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7 Dec 2011

Volume 135, Issue 21, Articles (21xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 135, 214501 (2011); http://dx.doi.org/10.1063/1.3652863 (4 pages)

Thomas Scheler, Olga Degtyareva, and Eugene Gregoryanz
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back to top Theoretical Methods and Algorithms
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Coarse-graining entropy, forces, and structures

Joseph F. Rudzinski and W. G. Noid

J. Chem. Phys. 135, 214101 (2011); http://dx.doi.org/10.1063/1.3663709 (15 pages) | Cited 1 time

Online Publication Date: 2 December 2011

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Coarse-grained (CG) models enable highly efficient simulations of complex processes that cannot be effectively studied with more detailed models. CG models are often parameterized using either force- or structure-motivated approaches. The present work investigates parallels between these seemingly divergent approaches by examining the relative entropy and multiscale coarse-graining (MS-CG) methods. We demonstrate that both approaches can be expressed in terms of an information function that discriminates between the ensembles generated by atomistic and CG models. While it is well known that the relative entropy approach minimizes the average of this information function, the present work demonstrates that the MS-CG method minimizes the average of its gradient squared. We generalize previous results by establishing conditions for the uniqueness of structure-based potentials and identify similarities with corresponding conditions for the uniqueness of MS-CG potentials. We analyze the mapping entropy and extend the MS-CG and generalized-Yvon-Born-Green formalisms for more complex potentials. Finally, we present numerical calculations that highlight similarities and differences between structure- and force-based approaches. We demonstrate that both methods obtain identical results, not only for a complete basis set, but also for an incomplete harmonic basis set in Cartesian coordinates. However, the two methods differ when the incomplete basis set includes higher order polynomials of Cartesian coordinates or is expressed as functions of curvilinear coordinates.
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31.15.-p Calculations and mathematical techniques in atomic and molecular physics
02.10.De Algebraic structures and number theory
05.70.Ce Thermodynamic functions and equations of state

Efficient and accurate local single reference correlation methods for high-spin open-shell molecules using pair natural orbitals

Andreas Hansen, Dimitrios G. Liakos, and Frank Neese

J. Chem. Phys. 135, 214102 (2011); http://dx.doi.org/10.1063/1.3663855 (20 pages) | Cited 1 time

Online Publication Date: 2 December 2011

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A production level implementation of the high-spin open-shell (spin unrestricted) single reference coupled pair, quadratic configuration interaction and coupled cluster methods with up to doubly excited determinants in the framework of the local pair natural orbital (LPNO) concept is reported. This work is an extension of the closed-shell LPNO methods developed earlier [F. Neese, F. Wennmohs, and A. Hansen, J. Chem. Phys. 130, 114108 (2009)10.1063/1.3086717; F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys. 131, 064103 (2009)10.1063/1.3173827]. The internal space is spanned by localized orbitals, while the external space for each electron pair is represented by a truncated PNO expansion. The laborious integral transformation associated with the large number of PNOs becomes feasible through the extensive use of density fitting (resolution of the identity (RI)) techniques. Technical complications arising for the open-shell case and the use of quasi-restricted orbitals for the construction of the reference determinant are discussed in detail. As in the closed-shell case, only three cutoff parameters control the average number of PNOs per electron pair, the size of the significant pair list, and the number of contributing auxiliary basis functions per PNO. The chosen threshold default values ensure robustness and the results of the parent canonical methods are reproduced to high accuracy. Comprehensive numerical tests on absolute and relative energies as well as timings consistently show that the outstanding performance of the LPNO methods carries over to the open-shell case with minor modifications. Finally, hyperfine couplings calculated with the variational LPNO-CEPA/1 method, for which a well-defined expectation value type density exists, indicate the great potential of the LPNO approach for the efficient calculation of molecular properties.
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31.15.V- Electron correlation calculations for atoms, ions and molecules
31.30.Gs Hyperfine interactions and isotope effects
33.15.Pw Fine and hyperfine structure
31.15.bw Coupled-cluster theory
31.15.E- Density-functional theory

A pseudopotential-based composite method: The relativistic pseudopotential correlation consistent composite approach for molecules containing 4d transition metals (Y–Cd)

