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Protonation: pka inconsistency
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Stephan

Joined: 04 Nov 2015
Posts: 2

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Link to postPosted: Wed Nov 04, 2015 2:29 pmPost subject: Protonation: pka inconsistency Reply with quote

Hi,

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).

N(C1=NNC=N1)C1=CC=CC=C1
C1=CC=CC=C1N(C1=NNC=N1)

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,

Stephan

tfazekas
ChemAxon personnel
Joined: 11 Oct 2012
Posts: 98

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Link to postPosted: Wed Nov 04, 2015 4:45 pmPost subject: Reply with quote

Hi Stephan,

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

Regards,

Tamas Fazekas-Vigh 

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

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Link to postPosted: Thu Nov 05, 2015 11:09 amPost subject: Reply with quote

Hi, 

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.

Daniel 

Stephan

Joined: 04 Nov 2015
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Link to postPosted: Thu Nov 05, 2015 11:49 amPost subject: Reply with quote

Hi,

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

I'll wait for the next release.

Stephan

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