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7 Mar 2007

Volume 126, Issue 9, Articles (09xxxx)

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Nonequilibrium GW approach to quantum transport in nano-scale contacts

Kristian S. Thygesen and Angel Rubio

J. Chem. Phys. 126, 091101 (2007); http://dx.doi.org/10.1063/1.2565690 (4 pages) | Cited 36 times

Online Publication Date: 2 March 2007

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Correlation effects within the GW approximation have been incorporated into the Keldysh nonequilibrium transport formalism. We show that GW describes the Kondo effect and the zero-temperature transport properties of the Anderson model fairly well. Combining the GW scheme with density functional theory and a Wannier function basis set, we illustrate the impact of correlations by computing the I-V characteristics of a hydrogen molecule between two Pt chains. Our results indicate that self-consistency is fundamental for the calculated currents, but that it tends to wash out satellite structures in the spectral function.
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73.23.Hk Coulomb blockade; single-electron tunneling
72.10.Fk Scattering by point defects, dislocations, surfaces, and other imperfections (including Kondo effect)

Complete characterization of molecular vibration using frequency resolved gating

Xiaoji G. Xu, Stanislav O. Konorov, Sergey Zhdanovich, John W. Hepburn, and Valery Milner

J. Chem. Phys. 126, 091102 (2007); http://dx.doi.org/10.1063/1.2712839 (5 pages) | Cited 8 times

Online Publication Date: 2 March 2007

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The authors propose a new approach to vibration spectroscopy based on the coherent anti-Stokes Raman scattering of broadband ultrashort laser pulses. The proposed method reveals both the amplitude and the phase of molecular vibrations by utilizing the cross-correlation frequency resolved optical gating (XFROG) technique. The spectrum of the anti-Stokes pulse is measured as a function of the time delay between the laser-induced molecular vibrations and a well characterized broadband femtosecond probe pulse. The iterative XFROG algorithm provides a simultaneous complete characterization of molecular vibrations both in frequency and time domains with high resolution. They demonstrate experimentally the feasibility of the proposed method and show one of its potential applications in disentangling the time behavior of a mixture of vibrationally excited molecules. The technique of femtosecond pulse shaping is used for further improvement of accuracy and stability against noise.
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33.20.Fb Raman and Rayleigh spectra (including optical scattering)
33.15.Mt Rotation, vibration, and vibration-rotation constants
42.65.Re Ultrafast processes; optical pulse generation and pulse compression
33.80.-b Photon interactions with molecules

Phase separation of acetonitrile-water mixtures and minimizing of ice crystallites from there in confinement of MCM-41

Shigeharu Kittaka, Miki Kuranishi, Shinji Ishimaru, and Osamu Umahara

J. Chem. Phys. 126, 091103 (2007); http://dx.doi.org/10.1063/1.2712432 (4 pages) | Cited 5 times

Online Publication Date: 2 March 2007

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The effect of confinement of an acetonitrile-water mixture, whose correlation length was comparable to the pore size of the mesopores of MCM-41 (d = 2.4–3.6 nm), on the phase changes was studied. Used techniques were low temperature differential scanning calorimetry and Fourier transform infrared spectroscopy, where the phase separation, lowering of the freezing and melting temperatures, and phase transitions of the acetonitrile were detected. The latter occurred in the mesopores at temperatures similar to that of the pure liquid, while the melting temperature of the water in the mesopores <3.1 nm decreased markedly at higher acetonitrile contents, suggesting a marked lowering of ice crystallite size.
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64.75.-g Phase equilibria
78.30.C- Liquids
64.70.Ja Liquid-liquid transitions

First-order conformation transition of single poly(2-vinylpyridine) molecules in aqueous solutions

Shengqin Wang and Jiang Zhao

J. Chem. Phys. 126, 091104 (2007); http://dx.doi.org/10.1063/1.2711804 (4 pages) | Cited 9 times

Online Publication Date: 6 March 2007

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By measuring diffusion rate, the conformation change of single poly(2-vinylpyridine) chain in aqueous solution was studied by fluorescence correlation spectroscopy. The data showed a stepwise change of hydrodynamic radius when pH value was tuned, reflecting a sign of first-order conformation transition, and a continuous change was found at varying salt concentration.
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61.25.H- Macromolecular and polymers solutions; polymer melts
66.10.C- Diffusion and thermal diffusion
36.20.Ey Conformation (statistics and dynamics)
36.20.Fz Constitution (chains and sequences)
36.20.Hb Configuration (bonds, dimensions)
36.20.Kd Electronic structure and spectra

