Ways of Looking

From WikidChem

There are many ways of looking at a molecule (or an elephant). When we look at the electron-density contour map of H2, we can look at the molecule from the perspective of several different contours.

Looking at the high e-density contour, we just see two atoms – slightly distorted atoms, but still two distinct entities. We can call this ‘molecule as atoms’.

Looking at the medium e-density contour, we see a sort of figure eight electron density contour. Here, we clearly have two centers of electron density, but they clearly share some e-density. The molecule looks, from this perspective, like atoms with weak bonding. We can call this ‘molecule from atom’.

Looking at the low e-density contour, we just see one big mass. The molecule looks like an atom! We can call this ‘molecule as atom’ or the 'United Atom'.

But the atom’s e-density looks distorted. This is because we can think of the nucleus – the positive charge – as being broken up into several (here, two) parts. We can think of the nuclei as being positively-charged spheres embedded in a cloud of negative charge – electrons dispersed and noded by kinetic energy. This is reminiscent of the ‘plum-pudding’ model of the atom, except that the charges are reversed – in the ‘plum-pudding atom’ the electrons are embedded in a sphere of positive charge.

what does "noded by kinetic energy" mean? In the Oxford English Dictionary "node" as a verb is said to be "rare and obsolete" and means "to form a knot". - JMM

I think that what this means is that we have invented a new verb. The cloud of negative charge is not just vaguely nebulous. Rather, because we are thinking of the molecule as an atom, with orbitals like those of an atom, the molecules has orbitals. These orbitals have shapes, just like those of atoms. And these shapes are derived from nodes in the ψ curve - thus, these shapes are 'noded'. If an electron around a nucleus - one positive sphere - has a particular ψ and so a particularly shaped orbital, an electron around two postive spheres - two nuclei in a molecule - will have a similar shape. Of course, things - primarily the value of Z - can distort the shape. For some happy visuals, see slides 18 through 23 of this lecture (100906) or, for more complicated visuals, most of next lecure (101106). - JBA

We can take advantage of the 'United Atom' model to predict the electron orbitals around even complicated molecules like methane and ammonia.