Tutorial on Umbrella Sampling Simulation with a Combined QM/MM Potential: The Potential of Mean Force for an S_N2 Reaction in Water.

ABSTRACT: We present a tutorial to carry out umbrella-sampling free-energy simulations with a combined quantum mechanical and molecular mechanical (QM/MM) potential, which may also be used in a computational or biophysical chemistry curriculum for first-year graduate and undergraduate students. In this article, we choose the Type II S_N2 Menshutkin reaction between ammonia and chloromethane to construct the potential of mean force (PMF) for the reaction in aqueous solution. In this exercise, we wish to accomplish three tasks: (1) an understanding of the concept of PMF and the umbrella-sampling free-energy simulation method, (2) the use of a combined QM/MM potential in molecular dynamics simulation of chemical reactions, and (3) an understanding of solvent effects and intermolecular interac

SUBMITTER: Liu C 

PROVIDER: S-EPMC12765577 | biostudies-literature | 2024 Oct

REPOSITORIES: biostudies-literature