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When referring to a particular atom, both in text and when using a graphical representation, several conventions are being applied.

In the field of crystallography an arabic numeral either follows the element symbol without any space, e.g. $\mathrm{C}42$ for carbon atom number $42$ (usually assigned during solve/refine routine by SHELX), or is being placed in braces, e.g. $\mathrm{C}(42).$ Sometimes hydrogens attached to the same carbon atom inherit its number and receive an additional letter, e.g. $\mathrm{H42c}$ for the third hydrogen in $\mathrm{C42}$ methyl group.

In NMR spectroscopy an element is normally labeled with a script-sized symbol (arabic number or lowercase letter) in the bottom right corner, e.g. $\ce{H_3}$ or $\ce{H_c}.$ Mestrelab Mnova places numerical labels underneath the element symbol, e.g. $\underset{3}{\ce{H}}$, or directly in place of the element if the symbol for the latter is hidden (carbon, in most cases): ${\scriptsize 3}.$

These labeling schemes used in both instrumental methods (which I cherry-picked solely for the illustrative purposes) seem to work OK in a sense that they are compatible with expanded AZE-notation required to depict any element and its attributes, such as chemical symbol $\ce{El},$ mass number $A,$ atomic number $Z,$ oxidation number O.N., charge $q$ and number of atoms of given kind $x$:

$$\Large\ce{\overset{\text{O.N.}}{^{$A$}_{$Z$}El^{$q$}_x}}$$

and won't cause any confusion (except for $\ce{H_3},$ maybe). However, it would be nice to know whether there is a standardized way to attribute a label to an element that can be uniformly displayed and recognized (main text, titles, structures, illustrations etc.). Does such robust labeling scheme exist?

P.S. If you are a software developer and read this, also feel free to comment or add an answer as to which labeling scheme you've came up with for calling out a particular atom.

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  • $\begingroup$ IUPAC's green book "Quantities Units and Symbols in Physical Chemistry" might be worth a look. It is a 165-paged book. $\endgroup$ – M. Farooq Dec 23 '19 at 16:41
  • $\begingroup$ @M.Farooq Already did. According to the Green Book, labels (in general) must be typed in upright typeface, that's all I found. $\endgroup$ – andselisk Dec 23 '19 at 16:44
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    $\begingroup$ I can imagine that this can become a headache for a reader if the numbering scheme is not obvious, but that does not appear to be a consideration in this question. To draw a comparison, protein sequences are numbered N->C ie Ala42 is the C-terminal residue in the A$\beta$(1-42) peptide. This rarely is a problem although numbering conventions may refer to the original gene rather than a specific construct such as the A$\beta$ in question. But since the sequences are linear the numbering convention is otherwise clear. Now consider branching and rings in compounds and the story changes. $\endgroup$ – Buck Thorn Dec 23 '19 at 19:54
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    $\begingroup$ In any case your question is about convention, not about the best way to do this for the sake of clarity. I would say stick to the crystallography convention but if the molecule is complex provide a structure file or figure with numbering. $\endgroup$ – Buck Thorn Dec 23 '19 at 19:56
  • $\begingroup$ @BuckThorn Yeah, I have the same feeling that crystallographic notation would be easier to maintain. And I actually do care about reader's ergonomics, but I'd put standards/recommendations/guidelines first, if there are any, to avoid confusion and develop a coherent labeling scheme. Ideally, the one that is interdisciplinary understood:) $\endgroup$ – andselisk Dec 23 '19 at 20:00

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