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7 Jan 2012

Volume 136, Issue 1, Articles (01xxxx)

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J. Chem. Phys. 136, 014501 (2012); http://dx.doi.org/10.1063/1.3665140 (8 pages)

Minbiao Ji, Robert W. Hartsock, Zheng Sung, and Kelly J. Gaffney
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back to top Theoretical Methods and Algorithms

Stochastic simulation of chemically reacting systems using multi-core processors

Colin S. Gillespie

J. Chem. Phys. 136, 014101 (2012); http://dx.doi.org/10.1063/1.3670416 (8 pages)

Online Publication Date: 3 January 2012

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In recent years, computer simulations have become increasingly useful when trying to understand the complex dynamics of biochemical networks, particularly in stochastic systems. In such situations stochastic simulation is vital in gaining an understanding of the inherent stochasticity present, as these models are rarely analytically tractable. However, a stochastic approach can be computationally prohibitive for many models. A number of approximations have been proposed that aim to speed up stochastic simulations. However, the majority of these approaches are fundamentally serial in terms of central processing unit (CPU) usage. In this paper, we propose a novel simulation algorithm that utilises the potential of multi-core machines. This algorithm partitions the model into smaller sub-models. These sub-models are then simulated, in parallel, on separate CPUs. We demonstrate that this method is accurate and can speed-up the simulation by a factor proportional to the number of processors available.
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82.20.Wt Computational modeling; simulation

Extended hydrodynamic approach to quantum-classical nonequilibrium evolution. II. Application to nonpolar solvation

Keith H. Hughes, Sean N. Baxter, David Bousquet, Padmanaban Ramanathan, and Irene Burghardt

J. Chem. Phys. 136, 014102 (2012); http://dx.doi.org/10.1063/1.3671378 (10 pages)

Online Publication Date: 3 January 2012

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The mixed quantum-classical formulation derived in our companion paper [D. Bousquet, K. H. Hughes, D. Micha, and I. Burghardt, J. Chem. Phys. 134, 064116 (2011)]10.1063/1.3553174, which is based upon a hydrodynamic representation of the classical sector, is applied to nonequilibrium nonpolar solvation dynamics as exemplified by the solvation of the electronically excited NO molecule in a rare gas environment. Derived from a partition of the Hamiltonian into a primary (quantum) part and a secondary (classical) part the hydrodynamic equations are formulated for multi-quantum states and result in explicit equations of motion for populations and coherences. The hierarchy of hydrodynamic equations is truncated by the following approximate closure schemes: Gauss-Hermite closure, dynamical density functional theory approximation, and a generalized Maxwellian closure. A comparison of the dynamics using these three closure methods showed that the suitability of a particular closure scheme was dependent on the initial conditions and the nonequilibrium character of the dynamics.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions

Basis set dependence of higher-order correlation effects in π-type interactions

Emily J. Carrell, Cara M. Thorne, and Gregory S. Tschumper

J. Chem. Phys. 136, 014103 (2012); http://dx.doi.org/10.1063/1.3671950 (11 pages)

Online Publication Date: 3 January 2012

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The basis set dependence of higher-order correlation effects on π-type interaction energies was examined by scanning the potential energy surfaces of five dimer systems. The dimers of acetylene (H−C≡C−H), diacetylene (H−C≡C−C≡C−H), cyanogen (N≡C−C≡N), diphosphorous (P≡P), and 1,4-diphosphabutadiyne (P≡C−C≡P) were studied in three different configurations: cross, parallel-displaced, and t-shaped. More than 800 potential energy curves (PECs) were generated by computing the interaction energies for all 15 dimer configurations over a range of intermolecular distances with the MP2, coupled-cluster single double (CCSD), and coupled-cluster single double triple (CCSD(T)) methods in conjunction with 21 basis sets ranging from a small 6-31G*(0.25) split-valence basis set to a large aug-cc-pVQZ correlation consistent basis set. Standard extrapolation techniques were also used to construct MP2, CCSD, and CCSD(T) complete basis set (CBS) limit PECs as well as CBS limit higher-order correlation corrections based on the differences between CCSD(T) and MP2 interaction energies, denoted δ MP 2 CCSD (T), and the corresponding differences between CCSD(T) and CCSD interactions energies, denoted δ CCSD CCSD (T). Double-ζ basis sets struggled to reproduce the former but provided quite reasonable descriptions of the latter as long as diffuse functions were included. The aug-cc-pVDZ basis deviated from the δ CCSD CCSD (T) CBS limit by only 0.06 kcal mol−1 on average and never by more than 0.24 kcal mol−1, whereas the corresponding deviations were approximately twice that for the δ MP 2 CCSD (T) term. While triple-ζ basis sets typically improved results, only aug-cc-pVTZ provided appreciable improvement over utilizing the aug-cc-pVDZ basis set to compute δ CCSD CCSD (T). Counterpoise (CP) corrections were also applied to all double- and triple-ζ basis sets, but they rarely yielded a better description of these higher-order correlation effects. CP corrections only consistently improved results when the aug-cc-pVDZ basis set was used to compute δ MP 2 CCSD (T), yielding mean and maximum absolute deviations from the CBS values of 0.10 and 0.39 kcal mol−1, respectively, for all five dimer systems.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
31.50.-x Potential energy surfaces
31.15.bw Coupled-cluster theory
31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.xp Perturbation theory

