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21 Dec 2009

Volume 131, Issue 23, Articles (23xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 131, 234501 (2009); http://dx.doi.org/10.1063/1.3268766 (10 pages)

Mirco Zerbetto, Antonino Polimeno, Dmytro Kotsyubynskyy, Leila Ghalebani, Jozef Kowalewski, Eva Meirovitch, Ulrika Olsson, and Göran Widmalm
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Koopmans’ springs to life

Ulrike Salzner and Roi Baer

J. Chem. Phys. 131, 231101 (2009); http://dx.doi.org/10.1063/1.3269030 (4 pages) | Cited 12 times

Online Publication Date: 16 December 2009

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The meaning of orbital energies (OOEs) in Kohn–Sham (KS) density functional theory (DFT) is subject to a longstanding controversy. In local, semilocal, and hybrid density functionals (DFs) a Koopmans’ approach, where OOEs approximate negative ionization potentials (IPs), is unreliable. We discuss a methodology based on the Baer–Neuhauser–Livshits range-separated hybrid DFs for which Koopmans’ approach “springs to life.” The OOEs are remarkably close to the negative IPs with typical deviances of ±0.3 eV down to IPs of 30 eV, as demonstrated on several molecules. An essential component is the ab initio motivated range-parameter tuning procedure, forcing the highest OOE to be exactly equal to the negative first IP. We develop a theory for the curvature of the energy as a function of fractional occupation numbers to explain some of the results.
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31.15.E- Density-functional theory
31.15.A- Ab initio calculations
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Computing absolute free energies of disordered structures by molecular simulation

T. Schilling and F. Schmid

J. Chem. Phys. 131, 231102 (2009); http://dx.doi.org/10.1063/1.3274951 (4 pages) | Cited 2 times

Online Publication Date: 17 December 2009

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We present a Monte Carlo simulation technique by which the free energy of disordered systems can be computed directly. It is based on thermodynamic integration. The central idea is to construct an analytically solvable reference system from a configuration which is representative for the state of interest. The method can be applied to lattice models (e.g., the Ising model) as well as off-lattice molecular models. We focus mainly on the more challenging off-lattice case. We propose a Monte Carlo algorithm, by which the thermodynamic integration path can be sampled efficiently. At the examples of the hard sphere liquid and a hard disk solid with a defect, we discuss several properties of the approach.
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61.43.Bn Structural modeling: serial-addition models, computer simulation
61.20.Ja Computer simulation of liquid structure
65.60.+a Thermal properties of amorphous solids and glasses: heat capacity, thermal expansion, etc.
65.20.-w Thermal properties of liquids
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Single chain contraction and re-expansion of polystyrene sulfonate: A study on its re-entrant condensation at single molecular level

Pengxiang Jia and Jiang Zhao

J. Chem. Phys. 131, 231103 (2009); http://dx.doi.org/10.1063/1.3276278 (4 pages) | Cited 3 times

Online Publication Date: 18 December 2009

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Single chain conformation of a polyelectrolyte (polystyrene sulfonate, PSS−Na+) during its re-entrant condensation was studied by fluorescence correlation spectroscopy (FCS) with single molecule sensitivity. The contraction and re-expansion of PSS−Na+ chain were observed with the addition of counterions of different valencies. The formation of aggregation and precipitation of PSS−Na+ and its redissolution were observed in accordance with the chain contraction and re-expansion process for the PSS−Na+ chain upon the addition of trivalent La3+ ion. Chain contraction and re-expansion of the PSS−Na+ chain were also observed with the addition of monovalent Cs+ and divalent Ca2+ ions, under which condition, the re-entrant condensation was not observed. The results demonstrate that the high sensitivity of FCS can really study single PSS−Na+ chain under extremely dilute situation.
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61.25.he Polymer solutions
78.55.Bq Liquids
82.45.Gj Electrolytes
82.35.Rs Polyelectrolytes
64.75.Bc Solubility
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back to top Theoretical Methods and Algorithms

Towards an accurate description of the electronic properties of the biphenylthiol/gold interface: The role of exact exchange

