>Since we do not have a microscope powerful enough to actually look at the atoms in a molecule
[Excuse you..](https://www.youtube.com/watch?v=pGWSX6pStd0)
The key is in the word *look*. At subatomic scales, we’re not talking about magnifying light anymore. We use electron microscopes which fire a beam of electrons at the object.
Yet your question still stands: how did we know those things before the invention of the electron microscope? Well, it’s a whole subject we call valence shell electron pair repulsion theory. In essence, the way the particle behaves and what atoms comprise it can be used to infer details about its geometry. The simplest one is water: we know the angle between the two hydrogen atoms is bigger than 90° because the lone pair electron repulsions are greater than the bond pair ones.
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