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7 Dec 2008

Volume 129, Issue 21, Articles (21xxxx)

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Experimental determination of the third derivative of G. I. Enthalpic interaction

Peter Westh, Akira Inaba, and Yoshikata Koga

J. Chem. Phys. 129, 211101 (2008); http://dx.doi.org/10.1063/1.3033366 (4 pages) | Cited 1 time

Online Publication Date: 3 December 2008

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The solute (i)—solute interaction in terms of enthalpy, Hi−iE = N(∂2HE/∂ni2) = (1−xi)(∂2HE/∂ni∂xi), the third derivative of G, was experimentally determined using a Thermal Activity Monitor isothermal titration calorimeter for aqueous solutions of 2-butoxyethanol (BE) and 1-propanol (1P). This was done using both calorimetric reference and sample vessels actively. We simultaneously titrate small and exactly equal amounts of solute i ( = BE or 1P) into both cells which contain the binary mixtures at an average mole fraction, xi, which differs by a small amount Δxi. The appropriate amount of titrant δni was chosen so that the quotient (δHE/δni) can be approximated as (∂HE/∂ni), and so that the scatter of the results is reasonable. δHE is the thermal response from an individual cell on titration, and we measure directly the difference in the thermal response between the two cells, Δ(δHE). The resulting quotient, Δ(δHE)/δni/Δxi, can be approximated as (∂2HE/∂ni∂xi) and hence provides a direct experimental avenue for the enthalpy interaction function. We varied the value of Δxi to seek its appropriate size. Since HE contains the first derivative of G with respect to T, the result is the third derivative quantity. Thus we present here a third derivative quantity directly determined experimentally for the first time.
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82.60.Lf Thermodynamics of solutions
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Implementation of transition moments between excited states in the approximate coupled-cluster singles and doubles model

Mathias Pabst and Andreas Köhn

J. Chem. Phys. 129, 214101 (2008); http://dx.doi.org/10.1063/1.3023118 (12 pages) | Cited 9 times

Online Publication Date: 2 December 2008

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An implementation of transition moments between excited states for the approximate coupled-cluster singles and doubles model (CC2) using the resolution of the identity (RI) approximation is reported. The accuracy of the RI approximation is analyzed for a testset of 7 molecules and 76 transitions. The RI error is found to be very small for both transition moments and oscillator strengths. Furthermore, the performance of the CC2 model in comparison with coupled-cluster singles and doubles (CCSD) is studied for 40 transitions of the same testset, yielding deviations of about 12% for the transition moments and 24% for the oscillator strengths. In addition, for 13 transitions of the testset the behavior of the transition moments with respect to seven different basis sets (Dunnings xaug-cc-pVXZ, with x = 0,1,2 for X = D,T and x = 2 for X = 5) is analyzed, showing a strong dependence on the degree of augmentation x and a rather small effect of the cardinal number X. First applications are presented for the triplet-triplet transition moments of benzene and polyacenes (naphthalene to pentacene), showing good agreement with experimental and theoretical results for transitions between single excitation dominated states. Somewhat problematic is the insufficient description of double-excitation dominated states by the CC2 model. As transitions to such states may be strongly allowed, unlike for excitations out of the ground state, important features of transient spectra may be missed. For triplet-triplet excitations the problem is less evident as the lowest doubly excited triplet states are expected at higher energies.
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33.50.-j Fluorescence and phosphorescence; radiationless transitions, quenching (intersystem crossing, internal conversion)
31.15.bw Coupled-cluster theory
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors

A tight-binding potential for helium in carbon systems

Rebecca Granot and Roi Baer

J. Chem. Phys. 129, 214102 (2008); http://dx.doi.org/10.1063/1.3025241 (5 pages)

Online Publication Date: 2 December 2008

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The presence of helium in carbon systems, such as diamonds and fullerenes is of interest for planetary sciences, geophysics, astrophysics, and evolution biology. Such systems typically involve a large number of atoms and require a fast method for assessing the interaction potential and forces. We developed a tight-binding approach, based on density functional calculations, which includes a many-body potential term. This latter term is essential for consolidating the density functional results of helium in bulky diamond and Helium passing through a benzene ring which is important for helium-fullerene applications. The method is simple to apply and exhibits good transferability properties.
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71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)
71.15.Mb Density functional theory, local density approximation, gradient and other corrections

Efficient elimination of response parameters in molecular property calculations for variational and nonvariational energies

