Automated exploration of the conformational degrees of freedom along reaction profiles - driving a FASTCAR

Abstract

This publication aims at presenting a Python-based workflow designed to enable a fully automatised and exhaustive exploration of the conformational degrees of freedom within the calculation of reaction paths in molecular systems. The proposed strategy focuses on effectively representing the lowest energy conformers for intricate, highly rotatable, and non-intuitive transition states, reagents and products, using existing computational tools. The article presents a workflow that is demonstrated through the application of three chemical reactions: a Diels-Alder reaction involving 4,4-dimethyl-3-methylenepent-1-ene and (E)-dec-5-ene, a diastereoselective intramolecular acid-catalysed cyclization reaction of an polycyclic azocane derivative and an enantioselective organo-catalysed Black rearrangement of benzofuran derivatives, which prove to be challenging to study "by hand". The proposed methodology is expected to be of a great help in the modelling of state-of-the art organic chemistry reactions, whose complexity is ever increasing.