Eli5, How do we know a molecules’s shape?

Question

I was reading the other post about H2O vs H2O2, and someone mentioned that H2O2 is structured like HOOH. How do we know this? Why not OHHO? Is it process of elimination from knowing that certain atoms don’t form bonds in a certain way?

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Answer 1

To answer this requires a bit more a background in chemistry but it’s two pieces.

First, we know *why* atoms bond together, which has to do with the number of electrons they have and how they are arranged. In a very simple example, you might understand that electrons repel each other like magnets. So if I have 3 electrons around me in a circle, and they all repel each other, they push themselves in 120^(0) angles. Because 3*120=360, so they evenly push each other apart. Long story short, we now know enough about chemistry to predict the shape of molecules based on our knowledge of each atom’s specific electron situation and how it would interact with another atom’s electron situation.

As a good visualization example, oxygen “wants” to have a 4 electron “situation” (this is another chemistry conversation, let’s agree we know this from a previous school lesson), but it only has 2. So desires bonds with 2 hydrogen atoms which give it the desired 4 electron situation. But in our visual models of water, we wouldn’t draw the 2 electrons oxygen started with, only the 2 new hydrogen atoms. Since 360/4 = 90, we can imagine a water molecule as looking like 2 invisible electrons on the bottom and 2 visible hydrogen atoms on top, all 90 degrees apart, this would be the Micky Mouse Head kind of appearance of water. (Note, this is idealized, there more going on and the hydrogen atoms in water are closer to 110 degrees apart, but that’s tomorrow’s chemistry lesson).

So in the end for basic molecules, we can use our knowledge of electrons, chemistry, and trigonometry to visualize them. This gets much, much more complicated when you get to huge molecules because we’re less sure of how everything connects to together, but we have other, future-lesson complicated type stuff, ways of visualizing those molecules too.