Representing catalytic mechanisms with rule composition

Abstract

Understanding the underlying chemistry of a catalytic process is essential for advancing of its medical and industrial applications. A well defined and compact representation of a catalytic process is becoming exceedingly valuable in face of the growth in computer assisted development strategies. A step-wise partition of a catalytic process is traditional in organic chemistry. We argue, however, that such a description remains incomplete, especially in face of automation and formal methods. In this contribution-based on enzymatic reaction mechanisms-we fully formalize the step-wise notion of a catalytic process within the mathematical framework of graph transformation, and propose a concise representation as an overlay graph (OG). We formally define this concept in a dual form as an OG itself and an overlay rule. The former representing a static summary of the process, and the latter being an executable in the graph transformation formalism. We demonstrate that OGs readily expose the underlying chemistry and facilitate the interpretation of catalytic processes. The emergence of electron flow patterns, for instance, provides an excellent stage for classification efforts. We further show how the executable overlay rules can be employed to automatically assign a fully specified mechanism to a reaction with only an overall description, i.e. educt and product molecules.