Denaturation of hen egg white lysozyme in electromagnetic fields: A molecular dynamics study

Niall J. English and Damian A. Mooney

J. Chem. Phys. 126, 091105 (2007); http://dx.doi.org/10.1063/1.2515315 (4 pages) | Cited 13 times

Online Publication Date: 6 March 2007

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Nonequilibrium molecular dynamics simulations of hen egg white lysozyme have been performed in the canonical ensemble at 298 K in the presence of external electromagnetic fields of varying intensity in the microwave to far-infrared frequency range. Significant nonthermal field effects were noted, such as marked changes in the protein’s secondary structure which led to accelerated incipient local denaturation relative to zero-field conditions. This occurred primarily as a consequence of alignment of the protein’s total dipole moment with the external field, although the enhanced molecular mobility and dipolar alignment of water molecules is influential on sidechain motion in solvent-exposed regions. The applied field intensity was found to be highly influential on the extent of denaturation in the frequency range studied, and 0.25–0.5 V Årms−1 fields were found to induce initial denaturation to a comparable extent to thermal denaturation in the 400 to 500 K range. In subsequent zero-field simulations following exposure to the e/m field, the extent of perturbation from the native fold and the degree of residual dipolar alignment were found to be influential on incipient folding.
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87.15.A- Theory, modeling, and computer simulation
87.15.B- Structure of biomolecules
87.15.H- Dynamics of biomolecules
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back to top Theoretical Methods and Algorithms

Parallel implementation of a direct method for calculating electrostatic potentials

Jonas Jusélius and Dage Sundholm

J. Chem. Phys. 126, 094101 (2007); http://dx.doi.org/10.1063/1.2436880 (9 pages) | Cited 7 times

Online Publication Date: 2 March 2007

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The authors present a method for calculating the electrostatic potential directly in a straightforward manner. While traditional methods for calculating the electrostatic potential usually involve solving the Poisson equation iteratively, the authors obtain the electrostatic interaction potential by performing direct numerical integration of the Coulomb-law expression using finite-element functions defined on a grid. The singularity of the Coulomb operator is circumvented by an integral transformation and the resulting auxiliary integral is obtained using Gaussian quadrature. The three-dimensional finite-element basis is constructed as a tensor (outer) product of one-dimensional functions, yielding a partial factorization of the expressions. The resulting algorithm has, without using any prescreening or other computational tricks, a formal computational scaling of O(N4/3), where N is the size of the grid. The authors show here how to implement the method for efficiently running on parallel computers. The matrix multiplications of the innermost loops are completely independent, yielding a parallel algorithm with the computational costs scaling practically linearly with the number of processors.
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31.15.E- Density-functional theory
31.15.xf Finite-difference schemes
02.30.Jr Partial differential equations
02.60.Jh Numerical differentiation and integration

Electron number probability distributions for correlated wave functions

E. Francisco, A. Martín Pendás, and M. A. Blanco

J. Chem. Phys. 126, 094102 (2007); http://dx.doi.org/10.1063/1.2709883 (13 pages) | Cited 12 times

Online Publication Date: 5 March 2007

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Efficient formulas for computing the probability of finding exactly an integer number of electrons in an arbitrarily chosen volume are only known for single-determinant wave functions [ E. Cancès et al., Theor. Chem. Acc. 111, 373 (2004) ]. In this article, an algebraic method is presented that extends these formulas to the case of multideterminant wave functions and any number of disjoint volumes. The derived expressions are applied to compute the probabilities within the atomic domains derived from the space partitioning based on the quantum theory of atoms in molecules. Results for a series of test molecules are presented, paying particular attention to the effects of electron correlation and of some numerical approximations on the computed probabilities.
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31.15.V- Electron correlation calculations for atoms, ions and molecules
02.50.Cw Probability theory

