From chemistry-request@server.ccl.net Thu Jan 20 10:52:55 2000 Received: from coch11.chm.tu-dresden.de (mann@coch11.chm.tu-dresden.de [141.30.9.111]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA15537 for ; Thu, 20 Jan 2000 10:52:54 -0500 Received: from localhost (localhost [[UNIX: localhost]]) by coch11.chm.tu-dresden.de (8.9.3/8.9.3) id PAA13611 for chemistry@ccl.net; Thu, 20 Jan 2000 15:50:02 +0100 From: Matthias Mann Reply-To: Matthias.Mann@chemie.tu-dresden.de To: chemistry@ccl.net Subject: Summary: MOPAC97 on AIX or Linux Date: Thu, 20 Jan 2000 15:32:12 +0100 X-Mailer: KMail [version 1.0.17] Content-Type: text/plain MIME-Version: 1.0 Message-Id: <00012015500200.13609@coch11> Content-Transfer-Encoding: 8bit Hi all, some weeks ago I posted the question, if anybody had success in installing the MOPAC97 source on IBM AIX or Linux machines. There seems to be not so much people dealing with this combinations, but I have received this very helpful email: > You should change those: > > MALLOC(NEED) -> MALLOC(%VAL(NEED)) > FREE(P1) -> FREE(%VAL(P1)) > FDATE(IDATE) -> FDATE_(IDATE) > ETIME(CPU) -> ETIME_(CPU) > SLEEP(2) -> SLEEP_(2) > NAMES='????' -> NAMES='XXXX' > > Yutaka TACHIKAWA (yutaka-tachikawa@ma.dic.co.jp) Making this changes in the source results in an working binary on IBM AIX machines. Many thanks ! However, until now I have no success on Linux. The binaries crash with "Memory fault" message. Any suggestion for this case is welcome also in future. Thank you, Matthias -- Dr. Matthias Mann Fachrichtung Chemie der TU Dresden D-01069 Dresden, Mommsenstr. 13 Tel.: +49 (351) 463-4286 / Fax: -7030 Email: Matthias.Mann@chemie.tu-dresden.de From chemistry-request@server.ccl.net Thu Jan 20 11:26:55 2000 Received: from sun.fqspl.com.pl ([212.244.147.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA15703 for ; Thu, 20 Jan 2000 11:26:54 -0500 Received: from victor by sun.fqspl.com.pl (SMI-8.6/SMI-SVR4) id QAA29553; Thu, 20 Jan 2000 16:19:30 +0100 Message-ID: <001801bf6359$afb7ca00$050a0a0a@victor.fqspl-in.com.pl> From: "Victor Anisimov" To: Subject: Re: CCL:Summary: MOPAC97 on AIX or Linux Date: Thu, 20 Jan 2000 16:19:03 +0100 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Matthias Mann wrote: >However, until now I have no success on Linux. The binaries >crash with "Memory fault" message. Any suggestion for this >case is welcome also in future. MOPAC97 is an obsolete MOPAC code that may be a reason why there is no much interest to it on non-Windows platforms. If you use g77 compiler under Linux I would recommend you to change it on something like PGI or Fujitsu fortran compiler. www.tools.fujitsu.com www.pgroup.com Shure it will help. Best regards, Victor. ========================================================================= Victor Anisimov, PhD, Software Researcher - Computational Chemistry FQS Poland, Palac Pugetow, ul. Starowislna 13-15, 31-038 Krakow, Poland Email: victor@fqspl.com.pl Tel.(+48 12) 429 4345 Fax(+48 12) 429 6124 ========================================================================= From chemistry-request@server.ccl.net Thu Jan 20 11:37:46 2000 Received: from mailsrv.rz.fh-merseburg.de (nowak@mailsrv.rz.fh-merseburg.de [149.205.18.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA15788 for ; Thu, 20 Jan 2000 11:37:45 -0500 Received: from localhost (nowak@localhost) by mailsrv.rz.fh-merseburg.de (8.9.3/8.9.1) with ESMTP id QAA25175 for ; Thu, 20 Jan 2000 16:33:22 +0100 (MET) X-Authentication-Warning: mailsrv.rz.fh-merseburg.de: nowak owned process doing -bs Date: Thu, 20 Jan 2000 16:33:22 +0100 (MET) From: Thomas Nowak X-Sender: nowak@mailserv To: chemistry@ccl.net Subject: ionicity of a bond Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I want to study various Nd complexes of the type Nd(L)3-olefin with DFT calculation. I want to characterize the Nd-olefin bond. The main contribution of the bond should be an ionic quadropole interaction. But I am looking for a tool to get a quantity of this ionic part and the covalent part ( donation from olefin pi-bond to the Nd ). I have tried to get the ionic part by an interaction of a point charge with the olefin, but because of the ligands I don't know exactly how big this charge must be. Thanks in advance, Thomas Nowak Martin-Luther Universitaet Halle FB Chemie (Merseburg) IPC 06099 Halle email: nowak@chemie.uni-halle.de From chemistry-request@server.ccl.net Thu Jan 20 05:43:19 2000 Received: from cfalfa.chfi.unipd.it (cfalfa.chfi.unipd.it [147.162.53.