From HMOLIN@astra.se Fri Aug 5 03:29:46 1994 Received: from cthnet.chalmers.se for HMOLIN@astra.se by www.ccl.net (8.6.9/930601.1506) id CAA22430; Fri, 5 Aug 1994 02:37:41 -0400 Date: Fri, 5 Aug 94 08:43 +0200 From: "HAKAN MOLIN, TEL. +46 8 553 261 22, EMAIL: HMOLIN@ASTRA.SE" Subject: Structure display in red/geen stereo To: chemistry@ccl.net X-VMS-To: INTERNET::"chemistry@ccl.net" Message-Id: <1994Aug05.084310.33.00013A71@astra.se> Dear Netters, Does anyone know or have heard of a (preferrably free) program for displaying (3D-)structures as stick models in red/green stereo? Hakan Molin hmolin@astra.se From hodgkina@vax.ox.ac.uk Fri Aug 5 07:29:52 1994 Received: from oxmail2.ox.ac.uk for hodgkina@vax.ox.ac.uk by www.ccl.net (8.6.9/930601.1506) id HAA23815; Fri, 5 Aug 1994 07:02:29 -0400 From: Received: from vax.ox.ac.uk by oxmail2.ox.ac.uk. with SMTP (PP) id <01986-0@oxmail2.ox.ac.uk.>; Fri, 5 Aug 1994 12:06:42 +0100 Received: by vax.ox.ac.uk (MX V4.1 VAX) id 13; Fri, 05 Aug 1994 12:07:36 +0100 Sender: hodgkina@vax.ox.ac.uk Date: Fri, 05 Aug 1994 12:07:35 +0100 To: CHEMISTRY@ccl.net Message-ID: <009827E3.0AE87C24.13@vax.ox.ac.uk> Subject: Please no more testers for gNMR Dear Netters Thank you very much for your help in regard to our NMR simulation program: gNMR. We have had 25 offers in the first six hours, more than we can cope with. We have asked 6 of the early respondents to help us. We will keep you informed of the release date. Some points of information on matters that I have not managed to make individual replies: A Windows version is in prospect, but it may take us a year to get it ready. No JEOL format yet but we would like to improve the range of options, so we are working on it. The developer is Dutch. Thanks again for your help Adam If you need further information contact us at: Cherwell Scientific The Magdalen Centre Oxford Science Park Oxford OX4 4GA Tel: 44-865-784800 Fax: 44-865-784801 adam.hodgkin@queens.oxford.ac.uk From toukie@zui.unizh.ch Fri Aug 5 08:29:49 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id HAA24212; Fri, 5 Aug 1994 07:51:15 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA01583; Fri, 5 Aug 94 13:56:38 +0200 X-Nupop-Charset: British Date: Fri, 5 Aug 1994 12:52:29 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <46375.toukie@zui.unizh.ch> To: chemistry@ccl.net Subject: ROH confign. by MS? Dear Colleagues; If anyone has any references to journal articles in which mass spectro- metry was used to experimentally determine the configuration of a chiral secondary or tertiary alcohol, would you be kind enough to send me the cita- tions? Thanks to all responders in advance. Sincerely, S. Shapiro Institut fuer orale Mikrobiologie Zentrum fuer Zahn-, Mund- und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich, Switzerland Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From djh@ccl.net Fri Aug 5 09:29:54 1994 Received: for djh@ccl.net by www.ccl.net (8.6.9/930601.1506) id JAA26398; Fri, 5 Aug 1994 09:27:41 -0400 Date: Fri, 5 Aug 1994 09:27:41 -0400 From: David Heisterberg Message-Id: <199408051327.JAA26398@www.ccl.net> To: chemistry@ccl.net Subject: Froese-Fischer's atomic MCHF code I would like to find a copy of Froese-Fischer's atomic MCHF code. I believe it dates from about 1969. Thanks for any pointers. -- David J. Heisterberg (djh@ccl.net) Gee, it's so beautiful, I gotta The Ohio Supercomputer Center give somebody a sock in the jaw. Columbus, Ohio -- Little Skippy (Percy Crosby) From vkitzing@sunny.mpimf-Heidelberg.mpg.de Fri Aug 5 10:29:54 1994 Received: from foxy.