From owner-chemistry@ccl.net Thu May 15 03:40:00 2008 From: "jacquie cawthray jacqueline.cawthray]^[adelaide.edu.au" To: CCL Subject: CCL: Problems with NBO analysis of intramolecular hydrogen bonds Message-Id: <-36967-080515033912-11161-K0H6fmH09svLzZmAjboa7w(_)server.ccl.net> X-Original-From: "jacquie cawthray" Date: Thu, 15 May 2008 03:39:08 -0400 Sent to CCL by: "jacquie cawthray" [jacqueline.cawthray^^^adelaide.edu.au] Hi everyone. I've been investigating a series of molecules with strong intramolecular hydrogen bonds using NBO. In the NBO output for many of the molecules, the H in the O-H--O fragment is treated as another unit and the O-H bond is not recognized. The NBO for H is given as LP*(1). For simple molecules containing an intramolecular hydrogen bond, it works fine. Any help or comments would be appreciated. From owner-chemistry@ccl.net Thu May 15 06:55:00 2008 From: "Anica anica~~chem.uni-potsdam.de" To: CCL Subject: CCL: AW: Problems with NBO analysis of intramolecular hydrogen bonds Message-Id: <-36968-080515054717-14367-WlpKDLEnrUOcdNqQaJA3sA^server.ccl.net> X-Original-From: "Anica" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 15 May 2008 10:56:02 +0200 MIME-Version: 1.0 Sent to CCL by: "Anica" [anica---chem.uni-potsdam.de] Hallo Jacquie, it seems that I had the same problem as you. Do you have a strong = electron delocalization? Try the key word $CHOOSE! Examples how to create the = input file you may find in the NBO Program manual. Best wishes, Anica -----Urspr=FCngliche Nachricht----- Von: owner-chemistry-$-ccl.net [mailto:owner-chemistry-$-ccl.net]=20 Gesendet: Donnerstag, 15. Mai 2008 09:39 An: L=C3=A4mmermann, Anica Betreff: CCL: Problems with NBO analysis of intramolecular hydrogen = bonds Sent to CCL by: "jacquie cawthray" = [jacqueline.cawthray^^^adelaide.edu.au] Hi everyone. I've been investigating a series of molecules with strong intramolecular hydrogen bonds using NBO. In the NBO output for many of the molecules, = the H in the O-H--O fragment is treated as another unit and the O-H bond is = not recognized. The NBO for H is given as LP*(1). For simple molecules containing an intramolecular hydrogen bond, it works fine. Any help or comments would be appreciated. -=3D This is automatically added to each message by the mailing script = =3D-=look up = the X-Original-From: line in the mail header.http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txtNo virus found in this incoming message. Checked by AVG.=20 Version: 7.5.524 / Virus Database: 269.23.16/1433 - Release Date: = 14.05.2008 16:44 =20 No virus found in this outgoing message. Checked by AVG.=20 Version: 7.5.524 / Virus Database: 269.23.16/1433 - Release Date: = 14.05.2008 16:44 =20 From owner-chemistry@ccl.net Thu May 15 08:42:01 2008 From: "Patrik Rydberg pry(0)farma.ku.dk" To: CCL Subject: CCL:G: Angle force constant Message-Id: <-36969-080515035837-20444-9ZBvrVZTzxE/BeRoZ6Ga8Q^^server.ccl.net> X-Original-From: "Patrik Rydberg" Content-Language: sv Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 15 May 2008 09:26:06 +0200 MIME-Version: 1.0 Sent to CCL by: "Patrik Rydberg" [pry,,farma.ku.dk] Hi, I know that the program Hess2FF can do this. It is described in an = article by K. Nilsson, D. Lecerof, E. Sigfridsson and U. Ryde, http://dx.doi.org/10.1107/S0907444902021431 . The article says that the program is available from the authors on request. It is very likely that there are other programs that can do this as well = but I only know of Hess2FF. Best