From chemistry-request@ccl.net Mon Dec 6 02:27:34 2004 Received: from mrbusi2.netcologne.de (mrbusi2.netcologne.de [194.8.194.214]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iB67RXGQ009701 for >ccl.net>; Mon, 6 Dec 2004 02:27:34 -0500 Received: from cosmologic.de (xdsl-213-196-255-178.netcologne.de [213.196.255.178]) by mrbusi2.netcologne.de (Postfix) with ESMTP id 33A382401D7; Mon, 6 Dec 2004 08:42:40 +0100 (CET) Message-ID: <41B40D6E.2010203<>cosmologic.de> Date: Mon, 06 Dec 2004 08:42:38 +0100 From: Andreas Klamt >cosmologic.de> 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: Edgar Luttmann >mpi-bpc.mpg.de> Cc: CHEMISTRY<>ccl.net Subject: Re: CCL:DMSO, counter ions and ionization state References: <41B03028.1050003<>mpi-bpc.mpg.de> In-Reply-To: <41B03028.1050003<>mpi-bpc.mpg.de> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=4.4 required=7.5 tests=MY_BAD_DOT,MY_DSL, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Edgar, is it dry (water free) DMSO? Then the only way of deprotonation is producing DMSO-H+ ions and for protonation building DMSO anions. We have proposed a pKa model in DMSO in our paper J. Phys. Chem. A 2003, 107, 9380-9386: "First Principles Calculations of Aqueous pKa Values for Organic and Inorganic Acids Using COSMO-RS Reveal an Inconsistency in the Slope of the pKa Scale Andreas Klamt,* Frank Eckert, and Michael Diedenhofen, Michael E. Beck This may outline the way how to do it based on our COSMO-RS method. Andreas Luttmann wrote: > Dear all, > > does anyone have experiences with the treatment of charges during > peptide MD simulations (with gromacs) in DMSO? > > The pka of the sidechains as well as the termini might be > significantly different in DMSO compared to water and thus I wonder if > there is a convenient way to estimate the ionization state of the > residues. Furthermore would you just put counter ions into the DMSO - > or would you keep the peptide neutral? > > Any suggestions are welcome and thanks in advance.. > > Edgar > -- -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt=at=cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics --------------------------------------------------------------------------------