Automated chemical resonance generation and structure filtration for kinetic modeling

• Published in: International journal of chemical kinetics Vol. 51; no. 10; pp. 760 - 776
• Main Authors: Grinberg Dana, Alon, Liu, Mengjie, Green, William H.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc 01.10.2019; Wiley Blackwell (John Wiley & Sons)
• Subjects: Algorithms; automated localized structure filtration; automatic reaction mechanism generation; Automation; chemical kinetics modeling; Chemical reactions; chemical resonance; electron delocalization; Filtration; Organic chemistry; Quantum chemistry; Reaction mechanisms; resonance weights
• ISSN: 0538-8066; 1097-4601; 1097-4601
• DOI: 10.1002/kin.21307

This work discusses efficient and automated methods for constructing a set of representative resonance structures for arbitrary chemical species, including radicals and biradicals, consisting of the elements H, C, O, N, and S. Determining the representative reactive structures of chemical species is crucial for identification of reactive sites and consequently applying the correct reaction templates to generate the set of important reactions during automated chemical kinetic model generation. We describe a fundamental set of resonance pathway types, accounting for simple resonating structures, as well as global approaches for polycyclic aromatic species. Automatically discovering potential localized structures along with filtration to identify the representative structures was shown to be robust and relatively fast. The algorithms discussed here were recently implemented in the Reaction Mechanism Generator (RMG) software. The final structures proposed by this method were found to be in reasonable agreement with quantum chemical computation results of localized structure contributions to the resonance hybrid.