This paper describes a new method for incorporating the extra mean force terms of solvent including the Coulombic interactions with the induced surface charge and surface pressure of solvent into stochastic dynamics simulation. The boundary element method based on the classical continuum approximation has been used to evaluate those mean force terms. Calculations with our method have been perfo...

Photofragmentation of size-selected I2(CO2)n cluster ions and the subsequent cage recombination of the photodissociated I2 chromophore are observed to occur with high efficiency and on a ps time scale, for even partially solvated ions. This result is observed for dissociation on either ground state (I– + I) or spin-orbit excited (I– + I*) state surfaces. With intimate interplay between theory a...

We investigate the solvent-mediated interactions between nanoparticles adsorbed at a liquid-vapor interface in comparison to the solvent-mediated interactions in the bulk liquid and vapor phases of a Lennard-Jones solvent. Molecular dynamics simulation data for the latter are in good agreement with results from integral equations in the reference functional approximation and a simple geometric ...

The molecular mechanisms in both vibrational relaxation and proton transfer (PT) associated with infrared (IR)-induced PT in a dilute hydrofluoric acid solution at ambient temperature are studied by molecular dynamics (MD) simulations with the multistate empirical valence bond model. To investigate the solvation dynamics, a collective solvent coordinate and its perpendicular bath modes are defi...

A method for determining the activity of the solvent in electrolyte solutions by molecular dynamics simulations is presented. The electrolyte solution is simulated in contact with the pure solvent. Between the two phases, there is a virtual membrane, which is permeable only for the solvent. In the simulation, this is realized by an external field which acts only on the solutes and confines them...

Recent work has shown that the nature of hydration of pure hydrophobic surfaces changes with the length scale considered: water hydrogen-bonding networks adapt to small exposed hydrophobic species, hydrating or "wetting" them at relatively high densities, whereas larger hydrophobic areas are "dewetted" [Chandler D (2005), Nature 29:640-647]. Here we determine whether this effect is also present...

Human carbonic anhydrase II (HCA II) is a zinc-metalloenzyme that catalyzes the reversible interconversion of CO2 and HCO3-. The rate-limiting step of this catalysis is the transfer of a proton between the Zn-bound solvent molecule and residue His64. In order to fully characterize the active site structural features implicated in the proton transfer mechanism, the refined X-ray crystal structur...

Adequate sampling of conformation space remains challenging in atomistic simulations, especially if the solvent is treated explicitly. Implicit-solvent simulations can speed up conformational sampling significantly. We compare the speed of conformational sampling between two commonly used methods of each class: the explicit-solvent particle mesh Ewald (PME) with TIP3P water model and a popular ...