Marie L. Laury, Nathan J. DeYonker, Wanyi Jiang, and Angela K. Wilson

J. Chem. Phys. 135, 214103 (2011); http://dx.doi.org/10.1063/1.3662415 (10 pages)

Online Publication Date: 5 December 2011

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The correlation consistent composite approach (ccCA) has proven to be an effective first-principles-based composite approach for main group and first-row transition metal species. By combining relativistic pseudopotentials and ccCA, accurate energetic and thermodynamic data for heavier elements, including transition metals, is obtainable. Relativistic pseudopotential ccCA (rp-ccCA) was formulated and tested on 25 molecules from the G3/05 set that contain 4p elements (Ga-Kr). A 32.5% time savings was obtained using rp-ccCA, relative to ccCA employing all-electron basis sets. When implementing rp-ccCA to compute dissociation energies and enthalpies of formation for molecules from the 4p block, rp-ccCA results in a mean absolute deviation of 0.89 kcal mol−1 from experimental data. rp-ccCA was also applied to a set of 30 4d transition metal-containing molecules, ranging from diatomics to Mo(CO)6, and enthalpies of formation for these species were obtained with a mean absolute deviation of 2.89 kcal mol−1 in comparison to experimental data. Based on quality of the experimentally available enthalpies of formation, where the average value of reported experimental error bars is 3.43 kcal mol−1, rp-ccCA is within transition metal chemical accuracy for the 4d molecule set. rp-ccCA is a pseudopotential-based composite method for transition metals and is shown to yield accurate thermodynamic results for molecules containing heavy elements Ga–Kr and Y–Cd.
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31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
33.15.Fm Bond strengths, dissociation energies

Accurate variational calculations of the ground 2Po(1s22s22p) and excited 2S(1s22s2p2) and 2Po(1s22s23p) states of singly ionized carbon atom

Sergiy Bubin and Ludwik Adamowicz

J. Chem. Phys. 135, 214104 (2011); http://dx.doi.org/10.1063/1.3664900 (4 pages)

Online Publication Date: 5 December 2011

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In this article we report accurate nonrelativistic variational calculations of the ground and two excited states of C+ ion. We employ extended and well optimized basis sets of all-electron explicitly correlated Gaussians to represent the wave functions of the states. The optimization of the basis functions is performed with a procedure employing the analytic gradient of the energy with respect to the nonlinear parameters of the Gaussians. The calculations explicitly include the effects due to the finite nuclear mass. The calculated transition energies between the three states are compared to the experimentally derived values. Finally, we present expectation values of some small positive and negative powers of the interparticle distances and contact densities.
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31.15.xt Variational techniques
31.15.ve Electron correlation calculations for atoms and ions: ground state
31.15.vj Electron correlation calculations for atoms and ions: excited states

SF-[2]R12: A spin-adapted explicitly correlated method applicable to arbitrary electronic states

Liguo Kong and Edward F. Valeev

J. Chem. Phys. 135, 214105 (2011); http://dx.doi.org/10.1063/1.3664729 (7 pages)

Online Publication Date: 5 December 2011

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The [2]R12 method [M. Torheyden and E. F. Valeev, J. Chem. Phys. 131, 171103 (2009)10.1063/1.3254836] is an explicitly correlated perturbative correction that can greatly reduce the basis set error of an arbitrary electronic structure method for which the two-electron density matrix is available. Here we present a spin-adapted variant (denoted as SF-[2]R12) that is formulated completely in terms of spin-free quantities. A spin-free cumulant decomposition and multi-reference generalized Brillouin condition are used to avoid three-particle reduced density matrix completely. The computational complexity of SF-[2]R12 is proportional to the sixth power of the system size and is comparable to the cost of the single-reference MP2-R12 method. The SF-[2]R12 method is shown to decrease greatly the basis set error of multi-configurational wave functions.
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31.15.xp Perturbation theory

Local pair natural orbitals for excited states

Benjamin Helmich and Christof Hättig

J. Chem. Phys. 135, 214106 (2011); http://dx.doi.org/10.1063/1.3664902 (11 pages)

Online Publication Date: 6 December 2011

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We explore how in response calculations for excitation energies with wavefunction based (e.g., coupled cluster) methods the number of double excitation amplitudes can be reduced by means of truncated pair natural orbital (PNO) expansions and localized occupied orbitals. Using the CIS(D) approximation as a test model, we find that the number of double excitation amplitudes can be reduced dramatically with minor impact on the accuracy if the excited state wavefunction is expanded in state-specific PNOs generated from an approximate first-order guess wavefunction. As for ground states, the PNO truncation error can also for excitation energies be controlled by a single threshold related to generalized natural occupation numbers. The best performance is found with occupied orbitals which are localized by the Pipek-Mezey localization. For a large test set of excited states we find with this localization that already a PNO threshold of 10−8–10−7, corresponding to an average of only 40–80 PNOs per pair, is sufficient to keep the PNO truncation error for vertical excitation energies below 0.01 eV. This is a significantly more rapid convergence with the number doubles amplitudes than in domain-based local response approaches. We demonstrate that the number of significant excited state PNOs scales asymptotically linearly with the system size in the worst case of completely delocalized excitations and sub-linearly whenever the chromophore does not increase with the system size. Moreover, we observe that the flexibility of state-specific PNOs to adapt to the character of an excitation allows for an almost unbiased treatment of local, delocalized and charge transfer excited states.
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31.15.am Relativistic configuration interaction (CI) and many-body perturbation calculations
31.15.bw Coupled-cluster theory
31.15.ve Electron correlation calculations for atoms and ions: ground state
31.15.vj Electron correlation calculations for atoms and ions: excited states
34.70.+e Charge transfer

Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups

Arvid Conrad Ihrig, Christoph Schiffmann, and Daniel Sebastiani

J. Chem. Phys. 135, 214107 (2011); http://dx.doi.org/10.1063/1.3664300 (7 pages)

Online Publication Date: 6 December 2011

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We present a series of capping-potentials designed as link atoms to saturate dangling bonds at the quantum/classical interface within density functional theory-based hybrid QM/MM calculations. We aim at imitating the properties of different carbon-carbon bonds by means of monovalent analytic pseudopotentials. These effective potentials are optimized such that the perturbations of the quantum electronic density are minimized. This optimization is based on a stochastic scheme, which helps to avoid local minima trapping. For a series of common biomolecular groups, we find capping-potentials that outperform the more common hydrogen-capping in view of structural and spectroscopic properties. To demonstrate the transferability to complex systems, we also benchmark our potentials with a hydrogen-bonded dimer, yielding systematic improvements in structural and spectroscopic parameters.
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87.15.B- Structure of biomolecules
36.20.Hb Configuration (bonds, dimensions)
02.50.Ey Stochastic processes
87.15.Fh Bonding; mechanisms of bond breakage
87.15.M- Spectra of biomolecules

Fighting the curse of dimensionality in first-principles semiclassical calculations: Non-local reference states for large number of dimensions

Michele Ceotto, Gian Franco Tantardini, and Alán Aspuru-Guzik

J. Chem. Phys. 135, 214108 (2011); http://dx.doi.org/10.1063/1.3664731 (11 pages)

Online Publication Date: 6 December 2011

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Semiclassical methods face numerical challenges as the dimensionality of the system increases. In the general context of the theory of differential equations, this is known as the “curse of dimensionality.” In the present manuscript, we apply the recently-introduced multi-coherent states semiclassical initial value representation (MC-SC-IVR) approach to extend the applicability of first-principles semiclassical calculations. The proposed strategy involves the use of non-local coherent states with the goal of increasing accuracy in the Fourier transforms, and on the other hand, allows for the selection of peaks of different frequencies. The ability to filter desired peaks is important for analyzing the power spectra of complex systems. The MC-SC-IVR approach allows us to solve a 19-dimensional test system and to resolve on-the-fly the power spectra of the formaldehyde molecule with very few classical trajectories.
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31.15.ae Electronic structure and bonding characteristics

Calculation of chemical potentials of chain molecules by the incremental gauge cell method

Christopher J. Rasmussen, Aleksey Vishnyakov, and Alexander V. Neimark

J. Chem. Phys. 135, 214109 (2011); http://dx.doi.org/10.1063/1.3657438 (14 pages)

Online Publication Date: 6 December 2011

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The gauge cell Monte Carlo method is extended to calculations of the incremental chemical potentials and free energies of linear chain molecules. The method was applied to chains of Lennard-Jones beads with stiff harmonic bonds up to 500 monomers in length. We show that the suggested method quantitatively reproduces the modified Widom particle insertion method of Kumar et al. [S. K. Kumar, I. Szleifer, and A. Z. Panagiotopoulos, Phys. Rev. Lett. 66(22), 2935 (1991)]10.1103/PhysRevLett.66.2935, and is by an order of magnitude more efficient for long chains in terms of the computational time required for the same accuracy of chemical potential calculations. The chain increment ansatz, which suggests that the incremental chemical potential is independent of the chain length, was tested at different temperatures. We confirmed that the ansatz holds only for coils above the θ temperature. Special attention is paid to the effects of the magnitude of adsorption potential and temperature on the behavior of single chains in confinements that are comparable in size with the free chain radius of gyration. At sufficiently low temperatures, the dependence of the incremental chemical potential on the chain length in wetting pores is superficially similar to a capillary condensation isotherm, reflecting monolayer formation following by pore volume filling, as the chain length increases. We find that the incremental gauge cell method is an accurate and efficient technique for calculations of the free energies of chain molecules in bulk systems and nanoconfinements alike. The suggested method may find practical applications, such as modeling polymer partitioning on porous substrates and dynamics of chain translocation into nanopores.
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36.20.Fz Constitution (chains and sequences)
36.20.Hb Configuration (bonds, dimensions)
31.15.-p Calculations and mathematical techniques in atomic and molecular physics
33.15.Fm Bond strengths, dissociation energies
34.20.-b Interatomic and intermolecular potentials and forces, potential energy surfaces for collisions
36.20.Ey Conformation (statistics and dynamics)
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A data-integrated method for analyzing stochastic biochemical networks

