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Given a connection table (that is, a list of atoms, their connectivities/bonds, and the type of bonds), how can I detect the presence of an aromatic ring?

For reference, the aromatic rings in the structure will always be depicted in Kekule form (alternating single and double bonds).

It is simple enough for me to use a cycle finding algorithm on the graph representing the bonds to find candidates. The problem is now recognizing which of those rings can be aromatic.

A naive approach for at least six-membered carbocyclic rings would be to check if the ring bonds alternate between single and double bonds. But, the structures below would be problematic:

where the center ring in phenanthrene and the six-membered ring in 2H-indene are decidedly aromatic, even if there is no complete alternation of single and double bonds. If you try to check exocyclic double bonds, the leftmost structure could be a false positive.

Pointers to algorithms would be very much appreciated. I am ignoring heterocyclics like thiophene or imidazole, or cations like tropylium for now, but if you know how to handle them too, it would be a nice bonus.

I haven't gotten an adequate explanation of why people thought the question was "too broad"; thus, to restrict the question, here is a drastically short reformulation:

Given a connection table for a molecule that contains any number of six-membered rings (possibly fused, spiro, etc.) and is represented in Kekule form, can one write an algorithm to determine which rings are aromatic and which are not? Atomic coordinates are available if necessary.

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  • $\begingroup$ Wouldn't simply checking for hybridization of all ring carbons solve all 3 problems presented here? Do you need to differentiate aromatic/antiaromatic? $\endgroup$
    – DSVA
    Sep 9, 2018 at 22:24
  • $\begingroup$ This may be me being slow, but all the carbon atoms in the six-membered rings in all three atoms are sp2-hybridized, yes? But, the six-membered ring in the first structure shouldn't be aromatic... and yes, excluding antiaromatics would be immensely useful. $\endgroup$
    – derek correa
    Sep 9, 2018 at 22:32
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    $\begingroup$ Well, when looking at aromaticity of fulvalenes and similar structures I don't think I can be sure if that exact structure would be aromatic, antiaromatic or non-aromatic. And another question, are you looking into what ring is aromatic or if the structure contains at least one aromatic ring? $\endgroup$
    – DSVA
    Sep 9, 2018 at 22:47
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    $\begingroup$ I wouldn't say 2H-indene is aromatic, much like 1,2-benzoquinone also isn't. $\endgroup$
    – Mithoron
    Sep 9, 2018 at 23:07
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    $\begingroup$ Since I'm pretty sure it is done in context of QSAR, I suggest to move from analysis of aromaticity to analysis of conjugated pi-systems in general. I also have to say that connectivity matrix lacks information of 3d structure and it can easily missdetect some cases of aromaticity/conjugation. $\endgroup$
    – permeakra
    Sep 10, 2018 at 5:35

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I will reiterate what I have written in a comment earlier, as of why I find this a bit problematic (especially for a cheminformatics approach).

There still is no clear cut definition of aromaticity, there even is an (at the time of writing) upcoming conference Aromaticity 2018 to get more clarity on the matter.

There are a couple of questions on the site, where I have written an answer for which demonstrate the issue. I don't want to be shamelessly promoting my own posts, but I also don't want to repeat myself. I think one of the crucial examples is How to explain (non-/anti-) aromaticity in fulvene with the help of resonance structures?

From examples like this, it seems clear that from structure and Kekule form alone it appears impossible to determine whether a ring has aromatic character or not. Mithoron stated in the comments something quite categorical, which I find in its extend debatable; but I wouldn't want to dismiss it either:

I wouldn't say 2H-indene is aromatic, much like 1,2-benzoquinone also isn't.

Take the first as an example, it has a high C-H acidity (higher than indene), because the resulting structure would have a fully conjugated system very closely related to naphthalene. This structure is undoubtedly more aromatic (handwavy, but if you could quantify it, it probably would), so any kind of structural diagram, yes/no-parameter would misrepresent that.

Given a connection table for a molecule that contains any number of six-membered rings (possibly fused, spiro, etc.) and is represented in Kekule form, can one write an algorithm to determine which rings are aromatic and which are not? Atomic coordinates are available if necessary.

I'm afraid the answer to this question is no.

What you could do, and where you'll probably be right many times is using the bond lengths as an indicator. The bonds in such rings should all be very, very similar (maybe ±10%), an given Pekka Pyykkö's data (pdf from his homepage) fall somewhere around 140 pm. Couple that with the ring-finder and I would assume it's going to be close many times.

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