From Fredrik.Bokman@akka.kemi.uu.se Mon Nov 25 04:49:07 1996 Received: from akka.kemi.uu.se for Fredrik.Bokman@akka.kemi.uu.se by www.ccl.net (8.8.3/950822.1) id EAA12624; Mon, 25 Nov 1996 04:25:49 -0500 (EST) Received: from donau.kemi.uu.se by akka.kemi.uu.se with SMTP id AA00877 (5.67a8/IDA-1.5 for ); Mon, 25 Nov 1996 10:24:44 +0100 Received: from localhost by donau.kemi.uu.se; (5.65/1.1.8.2/06Jul95-0509PM) id AA27588; Mon, 25 Nov 1996 10:26:48 +0100 Sender: fredrik@donau.kemi.uu.se Message-Id: <32996657.41C6@kemi.uu.se> Date: Mon, 25 Nov 1996 10:26:47 +0100 From: Fredrik B|kman X-Mailer: Mozilla 3.0 (X11; I; OSF1 V3.2 alpha) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: fortran/PC Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL fellows, Hints on what FORTRAN compilers that are good (or even: available) for pentium/windows95 systems would be greatly appreciated. Thanks, Fredrik B|kman Dept of Organic Chemistry, Uppsala University Fredrik.Bokman@kemi.uu.se From herbert.homeier@rchs1.chemie.uni-regensburg.de Mon Nov 25 05:49:07 1996 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by www.ccl.net (8.8.3/950822.1) id FAA12768; Mon, 25 Nov 1996 05:18:42 -0500 (EST) Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA27199 (5.65c/IDA-1.4.4 for ); Mon, 25 Nov 1996 11:16:32 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA26119; Mon, 25 Nov 96 12:17:01 +0100 Date: Mon, 25 Nov 96 12:17:01 +0100 From: Herbert Homeier t4720 Message-Id: <9611251117.AA26119@rchs1.chemie.uni-regensburg.de> To: chemistry@www.ccl.net Subject: Anharmonicity Cc: jsl@virgil.ruc.dk X-Url: http://rchs1.uni-regensburg.de/~maillist/data/ Please excuse if you receive this message twice. "Jens Spanget-Larsen" wrote: --------------------------- CCL: On Friday, 15 Nov 1996, I posted the following question: > In a study of molecular vibrational structure I have encountered a > normal mode with a "symmetrical" anharmonic potential V of the form: > > V(Q) = a*Q^2 + b*Q^4 > > i.e., the potential V as a function of the normal coordinate Q can be > approximated by a fourth order polynomial in Q, containing only the > second and the fourth power. What are the solutions to the > vibrational eigenvalue problem with this potential function? I would > be most grateful for information on literature that deals with this > problem. I immediately received a number of useful replies, that are summarized below. Thank you to all that replied! Yours, Jens >--< (summary omitted) -------------------------- It may be of interest that there are a number of results of Weniger and Meissner regarding this type of anharmonic oscillator that are online available via our server at http://www.chemie.uni-regensburg.de/preprint.html These are based on perturbation theory (Weniger. Beware: the usual perturbation series as sketched in one of the responses in the summary is strongly divergent. This, however, does not mean that it is useless. The problems can be handled.) and the generalized Bloch equation that can be solved iteratively (Meissner). There is also a poster of Meissner at ECCC3 ---accessible via http://hackberry.chem.niu.edu:8000 http://www.chemie.uni-regensburg.de:8000 (mirror) --- that summarizes some of his results. -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg, D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX: +49-941-943 4719/+49-941-943 2305 email: herbert.homeier@na-net.ornl.gov WWW: http://rchs1.uni-regensburg.de/~c5008 --------------------------------------------------------------- From kessler@mpi-muelheim.mpg.de Mon Nov 25 06:11:22 1996 Received: from dsa.mpi-muelheim.mpg.de for kessler@mpi-muelheim.mpg.de by www.ccl.net (8.8.3/950822.1) id FAA12797; Mon, 25 Nov 1996 05:35:44 -0500 (EST) Received: from dsa.mpi-muelheim.mpg.de by dsa.mpi-muelheim.mpg.de; (5.65v3.2/1.1.8.2/20Mar95-0228PM) id AA29128; Mon, 25 Nov 1996 11:37:13 +0100 Sender: kessler@dsa.mpi-muelheim.mpg.de Message-Id: <329976D9.41C6@mpi-muelheim.mpg.de> Date: Mon, 25 Nov 1996 11:37:13 +0100 From: Magnus Kessler Organization: Max-Planck-Institut fuer Kohlenforschung X-Mailer: Mozilla 2.01 (X11; I; OSF1 V4.0 alpha) Mime-Version: 1.0 To: Computational Chemistry List Subject: CCL: Summary:Atoms In Molecules for transition metal complexes Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers Thank you to all who have helped me with their comments, suggestions and literature citations concerning Atoms In Molecules of Transition Metals. Before I come to the summary, I must apologize for my statement, that the AIM command in G94 cannot handle d functions -- of course it can as Douglas Fox from Gaussian Inc. and Pierre J.