iopromide pKa: difference and Marvin 5.11.1

User e9595e93a3

18-10-2012 08:46:47

iopromide: COCC(O)=NC1=C(I)C(C(O)=NCC(O)CO)=C(I)C(C(=O)N(C)CC(O)CO)=C1I


In Marvin 5.11.1, I get the following:


On the website, I get:

Notice the difference...

Additionally, on the website, the N and O 'groups' (indicated) do not have a value...

Hence, also the species distribution is different.


Which one is the correct one? I assume the Marvin 5.11.1 one?


Best regards

User 851ac690a0

18-10-2012 09:56:50



The Website pKa calcualtor try to follow the "golden mean" even in case of  the minor tauotmeric form had submitted for calculating pKa values. It means that only the most  interesting pKa values are reported . Usually this strategy provides reasonable pKa result, providing that the submitted molecule is not too far from the  dominant tauotmeric form. 

On the other side , in MarvinView the pKa calcualtion is  "liberal" enough.  User has a chance to choose options and decide what to do with the structure before of  submittion to the  pKa calculator. 

For example incase of  iopromide the best choice of options seems to take the "consider tauotmerization" option.




User e9595e93a3

18-10-2012 10:05:14

I see!

Thank you