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28 May 2012

Volume 136, Issue 20 (partial)

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J. Chem. Phys. 136, 204301 (2012); http://dx.doi.org/10.1063/1.4714347 (9 pages)

Peter Botschwina and Rainer Oswald
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back to top Theoretical Methods and Algorithms

Many-body calculations of low-energy eigenstates in magnetic and periodic systems with self-healing diffusion Monte Carlo: Steps beyond the fixed phase

Fernando Agustín Reboredo

J. Chem. Phys. 136, 204101 (2012); http://dx.doi.org/10.1063/1.4711023 (16 pages)

Online Publication Date: 22 May 2012

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The self-healing diffusion Monte Carlo algorithm (SHDMC) [F. A. Reboredo, R. Q. Hood, and P. R. C. Kent, Phys. Rev. B 79, 195117 (2009);10.1103/PhysRevB.79.195117 F. A. Reboredo, Phys. Rev. B 80, 125110 (2009)10.1103/PhysRevB.80.125110] is extended to study the ground and excited states of magnetic and periodic systems. The method converges to exact eigenstates as the statistical data collected increase if the wave function is sufficiently flexible. It is shown that the dimensionality of the nodal surface is dependent on whether phase is a scalar function or not. A recursive optimization algorithm is derived from the time evolution of the mixed probability density, which is given by an ensemble of electronic configurations (walkers) with complex weight. This complex weight allows the phase of the fixed-node wave function to move away from the trial wave function phase. This novel approach is both a generalization of SHDMC and the fixed-phase approximation [G. Ortiz, D. M. Ceperley, and R. M. Martin, Phys Rev. Lett. 71, 2777 (1993)10.1103/PhysRevLett.71.2777]. When used recursively it simultaneously improves the node and the phase. The algorithm is demonstrated to converge to nearly exact solutions of model systems with periodic boundary conditions or applied magnetic fields. The computational cost is proportional to the number of independent degrees of freedom of the phase. The method is applied to obtain low-energy excitations of Hamiltonians with magnetic field. Periodic boundary conditions are also considered optimizing wave functions with twisted boundary conditions which are included in a many-body Bloch phase. The potential applications of this new method to study periodic, magnetic, and complex Hamiltonians are discussed.
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02.70.Ss Quantum Monte Carlo methods
02.10.Ud Linear algebra
02.50.-r Probability theory, stochastic processes, and statistics

Phase diagram and universality of the Lennard-Jones gas-liquid system

Hiroshi Watanabe, Nobuyasu Ito, and Chin-Kun Hu

J. Chem. Phys. 136, 204102 (2012); http://dx.doi.org/10.1063/1.4720089 (7 pages)

Online Publication Date: 23 May 2012

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The gas-liquid phase transition of the three-dimensional Lennard-Jones particles system is studied by molecular dynamics simulations. The gas and liquid densities in the coexisting state are determined with high accuracy. The critical point is determined by the block density analysis of the Binder parameter with the aid of the law of rectilinear diameter. From the critical behavior of the gas-liquid coexisting density, the critical exponent of the order parameter is estimated to be β = 0.3285(7). Surface tension is estimated from interface broadening behavior due to capillary waves. From the critical behavior of the surface tension, the critical exponent of the correlation length is estimated to be ν = 0.63(4). The obtained values of β and ν are consistent with those of the Ising universality class.
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61.20.Ja Computer simulation of liquid structure
68.03.Cd Surface tension and related phenomena
64.60.F- Equilibrium properties near critical points, critical exponents
64.70.F- Liquid-vapor transitions

General formulation of spin-flip time-dependent density functional theory using non-collinear kernels: Theory, implementation, and benchmarks

