Reactive Coarse-Grained Molecular Dynamics

J Chem Theory Comput. 2020 Apr 14;16(4):2541-2549. doi: 10.1021/acs.jctc.9b01140. Epub 2020 Mar 10.


Coarse-grained (CG) models have allowed for the study of long time and length scale properties of a variety of systems. However, when a system undergoes chemical reactions, current CG models are not able to capture this behavior because of their fixed bonding topology. In order to develop CG models capable of taking into account such chemical changes, a model must be able to adapt its bonding topology and CG site-site interactions to switch between multiple bonding structures (i.e., topologies). This challenge particularly impacts "bottom-up" CG models developed from the fundamental underlying atomistic-scale interactions. In this paper, a reactive coarse-grained (RCG) method is developed which utilizes all-atom (AA) data to create a CG model able to represent chemical reactions by undergoing changes in bonding topology. As an example, the RCG method was applied to a model of SN2 reactions of 1-chlorobutane with a chloride ion and 1-iodobutane with an iodide ion in a methanol solvent. An asymmetric reaction was also modeled by incorporating a constant energy offset to the 1-iodobutane model. In each case, the calculated CG potential of mean force (PMF) results in good agreement with the fully AA PMF for the reactions.