From jon@dougal.chem.soton.ac.uk Thu Feb 27 04:25:53 1997 Received: from dougal.chem.soton.ac.uk for jon@dougal.chem.soton.ac.uk by www.ccl.net (8.8.3/950822.1) id EAA10763; Thu, 27 Feb 1997 04:21:25 -0500 (EST) Received: by dougal.chem.soton.ac.uk (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id JAA04160; Thu, 27 Feb 1997 09:20:03 GMT Date: Thu, 27 Feb 1997 09:20:03 GMT From: jon@dougal.chem.soton.ac.uk (Jonathan Essex) Message-Id: <199702270920.JAA04160@dougal.chem.soton.ac.uk> To: chemistry@www.ccl.net Subject: Bioinformatics Meeting Molecular Graphics and Modelling Society Bioinformatics and Drug Discovery University of Manchester, 2-4th April 1997 2nd call for contributions A two and a half day meeting covering the use of bioinformatics in all aspects of drug discovery from the application of genomics for rational target identification to structure-function prediction. Abstracts: Oral contributions and poster presentations are invited; abstracts should be submitted to Dr. Andy Brass by March 14th, 1997. A limited number of bursaries are available; students should indicate that they wish to be considered for a bursary when they submit their abstract. e-mail: andy.brass@man.ac.uk FAX: (33) 161 275 5082 mail: Dr Andy Brass School of Biological Sciences 2.205 Stopford Building University of Manchester Oxford Road Manchester M13 9PT UK Further details on the conference and instructions for abstracts are available at http://mbisg2.sbc.man.ac.uk/hssp/mgms.html Invited Speakers: "Protein structure similarities and structure prediction" Dr Geoff Barton, Univ. of Oxford, UK "2-hybrid methods for identifying protein-protein interactions" Dr Roger Brent, Massachusetts General Hospital, USA "Integrated Resources for Bioinformatics" Dr Peter Buneman, Univ. of Pennsylvania, USA "Integrating and visualising biological databases" Dr Tom Flores, European Bioinformatics Institute. "Hidden Markoff Models" Dr Tim Hubbard, MRC Centre for Protein Engineering, UK "Metabolic databases" Dr Peter Karp, Artificial Intelligence Center, SRI, USA "The yeast genome database" Dr H Werner Mewes, MIPS, Max-Planck Institut fur Biochemie, Germany "Bioinformatics: A powerful resource for drug discovery" Dr David Parry-Smith, Pfizer Central Research, UK "Automated homology modelling" Dr Mansoor Saqi, Glaxo-Wellcome Research, Stevenage, UK "Recognition of Analogous and Homologous Protein Folds using FOLDFIT" Dr Michael Sternberg, Imperial Cancer Research Fund, UK. (some of the titles are still provisional) From Alan.Shusterman@directory.Reed.EDU Thu Feb 27 12:25:57 1997 Received: from reed.edu for Alan.Shusterman@directory.Reed.EDU by www.ccl.net (8.8.3/950822.1) id MAA13399; Thu, 27 Feb 1997 12:00:18 -0500 (EST) Received: from isis.Reed.EDU [134.10.2.1 no identification] by reed.edu (/\oo/\ Smail3.1.29.1osf1 #29.2) id ; Thu, 27 Feb 97 09:00 PST Message-id: <2668583@isis.Reed.EDU> Date: 27 Feb 97 09:00:23 PST From: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman) Subject: Re: methane dimer To: CHEMISTRY@www.ccl.net I had written: > > Can anyone tell me the experimental CC distance in methane dimer, and the > binding energy of the dimer relative to the individual molecules? Literature > refs, if you can easily lay your hands on them, are also much appreciated. > Thanks, > > Alan Shusterman Here is a summary of the replies that I received (the order of the replies is not significant). Thanks for all of your help. Alan Department of Chemistry Reed College Portland, OR ---------------------------------------- As far as I know there is no experimental structure of the methane dimer in the gas phase available ( It would be a very ambitious experiment !). But I have at least 2 experimental papers: Baflie, Ubaldo; Ulivi, Lorenzo; Zoppi, Marco; Barocchi, Fabrizio; Frommhold, Lothar. Interaction-induced light scattering by gaseous methane: the bound dimer contribution (CH4)2. Phys. Rev. A: At., Mol., Opt. Phys. (1994), 50(2-A), 1172-7 Prengel, Alex