normal equilibrium densities logD

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8 years 10 months ago #4541 by satti
equilibrium densities logD was created by satti
Hello,
thanks for an excellent tutorial on parametrizing new molecules. The tutorial,
at the end, mentions about another tutorial in preparation on calculating
partitioning free energies. Would it be possible for anyone to briefly outline
the procedure, especially the way to obtain the equilibrium densities?

I have been working on parametrizing a molecule with three
heterocyclic rings for which I also have the logD value for octanol/water
partitioning. One of the rings has a charged (amine) substituent.
I am following the procedure for calculating the free energies of
partioning as outlined in the Martini paper(J. Phys. Chem. B 2007, 111, 7812) using a oct/water box. I am not certain how to obtain equilibrium densities of the compound of my interest in the two phases as this compund lies at the oct/water interface.
Since the compund is charged, would it be required that I run oct/wat systems for both charged and uncharged species to get logD vlaues. I would like to hear your opinion on this too.

thanks for reading,

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8 years 10 months ago #4558 by jaakko
Replied by jaakko on topic equilibrium densities logD
Hi satti,

have a look at how the partition coefficients were calculated in the Dry Martini paper dx.doi.org/10.1021/ct500477k . Calculating the free energy of solvation in both (hydrated) octanol and water is faster and more accurate and also doesn't have problems with molecules stuck at the interface.

Unless you know what ratio of the compound is charged in the experiment just run the version of the molecule that you're going to use in simulations. There are no charges in the water/octanol anyway so at infinite dilution the difference would only come from the different bead type in the uncharged molecule (that you apparently don't need).

- Jaakko

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8 years 10 months ago #4560 by satti
Replied by satti on topic equilibrium densities logD
Dear Jaakko,
thanks a lot for the suggestion and pointing out the dry martini paper. As a start and a test case I would be doing the partitioning of Qa particle as in dry martini paper.

t.,
satyan

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