Molecular Dynamics Simulations for Organic Chemists – It’s About Time!

Molecular dynamics simulations model chemical reactions as continuous changes in molecular structure over time in-stead of static minima and transition states. This perspective argues that time-dependent structural change is a crucial, but often overlooked, mechanistic feature as many reactions simply do not follow a single, equilibrated minimum-energy path. We highlight examples where traditional transition state theory fails, typically cases involving short-lived interme-diates, non-equilibrium solvation, momentum-controlled selectivity, post-transition state bifurcations, and “hidden” dy-namic intermediates and show how molecular dynamics can reveal the actual sequence of structural change which gov-erns a reaction outcome. We also discuss emerging machine learning-based molecular dynamics which have found appli-cations in photochemistry and solvent modelling. While molecular dynamics will not replace methods based on transi-tion state theory, it offers organic chemists a time-resolved view of molecular structure which can be crucial to under-standing a given reaction. However, a central barrier for organic chemists is to understand when and why to apply an ad-vanced computational technique such as molecular dynamics simulations. In this perspective, we aim to introduce the methodology in sufficient detail to enable organic chemists to make this assessment and gain an appreciation for the im-portance of time in reaction mechanisms.