Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

TL;DR

This paper introduces a modified CHARMM force field integrated into MBN Explorer, enabling simulations of biomolecular systems with dynamic topologies, such as bond rupture and fragmentation processes.

Contribution

The paper presents a novel modification of the CHARMM force field for dynamic topologies, implemented in MBN Explorer, with case studies demonstrating its application in bond rupture and biomolecular damage.

Findings

Modified force field supports bond-breaking simulations.

Application demonstrated in irradiation and collision damage studies.

Enables modeling of biomolecular transformations involving topological changes.

Abstract

The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, we provide several illustrative case studies where dynamical topology is necessary. In particular, it is shown that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems.