Donald K. Phelps

Solvent Dynamical Effects in Electron Transfer: Molecular Dynamics Simulations of Reactions in Methanol

Abstract Molecular-dynamics simulations of solvation dynamics accompanying activated electron-transfer (ET) reactions in methanol have been undertaken in order to explore the physical nature of the solvent dynamics coupled to ET barrier crossing, and to probe some underlying reasons for the facile kinetics observed in this solvent. The reactant is modeled by a pair of Lennard-Jones (LJ) spheres in contact, of varying diameter (4 or 5 A), and containing a univalent charge (cation or anion) on one site so to probe possible effects of the ionic charge sign. Following equilibration, the collective solvent response to a sudden charge transfer between the spherical sites is followed, and described in terms of the response function C ( t ), describing the difference in the solvent-induced electrostatic potential between the initial and final solute states. In all cases, the C ( t ) curves exhibit a very rapid (50–100 fs) initial decay component associated with hydroxyl inertial motion, followed by components arising from hydrogen-bond librational and diffusive motions. Interestingly, the dynamics and relative importance of these relaxation modes are dependent on the charge sign as well as size of the solute pair. The molecular-level origins of these sensitivities are explored by examining time-dependent radial distribution functions, which implicate the dominance of short-range solvation in the rapid relaxation dynamics. In particular, the initial very rapid C ( t ) component for the smaller anion-neutral reactant pair is seen to arise chiefly from dissipation of the hydroxyl solvent polarization around the newly formed neutral site following ET, being accompanied by a slower build up of solvent structuring around the adjacent anionic site. The simulated ET reorganization energies are also shown to be dependent upon the reactant size and charge type. Some more general implications of these and other MD simulation results to the elucidation of dynamical solvent effects in activated ET processes are also noted.

Nonlocal electrostatic effects on polar solvation dynamics

A phenomenological theory of polar solvation dynamics in electron transfer that accounts for the spatial‐ and frequency‐dependent dielectric function of the solvent is developed and described in a format appropriate to time‐dependent fluorescence Stokes shifts. The basic features of the relaxation dynamics are explored by using various analytical expressions for the dielectric function. The presence of spatial correlations persisting to frequencies higher than those corresponding to longitudinal solvent relaxation, τ−1L, yields significant or even substantial decay components with relaxation times shorter than τL. These are associated with motions of individual molecules within the solvent structural network. The implications of these predictions for solvation dynamics in activated charge‐transfer processes are noted.

Theoretical studies of viral capsid proteins.

Recent results in structural biology and increases in computer power have prompted initial theoretical studies on capsids of nonenveloped icosahedral viruses. The macromolecular assembly of 60 to 180 protein copies into a protein shell results in a structure of considerable size for molecular dynamics simulations. Nonetheless, progress has been made in examining these capsid assemblies from molecular dynamics calculations and kinetic models. The goals of these studies are to understand capsid function and structural properties, including quarternary structural stability, effects of antiviral compounds that bind the capsid and the self-assembly process. The insight that can be gained from the detailed information provided by simulations is demonstrated in studies of human rhinovirus; an entropic basis for the antiviral activity of hydrophobic compounds, predicted from calculated compressibility values, has been corroborated by experimental measurements on poliovirus.

First principle and ReaxFF molecular dynamics investigations of formaldehyde dissociation on Fe(100) surface.

Detailed formaldehyde adsorption and dissociation reactions on Fe(100) surface were studied using first principle calculations and molecular dynamics (MD) simulations, and results were compared with available experimental data. The study includes formaldehyde, formyl radical (HCO), and CO adsorption and dissociation energy calculations on the surface, adsorbate vibrational frequency calculations, density of states analysis of clean and adsorbed surfaces, complete potential energy diagram construction from formaldehyde to atomic carbon (C), hydrogen (H), and oxygen (O), simulation of formaldehyde adsorption and dissociation reaction on the surface using reactive force field, ReaxFF MD, and reaction rate calculations of adsorbates using transition state theory (TST). Formaldehyde and HCO were adsorbed most strongly at the hollow (fourfold) site. Adsorption energies ranged from −22.9 to −33.9 kcal/mol for formaldehyde, and from −44.3 to −66.3 kcal/mol for HCO, depending on adsorption sites and molecular direction. The dissociation energies were investigated for the dissociation paths: formaldehyde → HCO + H, HCO → H + CO, and CO → C + O, and the calculated energies were 11.0, 4.1, and 26.3 kcal/mol, respectively. ReaxFF MD simulation results were compared with experimental surface analysis using high resolution electron energy loss spectrometry (HREELS) and TST based reaction rates. ReaxFF simulation showed less reactivity than HREELS observation at 310 and 523 K. ReaxFF simulation showed more reactivity than the TST based rate for formaldehyde dissociation and less reactivity than TST based rate for HCO dissociation at 523 K. TST‐based rates are consistent with HREELS observation.