E. Fabiano, M. Piacenza, S. D’Agostino, and F. Della Sala

J. Chem. Phys. 131, 234101 (2009); http://dx.doi.org/10.1063/1.3271393 (10 pages) | Cited 9 times

Online Publication Date: 15 December 2009

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We investigate the role of the exact exchange in describing the biphenylthiol/gold interface. The study is performed by simulating the electronic properties of mercaptobiphenylthiol and aminobiphenylthiol molecules adsorbed on a Au23 cluster, using local, semilocal and hybrid functionals and an effective exact exchange method, namely, the localized Hartree–Fock (LHF). We find that the local/semilocal functionals strongly underestimate the charge transfer and the bond dipole at the interface due to the self-interaction-error (SIE), which alters the correct level alignment. On the other hand the LHF method is SIE free and predicts a larger charge transfer and bond dipole. We also found that LHF results can be reproduced using hybrid functionals and that conventional local/semilocal correlation functionals are unable to improve over the exchange-only description.
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73.20.Hb Impurity and defect levels; energy states of adsorbed species
73.22.Lp Collective excitations
71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)
71.70.Gm Exchange interactions

New shooting algorithms for transition path sampling: Centering moves and varied-perturbation sizes for improved sampling

Christopher N. Rowley and Tom K. Woo

J. Chem. Phys. 131, 234102 (2009); http://dx.doi.org/10.1063/1.3274203 (11 pages)

Online Publication Date: 15 December 2009

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Transition path sampling has been established as a powerful tool for studying the dynamics of rare events. The trajectory generation moves of this Monte Carlo procedure, shooting moves and shifting modes, were developed primarily for rate constant calculations, although this method has been more extensively used to study the dynamics of reactive processes. We have devised and implemented three alternative trajectory generation moves for use with transition path sampling. The centering-shooting move incorporates a shifting move into a shooting move, which centers the transition period in the middle of the trajectory, eliminating the need for shifting moves and generating an ensemble where the transition event consistently occurs near the middle of the trajectory. We have also developed varied-perturbation size shooting moves, wherein smaller perturbations are made if the shooting point is far from the transition event. The trajectories generated using these moves decorrelate significantly faster than with conventional, constant sized perturbations. This results in an increase in the statistical efficiency by a factor of 2.5–5 when compared to the conventional shooting algorithm. On the other hand, the new algorithm breaks detailed balance and introduces a small bias in the transition time distribution. We have developed a modification of this varied-perturbation size shooting algorithm that preserves detailed balance, albeit at the cost of decreased sampling efficiency. Both varied-perturbation size shooting algorithms are found to have improved sampling efficiency when compared to the original constant perturbation size shooting algorithm.
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82.20.Db Transition state theory and statistical theories of rate constants
82.20.Pm Rate constants, reaction cross sections, and activation energies

Optimizing core-shell nanoparticle catalysts with a genetic algorithm

Nathan S. Froemming and Graeme Henkelman

J. Chem. Phys. 131, 234103 (2009); http://dx.doi.org/10.1063/1.3272274 (7 pages) | Cited 8 times

Online Publication Date: 16 December 2009

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A genetic algorithm is used with density functional theory to investigate the catalytic properties of 38- and 79-atom bimetallic core-shell nanoparticles for the oxygen reduction reaction. Each particle is represented by a two-gene chromosome that identifies its core and shell metals. The fitness of each particle is specified by how close the d-band level of the shell is to that of the Pt(111) surface, a catalyst known to be effective for oxygen reduction. The genetic algorithm starts by creating an initial population of random core-shell particles. The fittest particles are then bred and mutated to replace the least-fit particles in the population and form successive generations. The genetic algorithm iteratively refines the population of candidate catalysts more efficiently than Monte Carlo or random sampling, and we demonstrate how the average energy of the surface d-band can be tuned to that of Pt(111) by varying the core and shell metals. The binding of oxygen is a more direct measure of catalytic activity and is used to further investigate the fittest particles found by the genetic algorithm. The oxygen binding energy is found to vary linearly with the d-band level for particles with the same shell metal, but there is considerable variation in the trend across different shells. Several particles with oxygen binding energies similar to Pt(111) have already been investigated experimentally and found to be active for oxygen reduction. In this work, many other candidates are identified.
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82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.15.Nc Total energy and cohesive energy calculations
73.20.At Surface states, band structure, electron density of states
73.22.-f Electronic structure of nanoscale materials and related systems
82.30.-b Specific chemical reactions; reaction mechanisms

Analytical formulas for low-fluence non-line-narrowed hole-burned spectra in an excitonically coupled dimer

