Hi, I still believe that Acepentalene should not be recognized by RDKit as aromatic, because there is no ring that contains 4n+2 electrons. The fact that counting bonds not in the outer ring gives 10 electrons should not make the outer ring aromatic. Moreover, RDKit seems to perceive aromaticity correctly (using this criterion) in several similar systems which have 4n+2 electrons in the outer ring but in which counting additional electrons in bonds not in the ring would, following Greg's interpretation, make them non-aromatic.
Here are several examples, starting with a recap of Acepentalene. For Acepentalene itself, as Greg pointed out, there are 9 electrons in the outer ring, but since no single ring contains 4n+2 electrons, I do not believe it should be considered aromatic. [image: acepentalene.png] --- Now consider the closely related compound created by making one of those 5-membered rings a 7-membered ring. It's called aceazulylene (yes, I had to look this up! 😉). The outer ring is aromatic in my view, because it has 10 (i.e., 4n+2) electrons. The ring system has 12 electrons, and so it would seem that based on Greg's discusiion of acepentalene, it should be perceived as non-aromatic. Yet RDKit perceives it as aromatic — correctly, in my view. As a side issue, I would have thought that, as in azulene, the internal bonds and the central carbon would not have been perceived as aromatic by RDKit; this is the same issue that Andrew originally raised for Acepentalene. [image: aceazulylene.png] --- Now consider dicyclopenta[cd,gh]pentalene from Schleyer's paper (referenced in Andrew Dalke's recent email). Again, this molecule has 12 electrons in total, so that again, based on Greg's discussion of acepentalene, I'd have thought RDKit would consider it non-aromatic. But the outer ring consists of a pi system containing 4n+2 electrons, and so, in my view, it should be considered aromatic. Schleyer's calculations agree. And again, as in aceazulylene, RDKit in fact correctly perceives it as aromatic, although, as in aceazulylene,, the internal bonds and carbons should probably not be perceived as aromatic. [image: dicyclopenta[cd,gh]pentalene.png] As a closing comment, it seems to me that if ring bonds are counted and off-ring bonds are ignored, electron counting would correctly infer the aromaticity or not of these compounds. MO calculations, as per Schleyer, would not be required for this purpose – at least for these compounds! -P. On Wed, Jan 22, 2020 at 8:50 AM Andrew Dalke <da...@dalkescientific.com> wrote: > On Jan 22, 2020, at 14:12, Greg Landrum <greg.land...@gmail.com> wrote: > > As an aside: it's not particularly relevant to this discussion, but I > don't understand why the wikipedia page says that the compound is > anti-aromatic. I think the standard definition of anti-aromaticity (agrees > with the one linked to from the acepentalene page) requires the ring system > to have 4n electrons. That definitely doesn't apply here to either the > individual rings or the system as a whole. The system as a whole has 10 > electrons (4n+2), the individual rings each have 5 (neither aromatic nor > anti-aromatic), and the outer envelope has 9 (again, neither aromatic nor > anti-aromatic). > > Because I didn't know either, I looked into it. > > I think that's because (to quote "Towards experimental determination of > conical intersection properties:a twin state based comparison with bound > excited states", Phys. Chem. Chem. Phys., 2011,13, 11872–11877 [*] ) > > > A Hückel MO analysis[21] leads to the conclusion that the ground state > of the conjugated tricyclic acepentalene I is a triplet state. DFT > calculations corrected this picture and showed a singlet global minimum > distorted to C_s symmetry with alternated single and double bonds,[22] > which are well described by the Lewis structures A(B,C). According to a > B3LYP/6-31G* calculation the lowest triplet state has also a high symmetric > C_3v configuration and lies 3.9 kcal/mol above the singlet ground state > minimum. Acepentalene I was characterized as an antiaromatic system [23] > despite being formally an aromatic 10 electron system: the resonance > between each pair of Kekule structures in this case involves only 4 > electron pairs of the pentalene fragments and it averts the resonance with > the additional fifth electron pair common for both the structures. Such a > resonance is described as an anti-combination of two Kekule structures: > (A–B), (C–B) and (C–A). > > Just need to add B3LYP/6-31G* calculations to RDKit's aromaticity > perception algorithm and everything will be fine. :) > > The "characterized as an antiaromatic system[23]" is "T. K. Zywietz, H. > Jiao, P. v. R. Schleyer and A. de Meijere, J. Org.Chem., 1998, 63, 3417" at > https://pubs.acs.org/doi/abs/10.1021/jo980089f . > > > Cheers, > > Andrew > da...@dalkescientific.com > > [*] > https://www.researchgate.net/profile/Shmuel_Zilberg/publication/51175586_Towards_experimental_determination_of_conical_intersection_properties_A_twin_state_based_comparison_with_bound_excited_states/links/561bb5bc08ae6d17308b037f/Towards-experimental-determination-of-conical-intersection-properties-A-twin-state-based-comparison-with-bound-excited-states.pdf > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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