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Subtle is the Lord by Abraham Pais (1982) page 85:
However, it became increasingly difficult in chemical circles to deny the reality of molecules after 1874, the year in which Jacobus Henricus van't Hoff and Joseph Achille Le Bel independently explained the isomerism of certain organic substances in terms of stereochemical properties of carbon compounds.
so it is quite cool to see that organic chemistry is one of the things that pushed atomic theory forward. Because when you start to observe that isomers has different characteristics, despite identical proportions of atoms, this is really hard to explain without talking about the relative positions of the atoms within molecules!
TODO: is there anything even more precise that points to atoms in stereoisomers besides just the "two isomers with different properties" thing?