Continuum treatment of electronic polarization effect

Yu-Hong Tan and Ray Luo

J. Chem. Phys. 126, 094103 (2007); http://dx.doi.org/10.1063/1.2436871 (6 pages) | Cited 3 times

Online Publication Date: 5 March 2007

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A continuum treatment of electronic polarization has been explored for in molecular mechanics simulations in implicit solvents. The dielectric constant for molecule interior is the only parameter in the continuum polarizable model. A value of 4 is found to yield optimal agreement with high-level ab initio quantum mechanical calculations for the tested molecular systems. Interestingly, its performance is not sensitive to the definition of molecular volume, in which the continuum electronic polarization is defined. In this model, quantum mechanical electrostatic field in different dielectric environments from vacuum, low-dielectric organic solvent, and water can be used simultaneously in atomic charge fitting to achieve consistent treatment of electrostatic interactions. The tests show that a single set of atomic charges can be used consistently in different dielectric environments and different molecular conformations, and the atomic charges transfer well from training monomers to tested dimers. The preliminary study gives us the hope of developing a continuum polarizable force field for more consistent simulations of proteins and nucleic acids in implicit solvents.
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87.14.E- Proteins
87.15.B- Structure of biomolecules
87.15.K- Molecular interactions; membrane-protein interactions
36.20.Ey Conformation (statistics and dynamics)
33.15.Bh General molecular conformation and symmetry; stereochemistry

Chemical reaction rates using the semiclassical Van Vleck initial value representation

Charulatha Venkataraman and William H. Miller

J. Chem. Phys. 126, 094104 (2007); http://dx.doi.org/10.1063/1.2567200 (8 pages) | Cited 7 times

Online Publication Date: 6 March 2007

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A semiclassical initial value representation formulation using the Van Vleck [Proc. Natl. Acad. Sci. U.S.A. 14, 178 (1928)] propagator has been used to calculate the flux correlation function and thereby reaction rate constants. This Van Vleck formulation of the flux-flux correlation function is computationally as simple as the classical Wigner [Trans. Faraday Soc. 34, 29 (1938)] model. However, unlike the latter, it has the ability to capture quantum interference/coherence effects. Classical trajectories are evolved starting from the dividing surface that separates reactants and products, and are evolved negatively in time. This formulation has been tested on model problems ranging from the Eckart barrier, double well to the collinear H+H2.
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82.20.Ln Semiclassical theory of reactions and/or energy transfer
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions

Photonic reagent control of dynamically homologous quantum systems

Vincent Beltrani, Jason Dominy, Tak-San Ho, and Herschel Rabitz

J. Chem. Phys. 126, 094105 (2007); http://dx.doi.org/10.1063/1.2434177 (10 pages) | Cited 4 times

Online Publication Date: 7 March 2007

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The general objective of quantum control is the manipulation of atomic scale physical and chemical phenomena through the application of external control fields. These tailored fields, or photonic reagents, exhibit systematic properties analogous to those of ordinary laboratory reagents. This analogous behavior is explored further here by considering the controlled response of a family of homologous quantum systems to a single common photonic reagent. A level set of dynamically homologous quantum systems is defined as the family that produces the same value(s) for a target physical observable(s) when controlled by a common photonic reagent. This paper investigates the scope of homologous quantum system control using the level set exploration technique (L-SET). L-SET enables the identification of continuous families of dynamically homologous quantum systems. Each quantum system is specified by a point in a hypercube whose edges are labeled by Hamiltonian matrix elements. Numerical examples are presented with simple finite level systems to illustrate the L-SET concepts. Both connected and disconnected families of dynamically homologous systems are shown to exist.
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42.50.-p Quantum optics
32.80.Qk Coherent control of atomic interactions with photons
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Theoretical study of the double Renner effect for math 2Π MgNC/MgCN: Higher excited rovibrational states

Tina Erica Odaka, Vladlen V. Melnikov, Per Jensen, Tsuneo Hirano, Bruno Lang, and Peter Langer