Kasper Kristensen, Poul Jørgensen, Andreas J. Thorvaldsen, and Trygve Helgaker

J. Chem. Phys. 129, 214103 (2008); http://dx.doi.org/10.1063/1.3023123 (7 pages) | Cited 8 times

Online Publication Date: 2 December 2008

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A general method is presented for the efficient elimination of response parameters in molecular property calculations for variational and nonvariational energies. For variational energies, Wigner’s 2n+1 rule is obtained as a special case of the more general k2n+1 rule, which states that for a subset of k perturbations within a total set of z ≥ k perturbations, response parameters may be eliminated according to the 2n+1 rule (normally applied to the full set of perturbations). Nonvariational energies may be treated by introducing Lagrange multipliers that satisfy the stronger 2n+2 rule for the k perturbations, while the wave-function parameters still satisfy the 2n+1 rule for the k perturbations. The corresponding rule for nonvariational energies is referred to as the k2n+1,2n+2 rule. For k = z, the well-known 2n+2 rule for the multipliers is reproduced, while the wave-function parameters satisfy the 2n+1 rule. The application of the k2n+1 and k2n+1,2n+2 rules minimizes the total number of response equations to be solved when the molecular property contains k extensive perturbations (e.g., geometrical derivatives) and z−k intensive perturbations (e.g., electric fields).
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31.15.-p Calculations and mathematical techniques in atomic and molecular physics

Photon-exposure-dependent photon-stimulated desorption for obtaining photolysis cross section of molecules adsorbed on surface by monochromatic soft x-ray photons

L.-C. Chou, C.-Y. Jang, Y.-H. Wu, W.-C. Tsai, S.-K. Wang, J. Chen, S.-C. Chang, C.-C. Liu, Y. Shai, and C.-R. Wen

J. Chem. Phys. 129, 214104 (2008); http://dx.doi.org/10.1063/1.3026598 (13 pages) | Cited 3 times

Online Publication Date: 2 December 2008

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Photon-exposure-dependent positive- and negative-ion photon-stimulated desorption (PSD) was proposed to study the photoreactions and obtain the photolysis cross sections of molecules adsorbed on a single-crystal surface by monochromatic soft x-ray photons with energy near the core level of adsorbate. The changes in the F+ and F− PSD ion yields were measured from CF3Cl molecules adsorbed on Si(111)-7×7 at 30 K (CF3Cl dose = 0.3×1015 molecules/cm2, ∼ 0.75 monolayer) during irradiation of monochromatic soft x-ray photons near the F(1s) edge. The PSD ion yield data show the following characteristics: (a) The dissociation of adsorbed CF3Cl molecules is due to a combination of direct photodissociation via excitation of F(1s) core level and substrate-mediated dissociation [dissociative attachment and dipolar dissociation induced by the photoelectrons emitting from the silicon substrate]. (b) the F+ ion desorption is associated with the bond breaking of the surface CF3Cl, CF2Cl, CFCl, and SiF species. (c) the F− yield is mainly due to DA and DD of the adsorbed CF3Cl molecules. (d) The surface SiF is formed by reaction of the surface Si atom with the neutral fluorine atom, F+, or F− ion produced by scission of C–F bond of CF3Cl, CF2Cl, or CFCl species. A kinetic model was proposed for the explanation of the photolysis of this submonolayer CF3Cl-covered surface. Based on this model and the variation rates of the F+/F− signals during fixed-energy monochromatic photon bombardment at 690.2 and 692.6 eV [near the F(1s) edge], the photolysis cross section was deduced as a function of energy.
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68.43.Tj Photon stimulated desorption
82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
61.80.Cb X-ray effects
79.20.Rf Atomic, molecular, and ion beam impact and interactions with surfaces
82.50.-m Photochemistry

Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions

Dahlia A. Goldfeld, Arteum D. Bochevarov, and Richard A. Friesner

J. Chem. Phys. 129, 214105 (2008); http://dx.doi.org/10.1063/1.3008062 (13 pages) | Cited 3 times

Online Publication Date: 2 December 2008

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This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [ R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006) ; E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006) .] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT’s inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G∗, 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.
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82.60.Cx Enthalpies of combustion, reaction, and formation
82.20.Db Transition state theory and statistical theories of rate constants
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions

On collisional energy transfer in recombination and dissociation reactions: A Wiener–Hopf problem and the effect of a near elastic peak

