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

Chemical reactions are ubiquitous in both materials andthe biophysicalsciences. While coarse-grained (CG) molecular dynamics simulationsare often needed to study the spatiotemporal scales present in thesefields, chemical reactivity has not been explored thoroughly in CGmodels. In this work, a new approach to model chemical reactivityis presented for the widely used Martini CG Martini model. Employingtabulated potentials with a single extra particle for the angle dependence,the model provides a generic framework for capturing bonded topologychanges using nonbonded interactions. As a first example application,the reactive model is used to study the macrocycle formation of benzene-1,3-dithiolmolecules through the formation of disulfide bonds. We show that startingfrom monomers, macrocycles with sizes in agreement with experimentalresults are obtained using reactive Martini. Overall, our reactiveMartini framework is general and can be easily extended to other systems.All of the required scripts and tutorials to explain its use are providedonline.