Automatic potential energy surface exploration by accelerated reactive MD simulations: from pyrolysis to oxidation chemistry

Automatic potential energy surface (PES) exploration is important to better understand reaction mechanisms. Existing automatic PES mapping tools usually rely on predefined knowledge or on computationally expensive on-the-fly quantum-chemical calculations. In this work, we have developed a method for discovering novel reaction pathways and automatically mapping out the PES when only being given a starting species. We have therefore extended the reactive molecular dynamics simulation tool ChemTraYzer2.0 (Chemical Trajectory Analyzer, CTY) for this PES-mapping algorithm. To explore PESs with low-temperature reactions, we applied the acceleration method Collective Variable-driven Hyperdynamics (CVHD). This involved the development of tailored collective variable (CV) templates, which are discussed in this study. The PES mapping algorithm can generate new seed species, automatically start replica simulations for new pathways, and stop the simulation when a reaction has been found, reducing the computational cost of the algorithm. It is validated for known pathways in various pyrolysis and oxidation systems: hydrocarbon isomerization and dissociation (C4H7 and C8H7 PES), mostly dominant at high temperatures, 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 minutes wall time and low-temperature chemistry such as the internal H-shift of RO2 → QO2H within one day wall time. Furthermore, since CTY keeps track of all found geometries of the reactants, transition states, and products, PES mapping facilitates automated higher-level calculations without a priori knowledge. Lastly, we applied PES mapping to the oxidation of the recently proposed bio-hybrid 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.