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA13706 for ; Thu, 20 Jan 2000 05:43:17 -0500 Received: by cfalfa.chfi.unipd.it; (5.65v3.2/1.1.8.2/02Nov95-0925AM) id AA01645; Thu, 20 Jan 2000 09:48:17 GMT Date: Thu, 20 Jan 2000 09:48:16 +0000 (GMT) From: Stephen Todd To: chemistry@ccl.net Subject: Summary: stories etc... Message-Id: Plese find attached the summary of answers to my question about stories and anecdotes. Thanks alot to everyone who answered, Steve Email: S.Todd@chfi.unipd.it Snailmail: Dr Stephen Todd c/o Gruppo di Chimica Teorica Dipartimento di Chimica Fisica Universita' degli Studi di Padova Via Loredan 2 I-35131 Padova Italy ===================================================================== Thanks to all those who replied to my question concerning stories. I haven't had time to check out all the replies yet but they look useful. Thanks again, Steve My original question was >Hi all, > >I am currently beginning to write some training materials for a >computational chemistry course and I want to "liven" them up a little. >Therefore, I was wondering if anyone knew of a good source of stories, > anecdotes or historical notes that I can drop into my presentations to >give them a real life touch. > >These can either be in books or preferably on the web. ****************************************************************** Well, I have some stories on http://www.ch.ic.ac.uk/local/organic/mod/ But they are more like case studies, than actual stories There are about 15 there, and I will be adding a few more shortly. In turn, if you have any good stories, I would be delighted to point my students at them! Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0)20 7594 5804 (Fax) Dept. Chemistry, Imperial College, London, SW7 2AY, UK. http://www.ch.ic.ac.uk/rzepa/ ******************************************************************* Well, have a look at Levine, "Quantum Chemistry" There is a story about Hartree and his Father and some other funny remarks -- I think. Bye, Robert ----------------------------------------------- Robert P. Krawczyk Lehrstuhl fuer Theoretische Chemie TU Muenchen Lichtenbergstr. 4 85747 Garching Tel.: +49 89 289 - 13618 Fax.: +49 89 289 - 13622 e-mail: robert.krawczyk@gmx.de ----------------------------------------------- ******************************************************************** You should definitely take a look at R.L. Weber, "A random walk in science" and "More random walks in science". They are slightly old, and some of the stories are from other areas of physics. But some of the stories should be perfect. And the rest is well worth the price, simply for your own joy! A short example. Once in Russia, in a physics exam, the professor wrote the equation E=hv and asked the student: 'What is v?' 'Planck's constant.' 'And h?' 'The length of the plank.' The books are still available from IOP, or check you library. Regards, Finn Drablos finn.drablos@unimed.sintef.no SINTEF UNIMED MR Center http://www.sintef.no/ N-7465 TRONDHEIM phone +47 73 59 05 31 NORWAY fax +47 73 86 77 08 ******************************************************************** In response to your CCL posting, you might take a look at one of the NetSci articles on the mergers and acquisitions that have taken place in computational chemistry. The article is only current through '98, but gives a lot of historical data on the market. The address is: http://www.netsci.org/Science/Compchem/feature17.html Regards, Merry Ambos <==============================================================> Allen Richon, Ph.D. & Merry Ambos e-mail: netsci@awod.com Molecular Solutions/Network Science 843-886-8775, 843-886-5924 (FAX) URL: http://www.netsci.org ************************************************************************ I would be very interested in these stories also, please forward any responses you get. I know Dudley Herschbach at Harvard has an interesting story about how Otto Hahn and Walter Gerlach discovered electron spin. This may not be appropriate for your course, however. Dave ************************************************************************* You will find some stories and histories in Reviews in Computational Chemistry. Are you familiar with this book series? It contains tutorials, plus some interesting "extras" like histories of comp chem in various nations, including the US, UK, and France. Also the prefaces in some volumes have commentaries and anecdotes. Good luck, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu ************************************************************************** For anecdotes, etc, see book: M. J. S. Dewar "A Semiempirical Life", ACS Profiles and Pathways series. Best Wishes, E. Lewars ===== ************************************************************************** I am teaching a comp chem course this winter, and am just now updating my stuff. http://chem.csusb.edu/~kcousins/chem500b/chem500b.html Mike Colvin has some historical stuff in his intro; http://gutenberg.llnl.gov/~colvin/ (follow "quantum chemistry notes" then "introduction" The interview with Pople is informative http://www.rdmag.com/features/0699rd/06pople.htm And the NPR interview with Kollman might be useful: http://www.AMBER.ucsf.edu/ I assemble stuff as I go along, so if you wish to share other sources, I would appreciate it! Kimberley Cousins Associate Professor of Chemistry California