Chemical applications of discrete mathematics and graph theory are briefly reviewed, including philosophical implications. Using the concept of dualist (inner graph-theoretical duals) it was possible to classify (cata-peri-corona classes) and enumerate benzenoid and diamondoid hydrocarbons. By associating numbers with molecular graphs, one can use these numbers (topological indices) for correlations with properties of chemical compounds − an early, simple, and rapid approach to drug design. The two types of atoms (metals and non-metals), are connected by three types pf chemical bonds (ionic, metallic, and covalent) that lead to four types pf lattices (ionic, metallic, atomic and molecular), allowing quick "2-3-4 grasp" of chemistry. The Periodic System of Elements, which is the cornerstone of chemistry and atomic physics, is in danger of being presented wrongly, devoid of the symmetry based on electronic s, p, d, and f shells; several possibilities for showing correctly these shells are discussed.