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I was reading about atropisomers and their impacts on drug design, and I started wondering whether we have a formal definition for identical molecules. Atropisomers are not the same molecules because they can’t easily interconvert, so I was thinking a definition of “identical” might involve conformations, as it seems like conformers are chemically different (for example, only certain (cyclo)alkyl bromide conformers can undergo elimination via an E2 pathway).

One definition that I think could work would be that two molecules are identical if they can quickly interconvert between the same set of conformers (though I imagine the timescale of the interconversion necessary for the molecules to be identical depends on the purpose of the molecule). Two conformers would be considered the same if they are geometrically identical and could be superimposed upon each other. Would a definition like this differentiate all isomers, or would it classify some isomers as identical? Is there an accepted definition of identical? Is it something that is defined based on the context of the situation?

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    $\begingroup$ related chemistry.stackexchange.com/questions/89909/… $\endgroup$
    – Mithoron
    Commented Nov 7, 2022 at 17:29
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    $\begingroup$ Typical cut-off for atropoisomers is 1000 seconds, afaik. en.wikipedia.org/wiki/Atropisomer $\endgroup$
    – Mithoron
    Commented Nov 7, 2022 at 17:43
  • $\begingroup$ Following up on Mithoron's comment, atropisomers are "identical" in that you don't have to worry about the conformational energy barrier when you interconvert them on paper or in your mind. However, in practice, a sample containing atropisomers will contain molecules with different physical properties relevant for instance when interacting with a biomolecule binding site. It's all about the timescale. $\endgroup$
    – Buck Thorn
    Commented Nov 7, 2022 at 18:22

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