Need to clarify search with/without charge

Hi,

Currenly we use JChem 5.6.0.2 in Oracle Database 10.2.0.5 x86_64.

We have N-Alkylpicoline.mol in table with JCHem index with parameters: 'structureType=anyStructures,fp_size=32,fp_bit=2,pat_length=6,duplicateFiltering=n

We tried to find N-Alkylpicoline_without_charge.mol, that differs from first with charges only.

So, we used these search options for jc_compare:

t:f charge:d
t:f charge:i
t:d charge:d
t:d charge:i

without any result.

Pavel

Hi Pavel,

The problem is that the charged molecule is recognized as aromatic, while the uncharged as non-aromatic. It seems to me that the uncharged version also has a valence error. This might cause the problem, but my colleague will confirm.

 

Best regards,

Szabolcs

Szabolcs wrote:

Hi Pavel, The problem is that the charged molecule is recognized as aromatic, while the uncharged as non-aromatic. It seems to me that the uncharged version also has a valence error. This might cause the problem, but my colleague will confirm.   Best regards, Szabolcs

Thanks for reply, Szabolcs. I'll send your comment to our chemists (I don't know about a half of words from comment :))

Yes I confirm Szabolcs's note. The non-charged version is not aromatized due to the missing positive charge.

If you manually add the missing positive charge (see my attachment) then the molecule will be aromatized.