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Even as Hückel's rule is not applicable in every scenario, especially in metallic clusters, it seems that organic structure need to be planar to show aromaticity. That being the case, Pubchem's representation of Phthalocyanine shows a non-planar structure. Part of it is completely out of phase and perpendicular to the whole structure, just as in Biphenyl, with this making the latter experimentally confirmed as non-aromatic (the whole molecule, not each phenyl ring):

Phthalocyanine Pubchem

Is this representation mistaken or is there something more to this?

C-Consciousness
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  • Related: https://chemistry.stackexchange.com/questions/51484/does-aromaticity-require-a-co-planar-pi-system/51485#51485 – Ivan Neretin Oct 25 '21 at 16:51
  • As mentioned in that link, they can be twisted to a degree and be aromatic. Yet in Phthalocyanine part of the side is completely out of phase with the rest just as in Biphenyl, which should render it non-aromatic. – C-Consciousness Oct 25 '21 at 17:12
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    Is it really? Why did you look at a lame molecule viewer and not crystal structure? It's flat all right and even if it wasn't flat as a whole then a single aromatic ring would make it aromatic. – Mithoron Oct 25 '21 at 17:26
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    Aromaticity, especially if you consider systems with more than a single cyclic structure (e.g., benzene, pyridine, pyrole, thiophene, furane, cyclopentadienyl anion), isn't on/off like like a light switch. See, for example [18]annulene (wikipedia entry here). For phthalocyanines, it actually equally matters if these are empty or complex a transition metal. Thus, related. – Buttonwood Oct 25 '21 at 17:40
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    In addition, many of PubChem's 3D structure entries are the result of putting the atoms together (in a computer) and optimizing the structure in a molecular force field at low computational cost. This may, but need not be the most favourable conformation in solution, and even less in the solid/crystalline state experimentally recorded. – Buttonwood Oct 25 '21 at 17:45
  • Mithoron/Buttonwood, I was not aware of such compromises and limitations of 3D singular molecular representation. Makes more sense now on it planarity. I believe this question can be closed, unless someone wants to add anything else. Thank you! – C-Consciousness Oct 25 '21 at 18:22
  • Just to add a little on the Huckel's rule: it CAN be applicable to aromatic all-metal clusters as well. ;-) – Aleksey Kuznetsov Oct 25 '21 at 22:06
  • Just to be precise: this is the protonated form, and I think you are interested in the deprotonated form coordinating to some metal ion, aren't you. – Greg Oct 25 '21 at 22:15
  • You read my mind Greg. Any suggestions on good modelling software for this that is free and accessible? – C-Consciousness Oct 26 '21 at 00:00
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    @C-Consciousness I'd recommend using xtb which is a fast approximate quantum method available on Linux, Mac, etc. and Avogadro but I admit to being biased as an Avogadro developer. – Geoff Hutchison Oct 26 '21 at 00:11

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Phthalocyanine is flat, for example in the crystal structure (linked on PubChem) or PQR or Wikipedia

enter image description here

As noted in the comments, PubChem uses an efficient force field (MMFF94) which does not consider aromaticity. Since the record you linked is protonated (though strangely in a cis-oid configuration, not the typical trans-oid depiction) the steric considerations between the nitrogen atoms and the protons break planarity.

In reality, due to delocalization around the macrocycle, breaking planarity and aromaticity is energetically disfavored.

While there are a few force fields which consider aromaticity effects (e.g., MM3 / MM4) generally one needs at least an approximate quantum chemical method. PQR (which I used for the image) uses OpenMOPAC and XTB / GFN2.

Geoff Hutchison
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