Count of positive or negative ionisable groups.

Hello,

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?

Regards,

Tim Ritchie, GlaxoSmithKline UK.

JChem for Excel 5.3.8.15
Marvin Sketch 5.4.0.1
Windows XP Professional SP3

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,
Laszlo

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,

Tim.

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

Hi,

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.)

BR,
Laszlo

Hello Laszlo,

Great. They work fine.

Many thanks for your help.

Regards,

Tim.