wishes, Patrik -------------------------------------------------------------------------= - Patrik Rydberg, Post-doc, Ph.D. Biostructural Research Group Department of Medicinal Chemistry Faculty of Pharmaceutical=A0 Sciences University of Copenhagen DK-2200 Copenhagen http://www.farma.ku.dk/index.php/Patrik-Rydberg/5304/0/ -----Original Message----- > From: owner-chemistry||ccl.net [mailto:owner-chemistry||ccl.net]=20 Sent: den 14 maj 2008 18:52 To: Rydberg, Patrik Subject: CCL:G: Angle force constant Sent to CCL by: "M Qaiser Fatmi" [qaiser_fatmi-x-yahoo.com] Hi, I performed a geometry optimisation followed by a frequency calculations = of Fe(II), complexed with three imidazole and one acetate group using = gaussian 03. My question is regarding the calculation of angle force constant. = Can anyone suggest me how to read the angle force constant from the gaussian output file. Thanking in advance Qaiser -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu May 15 11:08:00 2008 From: "Oluwakemi.Oloba#mail.uh.edu" To: CCL Subject: CCL: he largest beta MO coefficient Message-Id: <-36970-080515110609-3006-0E/fSw9VbnPfRrKuwPUHqw[#]server.ccl.net> X-Original-From: Oluwakemi.Oloba-x-mail.uh.edu Content-language: en Content-type: multipart/alternative; boundary="Boundary_(ID_4rTB9KynscuoRr1o0uq7KQ)" Date: Thu, 15 May 2008 10:01:40 -0500 MIME-version: 1.0 Sent to CCL by: Oluwakemi.Oloba ~~ mail.uh.edu This is a multi-part message in MIME format. --Boundary_(ID_4rTB9KynscuoRr1o0uq7KQ) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: QUOTED-PRINTABLE Content-disposition: inline Pls help what does this mean =A0 **** Warning!!: The largest alpha MO coefficient is=A0 0.13972408= D+02 =A0**** Warning!!: The smallest alpha delta epsilon is=A0 0.99566194D= -01 =A0**** Warning!!: The largest beta MO coefficient is=A0 0.14294959D+= 02 thanks for your reply --Boundary_(ID_4rTB9KynscuoRr1o0uq7KQ) Content-type: text/html; charset=us-ascii Content-transfer-encoding: 7BIT Content-disposition: inline Pls help what does this mean

  **** Warning!!: The largest alpha MO coefficient is  0.13972408D+02


 **** Warning!!: The smallest alpha delta epsilon is  0.99566194D-01


 **** Warning!!: The largest beta MO coefficient is  0.14294959D+02

thanks for your reply

--Boundary_(ID_4rTB9KynscuoRr1o0uq7KQ)-- From owner-chemistry@ccl.net Thu May 15 11:42:01 2008 From: "Renata Kwiecien renee###p.lodz.pl" To: CCL Subject: CCL: modeling adsorption on silica surface Message-Id: <-36971-080515104226-32421-PQGpG1Rv7ihgw84RWXtJxA- -server.ccl.net> X-Original-From: "Renata Kwiecien" Date: Thu, 15 May 2008 10:42:22 -0400 Sent to CCL by: "Renata Kwiecien" [renee[*]p.lodz.pl] Dear CCL'ers, I want to simulate adsorption of several substituted benzylaldehyde molecules on a silica gel models. This is to get quantitative and qualitative information about interactions between silanol hydroxyl groups and substituted benzylaldehydes, and to determine how those interactions influence observed isotope effects. There is a lot of information about non covalent isotope effects in the literature, but measured or calculated for enzymes. What I am looking for are publications which describe calculated interactions of aromatic molecules with the silica gel surface. Also, computational and experimental results with isotope effects would be useful. Thank you, Renata Kwiecien Universit de Nantes From owner-chemistry@ccl.net Thu May 15 13:46:01 2008 From: "Ekram Hossain ehossain+*+indiana.edu" To: CCL