Zhaoyan Zhu and R. A. Marcus

J. Chem. Phys. 129, 214106 (2008); http://dx.doi.org/10.1063/1.3026605 (10 pages) | Cited 4 times

Online Publication Date: 2 December 2008

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The effect of the large impact parameter near-elastic peak of collisional energy transfer for unimolecular dissociation/bimolecular recombination reactions is studied. To this end, the conventional single exponential model, a biexponential model that fits the literature classical trajectory data better, a model with a singularity at zero energy transfer, and the most realistic model, a model with a near-singularity, are fitted to the trajectory data in the literature. The typical effect of the energy transfer on the recombination rate constant is maximal at low pressures and this region is the one studied here. The distribution function for the limiting dissociation rate constant k0 at low pressures is shown to obey a Wiener–Hopf integral equation and is solved analytically for the first two models and perturbatively for the other two. For the single exponential model, this method yields the trial solution of Troe. The results are applied to the dissociation of O3 in the presence of argon, for which classical mechanical trajectory data are available. The k0’s for various models are calculated and compared, the value for the near-singularity model being about ten times larger than that for the first two models. This trend reflects the contribution to the cross section from collisions with larger impact parameter. In the present study of the near-singularity model, it is found that k0 is not sensitive to reasonable values for the lower bound. Energy transfer values 〈ΔE〉’s are also calculated and compared and can be similarly understood. However, unlike the k0 values, they are sensitive to the lower bound, and so any comparison of a classical trajectory analysis for 〈ΔE〉’s with the kinetic experimental data needs particular care.
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82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.20.Nk Classical theories of reactions and/or energy transfer
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.30.Nr Association, addition, insertion, cluster formation

Molecular dynamics with time dependent quantum Monte Carlo

Ivan P. Christov

J. Chem. Phys. 129, 214107 (2008); http://dx.doi.org/10.1063/1.3031214 (8 pages) | Cited 2 times

Online Publication Date: 3 December 2008

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In this paper we propose an ab initio method to solve quantum many-body problems of molecular dynamics where both electronic and nuclear degrees are represented by ensembles of trajectories and guiding waves in physical space. Both electrons and nuclei can be treated quantum mechanically where the guiding waves obey a set of coupled Schrödinger equations (quantum-quantum description) or, alternatively, coupled Schrödinger–Newtonian equations are solved for the quantum-classical approximation. The method takes into account local and nonlocal quantum correlation effects in a self-consistent manner. The general formalism is applied to one- and two-dimensional hydrogen molecules subjected to a strong ultrashort optical pulse. Comparison is made with the results from the “exact” Ehrenfest molecular dynamics for the molecular ionization and for the evolution of the internuclear distance as the molecule dissociates.
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33.80.Eh Autoionization, photoionization, and photodetachment
33.80.Gj Diffuse spectra; predissociation, photodissociation
31.15.xv Molecular dynamics and other numerical methods
31.15.at Molecule transport characteristics; molecular dynamics; electronic structure of polymers
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations

A density matrix-based quasienergy formulation of the Kohn–Sham density functional response theory using perturbation- and time-dependent basis sets

Andreas J. Thorvaldsen, Kenneth Ruud, Kasper Kristensen, Poul Jørgensen, and Sonia Coriani

J. Chem. Phys. 129, 214108 (2008); http://dx.doi.org/10.1063/1.2996351 (27 pages) | Cited 26 times

Online Publication Date: 3 December 2008

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A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn–Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability.
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31.15.E- Density-functional theory
31.15.xr Self-consistent-field methods
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.xt Variational techniques
31.15.xp Perturbation theory

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit

H. Lee Woodcock, Wenjun Zheng, An Ghysels, Yihan Shao, Jing Kong, and Bernard R. Brooks

J. Chem. Phys. 129, 214109 (2008); http://dx.doi.org/10.1063/1.3013558 (9 pages) | Cited 10 times

Online Publication Date: 3 December 2008

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A new vibrational subsystem analysis (VSA) method is presented for coupling global motion to a local subsystem while including the inertial effects of the environment. The premise of the VSA method is a partitioning of a system into a smaller region of interest and a usually larger part referred to as environment. This method allows the investigation of local-global coupling, a more accurate estimation of vibrational free energy contribution for parts of a large system, and the elimination of the “tip effect” in elastic network model calculations. Additionally, the VSA method can be used as a probe of specific degrees of freedom that may contribute to free energy differences. The VSA approach can be employed in many ways, but it will likely be most useful for estimating activation free energies in QM/MM reaction path calculations. Four examples are presented to demonstrate the utility of this method.
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33.20.Tp Vibrational analysis
31.15.V- Electron correlation calculations for atoms, ions and molecules

Dimensional scaling treatment of stability of simple diatomic molecules induced by superintense, high-frequency laser fields

Qi Wei, Sabre Kais, and Dudley Herschbach

J. Chem. Phys. 129, 214110 (2008); http://dx.doi.org/10.1063/1.3027451 (8 pages) | Cited 1 time

Online Publication Date: 3 December 2008

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We present results obtained using dimensional scaling with high-frequency Floquet theory to evaluate the stability of gas phase simple diatomic molecules in superintense laser fields. The large-D limit provides a simple model that captures the main physics of the problem, which imposes electron localization along the polarization direction of the laser field. This localization markedly reduces the ionization probability and can enhance chemical bonding when the laser strength becomes sufficiently strong. We find that energy and structure calculations at the large-dimensional limit (D→∞) for stabilities of H2+, H2, and He2 in superintense laser fields are much simpler than at D = 3, yet yield similar results to those found from demanding ab initio calculations. We also use the large-D model to predict the stability of H2− and the field strength needed to bind the “extra” electron to the H2 molecule.
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33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
31.15.ae Electronic structure and bonding characteristics