Mike Reppert, Virginia Naibo, and Ryszard Jankowiak

J. Chem. Phys. 131, 234104 (2009); http://dx.doi.org/10.1063/1.3270394 (11 pages) | Cited 4 times

Online Publication Date: 16 December 2009

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We present exact equations for the low-fluence non-line-narrowed (NLN) nonphotochemical hole-burning (NPHB) spectrum of an excitonically coupled dimer (for arbitrary coupling strength) under the assumption that postburn and preburn site energies are independent. The equations provide a transparent view into the contributions of various effects to the NPHB spectrum. It is demonstrated that the NPHB spectrum in dimers is largely dominated by the statistical reshuffling of site energies and by altered excitonic transition energies of both excitonic states (in contrast with only the lowest state). For comparison of these results with those from larger excitonically coupled systems, the low-fluence NLN NPHB spectrum obtained for the CP47 complex (a 16-pigment core antenna complex of Photosystem II) is also calculated using Monte Carlo simulations. In this larger system it is shown that the NPHB spectra for individual excitonic states are not entirely conservative (although the changes in average oscillator strength for the higher excitonic states are in most cases less than 1%), a feature which we argue is due primarily to reordering of the contributions of various pigments to the excitonic states. We anticipate that a better understanding of NPHB spectra obtained for various photosynthetic complexes and their simultaneous fits with other optical spectra (e.g., absorption, emission, and circular dichroism spectra) will provide more insight into the underlying electronic structures of various photosynthetic systems.
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78.47.nd Hole burning spectroscopy
78.40.-q Absorption and reflection spectra: visible and ultraviolet
71.35.Gg Exciton-mediated interactions
71.15.Pd Molecular dynamics calculations (Car-Parrinello) and other numerical simulations

Two-scale Brownian dynamics of suspensions of charged nanoparticles including electrostatic and hydrodynamic interactions

V. Dahirel, M. Jardat, J. F. Dufrêche, and P. Turq

J. Chem. Phys. 131, 234105 (2009); http://dx.doi.org/10.1063/1.3273871 (10 pages) | Cited 2 times

Online Publication Date: 16 December 2009

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We propose here a multiscale strategy based on continuous solvent Brownian dynamics (BD) simulations to study the dynamical properties of aqueous suspensions of charged nanoparticles. We extend our previous coarse-graining strategy [ V. Dahirel et al., J. Chem. Phys. 126, 114108 (2007) ] to account for hydrodynamic interactions between solute particles. Within this new procedure, two BD simulations are performed: (1) The first one investigates the time scales of the counterions and coions (the microions) with only one nanoparticle in the simulation box but explicit microions, (ii) the second one investigates the larger time scale of the nanoparticles with numerous nanoparticles in the simulation box but implicit microions. We show how individual and collective transport coefficients can be computed from this two-scale procedure. To ensure the validity of our procedure, we compute the transport coefficients of a 10-1 model electrolyte in aqueous solution with a 1-1 added salt. We do a systematic comparison between the results obtained within the new procedure and those obtained with explicit BD simulations of the complete system containing several nanoparticles and explicit microions. The agreement between the two methods is found to be excellent: Even if the new procedure is much faster than explicit simulations, it allows us to compute transport coefficients with a good precision. Moreover, one step of our procedure also allows us to compute the individual transport coefficients relative to the microions (self-diffusion coefficients and electrophoretic mobility).
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82.70.Kj Emulsions and suspensions
66.10.cg Mass diffusion, including self-diffusion, mutual diffusion, tracer diffusion, etc.
61.46.Df Structure of nanocrystals and nanoparticles ("colloidal" quantum dots but not gate-isolated embedded quantum dots)

Nonlinear diffusion in two-dimensional ordered porous media based on a free volume theory

A. Godec, M. Gaberscek, J. Jamnik, and F. Merzel

J. Chem. Phys. 131, 234106 (2009); http://dx.doi.org/10.1063/1.3274638 (12 pages) | Cited 4 times

Online Publication Date: 17 December 2009

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A continuum nonlinear diffusion model is developed to describe molecular transport in ordered porous media. An existing generic van der Waals equation of state based free volume theory of binary diffusion coefficients is modified and introduced into the two-dimensional diffusion equation. The resulting diffusion equation is solved numerically with the alternating-direction fully implicit method under Neumann boundary conditions. Two types of pore structure symmetries are considered, hexagonal and cubic. The former is modeled as parallel channels while in case of the latter equal-sized channels are placed perpendicularly thus creating an interconnected network. First, general features of transport in both systems are explored, followed by the analysis of the impact of molecular properties on diffusion inside and out of the porous matrix. The influence of pore size on the diffusion-controlled release kinetics is assessed and the findings used to comment recent experimental studies of drug release profiles from ordered mesoporous silicates.
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66.30.Dn Theory of diffusion and ionic conduction in solids
61.43.Gt Powders, porous materials
64.10.+h General theory of equations of state and phase equilibria
66.30.J- Diffusion of impurities

Extensive regularization of the coupled cluster methods based on the generating functional formalism: Application to gas-phase benchmarks and to the SN2 reaction of CHCl3 and OH− in water