Long-range correlation energies from frequency-dependent weighted exchange-hole dipole polarisabilities

Andreas Heßelmann

J. Chem. Phys. 136, 014104 (2012); http://dx.doi.org/10.1063/1.3672236 (15 pages)

Online Publication Date: 4 January 2012

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Long-range correlation energies are calculated using an approximation of the single-particle density-density response function of the system that leads to an expression requiring only occupied orbitals and eigenvalues. Dipole-dipole polarisabilities and isotropic leading-order dispersion coefficients obtained from this approximation are shown to be in a reasonable agreement with corresponding values from the experiment or dipole oscillator strength distributions. The localised polarisabilities were used to calculate a long-range correlation correction to a hybrid-generalised gradient approximation functional using a proper damping function at short ranges. It was found that the hybrid density-functional theory+dispersion method obtained in this way has a comparable accuracy than high-level ab initio wave function methods at a much lower computational cost. This has been analysed for a number of systems from the GMTKN30 database including subsets for noncovalently bound complexes, relative energies for sugar conformers and reaction energies and barrier heights of pericyclic reactions of some medium sized organic molecules.
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31.15.eg Exchange-correlation functionals (in current density functional theory)
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

The divide-expand-consolidate family of coupled cluster methods: Numerical illustrations using second order Møller-Plesset perturbation theory

Ida-Marie Høyvik, Kasper Kristensen, Branislav Jansik, and Poul Jørgensen

J. Chem. Phys. 136, 014105 (2012); http://dx.doi.org/10.1063/1.3667266 (16 pages)

Online Publication Date: 4 January 2012

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Previously, we have introduced the linear scaling coupled cluster (CC) divide-expand-consolidate (DEC) method, using an occupied space partitioning of the standard correlation energy. In this article, we show that the correlation energy may alternatively be expressed using a virtual space partitioning, and that the Lagrangian correlation energy may be partitioned using elements from both the occupied and virtual partitioning schemes. The partitionings of the correlation energy leads to atomic site and pair interaction energies which are term-wise invariant with respect to an orthogonal transformation among the occupied or the virtual orbitals. Evaluating the atomic site and pair interaction energies using local orbitals leads to a linear scaling algorithm and a distinction between Coulomb hole and dispersion energy contributions to the correlation energy. Further, a detailed error analysis is performed illustrating the error control imposed on all components of the energy by the chosen energy threshold. This error control is ultimately used to show how to reduce the computational cost for evaluating dispersion energy contributions in DEC.
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31.15.bw Coupled-cluster theory
31.15.xp Perturbation theory

Constrained adiabatic trajectory method: A global integrator for explicitly time-dependent Hamiltonians

A. Leclerc, G. Jolicard, D. Viennot, and J. P. Killingbeck

J. Chem. Phys. 136, 014106 (2012); http://dx.doi.org/10.1063/1.3673320 (14 pages)

Online Publication Date: 4 January 2012

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The constrained adiabatic trajectory method (CATM) is reexamined as an integrator for the Schrödinger equation. An initial discussion places the CATM in the context of the different integrators used in the literature for time-independent or explicitly time-dependent Hamiltonians. The emphasis is put on adiabatic processes and within this adiabatic framework the interdependence between the CATM, the wave operator, the Floquet, and the (t, t′) theories is presented in detail. Two points are then more particularly analyzed and illustrated by a numerical calculation describing the H2+ ion submitted to a laser pulse. The first point is the ability of the CATM to dilate the Hamiltonian spectrum and thus to make the perturbative treatment of the equations defining the wave function possible, possibly by using a Krylov subspace approach as a complement. The second point is the ability of the CATM to handle extremely complex time-dependencies, such as those which appear when interaction representations are used to integrate the system.
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33.80.-b Photon interactions with molecules
31.15.xp Perturbation theory
03.65.Ge Solutions of wave equations: bound states

Stockholder projector analysis: A Hilbert-space partitioning of the molecular one-electron density matrix with orthogonal projectors