Subject: CCL: Franck-Condon Simulation. Message-Id: <-36972-080515125931-31991-CglknIgecFvzZMTVLsr37w:+:server.ccl.net> X-Original-From: "Ekram Hossain" Date: Thu, 15 May 2008 12:59:27 -0400 Sent to CCL by: "Ekram Hossain" [ehossain++indiana.edu] Hi, Does anyone know of any software which can generate Feanck-Condon Simulation spectra? Thanks for your time. Ekram. From owner-chemistry@ccl.net Thu May 15 14:21:02 2008 From: "James G Prudhomme jprudhomme=healthtech.com" To: CCL Subject: CCL: CHI's Structure-Based Drug Design Conference Message-Id: <-36973-080514153653-29368-vM3/tXIrCgSWsd3ROYoPGA_._server.ccl.net> X-Original-From: "James G Prudhomme" Date: Wed, 14 May 2008 15:36:49 -0400 Sent to CCL by: "James G Prudhomme" [jprudhomme||healthtech.com] CHI's Stucture-Based Drug Design June 25-27, 2008 The World Trade Center, Boston, Massachusetts Advanced registration discount ends May 23. Register at www.healthtech.com/sbd/overview.aspx Session Topics: * Structure-Based Modeling of GPCRs * Determination of Protein-Protein Interaction Sites * Computational-Based Protein Design * Hit and Lead Optimization * Accounting for Receptor Flexibility in Ligand Binding * Challenges of Docking and Screening * Experimental Approaches * Case Studies Distinguished Faculty: * Matthew Clark, Ph.D., Senior Director of Scientific Computation, Locus Pharmaceuticals * David Dalgarno, Ph.D., Vice President, Research Technologies, ARIAD Pharmaceuticals Inc. * Stefan Geschwindner, Ph.D., Principal Scientist and Team Leader, Protein Engineering, Global Structural Chemistry, AstraZeneca R&D * Andrew Good, Ph.D., Principal Scientist, Computer Assisted Drug Design, Bristol-Myers Squibb * Andreas Gosberg, Ph.D., Senior Scientist II, Medicinal Chemistry, SGX Pharmaceuticals * Roderick E. Hubbard, Senior Fellow, Vernalis and Professor, University of York * Paul Labute, Ph.D., President, Chemical Computing Group Inc. * Jonathan S. Mason, Ph.D., Chief Scientist & Divisional Director, Computational Chemistry & Structural Biology, Lundbeck Research (Denmark) * Stephen Mayo, Ph.D., Professor of Biology and Chemistry, California Institute of Technology * Stefan Modeling, Ph.D., Head of Molecular Modeling Unit, Laboratory of Biological Modeling, NIH, NIDDK * Xavier J. Morelli, Ph.D., Principal Investigator, NMR and Drug Design, National Center for Scientific Research (CNRS) * Mark Mulvihill, Ph.D., Associate Director of Chemistry, Oncology, OSI Pharmaceuticals * Jennifer Nemeth, Ph.D., Principal Research Scientist, Protein Engineering, Centocor Research and Development * Christopher Phillips, Ph.D., Senior Principal Scientist, Exploratory Medicinal Sciences, Pfizer Global Research and Development * Alan C. Rigby Ph.D., Assistant Professor of Medicine, Harvard Medical School * Tomi Sawyer, Ph.D., Chief Scientific Officer, AILERON Therapeutics; Editor-in-Chief, Chemical Biology & Drug Design * Sharon Shacham, Ph.D., Vice President, Drug Development, EPIX Pharmaceuticals * B. Woody Sherman, Ph.D., Director, Applications Science, Schrodinger, Inc. * Lena Tagmose, Ph.D., Head of Section, Computational Chemistry, Lundbeck Research (Denmark) * Gergely Toth, Ph.D., Scientist, Computational Chemistry and Biology, Elan Pharmaceuticals * Thomas J. Tucker, Ph.D., Senior Research Fellow, Dept. of Medicinal Chemistry, Merck Research Laboratories * T. R. Vedananda, Ph.D., Program Head, Diabetes & Metabolism, Novartis * C.M. (Venkat) Venkatachalam, Ph.D., Fellow, Accelrys, Inc. * Zsolt Zsoldos, Co-Founder and