Yves A. Bernard, Yihan Shao, and Anna I. Krylov

J. Chem. Phys. 136, 204103 (2012); http://dx.doi.org/10.1063/1.4714499 (17 pages)

Online Publication Date: 23 May 2012

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We report an implementation of the spin-flip (SF) variant of time-dependent density functional theory (TD-DFT) within the Tamm-Dancoff approximation and non-collinear (NC) formalism for local, generalized gradient approximation, hybrid, and range-separated functionals. The performance of different functionals is evaluated by extensive benchmark calculations of energy gaps in a variety of diradicals and open-shell atoms. The benchmark set consists of 41 energy gaps. A consistently good performance is observed for the Perdew-Burke-Ernzerhof (PBE) family, in particular PBE0 and PBE50, which yield mean average deviations of 0.126 and 0.090 eV, respectively. In most cases, the performance of original (collinear) SF-TDDFT with 50-50 functional is also satisfactory (as compared to non-collinear variants), except for the same-center diradicals where both collinear and non-collinear SF variants that use LYP or B97 exhibit large errors. The accuracy of NC-SF-TDDFT and collinear SF-TDDFT with 50-50 and BHHLYP is very similar. Using PBE50 within collinear formalism does not improve the accuracy.
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31.15.ee Time-dependent density functional theory

Sensitivity of the properties of ruthenium “blue dimer” to method, basis set, and continuum model

Abdullah Ozkanlar and Aurora E. Clark

J. Chem. Phys. 136, 204104 (2012); http://dx.doi.org/10.1063/1.4719937 (7 pages)

Online Publication Date: 23 May 2012

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The ruthenium “blue dimer” [(bpy)2RuIIIOH2]2O4+ is best known as the first well-defined molecular catalyst for water oxidation. It has been subject to numerous computational studies primarily employing density functional theory. However, those studies have been limited in the functionals, basis sets, and continuum models employed. The controversy in the calculated electronic structure and the reaction energetics of this catalyst highlights the necessity of benchmark calculations that explore the role of density functionals, basis sets, and continuum models upon the essential features of blue-dimer reactivity. In this paper, we report Kohn-Sham complete basis set (KS-CBS) limit extrapolations of the electronic structure of “blue dimer” using GGA (BPW91 and BP86), hybrid-GGA (B3LYP), and meta-GGA (M06-L) density functionals. The dependence of solvation free energy corrections on the different cavity types (UFF, UA0, UAHF, UAKS, Bondi, and Pauling) within polarizable and conductor-like polarizable continuum model has also been investigated. The most common basis sets of double-zeta quality are shown to yield results close to the KS-CBS limit; however, large variations are observed in the reaction energetics as a function of density functional and continuum cavity model employed.
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31.15.E- Density-functional theory
82.30.Nr Association, addition, insertion, cluster formation
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry
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Complexes of type C6H7+·L (L = N2 and CO2) studied by explicitly correlated coupled cluster theory

Peter Botschwina and Rainer Oswald

J. Chem. Phys. 136, 204301 (2012); http://dx.doi.org/10.1063/1.4714347 (9 pages)

Online Publication Date: 22 May 2012

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Complexes of the benzenium ion (C6H7+) with N2 or CO2 have been studied by explicitly correlated coupled cluster theory at the CCSD(T)-F12x (x = a, b) level [T. B. Adler et al., J. Chem. Phys. 127, 221106 (2007)10.1063/1.2817618] and the double-hybrid density functional B2PLYP-D [T. Schwabe and S. Grimme, Phys. Chem. Chem. Phys. 9, 3397 (2007)10.1039/b704725h]. Improved harmonic vibrational wavenumbers for C6H7+ have been obtained by CCSD(T*)-F12a calculations with the VTZ-F12 basis set. Combining them with previous B2PLYP-D anharmonic contributions we arrive at anharmonic wavenumbers which are in excellent agreement with recent experimental data from p-H2 matrix isolation IR spectroscopy [M. Bahou et al., J. Chem. Phys. 136, 154304 (2012)10.1063/1.3703502]. The energetically most favourable conformer of C6H7+·N2 shows a π-bonded structure similar to C6H7+·Rg (Rg = Ne, Ar) [P. Botschwina and R. Oswald, J. Phys. Chem. A 115, 13664 (2011)10.1021/jp207905t] with De ≈ 870 cm−1. For C6H7+·CO2, a slightly lower energy is calculated for a conformer with the CO2 ligand lying in the ring-plane of the C6H7+ moiety (De ≈ 1508 cm−1). It may be discriminated from other conformers through a strong band predicted at 1218 cm−1, red-shifted by 21 cm−1 from the corresponding band of free C6H7+.
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31.15.bw Coupled-cluster theory
31.15.E- Density-functional theory
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.20.Tp Vibrational analysis