Michael W. Chevalier and Hana El-Samad

J. Chem. Phys. 135, 214110 (2011); http://dx.doi.org/10.1063/1.3664126 (11 pages)

Online Publication Date: 7 December 2011

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Variability and fluctuations among genetically identical cells under uniform experimental conditions stem from the stochastic nature of biochemical reactions. Understanding network function for endogenous biological systems or designing robust synthetic genetic circuits requires accounting for and analyzing this variability. Stochasticity in biological networks is usually represented using a continuous-time discrete-state Markov formalism, where the chemical master equation (CME) and its kinetic Monte Carlo equivalent, the stochastic simulation algorithm (SSA), are used. These two representations are computationally intractable for many realistic biological problems. Fitting parameters in the context of these stochastic models is particularly challenging and has not been accomplished for any but very simple systems. In this work, we propose that moment equations derived from the CME, when treated appropriately in terms of higher order moment contributions, represent a computationally efficient framework for estimating the kinetic rate constants of stochastic network models and subsequent analysis of their dynamics. To do so, we present a practical data-derived moment closure method for these equations. In contrast to previous work, this method does not rely on any assumptions about the shape of the stochastic distributions or a functional relationship among their moments. We use this method to analyze a stochastic model of a biological oscillator and demonstrate its accuracy through excellent agreement with CME/SSA calculations. By coupling this moment-closure method with a parameter search procedure, we further demonstrate how a model's kinetic parameters can be iteratively determined in order to fit measured distribution data.
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87.15.R- Reactions and kinetics
87.15.ak Monte Carlo simulations
82.20.Uv Stochastic theories of rate constants
87.16.af Monte Carlo calculations
02.50.Ga Markov processes

Thinking outside the box: The uniform electron gas on a hypersphere

Pierre-François Loos and Peter M. W. Gill

J. Chem. Phys. 135, 214111 (2011); http://dx.doi.org/10.1063/1.3665393 (5 pages)

Online Publication Date: 7 December 2011

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We discuss alternative homogeneous electron gas systems in which a finite number n of electrons are confined to a D-dimensional sphere. We derive the first few terms of the high-density (rs → 0, where rs is the Seitz radius) energy expansions for these systems and show that, in the thermodynamic limit (n → ∞), these terms become identical to those of D-dimensional jellium.
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71.10.Ca Electron gas, Fermi gas
71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)
back to top Advanced Experimental Techniques

Structural dynamics of surfaces by ultrafast electron crystallography: Experimental and multiple scattering theory

Sascha Schäfer, Wenxi Liang, and Ahmed H. Zewail

J. Chem. Phys. 135, 214201 (2011); http://dx.doi.org/10.1063/1.3663963 (15 pages)

Online Publication Date: 2 December 2011

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Recent studies in ultrafast electron crystallography (UEC) using a reflection diffraction geometry have enabled the investigation of a wide range of phenomena on the femtosecond and picosecond time scales. In all these studies, the analysis of the diffraction patterns and their temporal change after excitation was performed within the kinematical scattering theory. In this contribution, we address the question, to what extent dynamical scattering effects have to be included in order to obtain quantitative information about structural dynamics. We discuss different scattering regimes and provide diffraction maps that describe all essential features of scatterings and observables. The effects are quantified by dynamical scattering simulations and examined by direct comparison to the results of ultrafast electron diffraction experiments on an in situ prepared Ni(100) surface, for which structural dynamics can be well described by a two-temperature model. We also report calculations for graphite surfaces. The theoretical framework provided here allows for further UEC studies of surfaces especially at larger penetration depths and for those of heavy-atom materials.
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68.35.B- Structure of clean surfaces (and surface reconstruction)
68.35.bp Fullerenes

