[gmx-users] Tautomer Prediction

[Mark Abraham]

On 12/01/2011 8:11 AM, Nancy wrote:
> Hi All,
>
> Using MarvinSketch v5.3.3 (ChemAxon software), the predicted pKa value 
> of the acidic hydrogen on the thiazolidinedione ring of pioglitazone 
> is 4.57 (see attached "Figure_1.gif").  Therefore, the predominant 
> species at pH 7.0 predicted by MarvinSketch is the one depicted in 
> "Figure_2.gif".  The different tautomeric forms predicted by 
> MarvinSketch are shown in "Figure_3.gif".
>
> Can anyone explain where these predictions come from, and if they are 
> correct?

Nancy, this is a forum for discussion of questions relating to the 
biomolecular simulation package GROMACS. Your questions would be more 
suited to a general chemistry discussion forum, though I can't suggest a 
particular one. At the very least, you would have to read the 
documentation of the software you've used, and any underlying scientific 
literature to start answering your own questions.

Mark