Technical Support Forum Index
Technical Support Forum
Access ChemAxon scientists and developers here. For registration and login issues contact website support.
Difference between JCAcidicpKa and JCAcidicpKaLargeMolecule?
To watch this topic for replies  Register (enables digests) or give email address:
Reply to topic
Display posts from previous:   
    View previous topic :: View next topic    
Author Message
wattsgp

Joined: 10 May 2011
Posts: 29

View user's profile

Back to top
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

Jozsi
ChemAxon personnel
Joined: 25 May 2004
Posts: 540

View user's profile

Back to top
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

hamoriviktor
ChemAxon personnel
Joined: 30 Aug 2008
Posts: 754

View user's profile

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

Thanks, Jozsi!

wattsgp

Joined: 10 May 2011
Posts: 29

View user's profile

Back to top
Link to postPosted: Tue Jun 07, 2011 5:36 pmPost subject: Reply with quote

yes, thank you very much for the explanation

wattsgp

Joined: 10 May 2011
Posts: 29

View user's profile

Back to top
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
ChemAxon personnel
Joined: 25 May 2004
Posts: 540

View user's profile

Back to top
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

Reply to topic
Page 1 of 1


To watch this topic for replies   Register (enables digests) or give email address  
Jump to:  
You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot vote in polls in this forum
You cannot attach files in this forum
You can download files in this forum