From chemistry-request@ccl.net Fri Jul 8 01:33:33 2005 Received: from mrbusi1.netcologne.de (mrbusi1.netcologne.de [194.8.194.213]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j685XTsW005614 for ; Fri, 8 Jul 2005 01:33:30 -0400 Received: from cosmologic.de (xdsl-213-196-241-161.netcologne.de [213.196.241.161]) by mrbusi1.netcologne.de (Postfix) with ESMTP id 483F01A0028 for ; Fri, 8 Jul 2005 07:33:27 +0200 (CEST) Message-ID: <42CE1025.8080803 _()_ cosmologic.de> Date: Fri, 08 Jul 2005 07:33:25 +0200 From: Andreas Klamt User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6b) Gecko/20031205 Thunderbird/0.4 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry _()_ ccl.net Subject: Re: CCL: W:Solvation free energy for aromatic hydrocarbon References: <200507072007.j67K7coC007174 _()_ server.ccl.net> In-Reply-To: <200507072007.j67K7coC007174 _()_ server.ccl.net> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=1.1 required=5.0 tests=FORGED_RCVD_HELO, RCVD_IN_NJABL_PROXY autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hi Bond, the concepts of the solavtion models are right. You must take into account the van der Waals (vdW) energies, which to first order can be considered as a kind of vdWs surface energy. More or less accidentally, for water vdWs energy and surface tension (cavity formation free energy) almost cancel, so that hydration free energies of alkanes are very slightly positive. Since aromatics (due to the quadrupole moment) are slightly more polar than alkanes, hydration free energies of aromatics are slightly negative, as you say. In a less polar solvent than water the cavitation free energy is much less positive (typically close to zero). Thus the solavtion free energy in such solvent would be much more negative that it is into water, and thus the ballance of the transfer of aromatics from water to less polar solvents is much in favor of the non-polar solvent. You can study these terms in detail in our solvation model COSMO-RS (see www.cosmologic.de). Regards Andreas Chemical, , Bond wrote: >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 _()_ ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST _()_ 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 >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt _()_ cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -----------------------------------------------------------------------------