S-Graphs and Synthons

The concepts of a graph and molecular graph were introduced in the previous chapter. These terms will be generalized in such a way that some vertices are distinguished from others and are called the virtual vertices. We remember that in graph theory [1] such a process is called rooting and the distinguished vertices are called the roots. In the original approach employing the molecular graphs the concept of chemical transformation is determined for pairs of graphs that are isomeric, i.e. in the course of the chemical transformation the numbers of atoms and valence electrons are conserved; the chemical transformations are strictly stoichiometric. This prominent feature of the theory may cause some formal difficulties should we wish to implement in the model the fruitful idea of general organic chemistry, in particular, the notion of the synthon. The description of chemical transformations may be limited to so-called synthons that represent the necessary minimal fragment of the molecular system for the given chemical transformation. The concept of synthon was initially formulated by Corey [2] in 1967 for the purposes of computer-assisted organic synthesis design.