From chemistry-request@server.ccl.net Fri Jul 14 14:07:24 2000 Received: from genxy.com (mailhub.genxy.com [207.137.9.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA00772 for ; Fri, 14 Jul 2000 14:07:23 -0400 Received: from genxy.com (genxy5-50.genxy.com [172.20.5.50]) by genxy.com (8.9.1b+Sun/8.9.1) with ESMTP id LAA03129 for ; Fri, 14 Jul 2000 11:11:53 -0700 (PDT) Message-ID: <396F5600.19AC572D@genxy.com> Date: Fri, 14 Jul 2000 11:03:44 -0700 From: Iraj Daizadeh X-Mailer: Mozilla 4.73 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: protein folding/sequence. Content-Type: multipart/mixed; boundary="------------51254766772CE1360B5C38A4" This is a multi-part message in MIME format. --------------51254766772CE1360B5C38A4 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I hear that if two sequences have homology (biological sequence similarity) greater than 20%, then their 3-d structures will be almost identical. Is this true? If so, can someone point me to some seminal papers discussing this... Thanks in advance. I will summarize if enough interest is shown. Best Wishes, Iraj. --------------51254766772CE1360B5C38A4 Content-Type: text/x-vcard; charset=us-ascii; name="iraj.daizadeh.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Iraj Daizadeh Content-Disposition: attachment; filename="iraj.daizadeh.vcf" begin:vcard n:Daizadeh;Iraj tel;fax:858-551-3001 tel;work:858-551-3030 x-mozilla-html:FALSE org:Genset Corporation;Statistical Genomics version:2.1 email;internet:iraj.daizadeh@genxy.com title:Patent Liaison adr;quoted-printable:;;875 Prospect Street, Suite 206=0D=0A;La Jolla;CA;92037; fn:Iraj Daizadeh end:vcard --------------51254766772CE1360B5C38A4-- From chemistry-request@server.ccl.net Fri Jul 14 23:36:22 2000 Received: from smtp.mail.yahoo.com (smtp.mail.yahoo.com [128.11.68.32]) by server.ccl.net (8.8.7/8.8.7) with SMTP id XAA00653 for ; Fri, 14 Jul 2000 23:36:21 -0400 Received: from s10062.pc.nus.edu.sg (HELO scip8239) (137.132.24.189) by smtp.mail.yahoo.com with SMTP; 15 Jul 2000 03:31:38 -0000 X-Apparently-From: Message-ID: <000001bfee0d$30254e40$bd188489@nus.edu.sg> From: "Li Zhenhua" To: "G. Naga Srinivas" , "CCL" References: <396DE4C1.11C0E0B0@jamie.chem.unt.edu> Subject: Re: CCL:CO frequencies in Organometallics Date: Sat, 15 Jul 2000 10:07:08 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4029.2901 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4029.2901 Hi, A paper by Bytheway I and Wong MW is about the scaling factors of DFT method for inorganic compounds. Hope it can help you. The prediction of vibrational frequencies of inorganic molecules using density functional theory CHEM PHYS LETT 282: (3-4) 219-226 JAN 16 1998 ----- Original Message ----- From: "G. Naga Srinivas" To: Sent: Thursday, July 13, 2000 11:48 PM Subject: CCL:CO frequencies in Organometallics > Hi > I am trying to compare the calculated CO vibrational frequencies > with experimental > frequencies in Organometallics. But the scaling factors suggested for > organic compounds > in J. Phys. Chem. 1996, 100, 16052 producing large errors. Are there > any special scaling > factors for organometallic CO vibrational frequencies. I will > summarize. > > Thanks > Srinivas > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > __________________________________________________ Do You Yahoo!? Talk to your friends online with Yahoo! Messenger. http://im.yahoo.com From chemistry-request@server.ccl.net Fri Jul 14 23:56:53 2000 Received: from cosmos.cosm.sc.edu (cosmos.cosm.sc.edu [129.252.40.