-L. Plourde from the Dalhousie University, Halifax correctly stated. To my knowledge it just cannot handle f functions which may be present in basis sets for TM's. The summary follows Magnus Kessler =============================================================================== SUMMARY: The question was: Dear CCLer's I would like to do a bonding analysis with Bader's "atoms in molecules" (AIM) concept on transition metal complexes. Two questions arise: 1. Which software is capable to do such an analysis. (According to the manual, AIM in G94 Rev. B3 cannot handle d-electrons; BTW the AIM functionality seems not to be implemented in G94 Rev. B3) 2. Has anyone made any experience with AIM analysis on transition metals? Any information will be greatly appreciated Thanks a lot in advance Magnus Kessler =============================================================================== From Douglas J. Fox: The AIM implementation in G94 can handle s, p and d functions and this is as documented in the User's Reference. I would be curious what page of the manual you found the comment that lead you to believe that d functions could not be dealt with. The AIM functionality was not present in Rev. B.3 (...) [but in newer versions, MK] I am not aware of much work with AIM and transition metals. These methods are numerically quite delicate but they are quite insensitive to the nature of the underlying elements so if there were not numerical problems I expect they will work quite well. Douglas J. Fox Director of Technical Support help@gaussian.com =============================================================================== From Pierre J.-L. Plourde: According to version 5.0 (Jan 95) of the G94 manual, G94's implementation of AIM can handle s, p and d functions, but not f or higher. Having done AIM calculations on a couple of systems, I know it is implemented in G94 Rev B.2, and I would assume it is as well in B.3, though I may be wrong on that count. Pierre J.-L. Plourde Ph.D. student Theoretical and Computational Chemistry Centre Room 322B, Chemistry Building Department of Chemistry, Dalhousie University Halifax, Nova Scotia, Canada Tel: (902) 494-7021 Fax: (902) 494-1310 Email: pplourde@is2.dal.ca =============================================================================== From Carles Bo: For the latest AIM program version ask Prof. Bader group. You can reach them from http://www.chemistry.mcmaster.ca/faculty/bader/ I don't know if G94 can do AIM analysis, but you can produce an WFN file which is the input to Bader programs. 2. Has anyone made any experience with AIM analysis on transition metals? We have analyzed many molecules containing transition metals. If our experience can help you, don't doubt to contact me. ________________________________________________________________ Dr. Carles Bo Dept. de Quimica Universitat Rovira i Virgili Voice (34) (77) 55 95 69 Pl. Imperial Tarraco, 1 FAX (34) (77) 55 95 63 43005 - Tarragona SPAIN ________________________________________________________________ =============================================================================== From Jauoad El Bahraoui: they are no problem to do it, you can do it with the AIMPAC program of Bader and cols, this program it free of charge Email:bader@mcmaster.ca | Jaouad El-Bahraoui , Ph.D | | Instituto de Biotecnologma | | GMDM, UNIV Granada | | Granada 18071, Spain | | Tel/Fax +34-58-243186 | | jaouad@goliat.ugr.es | |http ://dalila.ugr.es/~jaouad/| =============================================================================== From Fernando Martin: I am a pHD student of professor Bader and it was brought to my attention that you are having trouble doing an AIM assessment of transition metals. You seem to be using the routines in g94. Unfortunaltely they seem to be limited in what they can do and sometimes don't even work. I am also not sure by what you mean as "bonding analysis". Do you want to find the critical points, integrate for atomic properties, ...?. Let me know in more detail what you are up to. The students that have circulated through this lab have created routines that might be of help to you, these are free of cost, all we need is an e-mail address to send them to. If you are interested in the programs, let me