Karol Kowalski and Marat Valiev

J. Chem. Phys. 131, 234107 (2009); http://dx.doi.org/10.1063/1.3270957 (12 pages) | Cited 1 time

Online Publication Date: 17 December 2009

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The recently introduced energy expansion based on the use of generating functional (GF) [ K. Kowalski and P. D. Fan, J. Chem. Phys. 130, 084112 (2009) ] provides a way of constructing size-consistent noniterative coupled cluster (CC) corrections in terms of moments of the CC equations. To take advantage of this expansion in a strongly interacting regime, the regularization of the cluster amplitudes is required in order to counteract the effect of excessive growth of the norm of the CC wave function. Although proven to be efficient, the previously discussed form of the regularization does not lead to rigorously size-consistent corrections. In this paper we address the issue of size-consistent regularization of the GF expansion by redefining the equations for the cluster amplitudes. The performance and basic features of proposed methodology are illustrated on several gas-phase benchmark systems. Moreover, the regularized GF approaches are combined with quantum mechanical molecular mechanics module and applied to describe the SN2 reaction of CHCl3 and OH− in aqueous solution.
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82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.20.Uv Stochastic theories of rate constants

Derivatives of spin dynamics simulations

Ilya Kuprov and Christopher T. Rodgers

J. Chem. Phys. 131, 234108 (2009); http://dx.doi.org/10.1063/1.3267086 (8 pages) | Cited 5 times

Online Publication Date: 17 December 2009

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We report analytical equations for the derivatives of spin dynamics simulations with respect to pulse sequence and spin system parameters. The methods described are significantly faster, more accurate, and more reliable than the finite difference approximations typically employed. The resulting derivatives may be used in fitting, optimization, performance evaluation, and stability analysis of spin dynamics simulations and experiments.
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75.40.Gb Dynamic properties (dynamic susceptibility, spin waves, spin diffusion, dynamic scaling, etc.)

Automatic derivation and evaluation of vibrational coupled cluster theory equations

Peter Seidler and Ove Christiansen

J. Chem. Phys. 131, 234109 (2009); http://dx.doi.org/10.1063/1.3272796 (15 pages) | Cited 6 times

Online Publication Date: 18 December 2009

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A scheme for automatic derivation and evaluation of the expressions occurring in vibrational coupled cluster theory is introduced. The method is based on a Baker–Campbell–Hausdorff expansion of the similarity transformed Hamiltonian and is general both with respect to the excitation level in the parameter space and the mode coupling level in the Hamiltonian. In addition to deriving general expressions, intermediates that lower the computational scaling are automatically detected. The final equations are then evaluated. Due to the commutator based nature of the algorithm, it is also applicable to the evaluation of quantities needed for response theory. Different aspects of the theory and implementation are illustrated by calculations on model systems. Furthermore, all fundamental excitation energies of ethylene oxide are calculated.
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31.15.bw Coupled-cluster theory
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Tp Vibrational analysis

A density-division embedding potential inversion technique

O. Roncero, A. Zanchet, P. Villarreal, and A. Aguado

J. Chem. Phys. 131, 234110 (2009); http://dx.doi.org/10.1063/1.3274823 (7 pages) | Cited 10 times

Online Publication Date: 18 December 2009

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A new method is proposed to partition the density of a system in two portions. The density on each subsystem is the solution of a Fock equation modified by the addition of an embedding potential. This embedding potential is obtained iteratively by minimizing the difference between the electronic densities of the total system and the sum of the subsystems. Thus, the electronic density partition and the embedding potential are obtained at the same time within the procedure, guarantying the v-representability of the densities partitioned. This fact is a considerable improvement of a recently proposed embedding potential inversion technique, [ O. Roncero, M. P. de Lara-Castells, P. Villarreal, F. Flores, J. Ortega, M. Paniagua, and A. Aguado, J. Chem. Phys. 129, 184104 (2008) ], in which the embedding potential is obtained once the electronic density is previously partitioned. The method is first applied to a linear H10 chain to illustrate how it works. The orbitals obtained are localized on each subsystem, and can be used to include local electronic correlation with currently available ab initio programs. Finally, the method is applied to include the electronic correlation needed to describe the van der Waals interaction between H10 chains and H2 molecules, of ≈12 meV, giving very accurate results.
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31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.A- Ab initio calculations
34.20.Gj Intermolecular and atom-molecule potentials and forces

