Hyle 19 (1):107 - 134 (2013)

Abstract
The development of chemical applications of graph theory is reviewed from a personal perspective. Graph-theoretical methods for finding all graphs fulfilling certain mathematical conditions followed by eliminating chemically impossible solutions are equivalent to the ‘Sherlock Holmes principle’. For molecular graphs, this is illustrated by monocyclic aromatic systems and by valence isomers of annulenes. Using dualist graphs for benzenoids and diamond hydrocarbons it was possible to develop simple encoding systems that allowed convenient enumerations of isomers. Starting with the invention of reaction graphs in 1966 that included the Petersen graph which is also the 5-cage (the smallest graph with girth 5) two gaps were filled by discovering the first 10-cage and the unique 11-cage, showing how chemical clues can lead to interesting mathematical developments. Graphs of a third type are represented by synthon graphs that are helping chemical synthesis. Connections between chemical structure and molecular properties allow the design of biologically active substances on the basis of quantitative structure-activity relationships (QSARs). Some of the simplest tools for QSAR are topological indices and they are briefly discussed
Keywords Philosophy of Chemistry  mathematical chemistry  molecular graphs  reaction graphs  synthon graphs  topological indices  QSAR
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