Multistage Zeeman deceleration of metastable neon

Alex W. Wiederkehr, Michael Motsch, Stephen D. Hogan, Markus Andrist, Hansjürg Schmutz, Bruno Lambillotte, Josef A. Agner, and Frédéric Merkt

J. Chem. Phys. 135, 214202 (2011); http://dx.doi.org/10.1063/1.3662141 (14 pages)

Online Publication Date: 5 December 2011

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A supersonic beam of metastable neon atoms has been decelerated by exploiting the interaction between the magnetic moment of the atoms and time-dependent inhomogeneous magnetic fields in a multistage Zeeman decelerator. Using 91 deceleration solenoids, the atoms were decelerated from an initial velocity of 580 m/s to final velocities as low as 105 m/s, corresponding to a removal of more than 95% of their initial kinetic energy. The phase-space distribution of the cold, decelerated atoms was characterized by time-of-flight and imaging measurements, from which a temperature of 10 mK was obtained in the moving frame of the decelerated sample. In combination with particle-trajectory simulations, these measurements allowed the phase-space acceptance of the decelerator to be quantified. The degree of isotope separation that can be achieved by multistage Zeeman deceleration was also studied by performing experiments with pulse sequences generated for 20Ne and 22Ne.
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32.60.+i Zeeman and Stark effects
32.80.-t Photoionization and excitation
32.10.Bi Atomic masses, mass spectra, abundances, and isotopes
32.30.-r Atomic spectra
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Effect of microhydration on the guanidinium⋯benzene interaction

Enrique M. Cabaleiro-Lago, Jesús Rodríguez-Otero, and Ángeles Peña-Gallego

J. Chem. Phys. 135, 214301 (2011); http://dx.doi.org/10.1063/1.3663277 (9 pages)

Online Publication Date: 1 December 2011

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The effect of microhydration on the interaction of guanidinium cation with benzene has been studied by employing ab initio calculations. Four different structural arrangements were considered for the guanidinium⋯benzene interaction to which up to six water molecules were added. T-shaped structures are usually the most stable, but as water molecules are included the energy differences with the parallel structures decrease, reaching a point where parallel complexes are even more stable than T-shaped ones. Therefore, the inclusion of water molecules promotes a change in the structure of the cation⋯π contact. The analysis reveals that these stability changes are more related with the structure of the hydrating water molecules than to a modulation of the cation⋯π interaction. Already with three water molecules, one water molecule in the T-shaped complex has to be located in the second solvation shell, whereas in parallel structures this occurs with four water molecules. As a consequence energy differences among structures decrease. The calculations show that the nature of the interaction is almost unaffected in T-shaped structures, whereas an important dispersion increment is observed in parallel ones, though its overall effect is small.
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82.30.Nr Association, addition, insertion, cluster formation
31.15.bw Coupled-cluster theory
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
34.20.Gj Intermolecular and atom-molecule potentials and forces
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.A- Ab initio calculations

Influence of higher-order dispersion coefficients on near-threshold bound and continuum states: Application to 88Sr2

Alexander Kaiser, Tim-Oliver Müller, and Harald Friedrich

J. Chem. Phys. 135, 214302 (2011); http://dx.doi.org/10.1063/1.3664311 (8 pages)

Online Publication Date: 2 December 2011

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We give a simple description of quantum states near the dissociation threshold of deep interatomic potentials. The influence of the potential tail is separated from effects due to the interaction at short distances. We present a general formalism which is valid for weakly bound and low-energy continuum states, both for vanishing and non-vanishing angular momentum. Its applicability is demonstrated for the example of the electronic ground state of the strontium dimer 88Sr2. With an appropriate choice of the potential tail that includes higher-order dispersion coefficients, all short-range effects are incorporated via the threshold quantum number vD and one further parameter accounting for residual short-range effects.
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03.65.Ge Solutions of wave equations: bound states
33.15.Fm Bond strengths, dissociation energies

Vibrational frequencies and spectroscopic constants from quartic force fields for cis-HOCO: The radical and the anion

Ryan C. Fortenberry, Xinchuan Huang, Joseph S. Francisco, T. Daniel Crawford, and Timothy J. Lee

