We have been using cxcalc pka to determine the pKa values using sdf files containing many thousands of compounds. (JChem version 5.5.1, unix-based system) The output allows us to determine how many acidic and basic groups are relevant given the pH range we are interested in. We also plot pKa distributions for compounds that contain a single acidic group and those with a single basic group.
What we'd like to do is to identify the functional group associated with the pKa value. If that could be classified into groups such as, carboxylic acid, sulfonamide, tetrazole, phenol, this would be advantageous. Similarly for compounds with a single basic group, primary amines, secondary amines, tertiary amines, aromatic amines, heterocycles, amidines, guanidines, etc.
We've had a look at doing this, but were hoping there is a reporting facility that can list the pKa value and the type of functional group asociated with that value. Hope you can help.
David Manallack, Monash University