How do Scientists study small objects like molecules and atoms?
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There are so many ways, no ELI5 comment could cover all of them. But here are a few interesting ones.
The geiger-marsden experiment is why we think atoms have nuclei. If you take a really thin sheet of gold (gold foil can be made almost atomically thin), and fire a beam of alpha particles at it, occasionally they will bounce back. This was not the expected result – it suggested a small, concentrated electric charge for the particles to bounce off, which we now call a nucleus.
If you have a molecule and want to weigh it, you can use mass spectroscopy. Typically, this means ionising what you have so that it has a charge, then firing the ions through a magnetic field. The ions will be redirected by the field – but heavier ions will be deflected less.
If you want to actually keep track of individual atoms, you need to used a microscope. Not an optical one that uses light, but a fancy one that uses other means to “see”. One type is electron microscopes – these use electrons instead of light, as electrons can have a shorter wavelength, which allows a higher resolution.
Too many ways for a single answer. Here’s one way:
Usually we’re interested in how molecules or atoms react with other chemicals, and that’s usually determined by what the outer shell of electrons is doing.
We can learn about what’s going on with the electron shell of a molecule with a technique called nuclear magnetic resonance.
When you put a sample of something into a very strong magnetic field, and manipulate that field in a specific way, some nuclei behave like tiny bar magnets and generate a signal that can be measured.
Electrons flying around generate their own tiny magnetic fields and interfere with the signal, so what you actually measure is a slightly different signal for every nucleus in the sample that has a different environment around it.
You can put all those different signals together like a puzzle into a structure of the molecule in three dimensions. For really big molecules like proteins, you can even see signals between nuclei that aren’t directly bound to each other but are held close together by secondary structure.
Edit: You can get different types of information from different NMR experiments, which you can then combine into structural details. The most common experiments look at hydrogen nuclei, carbon-13 nuclei or nitrogen-15 nuclei, which are in almost all organic molecules.
You can learn what the proportions of each kind of nucleus are, which nuclei are directly bound to each other, which ones are held in specific angular rotations to each other, and which ones are close to each other in space.
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