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14 Oct 2009

Volume 131, Issue 14, Articles (14xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 131, 144503 (2009); http://dx.doi.org/10.1063/1.3225270 (11 pages)

Jessica C. Johnston, Robbie J. Iuliucci, Julio C. Facelli, George Fitzgerald, and Karl T. Mueller
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back to top Theoretical Methods and Algorithms

Atomic charge densities generated using an iterative stockholder procedure

Timothy C. Lillestolen and Richard J. Wheatley

J. Chem. Phys. 131, 144101 (2009); http://dx.doi.org/10.1063/1.3243863 (6 pages) | Cited 10 times

Online Publication Date: 8 October 2009

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A simple computational technique is introduced for generating atomic electron densities using an iterated stockholder procedure. It is proven that the procedure is always convergent and leads to unique atomic densities. The resulting atomic densities are shown to have chemically intuitive and reasonable charges, and the method is used to analyze the hydrogen bonding in the minimum energy configuration of the water dimer and charge transfer in the borazane molecule.
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31.15.xv Molecular dynamics and other numerical methods
02.60.-x Numerical approximation and analysis
33.15.Fm Bond strengths, dissociation energies
33.15.Bh General molecular conformation and symmetry; stereochemistry
34.70.+e Charge transfer

Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach

Li-Tien Cheng, Zhongming Wang, Piotr Setny, Joachim Dzubiella, Bo Li, and J. Andrew McCammon

J. Chem. Phys. 131, 144102 (2009); http://dx.doi.org/10.1063/1.3242274 (10 pages) | Cited 12 times

Online Publication Date: 9 October 2009

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A model nanometer-sized hydrophobic receptor-ligand system in aqueous solution is studied by the recently developed level-set variational implicit solvent model (VISM). This approach is compared to all-atom computer simulations. The simulations reveal complex hydration effects within the (concave) receptor pocket, sensitive to the distance of the (convex) approaching ligand. The ligand induces and controls an intermittent switching between dry and wet states of the hosting pocket, which determines the range and magnitude of the pocket-ligand attraction. In the level-set VISM, a geometric free-energy functional of all possible solute-solvent interfaces coupled to the local dispersion potential is minimized numerically. This approach captures the distinct metastable states that correspond to topologically different solute-solvent interfaces, and thereby reproduces the bimodal hydration behavior observed in the all-atom simulation. Geometrical singularities formed during the interface relaxation are found to contribute significantly to the energy barrier between different metastable states. While the hydration phenomena can thus be explained by capillary effects, the explicit inclusion of dispersion and curvature corrections seems to be essential for a quantitative description of hydrophobically confined systems on nanoscales. This study may shed more light onto the tight connection between geometric and energetic aspects of biomolecular hydration and may represent a valuable step toward the proper interpretation of experimental receptor-ligand binding rates.
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87.15.kp Protein-ligand interactions
87.15.kr Protein-solvent interactions
87.15.R- Reactions and kinetics
87.14.E- Proteins
87.15.ap Molecular dynamics simulation
87.15.H- Dynamics of biomolecules

The quantum normal form approach to reactive scattering: The cumulative reaction probability for collinear exchange reactions

Arseni Goussev, Roman Schubert, Holger Waalkens, and Stephen Wiggins

J. Chem. Phys. 131, 144103 (2009); http://dx.doi.org/10.1063/1.3245402 (8 pages) | Cited 4 times

Online Publication Date: 9 October 2009

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The quantum normal form approach to quantum transition state theory is used to compute the cumulative reaction probability for collinear exchange reactions. It is shown that for heavy-atom systems such as the nitrogen-exchange reaction, the quantum normal form approach gives excellent results and has major computational benefits over full reactive scattering approaches. For light atom systems such as the hydrogen-exchange reaction however, the quantum normal approach is shown to give only poor results. This failure is attributed to the importance of tunneling trajectories in light atom reactions that are not captured by the quantum normal form as indicated by the only very slow convergence of the quantum normal form for such systems.
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82.20.Db Transition state theory and statistical theories of rate constants
82.20.Ej Quantum theory of reaction cross section
82.30.Hk Chemical exchanges (substitution, atom transfer, abstraction, disproportionation, and group exchange)

Benchmarking density-functional-theory calculations of rotational g tensors and magnetizabilities using accurate coupled-cluster calculations

Ola B. Lutnæs, Andrew M. Teale, Trygve Helgaker, David J. Tozer, Kenneth Ruud, and Jürgen Gauss

