TBI-Preprint 02-09-045

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A Graph-Based Toy Model of Chemistry

Gil Benkö, Christoph Flamm, Peter F. Stadler

Submitted to:
J. Chem. Inf. Comput. Sci., 43, 1085-1093 (2003)

Large scale chemical reaction networks are a ubiquitous phenomenon, from the metabolism of living cells to processes in planetary atmospheres and chemical technology. At least some of these networks exhibit distinctive global features such as the ''small world'' behavior. The systematic study of such properties, however, suffers from substantial sampling biases in the few networks that are known in detail. A computational model for generating them is therefore required.
Here we present a Toy Model that provides a consistent framework in which generic properties of extensive chemical reaction networks can be explored in detail and that at the same time preserves the ''look-and-feel'' of chemistry: Molecules are represented as labeled graphs, i.e., by their structural formulae; their basic properties are derived by a caricature version of the Extended Hückel MO theory that operates directly on the graphs; chemical reaction mechanisms are implemented as graph rewriting rules acting on the structural formulae; reactivities and selectivities are modeled by a variant of the Frontier Molecular Orbital Theory based on the Extended Hückel scheme. The approach is illustrated for two types of reaction networks: Diels-Alder reactions and the formose reaction implicated in prebiotic sugar synthesis.

reaction networks, graph grammar, extended Hückel MO theory, chemistry toy model, artificial chemistry

Alternative Numbers:
SFI 02-09-045, BIOINF 02-001

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