know. ______________________________________________________________________________ Fernando Martin phone: (905)525 9140 ext. 22502 Department of Chemistry, box 109. fax: (905)522 2509 McMASTER UNIVERSITY Hamilton, Ontario, Canada. L8S 4M1 martif@mcmail.cis.mcmaster.ca ______________________________________________________________________________ =============================================================================== From Jan Hrusak: You may have look to our recent paper in J. Chem. Phys 100 (1996) 12253 Where we present the results for Bader Analysis for the Metal-Ethene cations. Additional information might be provided by R. Hertwig in TU Berlin. (hert0531@argon.chem.tu-berlin.de Regards Jan Hrusak "Dr. Jan Hrusak" =============================================================================== From Ian Bytheway: I would suggest that you get hold of either the AIMPAC suite of programs from Prof Bader (bader@mcmail.cis.mcmaster.ca), or MORPHY from Dr Paul Popelier (pla@umist.ac.uk). I use MORPHY to locate critical points in rho and del2rho, as well as to produce plots. The proaim part of AIMPAC is useful for calculating integrated atomic charges, although I believe a soon-to-be-released version of MORPHY will do this. Using either of these packages requires a wfn file, which can be generated from a g94 run with output=psi specified, and a file name at the end of the input (see the manual for specific details). I've appended a list of papers of mine which you might find interesting and relevant. Some deal with AIM analyses exclusively, while others have AIM as only a small part of the overall study. I hope this information is of some use, please feel free to contact me again if you'd like more info! R.J. Gillespie, I. Bytheway, R.S. DeWitte, R.F.W. Bader "Trigonal Bipyramidal and Related Molecules of Main Group Elements: An Investigation of Apparent Exceptions to the VSEPR Model Through the Analysis of the Laplacian of the Electron Density", Inorganic Chemistry, 1994, 33, 2115-2121. I. Bytheway, R.J. Gillespie, R.F.W. Bader, T.-H. Tang "Core Polarizability and the Geometry of the Calcium Difluoride Molecule" Inorganic Chemistry, 1995, 34, 2407-2414. I. Bytheway, M.B. Hall "Electronic Structures of Peroxonickel(II) bis(isocyanide) Complexes" Inorganic Chemistry, 1995, 34, 3741-3746. Z. Lin, I. Bytheway "The Stereochemistry of Seven-coordinate d0-Transition Metal and Main Group Molecules" Inorganic Chemistry, 1996, 35, 594-603. I. Bytheway, G.B. Bacskay, N.S. Hush "Quantum Chemical Study of the Properties of Molecular Hydrogen Complexes of Osmium(II): A Comparison of Density Functional and Conventional Ab Initio Methods" Journal of Physical Chemistry, 1996, 100, 6023-6031. R.J. Gillespie, I. Bytheway, T-H. Tang, R.F.W. Bader, R.S. DeWitte "Geometry of the Fluorides, Oxofluorides, Hydrides and Methanides of Vanadium (V), Chromium (VI) and Molybdenum(VI): Understanding the Structures of Some non-VSEPR Molecules in Terms of Core Distortion" Inorganic Chemistry, 1996, 35 , 3954-3963. I. Bytheway, P.L.A. Popelier, R.J. Gillespie "Topological Studies of the Charge Density of Some Group 2 Metallocenes, M(eta5-C5H5)2 (M = Mg or Ca)" Canadian Journal of Chemistry, 1996, 74, 1059-1071. Ian Bytheway =============================================================================== From Preston J. MacDougall: I did my Ph.D. with Richard Bader, and part of my research involved transition metal complexes. My thesis was not published, but I copies available. Some later work was published in Can. J. Chem., vol. 67, p. 1842 (1989), and in Trans. Amer. Cryst. Assoc., vol. 26, p. 105 (1990) (Many crystallographers get these Transactions). Others have performed AIM studies of transition metal complexes. M. B. Hall, G. Frenking, M. Benard, C. Bo, are some who have published interesting papers using AIM on a wide range of systems. Richard Bader has recently published some papers in Inorg. Chem. concerning transition- metal complexes. About software, Professor Bader distributes the programs that run off of .wfn files that all recent Gaussian versions output (since G92). Including d functions (f functions are probably handled by the software that Bader distributes). I have forwarded your posting to his group, they usually respond quickly. Good luck, and I'm sure you will find the analysis very helpful in your studies! Preston J. MacDougall Assistant Professor Department of Chemistry, Box X-101 Middle Tennessee State University Murfreesboro, TN 