Angular and energy distribution of fragment ions in dissociative double photoionization of acetylene molecules at 39 eV

M. Alagia, C. Callegari, P. Candori, S. Falcinelli, F. Pirani, R. Richter, S. Stranges, and F. Vecchiocattivi

J. Chem. Phys. 136, 204302 (2012); http://dx.doi.org/10.1063/1.4720350 (6 pages)

Online Publication Date: 22 May 2012

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The two-body dissociation reactions of the dication, C2H22+, produced by 39.0 eV double photoionization of acetylene molecules, have been studied by coupling photoelectron-photoion-photoion coincidence and ion imaging techniques. The results provide the kinetic energy and angular distributions of product ions. The analysis of the results indicates that the dissociation leading to C2H++H+ products occurs through a metastable dication with a lifetime of 108 ± 22 ns, and a kinetic energy release (KER) distribution exhibiting a maximum at ∼4.3 eV with a full width at half maximum (FWHM) of about 60%. The reaction leading to CH 2++C+ occurs in a time shorter than the typical rotational period of the acetylene molecules (of the order of 10−12 s). The KER distribution of product ions for this reaction, exhibits a maximum at ∼4.5 eV with a FWHM of about 28%. The symmetric dissociation, leading to CH+ + CH+, exhibits a KER distribution with a maximum at ∼5.2 eV with a FWHM of 44%. For the first two reactions the angular distributions of ion products also indicate that the double photoionization of acetylene occurs when the neutral molecule is mainly oriented perpendicularly to the light polarization vector.
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82.50.-m Photochemistry
33.80.Gj Diffuse spectra; predissociation, photodissociation
82.53.Eb Pump probe studies of photodissociation

Vibrationally averaged isotropic dispersion energy coefficients of the parahydrogen dimer

Timothy C. Lillestolen and Robert J. Hinde

J. Chem. Phys. 136, 204303 (2012); http://dx.doi.org/10.1063/1.4708807 (4 pages)

Online Publication Date: 22 May 2012

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We compare the sum-over-states and coupled cluster linear response formalisms for the determination of imaginary-frequency polarizabilities of H2. Using both approaches, we compute isotropic dispersion energy coefficients Cn (n = 6, 8, 10) for H2–H2 molecular pairs over a wide range of H2 bond lengths. We present vibrationally averaged dispersion energy coefficients for H2–H2, H2–D2, and D2–D2 molecular pairs and examine the coefficients’ convergence with respect to basis set.
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31.15.vn Electron correlation calculations for diatomic molecules
31.15.bw Coupled-cluster theory
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Dj Interatomic distances and angles

Comprehensive vacuum ultraviolet photoionization study of the CF3• trifluoromethyl radical using synchrotron radiation

Héloïse Dossmann (Soldi-Lose), Gustavo A. Garcia, Laurent Nahon, Barbara K. C. de Miranda, and Christian Alcaraz

