From chemistry-request@ccl.net Fri Jul 8 11:06:35 2005 Received: from smtp1.kodak.com (smtp1.kodak.com [192.232.121.200]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j68F6WaX002258 for ; Fri, 8 Jul 2005 11:06:33 -0400 Received: from roc-us-e1000-110.kodak.com (roc-us-e1000-110.kodak.com [192.232.121.190]) by smtp1.kodak.com (8.11.3/8.11.1) with SMTP id j68F6VL21345 for ; Fri, 8 Jul 2005 11:06:31 -0400 (EDT) Received: from (150.221.122.53) by roc-us-e1000-110.kodak.com via smtp id 5c63_dddd707e_efc1_11d9_930a_0002b3eef597; Fri, 08 Jul 2005 11:06:30 -0400 To: chemistry/at/ccl.net Subject: Re: CCL: W:Solvation free energy for aromatic hydrocarbon X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Message-ID: From: david.giesen/at/kodak.com Date: Fri, 8 Jul 2005 11:06:29 -0400 X-MIMETrack: Serialize by Router on KNOTES2/ISBP/EKC(652HF120|July 29, 2004) at 07/08/2005 11:06:31 AM, Serialize complete at 07/08/2005 11:06:31 AM MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net 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" Sent by: "Computational Chemistry List" 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 -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY/at/ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+