I'm drawing the generic structure of several different organic molecules in my thesis. They share some features, one of which is a carbonyl carbon attached to either an oxygen atom (i.e. ester) or an $\ce{-NH}$ (i.e. amide).

My first instinct was to draw it like this: $\ce{R-X-C(=O)-R'}$

But I wonder if X wrongly implies that it's a halogen? In which case, what would be the correct letter or symbol to use? I've seen Z used sometimes when X is used elsewhere, would that be more appropriate? Or perhaps Q for heteroatom, as in Reaxys? Or A for 'any'?

I'm actually drawing in ChemDraw, this is simplified for the sake of the question

Edit: corrected mistake (nitrogen atom -> $\ce{-NH}$ group)


1 Answer 1


Oxygen and nitrogen have different valencies, so you can't use the same letter to denote literally an $\ce{O}$ or an $\ce{N}$ atom, as they can't be directly substituted for one another.

You should use the same letter to denote $\ce{O}$ or $\ce{NH}$, for example. It's perfectly permissible to write $\ce{R-X-C(O)-R'}$ and say $\ce{X} = \ce{O}, \ce{NH}$. This approach is commonly used in the literature. If your amide is tertiary then write something like $\ce{X} = \ce{O}, \ce{NH}, \ce{NR}$. The same applies to structures drawn in ChemDraw.

Beyond that, the choice of letter is arbitrary (as long as you define it!) so $\ce{X}$ is perfectly fine, although you should obviously avoid letters which already represent a chemical element (e.g. $\ce{B}$, $\ce{C}$, ...).

What one might consider the "official rules" are given in: Brecher, J. Graphical representation standards for chemical structure diagrams (IUPAC Recommendations 2008). Pure and Applied Chemistry 2008, 80 (2), 277–410. DOI: 10.1351/pac200880020277 (free version provided here). See especially section GR-2.2. However, there isn't really much in there that constrains you; a lot of it is "common sense".

  • 1
    $\begingroup$ Of course I meant NH and feel very silly now... Edited my question for the sake of future readers. Thank you for the excellent answer! $\endgroup$
    – Oded R.
    Commented Sep 9, 2021 at 17:19

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