J. Chem. Phys. 126, 094301 (2007); http://dx.doi.org/10.1063/1.2464094 (9 pages) | Cited 5 times

Online Publication Date: 1 March 2007

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The authors report here the implementation of a newly developed, highly efficient matrix diagonalization routine in the DR program [ T. E. Odaka et al., J. Mol. Struct. 795, 14 (2006) ]. The DR program solves the rovibronic Schrödinger equation for a triatomic molecule with a double Renner effect, i.e., with two accessible linear arrangements of the nuclei at which the electronic energy is doubly degenerate. With the new routines, the authors can extend the DR calculations of rovibronic energies for math 2Π MgNC/MgCN by considering a much larger set of rovibronic states, in particular, states at higher J values, than the authors were able to access previously.
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33.20.Vq Vibration-rotation analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.A- Ab initio calculations
31.50.Df Potential energy surfaces for excited electronic states

State dynamics of acetylene excited to individual rotational level of the V 12K10,1,2 subbands

Vladimir I. Makarov, Sergei A. Kochubei, and Igor V. Khmelinskii

J. Chem. Phys. 126, 094302 (2007); http://dx.doi.org/10.1063/1.2437205 (12 pages)

Online Publication Date: 1 March 2007

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The dynamics of the IR emission induced by excitation of the acetylene molecule at the 32 Ka2, math 1Au←41 la1, math 1Σg+ transition was investigated. Vibrationally resolved IR emission spectra were recorded at different delay times after the laser excitation pulse. The observed IR emission was assigned to transitions between vibrational levels of the acetylene molecule in the ground state. Values of the relaxation parameters of different vibrational levels of the ground state were obtained. The Ti→Tj transition was detected by cavity ring-down spectroscopy in the 455 nm spectral range after excitation of the acetylene molecule at the 32 K�asame transition. Rotationally resolved spectra of the respective transition were obtained and analyzed at different delay times after the laser excitation pulse. The dynamics of the S1→Tx→T1→S0 transitions was investigated, and the relaxation parameter values were estimated for the T1 state.
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33.20.Ea Infrared spectra
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.50.Df Potential energy surfaces for excited electronic states

Effects of solvation on one- and two-photon spectra of coumarin derivatives: A time-dependent density functional theory study

Kiet A. Nguyen, Paul N. Day, and Ruth Pachter

J. Chem. Phys. 126, 094303 (2007); http://dx.doi.org/10.1063/1.2464110 (10 pages) | Cited 15 times

Online Publication Date: 5 March 2007

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We report one- and two-photon absorption excitation energies and cross sections for a series of 7-aminocoumarins using time-dependent density functional theory with various basis sets and functionals, including exchange-correlation functionals using the Coulomb-attenuating method, to evaluate their performance in the gas phase and in solvents. Except for the results of one functional, the computed one-photon excitation energies and transition dipole moments are in good agreement with experiment. The range of errors obtained from various functionals is discussed in detail. The relationship of donor and acceptor groups with the one- and two-photon resonances and intensities is also discussed.
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31.15.E- Density-functional theory
33.80.-b Photon interactions with molecules
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors

Photodissociation of vibrationally excited SH and SD radicals at 288 and 291 nm: The S(1D2) channel

Liesbeth M. C. Janssen, Mark P. J. van der Loo, Gerrit C. Groenenboom, Shiou-Min Wu, Dragana Č. Radenović, André J. A. van Roij, Ivan Anton Garcia, and David H. Parker

J. Chem. Phys. 126, 094304 (2007); http://dx.doi.org/10.1063/1.2646522 (8 pages) | Cited 8 times

Online Publication Date: 6 March 2007

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Ultraviolet photodissociation of SH (X 2Π, υ″ = 2–7) and SD (X 2Π, υ″ = 3–7) has been studied at 288 and 291 nm, using the velocity map imaging technique to probe the angular and speed distributions of the S(1D2) products. Photodissociation cross sections for the A 2Σ+←X 2Π(υ″) and 2Δ←X 2Π(υ″) transitions have been obtained by ab initio calculations at the CASSCF-MRSDCI/aug-cc-pV5Z level of theory. Both the experimental and theoretical results show that SH/SD photodissociation from X 2Π (υ″ ⩽ 7) proceeds via the repulsive wall of the A 2Σ+ state. The angular distributions of S(1D2) indicate that the dissociation approaches the sudden recoil limit of the A 2Σ+ state, yielding strongly polarized fragments. The S(1D2) atoms are predominantly produced with total electronic angular momentum perpendicular to the recoil axis.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
33.15.Mt Rotation, vibration, and vibration-rotation constants
31.15.xr Self-consistent-field methods
31.15.A- Ab initio calculations

