Subject: W:Solvation free energy for aromatic hydrocarbon

From: "Chemical, , Bond" <chemicalbond001 _+_ yahoo.com>
Date: Thu, 7 Jul 2005 16:07:38 -0400

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