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-Heidelberg.mpg.de by www.ccl.net (8.6.9/930601.1506) id JAA26642; Fri, 5 Aug 1994 09:37:00 -0400 Received: from sunny.mpimf-heidelberg.mpg.de by foxy.mpimf-heidelberg.mpg.de (5.65+/1.34) id AA01477; Fri, 5 Aug 94 15:42:06 +0200 Received: from [192.109.43.34] (mac10) by sunny.mpimf-Heidelberg.mpg.de (4.1/SMI-4.1) id AA23871; Fri, 5 Aug 94 15:36:30 +0200 Date: Fri, 5 Aug 94 15:36:30 +0200 Message-Id: <9408051336.AA23871@sunny.mpimf-Heidelberg.mpg.de> To: K Bryson , CHEMISTRY@ccl.net (Computational Chemistry List) From: vkitzing@sunny.mpimf-Heidelberg.mpg.de (Eberhard von Kitzing) X-Sender: vkitzing@sunny.MPImF-Heidelberg.mpg.de (Unverified) Subject: Re: CCL:MD & MC; Modelling of counterions effects in polyelectrolytes. Dear netters, I would like to provide a late resonse to this subject. As long as only the structure of the DNA is considered the proposed "tricks" to deal with counterions may work. For instance if one is interested in the stability of the DNA molecule as a function of ionic concentration more fancy methods have to be used. The most simple one is the potential of mean force approach. Here only screened electrostatic interactions are considered. At low ionic strength, the electrostatic interaction would be screened by the Debye-Hueckel function. At higher concentrations MSA or even more advanced potentials must be introduced. By this means it is possible to calculate the B-Z transition as a function of ionic concentration and ionic radii or the distributions of ions around the molecule; see: %0 Journal Article %A Soumpasis, Dikeos Mario %D 1984 %T Statistical mechanics of the B-Z transition of DNA: Contribution of diffuse ionic interations %J Proceedings of the National Academy of Sciences of the USA %V 81 %P 5116-5120 %K DNA polymorphism, polyelectrolytes, diffuse ion cloud, free energy of conformational stability, DNA B-Z transition, potential of mean force, MSA approximation, mean spherical approximation, hypernetted chain equation, Kirkwood superposition approximation %0 Journal Article %A Klement, Reinhard %A Soumpasis, Dikeos Mario %A Kitzing, Eberhard v. %A Jovin, Thomas M. %D 1990 %T Inclusion of ionic interactions in force field calculations of charged biomolecules - DNA structural transitions %J Biopolymers %V 29 %P 1089-1103 %K force field, potential of mean force, pair correlation function, MSA theory, mean sperical approximation, electrolyte theory, screened interactions %0 Journal Article %A Klement, Reinhard %A Soumpasis, Dikeos Mario %A Jovin, Thomas M. %D 1991 %T Computation of ionic destributions around charged biomolecular structures: Results for right-handed and left-handed DNA %J Proceedings of the National Academy of Sciences of the USA %V 88 %P 4631-4635 %K force field, potential of mean force, pair correlation function, MSA theory, mean sperical approximation, electrolyte