Counting chemical isomers with multivariate generating functions

Abstract Counting the number of isomers of a chemical molecule is one of the formative problems of graph theory. However, recent progress has been slow, and the problem has largely been ignored in modern network science. Here we provide an introduction to the mathematics of counting network structures and then use it to derive results for two new classes of molecules. In contrast to previously studied examples, these classes take additional chemical complexity into account and thus require the use of multivariate generating functions. The results illustrate the elegance of counting theory, highlighting it as an important tool that should receive more attention in network science.