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Figure 3 | Journal of Systems Chemistry

Figure 3

From: Evolution of metabolic networks: a computational frame-work

Figure 3

Reactions as Graph Grammars. Chemical transformations very naturally translate into graph transformation rules. As an example the Cope rearrangement, a concerted pericyclic [3,3]-sigmatrope rearrangement, is shown (a). A graph rewrite rule consists of 3 graphs: (i) the left graph which is composed of all the atoms and bonds which vanish during the reaction (ii) the context graph comprised of all atoms and bonds which do not change (iii) the right graph consists of all the atoms and bonds which are formed during the reaction. The conjunction of left and context graph forms the pre-condition for the applicability of the rewrite rule. The rules for the Cope and oxy-Cope rearrangement are shown (b). The context sensitivity of graph rewrite rules is illustrated by Wender's methatese, a tandem reaction (oxy-Cope rearrangement followed by Cope rearrangement). While the Cope rule applies to both steps, the oxy-Cope rule is only applicable to the first step of the tandem reaction (c).

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