User 9ef27c545f
09-07-2012 21:21:31
I was wondering why the logP calculator plugin gives different results for different pHs?
I thought that the partition coefficient does not depend on pH: http://www.chemaxon.com/marvin/help/calculations/logPlogD.html
Thanks!
Robert
User 851ac690a0
11-07-2012 09:09:22
Hi,
The "logP" is the partition coefficient of the unionized molecular
form between octanol water solvents . It is independent on the pH.
The "logD" is the distribution coefficient of the unionized and the
ionized molecular forms together between octanol water solvents at given
pH. It is also called as pH-partition coefficient in the literature.
Fig1. Partitioning menu has two parts: logP and logD
Fig2.logP and logD have separate options panel
Fig3.under the display option tage the pH range can be adjusted in case of the logD calculation
Fig4. benzene has not got ionizable atom ,this is why its logP
coincide with its logD in the whole pH range as it is indicated with the
orange line on the logD plot.
Fig5. phenol is a weak acid this is why its logD value depends on the pH
Jozsi
User 9ef27c545f
11-07-2012 10:54:37
Hi Jozsi,
I agree with you: logP is not pH dependent. However, according to the documentation, you can calculate logP (not logD) at a certain pH by the cxcalc command, see:
https://www.chemaxon.com/marvin/help/applications/cxcalc-calculations.html#logp
Robert
User 851ac690a0
11-07-2012 12:49:49
Hi,
Yes, you are right. The documentation is not correct in this form.
The logP at given pH is calculated in this way:
The input molecule is transformed into its major ionic form at the pH specified by the user. And subsequently the "ionic logP" is calculated .
For Example:
The major form of acetic acid at pH=5.0 is deprotonated. This is why the calculated logP of acetic acid is - 3.75 which is coincide with the ionic logP of acetate anion.
cxcalc logP -H 5.0 "CC(O)=O" //acetic acid
id logP
1 -3,75
cxcalc logP -t logPMicro "CC([O-])=O" //acetate anion
id logP of ionic species
1 -3,75
We will modify the documentation according to the above notes.
Jozsi
User 9ef27c545f
11-07-2012 13:00:38
Thanks!
Robert