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

Chapter 6
Computational results
When the three components molecules, reactions, and network simulation
are put together, it is possible to build a CRN performing molecular property
prediction and model reduction on the fly, given only a list of initial
SMILES. For the following CRNs, regioselectivity was simulated using the
simple equations described at the end of section 3.6.
6.1 Repetitive Diels-Alder reactions
The Diels-Alder reaction [25] has been extensively studied thanks to its importance
in natural products synthesis and because it is easily tractable by
simple semi-empirical methods. It is the typical test reaction for a semiempirical
quantum calculation methods such as ours, and furthermore for
the numerous approaches of reaction description [110]. It involves the reaction
between two linear π-systems of length 2 and 4, called dienophiles
and dienes, and is thus called a [2+4]-cycloaddition. The product is again a
dienophile and may react again in a Diels-Alder reaction, then termed repetitive.
Indeed, the reaction is used for the synthesis of polymers [80]. The
CRN in fig. 6.1 is obtained by repetitive Diels-Alder reactions of a simple
initial mixture of dienes and dienophiles.
The rewrite rule is a bimolecular variant of the one described in fig. 4.2
(see appendix B). The simple constraints derived from FMO lead to a reaction
respecting the Woodward-Hoffmann rules [126]. Depending on which
choice makes |∆E FMO | smaller, the HOMO of the diene or dienophile reacts
with the LUMO of the complementary species. The orientation of the reactants
to each other is determined by the FMO coefficients. Model reduction
consisted in producing only one of regioisomers instead of both. A further
reduction was introduced by an enthalpy threshold of 20 eV.
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