Diederik Vanfleteren, Dimitri Van Neck, Patrick Bultinck, Paul W. Ayers, and Michel Waroquier

J. Chem. Phys. 136, 014107 (2012); http://dx.doi.org/10.1063/1.3673321 (13 pages)

Online Publication Date: 4 January 2012

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A previously introduced partitioning of the molecular one-electron density matrix over atoms and bonds [D. Vanfleteren et al., J. Chem. Phys. 133, 231103 (2010)] is investigated in detail. Orthogonal projection operators are used to define atomic subspaces, as in Natural Population Analysis. The orthogonal projection operators are constructed with a recursive scheme. These operators are chemically relevant and obey a stockholder principle, familiar from the Hirshfeld-I partitioning of the electron density. The stockholder principle is extended to density matrices, where the orthogonal projectors are considered to be atomic fractions of the summed contributions. All calculations are performed as matrix manipulations in one-electron Hilbert space. Mathematical proofs and numerical evidence concerning this recursive scheme are provided in the present paper. The advantages associated with the use of these stockholder projection operators are examined with respect to covalent bond orders, bond polarization, and transferability.
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31.15.E- Density-functional theory
33.15.Bh General molecular conformation and symmetry; stereochemistry

A simple scheme for magnetic balance in four-component relativistic Kohn–Sham calculations of nuclear magnetic resonance shielding constants in a Gaussian basis

Małgorzata Olejniczak, Radovan Bast, Trond Saue, and Magdalena Pecul

J. Chem. Phys. 136, 014108 (2012); http://dx.doi.org/10.1063/1.3671390 (13 pages) | Cited 1 time

Online Publication Date: 4 January 2012

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We report the implementation of nuclear magnetic resonance (NMR) shielding tensors within the four-component relativistic Kohn–Sham density functional theory including non-collinear spin magnetization and employing London atomic orbitals to ensure gauge origin independent results, together with a new and efficient scheme for assuring correct balance between the large and small components of a molecular four-component spinor in the presence of an external magnetic field (simple magnetic balance). To test our formalism we have carried out calculations of NMR shielding tensors for the HX series (X = F, Cl, Br, I, At), the Xe atom, and the Xe dimer. The advantage of simple magnetic balance scheme combined with the use of London atomic orbitals is the fast convergence of results (when compared with restricted kinetic balance) and elimination of linear dependencies in the basis set (when compared to unrestricted kinetic balance). The effect of including spin magnetization in the description of NMR shielding tensor has been found important for hydrogen atoms in heavy HX molecules, causing an increase of isotropic values of 10%, but negligible for heavy atoms.
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33.25.+k Nuclear resonance and relaxation
32.30.Dx Magnetic resonance spectra
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)

Linear dependence and energy conservation in Gaussian wavepacket basis sets

Scott Habershon

J. Chem. Phys. 136, 014109 (2012); http://dx.doi.org/10.1063/1.3671978 (8 pages)

Online Publication Date: 4 January 2012

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We propose a method for dealing with the problem of linear dependence in quantum dynamics simulations employing over-complete Gaussian wavepacket (GWP) basis sets. In particular, by periodically projecting out redundant basis functions using the matching pursuit algorithm whilst simultaneously introducing GWPs which avoid linear dependence with the current basis set, we find that numerical conditioning of the equations-of-motion can be readily controlled. In applications to particle tunnelling in one- and two-dimensional potentials, this method allows us to reproduce the exact quantum-mechanical results with fewer GWP basis functions than similar calculations with non-adaptive basis sets, a result which we trace back to the improved energy conservation of our adaptive approach.
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31.15.X- Alternative approaches

Considerations on describing non-singlet spin states in variational second order density matrix methods

Helen van Aggelen, Brecht Verstichel, Patrick Bultinck, Dimitri Van Neck, and Paul W. Ayers

J. Chem. Phys. 136, 014110 (2012); http://dx.doi.org/10.1063/1.3672087 (9 pages)

Online Publication Date: 5 January 2012

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Despite the importance of non-singlet molecules in chemistry, most variational second order density matrix calculations have focused on singlet states. Ensuring that a second order density matrix is derivable from a proper N-electron spin state is a difficult problem because the second order density matrix only describes one- and two-particle interactions. In pursuit of a consistent description of spin in second order density matrix theory, we propose and evaluate two main approaches: we consider constraints derived from a pure spin state and from an ensemble of spin states. This paper makes a comparative assessment of the different approaches by applying them to potential energy surfaces for different spin states of the oxygen and carbon dimer. We observe two major shortcomings of the applied spin constraints: they are not size consistent and they do not reproduce the degeneracy of the different states in a spin multiplet. First of all, the spin constraints are less strong when applied to a dissociated molecule than when they are applied to the dissociation products separately. Although they impose correct spin expectation values on the dissociated molecule, the dissociation products do not have correct spin expectation values. Secondly, both under “pure spin state conditions” and under “ensemble spin state” conditions is the energy a convex function of the spin projection. Potential energy surfaces for different spin projections of the same spin state may give a completely different picture of the molecule's bonding. The maximal spin projection always gives the most strongly constrained energy, but is also significantly more expensive to compute than a spin-averaged ensemble. In the dissociation limit, both the problem of nondegeneracy of equivalent spin projections, size-inconsistency and unphysical dissociation can be corrected by means of subspace energy constraints.
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31.15.E- Density-functional theory
31.50.-x Potential energy surfaces
31.15.xt Variational techniques