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA00716 for ; Fri, 14 Jul 2000 23:56:53 -0400 Received: (from jorge@localhost) by cosmos.cosm.sc.edu (8.9.3/8.9.3) id XAA795394; Fri, 14 Jul 2000 23:51:52 -0400 (EDT) From: Jorge Seminario Message-Id: <200007150351.XAA795394@cosmos.cosm.sc.edu> Subject: Zerner Conference To: chemistry@ccl.net Date: Fri, 14 Jul 2000 23:51:51 -0400 (EDT) Cc: jorge@mail.chem.sc.edu X-Mailer: ELM [version 2.5 PL2] MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Colleagues, The International Society of Quantum Biology and Pharmacology, is organizing the Zerner Conference, in New Orleans, Louisiana, on August 17-19, 2000. (http://www.chem.uno.edu/Politzer_files/ISQBP.htm) Registration and abstract submission for poster presentations are still open. Articles will be published in the Proceedings (International Journal of Quantum Chemistry) of The International Society of Quantum Biology and Pharmacology. Hotel Information The conference will be held in the Queen and Crescent Hotel, located at 344 Camp Street. It is in a 100-year-old historic building within walking distance of the French Quarter, the arts district and the casino. (For more on-line information about New Orleans, visit http://www.nola.com.) The rate for a double room will be $69 per night for August 16 and 17 and $89 per night for August 18 and 19. A third and a fourth person can be accommodated in a room for an additional$10 per person per night. A block of rooms at these rates is being held until June 15, 2000. For room reservations, contact the hotel at1-800-975-6652 or 1-504-587-9700; their fax number is 1-504-587-9701. In order to receive the special rate, conference attendees should mention the University of New Orleans conference. Conference Fees: * ISQBP Members: $100 * Nonmembers: $125 * Students: $60 Organizer Dr. Peter Politzer, Department of Chemistry, University of New Orleans, New Orleans, Louisiana, 70148, USA. Conference Registration Form Name: ___________________________________________ Mailing Address: __________________________________ ________________________________________________ E-mail: __________________________________________ Telephone: _______________________________________ Fax: ____________________________________________ (This information will be included in the conference program unless you specify otherwise.) ISQBP member _____ Nonmember _____ Student _____ Registration fee enclosed? _____ Yes _____ No Please make check payable to the International Society of Quantum Biology and Pharmacology; it should preferably be drawn on a U.S. bank. Do you wish to present a poster? _____ Yes _____ No Tentative Title: _____________________________________ __________________________________________________ Do you plan to submit a contribution to the proceedings of the conference? _____Yes _____ No (Manuscripts should be written in the usual IJQC format and submitted on-site during the conference.) Plenary Sessions and Speakers: Enzyme Function: * David Beratan (University of Pittsburgh) - * Tim Clark (University of Erlangen) - Hybrid QM/MM Simulations of Enzyme Reaction Mechanisms. * Gilda Loew (Molecular Research Institute, Palo Alto) - Homology Modeling and Substrate Binding Study of Human CYP450 Enzymes. * Kenneth Merz (Penn State University) - Combined QM/MM Methodologies and Applications. Biochemical Nanocomputer Technologies: * Robert Birge (University of Connecticut) - Protein-Based Volumetric Memories and Associative Processors. * John Reif (Duke University) - Recent Advances and New Applications for Biomolecular Computations. * Joel Schnur (Naval Research Laboratory) - Sub-Micron Lipid Tubules and their Applications. Protein Structure: * Harold Scheraga (Cornell University) - Prediction of Protein Structure by Global Optimization of a Potential Function. * Eugene Shakhnovich (Harvard University) - Universally-Conserved Positions in Protein Folds: Reading Evolutionary Information about Protein Stability, Folding Kinetics and Function. * Jeffrey Skolnick (Donald Danforth Plant Science Center, St. Louis) - Prediction of Structure and Function on a Genomic Scale. * Devarajan Thirumalai (University of Maryland) - Stretching Proteins. Proton Pumps: * Daniel Borgis (Université Pierre et Marie Curie, Paris) - Transport and Spectroscopy of Protons in Aqueous Media. * Mark Tuckerman (New York University) - Identifying Quantum Effects in Aqueous Proton Transport and in "Intermediate-Barrier" Intramolecular Proton Transfer. * Arieh Warshel (University of Southern California) - Computer Simulations of Proton Transfer Processes in Proteins. The Energetics of Proton Translocation Processes. Membrane Proteins: * Frank Blaney (SmithKline Beecham) - Modelling of Voltage-Gated Calcium Channels and their Interactions with Small Peptide Neurotoxins. * Benoit Roux (Cornell Medical School) - Theoretical Studies of Ion Permeation. * Peter Tieleman (Oxford University) - Molecular Dynamics Simulations of Antimicrobial Peptides: From Membrane Binding to Transmembrane Channels. * Harel Weinstein (Mt. Sinai Medical School, New York) - Computer Experiments Reveal Signaling Mechanisms in Membrane Proteins: From Structural Motifs to Functional Microdomains. Modelling of Electrostatic Interactions: * Sergio Hassan (Mt. Sinai Medical School, New York) - Description of Solvent Effects in Proteins: A New and General Continuum Approach for Structure Calculations. * Ferran Sanz (IMIM/Universitat Pompeu Fabra) - Automatic Exploration of Similarities between Distributions of Molecular Interaction Potentials. * Rebecca Wade (European Molecular Biology Laboratory, Heidelberg) - Electrostatic Interactions in Protein-Protein Association: Insights from Brownian Dynamics Simulations and Protein Interaction Property Similarity Analysis. From chemistry-request@server.ccl.net Sat Jul 15 07:55:42 2000 Received: from smtp.email.msn.com (cpimssmtpu08.email.msn.com [207.46.181.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA03437 for ; Sat, 15 Jul 2000 07:55:41 -0400 Received: from oemcomputer - 199.35.91.98 by email.msn.com with Microsoft SMTPSVC; Sat, 15 Jul 2000 04:48:29 -0700 Message-ID: <002d01bfee5a$b882a420$625b23c7@oemcomputer> From: "NATHAN HARRIS" To: Cc: "Mao Xiang" References: <396E739A.A5548C23@iris.sipp.ac.cn> Subject: Re: CCL:deprotonation rate Date: Sat, 15 Jul 2000 07:46:37 -0500 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear Mao, The heterolytic dissociation reactions you are interested in are all impossible processes without the presence of a proton accepter (a base). For example, the gas phase dissociation of water H2O ==> H+ + OH- has an energy requirement of around 380 kcal/mol (this is the same as the ionization enthalpy except zero-point energy is not included). However, the reverse process has no barrier at all. Gas phase ionization doesn't happen unless there is some proton acceptor, as in H2O + B- ==> OH- + BH In aqueous solution the story is different because the ions are then solvated. ----- Original Message ----- From: Mao Xiang To: Sent: Thursday, July 13, 2000 8:57 PM Subject: CCL:deprotonation rate > Hello everyone: > I want to know about the activation free energy of the following > reaction: > > 1. H2O---> H+ + OH- > 2. CH3CH2OH----> CH3CH2O- + H+ > 3. NH2CH2CH2OH---> +NH3CH2CH2O- > > I think I calculate them with Arrhenius equation, but I do not know > where I can get the observed rate constants. > > Does anyone have some experients about my problem. Hope you can help me. > Thanks. > > > Regards, > mao > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > | Xiang Mao | > | Lab of Molecular Regulation for Microbial Secondary Metabolism | > | Shanghai institute of Plant Physiology, Academia Sinica | > | 300 Fenglin Road, Shanghai, China, 200032 | > | Tel: +86-21-64042090-4791 | > | Fax: +86-21-64042385 | > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Sat Jul 15 13:56:21 2000 Received: from mauve.csi.cam.ac.uk (exim@mauve.csi.cam.ac.uk [131.111.8.38]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA04619 for ; Sat, 15 Jul 2000 13:56:20 -0400 Received: from su4.phar.cam.ac.uk ([131.111.156.196]) by mauve.csi.cam.ac.uk with smtp (Exim 3.13 #1) id 13DW5T-0005Bu-00; Sat, 15 Jul 2000 18:50:51 +0100 Received: from pc1.phar.cam.ac.uk by su4.phar.cam.ac.uk (SMI-8.6/CS-SUB) id SAA29905; Sat, 15 Jul 2000 18:50:20 +0100 Received: from localhost by pc1.phar.cam.ac.uk; Sat, 15 Jul 2000 18:50:20 +0100 (BST) Date: Sat, 15 Jul 2000 18:50:20 +0100 (BST) From: James Smith X-Sender: js252@pc1.phar.cam.ac.uk To: Iraj Daizadeh cc: chemistry@ccl.net Subject: Re: CCL:protein folding/sequence. In-Reply-To: <396F5600.19AC572D@genxy.