“…Simulation methods, such as conventional molecular dynamics (MD), − Monte Carlo, , and discrete molecular dynamics , simulations, focus on the physical nonbonding interactions while neglecting possible chemical reactions, e.g., ionizable groups’ protonation/deprotonation equilibrium and thiol–Au interactions and chemisorption. The development of the reactive force field (ReaxFF), as a polarizable charge model based on the bond order, has made it possible to simulate chemical reactions, including combustion, , hydrocarbon pyrolysis, , thermal decomposition of polymers, the explosion of high-energy materials, , and the oxidation of solid surfaces and NPs . By allowing chemical bonds to form and break freely without fixing the rigid connectivity between atoms inside a molecule or fixing atoms’ partial charges, ReaxFF MD overcomes the deficiencies of conventional MD and the scale problem of quantum mechanics. , A recent study employed ReaxFF MD to study biomolecules, e.g., short peptides and small proteins in water .…”