Importance of the correlation contribution for local hybrid functionals: Range separation and self-interaction corrections

Alexei V. Arbuznikov and Martin Kaupp

J. Chem. Phys. 136, 014111 (2012); http://dx.doi.org/10.1063/1.3672080 (13 pages)

Online Publication Date: 6 January 2012

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Local hybrid functionals with their position-dependent exact-exchange admixture are a conceptually simple and promising extension of the concept of a hybrid functional. Local hybrids based on a simple mixing of the local spin density approximation (LSDA) with exact exchange have been shown to be successful for thermochemistry, reaction barriers, and a range of other properties. So far, the combination of this generation of local hybrids with an LSDA correlation functional has been found to give the most favorable results for atomization energies, for a range of local mixing functions (LMFs) governing the exact-exchange admixture. Here, we show that the choice of correlation functional to be used with local hybrid exchange crucially influences the parameterization also of the exchange part as well as the overall performance. A novel ansatz for the correlation part of local hybrids is suggested based on (i) range-separation of LSDA correlation into short-range (SR) and long-range (LR) parts, and (ii) partial or full elimination of the one-electron self-correlation from the SR part. It is shown that such modified correlation functionals allow overall larger exact exchange admixture in thermochemically competitive local hybrids than before. This results in improvements for reaction barriers and for other properties crucially influenced by self-interaction errors, as demonstrated by a number of examples. Based on the range-separation approach, a fresh view on the breakdown of the correlation energy into dynamical and non-dynamical parts is suggested.
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82.20.Db Transition state theory and statistical theories of rate constants
82.60.-s Chemical thermodynamics
82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)

A density matrix renormalization group method study of optical properties of porphines and metalloporphines

Manoranjan Kumar, Y. Anusooya Pati, and S. Ramasesha

J. Chem. Phys. 136, 014112 (2012); http://dx.doi.org/10.1063/1.3671946 (12 pages) | Cited 1 time

Online Publication Date: 6 January 2012

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The symmetrized density matrix renormalization group method is used to study linear and nonlinear optical properties of free base porphine and metalloporphine. Long-range interacting model, namely, Pariser-Parr-Pople model is employed to capture the quantum many-body effect in these systems. The nonlinear optical coefficients are computed within the correction vector method. The computed singlet and triplet low-lying excited state energies and their charge densities are in excellent agreement with experimental as well as many other theoretical results. The rearrangement of the charge density at carbon and nitrogen sites, on excitation, is discussed. From our bond order calculation, we conclude that porphine is well described by the 18-annulenic structure in the ground state and the molecule expands upon excitation. We have modeled the regular metalloporphine by taking an effective electric field due to the metal ion and computed the excitation spectrum. Metalloporphines have D4h symmetry and hence have more degenerate excited states. The ground state of metalloporphines shows 20-annulenic structure, as the charge on the metal ion increases. The linear polarizability seems to increase with the charge initially and then saturates. The same trend is observed in third order polarizability coefficients.
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33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
31.15.bu Semi-empirical and empirical calculations (differential overlap, Hückel, PPP methods, etc.)
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Beam broadening of polar molecules and clusters in deflection experiments

J. Bulthuis and V. V. Kresin

J. Chem. Phys. 136, 014301 (2012); http://dx.doi.org/10.1063/1.3673890 (8 pages)

Online Publication Date: 3 January 2012

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A beam of rotating dipolar particles (molecules or clusters) will broaden when passed through an electric or magnetic field gradient region. This broadening, which is a common experimental observable, can be expressed in terms of the variance of the distribution of the resulting polarization orientation (the direction cosine). Here, the broadening for symmetric-top and linear rotors is discussed. These two types of rotors have qualitatively different low-field orientation distribution functions, but behave similarly in a strong field. While analytical expressions for the polarization variance can be derived from first-order perturbation theory, for experimental guidance it is important to identify the applicability and limitations of these expressions, and the general dependence of the broadening on the experimental parameters. For this purpose, the analytical results are compared with the full diagonalization of the rotational Stark-effect matrices. Conveniently for experimental estimations, it is found that for symmetric tops, the dependence of the broadening parameter on the rotational constant, the axial ratio, and the field strength remains similar to the analytical expression even outside of the perturbative regime. Also, it is observed that the shape envelope, the centroid, and the width of the orientation distribution function for a symmetric top are quite insensitive to the value of its rotational constant (except at low rotational temperatures).
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36.40.Vz Optical properties of clusters
33.20.Sn Rotational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations

