How do we go from atoms to larger structures?

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I have gone deep into a rabbit hole and I’m now forgetting everything there is to know. Atoms are a unit of matter with a proton, neutron, and electron. First off, are protons and electrons physical objects, or are they just representing a positive and negative charge? Secondly, when atoms interact with each other via intermolecular forces to form molecules, what is physically interacting with each other?

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> First off, are protons and electrons physical objects, or are they just representing a positive and negative charge?

They’re a real thing that’s really there, but they’re, um, not exactly “physical objects”. They’re “standing waves” in a handful of quantum fields, which gets very convoluted to explain very quickly.

The not-exactly-true-but-true-*enough* way to put it is that you shouldn’t think of them as charged little balls, but more like charged regions of 3D space. For the very lowest-energy electrons this region is spherical (look up “electron cloud”) but at higher energies they form much weirder shapes. This region in space that the electron occupies is called the “electron orbital”.

> Secondly, when atoms interact with each other via intermolecular forces to form molecules, what is physically interacting with each other?

First, atoms do not interact via “intermolecular forces” – intermolecular forces by definition act *between* (*inter-*) two different molecules, not within (*intra-*) the same molecule.

Second, atoms link together to form a bond when their valence (=outermost) electrons’ orbitals overlap*. That is, when an Atom 1’s electron occupies some region of space, and Atom 2’s electron occupies *the same* region of space, they smoosh together into one big region of space that holds both electrons simultaneously and now you’ve got a *molecular orbital* (MO). Both atoms’ nuclei are trying to hold onto that MO at the same time via the electrostatic force (the “opposite charges attract” force), so you basically get this sort of tug-of-war between the two nuclei using the MO as the rope, and that’s what we call a “bond”.

(* and in-phase, yes I know what an anti-bonding MO is)

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