Atoms in molecules

The development of QTAIM was driven by the assumption that, since the concepts of atoms and bonds have been and continue to be so ubiquitously useful in interpreting, classifying, predicting and communicating chemistry, they should have a well-defined physical basis.

In addition to bonding, QTAIM allows the calculation of certain physical properties on a per-atom basis, by dividing space up into atomic volumes containing exactly one nucleus, which acts as a local attractor of the electron density.

In terms of an electron density distribution's gradient vector field, this corresponds to a complete, non-overlapping partitioning of a molecule into three-dimensional basins (atoms) that are linked together by shared two-dimensional separatrices (interatomic surfaces).

Because QTAIM atoms are always bounded by surfaces having zero flux in the gradient vector field of the electron density, they have some unique quantum mechanical properties compared to other subsystem definitions.

In these compounds, the distance between two ortho hydrogen atoms again is shorter than their van der Waals radii, and according to in silico experiments based on this theory, a bond path is identified between them.

In mainstream chemistry descriptions, close proximity of two nonbonding atoms leads to destabilizing steric repulsion but in QTAIM the observed hydrogen-hydrogen interactions are in fact stabilizing.

The classic explanations for this rotational barrier are steric repulsion between the ortho-hydrogen atoms (planar) and breaking of delocalization of pi density over both rings (perpendicular).

For example, covalent–bond force constants in a set of lysine-arginine advanced glycation end-products were derived using electronic structure calculations, and then bond paths were used to illustrate differences in each of the applied computational chemistry functionals.