There wasn’t a “jump”. It was a long process.
Benjamin Frankling found a method to measure the size of molecules in 1774. But he didn’t reach that conclusion, wich was added bei Lord Rayleight in 1890.
Stuff like electronegativity could be puzzled together by measuring the energy released by certain reactions, and the fact if certain reactions are even possible.
And for crystalline materials you could find the microstructure from the shape of the macrostructure.
All that was slowly pieced together and combined with knowledge from electrical physics to slowly get a better and better idea of what molecules look like.
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