# Using cxcalc to calculate pKa with their microspecies

User 460fd82ff5

07-08-2011 22:45:53

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,

ChemAxon e08c317633

09-08-2011 13:30:01

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

User 460fd82ff5

09-08-2011 13:52:06

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.

ChemAxon e08c317633

22-08-2011 16:32:09

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-ms1       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-ms1       4.54            3       CC(O)=O\$ cxcalc pka -a 1 -b 1 majorms --pH 5 "CC(O)=O"id      apKa1   bpKa1   atoms   major-ms1       4.54            3       CC([O-])=O`

Is this what you need?

Zsolt

User 460fd82ff5

22-08-2011 18:14:05

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.

User 851ac690a0

15-09-2011 19:27:51

Hi,

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

Jozsi