Hi,

I've had a problem with the structure AFUWEE, as shown in the attached script.  If I do standardise_aromatic_bonds(), standardise_delocalised_bonds(), kekulize(), I get a structure with a pentavalent carbon (atom 3), a C-H with 2 double bonds off it.  If I run the same three functions on _that_ molecule, I get aromatic (type 4) bonds for those two bonds, which is a bit odd for a kekulised structure.  Granted, the bonding for this molecule is a mess (possibly there should be a double bond to the phosporus?) but the inconsistent behaviour isn't great, either.  Mercury shows AFUWEE with a fully-aromatic 6,5 carbon system, which is also unexpected.

This is the case in the latest production version (1.0.0) and the 2017 beta version.

 

Regards,

Dave

 

Hi Dave,

I agree - or rather a friendly chemist agrees - that the structure is a bit rubbish.  The first kekulize misassigns the double bonds in the carbon you mentioned, so the second aromatic assignment does not regard these bonds as aromatic, then the second kekulize does not operate on the same structure as the first.  I agree that this is not ideal behaviour, but it is comprehensible.

The only solution I can think of is to assign all bond types:

mol.assign_bond_types('all')

where the double bond to the phosphorus is detected, the five membered ring is no longer aromatic and the kekulisation works as expected.

I have mailed the database group to see if they want to fix the bonds in the structure, but this will be too late for the forthcoming November release.

Best wishes

Richard

Hi Richard,

Thanks for looking into this.  The structure itself is not vitally important other than that it upset my script. I'm certainly happy with a system that gives rubbish for rubbish structures but I think that rather than produce a pentavalent carbon, as the kekulize function does in this case, it should produce an error.  Pentavalent carbons are quite unequivocally wrong, after all, and producing one is a clear sign that something's badly awry.

Regards,

Dave

 

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