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Difference between JCAcidicpKa and JCAcidicpKaLargeMolecule?
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Graham

Joined: 10 May 2011
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Link to postPosted: Fri Jun 03, 2011 9:09 pmPost subject: Difference between JCAcidicpKa and JCAcidicpKaLargeMolecule? Reply with quote

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 useJCAcidicpKaLargeMolecule?

Also, what are JCLogP and JCLogD?

Thank you,

Graham

Jozsef
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Link to postPosted: Tue Jun 07, 2011 12:25 amPost subject: Reply with quote

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" methodcan beused for calculating of the pKa values of a molecule.

The "JCAcidicpKaLargeMolecule" methodusually more slower then the "JCAcidicpKa" method. It is a "safe" way to use this "JCAcidicpKaLargeMolecule" methodfor 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. Forzwitterions 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

vhamori
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Link to postPosted: Tue Jun 07, 2011 7:09 amPost subject: Reply with quote

Thanks, Jozsi!

Graham

Joined: 10 May 2011
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Link to postPosted: Tue Jun 07, 2011 5:36 pmPost subject: Reply with quote

yes, thank you very much for the explanation

Graham

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Link to postPosted: Tue Jun 07, 2011 5:38 pmPost subject: Reply with quote

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

Jozsef
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Link to postPosted: Wed Jun 08, 2011 1:14 amPost subject: Reply with quote

Hi,

area and volume in Angstroms (squred and cubed?) 

Yes.

area unit is [ 2 ]

volume unit is [ 3]

Jozsi

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