State University, San Bernardino 5500 University Parkway San Bernardino, CA 92407 (909)880-5391 kcousins@csusb.edu http://chem.csusb.edu/~kcousins ************************************************************************** You can always write about the story of the methylene radical (CH2) whose structure (linear or bent?) and Te triplet-singlet energy gap was a matter of controversy for many years between theoreticians and experimentalists. I remember reading the story in an old H.F.Schaeffer book ("The electronic structure of atoms and molecules"), but I am sure it can be found in many modern textbooks. Some other interesting molecules are (CH5)+ and Cr2. There are two fairly recent papers (one of Schaeffer and von Schleyer and one of Kutzelnigg) which have some "funny" titles: Shaeffer and von Schleyer wrote: "CH5+: The never-ending story or the final word?" and after 4 years Kutzelnigg wrote: "CH5+: The story goes on....." Recently there was published in "Science" a paper with its IR spectrum for the first time. Cr2 is a legendary "black sheep" molecule of the qchem community. There is a review article in the 1987 Adv.Chem.Phys. volumes regarding the trouble dealing with this diatomic molecule. I believe that the story on these molecules will keep the students' attention during a presentation. If you want tell me, I have the references somewhere. If you get any other useful replies, I would be very much interested. Perhaps you could summarize for the group. Regards, John Ioannis S.K. Kerkines, MSc PhD Candidate in Physical Chemistry Department of Chemistry University of Athens, Greece Panepistimiopolis Zografou, 157 10 Tel: +301-727-4569, Fax: +301-723-3219 Email: jkerk@arnold.chem.uoa.gr From chemistry-request@server.ccl.net Thu Jan 20 20:08:22 2000 Received: from gate-sl1.mdli.com (ns2.mdli.com [208.200.221.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA17925 for ; Thu, 20 Jan 2000 20:08:22 -0500 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id QAA11931 for ; Thu, 20 Jan 2000 16:03:40 -0800 (PST) Received: from puffin.mdli.com(191.254.19.10) by gate-sl1.mdli.com via smap (V2.1) id xma011929; Thu, 20 Jan 00 16:03:37 -0800 Received: from shepherd.mdli.com by puffin.mdli.com (8.8.5/BCH1.0) id QAA16123; Thu, 20 Jan 2000 16:03:37 -0800 (PST) Received: by shepherd.mdli.com with Internet Mail Service (5.5.2650.21) id ; Thu, 20 Jan 2000 16:03:36 -0800 Message-ID: <8E13FBBA26A9DA119ED400A0C9AB2CE502F33B4E@shepherd.mdli.com> From: Guenter Grethe To: "'chemistry@ccl.net'" Cc: "'Guenter Grethe'" Subject: Call for Papers, Pacifichem2000 (Symposium #175, Use of Chemical Information in Organic Synthesis) Date: Thu, 20 Jan 2000 16:03:35 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" The following Call for Papers has been listed on several servers, I apologize for any duplication. CALL FOR PAPERS The 2000 International Chemical Congress of Pacific Basin Societies will take place in Honolulu, Hawaii, from December 14 - 19, 2000. The congress is cosponsored by the American Chemical Society , the Chemical Society of Japan, the Canadian Society for Chemistry, the New Zealand Institute of Chemistry and the Royal Australian Chemical Institute. Chemical Societies in the countries that border the Pacific Ocean will be Official Participating Organizations. Overall, 6,000 reports on current research and development will be presented in 179 symposia and in oral and poster general sessions in 10 topical areas. If previous congresses are any indication, this year's program should be highly interesting and attendance should be very large. You are invited to submit an abstract for a paper or poster to be considered for presentation at symposium #175 "Use of Chemical Information in Organic Synthesis", co-organized by Prof. Kimito Funatsu, Toyohashi University of Technology, Japan, Dr. David Winkler, CSRIO Division of Molecular Science, Australia, and Dr. Guenter Grethe, MDL Information Systems, Inc., USA. Abstracts of approximately 150 words must be submitted to the Congress Secretariat at ACS by April 3, 2000, for paper versions, or April 14 electronically. The congress abstract form is available for electronic retrieval and submission from the Pacifichem 2000 web site at http://www.acs.org/meetings/pacific2000 Paper forms can be obtained by contacting the Congress Secretariat at Pacifichem Congress Secretariat American Chemical Society 1155-16th S., N.W. Washington, DC 20036, USA e-mail: pacifichem@acs.org To encourage attendance at the congress by young chemistry professionals >from developing countries that border the Pacific Ocean, the sponsoring societies of Pacifichem 2000 are making available up to 40 grants of $1,000 (U.S.) plus complimentary registration to assist with travel and attendance costs. Details about the scholarship are to be found on the congress web site. Why is participation in this symposium essential for synthetic chemists and information