This is something that never actually got explained to me in chemstry lessons in school and I’ve always been curious about since.
How, before electron microscopes capable of seeing individual atoms, were scientists able to say for certain that some substances were only made of one type of atom (e.g. oxygen in oxygen gas/ozone, carbon in graphite/diamond, or iron) but others were made of multiple types (e.g. H2O)
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To be frank, scientists do not use electron microscopes to identify compounds.
There are several ways to determine the types of atoms in a molecule. A flame test is probably one of the oldest. One can determine nitrogen (Keldjahl analysis) or carbon and hydrogen and many other elements using destructive techniques like acid or flame digestion followed by qualitative analysis (there is a flow chart that we used to learn). Um…early scientists used to taste the compounds as well. I cannot endorse that.
Here is a small section on [qualitative analysis](https://chem.libretexts.org/Bookshelves/Analytical_Chemistry/Supplemental_Modules_(Analytical_Chemistry)/Qualitative_Analysis/Confirmatory_Tests). Libretexts has lots more.
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