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

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.