J. Chem. Phys. 136, 204304 (2012); http://dx.doi.org/10.1063/1.4719529 (8 pages)

Online Publication Date: 22 May 2012

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The trifluoromethyl radical, CF3•, is studied for the first time by means of threshold photoelectron spectroscopy (TPES). The radical is produced in the gas phase using the flash-pyrolysis technique from hexafluoroethane as a precursor. CF3+ total ion yield and mass-selected TPES of the radical are recorded using a spectrometer based upon velocity map imaging and Wiley-McLaren time-of-flight coupled to the synchrotron radiation. The high resolution of the instrument and of the photons allows the observation of rich vibrational progressions in the TPES of CF3•. By using Franck-Condon factors computed by Bowman and coworkers, we have been able to simulate the TPES. The initial vibrational temperature of the radical beam has been evaluated at 350 ± 70 K. The structures have been identified as transitions between (n1,n2) and (n1+,n2+) vibrational levels of CF3 and CF3+ with small excitation of the breathing mode, ν1+, and large excitation (n2+ = 10–26) of the umbrella mode, ν2+, in the cation. From the energy separation between the two resolved peaks of each band, a value of 994 ± 16 cm−1 has been derived for the ν1+ breathing frequency of CF3+. For the high-lying n2+ levels, the apparent ν2+ umbrella spacing, 820 ± 14 cm−1, is fairly constant. Taking into account the ν2+ anharmonicity calculated by Bowman and coworkers, we have deduced ν2+ = 809 ± 14 cm−1, and semi-empirical estimations of the adiabatic ionization energy IEad.(CF3•) are proposed in good agreement with most of previous works. A value of the vertical ionization potential, IEvert.(CF3•) = 11.02 eV, has been derived from the observation of a photoelectron spectrum recorded at a fixed photon energy of 12 eV.
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33.80.Eh Autoionization, photoionization, and photodetachment
33.60.+q Photoelectron spectra
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors

Imaging ion-molecule reactions: Charge transfer and C-N bond formation in the C+ + NH3 system

Linsen Pei and James M. Farrar

J. Chem. Phys. 136, 204305 (2012); http://dx.doi.org/10.1063/1.4719808 (7 pages)

Online Publication Date: 23 May 2012

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The velocity mapping ion imaging method is applied to the ion-molecule reactions occurring between C+ and NH3. The velocity space images are collected over the relative collision energy range from 1.5 to 3.3 eV, allowing both product kinetic energy distributions and angular distributions to be obtained from the data. The charge transfer process appears to be direct, dominated by long-range electron transfer that results in minimal deflection of the products. The product kinetic energy distributions are consistent with a process dominated by energy resonance. The kinetic energy distributions for C-N bond formation appear to scale with the total available energy, providing strong evidence that energy in the [CNH3]+ precursor to products is distributed statistically. The angular distributions for C-N bond formation show pronounced forward-backward symmetry, as expected for a complex that resembles a prolate symmetric top decaying along its symmetry axis.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
33.15.Fm Bond strengths, dissociation energies
34.70.+e Charge transfer
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Density and birefringence of a highly stable α,α,β-trisnaphthylbenzene glass

Shakeel S. Dalal, A. Sepúlveda, Greg K. Pribil, Zahra Fakhraai, and M. D. Ediger

J. Chem. Phys. 136, 204501 (2012); http://dx.doi.org/10.1063/1.4719532 (10 pages)

Online Publication Date: 23 May 2012

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Spectroscopic ellipsometry has been used to understand the properties of α,α,β-trisnaphthylbenzene (ααβ-TNB) glasses vapor-deposited at a substrate temperature of 295 K (0.85 Tg). In a single temperature ramping experiment, a range of properties of the as-deposited glass can be measured, including density, fictive temperature, onset temperature, thermal expansion coefficient, and birefringence. The vapor-deposited ααβ-TNB glass is 1.3% more dense than the ordinary glass prepared by cooling at 1 K/min, is found to be birefringent, has a fictive temperature 35 K below that of the ordinary glass, and an onset temperature 20 K above that of the ordinary glass. The thermal expansion coefficient of the vapor-deposited ααβ-TNB glass is 14% lower than that of the ordinary glass, indicating that lower portions of the potential energy landscape have more harmonic potential minima than the parts accessible to the ordinary glass.
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78.20.Fm Birefringence
78.66.Qn Polymers; organic compounds
81.05.Lg Polymers and plastics; rubber; synthetic and natural fibers; organometallic and organic materials
68.55.am Polymers and organics
65.40.De Thermal expansion; thermomechanical effects
back to top Surfaces, Interfaces, and Materials