specialists? During the last two decades various programs and databases, large comprehensive and smaller thematic ones, covering a broad range of synthetic chemistry, have been developed to assist synthetic chemists with their tasks. Additionally, these databases have the potential to serve as a rich source for extracting data into knowledge bases for reaction planning and reaction prediction programs. Speakers at the symposium will address issues important to the various areas of reaction information management, such as synthesis planning, reaction retrieval and prediction, reagent selection, integrated web-based information, information needs in combinatorial chemistry and other related topics. Emphasis of the symposium will be on the integration of various programs and data from multiple sources to simulate the working habits of synthetic chemists in gathering necessary information, thereby generating an environment in which they will use electronic tools comfortably and efficiently - the synthetic workbench of the future. Papers describing the use of the various tools and information sources available to synthetic chemists and information specialists alike are solicited. Presentations for contributed papers will be restricted to 25 minutes, including 5 minutes for Q & A. Following is a description of some of the topics we hope to cover in the symposium: Reaction retrieval Retrieval of relevant information from existing databases to plan the synthesis of discrete compounds or libraries and to search for applicable methodologies and efficient functional group transformations is the most frequently used and therefore the most important part of any reaction information system. Presentations on available systems and associated applications to facilitate their use, the contents of available reaction databases, efficient management of large datasets, such as classification, post-search tools to manage large hitlists and other retrieval related topics are invited. Reaction prediction Reaction prediction plays an important role in synthesis, particularly in process development and combinatorial chemistry. Presentations addressing the use of available programs and the generation of knowledge bases from reaction databases to assist in the validation of reaction proposals in the planning process will be part of the symposium. Other topics for discussion are applications of methodologies to use physico-chemical parameters in predicting the outcome of reactions and the importance of functional group perception and their dependency on reaction conditions as criteria for reagent selection and automated synthesis. Synthesis planning Synthesis planning is experiencing rejuvenation, largely due to developments in combinatorial chemistry. Emphasis of programs has shifted >from planning syntheses of complex molecules to generating efficient and economic preparations of libraries of compounds, frequently involving the use of solid-phase methodology. We invite speakers to discuss progress made in this important area as well as talk about validation procedures used in the planning process and methods to select viable starting materials. Combinatorial chemistry Combinatorial synthesis continues to have an immense impact on the developments in managing chemical information. Finding the most relevant methodologies, planning a library, and selecting the most viable reagents and solid supports are some of the important tasks to be carried out by the synthetic chemist. Presentations on these topics as well as discussions about the utilization of available information for automated synthesis and effective data management are desirable. Electronic workbench The future and success of using electronic information in synthesis is heavily dependent on the smooth integration of the required tools in an electronic workbench through friendly graphical interfaces and smooth operations. To guarantee good results, the workbench must provide easy access to large amounts of data in diversified databases - online and inhouse - and in electronic versions of the primary and secondary literature. The electronic labjournal must serve both as an archiving and registration tool. We are soliciting papers describing the use of any of these tools, particularly web-based applications. If you have any questions please contact any of the organizers at the addresses shown below: Dr. Guenter Grethe MDL Information Systems, Inc. 14600 Catalina Street San Leandro, CA 94577 (+1) 510-357-2222, ext. 1430 (voice) (+1) 510-614-3616 (fax) guenter@mdli.com Prof. Kimito Funatsu Department of Knowledge-Based Information Engineering Toyohashi University of Technology Tempaku, Toyohashi 441-8580 Japan (+81) 532-44-6879 (voice) (+81) 532-47-9315 (fax) funatsu@tutkie.tut.ac.jp Dr. David A. Winkler CSIRO Molecular Science Private Bag, Clayton South MDC 3169 Australia (+61) 3-9545-2477 (voice) (+61) 3-9545-2446 (fax) dave.winkler@mo9lsci.csiro.au