An integration of chemical graph theory and the quantum theory of atoms in molecules (QTAIM) is proposed. QTAIM localization and delocalization indices organized as matrices are shown useful in the modeling of ground and excited state molecular properties. The pK(a)'s of 14para-substituted benzoic acids and the lambda(max)'s of a subset of those are predicted with accuracy (pK(a): r(2) = 0.986, q(2) = 0.982; lambda(max): r(2) = 0.973, q(2) = 0.944). 'Super-atoms' obtained by pruning the branches of the substituents' graphs equalize the matrices of all molecules of the set. The pK(a) of p-dimethylaminobenzoic acid is found to be 5.02 rather than the reported value of 6.03. (C) 2014 Elsevier B.V. All rights reserved.