Re: [Rdkit-discuss] protonation states of small molecules

[Greg L. <gre...@gm...>]

Dear Soeren,

On Wed, Apr 6, 2011 at 1:28 PM, Sören Wacker <sw...@gw...> wrote:
>
> I am wondering whether you can use RDKit for the estimation of
> protonation states of chemical compounds, too.
> And if yes, how can you do that, and what do you think how reliable it is?
> Or is there a way to implement this?

No functionality like this is currently implemented in the RDKit. It's
a hard problem.

I would guess that it is possible to implement most of the
non-quantum-mechanical approaches for pKa estimation, but all of them
would require a fair amount of work.  Gordon Crippen published a
relatively simple pKa estimator for monoprotic molecules a couple of
years ago: http://dx.doi.org/10.1021/ci8001815
The SMARTS patterns used in the paper could certainly be translated to
work within the RDKit.

Best,
-greg