theory, screened interactions, counter ion cloud, radial distribution function If one does not want to used potentials of mean force, Brownian dynamics are required to get fairly the statistics of the ions: %0 Journal Article %A Cooper, Kim %A Jakobsson, Eric %A Wolynes, Peter %D 1985 %T The Theory of Ion Transport through Membrane Channels %J Progress in Biophysics and molecular Biology %V 46 %P 51-96 %K Nernst-Planck equation, Fokker-Planck equation, Smoluchowski equation, Kramer's equation, Eyring rate theory, ion-ion interaction, molecular dynamics, Brownian dynamics %O review %0 Journal Article %A Bek, S. %A Jakobsson, E. %D 1994 %T Brownian dynamics study of a multiply-occupied cation channel - application to understanding permeation in potassium channels %J Biophysical Journal %V 66 %N 4 %P 1028-1038 %K squid giant-axons; gramicidin channels; continuum theory; ion channel; k+ channel; membrane; diffusion; motion; model; pores; ------------------------------------------------------------------------- Eberhard von Kitzing Max-Planck-Institut fuer Medizische Forschung Jahnstr. 29, D69120 Heidelberg, FRG Carl-Zuckmayer Str. 17, D69126 Heidelberg (privat) FAX : +49-6221-486 459 (work) Tel.: +49-6221-486 467 (work) Tel.: +49-6221-385 129 (home) internet: vkitzing@sunny.MPImF-Heidelberg.mpg.de From FS300627@Sol.YorkU.CA Fri Aug 5 11:31:11 1994 Received: from Sol.YorkU.CA for FS300627@Sol.YorkU.CA by www.ccl.net (8.6.9/930601.1506) id KAA27794; Fri, 5 Aug 1994 10:43:42 -0400 From: Received: from Sol.YorkU.CA by Sol.YorkU.CA (PMDF #12410) id <01HFJPYFVTMO8YACC0@Sol.YorkU.CA>; Fri, 5 Aug 1994 10:48 EDT Date: Fri, 5 Aug 1994 10:48 EDT Subject: Elemental Analysis Programs To: chemistry@ccl.net Message-id: <01HFJPYFVTMO8YACC0@Sol.YorkU.CA> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Greetings! We are spending a lot of time analyzing our elemental analysis results. We are working with relatively low MW compound (MW around 300) and can have H2O, HCl and EtOH present. We are therefore looking for a program that would find all possible percentages of solvents etc. to fit our results. Anyone know of such a program? Thanks Patrick From OLIVER@psipsy.uct.ac.za Fri Aug 5 11:35:42 1994 Received: from ucthpx.uct.ac.za for OLIVER@psipsy.uct.ac.za by www.ccl.net (8.6.9/930601.1506) id KAA27824; Fri, 5 Aug 1994 10:45:24 -0400 Received: by ucthpx.uct.ac.za (/\==/\ Smail3.1.28.1 #28.8) id m0qWQbQ-000KHzC; Fri, 5 Aug 94 16:50 SAST Received: From ITS/WORKQ3 by charongw3.uct.ac.za via Charon-4.0A-VROOM with IPX id 100.940805164918.704; 05 Aug 94 16:49:00 -0200 Message-ID: To: chemistry@ccl.net From: "Hill, RO, Oliver, HLLROB010" Date: Fri, 5 Aug 1994 16:50:05 SAST-2 Subject: Animation of Vib Modes in GAMESS (US version) Priority: normal X-mailer: WinPMail v1.0 (R1) Dear CCL's Does anyone know of a program to read a GAMESS output file and produce a file suitible for animation (eg in XMol or VIBRAM) of one or more vibrational modes. Something along the lines of XVIBS but for GAMESS (US) not GAUSSIAN. A perl script would be great. Thanks in advance Oliver Hill ______________________________________________________________________ | Oliver Hill | | | Department of Chemistry | "The true scientist never | | University