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I know the basics of naming organic molecules, but this one is a bit more complex than I'm capable of. How can I number the atoms in strychnine?

Systematic IUPAC name: ($4$bR,$4$b$^1$S,$7$aS,$8$aR,$8$a$^1$R,$12$aS)-$4$b$^1$,$5$,$6$,$7$a,$8,8$a,$8$a$^1$,$11$,$12$a,$13$-Decahydro-$14$H-$12$-oxa-$7$,$14$a-diaza-$7$,$9$-methanocyclohepta[cd]cyclopenta[g]fluoranthen-$14$-one

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Martin - マーチン
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imrobert
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  • related https://chemistry.stackexchange.com/questions/169432/iupac-naming-of-lysergic-acid-diethylamide-lsd-heterocyclic-core-and-its-locan – Mithoron Mar 01 '24 at 14:43

1 Answers1

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Nomenclature for organic compounds (Blue Book, see nomenclature references on the resources site) equally agreed on how structure formulae of polycylic compounds should be presented, and oriented. For a couple of parent structures considered important enough, the numbering is defined, too. While illustrating rule P-101.6.7, the Blue Book displays strychnidine as the plausibly most similar parent structure to strychnine itself (note C10 does not carry a carbonyl group):

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(image credit to G. P. Moss' freely available, searchable compilation of the Blue Book, landing page, and link to the corresponding pdf of chapter P-10).

This depiction differs from the pattern you found / obtained by a computer program, for which bridge atoms (atoms belonging to multiple rings) are named with small letters (e.g., 12a) because the algorithm applied assigned a different stem systems (a motif of higher seniority), than by departing from strychnidine as parent structure.

For the numbering, one has to identify the largest ring to be oriented that vertically sketched bonds are as far as possible away of each other. Subsequently, the orientation has to sequentially consider a) as many as possible rings are oriented along a horizontal line, b) as many as possible rings are in the top right quadrant, c) as few as possible rings are below a horizontal line, and d) as many as possible rings are above a horizontal line in an intermediate coordinate system. The relevant set of rules in the Blue Book are e.g., P-25.3.3.1.1 and following, and P-25.3.2.3 and following.

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Once this is set, one seeks for the position which is topmost, in the cycle most to the right hand side, the atom most to the left hand side which is member of only one cycle; from there, count clockwise within this stem system. Rasmussen compiled a couple of examples, for instance

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Among the molecule editors, the template library of the freely available ACD ChemSketch actually contains a set of alkaloid scaffolds already numbered, ready for copy-paste and further edit:

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Rasmussen, S. C. The Nomenclature of Fused-Ring Arenes and Heterocycles: A Guide to an Increasingly Important Dialect of Organic Chemistry. ChemTexts 2016, 2, 16. https://doi.org/10.1007/s40828-016-0035-3 (open access).

Buttonwood
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  • thanks, i'm trying to apply this to the structure of strychnine but i need a little more. could you explain why C1 in morphinan is where it is and point me to C1 in strychnine? – imrobert Mar 05 '24 at 17:29
  • @imrobert With reference to the Blue Book and a editor which has strychnidine as a structure closer to strychnine itself, I attempted to provide an entry into the nomenclature about fused organic rings. It is complex. – Buttonwood Mar 06 '24 at 22:04