ChemAxon Forum Archive » Structure based predictions: Calculator Plugins & Chemical Terms

How do I get single pKa value via sql jc_evaluate?

User 8688ffe688

23-05-2007 17:56:24

Anybody know how to get single pka value throw JChem cartridge jc_evaluate call?

ChemAxon e08c317633

24-05-2007 09:38:56

mpustel wrote:
Anybody know how to get single pka value throw JChem cartridge jc_evaluate call?
Hi,





Get the strongest acidic pKa value of the input molecule:


Code:
select jc_evaluate(<input-molecule>, 'pka("acidic", "1")') from dual;






You can find some useful JChem Cartridge examples here: http://www.chemaxon.com/jchem/doc/guide/cartridge/cartapi.html#jc_evaluate





Chemical Terms reference table (with description of the parameters, examples): http://www.chemaxon.com/jchem/doc/user/EvaluatorTables.html#pkadesc





Best regards,


Zsolt

User 8688ffe688

24-05-2007 19:38:01

The strongest "acidic" pKa compared to single pKa values calculated from ACDLabs is very different. I'm comparing some standard know molecules such as acetic acid, pyridine, phenol, formic acid, guanidine and the values do not match.

User 851ac690a0

25-05-2007 06:58:32

Hi,
Quote:
I'm comparing some standard know molecules such as acetic acid, pyridine, phenol, formic acid, guanidine and the values do not match.



Could you list the pKa values of the above molecules that you obtained with our pKa calculator?





Thanks.





Jozsi

User 2347372188

29-05-2007 22:07:26

I attached a CSV file with a comparison of some of the properties computed by ACD/Labs and JChem.





Please let me know if you have any questions.





-&

User 851ac690a0

30-05-2007 09:34:51

Hi,





I got these pKa values for guanidine:





-13.2, -5.6, 12.5, 21.2





You need to calculate the most basic pKa. The situation is the same with pyridine.


See the attached figure.





I calculated the HBD/HBA parameters. They different form the values you obtained. E.g. guanidine, see the attached figure.








Jozsi

ChemAxon e08c317633

30-05-2007 12:06:42

Hi,





Strongest basic pKa value can be obtained with the following Cartridge call:





Code:
select jc_evaluate(<input-molecule>, 'pka("basic", "1")') from dual;






Alternatively this also can be used:


Code:
select jc_evaluate(<input-molecule>, 'basicpKa("1")') from dual;






Strongest basic pKa calculation (I will use Evaluator in my examples; the same Chemical Terms expressions can be used in JChem Cartridge) for guanidine and pyridine returns these results:





Code:
evaluate -e 'pka("basic", "1")' "NC(N)=N"


12.55


evaluate -e 'pka("basic", "1")' "C1=CC=NC=C1"


5.12






How did you calculate the HBD and HBA columns? What was the exact Chemical Terms expression you used? We have three related calculations:


acc / don


accSiteCount / donSiteCount


acceptorCount / donorCount





donorCount and acceptorCount of acetic acid and guanidine:


Code:
evaluate -e 'donorCount()' "CC(O)=O"   


1


evaluate -e 'acceptorCount()' "CC(O)=O"


2


evaluate -e 'donorCount()' "NC(N)=N"


3


evaluate -e 'acceptorCount()' "NC(N)=N"


3






donSiteCount and accSiteCount of acetic acid and guanidine:


Code:
evaluate -e 'donSiteCount()' "CC(O)=O"


1


evaluate -e 'accSiteCount()' "CC(O)=O"


3


evaluate -e 'donSiteCount()' "NC(N)=N"


5


evaluate -e 'accSiteCount()' "NC(N)=N"


3






Best regards,


Zsolt

User 8688ffe688

30-05-2007 16:36:21

Using the pH parameter in the acceptor and donor calculation is causing the difference in values. Should we not do this? Finally the regarding the pKa calculation, besides returning both basic and acidic pKa, any way of returning a single value?

ChemAxon e08c317633

31-05-2007 10:14:00

mpustel wrote:
Using the pH parameter in the acceptor and donor calculation is causing the difference in values. Should we not do this?
Of course you can use the pH parameter. I'm just not sure ACD/Labs can also take it in account, and I thought you want to count the hydrogen bond donors and acceptors of the input structure (and not its microspecies at a given pH), and compare the results with the results of ACD/Labs. Sorry for misunderstanding.





Best regards,


Zsolt

User 851ac690a0

31-05-2007 22:39:00

Hi,








Quote:
...any way of returning a single value?
The single value would be straightforward in the next three cases.





- If a molecule has only one significant pKa value


- If a molecule has only acidic groups


- If a molecule has only basic groups








The single value is biased, however, if the molecule is ampholyte or zwitterionic.





This is why we don’t recommend using a single value pKa function.





Jozsi