please comment on this carbanion produced by Marvin

Hi - 

I'm attaching screenshots of the input and output to the Marvin pKa/tautomer calculator. Can you help me figure out how this calculation was done, please?  Is there some way to work back to a literature reference to understand how the program got this amazing result?

I just used Tools -> Protonation -> pKa, all the defaults. 

Thanks

John

Please see attachments for input/output to Marvin pKa Calculator. I am interested in understanding how this result was calculated, including e.g. literature references for carbanions in this or similar contexts near physiological pH. Thank you.

I am trying to understand how this carbanion could be the dominant form at pH 7.4. 

To move along the discussion just slightly, I'd like to propose a theory. That is, that pKa values in neat DMSO have been used in the parameterization in addition to aqueous measurements. Those values would of course cannot be used for an aqueous prediction, and would need to be scaled, scaled so much that this molecule (see attachments) would not be a carbanion under physiological conditions. 

Thanks for reading.

John

Hi,

Thanks for reporting these bugs. 

The fixed version will be available in the next patch bug fix release.

The fixed calculation shown on the attached figures.

 

Jozsi

Hi Jozsi

That is outstanding, thank you! 

For your interest, we have a few related problems which I'll promptly run through your new code and let you know if any remain. 

Can you give me some idea of when the patch might be released? hours, days, or weeks?  Whatever it is, is fine, I'm just asking so I can plan. If you wish, I would be willing to beta test. We have thousands of problematic molecules, so I could get you some good statistics fast. 

Out of curiosity, was there any merit to my hunch that your model had been erroneously regressed against neat DMSO pKa's for at least one of these cases?  I have a wee bet going on here... 

Thanks again

John

Hi,

 

Sorry for the late answer!

For your interest, we have a few related problems which I'll promptly run through your new code and let you know if any remain

Oh, Thank you very much in advance!

Can you give me some idea of when the patch might be released?...  If you wish, I would be willing to beta test.  

If I know well we are planing  to do patch release next week. 

We will contact you with the details of the beta test , probably tomorrow.

The bug was a true "programing code" bug not related with the pKa issue in DMSO solution .

Thanks for looking/thinking  in this direction too.  

Jozsi

thanks. standing by...