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

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.

Keywords

• chemical graphs
• cheminformatics
• chemical reaction mechanisms
• atom-to-atom maps
• imaginary transition state
• condensed graph of the reaction