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How can I name this organic compound while adhering to the IUPAC standards?

A name could not be generated for this structure.

orthocresol
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Panglossian Oporopolist
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    Congratulations! This structure breaks my favorite structure editor (ChemDoodle) when I attempt to have it name this molecule... – Curt F. Feb 16 '16 at 14:07
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    Not many online editors worked... unfortunately. :/ – Panglossian Oporopolist Feb 16 '16 at 14:28
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    Hah! This is an awesome test case for chemical editors and layout engines. Layout seems particularly tricky for what should be a quite easy job. – gilleain Feb 16 '16 at 14:37
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    Also, it looks like https://en.wikipedia.org/wiki/Hexabenzocoronene minus some of the internal bonds. – gilleain Feb 16 '16 at 14:38
  • Yea. Removing some of the internal bonds and adding two other phenyl groups gives you this compound. – Panglossian Oporopolist Feb 16 '16 at 14:43
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    Congratulations, this structure breaks ChemDraw's structure-to-name feature too! I'll try LexiChem when I'm at work tomorrow. – Geoff Hutchison Feb 16 '16 at 16:11
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    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... – gilleain Feb 16 '16 at 16:31
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    Sorry, but I can't resist : sigma-aldritch site also fails, as does pubchem. only e-molecules seems to allow searches by drawing it! https://orderbb.emolecules.com/search/#?smiles=Cc1ccc(cc1)c1cccc(c1c1ccc(cc1)c1c(cccc1c1ccc(cc1)c1ccccc1)c1ccc(cc1)c1ccccc1)c1ccc(cc1)C&searchtype=si&similimit=0.8&system-type=BB&p=1 – gilleain Feb 16 '16 at 16:40
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    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 http://dx.doi.org/10.1039/c2sc20719b. –  Feb 16 '16 at 17:22
  • I get undecacyclo[?.?.?.?.?.?.?.?.?.?.?.?]tetrapentaconta-1,3(9),4(10),5(13),6(12),7(45),8(46),11(49),14(52),15(35),16(24),17(36),18(26),19(37),20(28),21(38),22(30),23(39),25(40),27(41),29(42),31(43),32(34),33(44),47,50(54),51(53)-heptacosaene from LexiChem. The "?" (actually BLAH) comes when LexiChem aborts numbering a complicated ring system. – Geoff Hutchison Feb 17 '16 at 16:56
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    I actually suggest issuing this as a Twitter challenge to ChemDraw, OpenEye, ChemDoodle, ACD, etc. – Geoff Hutchison Feb 17 '16 at 16:59
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    Even though this compound has no chiral center, the stereochemistry would be very interesting. – mykhal Apr 27 '17 at 17:22
  • Related https://chemistry.stackexchange.com/questions/73103/does-iupac-nomenclature-have-the-ability-to-name-all-organic-compounds – Pritt says Reinstate Monica Apr 28 '17 at 04:53

2 Answers2

21

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*

sample schema with structures and names

By abstracting to the bicyclo phane composed of nine benzene nodes ("superatoms") of three kinds, we get

schema with structures

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:

srtucture for the obsolete answer

1,5(1,2,3),2,4,6,8,9(1,4),3,7(1,2)-nonabenzenabicyclo[3.3.1]nonaphane

Publicly accessible references:

*) 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).

mykhal
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  • "[3.3.1] " What does it stand for? – Mockingbird Apr 29 '17 at 06:54
  • @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. – mykhal Apr 29 '17 at 07:46
  • @mykkhal what if there are substituents? Like Cl or Br joined to one molecule. – Mockingbird Apr 30 '17 at 13:12
  • @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)-nonabe‌​nzenabicyclo[3.3.1]n‌​onaphane – mykhal May 09 '17 at 21:45
  • "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? – Mockingbird May 10 '17 at 03:51
  • @Mockingbird, I am not sure I understand your recent question, the bicyclo skeleton name completely defines node ("superatom"), but does not define any "amplificant". Sorry that I could be more explanatory, so I attached reference links. – mykhal May 10 '17 at 07:14
  • I mean the sequence in the first parantheses of your example mattered only because those two benzene molecules are the start and endpoint of the 2 cycles. – Mockingbird May 10 '17 at 07:34
  • @Mockingbird, this is not the exact reason, but is related. It matters, because of symmetry or asymmetry. It matters, because the branches are different. It can be vaguely said that it matters because the three numbers in the square brackets are different. If the superatom amplificant would be e.g. pyridine, the order would matter also for those in-branch nodes (with only two locants in the parentheses), if they were bonded asymmetrically, which is not possible for benzenediyl, in this sense. – mykhal May 10 '17 at 07:58
  • I don't understand the order in the first parenthese is in basis of what? – Mockingbird May 10 '17 at 08:04
  • @Mockingbird, .. the order is based on several rules - lowest set of locants, bute more importantly, it is also based on the order of the number of superatom nodes in the parent skeleton, boned to the amplificant locations. Please read through the refs, and draw possible structures yourself, it is no room here for the deep explanation. See rule PhI-2.3.2.2 – mykhal May 10 '17 at 08:10
18

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!

von Baeyer name

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

Geoff Hutchison
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iclkevin
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    Although impressive, the name ignores the identity of benzenes and treats the compound as poly-alekene. – ssavec Feb 17 '16 at 20:13
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    Interesting, Marvin Sketch seems to agree with ChemDoodle and Chem Office can not generate a name at all. – HCSthe2nd Feb 24 '16 at 16:39