S···X halogen bonds and H···X hydrogen bonds in H2CS–XY (XY = FF, ClF, ClCl, BrF, BrCl, and BrBr) complexes: Cooperativity and solvent effect

Qingzhong Li, Ran Li, Zhongjun Zhou, Wenzuo Li, and Jianbo Cheng

J. Chem. Phys. 136, 014302 (2012); http://dx.doi.org/10.1063/1.3673540 (8 pages)

Online Publication Date: 3 January 2012

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Using ab initio calculations, we have studied the structures, properties, and nature of halogen bonds in H2CS–XY (XY = FF, ClF, ClCl, BrF, BrCl, and BrBr) complexes. The results show that the ring-shaped complexes are formed by a halogen bond (S···X) and a secondary hydrogen bond (H···X). We also analyzed the H2CS–ClF–ClF and FCl–H2CS–ClF complexes to investigate the cooperative and diminutive halogen bonding. The cooperative effect of halogen bonding is found in the former, while the diminutive effect is present in the latter. We finally considered the solvent effect on the halogen bond in H2CS–BrCl complex and found that the solvent has a prominent enhancing effect on it. The complexes have also been analyzed with natural bond orbital, atoms in molecules, and symmetry adapted perturbation theory method.
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31.70.Dk Environmental and solvent effects
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Fm Bond strengths, dissociation energies
33.70.Jg Line and band widths, shapes, and shifts
31.15.ae Electronic structure and bonding characteristics
31.15.xp Perturbation theory

Dynamic (hyper)polarizabilities of the sulphur dioxide molecule: Coupled cluster calculations including vibrational corrections

Emílio S. Naves, Marcos A. Castro, and Tertius L. Fonseca

J. Chem. Phys. 136, 014303 (2012); http://dx.doi.org/10.1063/1.3673569 (7 pages)

Online Publication Date: 3 January 2012

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In this work we report results for dynamical (hyper)polarizabilities of the sulphur dioxide molecule with inclusion of vibrational corrections. The electronic contributions were computed analytically at the single and double coupled cluster level through response theories for the frequencies 0, 0.0239, 0.0428, 0.0656, 0.0720, and 0.0886 hartree. Contributions of the connected triple excitations to the dynamic electronic properties were also estimated through the multiplicative correction scheme. Vibrational corrections were calculated by means of the perturbation theoretical method. The results obtained show that the zero point vibrational correction is very small for all properties studied while the pure vibrational correction is relevant for the dc-Pockels effect, intensity dependent refractive index, and dc-Kerr effect. For these nonlinear optical processes, the pure vibrational corrections represent approximately 75%, 13%, and 6% of the corresponding electronic contributions for the higher frequencies quoted. The results presented for the polarizability are in good agreement with experimental values available in the literature. For the hyperpolarizabilities we have not obtained experimental results with precision sufficient for comparison.
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33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis
31.15.bw Coupled-cluster theory
32.30.-r Atomic spectra

Isotope effect in normal-to-local transition of acetylene bending modes

Jianyi Ma, Dingguo Xu, Hua Guo, Vivian Tyng, and Michael E. Kellman

J. Chem. Phys. 136, 014304 (2012); http://dx.doi.org/10.1063/1.3673570 (7 pages)

Online Publication Date: 3 January 2012

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The normal-to-local transition for the bending modes of acetylene is considered a prelude to its isomerization to vinylidene. Here, such a transition in fully deuterated acetylene is investigated using a full-dimensional quantum model. It is found that the local benders emerge at much lower energies and bending quantum numbers than in the hydrogen isotopomer HCCH. This is accompanied by a transition to a second kind of bending mode called counter-rotator, again at lower energies and quantum numbers than in HCCH. These transitions are also investigated using bifurcation analysis of two empirical spectroscopic fitting Hamiltonians for pure bending modes, which helps to understand the origin of the transitions semiclassically as branchings or bifurcations out of the trans- and cis-normal bend modes when the latter become dynamically unstable. The results of the quantum model and the empirical bifurcation analysis are in very good agreement.
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82.20.Tr Kinetic isotope effects including muonium
82.30.Qt Isomerization and rearrangement
31.30.Gs Hyperfine interactions and isotope effects
33.20.Sn Rotational analysis