of Cape Town | loses the faculty of | | Rondebosch, 7700 | amazement. It is the essence | | SOUTH AFRICA | of his being." | | OLIVER@PSIPSY.UCT.AC.ZA (internet) | - HANS SELYE | | | | | Tel. +27-21-650-2527 | | | Fax. +27-21-650-3788 | | |____________________________________|_______________________________| From er29+@andrew.cmu.edu Fri Aug 5 15:29:54 1994 Received: from po2.andrew.cmu.edu for er29+@andrew.cmu.edu by www.ccl.net (8.6.9/930601.1506) id OAA02309; Fri, 5 Aug 1994 14:43:20 -0400 Received: (from postman@localhost) by po2.andrew.cmu.edu (8.6.7/8.6.6) id OAA16658 for CHEMISTRY@ccl.net; Fri, 5 Aug 1994 14:48:48 -0400 Received: via switchmail; Fri, 5 Aug 1994 14:48:46 -0400 (EDT) Received: from pcs16.andrew.cmu.edu via qmail ID ; Fri, 5 Aug 1994 14:47:34 -0400 (EDT) Received: from pcs16.andrew.cmu.edu via qmail ID ; Fri, 5 Aug 1994 14:47:21 -0400 (EDT) Received: from mms.4.60.Nov..4.1993.10.47.44.sun4c.411.EzMail.PC.2.0.CUILIB.3.45.SNAP.NOT.LINKED.pcs16.andrew.cmu.edu.sun4c.411 via MS.5.6.pcs16.andrew.cmu.edu.sun4c_411; Fri, 5 Aug 1994 14:47:20 -0400 (EDT) Message-ID: Date: Fri, 5 Aug 1994 14:47:20 -0400 (EDT) From: "Eric M. Rehder" To: Outbound News , CHEMISTRY@ccl.net Subject: Data Acquisition Cards Hello, I'm going to be getting a DAC card and some accompanying software for a PC in a couple weeks, and was wondering if anyone has any info they might think is helpful. I'm not exactly sure what we will be doing with it. However, this is what I know so far: the card will be used to control a mass spec and sample the data. Therefore we need input and output capabilities. Most importantly i have no idea what sampling rate we need, nor the precision. General Info is what I'm looking for, tell me the name of a company that gave you real good service, or a good software package with lots of versatility... eRic From aiba@volta.vmsmail.ethz.ch Fri Aug 5 15:36:42 1994 Received: from bernina.ethz.ch for aiba@volta.vmsmail.ethz.ch by www.ccl.net (8.6.9/930601.1506) id PAA02710; Fri, 5 Aug 1994 15:06:36 -0400 Message-Id: <199408051906.PAA02710@www.ccl.net> Received: from VOLTA.vmsmail.ethz.ch by bernina.ethz.ch id <17300-0@bernina.ethz.ch>; Fri, 5 Aug 1994 21:12:02 +0200 X-Vms-To: ethz::"chemistry@ccl.net" To: chemistry@ccl.net From: aiba@volta.vmsmail.ethz.ch (Aiaz Bakassov, Phys. Chem., ETH Zurich) Subject: RE: Froese-Fischer's atomic MCHF code Date: Fri, 5 Aug 1994 21:12:02 +0200 Froese-Fischer's (working) e-mail is this: cff@vuse.vanderbilt.edu Major journal publications (in my opinion) are these, especially the first three: 1) Comp. Phys. Rep. 3 (1986) 273-326; 2) Comp. Phys. Comm. 43 (1987) 355-365; 3) Comp. Phys. Comm. 64 (1991) 369-398; 4) Comp. Phys. Comm. 64 (1991) 431-454; 5) Comp. Phys. Comm. 64 (1991) 399-405; 406-416; 417-430; 455-472; 473-485; 486-500; 501-519; 6) Comp. Phys. Comm. 74 (1993) 381-398; 399-414; 415-431; 432-440. All papers, customarily for the Comp. Phys. Comm., contain the source where the code may be requiested from. There is a book published, the reference could be found in these papers. It might be there are more of her recent works, but I didn't look at the recent issues of Comp. Phys. Comm. yet, sorry. Sincerely, Ayaz Bakasov. From avs@iris97.biosym.com Fri