Using cxcalc to calculate pKa with their microspecies

Hi,

 

I can manage to use cxcalc to get a list of pKas for a compound, and also generate a list of the microspecies using msdistr. However, it is not trivial to match each pKa with the pair of microspecies that correspond to it. Is there a way for cxcalc to output this data directly and with a single call?

 

Regards,

Elad

Hi,

Please explain what do you mean by "to match each pKa with the pair of microspecies that correspond to". Could you provide an example?

Zsolt

Hi,

 

For each pKa, I would like to know what the charge of the atom is before and after the protonation.

For example, acetate CC(=O)O changes to CC(=O)[O-] at a pKa of 4.54.

Now, all I have is the index to the atom being protonated.

 

Thanks. Elad.

cxcalc currently supports predicting
 - pKa,
 - major microspecies of a molecule (all),
 - major microspecies at given pH,
 - microspecies distribution at given pH.

 I think we cover all reasonable use cases with these calculations.

cxcalc can run multiple calculations in a single call.

Examples:

$ cxcalc pka -a 1 -b 1 majorms "CC(O)=O"
id      apKa1   bpKa1   atoms   major-ms
1       4.54            3       CC(O)=O.CC([O-])=O

$ cxcalc pka -a 1 -b 1 majorms --pH 4 "CC(O)=O"
id      apKa1   bpKa1   atoms   major-ms
1       4.54            3       CC(O)=O

$ cxcalc pka -a 1 -b 1 majorms --pH 5 "CC(O)=O"
id      apKa1   bpKa1   atoms   major-ms
1       4.54            3       CC([O-])=O

Is this what you need?

Zsolt

Hi,

This solution is exactly what I was looking for.

I have another question though. Is there a way to compensate for mutarotation in compounds, e.g. given the linear form of D-glucose the major tautomer would be alpha-D-glucopyranose? The --majortautomer flag doens't seem to do this.

 

-- Elad

Hi,

The "ring-chain" tautomerization is not available at this time. We are working on this topic. 

Jozsi