Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations

Citation (APA 7)

Sami, S., & Marrink, S. J. (2023). Reactive Martini: Chemical Reactions in Coarse-Grained Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 19(13), 4040-4046.

Abstract

Chemical reactions are ubiquitous in both materials and the biophysical sciences. While coarse-grained (CG) molecular dynamics simulations are often needed to study the spatiotemporal scales present in these fields, chemical reactivity has not been explored thoroughly in CG models. In this work, a new approach to model chemical reactivity is presented for the widely used Martini CG Martini model. Employing tabulated potentials with a single extra particle for the angle dependence, the model provides a generic framework for capturing bonded topology changes using nonbonded interactions. As a first example application, the reactive model is used to study the macrocycle formation of benzene-1,3-dithiol molecules through the formation of disulfide bonds. We show that starting from monomers, macrocycles with sizes in agreement with experimental results are obtained using reactive Martini. Overall, our reactive Martini framework is general and can be easily extended to other systems. All of the required scripts and tutorials to explain its use are provided online.