Thermodynamics of droplet formation around a soluble condensation nucleus in the atmosphere of a solvent vapor

A. K. Shchekin, I. V. Shabaev, and A. I. Rusanov

J. Chem. Phys. 129, 214111 (2008); http://dx.doi.org/10.1063/1.3021078 (8 pages) | Cited 6 times

Online Publication Date: 4 December 2008

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An expression for the work of formation of a spherical droplet condensing on a soluble condensation nucleus out of a solvent vapor is derived. The dependence of the formation work on the solvent vapor chemical potential and the droplet and the nucleus residue sizes is analyzed. The balance of the solute matter between the liquid film and the nucleus residue and the effect of overlapping the surface layers of the thin film have been taken into account. It is shown that the equations of the chemical equilibrium of a solute and a solvent in the droplet, resulting from the generating properties of the formation work, coincide with the generalized Gibbs–Kelvin–Köhler and Ostwald–Freundlich equations. The numerical solution of these equations at a fixed number of molecules of the nucleus matter (at an initial size of the nucleus specified) has been performed in the case of the solvent vapor undersaturated over the bulk liquid solvent phase. The solution links the equilibrium sizes of the droplet and the soluble nucleus residue with the chemical potential or the pressure of the solvent vapor saturated over the droplet. It also determines the limiting sizes of the droplet with small nucleus residue above which the chemical equilibrium of the residue surface and the solution film does not exist. The existence of the limiting sizes is responsible for the specific behavior of the droplet thermodynamic characteristics and the work of droplet formation at deliquescence transition from the droplet state with a partly dissolved nucleus to the state of complete dissolution of the nucleus.
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82.60.Lf Thermodynamics of solutions
68.15.+e Liquid thin films
64.75.Bc Solubility
64.70.fm Thermodynamics studies of evaporation and condensation
47.55.db Drop and bubble formation
82.60.Hc Chemical equilibria and equilibrium constants

Estimating errors in free energy calculations from thermodynamic integration using fitted data

Enrique de Miguel

J. Chem. Phys. 129, 214112 (2008); http://dx.doi.org/10.1063/1.3023062 (6 pages) | Cited 2 times

Online Publication Date: 4 December 2008

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A procedure to estimate the statistical uncertainties associated with free energies computed from thermodynamic integration using fitted data is described. The method involves generating synthetic data sets from the actual simulation data and performing an analysis of the resulting distribution of free energy values. These values follow a Gaussian distribution, and the corresponding standard deviation is associated with the error in the computed value of the free energy. The impact of these uncertainties on the coexistence pressure is examined for first-order transitions. The approach is demonstrated with an examination of finite-size effects at the freezing transition of hard spheres.
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05.70.Ce Thermodynamic functions and equations of state
02.60.-x Numerical approximation and analysis
02.50.Ng Distribution theory and Monte Carlo studies
05.70.Fh Phase transitions: general studies

A unified theoretical framework for fluctuating-charge models in atom-space and in bond-space

Jiahao Chen, Dirk Hundertmark, and Todd J. Martínez

J. Chem. Phys. 129, 214113 (2008); http://dx.doi.org/10.1063/1.3021400 (11 pages) | Cited 6 times

Online Publication Date: 4 December 2008

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Our previously introduced QTPIE (charge transfer with polarization current equilibration) model [ J. Chen and T. J. Martínez, Chem. Phys. Lett. 438, 315 (2007) ] is a fluctuating-charge model with correct asymptotic behavior. Unlike most other fluctuating-charge models, QTPIE is formulated in terms of charge-transfer variables and pairwise electronegativities, not atomic charge variables and electronegativities. The pairwise character of the electronegativities in QTPIE allows us to avoid spurious charge transfer when bonds are broken. However, the increased number of variables leads to considerable computational expense and a rank-deficient set of working equations, which is numerically inconvenient. Here, we show that QTPIE can be exactly reformulated in terms of atomic charge variables, leading to a considerable reduction in computational complexity. The transformation between atomic and bond variables is generally applicable to arbitrary fluctuating charge models and uncovers an underlying topological framework that can be used to understand the relation between fluctuating-charge models and the classical theory of electrical circuits.
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34.70.+e Charge transfer
31.15.-p Calculations and mathematical techniques in atomic and molecular physics

