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Difference between JCAcidicpKa and JCAcidicpKaLargeMolecule?
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wattsgp

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 useáJCAcidicpKaLargeMolecule?

á

Also, what are JCLogP and JCLogD?

á

Thank you,

Graham

Jozsi
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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"á then the ádefault method called as "JCAcidicpKa"ááwill be used for the pKa calculation.

In those other ácases if the number ofá the ionizable groups is larger than "8" then the so called "JCAcidicpKaLargeMolecule" methodácan beáused for calculating of the pKa values of a molecule.

The "JCAcidicpKaLargeMolecule"á methodááusually more slower then the "JCAcidicpKa"á method. It is a "safe" way to use this á"JCAcidicpKaLargeMolecule"á methodááfor árelatively large moleules (with molecular áweight ofá 300-500 g/mol) just in case the number of the expected pKaá values are above ofá "8".á

á

Also, what are JCLogP and JCLogD? 

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

Zwitterions are exceptionsá since their neutral form is not known in the "0-14 pH" range. Forááázwitterions theá "JCLogD " is calculated automatically and will be returned.ááá

Theá "JCLogD " is the "logP" value of a molecule at an optional ápH in the "0-14" range.ááá
áááá

Jozsi

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

Thanks, Jozsi!

wattsgp

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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

wattsgp

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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?)

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

Hi,

á

area and volume in Angstroms (squred and cubed?) 

Yes.á

area unit isá [ ┼2 ]

volume unit is [ ┼3]

Jozsi

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