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

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.

Martinoid: the peptoid martini force field

“…Recently Sami et al used this same tabulated potential based approach in a reactive Martini context. 65 The ∼100° well was set to be 4.35 kJ mol −1 higher than the 170° well which we set to 0.0 kJ mol −1 , with a barrier of 10.8 kJ mol −1 between the wells (Fig. 2d).…”

Block Chemistry for Accurate Modeling of Epoxy Resins

“…Although developed at the atomistic level, it may lay the foundations for new and systematic coarse-grained curing models, providing for easy and potentially less ambiguous back mapping. In future works, it will be interesting to coarse grain our atomistic systems with, e.g., the MARTINI scheme, − which was recently extended to incorporate reactivity . The MARTINI scheme incorporates Coulombic interactions, which will be crucial to describe the curing reaction and properties of epoxy resins.…”

Molecular Dynamics Simulation of In Situ Polymerization: Chain Conformation Transition

“…Coarse-grained molecular dynamics (CGMD) further simplifies the computational complexity of polymer systems by grouping heavy atoms and attaching hydrogen atoms to a coarse-grained bead. Numerous coarse-grained force fields for polymers have been developed and employed, − showcasing their close alignment with all-atom molecular dynamics for polymerization simulation at large scales of time and space.…”