Automatic Potential Energy Surface Exploration by Accelerated Reactive Molecular Dynamics Simulations: From Pyrolysis to Oxidation Chemistry

Automatic
potential energy surface (PES) exploration
is important
to a better understanding of reaction mechanisms. Existing automatic
PES mapping tools usually rely on predefined knowledge or computationally
expensive on-the-fly quantum-chemical calculations. In this work,
we have developed the PESmapping algorithm for discovering novel reaction
pathways and automatically mapping out the PES using merely one starting
species is present. The algorithm explores the unknown PES by iteratively
spawning new reactive molecular dynamics (RMD) simulations for species
that it has detected within previous RMD simulations. We have therefore
extended the RMD simulation tool ChemTraYzer2.1 (Chemical Trajectory
Analyzer, CTY) for this PESmapping algorithm. It can generate new
seed species, automatically start replica simulations for new pathways,
and stop the simulation when a reaction is found, reducing the computational
cost of the algorithm. To explore PESs with low-temperature reactions,
we applied the acceleration method collective variable (CV)-driven
hyperdynamics. This involved the development of tailored CV templates,
which are discussed in this study. We validate our approach for known
pathways in various pyrolysis and oxidation systems: hydrocarbon isomerization
and dissociation (C4H7 and C8H7 PES), mostly dominant at high temperatures and low-temperature
oxidation of n-butane (C4H9O2 PES) and cyclohexane (C6H11O2 PES). As a result, in addition to new pathways showing up
in the simulations, common isomerization and dissociation pathways
were found very fast: for example, 44 reactions of butenyl radicals
including major isomerizations and decompositions within about 30
min wall time and low-temperature chemistry such as the internal H-shift
of RO2 → QO2H within 1 day wall time.
Last, we applied PESmapping to the oxidation of the recently proposed
biohybrid fuel 1,3-dioxane and validated that the tool could be used
to discover new reaction pathways of larger molecules that are of
practical use.