Computer generated reaction networks: on-the-fly calculation of species properties using computational quantum chemistry

An algorithm for the translation of the chemically rich two-dimensional molecular graph into a three-dimensional internal coordinate representation of the relative positions of the atoms in space is described. This enables on-the-fly calculations of species properties during the computer generation of reaction networks. The algorithm systematically species bond distances, bond angles and dihedral angles. Geometric parameters for atoms belonging to cycles required the specification of predefined geometrical templates. Templates for six-membered rings of the types aromatic, cyclohexadienyl, cyclohexenyl and cyclohexyl were therefore developed and optimized. An algorithm was also developed for the identification of tight cycles and their member atoms. This was critical to categorize atoms as noncyclic or cyclic.