Topological reactivity method represents an effective mathematical tool in which the topological properties of a chemical system derived from the system adjacency or distance matrix are combined with its reactivity properties obtained with the aid of electronegativity and chemical hardness descriptors. The graph theoretical indices are very used as molecular descriptors in QSAR and QSPR studies. Recent studies in graph theory field proved that leads to the idea that the chemical properties of hexagonal ring systems can be influenced by the topology through the topological indices. The general topological descriptors are based on the adjacency matrix (entries in binary form) and the distance matrix (entries represents the sums of binary elements). Several polycyclic aromatic hydrocarbons structures were analyzed using the electro-topological coloring algorithm. The quantum topological molecular similarity method was proposed in order to test two sets of mutagenic compounds, i.e. halogenated hydroxyquinones and dimethyl heteroaromatic triazenes.