Intermolecular potential and second virial coefficient of the water-nitrogen complex

Akyl S. Tulegenov, Richard J. Wheatley, Matthew P. Hodges, and Allan H. Harvey

J. Chem. Phys. 126, 094305 (2007); http://dx.doi.org/10.1063/1.2446843 (11 pages) | Cited 12 times

Online Publication Date: 6 March 2007

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The authors construct a rigid-body (five-dimensional) potential energy surface for the water-nitrogen complex using the systematic intermolecular potential extrapolation routine. The intermolecular potential is then extrapolated to the limit of a complete basis set. An analytic fit of this surface is obtained, and, using this, the global minimum energy is found. The minimum is located in an arrangement in which N2 is near the H atom of H2O, almost collinear with the OH bond. The best estimate of the binding energy is 441 cm−1 (1 cm−1 ≈ 1.986 43×10−23 J). The extrapolated potential is then used to calculate the second cross virial coefficient over a wide temperature range (100–3000 K). These calculated second virial coefficients are generally consistent with experimental data, but for the most part the former have smaller uncertainties.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
31.15.A- Ab initio calculations
33.15.Fm Bond strengths, dissociation energies

Cross sections for the ionization continuum of H2 in the 15.3–17.2 eV energy range

M. Glass-Maujean, S. Klumpp, L. Werner, A. Ehresmann, and H. Schmoranzer

J. Chem. Phys. 126, 094306 (2007); http://dx.doi.org/10.1063/1.2435345 (3 pages) | Cited 1 time

Online Publication Date: 6 March 2007

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The absolute values for the cross sections of the ionization continuum of H2 had been measured at low energy (15.3–17.2 eV) Both absorption and ionization spectra were simultaneously recorded with linear response and absolute values, using a 10 m normal incidence monochromator installed on a synchrotron undulator beamline. The vibrational thresholds can be clearly seen as steps in the experimental data. The agreement between experimental values and theoretical ones is very good except around the first and second vibrational thresholds where the experimental data exceed the theoretical ones.
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33.80.Eh Autoionization, photoionization, and photodetachment
33.15.Mt Rotation, vibration, and vibration-rotation constants
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Gaussian excitations model for glass-former dynamics and thermodynamics

Dmitry V. Matyushov and C. Austen Angell

J. Chem. Phys. 126, 094501 (2007); http://dx.doi.org/10.1063/1.2538712 (19 pages) | Cited 18 times

Online Publication Date: 6 March 2007

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We describe a model for the thermodynamics and dynamics of glass-forming liquids in terms of excitations from an ideal glass state to a Gaussian manifold of configurationally excited states. The quantitative fit of this three parameter model to the experimental data on excess entropy and heat capacity shows that “fragile” behavior, indicated by a sharply rising excess heat capacity as the glass transition is approached from above, occurs in anticipation of a first-order transition—usually hidden below the glass transition—to a “strong” liquid state of low excess entropy. The distinction between fragile and strong behavior of glass formers is traced back to an order of magnitude difference in the Gaussian width of their excitation energies. Simple relations connect the excess heat capacity to the Gaussian width parameter, and the liquid-liquid transition temperature, and strong, testable, predictions concerning the distinct properties of energy landscape for fragile liquids are made. The dynamic model relates relaxation to a hierarchical sequence of excitation events each involving the probability of accumulating sufficient kinetic energy on a separate excitable unit. Super-Arrhenius behavior of the relaxation rates, and the known correlation of kinetic with thermodynamic fragility, both follow from the way the rugged landscape induces fluctuations in the partitioning of energy between vibrational and configurational manifolds. A relation is derived in which the configurational heat capacity, rather than the configurational entropy of the Adam–Gibbs equation, controls the temperature dependence of the relaxation times, and this gives a comparable account of the experimental observations without postulating a divergent length scale. The familiar coincidence of zero mobility and Kauzmann temperatures is obtained as an approximate extrapolation of the theoretical equations. The comparison of the fits to excess thermodynamic properties of laboratory glass formers, and to configurational thermodynamics from simulations, reveals that the major portion of the excitation entropy responsible for fragile behavior resides in the low-frequency vibrational density of states. The thermodynamic transition predicted for fragile liquids emerges from beneath the glass transition in case of laboratory water and the unusual heat capacity behavior observed for this much studied liquid can be closely reproduced by the model.
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65.20.-w Thermal properties of liquids
64.70.Ja Liquid-liquid transitions
64.70.P- Glass transitions of specific systems
64.70.Q- Theory and modeling of the glass transition
63.50.-x Vibrational states in disordered systems
61.25.Em Molecular liquids

