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Is there a recommended style how to designate an atom by its number according to the structure numbering (given by nomenclature, or any other one in the text context)?

The are (at least) two different styles used by IUPAC itself. E.g.[1]

Diastereoisomers of glycosides, hemiacetals or related cyclic forms of sugars, or related molecules differing in configuration only at C-1 of an aldose, C-2 of a 2-ketose, etc.

or[2]

Note: The configuration at C-4 (method 2) or C-1 (method 1) cannot be given because the attached substituent is unknown.

or[3]

Small substituents on the C-8 and C-9 atoms of steroids should be drawn within the ring system in this fashion even if there are no substituents on the adjacent fusion atoms C-10 and C-14.

vs[4]

The oxygen atom of the $\ce{CF3CO}$ portion of the ligand is attached to C2, while that of $\ce{MeCO}$ is attached to C4.

I can see some disadvantages for both of the styles.

With hyphen (dash):

  • Might be mistakenly thought, in favorable cases, that it is an isotope abbreviation. E.g. C-14 for carbon-14 ($\ce{^{14}C}$).
  • Not very likely, but eventually might be thought as a mathematical expression (e.g. when talking about 1st halogen atom X-1).

No hyphen:

  • When the text formatting was lost, it might be interconfused with molecular formula. Maybe not for carbon / organic chemistry, more likely for other elements in inorganic compounds, e.g. P4. Especially at chem.SE with Georgia font ☺.

References:

  1. Basic terminology of stereochemistry (IUPAC Recommendations 1996), p. 2199 (anomers, via IUPAC Gold Book)
  2. Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred Names 2013, p. 551
  3. Graphical representation standards for chemical structure diagrams (IUPAC Recommendations 2008), p. 356
  4. Nomenclature of Inorganic Chemistry (IUPAC Recommendations 2005), p. 156
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  • $\begingroup$ If I'd be really worried about possible lost formatting and other noise immunity issues, I'd go with C#1. $\endgroup$ – Ivan Neretin Oct 16 '18 at 14:19
  • $\begingroup$ @IvanNeretin … which then could be confused with some broken incomplete line formula notation (e.g. SMILES) with triple bond. $\endgroup$ – mykhal Oct 16 '18 at 14:48
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How about using the label plus the number encircled? Would be hard to confuse and misinterpret. I actually use this myself when writing on paper or typesetting on computers.

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