Abstract
Chemical graph theory (CGT) starts by defining matrices that represent the molecular graph then proceed to extract numbering-independent matrix invariants to be used as molecular descriptors in empirical quantitative structure to activity (or property) relationships (QSAR/QSPR). Two proposed matrix representations of molecular structure are presented in this chapter as alternatives to simple connectivity molecular graphs. Firstly, it is proposed to use a more “nuanced” connectivity matrix by weighing the “ones” entered in a CGT molecular graph matrix by the bond critical point electron densities associated with each bond path to yield what we term the “electron density-weighted adjacency/connectivity matrices (EDWAM/EDWCM)”. In a second approach, it is proposed to use the localization and delocalization indices of the quantum theory of atoms in molecules (QTAIM) to construct a richer representation of the molecular graph, a “fuzzy” graph, whereby an edge exists between any two atoms (measured by the delocalization index between them) whether they share a bond path or not. Such a fuzzy graph is represented by what we term “electron localization-delocalization matrix (LDM)”. We show that the LDM representations of a series of molecules provide a powerful tool for robust QSAR/QSPR modeling.
The development of chemistry has both led to, and been made possible by, the evolution of certain primary concepts. These concepts, without which there would be neither correlation nor prediction of the observations of descriptive chemistry, are: (1) the existence of atoms of functional groupings of atoms in molecules as evidenced by characteristic sets of properties; (2) the concept of bonding; and (3) the associated concepts of molecular structure and molecular shape. These concepts logically (but not historically) are consequences of fundamental topological properties of the charge distribution (electronic and nuclear) in a molecular system. In terms of the Born-Oppenheimer approximation the electronic distribution ρ( r ) is the scalar field defined in the real three-dimensional space with Euclidean metric. The universal topological properties of ρ( r ) are characterized by its gradient field ∇ ρ( r ) [1].
I.S. Dmitriev (1981)
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Acknowledgments
The authors thank Dr. Todd A. Keith, Professor Lou Massa, Dr. Nenad Trinajstić, Dr. Sonja Nikolić, and Mr. Matthew J. Timm for helpful discussions. Financial support of this work was provided by the Natural Sciences and Engineering Research Council of Canada (NSERC), Canada Foundation for Innovation (CFI), Saint Mary’s University, McMaster University, and Mount Saint Vincent University.
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Matta, C.F., Sumar, I., Cook, R., Ayers, P.W. (2016). Localization-Delocalization Matrices and Electron Density-Weighted Adjacency/Connectivity Matrices: A Bridge Between the Quantum Theory of Atoms in Molecules and Chemical Graph Theory. In: Chauvin, R., Lepetit, C., Silvi, B., Alikhani, E. (eds) Applications of Topological Methods in Molecular Chemistry. Challenges and Advances in Computational Chemistry and Physics, vol 22. Springer, Cham. https://doi.org/10.1007/978-3-319-29022-5_3
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