Theoretical chemistry has been dominated by quantum chemistry to such an extent that the potential of discrete mathematics has focused on combinatorial and topological properties of discrete objects. This book summarizes results related to chemical structures that go beyond molecular stability and energetics, addressing such topics as molecular similarity, QSAR, QSPR characterization of DNA and proteins, as well as DNA and protein alignment. Broad in scope, including bioinformatics topics and proteomics maps, it presents an outline of molecular descriptors that considers aromaticity of benzenoid and non-benzenoid compounds, properties of conjugated polymers, and stabilities of fullerenes.