From chemistry-request@ccl.net Sat Aug 28 12:13:54 2004 Received: from web52007.mail.yahoo.com (web52007.mail.yahoo.com [206.190.39.63]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i7SHDr3G010220 for ; Sat, 28 Aug 2004 12:13:53 -0500 Message-ID: <20040828172250.63398.qmail..at..web52007.mail.yahoo.com> Received: from [128.112.141.35] by web52007.mail.yahoo.com via HTTP; Sat, 28 Aug 2004 10:22:50 PDT Date: Sat, 28 Aug 2004 10:22:50 -0700 (PDT) From: Konstantin Kudin Subject: Re: CCL:SUMMARY: One negative eigenvalue - No imaginary frequency!!?? To: chemistry..at..ccl.net, Carlos Silva Lopez In-Reply-To: <412EAFB9.4030900..at..uvigo.es> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.2 required=7.5 tests=PLING_QUERY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --- Carlos Silva Lopez wrote: > In a nutshell, I am even more clueless than before even though I have > > received really nice and welcomed help from several netters. If > nobody > has any further idea about what's going on here I will eventually > re-converge everything within a continuum dielectric method to see if > it > counterbalances the anionic charge state and everything goes better. Carlos, There is not really anything out of ordinary in your particular case. If you look at the output, you'll see Full mass-weighted force constant matrix: Low frequencies --- -31.0607 0.0014 0.0024 0.0025 22.5484 25.9445 Low frequencies --- 42.3766 64.9775 107.1348 ... and normal coordinates: 1 2 3 A A A Frequencies -- 18.6726 63.9044 105.9740 Full mass-weighted numbers (at the top) include 3 translations and 3 rotations. Once these 6 coordinates projected out, one gets numbers that go under "Frequencies". While translational frequencies are usually close to hard 0s (you see 3 of those in the top output), rotational ones can be somewhere in the range -30 ... +30. This is normal, no need to panic. Numerical DFT grids are not perfectly rotationally invariant. Lowest true vibrations will inevitably mix with some rotations, that is why "42 65 107" became "19 64 106". In any event, such low lowest true frequencies indicate that the molecule you're looking at has very "soft" normal modes. If you do not like that, choose a better molecule! I hope that helps. Kostya __________________________________ Do you Yahoo!? Read only the mail you want - Yahoo! Mail SpamGuard. http://promotions.yahoo.com/new_mail From chemistry-request@ccl.net Sat Aug 28 16:32:14 2004 Received: from mxout6.cac.washington.edu (mxout6.cac.washington.edu [140.142.33.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7SLWD3G024055 for ; Sat, 28 Aug 2004 16:32:13 -0500 Received: from hymn02.u.washington.edu (hymn02.u.washington.edu [140.142.15.156]) by mxout6.cac.washington.edu (8.13.1+UW04.08/8.13.1+UW04.08) with ESMTP id i7SLf73p011727 for ; Sat, 28 Aug 2004 14:41:09 -0700 Received: from localhost (localhost [127.0.0.1]) by hymn02.u.washington.edu (8.13.1+UW04.08/8.13.1+UW04.08) with ESMTP id i7SLf4vK007226 for ; Sat, 28 Aug 2004 14:41:07 -0700 Date: Sat, 28 Aug 2004 14:41:04 -0700 (PDT) From: liaoyi_at_u.washington.edu To: chemistry_at_ccl.net Subject: calculation absorption band Message-ID: Received: from [140.142.172.106] by hymn02.u.washington.edu via HTTP; Sat, 28 Aug 2004 14:41:04 PDT MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Hi, Could any one suggest a software that can well calculate absorption band of chromophores? Thanks. From chemistry-request@ccl.net Sat Aug 28 13:47:50 2004 Received: from mail.interware.hu (mail.interware.hu [195.70.32.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7SIln3G015638 for ; Sat, 28 Aug 2004 13:47:49 -0500 Received: from caracas-2619.adsl.interware.hu ([213.178.110.59] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.34 #1 (Debian)) id 1C18Na-0000Ga-F3 for ; Sat, 28 Aug 2004 20:56:46 +0200 Message-ID: <005301c48d39$8f049130$0200a8c0@cthulhu> From: "Tamas E. Gunda" To: Subject: CCL: Mol2Mol 5.3 Date: Sat, 28 Aug 2004 20:59:31 +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 6.00.2800.1437 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL Members, The new 5.3.0 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 50 different file formats (including subtypes). By entering a format string practically every formats can be out/inputted. 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 PDB Chime subformat (with 1-2-3 bonds). Many molecular utilities. New in Mol2Mol 5.3: New utility: - Calculation of Gasteiger-Marsili charges, a simple procedure for calculating partial charges based on electron negativities. Supports organic molecules (C,H,N,O,S,P, halogen atoms). Best suited for systems with unconjugated double bonds only) New geometric utilities: - Calculation and dumping of geometrical data defined by named selections in HyperChem hin or hcs (Hyperchem conformation search) files. - Calculation of the dihedral angle of two best fitted mean planes. In previous versions only the angle of exact planes (defined by three atoms) could by calculated. Now the planes can be defined by any number of atoms. Several small corrections, bug fixes were also made. In the previous version Mol2Mol 5.2: New file format: Hyperchem HCS [conformation search] (read only) New utility: - Superimposing and rms comparison of two molecules; use of all atoms or only selected ones, optionally with different weight factors; it can be done automatically for all structures in multiple files; fitted molecules can be outputted to multiple files. New in POV-Ray format: - bond types are supported in vector mode too; - stereo bond types are supported; - support for rendering elemental symbols in vector mode; - support for rendering atom aliases in 2D sketch files in vector mode; and several bug fixes. 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: http://dragon.unideb.hu/~gundat/povraya.htm The program is available as 30 days unrestricted trial version or as shareware version. Dr. T. E. Gunda From chemistry-request@ccl.net Sat Aug 28 21:09:37 2004 Received: from pickering.cc.nd.edu (pickering.cc.nd.edu [129.74.250.225]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7T29aeo003049 for ; Sat, 28 Aug 2004 21:09:36 -0500 Received: from localhost (localhost [127.0.0.1]) by pickering.cc.nd.edu (Switch-3.1.6a/Switch-3.1.0) with ESMTP id i7T2IYRS015344 for ; Sat, 28 Aug 2004 21:18:34 -0500 (EST) Received: from piwnica.com (piwnica.com [66.93.212.2]) by webmail.nd.edu (IMP) with HTTP for ; Sat, 28 Aug 2004 21:18:34 -0500 Message-ID: <1093745914.41313cfa6907c)at(webmail.nd.edu> Date: Sat, 28 Aug 2004 21:18:34 -0500 From: Jan K Labanowski To: chemistry)at(ccl.net Subject: ECSOC-8 (8th electronic conference on synthetic organic chemistry MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 66.93.212.2 X-ND-MTA-Date: Sat, 28 Aug 2004 21:18:35 -0500 (EST) X-ND-Virus-Scan: engine v4.3.20; dat v4388 X-Spam-Status: No, hits=1.1 required=7.5 tests=FVGT_m_MULTI_ODD2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net ----- Forwarded message from "Julio A. Seijas" ----- Date: Mon, 19 Jul 2004 21:55:29 +0200 From: "Julio A. Seijas" Reply-To: "Julio A. Seijas" Subject: ECSOC-8 invitation To: jkl)at(ccl.net We should like to invite you to participate in the 8th electronic conference on synthetic organic chemistry organized by: Universidad de Santiago de Compostela MDPI Ocean University of China registration is free, and proceedings will be supplied in CD-ROM by a nominal fee, covering production and transport. THERE ARE SIX SECTIONS A. General Organic Synthesis B. Solid Phase Chemistry and Combinatorial Synthesis C. Bioorganic Chemistry and Natural Products D. Symposium on Selenium and Tellurium Chemistry E. Symposium on Microwave Assisted Synthesis F. Supramolecular Chemistry http://www.lugo.usc.es/~qoseijas/ECSOC-8/index.htm ORGANIZING COMMITTEE --------------------------------- Dr. Julio A. Seijas Vazquez, ECSOC-8 Chairman Departamento de Qummica Organica Universidad de Santiago de Compostela Facultad de Ciencias-Campus de Lugo Alfonso X el Sabio, 27002-Lugo, Spain. Phone +34 982 285 900; Fax +34 982 285 872; E-mail: qoseijas)at(lugo.usc.es http://www.lugo.usc.es/~qoseijas Dr. Shu-Kun Lin, ECSOC-8 Secretary MDPI, Matthaeusstrasse 11, CH-4057 Basel, Switzerland Phone +41 79 322 3379; Fax +41 61 302 8918; E-mail: lin)at(mdpi.org http://www.mdpi.org/lin Dr. De-Chun Ji, Editorial Assistant Molecules Editorial Office Ocean University of China Qingdao 266003, Shandong Province, China Tel. & fax ++86 532 203 1522 (office) E-mail: molecules)at(ouc.edu.cn http://molecules.ouc.edu.cn SCIENTIFIC COMMITTEE ---------------------------------- Dr. Rajive Gupta University of Jammu, India rajgupta)at(sancharnet.in Dr. Carmen Najera Domingo Universidad de Alicante, Spain cnajera)at(ua.es Dr. Ana Maria F. Oliveira-Campos Universidade do Minho. Portugal amcampos)at(quimica.uminho.pt Dr. Alice L. Pirez Sanchez Universidad de Costa Rica, Costa Rica. alperez)at(carian.ucr.ac.cr Dr. M. Pilar Vazquez Tato Universidad de Santiago de Compostela. Spain pilarvt)at(lugo.usc.es Dr. Miguel Angel Yus Astiz Universidad de Alicante, Spain yus)at(ua.es yours sincerely Julio A. Seijas chairman ====================================== Dr. JULIO A. SEIJAS V. Departamento de Quimica Organica FACULTAD DE CIENCIAS Universidad de Santiago de Compostela Campus de Lugo C/ Alfonso X el Sabio s/n 27002-LUGO. SPAIN ...................................... Aptdo.(P.O.Box) 280, 27080-Lugo.Spain ###################################### fax:+34 982 285 872. 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