OntoPESScan: an ontology for potential energy surface scans

Abstract

In this work, a new OntoPESScan ontology is developed for the semantic representation of one-dimensional potential energy surface (PES) scans, a central concept in computational chemistry. This ontology is developed in line with knowledge graph principles and The World Avatar (TWA) project. OntoPESScan is linked to other ontologies for chemistry in TWA, including OntoSpecies, which helps uniquely identify species along the PES and access their properties, and OntoCompChem, which allows the association of potential energy surfaces with quantum chemical calculations and the concepts used to derive them. A force-field fitting agent is also developed that makes use of the information in the OntoPESScan ontology to fit force fields to reactive surfaces of interest on the fly by making use of the empirical valence bond methodology. This agent is demonstrated to successfully parametrize two cases, namely, a PES scan on ethanol and a PES scan on a localized π-radical PAH hypothesized to play a role in soot formation during combustion. OntoPESScan is an extension to the capabilities of TWA and, in conjunction with potential further ontological support for molecular dynamics and reactions, will further progress toward an open, continuous, and self-growing knowledge graph for chemistry.