T., Jr. Raman scattering from colliding molecules and van der Waals dimers in gaseous methane and argon. (1976) 137 pp. Avail.: Xerox Univ. Microfilms, Ann Arbor, Mich., Order No. 76-25,319. From: Diss. Abstr. Int. B 1976, 37(5), 2343 And a lot of theoretical papers, e.g. : Tetzger, Thomas G.; Ferguson, David M.; Glauser, William A. A computational analysis of interaction energies in methane and neopentane dimer systems. J. Comput. Chem. (1997), 18(1), 70-79 Yin, Daxu; MacKerell, Alexander D. Jr. Combined ab initio/empirical approach for the optimization of lennard-jones parameters. Book of Abstracts, 210th ACS National Meeting, Chicago, IL, August 20-24 (1995),Issue Pt. 1, COMP-153 Publisher: American Chemical Society, Washington, D. C. Nagy, Jeno; Weaver, Donald F.; Smith, Vedene H., Jr. Ab initio methane dimer intermolecular potentials. Mol. Phys. (1995), 85(6), 1179-92 Nagy, Jenoe; Weaver, Donald F.; Smith, Vedene H., Jr. A Comprehensive Study of Alkane Nonbonded Empirical Force Fields. Suggestions for Improved Parameter Sets. J. Phys. Chem. (1995), 99(20), 8058-65 Nagy, Jeno; Smith, Vedene H., Jr.; Weaver, Donald F. Calculation of second virial coefficients of alkanes with the MM2 and MM3 force fields. Mol. Phys. (1994), 81(5), 1039-47 Tsuzuki, Seiji; Uchimaru, Tadafumi; Tanabe, Kazutoshi; Kuwajima, Satoru. Refinement of Nonbonding Interaction Potential Parameters for Methane on the Basis of the Pair Potential Obtained by MP3/6-311G(3d,3p)-Level ab Initio Molecular Orbital Calculations: The Anisotropy of H/H Interaction. J. Phys. Chem. (1994), 98(7), 1830-3 Novoa, Juan J.; Whangbo, Myung Hwan; Williams, Jack M. Interaction energies associated with short intermolecular contacts of C-H bonds.II.Ab initio computational study of the C-H...H-C interactions in methane dimer. J. Chem. Phys. (1991), 94(7), 4835-41 Tsuzuki, Seiji; Tanabe, Kazutoshi. Basis set effects on the intermolecular interaction energies of methane dimers obtained by the Moeller-Plesset perturbation theory calculation. J. Phys. Chem. (1991), 95(6), 2272-8 Szczesniak, M. M.; Chalasinski, G.; Cybulski, S. M.; Scheiner, S. Intermolecular potential of the methane dimer and trimer. J. Chem. Phys. (1990), 93(6), 4243-53 Williams, Donald E.; Craycroft, David J. Nonbonded hydrogen...hydrogen repulsion energy from ab initio SCF calculations of methane, ammonia, water, and methanol dimers. J. Phys. Chem. (1987), 91(25), 6365-73 Kolos, W.; Ranghino, G.; Clementi, E.; Novaro, O. Interaction of methane molecules. Int. J. Quantum Chem. (1980), 17(3), 429-48 Hope this helps, Ciao Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst CR&T Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main schiffer@msmwia.hoechst.com ---------------------------------------- A C-C distance of 3.88 A is reported in G. P. Matthews and E. B. Smith, Mol. Phys. 32 (1976) 1719 Good luck, Ole Swang ---------------------------------------- This may not be very helpful, but in the book "Molecular Theory of Gases and Liquids" by Hirschfelder, Curtis, and Bird (1954) they list constants for the Lennard-Jones potential determined from second virial coefficients. I would expect the equilibrium distance to be overestimated this way and the well depth to be underestimated. They list for CH4 : epsilon (the well depth) 148.2 K sigma 3.817 Angstrom (the minimum is at 2^(1/6) sigma or 4.284 Angstrom. Good Luck Dr. Russell D. Johnson III Research Chemist Physical and Chemical Properties Division National Institute of Standards and Technology Gaithersburg, MD 20899 voice 301+975-2513 fax 301+975-3670 email: russell.johnson@nist.gov ---------------------------------------- For a nice thoeretical study done with pretty high level MO calculations and a large number of orientations, etc., see: J. Chem. Phys., 93, 4243-4253, 1990 Hope this helps, Jay Ponder -------- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ ---------------------------------------- The following reference may be of some use: Journal of Computational Chemistry Volume 18 No. 1 p 70-79 (1997) Good luck, Tom Metzger metzger@mnb.nida.nih.gov From G.Raether@dkfz-heidelberg.de Thu Feb 27 13:25:57 1997 Received: from ns1.DKFZ-Heidelberg.de for G.Raether@dkfz-heidelberg.de by www.ccl.net (8.8.3/950822.1) id NAA13718; Thu, 27 Feb 1997 13:02:59 -0500 (EST) Received: from mbp-sun7.inet.dkfz-heidelberg.de (mbp-sun7.inet.dkfz-heidelberg.de [193.174.48.242]) by ns1.DKFZ-Heidelberg.de (8.7.3/DKFZ-8.6.4) with SMTP id TAA02620; Thu, 27 Feb 1997 19:00:53 +0100 (MET) Received: by mbp-sun7.inet.dkfz-heidelberg.de (5.x/SMI-SVR4) id AA06579; Thu, 27 Feb 1997 19:03:46 +0100 Date: Thu, 27 Feb 1997 19:03:46 +0100 Message-Id: <9702271803.AA06579@mbp-sun7.inet.dkfz-heidelberg.de> From: Gerd Raether To: info@gaussian.com, dok248@mbp-sun7.inet.dkfz-heidelberg.de Subject: Potential-energy integrals with PRISM Dear Sirs, For my project I need to work with the Potential-energy integral part in the subroutines PDENBAS and PRISM in Gaussian 94. For this work I would be very glad if you can provide me with a reverence about the "density basis set of delta functions"-method used in these subroutines. Thank you very much in advance, Best Regards, Gerd Raether --------------------------------------------> German Cancer Research Center (DKFZ) Department of Molecular Biophysics (0810) Head: Priv.Doz. Dr. Sandor Suhai Im Neuenheimer Feld 280 D-69120 Heidelberg, Germany Tel. +49-6221/422337, FAX: +49-6221/422333 email: G.Raether@dkfz-heidelberg.de <-------------------------------------------- From kanzaki@mxk.meshnet.or.jp Thu Feb 27 19:26:00 1997 Received: from meshsv81.tk.mesh.ad.jp for kanzaki@mxk.meshnet.or.jp by www.ccl.net (8.8.3/950822.1) id TAA20232; Thu, 27 Feb 1997 19:07:09 -0500 (EST) Received: from tw3181 (tkrz1DS07.stm.mesh.ad.jp [133.205.230.157]) by meshsv81.tk.mesh.ad.jp (8.8.4+2.7Wbeta4/3.5Wpl1-) with SMTP id JAA06688; Fri, 28 Feb 1997 09:07:02 +0900 (JST) Message-Id: <199702280007.JAA06688@meshsv81.tk.mesh.ad.jp> X-Sender: kanzaki@mxk.meshnet.or.jp X-Mailer: Windows Eudora Pro Version 2.2-Jr1 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-2022-JP" Date: Fri, 28 Feb 1997 09:10:23 +0900 To: CHEMISTRY@www.ccl.net From: =?ISO-2022-JP?B?IhskQj9AOmohITkvPCMbKEoiIA==?= Subject: summary:radical on aromatic ring Cc: kanzaki@mxk.meshnet.or.jp Hi, Following this, the answers I got to the questions stated below. Thank you very much to all who responded. ------------------------------------------------------------------- (1)Dear Koji, Generally I would tell you to go to a library and fish out the relevant papers. But since the question you pose is related to my own research, I may be of help. If given a choice, use ab initio methods, especially for "electronically demanding" systems like yours. Even at this level it is not easy to compute radical structures reliably. RHF or MP2 methods are very often not suitable due to sever spin contamination (is to be tested on your system). A reasonable compromise is offered my DFT methods, which I would advise you to use, in particular the B3LYP functional. We are in the process of finalizing a book chapter on carbenes and and also a publication on the topomerization of benzene which also encompassed some biradicals. I am working at the same time on dehydroaromatics (biradicals), and some SET reactions. It what context are you looking at these species? kind regards, Peter ********************************************************************** from Dr. Peter R. Schreiner Institut fuer Organische Chemie Georg-August Universitaet Goettingen Tammannstr. 2 Phone: +49-(0)551-393287 D-37077 Goettingen, Germany FAX: +49-(0)551-399475 http://www.ccc.uni-erlangen.de/ecc/private date Wed. 26 Feb 1997 10:32 -------------------------------------------------------- KANZAKI KOJI( Yoshitomi Pharmaceutical Industries, LTD ) 7-25 Koyata 3-chome, Iruma-shi, Saitama, 358, JAPAN e-mail: kanzaki@mxk.meshnet.or.jp Fax: +81-429-63-3121 Phone: +81-429-64-1906