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 MethodsTheoretical and Physical Chemistry > Reaction Dynamics and KineticsMolecular and Statistical Mechanics > Molecular Interactions
Highlights
Understanding atomistic and molecular details of chemical reactions is one of the cornerstones in chemistry and biology
Atomistic simulations have shown their value in providing molecular-level insights into the energetics and dynamics of chemical reactions for systems ranging from small molecules
This Hamiltonian needs to be diagonalized at every time step of an molecular dynamics (MD) simulation and the forces can be determined from the Hellmann-Feynman theorem. (Glowacki et al, 2015) The parametrization of the off-diagonal elements is the most demanding part in a concrete empirical valence bond (EVB)-application
Summary
Understanding atomistic and molecular details of chemical reactions is one of the cornerstones in chemistry and biology. An essential requirement for a meaningful contribution of computer-based work to understand and characterize chemical reactions is the quantitatively correct description of the intermolecular interactions along the entire reaction path This involves regions around the reactants, products and the transition state(s). There are two possible approaches for following chemical reactions using molecular dynamics (MD) simulations: those using quantum mechanics (QM)-based methods and those employing empirical force fields. The focus of the present review is on the use of empirical energy functions to follow chemical reactions in the gas- and condensed phase The motivation for this is twofold: first, due to their computational efficiency formulations based on empirical energy functions are expected to be suitable for situations where extensive sampling of the conformational space is required. Topical examples are discussed with a particular focus on relating the reactive dynamics with the time scales of elementary processes and the underlying conformational dynamics
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