Are individual atoms inside a molecule (covalent) still really EM neutral?

Question

I am not asking about ionic bonds. I am in this case asking about covalent bonds.

I have read this question:

Why do atoms repel when closer but attract when farther apart?

Where Swike says:

So, from where is this repulsive force coming? Well, it turns out that if you play enough with the mathematical foundations of quantum mechanics you arrive to the idea of Pauli exclusion. Therefore what exactly means that two electrons can't occupy the same place? Well, as it turns out it means that there is a repulsion between them that is proportional to the overlapping of the spreads of their existence. The repulsive force due to Pauli exclusion is what emerges when you try to get two electron clouds (the regions where the electrons are primarily existing) closer together.

I do understand that the PEP plays a role in the atoms' repulsion (so they cannot get too close) inside the molecule.

But this view is assuming that the original atoms before they entered the covalent bond (that were EM neutral) are the same atoms, with the same electron configuration inside the molecule.

Now the molecules share the valence electron shell's atoms when they enter the covalent bond and form a molecule.

But when they do that, they do something else too, they change their own electron configuration, to make the bond more stable, and the total energy of the molecule becomes smaller, the total electron configuration becomes more effective.

Now by doing that, the individual atoms' valence electron shells will become common, existing around the whole molecule as per QM.

Now this way, the individual atoms' electron configuration has changed. This will mean too, that (assuming they were EM neutral before the bond), they cannot be EM neutral as individual atoms when looking at them from inside the molecule.

If you look at each individual atom inside the molecule, these atoms' inner shells (specifically the most outer remaining inner shell) will be the one electron shells that will create the PEP repulsion.

Now but since these individual atoms (when looking at them inside the molecule), are not EM neutral anymore (since they now share some valence electrons, and they partially lost those negative charges), they must act like individual negative charges on their own inside the molecule (surrounded by a common valence shell).

So as I understand it, the repulsive force that counterbalances the attractive force of the bond itself (which comes from the QM phenomenon of van der waals and London forces) created by the sharing of some valence electrons, must be some part PEP and some part EM repulsion.

So the forces that act and create the bond:

1. attractive force, QM phenomenon, sharing of valence electrons, van der waals and London forces

2. PEP repulsive

3. EM repulsion between the individual (now not anymore EM neutral) inner atoms inside the molecule

Question:

1. Is this correct, does the repulsion inside the molecule between the individual atoms come from part PEP and part EM repulsion or just PEP?

2. Are the individual atoms inside the molecule still really EM neutral (after sharing valence electrons and changing their own electron configuration)?

Answer 1

Are the individual atoms inside the molecule still really EM neutral (after sharing valence electrons and changing their own electron configuration)?

When talking about a molecule the concept of a single atom is not valid with respect to electron distribution.

You need to distinguish between the (notional) position of the atom defined by the mass of the atom, made up almost entirely of a quite localized nucleus and the atom as a nucleus with electrons around it, where the electron cloud cannot be as well localized.

Thus you can identify an atom in a molecule in the sense of a well defined nuclear center with an associated nucleus and position, but it is not at all as simple to define the distribution of the electrons associated with each atom. As electrons cannot be distinguished it makes no sense to talk about an electrically neutral atom in a molecule. Only the overall neutrality of the molecule is meaningful.

does the repulsion inside the molecule between the individual atoms come from part PEP and part EM repulsion or just PEP?

When constructing a wafefunction for electrons in an atom or molecule you would use a form that allows for the PEP to be "embedded" in the structure of wavefunction. See for example this Wikipedia page on the Slater determinant.

So we don't explicitly have a force as a result of the PEP, but in order to satisfy the mathematical requirements PEP imposes on the wavefunction, the effect of PEP on energy levels falls out of solving the equations with these "emebedded" structures.

Typically we cannot analytically calculate wavefunctions like these and rely on numerical methods instead. Calculating the effect of PEP is therefore not practical. To do so would require calculating using an entirely different wavefunction structure which does not incorporate PEP principles, but you could not meaningfully relate the two sets of results. I not sure you could even say that the PEP is always repulsive in effect in a molecule.

So the results depends on the effects of electrical attraction (between electrons of nuclei), electrical repulsion (between electrons) and the effects of the PEP via the mathematical requirements for the structure of the wavefunction.