Count of positive or negative ionisable groups.

User fca09bdbff

12-11-2013 10:02:46


I would like to count the number of groups in a molecule that are likely to be ionised at pH7.4, both positively charged groups such as amines and negatively charged groups such as carboxylic acids.

Is there a way to do this using the JCAcidicpKa and JCBasicpKa functions, or the average microspecies charge?


Tim Ritchie, GlaxoSmithKline UK.

JChem for Excel
Marvin Sketch
Windows XP Professional SP3

ChemAxon 5fc3e8d7d0

18-11-2013 15:55:55

Dear Tim,

Try to use the following JChem for Excel functions:

JCChemicalTerms(MOLECULE;"count(filter('pka() > 0'))")
    - The function calculates the number of atoms in molecule, which pKa value greater than zero, but it does not consider the pH dependency.

JCChemicalTerms(MOLECULE;"count(filter('acidicpKa() <= 7.4 || basicpKa() >= 7.4'))")
    - This CT calculates the number of atoms, which are in ionised forms 50% or greater distribution at pH 7.4.
Are these solutions convenient for you?

Best regards,

User fca09bdbff

18-11-2013 18:54:38

Hello Laszlo,

Thanks for the code. The second example is more interesting to me.

Would it be possible to modify this to create two equations to count:

a) the number of acidic pKas within a particular range e.g. 3-5 and

b) the number of basic pKas within a particular range e.g. 7-10?

Thanks and regards,


PS. I had to replace the semicolon with a comma to get the code to work in Excel.

ChemAxon 5fc3e8d7d0

19-11-2013 11:11:08


Yes, it is possible.
a) JCChemicalTerms(MOLECULE;"count(filter('acidicpKa() >= 3 && acidicpKa() <= 5'))")
b) JCChemicalTerms(MOLECULE;"count(filter('basicpKa() >= 7 && basicpKa() <= 10'))")

(The semicolon - comma change is due to my Hungarian localization in Excel.)


User fca09bdbff

19-11-2013 15:47:30

Hello Laszlo,

Great. They work fine.

Many thanks for your help.