User 568550d85a

10-11-2015 07:46:23

Dear forum

From basic acid-base chemistry I know tat given a molecule and its pKa values per site it is possible to calculate the "macrospecies" distribution at any given pH.

Now the thing is that there might be multiple "microspecies" for a given "macrospecies". So for molecule with SMILES "NCNC" and formal charge 1 there exist 2 forms

NC[N+]C [N+]CNC

The question is how do I calculate the ratio between these two at a given pH?

I see that in the pKa plugin this can be achived, for the example compound I get the distribution of

pH 7

NCNC 2.8%

NC[N+]C 32.96%

[N+]CNC 52.3%

[N+]C[N+]C 11%

so a ratio of 52/32 or 1.6:1. It seems to me this ratio is constant, but how can I get that easily form Chemaxon API?

Cheers,

Lorenz

ChemAxon d51151248d

10-11-2015 10:16:14

Hi,

Thanks for this question. In MarvinSketch the pKa plugin is only able to display the pH-microspecies distribution plot, so you can't get the distribution at a specific pH. To do this the best solution would be to use the cxcalc command line tool, not the API. For your example:

cxcalc microspeciesdistribution -H 7.0 -f sdf "NCNC" | mview -

This will calculate the distribution of the microspecies for your input molecule at pH 7.0, and open the output in a MarvinView window.

However, you can also use the API of the pKa plugin. Here is the API example for this:

https://www.chemaxon.com/marvin/help/developer/beans/api/chemaxon/marvin/calculations/pKaPlugin.html

I hope this helps,

Daniel

User 568550d85a

10-11-2015 15:08:11

Dear Daniel

In the pKaPlugin API I found

double[] distr = plugin.getMsDistribution(i); // distr values for pHs

Which gives me the distribution for the microspecies at the given pH. The problem is for me: Is there any details how this distribution - these percentages - are computed? I know that it is possible to calculate the "macrospecies" distribution from the pKa values of a molecule, but not in detail how to calculate the "microspecies" distribution.

Cheers,

Lorenz

ChemAxon d51151248d

17-11-2015 10:08:39