I am studying nitrogen bases and their structures and roles in nucleotide, polynucleotides and nucleic acids formation. In the structures of the nitrogen bases like Adenine, Guanine, Cytosine and Thymine, the numbering is baffling me. Why are the atoms in these molecules numbered so? Can someone please specify the rules for numbering these four molecules? I am a biologist and I'm not so good at chemistry.

What is the reason behind this numbering system? Why is a particular nitrogen given number 1? Why not the other in the same ring?

  • 1
    $\begingroup$ A minor correction: I think cytosine has a single bond to nitrogen atom of the amino group at the 4-position. $\endgroup$ – Mick Jan 24 '17 at 6:35
  • $\begingroup$ This customary numbering is not systematic. doi.org/10.1351/goldbook.P04953 $\endgroup$ – Hekim Ağacı Dec 5 '20 at 14:49

ACDLabs maintains a nice summary of the IUPAC nomenclature rules with examples:

Heterocyclics (pyrimidine): http://www.acdlabs.com/iupac/nomenclature/79/r79_702.htm

Fused heterocycles (purine): http://www.acdlabs.com/iupac/nomenclature/79/r79_960.htm

Briefly, apply the following rules:

  1. Number your rings so that the nitrogens end up with the lowest number combination. Thus pyrimidines have (1,3).
  2. Number your rings so that other functional group have lowest possible numbers. Hence pyrimidine is numbered to the exocyclic carbonyl groups are (2,4).
  3. In a fused system, numbering should prefer (in this order): ring with more nitrogens, rings with other heteroatoms, larger rings, nitrogen atom closer to ring junction.
  4. Number toward the farther ring junction from where you started. Do not number junction positions.

Number 3 is fine and all, but purine seems to have a numbering scheme that does not match these rules, and it is supported by IUPAC. Likely, this represents a historical numbering pattern that predates the IUPAC rules. Everyone was using it and so it was adopted. You will likely just need to memorize it (or look it up when you need to).

  • $\begingroup$ Rule 4 clearly has some exceptions, one of which deals with non-carbon atoms (i.e. N) present at fused junctions. $\endgroup$ – user64410 May 21 '18 at 11:40

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