37132 ph: (615)898-2741, FAX: (615)898-5182 e-mail: pmacdougall@mtsu.edu Homepage: http://www.mtsu.edu/~chem/ =============================================================================== From Martin Kaupp: Gernot Frenking's Gruppe in Marburg macht viel AIM mit Uebergangsmetall-Systemen (Kontakt FRENKING@ps1515.chemie.uni-marburg.de). Da bekommen Sie sicher naehere Auskuenfte (u.a. wie man dies mit ECPs tut). Ich selbst verwende eher die Elektronenlokalisierungsfunktion (ELF) fuer aehnliche Zwecke (fuer Hgr. und Ueberg.elemente, mit und ohne ECPs). ------------------------------------------------------------------ | Dr. Martin Kaupp | | Max-Planck-Institut fuer Festkoerperforschung, | | Heisenbergstrasse 1, D-70569 Stuttgart, Germany, | | Tel.: country-code+711/689-1532 | | Fax.: country-code+711/689-1562 | | email: kaupp@vsibm1.mpi-stuttgart.mpg.de | | | | and Institut fuer Theoretische Chemie, Universitaet Stuttgart, | | Pfaffenwaldring 55, D-70569 Stuttgart, Germany | | Tel.: country-code+711/685-4408 | | Fax.: country-code+711/685-4442 | | http://www.theochem.uni-stuttgart.de/~kaupp/ | | email: kaupp@theochem.uni-stuttgart.de | ------------------------------------------------------------------ =============================================================================== Thank you again to all who have answered. Best wishes ======================================================================== Magnus Kessler kessler@mpi-muelheim.mpg.de PhD Student MPI fuer Kohlenforschung Lembkestrasse 5 Strukturchemie D-45470 Muelheim / Germany ======================================================================== From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de Mon Nov 25 07:49:11 1996 Received: from ns1.DKFZ-Heidelberg.de for tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de by www.ccl.net (8.8.3/950822.1) id GAA13293; Mon, 25 Nov 1996 06:57:52 -0500 (EST) Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.48.96]) by ns1.DKFZ-Heidelberg.de (8.7.3/DKFZ-8.6.4) with ESMTP id MAA18442 for ; Mon, 25 Nov 1996 12:55:17 +0100 (MET) Received: (tajkhors@localhost) by mbp-sgi7.inet.dkfz-heidelberg.de (940816.SGI.8.6.9/DKFZ-8.6.4) id MAA06350 for chemistry@www.ccl.net; Mon, 25 Nov 1996 12:54:25 +0100 From: "Emadeddin Tajkhorshid" Message-Id: <9611251254.ZM6348@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Mon, 25 Nov 1996 12:54:25 +0100 Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net (Computational Chemistry List) Subject: pKa calculation Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers I have calculated the energy (HF) of a set of protonated molecules and compared them with the ones of non protonated species. After inclusion of vibrational and thermal corrections you can get a figure which can be refered as 'proton affinity' of the studied molecule. I want to know if there is any relationship between this proton affinity and pKa of the molecule. Any comment in this regard will be appreciated. Thanx in advance -- Emad ********************************************************************* E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2339 Dept. Molecular Biophysics (0810) FAX: +49 6221 42 2333 P.O.Box 101949 Email: E.Tajkhorshid@DKFZ-Heidelberg.DE 69009 Heidelberg, FRG *********************************************************************** * A friend may well be reckoned a masterpiece of the nature (Emerson) * *********************************************************************** From jerry@Ramsey.chem.dal.ca Mon Nov 25 08:49:16 1996 Received: from Ramsey.chem.dal.ca for jerry@Ramsey.chem.dal.ca by www.ccl.net (8.8.3/950822.1) id IAA13747; Mon, 25 Nov 1996 08:47:11 -0500 (EST) Received: by Ramsey.chem.dal.ca (940816.SGI.8.6.9/940406.SGI.AUTO) id KAA21098; Mon, 25 Nov 1996 10:21:02 -0400 Date: Mon, 25 Nov 1996 10:20:55 -0400 (AST) From: "Jerry C.C. Chan" To: chemistry@www.ccl.net Subject: Summary: Transition metal Shielding Calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Below please find the summary of DFT shielding calculation of transition metal nuclei. Thanks are due to Pascal and Georg. Jerry --------------------------------------------------------------------------- Concerning the DeMon-NMR program which performs DFT calculations of chemical shielding : 1. V. G. Malkin, O. L. Malkina, M. E. Casida and D. R. Salahub, J. Am. Chem. Soc. , 116, 5898 (1994). 