From Y0H8797@ACS.TAMU.EDU Fri Mar 1 01:31:34 1996 Received: from VMS2.TAMU.EDU for Y0H8797@ACS.TAMU.EDU by www.ccl.net (8.7.1/950822.1) id BAA14574; Fri, 1 Mar 1996 01:18:02 -0500 (EST) Date: Fri, 1 Mar 1996 0:17:30 -0600 (CST) From: YONG HUANG To: CHEMISTRY@www.ccl.net Message-Id: <960301001730.22222de5@ACS.TAMU.EDU> Subject: reference to cinnamic acid derivative Does anybody know any computational work done on cinnamic acid derivatives? These compounds are important in laser mass spectrometry. I'll summarize responses. Thanks. Yong y0h8797@acs.tamu.edu From owner-chemistry@ccl.net Fri Mar 1 10:31:37 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id KAA18636; Fri, 1 Mar 1996 10:12:57 -0500 (EST) Received: from fair1.fairfield.edu for LSTEFFEN@fair1.fairfield.edu by bedrock.ccl.net (8.7.1/950822.1) id KAA21078; Fri, 1 Mar 1996 10:12:57 -0500 (EST) From: Received: from fair1.fairfield.edu by fair1.fairfield.edu (PMDF V4.3-7 #10178) id <01I1TJTXHFB48YAI9L@fair1.fairfield.edu>; Fri, 1 Mar 1996 10:10:29 EST Date: Fri, 01 Mar 1996 10:10:29 -0500 (EST) Subject: Molecular Modeling In the Classroom Symposium To: chemistry@ccl.net Message-id: <01I1TJTXJKGY8YAI9L@fair1.fairfield.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT (sorry for taken up bandwidth for those of you far from New England) "Molecular Modeling in the Classroom" A Symposium for Exchange of Ideas, Problems and Success Stories Regarding the Integration of Molecular Modeling into the Chemistry Curriculum To be held at the New England Regional Meeting of the ACS, Wednesday and Thursday, August 14th and 15th. Danbury, Connecticut. Have you begun to use a modeling programs in your organic, biochemistry, physical or inorganic courses? What have you been using? How have your students responded? Would you like to discuss the efforts of others in this area? The Symposium will include formal presentations (What works, What doesnUt work) and RbreakoutS sessions dedicated to simply exchanging ideas. INTERESTED? Want to present a Paper? Send a brief description of your proposed topic to the Program Chair for the NERM Meeting. Include your name, title, contact address and phone, and wether you prefer a paper or poster. Al Adler Department of Chemistry WCSU, Danbury CT 06810 (203) 938-2920 fax (203) 938-9541 OR you can respond directly to the Symposium Chair (email is fine): L. Kraig Steffen Dept. of Chemistry Fairfield University Fairfield, CT 06430 203 254 - 4000 x 2254 203 254 4034 (fax) email: lsteffen@fair1.fairfield.edu CHECK OUT the Western Connecticut WWW page for more information: WWW: http://192.160.244.139/chem/nerm26.html From stevensa@dax.biol.port.ac.uk Fri Mar 1 12:31:40 1996 Received: from dax.biol.port.ac.uk for stevensa@dax.biol.port.ac.uk by www.ccl.net (8.7.1/950822.1) id LAA20496; Fri, 1 Mar 1996 11:48:23 -0500 (EST) Received: by dax.biol.port.ac.uk (940816.SGI.8.6.9/940415.SGI.SS) for chemistry@www.ccl.net id QAA00314; Fri, 1 Mar 1996 16:46:57 GMT From: "Adrian Stevens" Message-Id: <9603011646.ZM312@dax.sci.port.ac.uk> Date: Fri, 1 Mar 1996 16:46:50 +0000 Return-Receipt-To: "Adrian Stevens" X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: Errors in Vibrational mode calcs... Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, (Appol's. for the length of the mail message!) I have a query with regard to the accuracy of calculated normal modes of vibration (as for example, determined via semi-empirical methods) A while back, there was some discussion on the list, of the calculation of normal modes of vibration. In particular, David Young (at Michigan State University, young@slater.cem.msu.edu) posted a short introduction to the subject, titled 'Computational Modeling of Molecular Vibrations' (see Sun, 13 Aug 1995 in the CCL archive for the full posting). In it, he highlighted that vibrational frequencies from semi-empirical calculations tend to be qualitative in that bond stretches have high frequencies, bond angle bending lower frequencies, torsions even lower, etc. However, he also pointed out that the actual values are often erratic. When compared with experiment, some values come close while others are either too low or too high. He also made mention that density-functional theory methods give frequencies with this same erratic behavior, albeit, with a somewhat smaller deviation from the experimental results. I have certainly experienced such erratic behaviour in my current work. I started off initially, deciding to do a calibration test of the MOPAC software against the experimentally observed values for benzene - a reasonable starting point for any study is to check the accuracy of the model being applied. Taking the whole task of actually trying to figure out which eigenvalue corresponded to the c-c mode of 1485 cm-1 for an unsubstituted ring (in a substituted ring, eg tolualdehyde, this is the ~1600 cm-1 peak), there was no value to my mind, within an acceptable margin (it was pointed out to me, that a value returned within *5%* of the experimental result is acceptable!). It has been suggested to me, that the main reason for the deviation from experiment is attributable (and this