A simple nonlocal model for exchange

Benjamin G. Janesko

J. Chem. Phys. 131, 234111 (2009); http://dx.doi.org/10.1063/1.3274824 (8 pages) | Cited 5 times

Online Publication Date: 18 December 2009

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This work presents a new nonlocal model for the exchange energy density. The model is obtained from the product of the Kohn–Sham one-particle density matrix used to construct exact [Hartree–Fock-like (HF)] exchange, and an approximate density matrix used to construct local spin-density approximation (LSDA) exchange. The proposed exchange energy density has useful formal properties, including correct spin and coordinate scaling and the correct uniform limit. It can readily be evaluated in finite basis sets, with a computational scaling intermediate between HF exchange and semilocal quantities such as the noninteracting kinetic energy density. Applications to representative systems indicate that its properties are typically intermediate between HF and LSDA exchange, and often similar to global hybrids of HF and LSDA exchange. The model is proposed as a novel “Rung 3.5” ingredient for constructing approximate exchange-correlation functionals.
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71.45.Gm Exchange, correlation, dielectric and magnetic response functions, plasmons
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.15.Ap Basis sets (LCAO, plane-wave, APW, etc.) and related methodology (scattering methods, ASA, linearized methods, etc.)

Isotope shift in the electron affinity of lithium

Sergiy Bubin, Jacek Komasa, Monika Stanke, and Ludwik Adamowicz

J. Chem. Phys. 131, 234112 (2009); http://dx.doi.org/10.1063/1.3275804 (5 pages) | Cited 7 times

Online Publication Date: 18 December 2009

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Very accurate electron affinity (EA) calculations of mathi and mathi (and mathi) have been performed using explicitly correlated Gaussian functions and a variational approach that explicitly includes the nuclear motion in the calculations (i.e., the approach that does not assume the Born–Oppenheimer approximation). The leading relativistic and quantum electrodynamics corrections to the electron affinities were also calculated. The results are the most accurate theoretical values obtained for the studied systems to date. Our best estimates of the mathi and mathi EAs are 4984.9842(30) and 4984.9015(30) cm−1, respectively, and of the mathi/mathi EA isotope shift is 0.0827 cm−1.
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32.70.Jz Line shapes, widths, and shifts
32.50.+d Fluorescence, phosphorescence (including quenching)
31.15.xt Variational techniques
12.20.Ds Specific calculations
31.30.J- Relativistic and quantum electrodynamic (QED) effects in atoms, molecules, and ions

Thermal conduction in molecular materials using coarse grain dynamics: Role of mass diffusion and quantum corrections for molecular dynamics simulations

Ya Zhou and Alejandro Strachan

J. Chem. Phys. 131, 234113 (2009); http://dx.doi.org/10.1063/1.3272028 (9 pages)

Online Publication Date: 21 December 2009

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We use a mesodynamical method, denoted dynamics with implicit degrees of freedom (DID), to characterize thermal transport in a model molecular crystal below and above its melting temperature. DID represents groups of atoms (molecules in this case) using mesoparticles and the thermal role of the intramolecular degrees of freedom (DoFs) are described implicitly using their specific heat. We focus on the role of these intramolecular DoFs on thermal transport. We find that thermal conductivity is independent of intramolecular specific heat for solid samples and a linear relationship between the two quantities in liquid samples with the coefficient of proportionality being the mass diffusivity of the mesoparticles. As the temperature of the liquids is increased, thermal conductivity exhibits an increased sensitivity with respect to the specific heat of the internal DoFs due to the enhanced molecular mobility. Based on these results, we propose a simple method to incorporate quantum corrections to thermal conductivity obtained from nonequilibrium molecular dynamics simulations of molecular liquids. Our results also provide insight into the development of thermally accurate coarse grain models of soft materials.
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61.43.Bn Structural modeling: serial-addition models, computer simulation
61.20.Ja Computer simulation of liquid structure
66.70.-f Nonelectronic thermal conduction and heat-pulse propagation in solids; thermal waves
66.25.+g Thermal conduction in nonmetallic liquids
65.20.-w Thermal properties of liquids
65.40.Ba Heat capacity
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Continuous-time random walks at all times

Anatoly B. Kolomeisky

J. Chem. Phys. 131, 234114 (2009); http://dx.doi.org/10.1063/1.3276704 (6 pages)

Online Publication Date: 21 December 2009

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Continuous-time random walks (CTRW) play an important role in understanding of a wide range of phenomena. However, most theoretical studies of these models concentrate only on dynamics at long times. We present a new theoretical approach, based on generalized master equations picture, which allowed us to obtain explicit expressions for Laplace transforms for all dynamic quantities for different CTRW models. This theoretical method leads to the effective description of CTRW at all times. Specific calculations are performed for homogeneous, periodic models and for CTRW with irreversible detachments. The approach to stationary states for CTRW is analyzed. Our results are also used to analyze generalized fluctuations theorem.
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05.40.Fb Random walks and Levy flights
02.30.Uu Integral transforms