J. Chem. Phys. 131, 144104 (2009); http://dx.doi.org/10.1063/1.3242081 (16 pages) | Cited 11 times

Online Publication Date: 12 October 2009

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An accurate set of benchmark rotational g tensors and magnetizabilities are calculated using coupled-cluster singles-doubles (CCSD) theory and coupled-cluster single-doubles-perturbative-triples [CCSD(T)] theory, in a variety of basis sets consisting of (rotational) London atomic orbitals. The accuracy of the results obtained is established for the rotational g tensors by careful comparison with experimental data, taking into account zero-point vibrational corrections. After an analysis of the basis sets employed, extrapolation techniques are used to provide estimates of the basis-set-limit quantities, thereby establishing an accurate benchmark data set. The utility of the data set is demonstrated by examining a wide variety of density functionals for the calculation of these properties. None of the density-functional methods are competitive with the CCSD or CCSD(T) methods. The need for a careful consideration of vibrational effects is clearly illustrated. Finally, the pure coupled-cluster results are compared with the results of density-functional calculations constrained to give the same electronic density. The importance of current dependence in exchange–correlation functionals is discussed in light of this comparison.
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33.20.Sn Rotational analysis
31.15.eg Exchange-correlation functionals (in current density functional theory)
33.20.Tp Vibrational analysis
31.15.bw Coupled-cluster theory
31.15.xp Perturbation theory

Decomposition of energy and free energy changes by following the flow of work along reaction path

Kevin Haas and Jhih-Wei Chu

J. Chem. Phys. 131, 144105 (2009); http://dx.doi.org/10.1063/1.3243080 (11 pages) | Cited 4 times

Online Publication Date: 12 October 2009

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To extract mechanistic information of activated processes, we propose to decompose potential energy and free energy differences between configurations into contributions from individual atoms, functional groups, or residues. Decomposition is achieved by calculating the mechanical work associated with the displacements and forces of each atom along a path that connects two states, i.e., following the flow of work. Specifically, we focus on decomposing energy or free energy differences along representative pathways such as minimum energy paths (MEPs) and minimum free energy paths (MFEPs), and a numerical metric is developed to quantify the required accuracy of the reaction path. A statistical mechanical analysis of energy decomposition is also presented to illustrate the generality of this approach. Decomposition along MEP and MFEP is demonstrated on two test cases to illustrate the ability to derive quantitative mechanistic information for different types of activated processes. First, the MEP of alanine dipeptide isomerization in vacuum and the MFEP of isomerization in explicit water is studied. Our analysis shows that carbonyl oxygen and amide hydrogen contribute to most of the energetic cost for isomerization and that explicit water solvation modulates the free energy landscape primarily through hydrogen bonding with these atoms. The second test case concerns the formation of tetrahedral intermediate during a transesterification reaction. Decomposition analysis shows that water molecules not only have strong stabilization effects on the tetrahedral intermediate but also constitute a sizable potential energy barrier due to their significant structural rearrangement during the reaction. We expect that the proposed method can be generally applied to develop mechanistic understanding of catalytic and biocatalytic processes and provide useful insight for strategies of molecular engineering.
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87.15.rs Dissociation
82.30.Qt Isomerization and rearrangement
87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.15.Fh Bonding; mechanisms of bond breakage
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Db Transition state theory and statistical theories of rate constants
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)

Density matrix treatment of combined instantaneous and delayed dissipation for an electronically excited adsorbate on a solid surface

Andrew S. Leathers, David A. Micha, and Dmitri S. Kilin

J. Chem. Phys. 131, 144106 (2009); http://dx.doi.org/10.1063/1.3246168 (13 pages) | Cited 6 times

Online Publication Date: 14 October 2009

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The interaction of an excited adsorbate with a medium undergoing electronic and vibrational transitions leads to fast dissipation due to electronic energy relaxation and slow (or delayed) dissipation from vibrational energy relaxation. A theoretical and computational treatment of these phenomena has been done in terms of a reduced density matrix satisfying a generalized Liouville–von Neumann equation, with instantaneous dissipation constructed from state-to-state transition rates, and delayed dissipation given by a memory term derived from the time-correlation function (TCF) of atomic displacements in the medium. Two representative applications are presented here, where electronic excitation may enhance vibrational relaxation of an adsorbate. They involve femtosecond excitation of (a) a CO molecule adsorbed on the Cu(001) metal surface and (b) a metal cluster on a semiconductor surface, Ag3Si(111):H, both electronically excited by visible light and undergoing electron transfer and dissipative dynamics by electronic and vibrational relaxations. Models have been parametrized in both cases from electronic structure calculations and known TCFs for the medium, which are slowly decaying in case (a) and fast decaying in case (b). This requires different numerical procedures in the solution of the integrodifferential equations for the reduced density matrix, which have been solved with an extension of the Runge–Kutta algorithm. Results for the populations of vibronic states versus time show that they oscillate due to vibrational coupling through dissipative interaction with the substrate and show quantum coherence. The total population of electronic states is, however, little affected by vibrational motions. Vibrational relaxation is important only at very long times to establish thermal equilibrium.
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68.43.-h Chemisorption/physisorption: adsorbates on surfaces
68.43.Mn Adsorption kinetics
71.20.-b Electron density of states and band structure of crystalline solids