CSO, SimBioSys Prior to the start of this conference will be a pre-conference workshop (Designing Kinase Inhibitors) on June 25. Visit our website for full details on the Structure-Based Drug Design conference and pre-conference workshop: www.healthtech.com/sbd/overview.aspx The industry has relied on CHI for many year's to deliver top-notch science and quality networking in drug design...Don't miss out! Be sure to register by May 23to receive the lowest conference registration fee. To register, visit our website, or call +1 781-972-5400 or toll-free in the U.S. 888-999-6288. Sponsorship and Exhibit Opportunities are Available: Exhibiting at this premier event allows you to showcase your expertise, brand your solutions and develop revenue-generating opportunities with qualified decision-makers. Sponsorship packages are designed to achieve your lead generation, business development and networking goals and objectives. Through your sponsorship, CHI will help your company meet these goals plus maximize exclusive sponsorship branding opportunity pre, post and while at the Structure-Based Design conference. Sponsorship features include pre-conference, at-conference and post-conference benefits providing a well-rounded marketing campaign. For details and to contract space, contact Katelin Fitzgerald at 781-972-5458 or kfitzgerald[*]healthtech.com Present a Poster: Delegates are encouraged to display their recent research and progress in structure-based design by displaying a poster. Your poster will be included in our conference CD that is distributed to all our delegates on-site. Submit a poster by June 8 and CHI will take an additional $50 off your conference registration. From owner-chemistry@ccl.net Thu May 15 14:56:01 2008 From: "Frank Neese neese]_[thch.uni-bonn.de" To: CCL Subject: CCL: Franck-Condon Simulation. Message-Id: <-36974-080515142004-24596-lNRRgAoSyrTgHw28gOE41w::server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 15 May 2008 20:19:15 +0200 MIME-Version: 1.0 Sent to CCL by: Frank Neese [neese+/-thch.uni-bonn.de] Ekram Hossain ehossain+*+indiana.edu schrieb: > Sent to CCL by: "Ekram Hossain" [ehossain++indiana.edu] > Hi, > Does anyone know of any software which can generate Feanck-Condon Simulation spectra? Thanks for your time. > > Dear Ekram, ORCA (http://www.thch.uni-bonn.de/tc/orca/) does that (orca_asa). The paper is: Petrenko, T.; Neese, F. (2007) A general efficient quantum chemical method for predicting absorption bandshapes, resonance Raman spectra and excitation profiles for larger molecules. J. Chem. Phys., 127, 164319 All the best, Frank > Ekram.> > -- --------------------------------------------------------------- Prof. Dr. Frank Neese Lehrstuhl fuer Theoretische Chemie Universitaet Bonn Wegelerstr. 12 D-53115 Bonn, Germany neese()thch.uni-bonn.de Phone: +49-28-732351 FAX: +49-(0)228-739064 --------------------------------------------------------------- From owner-chemistry@ccl.net Thu May 15 21:11:01 2008 From: "Diego G mez darkego21|-|yahoo.com" To: CCL Subject: CCL: MOPAC2007 Message-Id: <-36975-080515210851-22397-pa7anqTfydlIpDF1z2N/dA{:}server.ccl.net> X-Original-From: "Diego G mez" Date: Thu, 15 May 2008 21:08:47 -0400 Sent to CCL by: "Diego G mez" [darkego21:yahoo.com] hello! Currently, I am trying the MOPAC2007 program to do some calculations on solid materials. So, I want to know if anyone know a program to create the imput file for a solid calculations wiht MOPAC2007. thank a lot any suggestion!! best regards...