Reasoning about Chemical Reactions Using the Situation Calculus

We explore applicability of the situation calculus, the well-known logical framework developed in Artificial Intelligence for representation of dynamic systems, to the task of representing knowledge about processes, actions and events in the natural sciences. In this paper, we concentrate on a case study in the area of organic chemistry. More specifically, we adapt the situation calculus to the task of automating organic synthesis planning on a qualitative level, where the objective is to identify a chain of chemical reactions transforming the given initial molecules into the desired goal molecule. We present two approaches for reasoning about reactions in organic chemistry: a “micro” approach and a “macro” approach. The “micro” approach is a low level approach that explicitly represents the most elementary interactions between molecules during a single chemical reaction, namely the splitting and forming of bonds between atoms. In contrast, the“macro” approach is a higher level approach that treats each chemical reaction (a set of splits and formation of bonds) as an elementary action. Both approaches are implemented in PROLOG. Declarative heuristics are defined to reduce the search space and help the program to find the correct synthesis routes more quickly. We hope that the lessons learned from our successful case study can have discovery potential in other bio-medical sciences. We discuss briefly how the proposed approaches can contribute to solving other research problems and to communicating pathways.