Computer simulation of nucleation in a gas-saturated liquid

S. P. Protsenko, V. G. Baidakov, A. S. Teterin, and E. R. Zhdanov

J. Chem. Phys. 126, 094502 (2007); http://dx.doi.org/10.1063/1.2426345 (14 pages) | Cited 1 time

Online Publication Date: 6 March 2007

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Molecular dynamics methods have been used to investigate the kinetics of the liquid-gas phase transition in a two-component Lennard-Jones system at negative pressures and elastic stretches of the liquid to values close to spinodal ones. The molecular dynamics system consists of 2048 interacting particles with parameters of the Lennard-Jones potential for argon and neon. Density dependences of pressure and internal energy have been calculated for stable and metastable states of the mixture at a temperature T* ≈ 0.7±0.01 and three values of the concentration. The location of mechanical and the diffusion spinodals has been determined. It has been established that a gas-saturated mixture retains its stability against finite variations of state variables up to stretches close to the values near the diffusion spinodal. The statistic laws of the process of destruction of the metastable state have been investigated. The lifetimes of the metastable phase have been determined. It is shown that owing to the small height of the potential barrier that separates the microheterogeneous from the homogeneous state a system of finite size has a possibility to make the reverse transition from the microheterogeneous into the homogeneous state. The lifetimes of the system in the microheterogeneous state, as well as the expectation times of the occurrence of a critical nucleus, are described by Poissonian distributions.
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64.60.Q- Nucleation
64.60.My Metastable phases
64.70.F- Liquid-vapor transitions
64.60.Cn Order-disorder transformations

Induced thermal dynamics in the melt of glycerol and aerosil dispersions

Dipti Sharma and Germano S. Iannacchione

J. Chem. Phys. 126, 094503 (2007); http://dx.doi.org/10.1063/1.2539000 (6 pages) | Cited 8 times

Online Publication Date: 7 March 2007

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A high-resolution calorimetric spectroscopy study has been performed on pure glycerol and colloidal dispersions of an aerosil gel in glycerol covering a wide range of temperatures from 300 to 380 K, deep in the liquid phase of glycerol. The colloidal glycerol+aerosil samples with 0.07, 0.14, and 0.32 g of silica per cm3 of glycerol reveal activated energy (thermal) dynamics at temperatures well above the Tg of the pure glycerol. The onset of these dynamics appears to be due to the frustration or pinning imposed by the silica gel on the glycerol liquid and is apparently a long-range, cooperative phenomena. Since this behavior begins to manifest itself at relatively low silica densities (large mean void length compared to the size of a glycerol molecule) and speeds up with increasing density, these induced dynamics are likely due to a coupling between the flexible aerosil gel and large groups of glycerol molecules mediated by mutual hydrogen bonding. This is supported by the lack of such thermal dynamics in pure aerosil gels, pure glycerol, or aerosil gels dispersed in a non-glass-forming, non-hydrogen-bonding, liquid crystal under nearly identical experimental conditions. The study of such frustrated colloids may provide a unique avenue for illuminating the physics of glasses.
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82.70.Rr Aerosols and foams
82.70.Dd Colloids
82.70.Gg Gels and sols
66.25.+g Thermal conduction in nonmetallic liquids
back to top Surfaces, Interfaces, and Materials