A Bayesian statistics approach to multiscale coarse graining

Pu Liu, Qiang Shi, Hal Daumé, III, and Gregory A. Voth

J. Chem. Phys. 129, 214114 (2008); http://dx.doi.org/10.1063/1.3033218 (11 pages) | Cited 3 times

Online Publication Date: 5 December 2008

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Coarse-grained (CG) modeling provides a promising way to investigate many important physical and biological phenomena over large spatial and temporal scales. The multiscale coarse-graining (MS-CG) method has been proven to be a thermodynamically consistent way to systematically derive a CG model from atomistic force information, as shown in a variety of systems, ranging from simple liquids to proteins embedded in lipid bilayers. In the present work, Bayes’ theorem, an advanced statistical tool widely used in signal processing and pattern recognition, is adopted to further improve the MS-CG force field obtained from the CG modeling. This approach can regularize the linear equation resulting from the underlying force-matching methodology, therefore substantially improving the quality of the MS-CG force field, especially for the regions with limited sampling. Moreover, this Bayesian approach can naturally provide an error estimation for each force field parameter, from which one can know the extent the results can be trusted. The robustness and accuracy of the Bayesian MS-CG algorithm is demonstrated for three different systems, including simple liquid methanol, polyalanine peptide solvated in explicit water, and a much more complicated peptide assembly with 32 NNQQNY hexapeptides.
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87.15.ap Molecular dynamics simulation
87.15.R- Reactions and kinetics
87.16.D- Membranes, bilayers, and vesicles
87.14.Cc Lipids
87.14.ef Peptides

Elimination of fast variables in chemical Langevin equations

Yueheng Lan, Timothy C. Elston, and Garegin A. Papoian

J. Chem. Phys. 129, 214115 (2008); http://dx.doi.org/10.1063/1.3027499 (10 pages) | Cited 3 times

Online Publication Date: 5 December 2008

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Internal and external fluctuations are ubiquitous in cellular signaling processes. Because biochemical reactions often evolve on disparate time scales, mathematical perturbation techniques can be invoked to reduce the complexity of stochastic models. Previous work in this area has focused on direct treatment of the master equation. However, eliminating fast variables in the chemical Langevin equation is also an important problem. We show how to solve this problem by utilizing a partial equilibrium assumption. Our technique is applied to a simple birth-death-dimerization process and a more involved gene regulation network, demonstrating great computational efficiency. Excellent agreement is found with results computed from exact stochastic simulations. We compare our approach with existing reduction schemes and discuss avenues for future improvement.
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87.15.R- Reactions and kinetics
87.16.A- Theory, modeling, and simulations
87.16.Yc Regulatory genetic and chemical networks

H/D isotope effect in methyl torsional interaction of acetone as calculated by a multicomponent molecular orbital method

Takayoshi Ishimoto, Yasuyuki Ishihara, Hiroyuki Teramae, Masaaki Baba, and Umpei Nagashima

J. Chem. Phys. 129, 214116 (2008); http://dx.doi.org/10.1063/1.3028540 (8 pages) | Cited 2 times

Online Publication Date: 5 December 2008

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We analyzed the H/D isotope effect in the methyl torsional interactions accompanying two methyl internal rotations for acetone (CH3COCH3) and deuterated acetone (CD3COCD3 and CH3COCD3) in the ground state by means of the multicomponent molecular orbital (MC_MO) method, which directly accounts for the quantum effects of protons and deuterons. Our estimated rotational constants and moments of inertia for CH3COCH3 and CD3COCD3 agreed well with the experimental results because of the adequate treatment of protonic and deuteronic quantum effects afforded by the MC_MO method. Because the C–D bond distance in the CD3 group was shorter than the C–H distance in CH3 owing to the anharmonicity of the potential, the difference in potential energy surfaces of CH3COCH3, CD3COCD3, and CH3COCD3 was strongly related to the differences induced in geometrical parameters by the H/D isotope effect. The potential energy obtained by the MC_MO method was estimated as 290.88 cm−1 for CH3COCH3, which is in excellent agreement with the experimental results. For CH3COCD3, two potential energies were obtained for CH3 and CD3 internal rotations. The MC_MO method successfully elucidated the H/D isotope effect for methyl-methyl repulsive interactions by allowing the adequate treatment of protonic and deuteronic wave functions. The potential energies and bond distances associated with methyl internal rotation induced by the H/D isotope effect were also controlled by the distribution of wave functions of protons and deuterons.
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31.30.Gs Hyperfine interactions and isotope effects
33.20.Sn Rotational analysis
31.50.-x Potential energy surfaces
33.15.Dj Interatomic distances and angles
31.15.-p Calculations and mathematical techniques in atomic and molecular physics

Effect of the geometric phase on nuclear dynamics at a conical intersection: Extension of a recent topological approach from one to two coupled surfaces

