Do atoms in a molecule overlap?

Question

By this I mean do the electron clouds overlap so that the various nuclei are actually close to each other?

If they overlap, how close do the nuclei get to each other? That being the case, does the closeness of the nuclei determine the density of the element?

Answer 1

Your question is actually pretty advanced and complicated, so bear with me...

If you're talking about electron clouds then you presumably know that electrons are described by wavefunctions whose square describes their probability distribution. The wavefunction of essentially every single electron is the size of the universe. However, the vast bulk of that electron density resides very close to the nucleus, which is why when people talk about electron density and distribution they typically refer to a 90% cutoff, or a 95% or 99% cutoff. Because a 100% cutoff = the size of the universe.

The closest any nucleii ever get in a non nuclear-fusion type even is about one angstrom (hydrogen bonds). If you calculate the average number of atomic nucleii in a gas, for example, you'd realize that if they were statistically distributed you'd never have any bonds, because they'd be so far apart. Entropy, for example, dictates that they should be distributed randomly and generally pretty far apart, so there must be another force. That is the enthalpy, the attraction of one nucleus in an atom to the electrons of another atom. It is enough to bring atoms pretty close together, with occasionally a fairly significant attraction (that exothermic attraction in things like water and nitrogen and carbon dioxide is what you see when you burn anything or when things explode).

Now back to the wavefunctions: if you write the wavefunction for electrons in a molecule, then you see that the electrons for anything that is bonded together actually describe something that is the size of the bonded entity. For example, the two electrons in hydrogen (H2) are each the size of the hydrogen molecule. So if you think about the electrons at some reasonable probability cutoff (i.e. less than 100% which would be the size of the universe), then when you bring the two atoms together into a molecule suddenly the electrons get "bigger"--they are now the size of the bond. In a benzene molecule, for example, the pi electrons are each (all six of them), about the size of the benzene molecule. So the electrons of the individual atoms have now merged into an entity that is much bigger--the molecule. This is because those electrons are now stabilized by more than one nucleus. So the individual atoms, which especially in a random gas would be very far apart from each other, are now very much closer and their electrons overlap across different atoms.

The nucleii, on the other hand, never come closer than about one angstrom apart. Once you start bringing them closer than about one angstrom the repulsion is EXTREME. This is why nucleur fusion is hard, and rarely occurs outside stars (which are very big--extreme pressures, and very hot). Think about it this way: if two carbon atoms come together, then a part of the nucleus of each one of them is now supporting a part of the electron density of the other atom. If you are trying to fuse them together then you're trying to force two nucleii with multiple protons together. Just based on Coulomb's law, the force required to do that scales with the square of the charged and the inverse square of the distance. It's even harder than that, but that's why nucleii are hard to fuse.

Hope that helps you to understand. You've hit upon something that's in the borderline of chemistry, physics, and philosophy, so that's why my answer is so long (and still incomplete!!!). Good question.

Answer 2

Electron clouds overlap, but nuclei only overlap during nuclear fusion, in which case you no longer have two atoms any more, but one. How much electron clouds in a molecule overlap depends on the atoms and the molecule, as well as the energy states of the electrons.