Hydrogen bonds in the nucleobase-gold complexes: Photoelectron spectroscopy and density functional calculations

Guo-Jin Cao, Hong-Guang Xu, Ren-Zhong Li, and Weijun Zheng

J. Chem. Phys. 136, 014305 (2012); http://dx.doi.org/10.1063/1.3671945 (8 pages)

Online Publication Date: 3 January 2012

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The nucleobase-gold complexes were studied with anion photoelectron spectroscopy and density functional calculations. The vertical detachment energies of uracil-Au−, thymine-Au−, cytosine-Au−, adenine-Au−, and guanine-Au− were estimated to be 3.37 ± 0.08 eV, 3.40 ± 0.08 eV, 3.23 ± 0.08 eV, 3.28 ± 0.08 eV, and 3.43 ± 0.08 eV, respectively, based on their photoelectron spectra. The combination of photoelectron spectroscopy experiments and density functional calculations reveals the presence of two or more isomers for these nucleobase-gold complexes. The major isomers detected in the experiments probably are formed by Au anion with the canonical tautomers of the nucleobases. The gold anion essentially interacts with the nucleobases through N-H···Au hydrogen bonds.
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33.60.+q Photoelectron spectra
33.15.Hp Barrier heights (internal rotation, inversion, rotational isomerism, conformational dynamics)
33.15.Fm Bond strengths, dissociation energies
31.15.E- Density-functional theory

Structure, energetics, and reactions of alkali tetramers

Jason N. Byrd, H. Harvey Michels, John A. Montgomery, Jr., Robin Côté, and William C. Stwalley

J. Chem. Phys. 136, 014306 (2012); http://dx.doi.org/10.1063/1.3672646 (5 pages)

Online Publication Date: 4 January 2012

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Electronic structure calculations have been carried out for all possible alkali tetramers that can be formed from X2 + X2 → X2X2, X2 + Y2 → X2Y2, and XY + XY → X2Y2 alkali dimer association reactions. Vibrationally stable rhombic (D2h) and planar (Cs) structures are found for all possible tetramers formed from the alkali metals, Li to Cs. All tetramer formation reactions (from ground state singlet homonuclear or heteronuclear dimers) are found to be exothermic with binding energies ranging from 6282 cm−1 for Li2Li2 to 1985 cm−1 for Cs2Cs2. Extensive calculations, carried out at long-range for several reactant pairs, indicate that there are barrier-less pathways for the formation of tetramers from dimer association reactions. At low temperatures, direct formation of tetramers is unlikely, owing to the large exothermicity associated with these association reactions, but atom exchange reactions (X2 + Y2 ↔ XY + XY) are possible for some species.
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82.30.Nr Association, addition, insertion, cluster formation
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.20.Tp Vibrational analysis
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions

Photodissociation pathways and lifetimes of protonated peptides and their dimers

G. Aravind, B. Klærke, J. Rajput, Y. Toker, L. H. Andersen, A. V. Bochenkova, R. Antoine, J. Lemoine, A. Racaud, and P. Dugourd

J. Chem. Phys. 136, 014307 (2012); http://dx.doi.org/10.1063/1.3671943 (14 pages)

Online Publication Date: 4 January 2012

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Photodissociation lifetimes and fragment channels of gas-phase, protonated YAn (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of ∼200 ns while the protonated dimers show an additional slow dissociation component with a lifetime of ∼2 μs. Laser power dependence measurements enabled us to ascribe the fast channel in the monomer and the slow channel in the dimer to a one-photon process, whereas the fast dimer channel is from a two-photon process. The slow (1 photon) dissociation channel in the dimer was found to result in cleavage of the H-bonds after energy transfer through these H-bonds. In general, the dissociation of these protonated peptides is non-prompt and the decay time was found to increase with the size of the peptides. Quantum RRKM calculations of the microcanonical rate constants also confirmed a statistical nature of the photodissociation processes in the dipeptide monomers and dimers. The classical RRKM expression gives a rate constant as an analytical function of the number of active vibrational modes in the system, estimated separately on the basis of the equipartition theorem. It demonstrates encouraging results in predicting fragmentation lifetimes of protonated peptides. Finally, we present the first experimental evidence for a photo-induced conversion of tyrosine-containing peptides into monocyclic aromatic hydrocarbon along with a formamide molecule both found in space.
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87.15.mk Photodissociation
87.15.Fh Bonding; mechanisms of bond breakage
87.14.ef Peptides
82.50.Pt Multiphoton processes
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Hf Product distribution

Core-to-Rydberg band shift and broadening of hydrogen bonded ammonia clusters studied with nitrogen K-edge excitation spectroscopy

