From chemistry-request@server.ccl.net Mon Mar 31 06:40:16 2003 Received: from netra.ksu.edu.sa ([212.138.39.67]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2VBeDs02545 for ; Mon, 31 Mar 2003 06:40:14 -0500 Received: from sun1.ksu.edu.sa (localhost [127.0.0.1]) by netra.ksu.edu.sa (8.11.6+Sun/8.11.6) with ESMTP id h347cTB17499 for ; Mon, 31 Mar 2003 14:38:30 -1700 (Mideast/Riyadh) Received: from localhost (najallal@localhost) by sun1.ksu.edu.sa (8.9.0/8.7.3) with SMTP id OAA27344 for ; Mon, 31 Mar 2003 14:39:16 -0300 (GMT) Date: Mon, 31 Mar 2003 14:39:16 -0300 (GMT) From: "Nada A Al-Jallal Sci. College Malaz" X-Sender: najallal@sun1 To: chemistry@ccl.net Subject: conformational search of cation metal complexes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCl members: I did conformationl search on a cyclic molecule using the MM3 method which went ok. Then I wanted to do conformational search on the alkali metal complexes with this cyclic molecule but I found the the program doing the conformational search, CAChe, places the alkali metal cation at about 5 angstrom from the molecule ring, although experimentlly and ab initio calculations predicts only 2-3 angstrom. My question is just to make sure the the problem is that the MM3 method is not able to handle cation metal complexes. Any suggestions to go around this problem, I mean doing conformational search of cation metal complexes, is most appreciated. Best regards, Nada Al-Jallal From chemistry-request@server.ccl.net Mon Mar 31 09:49:06 2003 Received: from anor.ics.muni.cz ([147.251.4.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2VEn5s12225 for ; Mon, 31 Mar 2003 09:49:05 -0500 Received: from bilbo.chemi.muni.cz (bilbo.chemi.muni.cz [147.251.28.2]) by anor.ics.muni.cz (8.12.1/8.12.1) with ESMTP id h2VEn0hT005337 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NO) for ; Mon, 31 Mar 2003 16:49:00 +0200 Received: from pegas (pegas.chemi.muni.cz [147.251.28.96]) by bilbo.chemi.muni.cz (8.11.6/8.8.5) with SMTP id h2VEn0J11107 for ; Mon, 31 Mar 2003 16:49:00 +0200 (MEST) Message-ID: <004a01c2f795$9c9ce170$601cfb93@chemi.muni.cz> From: "TRITON" To: Subject: New Version of TRITON 3.0 Released Date: Mon, 31 Mar 2003 16:55:46 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 X-Muni-Virus-Test: Clean Dear CCLers: We are pleased to announce the official release of new 3.0 version of program TRITON. Program TRITON 3.0 is graphic software package for: - in silico construction of protein mutants by homology modelling using the external program MODELLER - modelling of enzymatic reactions using semi-empirical quantum-mechanic method of external program MOPAC - analysis of essential electrostatic interactions between enzyme amino acids and substrate using results from previous calculations. TRITON 3.0 provides integrated graphic interface and tools for: - preparation of the input data files - automatic running calculations and their monitoring - visualization and graphical analysis of the output data. Program TRITON 3.0 is being developed in the National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic and is provided free of charge to academic users. Current version is available for IRIX, Linux or NetBSD platforms. Program TRITON 3.0 is suitable tool not only for molecular biologists and biochemists, non-specialists in computer modeling, but it can be also found as interesting and useful tool for computational chemists. For more information concerning this program and for download of the program please visit TRITON 3.0 official web site at http://ncbr.chemi.muni.cz/triton/triton.html. New in version 3.0 http://ncbr.chemi.muni.cz/triton/triton.html#newinversion30 TRITON Development Team From chemistry-request@server.ccl.net Mon Mar 31 09:28:05 2003 Received: from web20708.mail.yahoo.com ([216.136.226.181]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h2VES4s11055 for ; Mon, 31 Mar 2003 09:28:05 -0500 Message-ID: <20030331142804.76499.qmail@web20708.mail.yahoo.com> Received: from [62.90.24.137] by web20708.mail.yahoo.com via HTTP; Mon, 31 Mar 2003 06:28:04 PST Date: Mon, 31 Mar 2003 06:28:04 -0800 (PST) From: sawsan salameh Subject: just a question To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-880345395-1049120884=:73921" --0-880345395-1049120884=:73921 Content-Type: text/plain; charset=us-ascii hello Sir how r u am a Ms.c student working on hyperchem program to study a theoretical characteristics, the compound which work on affected by a tempreture so it break to form another isomer how i could use this program to study the effect of tempreture on my compound please help me thanx sawsan --------------------------------- Do you Yahoo!? Yahoo! Platinum - Watch CBS' NCAA March Madness, live on your desktop! --0-880345395-1049120884=:73921 Content-Type: text/html; charset=us-ascii

hello Sir

how r u

am a Ms.c student working on hyperchem program to study a theoretical characteristics, the compound which  work on affected by a tempreture so it break to form another isomer how i could use this program to study the effect of tempreture on my compound

please help me

thanx

sawsan


Do you Yahoo!?
Yahoo! Platinum - Watch CBS' NCAA March Madness, live on your desktop! --0-880345395-1049120884=:73921-- From chemistry-request@server.ccl.net Mon Mar 31 04:31:15 2003 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2V9VEs31782 for ; Mon, 31 Mar 2003 04:31:14 -0500 Received: from eeb04.cup.uni-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP for CHEMISTRY@ccl.net; Mon, 31 Mar 2003 11:30:53 +0200 Received: from localhost by eeb04.cup.uni-muenchen.de (8.8.8/1.1.22.3/02Jul99-1017PM) id LAA0000024207; Mon, 31 Mar 2003 11:30:52 +0200 (MET DST) Date: Mon, 31 Mar 2003 11:30:52 +0200 (MET DST) From: Stefan Seidler To: Subject: Re: Calculation of chemical reactivity Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > I was asked to investigate the relative reactivities of various aniline > derivatives in the following reaction: > > Ph-NH2 -> Ph-NHOH -> Ph-NO > > where Ph are differently substituted Phenyl or Azaphenyl (Pyridine, Pyrimidine...) rings. > The reactivity of cmpds in redox reactions could be estimated by thermodynamic considerations: deltaG = nF(Udon - Uacc) U: redox potential For sure the oxidative reactions of organic cmpds include complex reaction mechanisms, but the most important step in the mechanism of the oxidation of aromatic amines is actually the electron transfer itself (no H transfer, no O addition; see german "Organikum" D.6). The redox potential is directly related to the energies of the frontier orbitals: a substrate should be more easy oxidizeable the higher the energy of the HOMO. Therefore the calculation of the HOMO energies might be useful for estimating the reactivity and ordering your series. Additional information regarding reactivity could be found in the bibliographies of "synthesis planning tools" like EROS (Gasteiger) and CAMEO (Jorgensen). Quantitative Prediction of Chemical Reactivity: http://www2.chemie.uni-erlangen.de/publications/publ_topics/publ_topics-10.html Regards, Stefan --- stefan.seidler AT cup.uni-muenchen.de From jkl@ccl.net Mon Mar 31 06:02:09 2003 -0500 Date: Mon, 31 Mar 2003 13:03:57 +0200 From: Peter Butler Subject: Book Announcement: An Introduction to Chemoinformatics To: chemistry@ccl.net Message-id: <6DFAA8CF01F3E243BE4D137CBF7E4F4F043F93E5@id192.wkap.nl> An Introduction to Chemoinformatics Co-authored by Andrew R. Leach & Valerie J. Gillet Dear Colleagues, We are pleased to announce this forthcoming book title. Please find below some brief details as well as an abbreviated Table of Contents. Please contact me if you require further information. Kind regards, Peter Butler Publishing Manager BioMedical Unit Kluwer Academic Publishers E-mail: peter.butler@wkap.nl =================================================================== Chemoinformatics is emerging as a key tool for managing and analysing the vast quantitites of data that are generated by techniques such as combinatorial chemistry and high-throughput screening. Chemoinformatics techniques provide the means to convert such data into information and facts and thence into knowledge and rules. Chemoinformatics also provides a vital link between the world of real, existing compounds and the immense virtual or in silico world of molecules that could be made. Chemoinformatics draws upon techniques from many disciplines including computer science, mathematics, graphics and visualisation and computational chemistry to tackle these problems. The text aims to provide an introduction to the major techniques of chemoinformatics. The first part of the book deals with the representation of 2D and 3D molecular structures, the calculation of molecular descriptors and the construction of mathematical models. The second part describes other important topics including molecular similarity and diversity, the analysis of large data sets, virtual screening, and library design. The book is aimed at graduate students, final-year undergraduates, and professional scientists who wish to learn more about the subject. No prior knowledge is assumed other than a familiarity with chemistry and some basic mathematical concepts. Key features include: * clearly written, assuming little prior knowledge * major concepts are accompanied by simple illustrative examples * supplemented with case studies from the literature * extensive list of references and suggestions for further reading * includes up-to-date methods Table of Contents 1. Representation and manipulation of 2D molecular structures 2. Representation and manipulation of 3D molecular structures 3. Molecular descriptors 4. Computational models 5. Similarity methods 6. Selecting diverse sets of compounds 7. Analysis of high-throughput screening data 8. Virtual screening 9. Combinatorial chemistry and library design Approximately 250 pages From chemistry-request@server.ccl.net Mon Mar 31 11:27:53 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2VGRrC17237 for ; Mon, 31 Mar 2003 11:27:53 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h2VGRpt06318 for ; Mon, 31 Mar 2003 11:27:51 -0500 (EST) Date: Mon, 31 Mar 2003 11:27:51 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net Subject: Report from the ACS in New Orleans (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Fri, 28 Mar 2003 13:02:57 +0000 From: "Rzepa, Henry" To: chemweb@ic.ac.uk Subject: Report from the ACS in New Orleans Its been a few years since I did one of these reports from an ACS meeting, but one item in particular caught my (and a lot of other ) eyes. CAChe were displaying LCD panel monitors which display true 3D images WITHOUT any need for glasses. The technology apparently comes in four flavours, each vying for market, which is a good omen for costs, which are expected to come spiraling down over the next 12 months. The largest display is a 40" (@$17,000), a 20" (@ around $8000) and most interestingly, a laptop to be released later this year. The effects were remarkable, although the depth of stereo vision is probably not (yet) as impressive as dedicated Crystaleyes systems Currently, it does need software drivers (openGL) and so specific software must be enabled. The CAChe software is so, and I gather a Powerpoint enabled 3D display is on the cards; I argued for enabling the Weh browser, perhaps Mozilla/Netscape will do it? >From what we saw, and with the predictions, it does seem that any serious molecular modeller or anyone interested in the 3D properties of molecules will be buying themselves these 3D LCD panels routinely in a years time or so! Apparently, a demonstration might be on the cards at Heathrow Airport on April 24. Anyone who is seriously interested in attending should contact Magda Karabon for free registration at + 48 12 429 43 45 or ccs@fqspl.com.pl -- Henry Rzepa. +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk) From chemistry-request@server.ccl.net Mon Mar 31 11:28:23 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2VGSNC17274 for ; Mon, 31 Mar 2003 11:28:23 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h2VGSNt06339 for ; Mon, 31 Mar 2003 11:28:23 -0500 (EST) Date: Mon, 31 Mar 2003 11:28:23 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net Subject: Report from the ACS in New Orleans. Part 2 (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Fri, 28 Mar 2003 14:19:18 +0000 From: "Rzepa, Henry" To: chemweb@ic.ac.uk Subject: Report from the ACS in New Orleans. Part 2 On more directly Web related matters, two sessions at the ACS had relevance, one on XML in Chemistry, and another on "The Scientific Article in the digital World". As it happens these CINF sessions also had counterparts in the COMP sections (indicating again the absurdity of trying to separation of modelling from informatics). The XML session included presentations from Peter Murray-Rust and myself (mine at http://www.ch.ic.ac.uk/rzepa/talks/acs03/ ) on the family of CML languages and the "road plan" for them. Apart from (passionate!) pleas for opendata, opensource, openservices I noted "beyond the article" developments and "beyond the browser" alerting services based on RDF-based metadata. Elsewhere, ThermoML was presented as a physicochemical markup XML language and in the COMP division Jesus Castagnetto talked about the metalloprotein database (MDB) and how XML is being used there. The talk should appear at http://metallo.scripps.edu/talks/ in due course. I was very impressed not only with what these guys are doing but the incredible momentum being generated in bioinformatics compared to chemistry. This latter talk was attended by perhaps 20 people; at a bioinformatics conference I feel 200+ would easily have been there. Its a mystery why chemistry continues to be dominated by a small number of (mostly commercial) providers who "move at the speed the market will bear", which in the case of chemistry continues to be defined as "slowly". The Biogrid/Bio-ontology movements continue to pave the way and put the chemistry community in this area to shame! Regarding the future of the "article", Steve Bachrach made an interesting point that finally an ACS journal has appeared with "supplemental information" comprising Web-activated 3D coordinates (eg. chime) some 9 years after the technology was demonstrated. The RSC by the way did this 8 years ago, in 1995! What is apparent is that "guided data capture" at the authoring point is coming, and that writing an article, or at very least the supplemental information for such, will benefit from an increasing variety of publisher and opensource tools. for example, with M$ Word V 11 coming out soon and being fully XML compliant, and with tools such as OpenOffice also so, along with opensource editors supporting XML and CML, I feel there are grounds for optimism that the "article" and what lies beyond it (see above) is now reinventing itself apace. Can I indulge in just one piece of "real chemistry". Paul Schleyer appears to have resolved one interesting and controversial aspect of aromaticity, ie that aromatic compounds show no bond localisation for annulenes up to around [22]. The X-ray structure of eg [18] annulene indeed shows the bonds to be the same length, to some a fundamental of aromaticity. well, Paul presented very convincing evidence that the structure of [18] annulene is wrong, it being effectively twinned with two superimposed alternating forms. Paul estimates the bond localisation starts at [14] annulene. -- Henry Rzepa. +44 (0870) 132 3747 (eFax) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk) From chemistry-request@server.ccl.net Mon Mar 31 11:40:10 2003 Received: from mail.interware.hu ([195.70.32.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2VGe7C17878 for ; Mon, 31 Mar 2003 11:40:07 -0500 Received: from caracas-0505.adsl.interware.hu ([213.178.101.249] helo=cthulhu) by mail.interware.hu with smtp (Exim 3.33 #1 (Debian)) id 1902KN-0004HG-00 for ; Mon, 31 Mar 2003 18:40:07 +0200 Message-ID: <002601c2f7ac$d1502000$0200a8c0@cthulhu> From: "Tamas E. Gunda" To: Subject: Mol2Mol 5.0 Date: Mon, 31 Mar 2003 18:41:52 +0100 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 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Dear CCL Members, The new 5.0 version of the molecule file conversion, manipulation and utility program Mol2Mol is now available > from http://web.interware.hu/frenzy/mol2mol as trial or shareware version. The current version of Mol2Mol recognizes, and interconverts about 40 different file formats (including subtypes). It can slice multiple structural files to single ones (such as PDB models or MDL SD files to single ones) and vice versa in several variations. Support for four PDB subformats. (with 1-2-3 bonds). Some new features: User defined totally free format (Cartesian, Z-matrix or polar; read & write) Tinker format (read); MDL rxn and rdf (read); Renumbering of molecules by several options; Assigning of H-bonds; Several new rotation and translation methods (turn selected atoms into plane, selected bond parallel with axis etc.); Calculation of the bounding box of the molecule; Selection/coloring of peptides by helix/sheet/turn in PDB files and POV-ray output; Adding of hydrogens: orientations of the water molecules are now randomized; and many more. It contains a simple graphical display module to inspect the currently loaded molecule. It possesses chemical intelligence for recognizing detailed atom types, hybridization and chemical environments, which is necessary for converting simpler formats (like X-ray crystallographic files) to more advanced ones, or when hydrogen atoms are automatically to be added. Calculation of pyramidalities, ring puckerings, checking for mistakes in protein backbones. Mol2Mol is a very handy set of tools for everybody dealing with molecular modelling. It is impossible to write here all of the features of Mol2Mol, but have a look at its home page: http://web.interware.hu/frenzy/mol2mol POV-Ray fans may also have a look at above or: http://dragon.klte.hu/~gundat/povraya.htm The program is available as 30 days unrestricted trial version or as shareware version. Dr. Tamas E. Gunda tamasgunda@tigris.klte.hu From chemistry-request@server.ccl.net Mon Mar 31 12:11:51 2003 Received: from apex.ibpc.fr ([193.49.234.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2VHBpC19158 for ; Mon, 31 Mar 2003 12:11:51 -0500 Received: from baaden.galaxy.ibpc.fr (baaden@serv-1B2A.galaxy.ibpc.fr [193.49.27.42]) by apex.ibpc.fr (8.9.3/jtpda-5.3.3) with ESMTP id TAA08949 for ; Mon, 31 Mar 2003 19:11:50 +0200 (MET DST) Message-Id: <200303311711.TAA08949@apex.ibpc.fr> X-Mailer: exmh version 2.5 07/13/2001 (debian 2.5-1) with nmh-1.0.4+dev To: chemistry@ccl.net Subject: (chemical) markup languages for writing scientific documents (RE: ACS report part II) X-image-url: http://crypt.u-strasbg.fr/marc/m-baaden.gif X-url: X-Face: -Nz&SN]%I8g9WFR#/!fe9se!_G_OndNloj@t+6jrGsoZ"z)?an0n P!Nls~*o?u7fy:]1N|^^(KX*uE>Nk{bHaCJ)(hXF~E#5)j.k0n4hgfIzpmn,[VY'\7X:;VOZ\CItIq G!2f8,k2`VLrkXQ:<.3LxEQ'E-;d:A)V# Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Mon, 31 Mar 2003 19:11:50 +0200 From: Marc Baaden Dear colleagues, jkl@ccl.net said: >> On more directly Web related matters, two sessions at the ACS had >> relevance, one on XML in Chemistry, and another on "The Scientific >> Article in the digital World". .. not immediately directly related, but still of relevance (I hope): what kind of authoring environment would be best adapted to the task of writing scientific papers, reports, abstracts etc. ? I have recently been playing around with docbook and refdb (both come in SGML and XML flavours), and was amazed how far one could get with those already. Especially for *computational* chemistry, docbook has all the nice tags for inclusion of code, screenshots, etc. But concerning the more chemical and or biological side, I am not sure. So I wonder: is SGML (or XML) the way forward ? And is there a more adapted DTD (and stylesheets etc.) for the (bio)-chemical (computational) field ? .. hoping to stimulate an interesting discussion .. regards, Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden@smplinux.de - http://www.marc-baaden.de FAX: +49 697912 39550 - Tel: +33 15841 5176 ou +33 609 843217 From chemistry-request@server.ccl.net Mon Mar 31 13:44:46 2003 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2VIikC22189 for ; Mon, 31 Mar 2003 13:44:46 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #13) id 1904H0-00085N-00 for chemistry@ccl.net; Mon, 31 Mar 2003 20:44:46 +0200 Message-ID: <3E888C9C.8070202@mpi-bpc.mpg.de> Date: Mon, 31 Mar 2003 20:44:44 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en, ro MIME-Version: 1.0 To: CCL Subject: plotting hbond occupancies during an MD trajectory Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear all: I have a data file that looks like this: 1 1 1 2 2 1 3 3 1 4 4 0 5 5 0 6 6 1 7 7 0 ..... I would like to represent as a diogonal (where x is the first column and y is the second) colored in two different colors depending if the third column is 1 or 0. Does anyone have any idea about a good freeware that can do that? Best wishes, Vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@server.ccl.net Mon Mar 31 14:41:44 2003 Received: from celebris04.cetem.gov.br ([200.20.105.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2VJfhC24283 for ; Mon, 31 Mar 2003 14:41:44 -0500 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Mon, 31 Mar 2003 16:48:22 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56AED@correio.cetem.gov.br> From: Ian Hovell To: "'chemistry@ccl.net'" Subject: Problems with convergence Date: Mon, 31 Mar 2003 16:48:22 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) 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 h2VJfiC24284 Dear CCLers, I am having problems with the convergence of the molecule below. I have tried, without sucess, all of the options found in the reference manual for SCF calculations. I feel I must be doing something wrong. Any help would be extremely welcome since I'm rapidly losing my hair over this problem. TIA Ian P.S. Will summarise answers if there is interest. %mem=6MW %nproc=1 %chk=solutes.chk # opt rhf/3-21g* scrf=(scipcm,dielectric=35.6) geom=connectivity Solvated Solutes : quinolinol 0 1 C C 1 B1 C 2 B2 1 A1 C 3 B3 2 A2 1 D1 C 4 B4 3 A3 2 D2 N 5 B5 4 A4 3 D3 C 6 B6 5 A5 4 D4 C 7 B7 6 A6 5 D5 C 8 B8 7 A7 6 D6 C 5 B9 4 A8 3 D7 O 8 B10 7 A9 6 D8 H 3 B11 2 A10 1 D9 H 4 B12 3 A11 2 D10 H 1 B13 2 A12 3 D11 H 2 B14 1 A13 10 D12 H 7 B15 6 A14 5 D13 H 9 B16 8 A15 7 D14 H 11 B17 8 A16 7 D15 B1 1.356319 B2 1.417031 B3 1.355411 B4 1.413911 B5 1.360091 B6 1.297613 B7 1.412651 B8 1.355149 B9 1.404556 B10 1.373424 B11 1.071439 B12 1.070129 B13 1.072393 B14 1.071859 B15 1.073740 B16 1.070263 B17 0.964342 A1 120.664144 A2 120.217668 A3 120.288571 A4 119.422755 A5 119.925604 A6 122.763646 A7 118.806597 A8 119.630176 A9 121.864491 A10 119.329860 A11 122.198637 A12 120.846283 A13 120.120605 A14 117.591735 A15 119.665739 A16 113.351613 D1 -0.003573 D2 0.005337 D3 179.993576 D4 -179.986182 D5 0.002305 D6 -0.011149 D7 -0.000978 D8 179.992503 D9 179.996463 D10 -179.998392 D11 -179.998655 D12 179.995120 D13 -179.994506 D14 -179.996324 D15 -0.165861 1 2 2.0 10 1.5 14 1.0 2 3 1.5 15 1.0 3 4 2.0 12 1.0 4 5 1.5 13 1.0 5 6 1.5 10 1.5 6 7 2.0 7 8 1.5 16 1.0 8 9 2.0 11 1.0 9 10 1.5 17 1.0 10 11 18 1.0 12 13 14 15 16 17 18 Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Ciência e da Tecnologia- MCT Avenida Ipê, No 900 - Cidade Universitaria Ilha do Fundão Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell@cetem.gov.br From chemistry-request@server.ccl.net Mon Mar 31 21:16:14 2003 Received: from puck.reed.edu ([134.10.2.8]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h312GEC01146 for ; Mon, 31 Mar 2003 21:16:14 -0500 Received: (qmail 20686 invoked from network); 1 Apr 2003 02:12:32 -0000 Received: from rosencrantz.reed.edu (134.10.2.31) by puck.reed.edu with SMTP; 1 Apr 2003 02:12:32 -0000 Message-id: <11647331@rosencrantz.reed.edu> Date: 31 Mar 2003 18:16:14 PST From: Alan.Shusterman@directory.reed.edu (Alan Shusterman) Subject: M-NO2 frequencies To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/enriched Content-Disposition: inline I'm trying to distinguish a Co-NO2 complex from a Co-O-NO complex using mid-IR. The complexes are low-spin, closed-shell, and I'm wondering what theoretical model might give reasonable predictions for the ligand's vibrational frequencies. Any experience with this problem or pointers to published articles would be appreciated. Thanks, -Alan ==== Alan Shusterman Department of Chemistry Reed College 3203 S.E. Woodstock Blvd. Portland, OR 97202 503-517-7699 From chemistry-request@server.ccl.net Mon Mar 31 16:22:24 2003 Received: from web20513.mail.yahoo.com ([216.136.174.44]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h2VLMNC27122 for ; Mon, 31 Mar 2003 16:22:23 -0500 Message-ID: <20030331212223.50677.qmail@web20513.mail.yahoo.com> Received: from [129.109.73.75] by web20513.mail.yahoo.com via HTTP; Mon, 31 Mar 2003 13:22:23 PST Date: Mon, 31 Mar 2003 13:22:23 -0800 (PST) From: Robert Smith Subject: IEJMD special issue dedicated to Professor Nenad Trinajstic To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Call for Papers: IEJMD special issue dedicated to Professor Nenad Trinajstic on the occasion of the 65th birtday Guest Editors: Professor Douglas J. Klein (Galveston, Texas) Dr Sonja Nikolic (Zagreb, Croatia) IEJMD - the Internet Electronic Journal of Molecular Design http://www.biochempress.com Email: iejmd@yahoo.com You are cordially invited to contribute a paper to the special issue of IEJMD, http://www.biochempress.com, dedicated to Professor Nenad Trinajstic. The topic of the paper can be any original contribution regarding computer-assisted molecular design applications in chemistry, biochemistry, biology, chemical and pharmaceutical industry. If you decide to contribute a paper, please note these important deadlines: Title of manuscript and authors submitted by Email to iejmd@yahoo.com : May 30, 2003 Submission: manuscript submitted by Email to iejmd@yahoo.com : July 30, 2003 If you want to contribute a paper, but need more time for the submission, send an E-mail with an estimated time of submission. If you have any questions regarding this special issue, please contact me by E-mail at: iejmd@yahoo.com To obtain a Word file with Instructions for Authors send an Email to iejmd@yahoo.com All papers published in IEJMD can be downloaded for free from: http://www.biochempress.com Best regards, Robert Smith __________________________________________________ Do you Yahoo!? Yahoo! Platinum - Watch CBS' NCAA March Madness, live on your desktop! http://platinum.yahoo.com