TY - JOUR
T1 - Partial Imaginary Transition State (ITS) Graphs
T2 - A Formal Framework for Research and Analysis of Atom-to-Atom Maps of Unbalanced Chemical Reactions and Their Completions
AU - González Laffitte, Marcos E.
AU - Weinbauer, Klaus
AU - Phan, Tieu Long
AU - Beier, Nora
AU - Domschke, Nico
AU - Flamm, Christoph
AU - Gatter, Thomas
AU - Merkle, Daniel
AU - Stadler, Peter F.
PY - 2024/9
Y1 - 2024/9
N2 - 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.
AB - 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.
KW - (chemical) graph alignment
KW - (sub)graph isomorphism
KW - atom-to-atom maps
KW - chemical graphs
KW - chemical reaction mechanisms
KW - cheminformatics
KW - condensed graph of the reaction
KW - hydrogen atom mapping
KW - imaginary transition state
KW - rebalancing of reactions
KW - tautomerization reactions
U2 - 10.3390/sym16091217
DO - 10.3390/sym16091217
M3 - Journal article
AN - SCOPUS:85205114128
SN - 2073-8994
VL - 16
JO - Symmetry
JF - Symmetry
IS - 9
M1 - 1217
ER -