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Often, single-crystal X-ray diffraction analysis determines the non-H atoms first, and eventually puts hydrogen atoms "as riding" on idealized positions in respect to heavier atoms (e.g., C, O, N), because the latters are easier to localize in the Fourier maps. This then considers both distance and geometry (e.g., 0.93 Å for an H attached to a sp-hybridized C) and temperature during the experiment, determined by other experiments (e.g., neutron diffraction).

Is there a particular name for a sum / Hill formula where the hydrogens are omitted, for example, when stating glucose as $\ce{C6O6}$ instead of a complete $\ce{C6H12O6}$ to describe just the backbone of the molecule?

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  • $\begingroup$ Not an answer, but what you are describing seems like a condensed version of SMILES strings if you were to remove the bond information. $\endgroup$
    – Tyberius
    Jan 28, 2019 at 16:36
  • $\begingroup$ @Tyberius Not so fast, please. In a "truncated Hill formula" $\ce{C6O6}$, constitutional information is lost. In a reduced Smiles representation lacking bond order, CC1CCCCC1Br is (at least) a valid representative for any stereoisomer of 1-bromo-2-methylcyclohexane, or 1-bromo-2-methylbenzene; diffrerent from a short $\ce{C7Br}$. $\endgroup$
    – Buttonwood
    Jan 28, 2019 at 17:09
  • $\begingroup$ Yeah I figure the route to what your looking for probably goes through the Hill formula rather than SMILES. I just figured it was another avenue to look into to see if someone has given a name to this type of notation. @Buttonwood $\endgroup$
    – Tyberius
    Jan 28, 2019 at 17:28
  • $\begingroup$ You might say it is a "united atom" representation, but I can't speak for the universality of this nomenclature. $\endgroup$
    – Buck Thorn
    Jan 28, 2019 at 17:54
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    $\begingroup$ Please note that the terminology 'sp-hybridi(s|z)ed C' is incorrect, atoms cannot be hybridised, only orbitals can be. Better options would be linear (diagonal)/ trigonal/ tetrahedral ((coordinated)) carbon (or atom in genearal). Otherwise one could write spˣ-C as an abbreviation for carbon atom with spˣ-hybridised orbitals. // P.S.: MathJax should not be used as a style element. $\endgroup$ Jan 28, 2019 at 17:59

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