Subject: Re: CCL: W:Solvation free energy for aromatic hydrocarbon

From: david.giesen/at/kodak.com
Date: Fri, 8 Jul 2005 11:06:29 -0400

I believe the confusion lies in the fact that a protein environment is not 
well described by assuming it is the same as the gas phase.  That phenyl 
group in the protein is still "solvated" by the surrounding protein.  The 
important energetic measure in that case is not the (de)solvation energy 
of the phenyl group in water, but the differential solvation energy of the 
phenyl group between water and the protein environment.

Given a standard state of 1M concentration in the gas phase and solution 
phase, and 298K, benzene has the following experimental solvation 
energies: -0.9 kcal/mol in water, -4.0 kcal/mol in n-hexane, and -4.6 
kcal/mol in benzene.

So you can see that transferring a benzene molecule from water to some 
hydrocarbon-like environment is exothermic by ~3-4 kcal/mol, and for 
similar reasons there is a negative (beneficial) energetic effect of 
transfering the phenyl ring from water into the protein environment.

Dave Giesen

"Chemical, , Bond" <chemicalbond001/at/yahoo.com>
Sent by: "Computational Chemistry List" <chemistry-request/at/ccl.net>
07/07/2005 04:07 PM
Please respond to chemistry

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        Subject:        CCL: W:Solvation free energy for aromatic hydrocarbon

Hi there,

I am confused with a single concept: what should be the sign for the 
solvation  free energy for a fragment like phenyl? 

There are many experimental data of solvation free energy for aromatic 
hydrocarbons, such as benzene, naphthalene, etc, but they are all negative 
surprisingly.  I looked at several papers with models of solvation energy, 
and their predictions all all have negative solvation energies for those 
compounds, just like the experiments.

Typically when a phenyl group is transfered from water into protein, we 
would like to say there is a negative(beneficial) desolvation energy, or 
the usual called hydrophobic effect.  And this has been used in tons of 
models for protein simulation or protein-ligand binding.  Note, in this 
context, the solvation energy (from gas into water) is positive! 

Is there something wrong over here?  Or just some artifact from the 
fitting?

Hope there would be some good comments.

Thanks a lot,
Bond

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