Volume 126, Issue 9, 07 March 2007
Index of content:
- Theoretical Methods and Algorithms
126(2007); http://dx.doi.org/10.1063/1.2436880View Description Hide Description
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 , where 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.
126(2007); http://dx.doi.org/10.1063/1.2709883View Description Hide Description
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.
126(2007); http://dx.doi.org/10.1063/1.2436871View Description Hide Description
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.
126(2007); http://dx.doi.org/10.1063/1.2567200View Description Hide Description
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 .
126(2007); http://dx.doi.org/10.1063/1.2434177View Description Hide Description
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.
- Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry
126(2007); http://dx.doi.org/10.1063/1.2464094View Description Hide Description
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 MgNC/MgCN by considering a much larger set of rovibronic states, in particular, states at higher values, than the authors were able to access previously.
126(2007); http://dx.doi.org/10.1063/1.2437205View Description Hide Description
The dynamics of the IR emission induced by excitation of the acetylene molecule at the , 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 transition was detected by cavity ring-down spectroscopy in the spectral range after excitation of the acetylene molecule at the same 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 transitions was investigated, and the relaxation parameter values were estimated for the state.
Effects of solvation on one- and two-photon spectra of coumarin derivatives: A time-dependent density functional theory study126(2007); http://dx.doi.org/10.1063/1.2464110View Description Hide Description
We report one- and two-photon absorptionexcitation 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.
126(2007); http://dx.doi.org/10.1063/1.2646522View Description Hide Description
Ultraviolet photodissociation of SH (, ) and SD (, ) has been studied at 288 and , using the velocity map imaging technique to probe the angular and speed distributions of the products. Photodissociation cross sections for the and 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 proceeds via the repulsive wall of the state. The angular distributions of indicate that the dissociation approaches the sudden recoil limit of the state, yielding strongly polarized fragments. The atoms are predominantly produced with total electronic angular momentum perpendicular to the recoil axis.
126(2007); http://dx.doi.org/10.1063/1.2446843View Description Hide Description
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 is near the H atom of , almost collinear with the OH bond. The best estimate of the binding energy is . The extrapolated potential is then used to calculate the second cross virial coefficient over a wide temperature range . These calculated second virial coefficients are generally consistent with experimental data, but for the most part the former have smaller uncertainties.
126(2007); http://dx.doi.org/10.1063/1.2435345View Description Hide Description
The absolute values for the cross sections of the ionization continuum of had been measured at low energy Both absorption and ionizationspectra were simultaneously recorded with linear response and absolute values, using a 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.
- Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation
126(2007); http://dx.doi.org/10.1063/1.2538712View Description Hide Description
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-liquidtransition 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 excitationentropy 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.
126(2007); http://dx.doi.org/10.1063/1.2426345View Description Hide Description
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 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.
126(2007); http://dx.doi.org/10.1063/1.2539000View Description Hide Description
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 , deep in the liquid phase of glycerol. The colloidal samples with 0.07, 0.14, and of silica per of glycerol reveal activated energy (thermal) dynamics at temperatures well above the of the pure glycerol. The onset of these dynamics appears to be due to the frustration or pinning imposed by the silicagel 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.
- Surfaces, Interfaces, and Materials
126(2007); http://dx.doi.org/10.1063/1.2464085View Description Hide Description
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 ML, very good agreement is obtained between theory and experiment when considering top sites only. For coverages beyond 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.
Mesoscopic simulations of the diffusivity of ethane in beds of NaX zeolite crystals: Comparison with pulsed field gradient NMR measurements126(2007); http://dx.doi.org/10.1063/1.2567129View Description Hide Description
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.
126(2007); http://dx.doi.org/10.1063/1.2710264View Description Hide Description
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 rings . For all the complexes considered, the hydrogen storage capacity is limited by the 18-electron rule. The maximum retrievable uptake predicted is using , slightly better than the hydrogen using , and much larger than the hydrogen with , where only four 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 bindings.
126(2007); http://dx.doi.org/10.1063/1.2566372View Description Hide Description
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.
126(2007); http://dx.doi.org/10.1063/1.2565769View Description Hide Description
Using the classical nucleation theory corrected with line tension and experimental data of heterogeneous nucleation of -nonane, -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.
Gold nanoparticle multilayer films based on surfactant films as a template: Preparation, characterization, and application126(2007); http://dx.doi.org/10.1063/1.2710265View Description Hide Description
Highly ordered goldnanoparticlemultilayerfilms 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. Goldnanoparticlemultilayerfilms were prepared by soaking the template in colloidalgold solution for . The well-ordered superlattice structure of the DDAB template and the goldnanoparticlemultilayerfilms was identified by x-ray diffraction. The characterizations of the goldnanoparticlemultilayerfilms by UV-vis spectroscopy, atomic force microscopy, and cyclic voltammerty were described in detail. The application of the as-prepared goldnanoparticlemultilayerfilms in surface-enhanced Raman spectroscopy (SERS) was investigated by using Rhodamine 6G as a probe molecule. It was found that the colloidalgoldnanoparticlemultilayerfilms exhibit remarkable enhancement ability and can be used as SERS substrates.