Photoelectron-photofragment coincidence ~PPC! spectroscopy has been used to study the dissociative photodetachment of H2O2 2 and D2O2 . The observed partitioning of photoelectron and photofragment translational energies provides information on the dynamics in the transition state region of the reaction between two hydroxyl radicals: OH1OH→O(P)1H2O. The data reveal vibrationally resolved product...

Ionization potential (ionization energy) is a fundamental quantity characterizing electronic structure of a molecule. It is known that the energy in solution phase is significantly different from that in the gas phase. In this report, vertical and adiabatic ionization processes in aqueous solution are studied based on a hybrid method of quantum chemistry and statistical mechanics called referen...

Transfer energetics from pure water to a urea-water mixture is examined for a set of amino acid analog solutes by using molecular dynamics simulation and free-energy calculation. The free energy of transfer from pure-water solvent to 8 M urea-water mixed solvent is calculated for each solute, and the urea-water mixture is shown to be a more favorable solvent than pure water. The correlation of ...

The folding kinetics of a seven-residue long alanine polypeptide are investigated using a fully atomic protein model and molecular dynamics simulations. The peptide adopts helical conformations in the native state when simulated in two different implicit solvents: a model with a distance dependent dielectric constant and the generalized Born (GB) model. Although the two solvation models correct...

In an implicit-solvent description of molecular solvation, the electrostatic free energy is given through the electrostatic potential. This potential solves a boundary-value problem of the Poisson-Boltzmann equation in which the dielectric coefficient changes across the solute-solvent interface-the dielectric boundary. The dielectric boundary force acting on such a boundary is the negative firs...

in this study, the effect of the secondary structure of the protein on the acid strength of three structures of random (r), alpha helix (α) and beta sheet (b) were investigated theoretically. these structures are related to the cationic amino acids of histidine and lysine in the polypeptide chain of eight-glycine residue. computational methods at the hf, b3lyp, x3lyp and m05-2x levels in the ga...

Successful applications of molecular dynamics ( MD ) to study the structure and function of a biomolecule depend on the quality of the underlying force fi eld and the sampling effi ciency of the simulation protocol. In particular, an accurate representation of the aqueous solvent environment is important to reproduce the structural, functional, and dynamic behavior of soluble biomolecule s. The...

We develop a model of electron transfer reactions at conditions of nonergodicity when the time of solvent relaxation crosses the observation time window set up by the reaction rate. Solvent reorganization energy of intramolecular electron transfer in a charge-transfer molecule dissolved in water and acetonitrile is studied by molecular dynamics simulations at varying temperatures. We observe a ...