Takeshi Yamanaka, Kiyohiko Tabayashi, Osamu Takahashi, Kenichiro Tanaka, Hirofumi Namatame, and Masaki Taniguchi

J. Chem. Phys. 136, 014308 (2012); http://dx.doi.org/10.1063/1.3673778 (11 pages)

Online Publication Date: 5 January 2012

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Nitrogen 1s (N ls) core-to-Rydberg excitation spectra of hydrogen-bonded clusters of ammonia (AM) have been studied in the small cluster regime of beam conditions with time-of-flight (TOF) fragment-mass spectroscopy. By monitoring partial-ion-yield spectra of cluster-origin products, “cluster” specific excitation spectra could be recorded. Comparison of the “cluster” band with “monomer” band revealed that the first resonance bands of clusters corresponding to N 1s → 3sa1/3pe of AM monomer are considerably broadened. The changes of the experimental core-to-Rydberg transitions ΔFWHM (N 1s → 3sa1/3pe) = ∼0.20/∼0.50 eV compare well with the x ray absorption spectra of the clusters generated by using density functional theory (DFT) calculation. The broadening of the core-to-Rydberg bands in small clusters is interpreted as being primarily due to the splitting of non-equivalent core-hole N 1s states caused by both electrostatic core-hole and hydrogen-bonding (H3N···H–NH2) interactions upon dimerization. Under Cs dimer configuration, core-electron binding energy of H−N (H-donor) is significantly decreased by the intermolecular core-hole interaction and causes notable redshifts of core-excitation energies, whereas that of lone-pair nitrogen (H-acceptor) is slightly increased and results in appreciable blueshifts in the core-excitation bands. The result of the hydrogen-bonding interaction strongly appears in the n−σ* orbital correlation, destabilizing H−N donor Rydberg states in the direction opposite to the core-hole interaction, when excited N atom with H−N donor configuration strongly possesses the Rydberg component of anti-bonding σ* (N−H) character. Contributions of other cyclic H-bonded clusters (AM)n with n ≥ 3 to the spectral changes of the N 1s → 3sa1/3pe bands are also examined.
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36.40.Mr Spectroscopy and geometrical structure of clusters
33.15.Fm Bond strengths, dissociation energies
33.70.Jg Line and band widths, shapes, and shifts
33.15.Ta Mass spectra
33.20.Rm X-ray spectra
31.15.E- Density-functional theory
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation
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Influence of solute-solvent coordination on the orientational relaxation of ion assemblies in polar solvents

Minbiao Ji, Robert W. Hartsock, Zheng Sung, and Kelly J. Gaffney

J. Chem. Phys. 136, 014501 (2012); http://dx.doi.org/10.1063/1.3665140 (8 pages)

Online Publication Date: 3 January 2012

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We have investigated the rotational dynamics of lithium thiocyanate (LiNCS) dissolved in various polar solvents with time and polarization resolved vibrational spectroscopy. LiNCS forms multiple distinct ionic structures in solution that can be distinguished with the CN stretch vibrational frequency of the different ionic assemblies. By varying the solvent and the LiNCS concentration, the number and type of ionic structures present in solution can be controlled. Control of the ionic structure provides control over the volume, shape, and dipole moment of the solute, critical parameters for hydrodynamic and dielectric continuum models of friction. The use of solutes with sizes comparable to or smaller than the solvent molecules also helps amplify the sensitivity of the measurement to the short-ranged solute-solvent interaction. The measured orientational relaxation dynamics show many clear and distinct deviations from simple hydrodynamic behavior. All ionic structures in all solvents exhibit multi-exponential relaxation dynamics that do not scale with the solute volume. For Lewis base solvents such as benzonitrile, dimethyl carbonate, and ethyl acetate, the observed dynamics strongly show the effect of solute-solvent complex formation. For the weak Lewis base solvent nitromethane, we see no evidence for solute-solvent complex formation, but still see strong deviation from the predictions of simple hydrodynamic theory.
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82.30.Nr Association, addition, insertion, cluster formation
77.84.Jd Polymers; organic compounds
78.47.D- Time resolved spectroscopy (>1 psec)
63.20.-e Phonons in crystal lattices
77.22.Ej Polarization and depolarization
64.75.Bc Solubility

Theoretical study of the aqueous solvation of HgCl2: Monte Carlo simulations using second-order Moller-Plesset-derived flexible polarizable interaction potentials

