pKa plugin applicability

User 3b79244224

26-04-2006 13:02:11

Hi all!

I am using the pkaPlugin and/or MajorMicrospeciesPlugin in my programs. When running on a large dataset and checking the results, I was wondering about a few discrepancies, for example guanine:

ChemAxon/MarvinBeans/bin/cxcalc pka "NC1=NC2=C(N=C[NH]2)C(=O)N1"

id apKa1 apKa2 bpKa1 bpKa2 atoms

1 6,56 12,40 4,11 0,66 8,11,3,6

From the experimental values, I would expect a distribution like this:

apka1 = 9.4 (atom 11)

apka2 = 12.6 (atom 8)

apkb1 = 10.8 (atom 6)

So my question is: do you have some criteria for discrimiation: for which molecules does the method work well and for which it does not? Maybe it is documented somewhere and I didn't find it - please give me a small hint in this case.

The previous version of the plugin (Marvin 3.3.3, I think) gave a totally different result. Has there been some change in the algorithm?

I am currently using JChem 3.1.6 / Marvin 4.0.5.


User 851ac690a0

26-04-2006 14:13:18

Dear Kai,

Calculated pKa 6.56 seems to be too low. I will check what is the problem.

I think 10.8 is pKb value. 14.0 - 10.8 ==> pKa= 3.2 .

Our pKa calculator fails to work if molecule is given as minor tautomeric form.

By the way the molecule you show is the major tautomeric form?


User 3b79244224

26-04-2006 14:26:40

Hi Jozsi,

indeed "apkb1 = 10.8 (atom 6)" should read "bpka1 = 10.8 (atom 6)".

I think it is the major tautomeric form.

User 851ac690a0

19-05-2006 11:58:39

Dear kai_h

Improved version of pKa calculator will be released in a couple of days.

Guanine's pKa was calculated with this improved version. See the attached figure.