Modeling the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics and molecular dynamics simulations

Nikolaos K. Voulgarakis, Siddarth Satish, and Jhih-Wei Chu

J. Chem. Phys. 131, 234115 (2009); http://dx.doi.org/10.1063/1.3273210 (8 pages) | Cited 4 times

Online Publication Date: 21 December 2009

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A multiscale computational method is developed to model the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics (FHD) and molecular dynamics (MD) simulations. To capture the elastic responses that emerge at small length scales, we attach an additional rheological model parallel to the macroscopic constitutive equation of a fluid. The widely used linear Maxwell model is employed as a working choice; other models can be used as well. For a fluid that is Newtonian in the macroscopic limit, this approach results in a parallel Newtonian–Maxwell model. For water, argon, and an ionic liquid, the power spectrum of momentum field autocorrelation functions of the parallel Newtonian–Maxwell model agrees very well with those calculated from all-atom MD simulations. To incorporate thermal fluctuations, we generalize the equations of FHD to work with non-Markovian rheological models and colored noise. The fluctuating stress tensor (white noise) is integrated in time in the same manner as its dissipative counterpart and numerical simulations indicate that this approach accurately preserves the set temperature in a FHD simulation. By mapping position and velocity vectors in the molecular representation onto field variables, we bridge the non-Markovian FHD with atomistic MD simulations. Through this mapping, we quantitatively determine the transport coefficients of the parallel Newtonian–Maxwell model for water and argon from all-atom MD simulations. For both fluids, a significant enhancement in elastic responses is observed as the wave number of hydrodynamic modes is reduced to a few nanometers. The mapping from particle to field representations and the perturbative strategy of developing constitutive equations provide a useful framework for modeling the nanoscale viscoelasticity of fluids.
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83.60.Bc Linear viscoelasticity
47.61.Fg Flows in micro-electromechanical systems (MEMS) and nano-electromechanical systems (NEMS)
61.20.Ja Computer simulation of liquid structure
62.10.+s Mechanical properties of liquids
47.11.Mn Molecular dynamics methods
47.57.Qk Rheological aspects
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Theoretical investigation of the ground and low-lying excited states of gallium and indium silicides, GaSi and InSi

Demeter Tzeli, Ioannis D. Petsalakis, and Giannoula Theodorakopoulos

J. Chem. Phys. 131, 234301 (2009); http://dx.doi.org/10.1063/1.3271244 (9 pages) | Cited 1 time

Online Publication Date: 15 December 2009

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The electronic structure and the bonding of 13 electronic states of the diatomic gallium silicide (GaSi) and indium silicide (InSi) have been studied by multireference configuration interaction and coupled clusters methods in conjunction with the basis set (aug-)cc-pwCVQZ(-PP). Potential energy curves have been constructed for all states. Binding energies, spectroscopic parameters, and dipole moments have been calculated. Moreover, the bonding in the different states is analyzed. The potential energy curves of the two molecules, GaSi and InSi, are similar. The binding energies and the bond distances of the ground states of the molecules, X 4Σ−, are De = 56.2 kcal/mol (GaSi) and 51.9 kcal/mol (InSi) and Re = 2.406 Å (GaSi) and 2.603 Å (InSi). The first excited state a 2Σ− is calculated at 17 kcal/mol above the ground state in both molecules.
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31.15.vn Electron correlation calculations for diatomic molecules
31.50.Bc Potential energy surfaces for ground electronic states
31.50.Df Potential energy surfaces for excited electronic states
33.15.Dj Interatomic distances and angles
31.15.bw Coupled-cluster theory
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility

Long-range collisional energy transfer between charge-transfer (ion-pair) states of I2, induced by H2O and I2(X)

