For example, if you take a sample of human bone and put it under a microscope, how do you know if the atoms you’re seeing are calcium atoms? You can’t exactly count the protons on the inside, can you? Also, how do you distinguish between protons and neutrons? Do they reflect different wavelengths of light and so have different colours or something? I’ve also heard people saying that we can’t actually see atoms using microscopes, is that true? If so, how can we say something is made out, say, carbon, when we can’t see it? If the answer to that is that we have tests (flame tests for metals, precipitate tests, pH tests, etc…), then how did we know it is that element/compound that results in the test turning out a certain way? I have so many questions!
P.S. I know that nuclei aren’t really perfect spherical balls, but rather collections of protons and neutrons, which are spheres, in a classical, non-quantum-mechanical sense.
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To figure out a number of protons and neutrons, we can first find atomic mass. That will give us the total number (protons + neutrons). We can figure out atomic mass from statistics of reactions (that’s how it was calculated by John Dalton in 1803), or we can make atom to have unit charge (by giving or taking an electron) and observing its behavior in magnetic field (mass spectrometry).
Figuring the number of protons is harder. We can strip all electrons from the atom and measure the charge. But it is not practical – stripping electrons is a lot of work.
In practice, atoms are identified by a spectroscopy. Instead of measuring the nucleus, we measure an electron cloud instead. Electrons cannot be seen, but “distances” between them can be – they consume wavelengths that just “right enough”. “Distances” between electrons (and therefore – absorbed wavelengths of light) depend on the number of protons, so if two atoms have the same absorption lines – they have the same number of protons.
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