J. Hernández-Cobos, A. Ramírez-Solís, L. Maron, and I. Ortega-Blake

J. Chem. Phys. 136, 014502 (2012); http://dx.doi.org/10.1063/1.3673780 (8 pages)

Online Publication Date: 3 January 2012

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A study of the solvation of HgCl2 including ab initio aggregates of up to 24 water molecules and the results of extensive Monte Carlo simulations for the liquid phase using MP2-derived interaction potentials is presented. The interaction potentials are flexible, polarizable, and include non-additive effects. We conclude that a cluster description of the solvation mechanism is limited when compared to the condensed phase. The molecular image derived from the MC simulations is peculiar. It resembles that of a hydrophobic solute, which explains the rather easy passage of this neutral molecule through the cell membrane; however, it also shows an intermittent binding of one, two, or three water molecules to HgCl2 in the fashion of a hydrophilic solute.
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82.30.Nr Association, addition, insertion, cluster formation
82.20.Wt Computational modeling; simulation
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Hf Product distribution
82.20.Fd Collision theories; trajectory models

Clusters dissolution of Yb3+ in codoped SiO2-Al2O3-P2O5 glass fiber and its relevance to photodarkening

T. Deschamps, N. Ollier, H. Vezin, and C. Gonnet

J. Chem. Phys. 136, 014503 (2012); http://dx.doi.org/10.1063/1.3673792 (4 pages)

Online Publication Date: 4 January 2012

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Using a combination of pulse electron paramagnetic resonance and photoluminescence spectroscopy, we demonstrate the major role of phosphorous rather than aluminium in the rare-earth dissolution process, an essential advance in telecommunication and solid laser fields. Our results also provide new insight into the micro-structural origin of the photodarkening process occurring in Yb doped fiber.
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78.55.Qr Amorphous materials; glasses and other disordered solids
76.30.Kg Rare-earth ions and impurities
61.43.Fs Glasses

Clusters in a mixture of an “amphiphilic” ionic liquid and a nonionic liquid: Theoretical study

Artem A. Aerov, Alexei R. Khokhlov, and Igor I. Potemkin

J. Chem. Phys. 136, 014504 (2012); http://dx.doi.org/10.1063/1.3670016 (12 pages)

Online Publication Date: 4 January 2012

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A Flory-Huggins type lattice approach is used to describe theoretically a heterogeneous mixture composed of an ionic liquid (IL) and a nonionic liquid (nIL). It is analyzed, how the behavior of the system depends on the difference in the affinities of the cations and the anions to the neutral molecules (i.e., on the “amphiphilicity” of the IL with respect to the nIL). It is proved that if the difference in the affinities is not large, two macrophases coexist in the mixture; if the difference exceeds a certain threshold value, the mixture becomes microheterogeneous: depending on its composition, it can turn either into ion clusters dispersed over the phase having low concentration of ions, or into clusters of neutral molecules dispersed over the phase having high concentration of ions. If the system is not close to the critical point, the ion clusters can be only small: the maximal ratio of their diameter to an ion diameter is of the order of ten; however, the clusters of nonionic molecules can be large, if the difference in the affinities has a certain value. It is predicted also that cavities can nucleate inside an IL, and clusters of ions can appear in a saturated vapor of an IL.
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61.20.Gy Theory and models of liquid structure
81.30.Dz Phase diagrams of other materials

Solute rotation in polar liquids: Microscopic basis for the Stokes-Einstein-Debye model

Amit Das, Ranjit Biswas, and J. Chakrabarti

J. Chem. Phys. 136, 014505 (2012); http://dx.doi.org/10.1063/1.3672508 (8 pages)

Online Publication Date: 4 January 2012

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Here, we develop a framework for a molecular level understanding of the celebrated Stokes-Einstein-Debye (SED) formula. In particular, we explore reasons behind the surprising success of the SED model in describing dipolar solute rotation in complex polar media. Relative importance of solvent viscosity and solute-solvent dipolar interaction is quantified via a self-consistent treatment for the total friction on a rotating solute where the hydrodynamic contribution is modified by the friction arising from the longer ranged solute-solvent dipolar interaction. Although the solute-solvent dipolar coupling is obtained via the Mori-Zwanzig formalism, the inclusion of solvent structure via the wave vector dependent viscosity in the hydrodynamic contribution incorporates solvent molecularity in the present theory. This approach satisfactorily describes the experimental rotation times measured using a dipolar solute, coumarin 153 (C153), in protic and aprotic polar liquids, and more importantly, provides microscopic explanation for insignificant contribution of electrical interactions on solute rotation, in contrast to the substantial role played by the translational dielectric friction in the context of ionic mobility. It is also discussed on how the present theory can be suitably extended to study the rotation of a realistic solute in media other than dipolar solvents.
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66.20.Cy Theory and modeling of viscosity and rheological properties, including computer simulation
77.22.Ch Permittivity (dielectric function)
72.20.Ee Mobility edges; hopping transport
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