J. Chem. Phys. 135, 214303 (2011); http://dx.doi.org/10.1063/1.3663615 (10 pages) | Cited 1 time

Online Publication Date: 2 December 2011

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The use of accurate quartic force fields together with vibrational configuration interaction recently predicted gas phase fundamental vibrational frequencies of the trans-HOCO radical to within 4 cm−1 of experimental results for the two highest frequency modes. Utilizing the same approach, we are providing a full list of fundamental vibrational frequencies and spectroscopic constants for the cis-HOCO system in both radical and anionic forms. Our predicted geometrical parameters of the cis-HOCO radical match experiment and previous computation to better than 1% deviation, and previous theoretical work agrees equally well for the anion. Correspondence between vibrational perturbation theory and variational vibrational configuration interaction for prediction of the frequencies of each mode is strong, better than 5 cm−1, except for the torsional motion, similar to what has been previously identified in the trans-HOCO radical. Among other considerations, our results are immediately applicable to dissociative photodetachment experiments which initially draw on the cis-HOCO anion since it is the most stable conformer of the anion and is used to gain insight into the portion of the OH + CO potential surface where the HOCO radical is believed to form, and we are also providing highly accurate electron binding energies relevant to these experiments.
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33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.80.Eh Autoionization, photoionization, and photodetachment
31.15.xp Perturbation theory
31.15.xt Variational techniques
33.15.Bh General molecular conformation and symmetry; stereochemistry

The electronic spectrum of SiH4: Jahn-Teller Rydberg series

A. M. Velasco, C. Lavín, A. M. J. Sánchez de Merás, and J. Sánchez Marín

J. Chem. Phys. 135, 214304 (2011); http://dx.doi.org/10.1063/1.3664629 (5 pages)

Online Publication Date: 2 December 2011

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The aim of the present theoretical work is to provide data necessary for a better understanding of the electronic spectrum of the silane molecule, which is affected by the Jahn-Teller effect. By selecting an adequate distorted C2v geometry of SiH4, the three lower Koopmans ionization potentials are evaluated with the equation of motion coupled cluster of singles and doubles method. Vertical excitation energies for the different Rydberg series converging to the three Jahn-Teller components are inferred from ab initio coupled cluster linear response calculations. Absorption oscillator strengths for dipole-allowed electronic transitions are also determined with the molecular-adapted quantum defect orbital methodology. Predictions of new spectroscopic data on SiH4 are reported.
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34.80.-i Electron and positron scattering
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.ag Excitation energies and lifetimes; oscillator strengths

Confirmed assignments of isomeric dimethylbenzyl radicals generated by corona discharge

Young Wook Yoon and Sang Kuk Lee

J. Chem. Phys. 135, 214305 (2011); http://dx.doi.org/10.1063/1.3663962 (6 pages) | Cited 1 time

Online Publication Date: 2 December 2011

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The controversial vibronic assignments of isomeric dimethylbenzyl radicals were clearly resolved by using different precursors. By employing corresponding dimethylbenzyl chlorides as precursors, we identified the origins of the vibronic bands of the dimethylbenzyl radicals generated by corona discharge of 1,2,4-trimethylbenzene. From the analysis of the spectra observed from the dimethylbenzyl chlorides in a corona excited supersonic expansion, we revised previous assignments of the 3,4-, 2,4-, and 2,5-dimethylbenzyl radicals. Spectroscopic data of electronic transition and vibrational mode frequencies in the ground electronic state of each isomer were accurately determined by comparing them with those obtained by an ab initio calculation and with the known vibrational data of 1,2,4-trimethylbenzene.
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82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
31.15.A- Ab initio calculations
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions

Heavy atom nitroxyl radicals. V. An experimental and ab initio study of the previously unknown H2PS free radical

Robert A. Grimminger, Dennis J. Clouthier, and Riccardo Tarroni

J. Chem. Phys. 135, 214306 (2011); http://dx.doi.org/10.1063/1.3662416 (8 pages)

Online Publication Date: 5 December 2011

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The math2A′−math2A′ transition of the prototypical thiophosphoryl radical, H2PS, was observed for the first time using laser-induced fluorescence and single vibronic level emission spectroscopy. H2PS and its deuterated isotopologues, D2PS and HDPS, were produced in a pulsed supersonic discharge jet from a precursor mixture of Cl3PS and H2 or D2 or an H2/D2 mixture in high-pressure argon. High level ab initio calculations of the lowest three doublet electronic states helped in the definitive assignment of the math−math transition, which involves electron promotion from the π to the π* orbital. Vibrational frequencies were determined for several modes of each isotopologue in the math and math states and found to be in accord with theoretical predictions. Although a line-by-line rotational analysis was not possible, the observed band contours are consistent with the geometries obtained from our ab initio calculations. Theory indicates that PS bond length increases upon electronic excitation, while the pyramidalization of the radical does not change significantly.
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31.15.ae Electronic structure and bonding characteristics
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Dj Interatomic distances and angles
33.20.Tp Vibrational analysis
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
33.50.Dq Fluorescence and phosphorescence spectra

