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We talk of electrons as particles and that they're in "orbits"--"orbital" is the term of art now--and these form shells. Then we talk about shapes for these orbitals--the first orbital is spherical, the second is sort of dumbell shaped, etc. The orbitals are lettered spdf.
But we understand that electons are also waves, and that we don't track individual points of matter. Instead, there are probabilities: The s-orbital isn't a sphere, it's an amorphous cloud, but where the electrons in the s-orbital are most likely to be is the sphere. The farther away from that region of space around the nucleus, the less likely the probability. And the odds fall off rather sharply, so the s-orbital is the place to bet to find an s-electron.
Each orbital contains a set number of pairs of electrons. And with each electron there's a minimum amount of energy that it has.
We just number the shells, 1, 2, 3, etc. And we recognize that the orbital for one shell comes very close to, or even goes beyond the s orbital for the next higher shell in the case of some f orbitals.
That's an atom at its resting state, minimum energy. If you pitch energy into the electron shell--in specific lumps--you can excite an electron. Then it can jump to a higher slot within its orbital, to a higher orbital, to a higher shell, or just escape entirely.
That's atoms.
When you talk molecules you're looking at hybridizing the orbitals, and this both biases the probabilities as to where a given electron in an orbital is likely to be, which is to say, it changes the shape of the orbital. I'm sure if you Google or just check out Wiki for "orbital" and "hybrid orbital" or even things like sp-orbital you'll get interesting attempts at showing the 3-D shapes. Just keep in mind that the orbital isn't a solid, that it's just likely that the electron "in" that orbital will be within the volume enclosed by that shape, and that the probability isn't the same for each bit of that volume.
Images that they've managed to get of atoms and molecules show fuzzy pieces of lint, since the electrons are very fast and the "shutter speed" not that small.
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