title: Averaging techniques for reaction barriers in QM/MM simulations.
abstract: Herein, we test and compare different techniques to obtain averaged reaction barriers from quantum mechanics/molecular mechanics (QM/MM) simulations based on snapshots taken from molecular dynamics. Reasonable values can be obtained from a fairly small sample of well-chosen snapshots if an exponential averaging, also called Boltzmann averaging, is used. Snapshots with geometries close to the expected transition state are to be picked preferentially. Exponential averaging, arithmetic averaging, and simply taking the minimum barrier are compared to free-energy calculations from umbrella sampling. Three reactions within a protein in a water environment are used as test cases.
authors.affiliation: Computational Biochemistry Group, Institute of Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart (Germany).
authors.forename: April M
authors.initials: AM
authors.lastname: Cooper
authors.forename: Johannes
authors.initials: J
authors.lastname: Kästner
mesh_terms: D007536:Isomerism; D056004:Molecular Dynamics Simulation; D064828:Prolyl Hydroxylases / Q000737:chemistry / Q000378:metabolism; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D064828:Prolyl Hydroxylases
keywords: computational chemistry; molecular mechanics; proteins; quantum mechanics; reaction barriers