Protonation: pka inconsistency

User ce5d71d2ad

04-11-2015 13:29:22


while calculating pKa values in MarvinSketch 15.9.28, I came across an unexpected behavior.

For the following two SMILES, the pKa of the bridging nitrogen atom is different (12.20 vs 13.14).


Simply drawing the structures in Marvin from 'left to right' or 'right to left' has the same effect on the pKa calculation. The behavior seems to require the triazole moiety to occur.

I would be grateful if anyone could shed any light on this behavior as this is a bit concerning.

Many thanks in advance,


ChemAxon 4fa3cf533c

04-11-2015 15:45:23

Hi Stephan,

I've moved your question to the corresponding forum, my colleagues will soon answer to you.


Tamas Fazekas-Vigh 

ChemAxon d51151248d

05-11-2015 10:09:13


Thank you for reporting this issue. We have managed to reproduce it and it is indeed a bug. 

The pKa values of a molecule should not depend on the order of the atoms. We will make a fix for this bug, which will be available in our next release.


User ce5d71d2ad

05-11-2015 10:49:34


thank you for the quick reply and confirmation of the issue.

I'll wait for the next release.