2. V. G. Malkin, O. L. Malkina, L. A. Eriksson and D. R. Salahub,"The calculation of NMR and ESR spectroscopy parameters using Density Functional Theory" in Modern Density Functional Theory : a tool for chemistry 2, Coll. Theoretical and computational chemistry J.M. Seminario and P. Politzer Eds. (Elsevier, Amsterdam, 1995). Regards ***************************************************************************** Pascal HEBANT Laboratoire d'Electrochimie et de Chimie Analytique Ecole Nationale Superieure de Chimie de Paris 11 rue Pierre et Marie Curie 75005 Paris FRANCE tel:+33 - 01 44 27 66 94 fax: +33 - 01 44 27 67 50 http://alcyone.enscp.jussieu.fr/Pages/LECA/Electrochimie.html ***************************************************************************** From schrecke@zinc.chem.ucalgary.caMon Nov 25 10:19:11 1996 Date: Wed, 20 Nov 1996 10:28:37 -0700 From: schrecke@zinc.chem.ucalgary.ca To: jerry@Ramsey.chem.dal.ca Cc: schrecke@zinc.chem.ucalgary.ca Subject: Re: CCL:Transition metal Shielding Calculation Hi Jerry, this is a subject that has been pursued only recently. We have done some work; so far mainly on the ligands of transition metal complexes and on 77Se (let me know if you need these references). We have one paper in print in Int.J.QuantumChem.1996 that contains calculations on M(C))6 and MO4n-, M=Cr,Mo,W, among others. Further, please look for papers by Michael Buhl (or Buehl, it is an "Umlaut u" that my ASCII can't do), he did quite a lot an metal NMR recently, e.g. Helvetica Chimica Acta 1996,79,742 (57Fe) or Organometallics 1996,91,778 (91Zr). Finally, a good place to look are the annual reviews on NMR calculations by C.Jameson, in Specialist Reports on NMR Spectroscopy, edited by G.A.Webb, Royal Society, London, (annually 1980 - ...). Please summarize your findings to the list! Yours, Georg -- ============================================================================== Georg Schreckenbach Tel: (Canada)-403-220 8204 Department of Chemistry FAX: (Canada)-403-289 9488 University of Calgary Email: schrecke@zinc.chem.ucalgary.ca 2500 University Drive N.W., Calgary, Alberta, Canada, T2N 1N4 ============================================================================== From avital@yfaat.ch.huji.ac.il Mon Nov 25 09:49:11 1996 Received: from shum.cc.huji.ac.il for avital@yfaat.ch.huji.ac.il by www.ccl.net (8.8.3/950822.1) id JAA13959; Mon, 25 Nov 1996 09:20:10 -0500 (EST) Received: from yfaat.ch.huji.ac.il (yfaat.ch.huji.ac.il [132.64.98.55]) by shum.cc.huji.ac.il (8.8.3/8.6.10) with SMTP id QAA14467 for ; Mon, 25 Nov 1996 16:19:34 +0200 (GMT+0200) Received: by yfaat.ch.huji.ac.il (AIX 3.2/UCB 5.64/4.03) id AA20642; Mon, 25 Nov 1996 16:20:15 +0200 Date: Mon, 25 Nov 1996 16:20:15 +0200 From: avital@yfaat.ch.huji.ac.il (Avital Shurki) Message-Id: <9611251420.AA20642@yfaat.ch.huji.ac.il> To: CHEMISTRY@www.ccl.net Subject: vibration coordinats. Dear natters, I need to get the movements of the different vibrations in the internal coordinates representation. Gaussian 94 gives me the movements in the cartesian coordinates. Does anyone know how can I get the vibrations in internal coordinates representation from Gaussian 94. Thanks in advance Avital From mariano@zeus.uncor.edu Mon Nov 25 10:12:30 1996 Received: from zeus.uncor.edu for mariano@zeus.uncor.edu by www.ccl.net (8.8.3/950822.1) id JAA14040; Mon, 25 Nov 1996 09:34:39 -0500 (EST) Received: by zeus.uncor.edu; id AA31056; Mon, 25 Nov 1996 11:39:23 -0200 Date: Mon, 25 Nov 1996 11:39:22 -0200 (EDT) From: "Domingo Mariano A. Vera" To: "Gustavo A. Mercier Jr" , CHEMISTRY@www.ccl.net Subject: Re : CC software/Linux/Motif? In-Reply-To: <199611202002.PAA10637@mail.med.upenn.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 20 Nov 1996, Gustavo A. Mercier Jr wrote: ... > I am interested in running CC applications in a P6 box running > Linux with XFree86. Many applications make use of OpenGL and Motif > which I understand are not available through the vanilla XFree86. > > I need to find out in what ways to extend (or replace) XFree86 > to support the widest range of CC applications, at a reasonable > added cost. For example, 3rd party Xserver software vendors that > include Motif and OpenGl, etc. > > Comments in this area are welcomed, particularly updates to > previous discussions on this topic. ... A recommended comercial alternative to XFree86 is XInside. You can get more information about it at info@xinside.com, or http://www.xinside.com You may also search for information about comercial application for Linux or SCO Unix (you can run such applications by means of the adequate emulator, for example iBCS2) reading the Comercial-HOWTO document ( I don't remember exactly its location, but you may search for it at Excite engine). Good luck! Best regards Mariano Domingo Mariano A. Vera mariano@zeus.uncor.edu PhD student at Facultad de Ciencias Quimicas, Universidad Nacional de Cordoba, Cordoba, Argentina. 