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id NAA04620 Homology does not mean "amino acid sequence similarity >20%" It is defined in terms of functionality (cf. analogy). For a clear definition see Attwood, T. K. & Parry-Smith, D. J. (1999). Introduction to bioinfomatics (Cell and Molecular biology Series), Addison Wesley Longman Ltd., Harlow, England. Comparative modelling methods require more than aligning protein sequences, constructing structural models against canonical quaternary, tertiary and secondary structural element templates or using threading methodologies and then minimisation. It is increasingly knowledge based, requiring more information on protein domain motions (normal mode analysis), catalytic group analysis, protein-protein activation and modification, expression and regulation. For seminal papers perform citation searches on the following publications and look for reviews that have used or criticised: Chou & Fasman (1978). Advances in Enzymology, 47, 45-148 Godzik et al (1993). J Computer-aided molecular design, 7, 397-438 Jones et al (1992). Nature 358, 86-89 Luthy et al (1992). Nature 356, 83-85 Mosimann et al (1995). Proteins 23, 301-317 Novotny et al (1988). Proteins 4, 19-30 good luck James Smith > I hear that if two sequences have homology (biological sequence > similarity) > greater than 20%, then their 3-d structures will be almost identical. > > Is this true? If so, can someone point me to some seminal papers > discussing > this... > > Thanks in advance. I will summarize if enough interest is shown. > > Best Wishes, Iraj. > _________________________________________________________________________ James Smith The Drug Design Group 01123 331 987 (Office) St.John's College Department of Pharmacology 01223 331 740 (Fax) Cambridge University of Cambridge 07625 395 084 (Pager) CB2 1TP CB2 1QJ js252@cam.ac.uk United Kingdom United Kingdom http://www.cus.cam.ac.uk/~js252 _________________________________________________________________________ From chemistry-request@server.ccl.net Sat Jul 15 23:03:13 2000 Received: from server.ccl.net (server.ccl.net [192.153.40.39]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA06993 for ; Sat, 15 Jul 2000 23:03:13 -0400 Date: Sat, 15 Jul 2000 23:03:13 -0400 (EDT) From: Computational Chemistry List To: chemistry@ccl.net Subject: Fatal Problem: The largest alpha MO coefficient is 0.17136284D+04 (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Computational Chemistry List http://www.ccl.net/chemistry Administration (chemistry-request@ccl.net) ftp://ftp.ccl.net/ Ohio Supercomputer Center ccl@ccl.net 1224 Kinnear Rd Columbus, Ohio 43212-1163 ---------- Forwarded message ---------- Content-Type: text/plain; charset="us-ascii" MIME-version: 1.0 Subject: Fatal Problem: The largest alpha MO coefficient is 0.17136284D+04 To: chemistry-request@ccl.net Date: Fri, 14 Jul 2000 12:22:25 -0400 From: Sompop Sanongraj Hi When I ran the MP2 single point calculation in g98 (A.7) e.g. # rmp2/6-31g+(d,P) maxdisk=1500mb or # rmp2/6-31g++(d) maxdisk=1500mb. I got the error message shown: **** Fatal Problem: The largest alpha MO coefficient is 0.17136284D+04 Error termination via Lnk1e in /local/gauss/g98-a7/g98/l801.exe. Could anybody tell me how to deal with this problem? Thanks sompop Sompop Sanongraj 208 Church Street Hancock MI 49930. TEL: (906) 482 9377