Stuart C. Althorpe, Thomas Stecher, and Foudhil Bouakline

J. Chem. Phys. 129, 214117 (2008); http://dx.doi.org/10.1063/1.3031215 (10 pages) | Cited 4 times

Online Publication Date: 5 December 2008

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A recent approach [ S. C. Althorpe, J. Chem. Phys. 124, 084105 (2006) ] for interpreting geometric phase (GP) effects in a nuclear wave function confined to the lower of two conically intersecting potential energy surfaces is extended to treat coupled dynamics on both surfaces. The approach is exact, and uses simple topology to separate the wave function into contributions from Feynman paths that wind different numbers of times, and in different senses, around the conical intersection. We derive the approach first, by mapping the time-dependent wave packet describing the coupled dynamics onto a double space, and second, by classifying the Feynman paths within a time-ordered expansion of the path integral. The approach is demonstrated numerically for a simple E×e Jahn–Teller system and for a model of the 1B1−S0 intersection in pyrrole. The approach allows one to investigate and interpret the effect of the GP on population transfer between the surfaces, and also to extract contributions to the coupled nuclear wave function from different reaction paths.
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82.20.Kh Potential energy surfaces for chemical reactions
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Anion photoelectron spectroscopy of transition metal- and lanthanide metal-silicon clusters: MSin− (n = 6–20)

Kiichirou Koyasu, Junko Atobe, Shunsuke Furuse, and Atsushi Nakajima

J. Chem. Phys. 129, 214301 (2008); http://dx.doi.org/10.1063/1.3023080 (7 pages) | Cited 13 times

Online Publication Date: 2 December 2008

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The electronic properties of silicon clusters containing a transition or lanthanide metal atom from group 3, 4, or 5, MSin, (M = Sc, Ti, V, Y, Zr, Nb, Lu, Tb, Ho, Hf, and Ta) were investigated by anion photoelectron spectroscopy at 213 nm. In the case of the group 3 elements Sc, Y, Lu, Tb, and Ho, the threshold energy of electron detachment exhibits local maxima at n = 10 and 16, while in case of the group 4 elements Ti, Zr, and Hf, the threshold energy exhibits a local minimum at n = 16, associated with the presence of a small bump in the spectrum. These electronic characteristics of MSin are closely related to a cooperative effect between their geometric and electronic structures, which is discussed, together with the results of experiments that probe their geometric stability via their reactivity to H2O adsorption, and with theoretical calculations.
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79.60.Bm Clean metal, semiconductor, and insulator surfaces
68.43.-h Chemisorption/physisorption: adsorbates on surfaces
71.20.Be Transition metals and alloys

Potential energy curves and electronic structure of 3d transition metal hydrides and their cations

Satyender Goel and Artëm E. Masunov

J. Chem. Phys. 129, 214302 (2008); http://dx.doi.org/10.1063/1.2996347 (14 pages) | Cited 9 times

Online Publication Date: 2 December 2008

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We investigate gas-phase neutral and cationic hydrides formed by 3d transition metals from Sc to Cu with density functional theory (DFT) methods. The performance of two exchange-correlation functionals, Boese–Martin for kinetics (BMK) and Tao–Perdew–Staroverov-Scuseria (TPSS), in predicting bond lengths and energetics, electronic structures, dipole moments, and ionization potentials is evaluated in comparison with available experimental data. To ensure a unique self-consistent field (SCF) solution, we use stability analysis, Fermi smearing, and continuity analysis of the potential energy curves. Broken-symmetry approach was adapted in order to get the qualitatively correct description of the bond dissociation. We found that on average BMK predicted values of dissociation energies and ionization potentials are closer to experiment than those obtained with high level wave function theory methods. This agreement deteriorates quickly when the fraction of the Hartree–Fock exchange in DFT functional is decreased. Natural bond orbital (NBO) population analysis was used to describe the details of chemical bonding in the systems studied. The multireference character in the wave function description of the hydrides is reproduced in broken-symmetry DFT description, as evidenced by NBO analysis. We also propose a new scheme to correct for spin contamination arising in broken-symmetry DFT approach. Unlike conventional schemes, our spin correction is introduced for each spin-polarized electron pair individually and therefore is expected to yield more accurate energy values. We derive an expression to extract the energy of the pure singlet state from the energy of the broken-symmetry DFT description of the low spin state and the energies of the high spin states (pentuplet and two spin-contaminated triplets in the case of two spin-polarized electron pairs). The high spin states are build with canonical natural orbitals and do not require SCF convergence.
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31.50.Df Potential energy surfaces for excited electronic states
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

Effects of intense femtosecond pumping on ultrafast electronic-vibrational dynamics in molecular systems with relaxation

