Free software for pKa calculation from chemical structure? - I would like to get one of those... (Jul/17/2011 )

Howdy folks!

I am looking for software (preferably free) to calculate pKa for several compounds based on their chemical structure (from file or drawing by hand).

Chemicalize.org seems to have that option but it still in the beta stage and all I'm getting is errors and crashing browser when I try to enter new structure.

Help?

Moka is another one, but not free. But these programs anyway only predict pka values more or less inaccurate (though I'm not sure how good the models used for calculations are now). Therefore, if you're not using new or uncommon compounds, why not looking them up from spreadsheets that use experimental data?

Thanks!

I'm no longer in academia so I can't count on getting cheap licence and my company won't pay for the licence so I can check out my hunch.

Those are kinda new compounds - products of pre-column derivatization (for HPLC) of rather rare amino acid derivative and several interfering compounds. Knowing their pKa I could attempt to optimize resolution without resorting to trial and error or guessing.