Enumerating molecules

Jean-Loup Faulon, Donald P. Visco, Jr., and Diana Roe  

Reviews in Computational Chemistry, Volume 21 edited by Kenny B. Lipkowitz, Raima Larter, and Thomas R. Cundari Copyright 2005 Wiley-VCH, John Wiley Sons, Inc. 

About four decades ago, with the advance of computer science, researchers started to look at the former definition of enumeration and devised computer codes to explicitly list molecules. Again, while studying this challenging problem, important concepts in computer science were developed. Artificial intelligence textbooks generally quote DENDRAL, a code to enumerate molecules, as the first expert system. 

Historically, molecular enumeration has brought a fertile groimd of research among chemistry, mathematics, and computer science. Still today new concepts and techniques are being developed at the interstice of these fields.  

The purpose of the final section of this chapter is to review the practical applications of molecular enumeration and to give the reader interested in any of these applications pointers to relevant codes and techniques. In particular, the numbers of isomers for a specific molecular series are given, popular structure elucidation codes are reviewed, computed-aided structure elucidation successes are surveyed, and the connections between structure enumeration and combinatorial library design are established. The field of molecular design with inverse quantitative structure activity relationship is also reviewed. We conclude the chapter outlining future research directions. 

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Faulon J-L, Carla J (2003) Churchwell the signature molecular descriptor. 2. Enumerating molecules from their extended valence sequences. J. Chem. Inf. Comput. Sci. 43 721-734. 

Techniques to enumerate molecules (including cyclic ones) from a molecular formula appeared in the 1970s. The first algorithm to do so, CONGEN, was a product of the DENDRAL project. The solution consisted of decomposing the molecular formula into cyclic substructmes, which were combined by bridges to get molecules. The cyclic substructmes were built from a database of 3000 elementary cycles. A second approach, simpler in principle, has been the technique chosen by the researchers involved in the CHEMICS project.In this approach, only canonical structmes are... 

Enumerating structures with molecular descriptors. Enumerating molecules matching molecular descriptors or topological descriptors is a longstanding problem. Surprisingly, few reports in the literature provide answers to the question. Most of the proposed techniques are stochastic in nature and are reviewed in the Sampling Structures section. In a series of five papers, Kier, et reconstruct molecular structures from the count of paths... 

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