How can I name this organic compound while adhering to the IUPAC standards?
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asked Feb 16, 2016 at 13:54
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27$\begingroup$ Congratulations! This structure breaks my favorite structure editor (ChemDoodle) when I attempt to have it name this molecule... $\endgroup$– Curt F.Commented Feb 16, 2016 at 14:07
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16$\begingroup$ Congratulations, this structure breaks ChemDraw's structure-to-name feature too! I'll try LexiChem when I'm at work tomorrow. $\endgroup$– Geoff HutchisonCommented Feb 16, 2016 at 16:11
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10$\begingroup$ I can't even search chemspider with the skeleton (non-aromatic rings) with similarity search (tanimoto 99%) - I get an error. This is the devil's own structure... $\endgroup$– gilleainCommented Feb 16, 2016 at 16:31
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8$\begingroup$ The preferred systematic name in phane nomenclature for the outer ring (without the “1,4-phenylene” bridge) is “1,3,5,7(1,2),2,4,6,8(1,4)-octabenzenacyclooctaphane”. By way of comparison, the similar [8]cycloparaphenylene with the systematic name “1,2,3,4,5,6,7,8(1,4)-octabenzenacyclooctaphane” is described in dx.doi.org/10.1039/c2sc20719b. $\endgroup$– user7951Commented Feb 16, 2016 at 17:22
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17$\begingroup$ I actually suggest issuing this as a Twitter challenge to ChemDraw, OpenEye, ChemDoodle, ACD, etc. $\endgroup$– Geoff HutchisonCommented Feb 17, 2016 at 16:59
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2 Answers
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It indeed can be named quite nicely using the recent "phane" nomenclature from the Nomenclature of Organic Chemistry: IUPAC Recommendations and Preferred Names 2013, here is the example*
By abstracting to the bicyclo phane composed of nine benzene nodes ("superatoms") of three kinds, we get
1,5(1,3,2),2,4,6,8,9(1,4),3,7(1,2)-nonabenzenabicyclo[3.3.1]nonaphane
Note that the "superatom" (more precise "amplificant") locant ordering matters. If the numbers in the first parentheses were sorted, it would mean a different structure, that is little bit hard to draw in 2D:
1,5(1,2,3),2,4,6,8,9(1,4),3,7(1,2)-nonabenzenabicyclo[3.3.1]nonaphane
Publicly accessible references:
- Phane Nomenclature, Part I: Phane Parent Names
- Phane Nomenclature, Part II: Modification of the Degree of Hydrogenation and Substitution Derivatives of Phane Parent Hydrides
*) Please note there is a mistake in the example from the book, the pyridine (4) has wrong internal ring numbering - 4 should be replaced with 5. The name is correct, though. (It is mentioned in errata, for page 310).
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$\begingroup$ "[3.3.1] " What does it stand for? $\endgroup$ Commented Apr 29, 2017 at 6:54
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$\begingroup$ @Mockingbird, "[3.3.1]" describes that the skeleton composed of two cycles (bicyclo) has three branches (that each begin and end in two distinct nodes - it is always the case; here they are X) (therefore three dot-separated numbers) that have 3, 3 (two identical (X)YZY(X) branches) and 1 ((X)Y(X) branch) nodes ("superatoms") respectively, excluding the X end points, total 9 (nonaphane). This type of naming is also used for hydrocarbons, etc. If X, Y and Z were just carbon atom (with hydrogens), it would be bicyclo[3.3.1]nonane. $\endgroup$– mykhalCommented Apr 29, 2017 at 7:46
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$\begingroup$ @mykkhal what if there are substituents? Like Cl or Br joined to one molecule. $\endgroup$ Commented Apr 30, 2017 at 13:12
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$\begingroup$ @Mockingbird, numbering is done by indicating the number of the "superatom" and the position on it as upper index, so this structure with chlorine on all peripheral positions would be 1⁴,1⁵,1⁶,2²,2³,3³,3⁴,3⁵,3⁶,4²,4³,5⁴,5⁵,5⁶,6²,6³,7³,7⁴,7⁵,7⁶,8²,8³-docosachloro-1,5(1,3,2),2,4,6,8,9(1,4),3,7(1,2)-nonabenzenabicyclo[3.3.1]nonaphane $\endgroup$– mykhalCommented May 9, 2017 at 21:45
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$\begingroup$ "Note that the "superatom" (more precise "amplificant") locant ordering matters. If the numbers in the first parentheses were sorted, it would mean a different structure, that is little bit hard to draw in 2D" Does it only matter for the superatoms by which the "[3.3.1]" is specified? $\endgroup$ Commented May 10, 2017 at 3:51
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ChemDoodle 8 can name this via the extended von Baeyer system, although the name is quite long. Thanks for putting up this nice example though!
Undecacyclo[18.18.6.22,5.212,15.221,24.231,34.240,43.06,11.016,44.025,30.035,39]tetrapentaconta-1(39),2,4,6,8,10,12,14,16(44),17,19,21,23,25(30),26,28,31,33,35,37,40,42,45,47,49,51,53-heptacosaene
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9$\begingroup$ Although impressive, the name ignores the identity of benzenes and treats the compound as poly-alekene. $\endgroup$– ssavecCommented Feb 17, 2016 at 20:13
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2$\begingroup$ Interesting, Marvin Sketch seems to agree with ChemDoodle and Chem Office can not generate a name at all. $\endgroup$ Commented Feb 24, 2016 at 16:39