TBI-Preprint 02-09-045
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Titel:
A Graph-Based Toy Model of Chemistry
Author(s):
Gil Benkö,
Christoph Flamm,
Peter F. Stadler
Submitted to:
J. Chem. Inf. Comput. Sci., 43, 1085-1093 (2003)
Abstract:
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.
Keywords:
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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Last modified: 2003-07-25 10:50:41 www