The word molecule was first used in a scientific sense by Avogadro in 1811 and was brought into English in 1794 when it meant "small particle" of any type. However, it was used for more than a century before that in French, and wasn't too different in Latin as molecula. Now we get semantic variation; molecula is a diminutive of moles, which meant "mass" (so a molecule is a "tiny mass") and is sort of related to Avogadro's mole, through German. Moles also had a secondary definition of "barrier", and that's important for explaining the Proto-Indo-European reconstruction: apparently it derives from the root mo, meaning "exertion", because it requires effort to overcome barriers. Usage of the word molecule in literature over time has been slowly decreasing since a peak in the 1960s.
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The Etymology Nerd