This is a very dense article that could use a little unpacking. The author presents NH3 ammonia as an example but it's worth looking at two others, molecular O2 and methane CH4. Molecular orbital theory explains O2 very nicely but there's still an ongoing debate about whether to use Lewis dot structures or MO theory to describe methane (a very important chemical) to undergraduate chemistry students. (MO is better, it's far closer to experimental reality). There are some interesting papers out there on whether undergrads should be told methane is a Lewis-dot model or a MO model, IIRC.

Really, though, the problem here is that molecules are so complex that exact solutions fail and this brings us into the realm of numerical solutions, group theory symmetry arguments, and so on. If you find this subject interesting I suggest getting your hands on a copy of PW Atkins / RS Friedman "Molecular Quantum Mechanics" and perhaps also PCW Davies semi-pop-sci-but-with-way-too-many-equations (1979) "The forces of nature". (doesn't cover molecules though is great on background)

https://www.amazon.com/Forces-Nature-P-C-Davies/dp/052131392...

This article could be trying to cover too much ground, but perhaps thats OK? It's hard enough to apply QM to electrons and their interactions without trying to bring the nuclear interactions in at the same time (beta decay defies pop-sci demos, for example, IIRC it's two 4D matrices interacting with each other and somehow out pops a neutrino, I guess Pauli understood it).

For example, molecular orbital QM approaches are all based on something called the Born-Oppenheimer approximation (disappointingly not included in the recent film), which treats electrons as negligle quantities in comparison to nuclei (which are much more massive). So if we ask chatbot something like (1);

> "system: explain the Born-Oppenheimer approximation, which takes note of the great difference in the masses of electrons and nuclei. Because of this difference, the electrons can respond almost instantaneously to the displacement of nuclei. Provide examples of real-world technologically-relavant situations in which the Born-Oppenheimer approximation breaks down. User: a graduate student in a solid-state physics program. Assistant: This complicated topic is worth careful analysis..."

So the chatbot tells us, probably better than I could summarize it:

> "Because electrons are much lighter than nuclei, they can respond rapidly to changes in the positions of nuclei. In other words, when the nuclei move, the electronic configuration of the system adjusts almost instantaneously to accommodate these movements. This allows us to consider the electronic structure as adapting instantaneously to changes in nuclear positions. This separation of timescales makes it possible to treat the electronic and nuclear motions as somewhat independent, greatly simplifying the quantum mechanical calculations."

But since I once worked down the hall from these quantum dot enthusiasts, I know to ask a follow-up:

> "Titanium nanodots are a system where the B-O approximation breaks down due to relativistic effects, is this correct?"

chatbot: "In heavy elements like titanium, which has a relatively high atomic number, the velocities of its electrons can approach relativistic speeds, particularly in systems with high electron density or high atomic confinement, such as nanodots. When this happens, the usual non-relativistic treatment of electron motion (as assumed in the Born-Oppenheimer approximation) becomes inadequate, and relativistic corrections need to be taken into account. Relativistic effects can lead to several interesting phenomena..."

That said the overall thesis (of the source article) that there's a ton of stuff apparently going on inside of even simple atoms like carbon is certainly true. I think Feynman talked about this a few times, he said something like he couldn't understand how all that activity could be taking place in such a tiny space or words to that effect.

Anyone trying to understand this stuff... there are rabbit holes inside the rabbit holes, and it's all a very active field of current scientific investigation.