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The numerical algorithms for the discrete variable representation (DVR) basis sets based ab initio molecular dynamics (AIMD) scheme are provided and the accuracy and stability of the implementation of the DVR/AIMD scheme are tested by performing a simulation of liquid water at ambient conditions. The results show that a DVR/AIMD simulation of liquid water in the complete basis set limit is possible with a relatively small number of grid points as compared to the plane wave (PW) basis sets/AIMD method.

The theoretical study of (LiMe)(sub n) aggregates using Car-Parrinello molecular dynamics was undertaken and with respect to a quantum chemical static treatment, this approach furnishes supplementary information about the structural parameters. Results found that parameter-free ab intio molecular dynamics method is introduced.

The (super 17)O NMR parameters of an amorphous calcium aluminisilicate (CAS) is computed from first-principles. The atomic coordinates of a CAS glass of composition (CaO)0.21(Al2O3)0.12(SiO2)0.67 were obtained by quenching a liquid to room temperature by the means of ab initio molecular-dynamics simulations of the Car-Parrinello type.

A study was conducted to investigate the isothermal-isobaric molecular dynamics methods in system subject to holonomic constraints with the goal of devising equations of motion in which the scaling is performed on atomic positions. The result demonstrates that the Kneller-Mulders equations generate an isothermal-isobaric ensemble distribution only for systems with nonzero total force.

The different methods to calculate the accurate vibrational energy relaxation rates for high-frequency modes from classical molecular dynamics simulations are presented. The features and advantages of Fermi's golden rule, a convenient starting point for calculating the vibrational energy relaxation rate constants, are discussed.

A study was conducted to examine the structural and thermodynamic properties of a water droplet enclosed in a spherical cavity embedded in a hydrophobic material. The results indicate that the structure of water near an impenetrable and purely repulsive surface at standard conditions of temperature and pressure is described as a dry, separated state.

A study was conducted to investigate the thermodynamic and structural properties of a Lennard-Jones liquid at a state very close to the triple point as the radius of a hard sphere solute is varied. The result reveals that the oscillatory profiles arise for small, molecular sized radii, where as for large radii smooth interfaces with a drying layer of low vapor density near the solute are seen.

The numerical calculations of the concentration of interstitials in hard-sphere crystals are presented. In a three-dimensional fcc hard-sphere crystal at the melting pint, the concentration of interstitials is 2.7(4) x 10(super -8).

The various important issues related to the implementation of the nonadiabatic dynamics methods in the situation, where quasi-nonavoided crossings take place and play a crucial role in determining the dynamics, are presented. The important connection between dynamics, local environmental symmetry, and electronic structure in determining nonadiabatic relaxation is discussed.

The method of ab initio molecular dynamics was used to study the structural, dynamical, and electronic properties of ionic defects in liquid ammonia at 260 K created by the addition or removal of a proton. The result reveals that the NH4(super +) exhibits a characteristic cationic solvation pattern, in which it donates four hydrogen bonds to neighboring ammonia molecules, giving it a coordination number of 4.

Investigation of crystalline nitric acid trihydrate properties at 195 K has been carried out by means of Car-Parrinello molecular dynamics calculations. Results demonstrate that a proton requires free energy to reach the center of the oxygen-oxygen pair.

The article explains the various mechanisms that are involved in the concerted proton-electron transfer (CPET) taking place during the homogeneous reduction of dioxygen to water. The CPET is shown to significantly decreases with decrease in the endergonicity of ET.

The synthesis, properties and the stability of the various intermolecular and enol tautomers of the Watson-Crick base pair models are discussed. These compounds are shown to be dynamically metastable.

The molecular dynamics simulations performed at constant temperature and pressure to explore ethanolamines pure components and in aqueous solutions are presented. The excess molar volume is slightly overestimated in diethanolamine (DEA) at all concentrations and in methyldiethanolamine (MDEA) at low concentrations of ethanolamine.

Density functional theory QM/MM studies were carried out on the deacetylation reaction catalyzed by histone-deacetylase-like-protein (HDLP) in order to characterize the catalytic mechanism for histone-deacetylase (HDACs). The calculations were based on the pseudobond ab initio QM/MM approach, which was successfully employed in the study of several enzymes and were carried out with modified versions of the Gaussian03 and TINKER programs.

Ab initio molecular dynamics simulations are employed to study the structural and proton transport properties of methanol-water mixtures. Structural characteristics analyzed at two different methanol mole fractions reveal enhanced structuring of water as the methanol mole fraction increases in agreement with recent neutron diffraction experiments.

Three popular density functionals have been used to perform a virtual experiment on how different proposed solvation patterns for OH-(aq) influence the microscopic transport mechanism. It suggests that the solvation pattern of OH (super -) (aq) is not analogues to that of H+ (aq), implying that its structural diffusion mechanism cannot be a simple mirror image picture of the later.

Adiabatic free-energy dynamics (AFED) are used to generate the Ramachandran free-energy surfaces of the alanine di- and tripeptides in a vacuum and in solution using the CHARMM22 force field. It was found that the AFED method could be a powerful tool for studying multidimensional free-energy surfaces in complex systems.

A finite temperature ab inito molecular dynamics (AIMD) study is undertaken using forces obtained 'on the fly' from electronic structure calculations to investigate the addition product distribution as well as the underlying mechanistic aspects of the reaction. The method highlights the predominance of a stepwise zwitterionic mechanism governing addition product formation on the Si(100)-2 X 1 surface.

The mechanism of the reaction pathway of the [4 + 2] Diels-Alder adduct formation on Si(100)-2x1 surface is described. The ab initio molecular dynamics (AIMD) study shows that forces are generated 'on the fly' from electronic structure calculations.

An ab initio molecular dynamics (MD) study, of concentration effects in an aqueous KOH solution, was conducted to investigate the effect of concentration on a directly measurable quantity named infrared (IR) spectrum, as well as on the proton transport mechanism. The result reveals the mechanisms are due to the mobility of both K(super +) and OD(super -) at higher concentration.

The hydrated morphology of either proton exchange membranes (PEMs) or anion exchange membranes (AEMs) determines many aspects of species transport. The present work seeks to understand the morphology and microstructure of a triblock copolymer, polystyrene-b-poly(ethylene-co-butylene)-b-polystyrene (SEBS), functionalized with alkyl-substituted quaternary ammonium groups. Mesoscale dissipative particle dynamics (DPD) simulations were utilized and parametrized by reproducing the experimental morphology of the SEBS copolymer. It was found that the AEM (i.e., quaternary ammonium-functionalized SEBS) phase separates into a functionalized polystyrene-rich phase that is hydrophilic and a hydrophobic phase consisting of the SEBS mid-blocks. The morphology was controlled by the water content and was transformed from perforated and interconnected lamellae to perfect lamellae and then to disordered bicontinuous domains by increasing the hydration level (λ = H2O/functional head group) from 4 to 20. The hydrophilic phase swelled upon the hydration of the membrane consistent with AFM phase imaging of a similar SEBS-based ionomer. Domains exclusively consisting of water were formed at high levels of hydration (λ = 16 and 20) within the hydrophilic phase. Changing the anion from OH– to Cl– resulted in larger water domains at the highest hydration levels. [ABSTRACT FROM AUTHOR]