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Calculate protomers/microspecies using experimental pKas?
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Ed

Joined: 01 Feb 2013
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Link to postPosted: Wed Aug 17, 2016 3:05 pmPost subject: Calculate protomers/microspecies using experimental pKas? Reply with quote

Hello all,

 

I'm aware that cxcalc can be used to produce the microspecies relative abundances for a given pH.  However, I gather this uses the ChemAxon pKa calculator do to this?  I wish to generate microspecies using in-house experimentally derived pKa values.  Is it possible that this can be done, at least using ChemAxon tools?  Can a ChemAxon pKa-trained model be used in addition?

 

Thank you in advance,

Ed.

Daniel
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Joined: 22 Jan 2012
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Link to postPosted: Thu Aug 18, 2016 3:01 pmPost subject: Reply with quote

Hi Ed, 

Yes, you can use cxcalc to predict the microspecies distribution of your molecules. All functions that are available in Marvin can be accessed via cxcalc as well.

However, you can't use in-house pKa data to predict microspecies distribution directly (that is you can't predict microspecies data solely based on your pKa values). The only way to do this is to train our predictor with your in-house pKa data. If the training is successful, your data will be taken into account. 

I hope this helps, 

Daniel

Ed

Joined: 01 Feb 2013
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Link to postPosted: Wed Aug 31, 2016 4:42 pmPost subject: Reply with quote

Hi Daniel.

 

Thank you for your response.  Actually I would like to know how you calculate the relative abundances for each microspecies.  I assume it's pKa-based (and pH-based), using variations of the Henderson-Hasselbalch equation like here:

https://www.boundless.com/chemistry/textbooks/boundless-chemistry-textbook/acids-and-bases-15/diprotic-and-polyprotic-acids-111/diprotic-and-polyprotic-acids-462-6574/

I'm guessing you're using linear algebra to solve a set of simultaneous equations/multiple unknowns in this case?  Details would be very helpful.

 

Thank you in advance,

Ed.

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
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Link to postPosted: Mon Sep 05, 2016 1:09 pmPost subject: Reply with quote

Hi Ed, 

These deep details of the ChemAxon pKa predictor and microspecies calculator are not public, so unfortunately I can't tell you more about them. 

Thank you for your understanding. 

Daniel

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