A Toy Model of Chemical Reaction Networks - TBI - Universität Wien

12 CHAPTER 2. ARTIFICIAL CHEMISTRIES
that is described. The imaginary transition structure [45] merges constant
and changing parts into a single representation, while the skeleton of transformation
[95] shows only the changing parts.
[83, 88] uses a hybrid approach with the Reaction Description Language.
This language encodes the steps of reaction site identification, reaction matching,
and reactant manipulation. The code is compiled and yields a hardcoded
function for each reaction.
I. Ugi and coworkers [113, 114] have developed a a formal theory of chemical
reactions called the Dugundji-Ugi-model. In this model, reactions are
interconversions between isomers of ’ensembles of molecules’ (EM). The concept
of stoichiometric transformation in this model is used in the reaction
simulation part of the Toy Model (see sect. 4.1). EM and reactions can be
represented as matrices BE and R, such that the reaction R from BE 1 to
BE 2 is equivalent to writing BE 2 = BE 1 + R. The off-diagonal entries of
BE are bond orders between atoms, diagonal entries are number of valence
electrons in lone pairs. Reaction generators (RG) may generate all R from
a given BE 1 (RGB) or all BE from a given R (RGR). The program IGOR
[39] is an RGR and generates new organic reactions and reaction networks
between known educts and products. Koča et al. have developed an extension
of the DU-Model, the synthon model [60, 73]. Here, lone electron pairs
are represented by loops.
[33, 43] review methods to reduce the combinatorial explosion of possible
reactions in formal models of CRNs. Reduction may be choosing a subset of
reaction through an educated guess or in accordance to experimental observation.
This subset may be a certain class of reaction, thus representing a
special chemistry, or it may be formed by picking one representative reaction
for each class of reactions. Finally, the subset used by [33] includes reactions
according to their contribution to the reaction dynamics, by their concentration
or by their rate constant. Thus the reaction mechanism reduction is
achieved simultaneously with the CRN generation.