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

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
         To:     chemistry/at/ccl.net
         cc:
         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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