Replica exchange Monte Carlo applied to hard spheres

Gerardo Odriozola

J. Chem. Phys. 131, 144107 (2009); http://dx.doi.org/10.1063/1.3244562 (5 pages) | Cited 8 times

Online Publication Date: 14 October 2009

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In this work a replica exchange Monte Carlo scheme which considers an extended isobaric-isothermal ensemble with respect to pressure is applied to study hard spheres (HSs). The idea behind the proposal is expanding volume instead of increasing temperature to let crowded systems characterized by dominant repulsive interactions to unblock, and so, to produce sampling from disjoint configurations. The method produces, in a single parallel run, the complete HS equation of state. Thus, the first order fluid-solid transition is captured. The obtained results well agree with previous calculations. This approach seems particularly useful to treat purely entropy-driven systems such as hard body and nonadditive hard mixtures, where temperature plays a trivial role.
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05.70.Ce Thermodynamic functions and equations of state
02.50.Ng Distribution theory and Monte Carlo studies

An improved long-range corrected hybrid functional with vanishing Hartree–Fock exchange at zero interelectronic distance (LC2gau-BOP)

Jong-Won Song, Mark A. Watson, and Kimihiko Hirao

J. Chem. Phys. 131, 144108 (2009); http://dx.doi.org/10.1063/1.3243819 (9 pages) | Cited 13 times

Online Publication Date: 14 October 2009

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We present a new long-range corrected (LC) density functional theory (DFT) scheme, named “LC2gau,” which combines the best features of our two recently developed hybrid functionals, “LCgau” [ J.-W. Song et al., J. Chem. Phys. 127, 154109 (2007) ] and “LCgau-core” [ J.-W. Song et al., J. Chem. Phys. 129, 184113 (2008) ]. By introducing a flexible mixing of Hartree–Fock and DFT exchange in the LCgau scheme, we showed that a DFT functional could simultaneously achieve high accuracy in the reproduction of thermochemical properties, molecular geometries, as well as charge transfer and valence-Rydberg excitation energies. With an alternative mixing of short-range exchange, LCgau-core can reproduce core excitations with high accuracy, especially in the C, N, and O atoms, but at the expense of slightly higher atomization energy errors. We now show that LC2gau can simultaneously perform well for all types of excitations, as well as thermochemistry. In contrast to the previously proposed LC functionals, a notable feature is the inclusion of 100% DFT exchange as the interelectronic distance vanishes, showing that pure DFT approximations can be successfully used at short range, and the importance of including an appropriate correction in the midrange. This is achieved using two Gaussian functions in combination with the error function to describe the exchange partitioning. We rationalize the success of LC2gau by demonstrating a near-linear behavior of the total energies of the C atom as a function of the fractional number of electrons, both in the valence and core regions, which indicates an alleviation of significant self-interaction errors observed with other functionals.
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31.15.E- Density-functional theory
31.15.xr Self-consistent-field methods
33.15.Bh General molecular conformation and symmetry; stereochemistry
34.70.+e Charge transfer
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

The molecular dissociation of formaldehyde at medium photoexcitation energies: A quantum chemistry and direct quantum dynamics study

Marta Araújo, Benjamin Lasorne, Alexandre L. Magalhães, Graham A. Worth, Michael J. Bearpark, and Michael A. Robb

J. Chem. Phys. 131, 144301 (2009); http://dx.doi.org/10.1063/1.3242082 (8 pages) | Cited 12 times

Online Publication Date: 8 October 2009

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The mechanisms of radiationless decay involved in the photodissociation of formaldehyde into H2 and CO have been investigated using complete active space self-consistent field (CASSCF) calculations and direct dynamics variational multiconfiguration Gaussian (DD-vMCG) quantum dynamics in the S1, T1, and S0 states. A commonly accepted scheme involves Fermi Golden Rule internal conversion from S1 followed by dissociation of vibrationally hot H2CO in S0. We recently proposed a novel mechanism [ M. Araujo et al., J. Phys. Chem. A 112, 7489 (2008) ] whereby internal conversion and dissociation take place in concert through a seam of conical intersection between S1 and S0 after the system has passed through an S1 transition barrier. The relevance of this mechanism depends on the efficiency of tunneling in S1. At lower energy, an alternative scheme to internal conversion involves intersystem crossing via T1 to regenerate the reactant before the S0 barrier to dissociation. We propose here a previously unidentified mechanism leading directly to H2 and CO products via T1. This channel opens at medium energies, near or above the T1 barrier to dissociation and still lower than the S1 barrier, thus making T1 a possible shortcut to molecular dissociation.
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82.50.-m Photochemistry
82.20.Uv Stochastic theories of rate constants
82.20.Xr Quantum effects in rate constants (tunneling, resonances, etc.)
82.20.Hf Product distribution

