Studying Chemical Reactions with Molecular Mechanics

摘要

The concept of a force fields has been instrumental to the investigation of protein structure and dynamics at an atomistic level. Over the past decade the application of force field-based methods has demonstrated that they are useful to understand and describe various processes including protein folding, protein-ligand interactions and protein dynamics at least at a qualitative level. Recent developments in capturing finer details of the intermolecular interactions which should pave the way for more quantitative studies are broadly summarized here. One of the most challenging problems in computational chemistry, structural biology and biophysics is to follow a complex system in executing its function. This is often accompanied by switching between a reactant and a product state which are connected by transition states and metastable states. Methods to studying chemical reactions in complex environments are presented and examples are discussed.