From chemistry-request@ccl.net Thu Jul 7 21:39:02 2005 Received: from rozz.csail.mit.edu (rozz.csail.mit.edu [128.30.2.16]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j681d0vT027121 for ; Thu, 7 Jul 2005 21:39:00 -0400 Received: from pool-70-19-174-107.bos.east.verizon.net ([70.19.174.107] helo=[192.168.2.100]) by rozz.csail.mit.edu with esmtpsa (TLSv1:RC4-MD5:128) (Exim 4.50) id 1Dqgjc-00049s-Pg for chemistry !! ccl.net; Thu, 07 Jul 2005 20:28:53 -0400 Message-ID: <42CDC8C1.3040206 !! mit.edu> Date: Thu, 07 Jul 2005 20:28:49 -0400 From: "David F. Green" User-Agent: Mozilla Thunderbird 1.0.2 (Windows/20050317) 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=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Aromatic systems are weakly polar. Certainly, compared to other groups in proteins --- hydroxyls, amides, carboxylic acids, amines and so on --- they are relatively hydrophobic. However, they are significantly more polar than aliphatic hydrocarbons. As you pointed out, this is borne out by the free energies of hydration, as well as by theoretical studies. However, the interior of a protein is a vacuum, and is not even entirely hydrophobic (at minimum, there are buried back-bone amides). Looking at transfer between water and octanol (a moderately non-polar enviroment), benzene falls out somwhere between propane and butane --- certainly preferring the more hydrophobic environment. This all works out as a result of the balancing of enthalpic (both electrostatic and van der Waals, in molecular mechanics' terms) interactions between the solute and solvent and entropic terms resulting > from solvent structure. More statistical frameworks (like hydrophobicity scales and the like) are really just capturing the same underlying physics, which is why you'll often here people refering to them in the same language (e.g. the hydrophobic effect). To give a quick example of how the vacuum to water transfer free energy may be negative, while the hydrophobic solvent to water transfer energy may be positive, just think about van der Waals interactions; there are none in vacuum, and plenty between an aromatic system in hydrophobic solvent. The weak dielectric response of hydrophobic solvents (around 2 at the very minimum) gives an added bonus, and as always, entropy is a hard one to deal with perfectly. But in a nutshell, aromatic certainly do have favorable hydration free energies despite generally considered "hydrophobic". It's not a misnomer, but more a difference in reference state. Of course, every thing is always a little more complicated than what anyone tells you, but that's what makes it all fun. +--------------------------------------------------------------------+ | David F. Green | | | Postdoctoral Associate | Office: 617-253-5438 | | Division of Bioengineering and Computer | Mobile: 617-953-3922 | | Science & Artificial Intelligence Lab | Fax: 617-252-1816 | | Massachusetts Institute of Technology | | | 32 Vassar St., 32-211 | E-mail: dfgreen !! mit.edu | | Cambridge, MA 02139 | | +--------------------------------------------------------------------+ 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 > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > >