Free software for calculation of pKa. Any help?

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Prabhakar R. Sharma Popular answer

Dear Sir

I also found this link useful

https://epoch.uky.edu/ace/public/pKa.jsp

Devulapally Srikrishna

it depends on the class of molecule, i.e. proteins, organic or inorganic acids/bases, phenols

Please go through these links may be useful for you.

http://www.moldiscovery.com/soft_moka.php

http://propka.ki.ku.dk/

http://www.acdlabs.com/products/percepta/predictors/pka/

http://www.chemaxon.com/marvin/help/calculations/pKa.html

Teodoro S Kaufman

Dear Colleague, Thank you for your answer.

Prabhakar R. Sharma

Manuel Petroselli

Dear Teodoro S. Kaufman,

The theoretical calculation of pKa is not so easy to get with high accuracy and it is influenced by several factors as molecular structure, involved solvent and involved hydrogen bonds.

Herein attached you can find a nice paper for the pKa calculation but I can tell you in advance that this procedure is valid only for small organic molecules (formic acid, acetic acid, ecc).

I tried to verify this protocol for bigger molecules as N-hydroxy compounds or other organic acids but it did not work very well. The error using the PCM model is often very large when the molecule is more complex respect to easy carboxilic acids.

I improved this protocol but it is still not enought accurate. Anyway I am still working on it.

I compute my study on Gaussian (not free computational softwate) but you can use any other free computational software that is able to compute the requested termodynamic data.

Obviously the better software will depend by your system (organic molecule, protein, complex, ecc).

Hope these info can help in your research,

Regards,

Dan Xu

Dear Sir, I have been trying to get the the pKa of N-hydroxy-2-acetamidofluorene in aqueous solution, but ends in vain. If you have any sources about this, would you please share with me? Thanks so much!

Best Regards!

Dear Dan Xu,

Which protocol did you use for the pKa calculation of your system? Which level of theory?

Have you already read the JACS paper that I attached?

Dear Manuel,

Thanks for the post. I finally solved my problem w(no great accuracy required) ith Chemaxon. It has a free feature that allows calculation of pKa values ans species distribution. I ignore the basis of its calculations; no Gaussian for sure.

Thanks for your answer. I have read the JACS paper. But it's really hard to for me understand without computational chemistry background. I'm sorry I have not tried to calculate before. It will be great if there is a simple software to get the rough pKa of N-hydroxy-2-acetamidofluorene for a novice like me in the calculations. Thanks again.

Regards.

Dear Dan,

Try with chemaxon (it is free) or send me the structure of your compound.

Please find attached the pKa of your compound.

Dear Professor Kaufman,

Thanks so much for your kind help. The effect of solvent is not considered in the calculation of the pKa, right?

Best wishes!

No effects of solvent are cnsidered. This program is too simple to do that. Good luck

Kim Eun Jae

Hi Kaufman,

I am MS student of university of Ulsan, south korea. I am getting trouble to calculate the pKa of the systems (attached below) due to some reason. Could you please help to figure out the problems.