54-51-33-4170 From mtulio@dragoeiro.uma.pt Mon Nov 25 10:49:12 1996 Received: from phobos.rccn.net for mtulio@dragoeiro.uma.pt by www.ccl.net (8.8.3/950822.1) id KAA14295; Mon, 25 Nov 1996 10:10:16 -0500 (EST) Received: from dragoeiro.uma.pt by phobos with SMTP (PP); Mon, 25 Nov 1996 15:09:13 +0000 Received: by dragoeiro.uma.pt (5.4R3.00/200.1.1.4) id AA19943; Mon, 25 Nov 1996 15:06:57 GMT Date: Mon, 25 Nov 1996 15:06:57 GMT Message-Id: <9611251506.AA19943@dragoeiro.uma.pt> Received: from quim96(193.136.232.96) by dragoeiro via smap (V1.3) id sma019935; Mon Nov 25 15:06:56 1996 X-Sender: mtulio@dragoeiro.uma.pt X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Mario Tulio Rosado Subject: PED programs Dear CCL, I am looking for FREE (preferably) program runing on a PC that can do PED analysis and possibly animation of vibrational modes obtained from MO programs (Gaussian, Mopac). Can anybody help me? Thanks in advance Mario Tulio Rosado Dept. of Chemistry University of Madeira PORTUGAL From robert@pauli.utmb.edu Mon Nov 25 12:49:13 1996 Received: from nmr.utmb.edu for robert@pauli.utmb.edu by www.ccl.net (8.8.3/950822.1) id MAA15709; Mon, 25 Nov 1996 12:48:46 -0500 (EST) Received: from pauli.utmb.edu by nmr.utmb.edu via SMTP (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA02140; Mon, 25 Nov 96 11:53:41 -0600 Received: (from robert@localhost) by pauli.utmb.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id LAA18858; Mon, 25 Nov 1996 11:47:58 -0600 From: "Robert Fraczkiewicz" Message-Id: <9611251147.ZM18856@pauli.utmb.edu> Date: Mon, 25 Nov 1996 11:47:58 -0600 In-Reply-To: avital@yfaat.ch.huji.ac.il (Avital Shurki) "CCL:G:vibration coordinats." (Nov 25, 4:20pm) References: <9611251420.AA20642@yfaat.ch.huji.ac.il> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: avital@yfaat.ch.HUJI.AC.IL (Avital Shurki), CHEMISTRY@www.ccl.net Subject: Re: CCL:G:vibration coordinats. Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Avital, On Nov 25, 4:20pm, Avital Shurki wrote: > Subject: CCL:G:vibration coordinats. > Dear natters, > > I need to get the movements of the different vibrations > in the internal coordinates representation. > Gaussian 94 gives me the movements in the cartesian > coordinates. > > Does anyone know how can I get the vibrations in internal > coordinates representation from Gaussian 94. In Wilson's GF-matrix formalism internal coordinate displacements (R) are approximated as linear combinations of their Cartesian counterparts (x): R=Bx where is the Wilson's B-matrix. It is just a matrix-vector multiplication, but you need B-matrix first. If you are a programmer consult "Molecular Vibrations" by E.B. Wilson, J.C. Decius and P.C. Cross for definitions and equations. If not, there are normal mode analysis programs that can compute B-matrices from known structure of molecules (e.g., well known GMAT by Schachtschneider). A few years ago I wrote such a program called RAMVIB; I am going to deposit it in CCL software archives pretty soon. I am no expert in Gaussian 94, maybe there is an option to compute B-matrix. Wishing you good luck, Robert Fraczkiewicz University of Texas Medical Branch robert@nmr.utmb.edu From jkl@ccl.net Mon Nov 25 15:02 EST 1996 Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.8.3/950822.1) id PAA25045; Mon, 25 Nov 1996 15:02:29 -0500 (EST) Received: for jkl@ccl.net by krakow.ccl.net (8.6.10/920428.1525) id PAA10553; Mon, 25 Nov 1996 15:02:29 -0500 From: Jan Labanowski Date: Mon, 25 Nov 1996 15:02:29 -0500 Message-Id: <199611252002.PAA10553@krakow.ccl.net> To: chemistry@www.ccl.net Subject: CCL needs your input NOW!!! Dear Netters, The good news is that we have full time person to work on the CCL improvement and Web site. David Tinapple joins the CCL staff on Monday, Nov. 25. He has substantial Web authoring experience in commercial, as well as, non-profit sector. He participated in creating several multimedia CD-ROMs, and we are told that he has a good sense of knowing where simplicity meats elegance in the Web site development. We already have great plans, and once