title: Determination of proton transfer rate constants using Ab initio, molecular dynamics and density matrix evolution calculations.
abstract: In this work we give an overview of the methodologies required to compute the rate of proton transfer in hydrogen bonded systems in solution. Using ab initio or density functional methods we determine proton potentials of a truncated system as a function of proton-donor proton-acceptor distance as well as nonbonding parameters. By classical molecular dynamics we evaluate a swarm of proton potentials with the proton fixed in the reactant well. The rate of proton transfer is calculated perturbatively using the Density Matrix Evolution (DME) method, going beyond the Born Oppenheimer approximation. The method is illustrated by two examples: hydrogen malonate and the active center of HIV-1 protease.
authors.affiliation: BIOSON Research Institute, Department of Biophysical Chemistry, University of Groningen, The Netherlands.
authors.forename: D
authors.initials: D
authors.lastname: van der Spoel
authors.forename: H J
authors.initials: HJ
authors.lastname: Berendsen
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D016333:HIV Protease / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D007700:Kinetics; D008314:Malonates / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D011522:Protons; D012984:Software
chemical_list: D008314:Malonates; D011506:Proteins; D011522:Protons; C030290:malonic acid; D016333:HIV Protease