Crystal structure characterisation


I have a rather large data set. I have used ChemAxon's pKa calculator (to calculate the pKa - obviously!) From there though I want to refine the data so that:

(a) only structures with at least one acid-base pair are retained and

(b) only structures in which a single proton is trainsferred (or where there is the potential transfer of the most acidic proton of acid to most basic atome of base) are kept.

Any guidance/suggestions regarding the most approproate nodes to impliment this is greatly appreciated.



Hi Lauren,

I think it all depends how these acid base pairs are formatted in the structure. I.e. Is the amine drawn with a charge or is the acid and base drawn separately.

you could use Rdkit nodes to do a substructure for N+

you could use Indigo nodes to strip out the second component, I.e. The acid salt, using feature remover node to remove mine component. And calculate the Mw before and after and then look for a difference to indicate there was an acid base pair. 

You could also use pKa calculator for acid and pKa Calculator for base. If you get a pKa in a sensible range for acid (I.e. <5) and base (I.e. >5), then that would indicate you have an acid base pair.


Thank you for your reply Simon. I now only have acid base pairs, the solution was a lot simpler than I thought :)