Reaction routes and chemical structure

This account of the LHASA and CAMEO programs has been necessarily very limited readers interested in further details should contact the suppliers of the software as listed in the Software appendix. Another approach to the problem of synthesis planning is to provide literature references to model reactions, thus allowing the chemist user to make his or her own assessment of feasibility, using his or her own expert system A number of reaction database systems are in common use (e.g., REACCS, 

SYNLIB, see Software appendix) and a combination of synthesis-planning software with literature reaction retrieval software is a powerful tool for synthetic chemistry. 

The prediction of three-dimensional chemical structure from a list of atoms in a molecule and their connectivity is a good example of a chemical problem that may be solved by an expert system. We have already seen (Fig. 9.2) how the SMILES interpreter can construct a two-dimensional representation of a structure from its one-dimensional representation as a SMILES string. The CONCORD program (CONnection table to CoORDinates) takes a SMILES string and, very rapidly, produces a three-dimensional model of an input molecule. This system is a hybrid between an expert system and a molecular mechanics program, molecular mechanics being the method by which molecular structures are minimized in most molecular modelling systems. The procedure operates as follows. 

The SMILES input string is checked for syntax errors and is made unique if it is not already (see Box 9.1). 

The atom symbols in the SMILES string are numbered sequentially and a connection table is constructed which indicates which atoms are bonded to each other. 

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