Dassia Egorova, Maxim F. Gelin, Michael Thoss, Haobin Wang, and Wolfgang Domcke

J. Chem. Phys. 129, 214303 (2008); http://dx.doi.org/10.1063/1.3026509 (11 pages) | Cited 9 times

Online Publication Date: 3 December 2008

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We investigate the influence of strong femtosecond optical pulses on the ultrafast dynamics of molecular systems. The study is based on a series of generic molecular models of increasing complexity, which incorporate multiple and mutually coupled electronic states, electronic-vibrational interaction, and vibrational relaxation. The influence of vibrational relaxation is treated using multilevel Redfield theory. Comparisons to benchmark results of the multilayer multiconfiguration time-dependent Hartree (ML-MCTDH) method demonstrate the validity of the field-free implementation of Redfield theory employed in this work for weak system-bath interaction. The calculated electronic population and vibrational wave-packet dynamics demonstrate the intricate interplay of strong-field excitation, laser-induced Rabi oscillations, electronic interaction, vibronic coupling, and dissipation. In particular, we show that the interaction with a strong laser pulse may result in pronounced coherent vibrational motion in a dissipative system, even for laser pulses that are longer than the vibrational period. Furthermore, vibrational relaxation in combination with strong laser pulse excitation can lead to revivals of the electronic population after the excitation pulse is over.
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33.80.Be Level crossing and optical pumping
33.20.Tp Vibrational analysis
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.15.xr Self-consistent-field methods
31.15.V- Electron correlation calculations for atoms, ions and molecules

An accurate global potential energy surface, dipole moment surface, and rovibrational frequencies for NH3

Xinchuan Huang, David W. Schwenke, and Timothy J. Lee

J. Chem. Phys. 129, 214304 (2008); http://dx.doi.org/10.1063/1.3025885 (16 pages) | Cited 22 times

Online Publication Date: 4 December 2008

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A global potential energy surface (PES) that includes short and long range terms has been determined for the NH3 molecule. The singles and doubles coupled-cluster method that includes a perturbational estimate of connected triple excitations and the internally contracted averaged coupled-pair functional electronic structure methods have been used in conjunction with very large correlation-consistent basis sets, including diffuse functions. Extrapolation to the one-particle basis set limit was performed and core correlation and scalar relativistic contributions were included directly, while the diagonal Born–Oppenheimer correction was added. Our best purely ab initio PES, denoted “mixed,” is constructed from two PESs which differ in whether the ic-ACPF higher-order correlation correction was added or not. Rovibrational transition energies computed from the mixed PES agree well with experiment and the best previous theoretical studies, but most importantly the quality does not deteriorate even up to 10 300 cm−1 above the zero-point energy (ZPE). The mixed PES was improved further by empirical refinement using the most reliable J = 0–2 rovibrational transitions in the HITRAN 2004 database. Agreement between high-resolution experiment and rovibrational transition energies computed from our refined PES for J = 0–6 is excellent. Indeed, the root mean square (rms) error for 13 HITRAN 2004 bands for J = 0–2 is 0.023 cm−1 and that for each band is always ⩽ 0.06 cm−1. For J = 3–5 the rms error is always ⩽ 0.15 cm−1. This agreement means that transition energies computed with our refined PES should be useful in the assignment of new high-resolution NH3 spectra and in correcting mistakes in previous assignments. Ideas for further improvements to our refined PES and for extension to other isotopolog are discussed.
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31.50.Df Potential energy surfaces for excited electronic states
33.20.Vq Vibration-rotation analysis
31.15.xp Perturbation theory
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure

Simulations of the emission spectra of fac-tris(2-phenylpyridine) iridium and Duschinsky rotation effects using the Herman–Kluk semiclassical initial value representation method

Yinghua Wu and Jean-Luc Brédas

J. Chem. Phys. 129, 214305 (2008); http://dx.doi.org/10.1063/1.3027514 (10 pages) | Cited 2 times

Online Publication Date: 4 December 2008

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The phosphorescent emission spectra of fac-tris(2-phenylpyridine) iridium [fac-Ir(ppy)3] due to the lowest triplet T1 and T2 states are simulated using the harmonic oscillator approximation for the S0, T1, and T2 potential energy surfaces (PESs) and taking the Duschinsky rotation into account. The simulations involve the propagation of 177-dimensional wave packets on the coupled PES according to the Herman–Kluk (HK) semiclassical (SC) initial value representation (IVR) method. The HK SC-IVR method is employed because of its accuracy for the PES with mode mixing and its efficiency in dealing with coupled degrees of freedom for large systems. The simulated emission spectrum due to T1 reproduces the structures of the emission spectra observed experimentally, while T2 is found very unlikely to participate in the phosphorescent emission. Although the effect of the Duschinsky mode mixing is small for the T1 state, neglecting it blueshifts the spectrum due to the T2 state by 800 cm−1 and changes the relative intensities, indicating that the importance of the Duschinsky rotation is rather unpredictable and should not be overlooked. The present simulations demonstrate that the simple harmonic oscillator approximation combined with the Duschinsky rotation can adequately describe the photophysics of fac-Ir(ppy)3 and that the HK SC-IVR method is a powerful tool in studies of this kind.
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78.55.Kz Solid organic materials
33.50.Dq Fluorescence and phosphorescence spectra
31.50.Df Potential energy surfaces for excited electronic states

