by laser illumination at room temperature.
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78.30.Hv Other nonmetallic inorganics
61.50.Ks Crystallographic aspects of phase transformations; pressure effects
62.50.-p High-pressure effects in solids and liquids
61.66.Fn Inorganic compounds
71.15.-m Methods of electronic structure calculations

Intermolecular polarizability dynamics of aqueous formamide liquid mixtures studied by molecular dynamics simulations

M. Dolores Elola and Branka M. Ladanyi

J. Chem. Phys. 126, 084504 (2007); http://dx.doi.org/10.1063/1.2446782 (13 pages) | Cited 7 times

Online Publication Date: 22 February 2007

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A molecular dynamics simulation study is presented for the relaxation of the polarizability anisotropy in liquid mixtures of formamide and water, using a dipolar induction scheme that involves the intrinsic polarizability and first hyperpolarizability tensors of the molecules, and the dipole-quadrupole polarizability of water species. The long time diffusive decay of the collective polarizability anisotropy correlations exhibits a substantial slowing down as the formamide mole fraction increases in the mixture. The diffusive times for the polarizability relaxation obtained from the authors’ simulations are in good agreement with optical Kerr effect experimental data, and they are found to correlate nearly linearly with the estimated mean lifetimes of the hydrogen bonds within the mixture, suggesting that the relaxation of the hydrogen bond network is responsible to some extent for the collective relaxation of the polarizability anisotropy of the mixture. The short time behavior of the polarizability anisotropy relaxation was investigated by computing the nuclear response function, R(t), which is very rapidly dominated by the formamide contribution as it is added to water, due to the much larger polarizability anisotropy of formamide molecules compared to that of water. Several contributions to the Raman spectrum were also analyzed as a function of composition, and the dynamical origin of the different bands was determined.
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64.75.-g Phase equilibria
61.25.Em Molecular liquids
78.30.C- Liquids
78.20.Jq Electro-optical effects
42.65.An Optical susceptibility, hyperpolarizability
61.20.Ja Computer simulation of liquid structure

Size dependence of the structures and energetic and electronic properties of gold clusters

Xi-Bo Li, Hong-Yan Wang, Xiang-Dong Yang, Zheng-He Zhu, and Yong-Jian Tang

J. Chem. Phys. 126, 084505 (2007); http://dx.doi.org/10.1063/1.2434779 (8 pages) | Cited 38 times

Online Publication Date: 26 February 2007

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The structures and stabilities of gold clusters with up to 14 atoms have been determined by density-functional theory. The structure optimizations and frequency analysis are performed with the Perdew-Wang 1991 gradient-corrected functional combined with the effective core potential and corresponding valence basis set (LANL2DZ). The turnover point from two-dimensional to three-dimensional geometry for gold clusters occurs at Au12. The energetic and electronic properties of the small gold clusters are strongly dependent on sizes and structures, which are in good agreement with experiment and other theoretical calculations. The even-odd oscillation in cluster stability and electronic properties predicted that the clusters with even numbers of atoms were more stable than the neighboring clusters with odd numbers of atoms. The stability and electronic structure properties of gold clusters are also characterized by the maximum hardness principle of chemical reactivity and minimum polarizability principle.
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36.40.Cg Electronic and magnetic properties of clusters
36.40.Mr Spectroscopy and geometrical structure of clusters
36.40.Qv Stability and fragmentation of clusters
31.15.E- Density-functional theory
33.15.Bh General molecular conformation and symmetry; stereochemistry

Rigid quantum Monte Carlo simulations of condensed molecular matter: Water clusters in the n = 2→8 range

Stephen F. Langley, E. Curotto, D. L. Freeman, and J. D. Doll

J. Chem. Phys. 126, 084506 (2007); http://dx.doi.org/10.1063/1.2484229 (15 pages) | Cited 10 times

Online Publication Date: 27 February 2007

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The numerical advantage of quantum Monte Carlo simulations of rigid bodies relative to the flexible simulations is investigated for some simple systems. The results show that if high frequency modes in molecular condensed matter are predominantly in the ground state, the convergence of path integral simulations becomes nonuniform. Rigid body quantum parallel tempering simulations are necessary to accurately capture thermodynamic phenomena in the temperature range where the dynamics are influenced by intermolecular degrees of freedom; the stereographic projection path integral adapted for quantum simulations of asymmetric tops is a significantly more efficient strategy compared with Cartesian coordinate simulations for molecular condensed matter under these conditions. The reweighted random series approach for stereographic path integral Monte Carlo is refined and implemented for the quantum simulation of water clusters treated as an assembly of rigid asymmetric tops.
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36.40.Mr Spectroscopy and geometrical structure of clusters
65.40.G- Other thermodynamical quantities
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