Abstract
Abstract Background Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach to modeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like merging, splitting, and isomerisation of molecules. It is often convenient, in particular in the analysis of larger systems, to summarize several subsequent reactions into a single composite chemical reaction. Results We introduce a generic approach for composing graph grammar rules to define a chemically useful rule compositions. We iteratively apply these rule compositions to elementary transformations in order to automatically infer complex transformation patterns. As an application we automatically derive the overall reaction pattern of the Formose cycle, namely two carbonyl groups that can react with a bound glycolaldehyde to a second glycolaldehyde. Rule composition also can be used to study polymerization reactions as well as more complicated iterative reaction schemes. Terpenes and the polyketides, for instance, form two naturally occurring classes of compounds of utmost pharmaceutical interest that can be understood as “generalized polymers” consisting of five-carbon (isoprene) and two-carbon units, respectively. Conclusion The framework of graph transformations provides a valuable set of tools to generate and investigate large networks of chemical networks. Within this formalism, rule composition is a canonical technique to obtain coarse-grained representations that reflect, in a natural way, “effective” reactions that are obtained by lumping together specific combinations of elementary reactions.
Highlights
Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach to modeling chemistry
If molecules are treated as edge and vertex labeled graphs, where the vertex labels correspond to atom types and the edge labels denote bond types, structural change of molecules during chemical reactions can be modeled as graph rewriting rules [3]
Understanding chemical reaction patterns usually requires spanning the chemical reaction networks based on such rules
Summary
We introduce a generic approach for composing graph grammar rules to define a chemically useful rule compositions. We iteratively apply these rule compositions to elementary transformations in order to automatically infer complex transformation patterns. As an application we automatically derive the overall reaction pattern of the Formose cycle, namely two carbonyl groups that can react with a bound glycolaldehyde to a second glycolaldehyde. Rule composition can be used to study polymerization reactions as well as more complicated iterative reaction schemes. For instance, form two naturally occurring classes of compounds of utmost pharmaceutical interest that can be understood as “generalized polymers” consisting of five-carbon (isoprene) and two-carbon units, respectively
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