Heavy atom nitroxyl radicals. VI. The electronic spectrum of jet-cooled H2PO, the prototypical phosphoryl free radical

Mohammed A. Gharaibeh, Dennis J. Clouthier, and Riccardo Tarroni

J. Chem. Phys. 135, 214307 (2011); http://dx.doi.org/10.1063/1.3664903 (10 pages)

Online Publication Date: 5 December 2011

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The previously unknown electronic spectrum of the H2PO free radical has been identified in the 407–337 nm region using a combination of laser-induced fluorescence and single vibronic level emission spectroscopy. High level ab initio predictions of the properties of the ground and first two excited doublet states were used to identify the spectral region in which to search for the electronic transition and were used to aid in the analysis of the data. The band system is assigned as the math2A′−math2A′ electronic transition which involves promotion of an electron from the π to the π* molecular orbital. The excited state r0 molecular structure was determined by rotational analysis of high resolution LIF spectra to be r(PO) = 1.6710(2) Å, r(PH) = 1.4280(6) Å, θ(HPO) = 105.68(7)°, θ(HPH) = 93.3(2)°, and the out-of-plane angle = 66.8(2)°. The structural changes on electronic excitation, which include substantial increases in the PO bond length and out-of-plane angle, are as expected based on molecular orbital theory and our previous studies of the isoelectronic H2AsO, Cl2PS, and F2PS free radicals.
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33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Sn Rotational analysis
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
33.50.Dq Fluorescence and phosphorescence spectra
31.15.ae Electronic structure and bonding characteristics
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Dj Interatomic distances and angles

Studies on the structure, stability, and spectral signatures of hydride ion-water clusters

M. Prakash, K. Gopalsamy, and V. Subramanian

J. Chem. Phys. 135, 214308 (2011); http://dx.doi.org/10.1063/1.3663708 (18 pages)

Online Publication Date: 5 December 2011

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The gas-phase structure, stability, spectra, and electron density topography of H−Wn clusters (where n = 1−8) have been calculated using coupled-cluster CCSD(T) and Møller-Plesset second-order perturbation (MP2) theory combined with complete basis set (CBS) approaches. The performance of various density functional theory (DFT) based methods such as B3LYP, M05-2X, M06, M06-L, and M06-2X using 6-311++G(d,p), and aug-cc-pVXZ (aVXZ, where X = D, T, and Q) basis sets has also been assessed by considering values calculated using CCSD(T)/CBS limit as reference. The performance of the functionals has been ranked based on the mean signed/unsigned error. The comparison of geometrical parameters elicits that the geometrical parameters predicted by B3LYP/aVTZ method are in good agreement with those values obtained at MP2/aVTZ level of theory. Results show that M05-2X functional outperform other functionals in predicting the energetics when compared to CCSD(T)/CBS value. On the other hand, values predicted by M06-2X, and M06 methods, are closer to those values obtained from MP2/CBS approach. It is evident from the calculations that H−Wn (where n = 5–8) clusters adopt several interesting structural motifs such as pyramidal, prism, book, Clessidra, cubic, cage, and bag. The important role played by ion-water (O–H⋅⋅⋅H−) and water-water (O–H⋅⋅⋅O) interactions in determining the stability of the clusters has also been observed. Analysis of the results indicates that the most stable cluster is made up of minimum number of O–H⋅⋅⋅H− interaction in conjugation with the maximum number of O–H⋅⋅⋅O interactions. The Bader theory of atoms in molecules (AIM) and natural bond orbital (NBO) analyses has also been carried out to characterize the nature of interactions between hydride ion and water molecules. It can be observed from the vibrational spectra of H−Wn clusters, the stretching frequencies involving ion-water interaction always exhibit larger redshift and intensities than that of water-water (inter solvent) interactions.
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36.40.Mr Spectroscopy and geometrical structure of clusters
31.15.E- Density-functional theory
31.15.xp Perturbation theory
32.70.Jz Line shapes, widths, and shifts
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.70.Jg Line and band widths, shapes, and shifts

Dissociative electron attachment to triflates

Sylwia Ptasińska, David Gschliesser, Peter Bartl, Ireneusz Janik, Paul Scheier, and Stephan Denifl

