Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins

A K Das; M Meuwly

doi:10.1016/bs.mie.2016.05.045

Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins

Methods Enzymol. 2016:577:31-55. doi: 10.1016/bs.mie.2016.05.045. Epub 2016 Jul 14.

Authors

A K Das¹, M Meuwly²

Affiliations

¹ University of Basel, Basel, Switzerland.
² University of Basel, Basel, Switzerland. Electronic address: m.meuwly@unibas.ch.

PMID: 27498633
DOI: 10.1016/bs.mie.2016.05.045

Abstract

Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed.

Keywords: Chemical reaction; Denitrification reaction; Force field; Molecular dynamics; Reactive molecular dynamics.

Publication types

Review
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Humans
Models, Chemical*
Molecular Dynamics Simulation*
Mycobacterium tuberculosis / metabolism
Proteins / chemistry*
Quantum Theory
Thermodynamics*

Substances

Proteins