Similarity of atoms in molecules is quantitatively assessed with a mea
sure that employs electron densities within respective atomic basins.
This atomic similarity measure does not rely on arbitrary assumptions
concerning basis functions or ''atomic orbitals'', is relatively inexp
ensive to compute, and has straightforward interpretation. Inspection
of similarities between pairs of carbon, hydrogen, and fluorine atoms
in the CH4, CH3F, CH2F2, CHF3, CF4, C2H2, C2H4, and C2H6, molecules, c
alculated at the MP2/6-311G* level of theory, reveals that the atomic
similarity is greatly reduced by a change in the number or the charac
ter of ligands (i.e. the atoms with nuclei linked through bond paths t
o the nucleus of the atom in question). On the other hand, atoms with
formally identical (i.e. having the same nuclei and numbers of ligands
) ligands resemble each other to a large degree, with the similarity i
ndices greater than 0.95 for hydrogens and 0.99 for non-hydrogens.