Fluorescence quenching near small metal nanoparticles

V. N. Pustovit and T. V. Shahbazyan

J. Chem. Phys. 136, 204701 (2012); http://dx.doi.org/10.1063/1.4721388 (6 pages)

Online Publication Date: 22 May 2012

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We develop a microscopic model for fluorescence of a molecule (or semiconductor quantum dot) near a small metal nanoparticle. When a molecule is situated close to metal surface, its fluorescence is quenched due to energy transfer to the metal. We perform quantum-mechanical calculations of energy transfer rates for nanometer-sized Au nanoparticles and find that nonlocal and quantum-size effects significantly enhance dissipation in metal as compared to those predicted by semiclassical electromagnetic models. However, the dependence of transfer rates on molecule's distance to metal nanoparticle surface, d, is significantly weaker than the d−4 behavior for flat metal surface with a sharp boundary predicted by previous calculations within random phase approximation.
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33.50.Dq Fluorescence and phosphorescence spectra
33.50.Hv Radiationless transitions, quenching
34.35.+a Interactions of atoms and molecules with surfaces
31.15.-p Calculations and mathematical techniques in atomic and molecular physics
back to top Polymers and Complex Systems

Driven Brownian coagulation of polymers

P. L. Krapivsky and Colm Connaughton

J. Chem. Phys. 136, 204901 (2012); http://dx.doi.org/10.1063/1.4718833 (13 pages)

Online Publication Date: 22 May 2012

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We present an analysis of the mean-field kinetics of Brownian coagulation of droplets and polymers driven by input of monomers which aims to characterize the long time behavior of the cluster size distribution as a function of the inverse fractal dimension, a, of the aggregates. We find that two types of long time behavior are possible. For 0 ≤ a<½ the size distribution reaches a stationary state with a power law distribution of cluster sizes having exponent math. The amplitude of this stationary state is determined exactly as a function of a. For ½<a ≤ 1, the cluster size distribution never reaches a stationary state. Instead a bimodal distribution is formed in which a narrow population of small clusters near the monomer scale is separated by a gap (where the cluster size distribution is effectively zero) from a population of large clusters which continue to grow for all time by absorbing small clusters. The marginal case, a = ½, is difficult to analyze definitively, but we argue that the cluster size distribution becomes stationary and there is a logarithmic correction to the algebraic tail.
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36.40.Mr Spectroscopy and geometrical structure of clusters
36.20.Hb Configuration (bonds, dimensions)
36.20.Ey Conformation (statistics and dynamics)
31.15.X- Alternative approaches
back to top Biological Molecules, Biopolymers, and Biological Systems

Modeling of solvent flow effects in enzyme catalysis under physiological conditions

Jeremy Schofield, Paul Inder, and Raymond Kapral

J. Chem. Phys. 136, 205101 (2012); http://dx.doi.org/10.1063/1.4719539 (14 pages)

Online Publication Date: 22 May 2012

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A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with absorbing boundaries are combined with densities obtained from explicit simulation to obtain the overall probability density for the total reaction cycle time of the enzymatic system. The method is used to investigate the catalytic transfer of a phosphoryl group in a phosphoglycerate kinase-ADP-bis phosphoglycerate system, one of the steps of glycolysis. The direct simulation of the enzyme-substrate binding and reaction is carried out using an elastic network model for the protein, and the solvent motions are described by multiparticle collision dynamics which incorporates hydrodynamic flow effects. Systems where solvent-enzyme coupling occurs through explicit intermolecular interactions, as well as systems where this coupling is taken into account by including the protein and substrate in the multiparticle collision step, are investigated and compared with simulations where hydrodynamic coupling is absent. It is demonstrated that the flow of solvent particles around the enzyme facilitates the large-scale hinge motion of the enzyme with bound substrates, and has a significant impact on the shape of the probability densities and average time scales of substrate binding for substrates near the enzyme, the closure of the enzyme after binding, and the overall time of completion of the cycle.
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87.15.kr Protein-solvent interactions
87.15.R- Reactions and kinetics
87.14.ej Enzymes
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