Trevor Ridley, Kenneth P. Lawley, and Robert J. Donovan

J. Chem. Phys. 131, 234302 (2009); http://dx.doi.org/10.1063/1.3272953 (12 pages) | Cited 3 times

Online Publication Date: 16 December 2009

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Long-range (resonant) energy transfer, between g/u charge-transfer states of molecular iodine [i.e., f0g+(3P0)→F0u+(3P0) and E0g+(3P2)→D0u+(3P2)], induced by collisions with H2O and I2(X) via multipole coupling, has been observed. Large rate constants, up to 5×10−9 molecules−1 cm3 s−1, for collisional transfer between a range of vibrational levels of the f0g+(3P0) and F0u+(3P0) ion-pair states of I2, by H2O, are reported. Some previously reported studies on E0g+(3P2)→D0u+(3P2) and f0g+(3P0)→F0u+(3P0) collisional transfer, induced by I2(X), have been repeated and revised rate data are presented; the range of initially excited vibrational states studied has also been extended. Much smaller rate constants for quenching by I2(X), compared to H2O, are found and it is proposed that H2O desorbed from the walls of the sample cell could have significantly affected much larger rate data previously reported in the literature. For both collision partners, a model is proposed in which long-range, near-resonant interactions can occur when there is close matching of the change in energy in the ion-pair states with the change in energy that accompanies the rotational transition undergone by the collision partner.
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34.70.+e Charge transfer
33.20.Sn Rotational analysis
33.20.Tp Vibrational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
34.50.Ez Rotational and vibrational energy transfer

A single molecule as a dielectric medium

A. Mandal and K. L. C. Hunt

J. Chem. Phys. 131, 234303 (2009); http://dx.doi.org/10.1063/1.3259576 (10 pages)

Online Publication Date: 16 December 2009

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For three molecules with weak or negligible charge overlap, we prove that the three-body interaction energy obtained from quantum perturbation theory (to leading order) fits a dielectric model with a nonlocal electronic screening function. The electronic charge cloud of each molecule acts as a dielectric medium for the interaction of the remaining two with the nonlocal dielectric function ε(r,r′) obtained by O. S. Jenkins and K. L. C. Hunt [J. Chem. Phys. 119, 8250 (2003) ], by considering the charge redistribution induced in a single molecule by an external perturbation. The dielectric function depends parametrically on the coordinates of the nuclei, within the Born–Oppenheimer approximation. We also prove that the force on each nucleus in molecule A depends on intramolecular dielectric screening within A. The potential from the charge distribution of B, screened by C acting as a dielectric medium, is further screened linearly within A; and similarly, with the roles of B and C reversed. In addition, the potential due to the unperturbed charge distribution of B and the potential due to the unperturbed charge distribution of C, acting simultaneously, are screened nonlinearly within A. The results show that nonlocal dielectric theory holds on the molecular level, provided that the overlap of the electronic charge distributions is weak.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
31.15.xp Perturbation theory
36.40.-c Atomic and molecular clusters

A new experimental absolute nuclear magnetic shielding scale for oxygen based on the rotational hyperfine structure of H217O

Cristina Puzzarini, Gabriele Cazzoli, Michael E. Harding, Juana Vázquez, and Jürgen Gauss

J. Chem. Phys. 131, 234304 (2009); http://dx.doi.org/10.1063/1.3274062 (11 pages) | Cited 8 times

Online Publication Date: 17 December 2009

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The hyperfine structure in the rotational spectrum of water containing 17O has been investigated experimentally and by means of quantum-chemical calculations. The Lamb-dip technique has been used to resolve the hyperfine structure due to spin-rotation as well as spin-spin interactions and allowed the determination of the corresponding hyperfine parameters with high accuracy. The experimental investigation and, in particular, the analysis of the spectra have been supported by quantum-chemical computations at the coupled-cluster level. The experimental 17O isotropic spin-rotation constant of H217O has been used in a further step for the determination of the paramagnetic part of the corresponding nuclear magnetic shielding constant, whereas the diamagnetic contribution as well as vibrational and temperature corrections have been obtained from quantum-chemical calculations. This joint procedure leads to a value of 325.3(3) ppm for the oxygen shielding in H217O at 300 K, in good agreement with pure theoretical predictions, and in this way provides the basis for a new absolute oxygen shielding scale.
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31.30.Gs Hyperfine interactions and isotope effects
33.15.Pw Fine and hyperfine structure
33.20.Sn Rotational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.15.bw Coupled-cluster theory
33.20.Tp Vibrational analysis

