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I was wondering if anyone can tell me how to number this molecule:

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This molecule is derived from azulene by addition of two sulfurs and two oxygens at positions 2, 6, 1, and 5 respectively. I would like to learn the proper procedure of numbering. I tried googling around and reading papers but could not find the correct terminology for this process.

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If your aim is to know just the chemical name, you may ask a computer.

  • If the chemical already is known, chances are you find it in a data base (e.g., reaxys by Elsevier, or Scifinder by The American Chemical Society). The later even has the option to draw a structure and to request a naming for it, even if there wasn't yet a publication indexed by SciFinder about said molecule. A resource you typically find in Chemistry departments.
  • There are standalone programs helping you to find a chemical name for this structure. 2,6-bis(sulfanyl)azulene-1,5-dione, if you ask ACD Chemsketch (here, the freeware was used [free in the naming up to 50 atoms]); but Perkin Elmer's ChemDraw, or ChemDoodle -- often accessible within a campus wide license program by an university -- likely find it / generate it equally well.

If you aim to learn the nomenclature by yourself, the handy pocket guide by Helmchen may be worth to consider. Portions of it may be seen in googles book preview, like the screen photo taken below.

enter image description here

(credit to Google books, p. 16)

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  • $\begingroup$ I really Appreciate the fruitful explanation. I have two questions: 1- I understand the meaning of 3a and 8a but when looking for the Vertex-Adjacency Matrix of Weighted Graph, should they not be 9 and 10 instead? 2- Speaking of Vertex-Adjacency Matrix of Weighted Graph, would you be capable of explaining why you have not numbered O and S like the carbons? In other words, would you be able to confirm that numbering is only for carbons? 3- To ask about the Vertex-Adjacency Matrix of Weighted Graph 2,6-dimercaptoazulene-1,5-dione can I ask here ? Or should I post a new question? $\endgroup$ – abed haidar Dec 2 '18 at 1:45
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The rules for numbering of bicyclic compounds such as azulene are given in Nomenclature of Organic Chemistry – IUPAC Recommendations and Preferred Names 2013 (Blue Book).

First, you need to generate a "preferred orientation" of the molecule:

P-25.3.2.3.2 Polycyclic fused ring systems are oriented in accordance with the following criteria considered in order until a decision is reached:
(a) maximum number of rings in a horizontal row;

Because of this, the two rings need to be horizontally aligned with each other in the preferred orientations. Note that this rule alone does not distinguish between the two orientations on the left.

Preferred orientation of azulene

Then, the numbering proceeds as follows:

P-25.3.3.1.1 The numbering of peripheral items in the preferred orientation starts from the uppermost ring. If there is more than one uppermost ring, the ring furthest to the right is chosen. Numbering starts from the nonfused atom most counterclockwise in the ring selected and proceeds in a clockwise direction around the system, including fusion heteroatoms but not fusion carbon atoms. Each fusion carbon atom is given the same number as the immediately preceding nonfusion skeletal atom, modified by a Roman letter 'a', 'b', 'c', 'd', etc.

This leads to two possible numbering systems for the two orientations above. Which one is preferred is given by a further rule

P-25.3.3.1.2 If alternative numberings for a ring system remain [...] the following criteria are applied in order until a decision is reached: [...]
(c) low locants are assigned to fusion carbon atoms;

Preferred numbering for azulene

The ketones in your molecule have greater seniority over the thiols (P-41), and hence the ketones are expressed as the suffix (leading to a name ending in "dione") instead of the thiols (a name ending in "dithiol"). Note that if the thiols are deprotonated this seniority ranking would be reversed, as anions have greater seniority over ketones (hence you would have a name ending in "bis(thiolate)").

The quinone derived from azulene is named as azulene-x,y-dione, where x and y are the locants of the two carbonyl carbons (P-64.2.2.2.3). The asymmetry in the quinone leads to ambiguity in the numbering, which is resolved by the next rule:

P-14.4 When several structural features appear in cyclic and acyclic compounds, low locants are assigned to them in the following decreasing order of seniority: [...]
(c) principal characteristic groups and free valences (suffixes);

Numbering of azulene quinone

Finally, the –SH groups are inserted as prefixes into the name, as they can no longer be suffixes. The appropriate prefix for –SH is 'sulfanyl'. The multiplier used is "bis" and not "di" to avoid ambiguity:

P-16.3.6 The prefixes 'bis', 'tris', 'tetrakis', etc. are also used to avoid ambiguity:
(a) before a mononuclear subset of a polynuclear acyclic structure;
Examples: bis(sulfanyl) (preferred prefix; defines two –SH groups, see P-63.1.5; whereas disulfanyl defines the –SSH group; see P-63.3.1)

Structure and PIN of 2,6-bis(sulfanyl)azulene-1,5-dione

As you can see, the manual generation of such names is in no way trivial. Most people use software to automatically generate names, which is generally sufficiently clear for the chemical community to understand them. However, it should be mentioned that these automatically generated names are not always the preferred IUPAC names: for example, ChemDraw 16 gives "2,6-dimercaptoazulene-1,5-dione" as the name, even though the prefix "mercapto" is no longer recommended (P-63.1.5).

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  • $\begingroup$ I really Appreciate the fruitful explanation. I have two questions: 1- I understand the meaning of 3a and 8a but when looking for the Vertex-Adjacency Matrix of Weighted Graph, should they not be 9 and 10 instead? 2- Speaking of Vertex-Adjacency Matrix of Weighted Graph, would you be capable of explaining why you have not numbered O and S like the carbons? In other words, would you be able to confirm that numbering is only for carbons? 3- To ask about the Vertex-Adjacency Matrix of Weighted Graph 2,6-dimercaptoazulene-1,5-dione can I ask here ? Or should I post a new question? $\endgroup$ – abed haidar Dec 2 '18 at 4:25
  • $\begingroup$ I’m afraid I have no idea what that graph is, and if you have a different question please ask a new question. $\endgroup$ – orthocresol Dec 2 '18 at 7:43
  • $\begingroup$ My last question would be why as a suffix SH and O are not numbered and only included? Are they because Hetero atoms? $\endgroup$ – abed haidar Dec 3 '18 at 2:23
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    $\begingroup$ @abedhaidar The numbering system is not applied to the molecule as a whole, but rather to the "senior parent structure", which in this case is azulene itself. $\endgroup$ – orthocresol Dec 3 '18 at 2:28

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