Abstract
The concept of an atom in a molecule is developed in the context of density functional theory and used to separate the energy of a molecule into intra-atomic and interatomic terms. The intra-atomic kinetic energy may then be calculated accurately in terms of one-electron orbitals while the interaction term is approximated by an explicit functional of the density. This formalism is applied to the molecules H2+ and H2 where it yields a self-consistent picture of a hydrogen atom in a molecule.