Water reactivity with tungsten oxides: H2 production and kinetic traps

Nicholas J. Mayhall, David W. Rothgeb, Ekram Hossain, Caroline Chick Jarrold, and Krishnan Raghavachari

J. Chem. Phys. 131, 144302 (2009); http://dx.doi.org/10.1063/1.3242294 (8 pages) | Cited 10 times

Online Publication Date: 12 October 2009

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In a recent mass spectrometry/photoelectron spectroscopy study on the reactions between W2Oy− (y = 2–6) and water, Jarrold and co-workers [J. Chem. Phys. 130, 124314 (2009)] observed interesting differences in the reactivity of the different cluster ions. Particularly noteworthy is the observation that the only product with the incorporation of hydrogens is a single peak corresponding to W2O6H2−. As reactions between metal oxide clusters and small molecules such as water have high potential for catalytic applications, we carried out a careful study to obtain a mechanistic understanding of this observed reactivity. Using electronic structure calculations, we identified and characterized multiple modes of reactivity between unsaturated tungsten oxide clusters [W2Oy− (y = 4–6)] and water. By calculating the free energy corrected reaction profiles, our results provide an explanation for the formation of W2O6H2−. We propose a mechanism in which water reacts with a metal oxide cluster and eliminates H2. The results from our calculations show that this is nearly a barrierless process for all suboxide clusters with the exception of W2O5−.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.30.Nr Association, addition, insertion, cluster formation
82.20.Wt Computational modeling; simulation
36.40.Jn Reactivity of clusters
36.40.Mr Spectroscopy and geometrical structure of clusters
36.40.Cg Electronic and magnetic properties of clusters

Low temperature photoelectron spectra of water cluster anions

Lei Ma, Kiran Majer, Fabien Chirot, and Bernd von Issendorff

J. Chem. Phys. 131, 144303 (2009); http://dx.doi.org/10.1063/1.3245859 (6 pages) | Cited 36 times

Online Publication Date: 12 October 2009

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Photoelectron spectra of cold (10 K) size selected water cluster anions (H2O)n− and (D2O)n− have been measured in the size range n = 20–120. A new isomer with a higher binding energy than the so-called isomer I has been identified, which appears in the size range n = 25–30 and for (H2O)n− becomes dominant at n = 46. Magic numbers observed in the mass spectra of the cluster anions provide evidence that this new isomer class consists of clusters with an internal electron.
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33.60.+q Photoelectron spectra
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Ta Mass spectra
36.40.Mr Spectroscopy and geometrical structure of clusters
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)

Probing royal demolition explosive (1,3,5-trinitro-1,3,5-triazocyclohexane) by low-energy electrons: Strong dissociative electron attachment near 0 eV

P. Sulzer, A. Mauracher, F. Ferreira da Silva, S. Denifl, T. D. Märk, M. Probst, P. Limão-Vieira, and P. Scheier

J. Chem. Phys. 131, 144304 (2009); http://dx.doi.org/10.1063/1.3230116 (7 pages) | Cited 6 times

Online Publication Date: 12 October 2009

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Low energy electron attachment to gas phase royal demolition explosive (RDX) (and RDX-A3) has been performed by means of a crossed electron-molecular beam experiment in an electron energy range from 0 to 14 eV with an energy resolution of ∼ 70 meV. The most intense signals are observed at 102 and 46 amu and assigned to C2H4N3O2− and NO2−, respectively. Anion efficiency curves of 16 anions have been measured. Product ions are observed mainly in the low energy region, near 0 eV arising from surprisingly complex reactions associated with multiple bond cleavages and structural and electronic rearrangement. The remarkable instability of RDX to electron attachment with virtually thermal electrons reflects the highly explosive nature of this compound. The present results are compared to other explosive aromatic nitrocompounds studied in our laboratory recently.
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34.80.Ht Dissociation and dissociative attachment
33.15.Fm Bond strengths, dissociation energies

Quantum control study of multilevel effect on ultrafast isotope-selective vibrational excitations

Yuzuru Kurosaki, Keiichi Yokoyama, and Atsushi Yokoyama

J. Chem. Phys. 131, 144305 (2009); http://dx.doi.org/10.1063/1.3245401 (9 pages) | Cited 4 times

Online Publication Date: 12 October 2009

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Quantum optimal control calculations have been carried out for isotope-selective vibrational excitations of the cesium iodide (CsI) molecule on the ground-state potential energy curve. Considering a gaseous isotopic mixture of 133CsI and 135CsI, the initial state is set to the condition that both 133CsI and 135CsI are in the vibrational ground level (v = 0) and the target state is that 133CsI is in the v = 0 level while 135CsI in the first-excited level (v = 1). We find that, using the density-matrix formalism, perfect isotope-selective excitations for multilevel systems including more than ten lowest vibrational states can be completed in much shorter time scales than those for two-level systems. It is likely that this multilevel effect comes from the large isotope shifts in the vibrational levels of v>1. To check the reliability of the calculation we also carry out optimal control calculations based on the conventional wave-packet formalism, where the wave-function amplitude is temporally propagated on the grid points in real space, and obtain almost the same results as those with the density-matrix formalism.
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33.15.Mt Rotation, vibration, and vibration-rotation constants
31.50.Bc Potential energy surfaces for ground electronic states
31.15.es Applications of density-functional theory (e.g., to electronic structure and stability; defect formation; dielectric properties, susceptibilities; viscoelastic coefficients; Rydberg transition frequencies)

