Information theory, atoms in molecules, and molecular similarity

Using information theory, it is argued that from among possible definitions of what an atom is when it is in a molecule, a particular one merits special attention. Namely, it is the atom defined by the "stockholders partitioning" of a molecule invented by Hirshfeld (1977) Theor. Chim. Acta 44, 129. The theoretical tool used is the minimum entropy deficiency principle (minimum missing information principle) of Kullback and Liebler (1951) Ann. Math. Stat. 22, 79. A corresponding analysis is given of the problem of assessing similarity between molecules or pieces of molecules.