J. Chem. Phys. 135, 214309 (2011); http://dx.doi.org/10.1063/1.3664784 (6 pages)

Online Publication Date: 5 December 2011

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Gas phase studies of dissociative electron attachment to simple alkyl (CF3SO3CH3) and aryl (C6H5SO3CF3 and CF3SO3C6H4CH3) triflates, model molecules of nonionic photoacid generators for modern lithographic applications, were performed. The fragmentation pathways under electron impact below 10 eV were identified by means of crossed electron-molecular beam mass spectrometry. Major dissociation channels involved C–O, S–O, or C–S bond scissions in the triflate moiety leading to the formation of triflate (OTf−), triflyl (Tf−), or sulfonate (RSO3−) anions, respectively. A resonance leading to C–O bond breakage and OTf− formation in alkyl triflates occurred at electron energies about 0.5 eV lower than the corresponding resonance in aryl triflates. A resonance leading to S–O bond breakage and Tf− formation in aryl triflates occurred surprisingly at the same electron energies as C–O bond breakage. In case of alkyl triflates S–O bond breakage required 1.4 eV higher electron energies to occur and proceeded with substantially lower yields than in aryl triflates. C–S bond scission occurred for all presently studied triflates at energies close to 3 eV.
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34.80.Ht Dissociation and dissociative attachment
33.15.Ta Mass spectra

Competitive ionization processes of anthracene excited with a femtosecond pulse in the multi-photon ionization regime

M. Goto and K. Hansen

J. Chem. Phys. 135, 214310 (2011); http://dx.doi.org/10.1063/1.3663618 (6 pages)

Online Publication Date: 6 December 2011

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To clarify the ionization mechanism of large molecules under multi-photon ionization conditions, photo-electron spectroscopic studies on anthracene have been performed with electron imaging technique. Electron kinetic energy distributions below a few eV reveal that three kinds of ionization channels coexist, viz., vertical ionization, ionization from Rydberg states, and thermionic hot electron emission. Their relative yield is determined by the characteristic of the laser pulse. The duration in particular influences the ratio between the first two processes, while for higher intensities the last process dominates. Our results provide strong evidence that internal conversion plays an important role for the ionization of the molecule.
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33.80.Eh Autoionization, photoionization, and photodetachment
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
32.80.Ee Rydberg states
33.60.+q Photoelectron spectra
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

On the effects of high temperature and high pressure on the hydrogen solubility in rhenium

Thomas Scheler, Olga Degtyareva, and Eugene Gregoryanz

J. Chem. Phys. 135, 214501 (2011); http://dx.doi.org/10.1063/1.3652863 (4 pages)

Online Publication Date: 1 December 2011

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In situ x-ray diffraction experiments on rhenium hydride compressed up to 46 GPa reveal a hydrogen solubility (x) significantly larger than the previously assumed saturation limit of x ∼ 0.38(4). In the layered anti-CdI2-type structure of rhenium hydride, the hydrogen solubility was found to increase to x ∼ 0.5 at 15 GPa over time. When heated to temperatures above 420 K at pressures above 23 GPa, rhenium hydride undergoes an isomorphous phase transition into the NiAs-type structure accompanied by an increase in hydrogen solubility to x ∼ 0.85. The formation of fully stoichiometric rhenium hydride is discussed.
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61.50.Ks Crystallographic aspects of phase transformations; pressure effects
64.70.K- Solid-solid transitions
62.50.-p High-pressure effects in solids and liquids
81.40.Gh Other heat and thermomechanical treatments
81.30.Hd Constant-composition solid-solid phase transformations: polymorphic, massive, and order-disorder
64.75.Bc Solubility

Topological origin of stretched exponential relaxation in glass

Marcel Potuzak, Roger C. Welch, and John C. Mauro

J. Chem. Phys. 135, 214502 (2011); http://dx.doi.org/10.1063/1.3664744 (7 pages)

Online Publication Date: 1 December 2011

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The physical origin of stretched exponential relaxation is considered by many as one of the oldest unsolved problems in science. The functional form for stretched exponential relaxation can be deduced from the axiomatic diffusion-trap model of Phillips. The model predicts a topological origin for the dimensionless stretching exponent, with two “magic” values emerging: β = 3/5 arising from short-range molecular relaxation pathways and β = 3/7 for relaxation dominated by longer-range interactions. In this paper, we report experimental confirmation of these values using microscopically homogeneous silicate glass specimens. Our results reveal a bifurcation of the stretching exponent, with β = 3/5 for stress relaxation and β = 3/7 for structural relaxation, both on macroscopic length scales. These results point to two fundamentally different mechanisms governing stress relaxation versus structural relaxation, corresponding to different effective dimensionalities in configuration space during the relaxation process.
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61.43.Fs Glasses
62.40.+i Anelasticity, internal friction, stress relaxation, and mechanical resonances
81.40.Jj Elasticity and anelasticity, stress-strain relations
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