Termination of the W2Oy−+H2O/D2O→W2Oy+1−+H2/D2 sequential oxidation reaction: An exploration of kinetic versus thermodynamic effects

David W. Rothgeb, Ekram Hossain, Nicholas J. Mayhall, Krishnan Raghavachari, and Caroline Chick Jarrold

J. Chem. Phys. 131, 144306 (2009); http://dx.doi.org/10.1063/1.3246833 (8 pages) | Cited 7 times

Online Publication Date: 12 October 2009

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Several mechanisms proposed and calculated for the sequential oxidation of tungsten suboxide clusters by H2O/D2O [ Mayhall et al., J. Chem. Phys. 131, 144302 (2009) ] are evaluated using anion photoelectron spectroscopy of an apparent intermediate, W2O6D2−. The spectrum of W2O6D2− is consistent with the W2O5−+D2O→W2O6−+D2 intermediate in which the initial water addition involves the interaction of the oxygen from D2O with a tungsten atom, approaching from a direction with the least repulsion from the W2O5− oxygen atoms, coupled with the interaction between a deuterium with a tungsten-tungsten bridging oxygen on the cluster. The presence of W2O6H2− and W2O6D2− suggests that there is insufficient internal energy in the complex to surmount the barrier for rearrangement required for tungsten hydride and hydroxide formation necessary for H2 or D2 evolution, which was calculated to be energetically favorable. The quality of the calculations is verified by direct comparison between experimental photoelectron spectra of W2O5− and W2O6− and spectral simulations generated from the lowest energy structures calculated for W2O5−, W2O6− and their corresponding neutrals. The results shed light on the importance of repulsion on the pathway a reaction follows under room temperature conditions.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.80.Dx Analytical methods involving electronic spectroscopy
82.60.-s Chemical thermodynamics
82.20.Tr Kinetic isotope effects including muonium
82.30.Qt Isomerization and rearrangement

Electronic spectra of the linear polyyne cations HC2nH+ (n = 2–8): An ab initio study

Jinglai Zhang, Xugeng Guo, and Zexing Cao

J. Chem. Phys. 131, 144307 (2009); http://dx.doi.org/10.1063/1.3247289 (7 pages) | Cited 10 times

Online Publication Date: 12 October 2009

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The B3LYP, CAM-B3LYP, and RCCSD(T) calculations have been used to determine the ground-state geometries of the linear polyyne cations HC2nH+ (n = 2–8). The CASSCF method has also been used to optimize the ground and first excited states. The present results indicate that these linear cations generally have an acetylenic structure H–C ≡ C–C ≡ C⋯C ≡ C–H+ with the ground state of X 2Πg for even-numbered n or X 2Πu for odd-numbered n. Moreover, the bond length alternation of HC2nH+ is less pronounced than the corresponding one of the neutral polyyne chains HC2nH. The CASPT2 approach has been employed to estimate the vertical excitation energies for the dipole-allowed (A⋯D) 2Πu/g←X 2Πg/u transitions in HC2nH+ (n = 2–8) clusters. The predicted A 2Πu/g←X 2Πg/u transition energies in the gas phase are 2.62, 2.14, 1.81, 1.52, 1.35, 1.22, and 1.10 eV, respectively, in excellent agreement with the corresponding observed values of 2.45, 2.07, 1.75, 1.52, 1.35, 1.20, and 1.08 eV. The present calculations show that the absorption wavelengths for the A 2Πu/g←X 2Πg/u transitions exhibit notably linear size dependence, as shown in previous experimental studies, quite different from the nonlinear λ-n relationship for origin bands in HC2nH.
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31.15.A- Ab initio calculations
31.50.Df Potential energy surfaces for excited electronic states
33.15.Dj Interatomic distances and angles

The ejection of triatomic molecular hydrogen ions H3+ produced by the interaction of benzene molecules with ultrafast laser pulses

