Early chemists based their ideas for theories of matter largely on intuition, observation, and measurement. For instance, matter was observed to be solid, mass was understood to be conserved (that is, neither created nor destroyed), and related substances had related weights and reactivity. Antoine Lavoisier taught us a lot about chemistry simply by measuring things very carefully!
The modern atomic theory literally began as an educated guess. The *details* were worked out over many years, and were only verified in the last century. Some examples (note that this is a very incomplete list):
- John Dalton (~1800) proposed that matter is made up of atoms that are indivisible and indestructible. This was an educated guess, and it was a good one—though not perfect!
- J. J. Thomson (~1900) used a cathode ray tube to show that an electrical current could create a stream of particles that were electrically negative; he called these particles “electrons.”
- Ernest Rutherford (1911) did an experiment where he found that radioactively emitted particles *usually* passed through an extremely thin sheet of gold foil, but *sometimes* would deflect. His remarkable conclusion from this was that there was a dense “nucleus” inside atoms. Since atoms were understood to be electrically neutral and the electron was understood to be electrically negative, the conclusion was that the nucleus was electrically positive.
- Albert Einstein demonstrated that electrons could only be ejected from atoms when bombarded with specific energies. This was dubbed the “photoelectric affect” and it is this work for which he was awarded his Nobel Prize. It was this concept of electrons having discrete energies in an atom that led Niels Bohr to his “planetary model” of the atom.
There has been much more theoretical work since the invention of quantum mechanics in the 1920s that has further refined our theories of how atoms and electrons work. (For instance, we now know that the planetary model is not entirely accurate!)
Our understanding of atoms (and therefore how we imagine atoms looking) is still largely theoretical. Even the most sensitive electron microscopes can just barely show us little bumps on the surface of metals that appear to be spherical atoms arranged in a grid. So “visualizing” things has *never* been part of how discoveries in chemistry are made. Hope this helps!