Publications - Published papers

Please find below publications of our group. Currently, we list 563 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

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A Graph-Based Toy Model of Chemistry

Gil Benkö, Christoph Flamm, Peter F. Stadler


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Status: Published

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