S. Kaziannis, I. Liontos, G. Karras, C. Corsi, M. Bellini, and C. Kosmidis

J. Chem. Phys. 131, 144308 (2009); http://dx.doi.org/10.1063/1.3246832 (9 pages) | Cited 2 times

Online Publication Date: 13 October 2009

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The ejection process of triatomic molecular hydrogen ions produced by the interaction of benzene with ultrafast laser pulses of moderate strong intensity ( ∼ 1014 W/cm2) is studied by means of TOF mass spectrometry. The H3+ formation can only take place through the rupture of two C–H bonds and the migration of hydrogen atoms within the molecular structure. The H3+ fragments are released with high kinetic energy (typically 2–8 eV) and at laser intensities ≥ 1014 W/cm2, well above that required for the double ionization of benzene, suggesting that its formation is taking place within multiply charged parent ions. The relative ejection efficiency of H3+ molecular hydrogen ions with respect to the atomic ones is found to be strongly decreasing as a function of the laser intensity and pulse duration (67–25 fs). It is concluded that the H3+ formation is only feasible within parent molecular precursors of relatively low charged states and before significant elongation of their structure takes place, while the higher multiply charged molecular ions preferentially dissociate into H+ ions. The ejection of H2+ ions is also discussed in comparison to the production of H3+ and H+ ions. Finally, by recording the mass spectra of two deuterium label isotopes of benzene (1,2-C6H4D2, 1,4-C6H4D2) it is verified that the ejection efficiency of some molecular fragments, such as D2H+, DH+, is dependent on the specific position of hydrogen atoms in the molecular skeleton prior dissociation.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
33.80.Eh Autoionization, photoionization, and photodetachment
33.15.Ta Mass spectra

Gas-phase reaction between calcium monocation and fluoromethane: Analysis of the potential energy hypersurface and kinetics calculations

Adrián Varela-Álvarez, V. M. Rayón, P. Redondo, C. Barrientos, and José A. Sordo

J. Chem. Phys. 131, 144309 (2009); http://dx.doi.org/10.1063/1.3247287 (11 pages) | Cited 4 times

Online Publication Date: 13 October 2009

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The gas-phase reaction between calcium monocation and fluoromethane: Ca++CH3F→CaF++CH3 was theoretically analyzed. The potential energy hypersurface was explored by using density functional theory methodology with different functionals and Pople’s, Dunning’s, Ahlrichs’, and Stuttgart–Dresden basis sets. Kinetics calculations (energy and total angular momentum resolved microcanonical variational/conventional theory) were accomplished. The theoretically predicted range for the global kinetic rate constant values at 295 K (7.2×10−11–5.9×10−10 cm3 molecule−1 s−1) agrees reasonably well with the experimental value at the same temperature [(2.6±0.8)×10−10 cm3 molecule−1 s−1]. Explicit consideration of a two transition state model, where the formation of a weakly bounded prereactive complex is preceded by an outer transition state (entrance channel) and followed by an inner transition state connecting with a second intermediate that finally leads to products, is mandatory. Experimental observations on the correlation, or lack of correlation, between reaction rate constants and second ionization energies of the metal might well be rationalized in terms of this two transition state model.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.20.Db Transition state theory and statistical theories of rate constants
82.20.Kh Potential energy surfaces for chemical reactions

Collision-induced dissociation studies of FemOn+ : Bond energies in small iron oxide cluster cations, FemOn+ (m = 1–3, n = 1–6)

Ming Li, Shu-Rong Liu, and P. B. Armentrout

J. Chem. Phys. 131, 144310 (2009); http://dx.doi.org/10.1063/1.3246840 (16 pages) | Cited 6 times

Online Publication Date: 14 October 2009

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A variety of iron oxide cluster cations is synthesized in a laser vaporization ion source. The kinetic energy dependence of the collision-induced dissociation (CID) of mass selected FemOn+ (m = 1–3, n = 1–6) clusters with Xe is studied in this work using a guided ion beam tandem mass spectrometer. Examination of the general dissociation behavior over a broad collision energy range (0–15 eV) shows that iron oxide clusters can dissociate via evaporation of neutral Fe and O atoms as well as fission by loss of neutral O2, FeO, FeO2, Fe2O2, and Fe2O3 fragments. Such fission pathways, which are not observed in the CID studies of pure Fe cluster cations and most other pure transition metal cluster cations, result from the strong iron oxygen bonds. In general, the predominant dissociation pathways are found to correlate with the oxidation state of the iron in the cluster. Thresholds for loss of neutral Fe, O, O2, FeO, FeO2, Fe2O2, and Fe2O3 from various iron oxide cluster cations are quantitatively determined. These values are used to determine bond energies and heats of formation for both neutral and cationic iron oxide clusters in this size range.
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36.40.Jn Reactivity of clusters
36.40.Mr Spectroscopy and geometrical structure of clusters
34.50.Lf Chemical reactions
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Fm Bond strengths, dissociation energies
33.15.Ta Mass spectra

Nature of the lowest excited states of neutral polyenyl radicals and polyene radical cations