he goes through the megabytes of stuff in CCL archives, and gets over the new hire red tape, we will see things happening faster. We know it, and you know it that CCL discussions get sometimes too broad for some subscribers. And beside, if we asked you what is computational chemistry, we would get a lot of different answers. So for those of you who are interested only in the subset of CCL messages on a given topic, we want to provide an automatic filter. How it will work? ================= The current list stays as it is for those who want it this way. Everybody sends messages to the normal address: chemistry@www.ccl.net. The text of incoming message is analyzed by the software for contents, and tagged according to the contents. It may happen that the message will belong to several subjects. For example, the message dealing with: "The basis set dependence of Force Field parameters for Molecular Mechanics derived with Density Functional approaches" may belong to many subjects, e.g., Molecular Mechanics, Density Functional Methods, Basis Sets, Quantum Chemistry. The example also shows that subjects chosen need not be "orthogonal", and can overlap a great deal, or even be embedded within other subject. Once we are finished, we will provide a new signup form for the CCL and you will be able to migrate from the "everything" CCL to a subject oriented delivery (we may also provide other options like: the maximum file size for the message, the "This subject but only if together with that subject", and others). Of course you will be able to choose as many subjects as you want. And even if message belongs to several subjects you belong to, you will only get one message. What we need from you? ====================== Vote!!! That is, tell us which subjects you would choose for yourself. and which you do not want to see ever {:-)} ("Never say never again"). Fill in the form at: http://www.ccl.net/ccl/ccl-subjects.html or simply send a message to jkl@ccl.net (Jan Labanowski) with subjects which you would be personally interested in receiving, and which subjects you would not like to see. We need your initial response to decide how many subjects we want to implement. WE NEED YOUR MASSIVE RESPONSE to really help us in making rational choices. So please, participate. BUT PLEASE SEND COMMUNICATIONS ABOUT IT TO jkl@ccl.net rather than the list. PLEASE. This survey at http://www.ccl.net/ccl/ccl-subjects.html will only take you a minute or so to answer unless you are my type, i.e., "paralysis of analysis"). But do not be pedantic, since we need general guidance at this time. Save your deliberations for the moment when we will ask you to make the actual choice. How we will approach the problem? ================================= While it looks simple, it is not. So if you know how such things are done let us know (jkl@ccl.net). We could use the sophisticated stuff spooks use with FFT and the like. But we are considering the following general approach. Each subject will be defined as a series of keywords (or actually flexible matches, called regular expressions in UNIX). These keywords will be checked against the text of the message to qualify message as belonging to a given subject. There also has to be some ranking mechanism, and keywords may be assigned different weight ("importance"). The proximity of other words can also be taken into account. Of course, one could use a training set of past messages in CCL archives, assign subjects to them and run neural net stuff on them. While we do not rule out this approach, we will probably do it in a more deterministic way to be able to use new buzzwords which appear every month to add to the keywords list. After we decide on subjects, we will create a Web form, and you will be asked again for help. This time to provide us with keywords typical for a given subject. We will also go through archives and assign past messages to subjects, split messages to words and rank the frequency of words in a given subject. While we are sure that "and", "molecule", etc. will be the leaders, we hope to find also some specific words which occur within subjects. Then we will do the software. The software has to be smart and especially distribution has to be well optimized. We also need to think about messages which are outside the scope of any field (did not rank high enough) -- we may simply handle them by hand and improve our keyword lists. We will also provide a way for the authors to