Direct mapping of recoil in the ion-pair dissociation of molecular oxygen by a femtosecond depletion method

Alexey V. Baklanov, Liesbeth M. C. Janssen, David H. Parker, Lionel Poisson, Benoit Soep, Jean-Michel Mestdagh, and Olivier Gobert

J. Chem. Phys. 129, 214306 (2008); http://dx.doi.org/10.1063/1.3026613 (9 pages) | Cited 6 times

Online Publication Date: 4 December 2008

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Time-resolved dynamics of the photodissociation of molecular oxygen, O2, via the 3Σu− ion-pair state have been studied with femtosecond time resolution using a pump-probe scheme in combination with velocity map imaging of the resulting O+ and O− ions. The fourth harmonic of a femtosecond titanium-sapphire (Ti:sapphire) laser (λ ≈ 205 nm) was found to cause three-photon pumping of O2 to a level at 18.1 eV. The parallel character of the observed O+ and O− images allowed us to conclude that dissociation takes place on the 3Σu− ion-pair state. The 815 nm fundamental of the Ti:sapphire laser used as probe was found to cause two-photon electron photodetachment starting from the O2 ion-pair state, giving rise to (O(3P)+O+(4S)) products. This was revealed by the observed depletion of the yield of the O− anion and the appearance of a new O+ cation signal with a kinetic energy Etransl(O+) dependent on the time delay between the pump and probe lasers. This time-delay dependence of the dissociation dynamics on the ion-pair state has also been simulated, and the experimental and simulated results coincide very well over the experimental delay-time interval from about 130 fs to 20 ps where two- or one-photon photodetachment takes place, corresponding to a change in the R(O+,O−) interatomic distance from 12 to about 900 Å. This is one of the first implementations of a depletion scheme in femtosecond pump-probe experiments which could prove to be quite versatile and applicable to many femtosecond time-scale experiments.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
33.80.Eh Autoionization, photoionization, and photodetachment
33.80.Be Level crossing and optical pumping
42.65.Re Ultrafast processes; optical pulse generation and pulse compression

Energetics and molecular dynamics of the reaction of HOCO with HO2 radicals

Hua-Gen Yu, Gabriella Poggi, Joseph S. Francisco, and James T. Muckerman

J. Chem. Phys. 129, 214307 (2008); http://dx.doi.org/10.1063/1.3028052 (9 pages) | Cited 2 times

Online Publication Date: 5 December 2008

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The energetics of the reaction of HOCO with HO2 have been studied using the quadratic configuration interaction with single and double excitations (QCISD(T)) method and a large basis set on the singlet and triplet potential energy surfaces of the system. The results show that the ground-state O2+HOC(O)H products can be produced by a direct hydrogen abstraction via a transition state with a small barrier (1.66 kcal/mol) on the lowest triplet surface. A similar hydrogen abstraction can occur on the singlet electronic surface, but it leads to the singlet O2(a1Δ) and HOC(O)H. On the singlet surface, a new stable intermediate, HOC(O)OOH, hydroperoxyformic acid, has been found. This intermediate is formed by the direct addition of the terminal oxygen atom in HO2 onto the carbon atom in HOCO in a barrierless reaction. The HOC(O)OOH intermediate may dissociate into either the CO2+H2O2 or CO3+H2O products through elimination reactions with four-center transition states, or into HOC(O)O+OH through an O–O bond cleavage. The heat of formation of HOC(O)OOH is predicted to be −118.9±1.0 kcal/mol. In addition, the dynamics of the HO2+HOCO reaction have been investigated using a scaling-all correlation couple cluster method with single and double excitation terms (CCSD) on the singlet potential energy surface. Reaction mechanisms have been studied in detail. It was found that the direct and addition reaction mechanisms coexist. For the addition mechanism, the lifetime of the HOC(O)OOH intermediate is predicted to be 880±27 fs. At room temperature, the calculated thermal rate coefficient is (6.52±0.44)×10−11 cm3 molecule−1 s−1 with the product branching fractions: 0.77 (CO2+H2O2), 0.15 (HOC(O)O+OH), 0.056 (CO3+H2O), 0.019 (O2(a1Δ)+HOC(O)H), and 0.01 (O2(X 3Σ)+HOC(O)H).
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)
82.30.Nr Association, addition, insertion, cluster formation
82.20.Kh Potential energy surfaces for chemical reactions
82.60.Cx Enthalpies of combustion, reaction, and formation
82.20.Bc State selected dynamics and product distribution
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