Partial Imaginary Transition State (ITS) Graphs: A Formal Framework for Research and Analysis of Atom-to-Atom Maps of Unbalanced Chemical Reactions and Their Completions

Marcos E. González Laffitte*, Klaus Weinbauer, Tieu Long Phan, Nora Beier, Nico Domschke, Christoph Flamm, Thomas Gatter, Daniel Merkle, Peter F. Stadler

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Abstract

Atom-to-atom maps (AAMs) are bijections that establish the correspondence of reactant and product atoms across chemical reactions. They capture crucial features of the reaction mechanism and thus play a central role in modeling chemistry at the level of graph transformations. AAMs are equivalent to so-called “imaginary transition state” (ITS) graphs, making it possible to reduce tasks such as the computational comparison of AAMs to testing graph isomorphisms. In many application scenarios, nonetheless, only partial information is available, i.e., only partial maps or, equivalently, only subgraphs of the ITS graphs, are known. Here, we investigate whether and how, and to what extent, such partial chemical data can be completed and compared. The focus of this contribution is entirely on the development of a solid mathematical foundation for the analysis of partial AAMs and their associated partial ITS graphs.

Original languageEnglish
Article number1217
JournalSymmetry
Volume16
Issue number9
ISSN2073-8994
DOIs
Publication statusPublished - Sept 2024

Keywords

  • (chemical) graph alignment
  • (sub)graph isomorphism
  • atom-to-atom maps
  • chemical graphs
  • chemical reaction mechanisms
  • cheminformatics
  • condensed graph of the reaction
  • hydrogen atom mapping
  • imaginary transition state
  • rebalancing of reactions
  • tautomerization reactions

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