pKa pb

Hi,


I think there is a problem in the display of the pKa of the following molecules: the lateral chains differ by an oxygen instead of a nitrogen (named NON and NNN respectively) in the central atom. In all cases the nitrogens have pKas around 9, except in the NNN case where it is 3.9 whereas the central N is 9.17. I think there is a problem in the display since both molecules are charged 4H+ (at the operipheral N) at pH=7.4.


I hope I am clear...


Nicolas

Hi,








Yes. The pKa of nitrogens in the 'red circle' should be transpose. We are investigating what can be done.





Jozsi

Ok, I figured... now I have another problem: based on the different molecules attached, the order of protonation is different, but I would expect that thay would all behave like in pka2, am I wrong? Are the values reliable in these cases?

Hi,

Quote:

...but I would expect that thay would all behave like in pka2, am I wrong? Are the values reliable in these cases?

Yes, you are right. We are going to further improve the pKa-'atom mapping' method in the pKa calculator.





The predicted pKa values are likely to be reliable.





Jozsi