Molecular Simulations as Tracking Tools for the Dynamics of Reactive Species: A Personal Retrospect

Abstract

Reactive oxygen and nitrogen species (RONS) govern critical processes in biology and atmospheric chemistry, yet their fleeting dynamics often elude experimental tracking. Quantum chemistry is the go-to method for studying RONS, but fully classical molecular dynamics (MD) simulations, though unconventional for such transient species, offer unique insights into their interactions at complex interfaces. This self-reflective review chronicles a decade of our group’s work developing the GROMOS-RONS force field, harnessing MD’s computational efficiency to explore RONS in lipid bilayers, aquaporin channels, and water-air interfaces. These studies challenge the view of RONS as mere diffusible threats, revealing their selective enrichment and prolonged residence at critical interfacial regions. Simulations uncover nitro-oxidative pathways and transport mechanisms that shed light on unresolved experimental questions. Applications in signaling, therapy, and aerosol chemistry are highlighted, alongside challenges and future directions. By showcasing the GROMOS-RONS model’s strengths for condensed-phase MD, we aim to inspire its broader application as a complementary tool to study RONS dynamics across diverse fields.