Phase diagram and adsorption-desorption kinetics of CO on Ru(0001) from first principles

J.-S. McEwen and A. Eichler

J. Chem. Phys. 126, 094701 (2007); http://dx.doi.org/10.1063/1.2464085 (14 pages) | Cited 8 times

Online Publication Date: 1 March 2007

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A kinetic lattice gas model is used to study the equilibrium properties and the desorption kinetics of CO on Ru(0001). The authors compute all relevant on-site binding and interaction energies of CO molecules within density functional theory and import them in two different models. The first model allows the CO molecules to adsorb upright on top and hollow sites. The authors calculate the phase diagram, coverage isobars, and temperature programed desorption spectra. Up to a coverage of 1/3 ML, very good agreement is obtained between theory and experiment when considering top sites only. For coverages beyond 1/3 ML, hollow sites are included and disagreement between theory and experiment occurs. The second model allows adsorption on top sites only but allows them to tilt and shift from their upright positions. The authors show that this model resolves many of the deficiencies of their first one. Furthermore, the authors demonstrate that this model is more consistent with experiment since it is the only model that is able to explain the results from IR-spectroscopy experiments.
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68.43.Mn Adsorption kinetics
68.43.Vx Thermal desorption
68.43.Bc Ab initio calculations of adsorbate structure and reactions
81.30.Dz Phase diagrams of other materials

Mesoscopic simulations of the diffusivity of ethane in beds of NaX zeolite crystals: Comparison with pulsed field gradient NMR measurements

George K. Papadopoulos, Doros N. Theodorou, Sergey Vasenkov, and Jörg Kärger

J. Chem. Phys. 126, 094702 (2007); http://dx.doi.org/10.1063/1.2567129 (8 pages) | Cited 6 times

Online Publication Date: 2 March 2007

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Mesoscopic kinetic Monte Carlo simulations and pulsed field gradient nuclear magnetic resonance (PFG NMR) measurements are compared in order to investigate the transport of ethane in a bed of NaX crystals. A novel molecular mechanics particle-based reconstruction method is employed for the digital representation of the bed, enabling for the first time a parallel study of the real system and of a computer model tailored to reproduce the void fraction, particle shape and average size of the real system. Simulation of the long-range diffusion of ethane in the bed over the Knudsen, transient, and molecular diffusion regimes is consistent with the PFG NMR measurements in yielding tortuosity factors which depend upon the regime of diffusion; more specifically, tortuosity factors defined in the conventional way are higher in the Knudsen than in the molecular diffusion regime. Detailed statistical analysis of the computed molecular trajectories reveals that this difference arises in a nonexponential distribution of the lengths and in a correlation between the directions of path segments traversed between collisions with the solid in the Knudsen regime. When the Knudsen tortuosity is corrected to account for these features, a single, regime-independent value is obtained within the error of the calculations.
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61.43.Bn Structural modeling: serial-addition models, computer simulation
66.30.H- Self-diffusion and ionic conduction in nonmetals
76.60.-k Nuclear magnetic resonance and relaxation

Computational study of hydrogen storage in organometallic compounds

Philippe F. Weck, T. J. Dhilip Kumar, Eunja Kim, and Naduvalath Balakrishnan

J. Chem. Phys. 126, 094703 (2007); http://dx.doi.org/10.1063/1.2710264 (6 pages) | Cited 31 times

Online Publication Date: 5 March 2007

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The authors have performed a systematic computational study of the hydrogen storage capacity of model organometallic compounds consisting of Sc, Ti, and V transition metal atoms bound to CmHm rings (m = 4–6). For all the complexes considered, the hydrogen storage capacity is limited by the 18-electron rule. The maximum retrievable H2 uptake predicted is 9.3 wt % using ScC4H4, slightly better than the 9.1 wt % hydrogen using TiC4H4, and much larger than the ∼ 7 wt % hydrogen with VC4H4, where only four H2 molecules can be adsorbed. The kinetic stability of these hydrogen-covered organometallic complexes is reviewed in terms of the energy gap between the highest occupied and lowest unoccupied molecular orbitals and the strength and nature of successive H2 bindings.
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84.60.-h Direct energy conversion and storage
68.43.Mn Adsorption kinetics
71.20.Rv Polymers and organic compounds

Simple density functional approach to adsorption of biomolecules on solid surfaces

K. Bucior, J. Fischer, A. Patrykiejew, R. Tscheliessnig, and S. Sokolowski

J. Chem. Phys. 126, 094704 (2007); http://dx.doi.org/10.1063/1.2566372 (10 pages) | Cited 7 times

Online Publication Date: 6 March 2007

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A simple density functional approach for modeling the adsorption of biomolecules is considered. The model comprises a three-component mixture consisting of spherical and differently charged ions and chain molecules. Spherical ions can form associative bonds with selected segments of a chain. To enable the formation of bonds between chain segments and spherical ions, the statistical associating fluid theory is applied. The present theory is used to study the structure of adsorbed layers, the excess adsorption isotherms, and the capacitance of the double layer.
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87.15.K- Molecular interactions; membrane-protein interactions
82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
82.45.Gj Electrolytes

Estimation of line tension and contact angle from heterogeneous nucleation experimental data

A. I. Hienola, P. M. Winkler, P. E. Wagner, H. Vehkamäki, A. Lauri, I. Napari, and M. Kulmala

J. Chem. Phys. 126, 094705 (2007); http://dx.doi.org/10.1063/1.2565769 (11 pages) | Cited 14 times

Online Publication Date: 6 March 2007

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Using the classical nucleation theory corrected with line tension and experimental data of heterogeneous nucleation of n-nonane, n-propanol, and their mixture on silver particles of three different sizes, the authors were able to estimate the line tensions and the microscopic contact angles for the above mentioned systems. To do this they applied generalized Young’s equation for the line tension and calculated the interfacial tensions using Li and Neumann's equation [Adv. Colloid Interface Sci. 39, 299 (1992) ]. It has been found that, for both unary and binary systems, the line tension is negative and the resulting microscopic contact angle derived from experimental nucleation data is most of the time larger than the macroscopic one. This is in contrast to earlier studies where the influence of line tension has not been accounted for. The values of the three phase contact line tension obtained in this way are of the same order of magnitude as the estimations for other systems reported in literature. The line tension effect also decreases considerably the nucleation barrier.
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64.60.Q- Nucleation
68.03.Cd Surface tension and related phenomena

Gold nanoparticle multilayer films based on surfactant films as a template: Preparation, characterization, and application

Yancai Li, Ji Zhou, Kai Zhang, and Changqing Sun

J. Chem. Phys. 126, 094706 (2007); http://dx.doi.org/10.1063/1.2710265 (7 pages) | Cited 2 times

Online Publication Date: 7 March 2007

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Highly ordered gold nanoparticle multilayer films were achieved conveniently using didodecyldimethylammonium bromide (DDAB) films as a template. The template was produced by casting DDAB chloroform solution onto the surface of a (3-aminopropyl)trimethoxysilane-modified indium tin oxide substrate and then evaporating the organic solvent. Gold nanoparticle multilayer films were prepared by soaking the template in 2.6 nm colloidal gold solution for 120 min. The well-ordered superlattice structure of the DDAB template and the gold nanoparticle multilayer films was identified by x-ray diffraction. The characterizations of the gold nanoparticle multilayer films by UV-vis spectroscopy, atomic force microscopy, and cyclic voltammerty were described in detail. The application of the as-prepared gold nanoparticle multilayer films in surface-enhanced Raman spectroscopy (SERS) was investigated by using Rhodamine 6G as a probe molecule. It was found that the colloidal gold nanoparticle multilayer films exhibit remarkable enhancement ability and can be used as SERS substrates.
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81.15.Lm Liquid phase epitaxy; deposition from liquid phases (melts, solutions, and surface layers on liquids)
68.55.-a Thin film structure and morphology
78.30.Er Solid metals and alloys
78.40.Kc Metals, semimetals, and alloys
78.66.Bz Metals and metallic alloys
78.67.Pt Multilayers; superlattices; photonic structures; metamaterials
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