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

Chapter 7
Conclusion and Outlook
The present Toy Model is at least close to a minimal implementation of
an artificial chemistry exhibiting what we consider the defining features of
“real” chemistry. Molecules were represented only by their connectivity information
and atom types, as labeled graphs, and their energy was defined
along the lines of quantum chemistry, using an extremely simplified function.
This energy model forms the basis of full-fledged chemical thermodynamics
and kinetics. Chemical reactions are implemented as graph rewriting rules
that have to obey the principle of conservation of matter. These features
distinguish the Toy Model from artificial chemistries that are defined on abstract
algebraic structures such as the λ calculus, Turing machines, or term
rewriting. The application of the model to examples of complex organic and
prebiotic chemistry allowed an quasi-ab initio simulation of the resulting
networks and prediction of their properties. Now the emergence of generic
properties of CRNs can be studied given only starting material, generic reactions
and atom and bond parameters. A true ab initio simulation would not
need the introduction the latter parameters for the energy calculation and
would simulate reactions without even specifying generic reactions. Yet both
“educated guesses” are founded on the results of quantum chemistry and
synthetic chemistry, and their validity could be estimated by the judicious
comparison of predicted to experimental results.
A number of extensions of the present Toy Model are desirable. For
instance, the addition of the corresponding parameters (see appendix A)
would extend the current implementation of the model, considering only
molecules composed of C, H, O, and N, to an expanded set of chemical
elements, most importantly S, P, Si, and the halogens. The inclusion of
charged particles and radicals also does not seem to pose problems in the
current framework. Charges situated on specific atoms can be indicated in
SMILES, e.g. HC([O−]) = O. In fact, it does not matter to which atom the
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