Reactive molecular dynamics: From small molecules to proteins

Abstract

The current status of reactive molecular dynamics (MD) simulations is summarized. Both, methodological aspects and applications to problems ranging from gas phase reaction dynamics to ligand‐binding in solvated proteins are discussed, focusing on extracting information from simulations that cannot easily be obtained from experiments alone. One specific example is the structural interpretation of the ligand rebinding time scales extracted from state‐of‐the art time‐resolved experiments. Atomistic simulations employing validated reactive interaction potentials are capable of providing structural information about the time scales involved. Both, merits and shortcomings of the various methods are discussed and the outlook summarizes possible future avenues such as reactive potentials based on machine learning techniques. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics Molecular and Statistical Mechanics > Molecular Interactions

Reactive atomistic simulations of Diels-Alder reactions: The importance of molecular rotations

“…27 These procedures will most likely bias the final result and do not allow the direct calculation of reaction rates. Gas-phase reactive molecular dynamics simulations starting from an equilibrated ensemble of a statistically significant number of initial conditions, on the other hand, have recently been shown to provide molecular-level details into reactions relevant to atmospheric chemistry 28,29 and reactions in the hypersonic regime. 30,31 From an experimental perspective, the most precise data on reaction mechanisms and dynamics can be gained from gas-phase studies performed under single-collision conditions.…”

Development of the ChIMES Force Field for Reactive Molecular Systems: Carbon Monoxide at Extreme Conditions

“…Reactive force field (FF) based methods, on the other hand, are far less constrained and can readily access problem space in the hundreds of nm and ns regime (for an indepth discussion of the numerous available reactive force fields, the reader is referred to [20][21][22]. In fact, numerous reactive force fields have been developed for C/O chemistry, such as ReaxFF [23][24][25][26][27] and REBO 28,29 among others 30 , however these models are parameterized for combustion conditions (i.e.…”

Exploration of Reaction Pathways and Chemical Transformation Networks

“…This issue can be overcome by the application of a reactive classical force-field (for a recent review see Ref. 34). 35,36 Unfortunately, apart from reduced accuracy, force-field parameters will, in general, not be available for any type of system which limits their applicability.…”