I'm told applies also to ab initio Hartree Fock calculations) mainly to the intrinsic over-estimation of the electron- electron repulsion terms in the Hartree-Fock approach (an electron correlation effect?). What I would really appreciate primarily, would be confirmation or rejection of this statement, but idealy, an explanation of the underlying reason, with possible work-arounds, corrections, etc. It certainly puzzles me, that DFT also returns this error, when it treats the electrons in such a different fashion to Hartree-Fock? If replies could be mailed to me directly (Stevensa@chem.port.ac.uk), I'll post a summary of the responses to the net (hopefully, with out too much delay on my part). Thanks in advance to all who contribute. Adrian. -- ----------------------------------------------------------------- | Centre for Molecular Design, Adrian Stevens | c/o SSRIU, | University of Portsmouth, Research Associate | Halpern House, | 1/2 Hampshire Terrace, | Portsmouth, | Hampshire, UK, PO1 2QF. ----------------------------------------------------------------- Voice: +44 (0) 1705 843623 E-mail: Stevensa@chem.port.ac.uk ----------------------------------------------------------------- From ms@chem11.basel.sgi.com Fri Mar 1 17:31:42 1996 Received: from deliverator.sgi.com for ms@chem11.basel.sgi.com by www.ccl.net (8.7.1/950822.1) id RAA26554; Fri, 1 Mar 1996 17:10:48 -0500 (EST) Received: from sgihub.corp.sgi.com by deliverator.sgi.com via ESMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) for <@external-mail-relay.sgi.com:chemistry@www.ccl.net> id OAA07883; Fri, 1 Mar 1996 14:10:05 -0800 Received: from sgba.basel.sgi.com by sgihub.corp.sgi.com via SMTP (950511.SGI.8.6.12.PATCH526/911001.SGI) for <@sgihub.corp.sgi.com:chemistry@www.ccl.net> id OAA01592; Fri, 1 Mar 1996 14:09:48 -0800 Received: from chem11.basel.sgi.com by sgba.basel.sgi.com via SMTP (920330.SGI/911001.SGI) for @sgihub.corp.sgi.com:chemistry@www.ccl.net id AA01320; Sat, 2 Mar 96 01:55:27 +0100 Received: by chem11.basel.sgi.com (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id BAA15636; Sat, 2 Mar 1996 01:54:56 +0100 From: "Michael Schlenkrich" Message-Id: <9603020154.ZM15634@chem11.basel.sgi.com> Date: Sat, 2 Mar 1996 01:54:45 +0100 X-Mailer: Z-Mail (3.2.1 6apr95 MediaMail) To: chemistry@www.ccl.net Subject: Yeast genome analysis on a SGI Supercomputer - demonstration Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii GeneCrunch: See genome analysis on a supercomputer as it happens. Watch the analysis of genome information live on the WWW, March 4-7, 1996. In a joint demonstration project between Silicon Graphics and scientists from the EMBL-Heidelberg/EMBL-EBI the GeneQuiz software system will analyze more than 6000 protein sequences from the genome of yeast (Saccharomyces cerevisiae) on a 64 processor SGI POWER CHALLENGEarray in just a few days. The project will demonstrate large-scale genome sequence analysis on an almost-complete set of yeast genes. The analysis will be repeated as soon as the international collaborative effort of yeast researchers releases to the public the complete genetic blueprint of yeast, scheduled for later this year. The results on the likely biological function of many new genes will be of interest to biological researchers in both academia and industry. The results will be published on two internet Web sites as the analysis progresses, starting March 4th, 1996: http://genecrunch.sgi.com http://genecrunch.sgi.ch In addition to the biological results of the analysis, the sites will also contain information describing the supercomputing and web technology used. GeneQuiz is an automated system for large-scale genome sequence analysis. It aims at adding value to biosequence information by predicting the biological function of the corresponding genes. GeneQuiz accesses up-to-date protein and DNA databases, derives information by sophisticated search and analysis methods, and interprets any findings in terms of biological function using expert rules. It also predicts three-dimensional structures of protein molecules when these can be inferred by homology . The predicted functions are made available in hyperlinked WWW tables and the predicted coordinates of 3D structures in Protein Data Bank format. GeneQuiz is a collaborative effort between the two EMBL institutes and former EMBL scientists at CNB Madrid, MDC Berlin, and SRI Meno Park. The POWER CHALLENGEarray used for this project is located at the Silicon Graphics European Supercomputing Technology Center in Cortaillod, Switzerland. The POWER CHALLENGEarray consists of 4 POWER CHALLENGE nodes each with 16 R8000 Processors linked together with the very fast HIPPI interfaces. Reinhard Schneider and Georg Casari Biological Structures and Biocomputing program EMBL-Heidelberg Chris Sander European Bioinformatics Institute EMBL-EBI -- ********************** PLEASE NOTE OUR NEW ADDRESS***************************** Dr. Michael Schlenkrich European Chemistry Technology Center Silicon Graphics SA Phone: (41) 061 - 716 67 67 Kaegenstrasse 17 Fax: (41) 061 - 716 67 10 CH-4153 Reinach e-mail: ms@basel.sgi.com Switzerland VM: 5-9461