Jan Hendrik Starcke, Michael Wormit, and Andreas Dreuw

J. Chem. Phys. 131, 144311 (2009); http://dx.doi.org/10.1063/1.3246350 (8 pages) | Cited 8 times

Online Publication Date: 14 October 2009

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Due to the close relation of the polyenyl radicals C2n+1H2n+3• and polyene radical cations C2nH2n+2•+ to the neutral linear polyenes, one may suspect their excited states to possess substantial double excitation character, similar to the famous S1 state of neutral polyenes and thus to be equally problematic for simple excited state theories. Using the recently developed unrestricted algebraic-diagrammatic construction scheme of second order perturbation theory and the equation-of-motion coupled-cluster method, the vertical excitation energies, their corresponding oscillator strengths, and the nature of the wave functions of the lowest excited electronic states of the radicals are calculated and analyzed in detail. For the polyenyl radicals two one-photon allowed states are found as D1 and D4 states, with two symmetry-forbidden D2 and D3 states in between, while in the polyene radical cations D1 and D2 are allowed and D3 is forbidden. The order of the states is conserved with increasing chain length. It is found that all low-lying excited states exhibit a significant but similar amount of doubly excited configuration in their wave functions of 15%–20%. Using extrapolation, predictions for the excitation energies of the five lowest excited states of the polyene radical cations are made for longer chain lengths.
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31.15.bw Coupled-cluster theory
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

Spin relaxation of fullerene C70 photoexcited triplet in molecular glasses: Evidence for onset of fast orientational motions of molecules in the matrix near 100 K

Mikhail N. Uvarov, Leonid V. Kulik, and Sergei A. Dzuba

J. Chem. Phys. 131, 144501 (2009); http://dx.doi.org/10.1063/1.3244983 (4 pages) | Cited 3 times

Online Publication Date: 8 October 2009

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Electron spin echo (ESE) was applied to study transversal spin relaxation of photoexcited triplet state of fullerene C70 molecules in glassy o-terphenyl and cis-/trans-decalin matrices (glass transition temperatures of 243 and 137 K, respectively). The relaxation rate T2−1 was found to increase sharply above 110 K in o-terphenyl and above 100 K in decalin. It is suggested that this increase arises from interaction of 3C70 pseudorotation with fast molecular librations in the matrix. Both these types of motion involve atomic vibrations and are uniaxial in their nature, the known literature data on Raman light scattering and others indicate that molecular librations may be thermally activated in glasses just near 100 K. The increase in T2−1 near 100 K is not observed for photoexcited triplet state of fullerene C60, for which pseudorotation is not uniaxial. As the fullerene molecule has a size much larger than that for glass solvent molecules, it is likely that molecular librations in the matrix are of collective nature.
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76.30.-v Electron paramagnetic resonance and relaxation
64.70.ph Nonmetallic glasses (silicates, oxides, selenides, etc.)
61.48.-c Structure of fullerenes and related hollow and planar molecular structures
78.30.Na Fullerenes and related materials
61.43.Fs Glasses

Temperature and density dependence of the structural relaxation time in water by inelastic ultraviolet scattering

F. Bencivenga, A. Cimatoribus, A. Gessini, M. G. Izzo, and C. Masciovecchio

J. Chem. Phys. 131, 144502 (2009); http://dx.doi.org/10.1063/1.3243314 (8 pages) | Cited 3 times

Online Publication Date: 8 October 2009

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The density and temperature dependence of the structural relaxation time (τ) in water was determined by inelastic ultraviolet scattering spectroscopy in the thermodynamic range (P = 1–4000 bars, T = 253–323 K), where several water anomalies take place. We observed an activation (Arrhenius) temperature dependence of τ at constant density and a monotonic density decrease at constant temperature. The latter trend was accounted for by introducing a density-dependent activation entropy associated to water local structure. The combined temperature and density behavior of τ indicates that differently from previous results, in the probed thermodynamic range, the relaxation process is ruled by a density-dependent activation Helmholtz free energy rather than a simple activation energy. Finally, the extrapolation of the observed phenomenology at lower temperature suggests a substantial agreement with the liquid-liquid phase transition hypothesis.
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61.25.Em Molecular liquids
78.40.Dw Liquids
64.70.Ja Liquid-liquid transitions
65.20.Jk Studies of thermodynamic properties of specific liquids

Intermolecular shielding contributions studied by modeling the 13C chemical-shift tensors of organic single crystals with plane waves

Jessica C. Johnston, Robbie J. Iuliucci, Julio C. Facelli, George Fitzgerald, and Karl T. Mueller

J. Chem. Phys. 131, 144503 (2009); http://dx.doi.org/10.1063/1.3225270 (11 pages) | Cited 16 times

Online Publication Date: 8 October 2009

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In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all 13C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm.
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76.60.Cq Chemical and Knight shifts
71.70.Jp Nuclear states and interactions
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.15.Dx Computational methodology (Brillouin zone sampling, iterative diagonalization, pseudopotential construction)
61.66.Hq Organic compounds
61.50.Lt Crystal binding; cohesive energy
75.30.Cr Saturation moments and magnetic susceptibilities