Aug 5 16:29:54 1994 Received: from bioc1.biosym.com for avs@iris97.biosym.com by www.ccl.net (8.6.9/930601.1506) id PAA03443; Fri, 5 Aug 1994 15:34:32 -0400 Received: from iris97.biosym.com by bioc1.biosym.com (5.64/0.0) id AA17578; Fri, 5 Aug 94 12:39:15 -0700 Received: by iris97.biosym.com (931110.SGI.ANONFTP/920502.SGI) for @bioc1.biosym.com:CHEMISTRY@ccl.net id AA28971; Fri, 5 Aug 94 12:39:25 -0700 From: avs@biosym.com (Ajay Shah) Message-Id: <9408051939.AA28971@iris97.biosym.com> Subject: CCL: Call For Papers: Bench Chemist Modeling Symposium To: CHEMISTRY@ccl.net Date: Fri, 5 Aug 94 12:39:25 PDT X-Mailer: ELM [version 2.4dev PL52] SYMPOSIUM ANNOUNCEMENT AND 1st CALL FOR PAPERS MOLECULAR MODELING FOR BENCH CHEMISTS American Chemical Society Meeting anaheim, ca april 2 - 7, 1995 Purpose: Once a forte of professional Molecular Modelers, molecular modeling techniques have become increasingly acceptable and popular among experimental chemists. The Experimental (Bench) Chemists are using modeling for structure prediction, structure elucidation, lead generation, activity prediction, property prediction etc. The purpose of this Symposium is to bring together Bench Chemists and Computational Chemists who have written or used bench chemistry related computational tools and explore the state of the art in molecular modeling for bench chemists. Invitation: All papers that fit the purpose mentioned above are invited. The target audience includes (but is certainly not limited to), computational chemists, medicinal bench chemists, synthetic organic and inorganic chemists, researchers in the area of QSAR, QSPR, etc. Sponsor: The Computers In Chemistry Division of the American Chemical Society. The symposium will be part of the COMP division program at the Spring (April 2-7) 1995 meeting of the American Chemical Society In Anaheim, Ca. Deadline: I need to have an estimate of no. of speakers by August 17. I realize that this is a relatively short notice. However, all you need to do by August 17, is send me the following information: Name: Institution/Organization Name: Topic: Summary: A two line summary of what the talk will be about Contact Address: Please send above information to: Ajay Shah E-mail: avs@biosym.com Fax: (619) 458-0136 Or mail it to: Ajay Shah 9685, Scranton Road, San Diego, CA 92121-3752 -- **************************************************** Ajay Shah Biosym Technologies avs@biosym.com ****************************************************** Have You Heard of the Symmetry Death of the Universe? ****************************************************** From CHMORA@LSUVAX.SNCC.LSU.EDU Fri Aug 5 17:30:21 1994 Received: from sn01.sncc.lsu.edu for CHMORA@LSUVAX.SNCC.LSU.EDU by www.ccl.net (8.6.9/930601.1506) id RAA05028; Fri, 5 Aug 1994 17:09:37 -0400 Received: from LSUVAX.SNCC.LSU.EDU by LSUVAX.SNCC.LSU.EDU (PMDF V4.2-14 #3426) id <01HFK1CVNCCW8WY0U4@LSUVAX.SNCC.LSU.EDU>; Fri, 5 Aug 1994 16:17:30 CST Date: Fri, 05 Aug 1994 16:17:30 -0600 (CST) From: CHMORA@LSUVAX.SNCC.LSU.EDU Subject: Studying Indoles with MOPAC. To: chemistry@ccl.net Message-id: <01HFK1CVNCCY8WY0U4@LSUVAX.SNCC.LSU.