Multiscale modeling of enzymes: QM-cluster, QM/MM, and QM/MM/MD: A tutorial review

Abstract

Exemplars of the state of the art in modeling enzymes are reviewed through a selection of works from leading schools using QM-only cluster models, QM/MM models and QM/MM/MD models. A computational protocol is proposed, intended to guide neophytes through the myriad of methodological choices that are necessary for the successful study of chemical reactions in the complex enzymatic environment.