CO chemisorption on the surfaces of the golden cages

Wei Huang, Satya Bulusu, Rhitankar Pal, Xiao Cheng Zeng, and Lai-Sheng Wang

J. Chem. Phys. 131, 234305 (2009); http://dx.doi.org/10.1063/1.3273326 (6 pages) | Cited 4 times

Online Publication Date: 18 December 2009

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We report a joint experimental and theoretical study of CO chemisorption on the golden cages. We find that the Au17− cage is highly robust and retains its cage structure in Au17(CO)−. On the other hand, the Au16− cage is transformed to a structure similar to Au17− upon the adsorption of CO. Au18− is known to consist of two nearly degenerate structures, i.e., a cage and a pyramidal isomer, which coexist in the cluster beam. However, upon CO chemisorption only the cage isomer is observed while the pyramidal isomer no longer exists due to its less favorable interaction with CO, compared to the cage isomer. We find that inclusion of the spin-orbit effects is critical in yielding simulated spectra in quantitative agreement with the experimental data and providing unequivocal structural information and molecular insights into the chemical interactions between CO and the golden cages.
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68.43.Mn Adsorption kinetics
81.30.Hd Constant-composition solid-solid phase transformations: polymorphic, massive, and order-disorder
82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
79.60.Dp Adsorbed layers and thin films
64.70.kd Metals and alloys
71.70.Ej Spin-orbit coupling, Zeeman and Stark splitting, Jahn-Teller effect

Conical Intersections, charge localization, and photoisomerization pathway selection in a minimal model of a degenerate monomethine dye

Seth Olsen and Ross H. McKenzie

J. Chem. Phys. 131, 234306 (2009); http://dx.doi.org/10.1063/1.3267862 (14 pages) | Cited 4 times

Online Publication Date: 18 December 2009

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We propose a minimal model Hamiltonian for the electronic structure of a monomethine dye, in order to describe the photoisomerization of such dyes. The model describes interactions between three diabatic electronic states, each of which can be associated with a valence bond structure. Monomethine dyes are characterized by a charge-transfer resonance; the indeterminacy of the single-double bonding structure dictated by the resonance is reflected in a duality of photoisomerization pathways corresponding to the different methine bonds. The possible multiplicity of decay channels complicates mechanistic models of the effect of the environment on fluorescent quantum yields, as well as coherent control strategies. We examine the extent and topology of intersection seams between the electronic states of the dye and how they relate to charge localization and selection between different decay pathways. We find that intersections between the S1 and S0 surfaces only occur for large twist angles. In contrast, S2/S1 intersections can occur near the Franck–Condon region. When the molecule has left-right symmetry, all intersections are associated with con- or disrotations and never with single bond twists. For asymmetric molecules (i.e., where the bridge couples more strongly to one end) the S2 and S1 surfaces bias torsion about different bonds. Charge localization and torsion pathway biasing are correlated. We relate our observations with several recent experimental and theoretical results, which have been obtained for dyes with similar structure.
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82.30.Qt Isomerization and rearrangement
82.50.-m Photochemistry
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
82.80.Dx Analytical methods involving electronic spectroscopy
82.20.Hf Product distribution
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

An integrated approach to NMR spin relaxation in flexible biomolecules: Application to β-D-glucopyranosyl-(1→6)-α-D-mannopyranosyl-OMe

Mirco Zerbetto, Antonino Polimeno, Dmytro Kotsyubynskyy, Leila Ghalebani, Jozef Kowalewski, Eva Meirovitch, Ulrika Olsson, and Göran Widmalm

J. Chem. Phys. 131, 234501 (2009); http://dx.doi.org/10.1063/1.3268766 (10 pages) | Cited 2 times

Online Publication Date: 15 December 2009

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The description of the reorientational dynamics of flexible molecules is a challenging task, in particular when the rates of internal and global motions are comparable. The commonly used simple mode-decoupling models are based on the assumption of statistical independence between these motions. This assumption is not valid when the time scale separation between their rates is small, a situation that was found to arise in oligosaccharides in the context of certain internal motions. To make possible the interpretation of NMR spin relaxation data from such molecules, we developed a comprehensive approach generally applicable to flexible rotators with one internal degree of freedom. This approach integrates a stochastic description of coupled global tumbling and internal torsional motion, quantum chemical calculations of the local potential and the local geometry at the site of the restricted torsion, and hydrodynamics-based calculations of the diffusive properties. The method is applied to the disaccharide β-D-Glcp-(1→6)-α-D-[6-math]-Manp-OMe dissolved in a DMSO-d6/D2O cryosolvent. The experimental NMR relaxation parameters, associated with the mathH2 probe residing at the glycosidic linkage, include math T1 and T2 and math-{math} nuclear Overhauser enhancement (NOE) as well as longitudinal and transverse dipole-dipole cross-correlated relaxation rates, acquired in the temperature range of 253–293 K. These data are predicted successfully by the new theory with only the H–C–H angle allowed to vary. Previous attempts to fit these data using mode-decoupling models failed.
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87.15.M- Spectra of biomolecules
87.15.Vv Diffusion
87.15.B- Structure of biomolecules
87.14.E- Proteins
87.15.ag Quantum calculations
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