Infrared absorption of GeNNO isolated in solid Ar

Zih-Min Jiang, Joerg Glatthaar, and Yuan-Pern Lee

J. Chem. Phys. 131, 144504 (2009); http://dx.doi.org/10.1063/1.3236384 (12 pages) | Cited 1 time

Online Publication Date: 8 October 2009

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Codeposition of thermally generated atomic germanium vapor and nitrous oxide (N2O) in Ar onto a substrate at 11 K produced infrared absorption lines in several sets. The most prominent comprises intense lines at 1443.7, 1102.4, and 784.0 cm−1 that become diminished upon irradiation with UV or visible light. These lines are attributed to ν1 (NO stretching), ν2 (NN+GeN stretching), and ν3 (NNO bending+NN stretching) modes of singlet GeNNO. Two additional weak features at 1238.1 and 2859.2 cm−1 are assigned as ν3+ν4 and 2ν1 of GeNNO, respectively. Weak doublet features at 1259.3/1255.5 and 1488.9/1486.4 cm−1 are tentatively assigned to ν2 of triplet GeONN and ν1 of singlet cyc-Ge-η2 [NN(O)], respectively. Quantum-chemical calculations on the Ge+N2O system with density-functional theory (B3LYP /aug-cc-pVTZ) predict five stable structures: GeNNO (singlet and triplet), singlet cyc-Ge-η2 [NN(O)], triplet cyc-Ge-η2 (NNO), GeONN (singlet and triplet), and singlet GeNON. Vibrational wavenumbers, relative IR intensities, and 15N-isotopic ratios for observed species are consistent with those computed. Irradiation of singlet GeNNO with λ = 248 or 193 nm or λ>525 nm yields GeO.
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78.30.Hv Other nonmetallic inorganics
61.80.Ba Ultraviolet, visible, and infrared radiation effects (including laser radiation)

Dynamical disorder in 2-methyl-4-nitroaniline and its deuterated analogue crystals studied by Fourier transform infrared and nuclear magnetic resonance

Urszula Okwieka, Krystyna Hołderna-Natkaniec, Tomasz Misiaszek, Wojciech Medycki, Jan Baran, and M. Magdalena Szostak

J. Chem. Phys. 131, 144505 (2009); http://dx.doi.org/10.1063/1.3243855 (7 pages) | Cited 6 times

Online Publication Date: 8 October 2009

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The Fourier transform infrared spectra of the thin layers of 2-methyl-4-nitroaniline (MNA) and its deuterated analog were recorded in the 500–4000 cm−1 region in the 10–300 K temperature range. Activation energies of the –CH3, –NH2, and –NO2 groups reorientations were estimated. The 1H-NMR spin-lattice relaxation time, T1, and the second moment of 1H-NMR resonance line, M2, measured in the 80–298 K temperature range, were used to determine the parameters of the –CH3 group motion. The experimental potential barriers for the amine, nitro, and methyl group reorientations are considered in the context of strengths of the N–H…O, C–H…O intermolecular hydrogen bonds, and other short contacts, recognized recently [ U. Okwieka et al., J. Raman Spectrosc. 39, 849 (2008) ], and they agree with the barriers calculated by quantum chemical methods. The dynamical disorder found in the MNA crystal in the large temperature range seems to be important from the point of view of its nonlinear optical and other properties.
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68.55.-a Thin film structure and morphology
78.66.Qn Polymers; organic compounds
78.30.Jw Organic compounds, polymers
76.60.Es Relaxation effects
42.70.Jk Polymers and organics
42.70.Mp Nonlinear optical crystals

Ab initio molecular dynamics study of supercritical carbon dioxide including dispersion corrections

Sundaram Balasubramanian, Axel Kohlmeyer, and Michael L. Klein

J. Chem. Phys. 131, 144506 (2009); http://dx.doi.org/10.1063/1.3245962 (4 pages) | Cited 6 times

Online Publication Date: 9 October 2009

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Density functional theory based ab initio molecular dynamics simulations with explicit inclusion of empirical van der Waals (vdW) corrections of supercritical carbon dioxide have been performed. Significant changes in the intermolecular pair correlation functions of the fluid modeled with the added vdW interactions are observed, particularly at lower densities. The closest neighbor to a molecule is seen to be oriented in a distorted T-shaped geometry, consistent with earlier experiments and simulations.
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31.15.ap Polarizabilities and other atomic and molecular properties
31.15.em Corrections for core-spin polarization, surface effects, etc.
31.15.xv Molecular dynamics and other numerical methods
34.20.Cf Interatomic potentials and forces
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