A categorical model for organic chemistry

Abstract

We introduce a mathematical framework for organic chemistry, with three interrelated perspectives on chemical processes: reaction schemes, formal reactions and disconnection rules. We apply the framework to retrosynthetic analysis, an important research method in synthetic chemistry. Our approach represents molecules as labelled graphs, while the interactions between them are represented either as double pushout graph rewriting, partial bijections or local edge rewrite rules. In particular, we show that the formal reactions are generated by reaction schemes using double pushout rewriting, and that the disconnection rules are sound, complete and universal with respect to chemical reactions. The mathematical formulation of retrosynthesis is based on layered props – a recently introduced categorical model for partial explanations in scientific reasoning.