multi ionization centers and pKa
pKa calculations return different values for molecules having multi-ionization centers. I am interested in getting a unique pKa value at physiological pH (~7.4). Below some reported experimental values for some molecules with multi-ionization centers and their reported experimental pKa :
O\N=C1\C2=CC=CC=C2N=C1C3=CC=CC=C3 [pKa_obs 7.7]
CC(=O)NC1=CC=C(C=C1)C(=O)NN2C=NN=C2 [pKa_obs 6.3]
COCCNCCN1C=NC2=C1C(=O)NC(=O)N2C [pKa_obs 9.62]
Thank you in advance for your help.
I calculated the pKa of your molecules with an improved version of the pKa calculator. This version will be released soon.
See the attached figures "many_pKa.png" and "few_pKa.png".
On the option panel of the pKa calculator you can set an upper and a lower limits for the pKa calculation.
The "many_pKa.png" figure was calculated with the options which are given on this figure "set1.png"
The "few_pKa.png" was calculated with the options which are given on this figure "set2.png"
I hope this help you.
If you have further questions please let us know.
Thank you for your reply. I am looking forward to test the new version with many other "problemtic" structures! When do you think this version will be released?
I was informed that the next release can be expected in two weeks.
Do you think the new version of pKa calculation will be available shortly ?
Thank you in advance
Yes. We are going to do release on friday.