Difference between JCAcidicpKa and JCAcidicpKaLargeMolecule?

What is the difference between JCAcidicpKa and JCAcidicpKaLargeMolecule? (how does the calculation differ?)

If I am working with moleules 300-500 g/mol I assume I should use JCAcidicpKaLargeMolecule?

 

Also, what are JCLogP and JCLogD?

 

Thank you,

Graham

Hi,

If the number of the ionizable groups in a molecule is less or equals with "8"  then the  default method called as "JCAcidicpKa"  will be used for the pKa calculation.

In those other  cases if the number of  the ionizable groups is larger than "8" then the so called "JCAcidicpKaLargeMolecule" method can be used for calculating of the pKa values of a molecule.

The "JCAcidicpKaLargeMolecule"  method  usually more slower then the "JCAcidicpKa"  method. It is a "safe" way to use this  "JCAcidicpKaLargeMolecule"  method  for  relatively large moleules (with molecular  weight of  300-500 g/mol) just in case the number of the expected pKa  values are above of  "8". 

 

Also, what are JCLogP and JCLogD? 

The  "JCLogP " is the "logP" value of the neutral form of a molecule.

Zwitterions are exceptions  since their neutral form is not known in the "0-14 pH" range. For   zwitterions the  "JCLogD " is calculated automatically and will be returned.   

The  "JCLogD " is the "logP" value of a molecule at an optional  pH in the "0-14" range.   
    

Jozsi

Thanks, Jozsi!

yes, thank you very much for the explanation

Also, are the units for the functions that give area and volume in Angstroms (squred and cubed?)

Hi,

 

area and volume in Angstroms (squred and cubed?) 

Yes. 

area unit is  [ Ų ]

volume unit is [ ų]

Jozsi