I have used Marvin, Calculator Plugin and
Chemical Terms Demo to calculate LogP and LogD for a number of compounds that I
am studying and I have a technical question regarding calculation of these
parameters. LogP is the ratio of concentrations of a compound in the two phases
of a mixture of two immiscible solvents at equilibrium; typically one of then
solvent is water while the second is octanol. This true when a practical
experiment is carried out, but what about the mathematical model used by your
software? Is it is still true that this LogP expresses affinity to water or
octanol? In literature there are some examples of LogP (established
practically) in water/ hydrocarbons, so I wonder which hydrophobic phase is
taken into account by your software. The same question goes for LogD, is
octanol considered as the hydrophobic phase in your calculation?
Also, I have another question in relation to the
size/type of molecules and calculation of logP/ logD by your software. I wanted
to calculate the logP value for a decapeptide (slightly alkaline properties as
a free base) and the calculated values obtained with your software and another
programme differed significantly, although in both cases the molecule was shown
to be hydrophobic. I was wondering if your software has any limitations to
calculate the logP value of relatively simple peptides and proteins? Obviously
these are not simple organic compounds any more, is the calculation of logP
applicable for these cases? Thanks you very much in advance for clarification.
Yes, both logP and logD calculations considers octanol as the hydrocarbon phase, i.e., Partitioning plugin calculates the octanol/water partition and distribution coefficients.
The calculation method is based on the publication of Viswanadhan, V. N.; Ghose, A. K.; Revankar, G. R.; Robins, R. K., J. Chem. Inf. Comput. Sci., 1989, 29, 163-172, but the referred algorithm was modified at several points.
You can read more about our Patritioning plugin here: http://www.chemaxon.com/marvin/help/calculations/partitioning.html
/>The logP and logD calculation background can be found here: http://www.chemaxon.com/marvin/help/calculations/logPlogD.html
To calculate the logP value, our software has no molecule size limitations.
Our logP and logD calculations were developed for small/drug molecules, that is the calculation results for peptides and proteins are not reliable by our method; however, logP plugin can be trained with your own (e.g., experimental) data to make a more precise calculation possible.
Find the training of logP and logD here: http://www.chemaxon.com/marvin/help/calculations/logp_training.html
I am using JChem for excel and I am trying to calculate LogP/LogD for list of compounds. I can insert Jchem function in an excel cell. IN the insert funsert box, it shows LogP for selected compound but when I actually insert it in the cell, it only shows formula not the calculated value of LogP.
How do I see value LogP for list of compounds?
An example how to display logP values for a list of compound in Excel:
The structures can be found in the column A of an Excel sheet and you would like to see the logP values in the column B next to the structures.
Please select the B1 cell and enter =JClogP(A1) into the B1 cell and press enter
>> the logP value (calculated for the structure in A1 cell) should be displayed in the B1 cell
Click on the bottom-right corner of the B1 cell, and copy the logP function from B1 cell to the B2, B3, B4, B5...... cells by dragging.
>> logP values - calculated for the structures in A2, A3, A4, A5 ... cells - should be displayed in B2, B3, B4, B5...... cells
Of course you can insert the JClogP function into the B1 cell by using the "Insert Function" function of the Excel.
In this case you have to select the JClogP function from the JChem_Protonation and Partitioning category on the Insert Function form.
Press OK and enter A1 as Molecule on the Function Arguments form and Press OK on the Function Arguments form
>> The calculated logP value should be displayed in B1 cell. You can copy the function into B2, B2, B3 cells by dragging.
just an additional thing to my previous post regarding the JClogP function:
Please make sure that the cell format is "General" for the cells where you would like to see the calculated logP values. The General is the default cell format.
You can see the "JClogP(A1)" in the cell instead of the calculated logP values if the cell format is set to "Text".
You can check the cell format in the following way:
Select the cell
Make a right mouse-click
Select the Format Cells context menu item
>> On the first tab of the Format Cells form you can see the actual cell format. Of course you can change the cell format here.