microspecies ratio

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


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?




ChemAxon d51151248d

10-11-2015 10:16:14


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:


I hope this helps, 


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.



ChemAxon d51151248d

17-11-2015 10:08:39

Hi Lorenz, 

First, sorry for the late answer. 

Yes, you are right. You can calculate the macrospecies distribution just based on the pKa values.

However, the very details of the algorithm that is used to predict the microspecies distribution are not public. 

We have some conference material that covered this topic and which is public:


That should give you the answer for your questions. 

I hope this helps,