From chemistry-request- at -ccl.net Mon Jun 30 17:03:52 2003 Received: from mail-gate.uni-paderborn.de ([131.234.22.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5UL3Yqe001580 for ; Mon, 30 Jun 2003 17:03:52 -0400 Received: from oc34 ([131.234.240.94]:3274 "EHLO upb.de") by mail.uni-paderborn.de with ESMTP id ; Mon, 30 Jun 2003 09:14:36 +0200 Message-ID: <3EFFE3C0.4040902/at/upb.de> Date: Mon, 30 Jun 2003 09:16:16 +0200 From: Edgar Luttmann User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; de-DE; rv:1.0.1) Gecko/20020823 Netscape/7.0 (BDP) X-Accept-Language: de-de, de MIME-Version: 1.0 To: ccl Subject: [Summary] CD spectrum simulation Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Here the Summary of the replies regarding my initial question: #################### I would like to know if there is any method to simulate (at least a rough) CD spectrum of a small peptide. I do have a PDB file (so I have 3D coordinates) and it would be great to predict a spectrum from this. Any hints are welcome and I will give a summary. #################### Here the different replies: #################### If you mean circular dichroism spectrum, you may contact SCM (http://www.scm.com), because there will be a new implementation available (later this year, I think) within the ADF program. You might look for papers by Jochen Autschbach (Jochen.Autschbach/at/chemie.uni-erlangen.de). #################### Hello, For ab initio calc of CD spectra see 1) P. J. Stephens et al, J Phys Chem, 1994, 98, 11623. 2) F. J. Devlin et al, J Phys Chem A, 1997, 101, 6322. E. Lewars #################### Hi Edgar, > I would like to know if there is any method to simulate (at least a > rough) CD spectrum of a small peptide. I do have a PDB file (so I have > 3D coordinates) and it would be great to predict a spectrum from this. If you have enough computer power you can calculate the spectrum ab initio // (TD)DFT. (Dalton, Gaussian'03). But currently it would need to be a very small peptide, and you'd need a good idea of conformational distribution in solution at your experimental conditions. Maybe someone has made or should make a semi-empirical extention of e.g. ZINDO that can do the required electric and magnetic transition dipole moments etc. Otherwise, there's empirical correlations. hope this helps, Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy/at/greenwood.net Department of Medicinal Chemistry bh +45 35306117 The Danish University of Pharmaceutical Sciences fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 ---------------------------------------------------------------------- #################### Hi Edgar, Simulation of CD spectra can be done by ab initio methods which are available in QC codes like Turbomole and Gaussian03. See f.x. J. Am. Chem. Soc., 122 (8), 1717-1724, 2000. You might also consider contacting Professor Fleischhauer at the RWTH in Aachen. He has developed software code for prediction of protein CD spectra using a semi-empirical approach. See: http://134.130.101.5/akflei/index.html However, I guess you are interested in simulating the solution CD spectrum. This is not so easy for a small peptide, since they often have no single well-defined structure in solution. The CD spectrum in solution will thus represent a weighted average of the spectra of a large number of conformers of the peptide. Obviously, this will require some effort to model. Good luck, Peter -- Peter W. Thulstrup Chemistry Department / Royal Veterinary and Agricultural University Thorvaldsensvej 40 / DK-1871 Frederiksberg C / Denmark Phone (Chemistry Dep't): +45 35282400 / Fax: +45 35282398 Phone (Office - direct): +45 35282464 / E-mail: pwt/at/kvl.dk #################### See C. Diedrich S. Grimme, Systematic investigation of Modern Quantum Chemical Methods to Predict Electronic Circular Dichroism Spectra, J. Phys. Chem. A, 107, (2003), 2524-2539. for a recent investigation. Stefan _________________________________________________________ Prof. Dr. Stefan Grimme Organisch-Chemisches Institut (Abt. Theoretische Chemie) Westfaelische Wilhelms-Universitaet, Corrensstrasse 40 D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax) Email:grimmes/at/uni-muenster.de http://www.uni-muenster.de/Chemie/OC/research/grimme/ #################### CD spectra for any closed-shell molecule with up to 50 to 100 atoms can be efficiently and accurately calculated with the Amsterdam Density Functional (ADF) program. For larger systems, the rest of the system ("environment") will need to be modeled in a more approximate way. Please have a look at the recent papers by Dr. Jochen Autschbach (currently in Erlangen) and Prof. Tom Ziegler in J. Chem. Phys. and other journals on CD spectra simulations with ADF. If you would like to obtain further information, let me know. Best regards, Stan van Gisbergen #################### Thanks again for all your help.