assign their messages to the subjects, but we do not want to enforce it. And beside, who knows what will show up in the process of doing this. But we think that it may be a nice and needed tool once we can make it work. If it works well enough, we may want to make it available, so you can use it as a filter for your other mailing lists and newsgroups. But do not be impatient as it will take some time to create it. So please help us (and help yourself too, in the process). Jan Labanowski CCL Admin jkl@ccl.net From edanoff@unm.edu Mon Nov 25 21:49:16 1996 Received: from ariel.unm.edu for edanoff@unm.edu by www.ccl.net (8.8.3/950822.1) id UAA20661; Mon, 25 Nov 1996 20:58:31 -0500 (EST) Received: from pharm161155.unm.edu(really [129.24.161.155]) by ariel.unm.edu via sendmail with smtp id for ; Mon, 25 Nov 1996 18:58:31 -0700 (MST) (Smail-3.2 1996-Jul-4 #6 built 1996-Jul-22) Message-ID: <329A50F2.3771@unm.edu> Date: Mon, 25 Nov 1996 19:07:46 -0700 From: Ed Danoff X-Mailer: Mozilla 3.0Gold (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Gaussian 94 Visualization Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello List folks- Please excuse me if I appear as too much of a dullard by asking this. I am doing a number of geometry optimizations using Gaussian94. I would like to visualize the results of these files graphically within hyperchem. As such, I need a file conversion program to convert the output from the G94 job to a hyperchem *.hin file. I have tried BABEL and it does not work with G94 (it wants to give me a multistructure answer when all I want is the final result). I would prefer an easily downloaded free-ware program, but commercial program information would also be appreciated. Any assistance that can be provided will be most appreciated. Please reply to my email directly as I do not have access to the list. robp@unm.edu Thank you for your help!! Robert Palmer, Ph.D. Assistant Professor Medicinal Chemistry and Toxicology University of New Mexico Albuquerque, NM 87131-1066 robp@unm.edu From korkin@qtp.ufl.edu Mon Nov 25 23:49:17 1996 Received: from qtp.ufl.edu for korkin@qtp.ufl.edu by www.ccl.net (8.8.3/950822.1) id XAA21165; Mon, 25 Nov 1996 23:31:05 -0500 (EST) Received: from white7.qtp.ufl.edu by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id XAA18288; Mon, 25 Nov 1996 23:30:59 -0500 From: "Anatoli Korkin" Received: by white7.qtp.ufl.edu (SMI-8.6/4.11) id XAA13262; Mon, 25 Nov 1996 23:30:53 -0500 Date: Mon, 25 Nov 1996 23:30:53 -0500 Message-Id: <199611260430.XAA13262@white7.qtp.ufl.edu> To: edanoff@unm.edu Subject: Re: CCL:G:Gaussian 94 Visualization Cc: ostlund@hyper.com, chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: zhwMuKLOvEm1XkhfpmBqsQ== > From chemistry-request@www.ccl.net Mon Nov 25 23:14 EST 1996 > X-Authentication-Warning: www.ccl.net: mail set sender to chemistry-request@www.ccl.net using -f > Date: Mon, 25 Nov 1996 19:07:46 -0700 > From: Ed Danoff > To: chemistry@www.ccl.net > Subject: CCL:G:Gaussian 94 Visualization > > Hello List folks- > Please excuse me if I appear as too much of a dullard by asking this. > > I am doing a number of geometry optimizations using Gaussian94. I would > like to visualize the results of these files graphically within > hyperchem. As such, I need a file conversion program to convert the > output from the G94 job to a hyperchem *.hin file. I have tried BABEL > and it does not work with G94 (it wants to give me a multistructure > answer when all I want is the final result). I would prefer an easily > downloaded free-ware program, but commercial program information would > also be appreciated. Any assistance that can be provided will be most > appreciated. > > Please reply to my email directly as I do not have access to the list. > robp@unm.edu > > Thank you for your help!! > > Robert Palmer, Ph.D. > Assistant Professor > Medicinal Chemistry and Toxicology > University of New Mexico > Albuquerque, NM 87131-1066 > robp@unm.edu > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: edanoff@unm.edu > -- Original Sender From: Address: edanoff@unm.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > Hi Robert, It is easy problem. You do not need a special program, because "newzmat" (read gaussian manual) can convert your z-matrix into pdb format. Hyperchem can read it. You only need to change the extention "pdb" into "ent". For some reasons pdb format files in Hyperchem have the extention "ent". regards, Anatoli Korkin