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi everybody, I want to study indole derivatives using MOPAC, but I don't know what approach would be the best, AM1 or PM3. If anyone has done such studies I would appreciate it if you share your results with me. Thanks. Sincerely, Guillermo A. Morales (chmora@sn01.sncc.lsu.edu) From elewars@alchemy.chem.utoronto.ca Fri Aug 5 19:29:56 1994 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.9/930601.1506) id TAA05798; Fri, 5 Aug 1994 19:00:39 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.9/8.6.9) id TAA21684 for chemistry@ccl.net; Fri, 5 Aug 1994 19:05:13 -0400 Date: Fri, 5 Aug 1994 19:05:13 -0400 From: "E. Lewars" Message-Id: <199408052305.TAA21684@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: CALCS ON HCN/HNC ISOMERIZATION ipcake@iisc.ernet asked about the HCN/HNC isomerization. Here are the results of some calcs: H / \ N-----C H--N--C H--C--N TS linear linear Semiempirical AM1 method 118.5 kcal/mol 48.8 kcal/mol 31.0 kcal/mol ZPE 6.440 " " ZPE 10.747 " " ZPE 10.950 " " NC 1.217 NH 0.967 CH 1.069 NH 1.399 NC 1.178 CN 1.160 CH 1.298 HNC 59.0 NHC 53.5 NCH 67.6 -1 imag. freq -1407 cm Ab Initio, HF/3-21G -92.246 04 H -92.339 71 H -92.354 08 H ZPE 6.549 kcal/mol ZPE 11.022 ZPE 11.531 kcal/mol NC 1.183 NH 0.983 CH 1.050 NH 1.407 NC 1.160 CN 1.137 CH 1.213 HNC 55.1 NHC 53.0 NCH 71.9 -1 imag. freq -1216 cm Ab Initio, HF/6-31G* -92.791 95 H -92.855 33 -92.875 20 ZPE 7.287kcal/mol ZPE 10.70 kcal/mol ZPE 11.287 kcal/mol NC 1.169 NH 0.985 CH 1.059 NH 1.454 NC 1.154 CN 1.133 CH 1.155 HNC 50.8 NHC 51.7 NCH 77.5 -1 imag. freq -1227 cm The geom's of HCN and HNC have probably been measured by microwave spec. For an indication of the reliability of these calcs, see Hehre et al, "Ab Initio Molecular Orbital Calculations". For good quantitative estimates of relative energies, you probably should do MP2/6-31G* optimizations, and then maybe MP4/6-31G* single-points on these, or (best) G1 or G2 single-points. The HF geom's are likely not bad, and the energies are in the right order anyway. Errol Lewars ===== From FR042008@YSUB.YSU.EDU Fri Aug 5 20:29:56 1994 Received: from phem3 for FR042008@YSUB.YSU.EDU by www.ccl.net (8.6.9/930601.1506) id TAA06120; Fri, 5 Aug 1994 19:51:31 -0400 Received: from YSUB.YSU.EDU (MAILER@YSUB) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HFK94X2QGG960430@phem3.acs.ohio-state.edu>; Fri, 5 Aug 1994 19:56:55 EDT Received: from YSUB.YSU.EDU (NJE origin FR042008@YSUB) by YSUB.YSU.EDU (LMail V1.1d/1.7f) with RFC822 id 9463; Fri, 5 Aug 1994 19:56:52 -0400 Date: Fri, 05 Aug 1994 19:56:33 -0400 (EDT) From: Janet Del Bene Subject: CH3CN and CH3NC To: chemistry@ccl.net Message-id: <01HFK94X2QGI960430@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Another relevant reference is an article that I wrote on CH3CN and CH3NC and their interactions with H+ and HCl. Structures were optimized at MP2/6-31+G(d,p) and single point energies obtained at MP4 with an augmented Dunning correlation-consistent polarized split-valence basis set. Experimental data are also given. See, J. E. Del Bene, J. Am. Chem. Soc. 115, 1610 (1993). Note that the level of theory used here is beyond that recommended by Lewars. Hope this helps. Janet E. Del Bene Note: This message was initially sent to "ipcake" but could not be delivered at the address given.