A Computer-Oriented Linear Canonical Notational System for the Representation of Organic Structures with Stereochemistry

Computer algorithms and programs have been developed for a simple and effective notational system for organic molecules. The main features of the system are as follows: (1) The name produced is canonical and linear and consists of two parts. The first part represents the constitution of the molecule, the second its stereochemistry. Two molecules that are constitutionally alike but stereochemically distinct (diastereomers) have identical constitutional representations but different stereochemical descriptors. (2) Atoms which are constitutionally equivalent are identified, as are those that are stereochemically equivalent. (3) Generalized Huckel-resonant substructures of the molecule are identified by the system, allowing different resonant forms of the same molecule to be given identical names. (4) The program accepts as input an easy to write stereochemical descriptor of the molecule which is in fact a noncanonical form of the canonical name. (5) Molecules which are mirror images of one another (enantiomers) are identifiable from their canonical names. (6) The smallest number of asymmetric carbons at which two diastereomers differ can readily be computed from their names. Few systems offer the depth, breadth, and algorithmic correctness in addition to easy bidirectional human-machine communication of organic molecules including their stereochemistry. Although the notational system described here was developed to provide a complete and independent canonical stereochemical descriptor of a molecular structure for the SYNCHEM2 organic synthesis discovery program and has been successfully used for several years, the stereochemical descriptors may be used in conjunction with other standard nomenclature systems to extend their range to include stereochemistry.