From wei@hermes.chpc.utexas.edu Mon May 3 18:14:21 1993 Date: Mon, 3 May 93 23:14:21 -0500 From: wei@hermes.chpc.utexas.edu (Tai-Guang Wei) Message-Id: <9305040414.AA15446@hermes.chpc.utexas.edu> To: chemistry@ccl.net Subject: Molecular Modeling software on PCs Greetings, everyone, a synthetic organic chemist is looking for a molecular modelling software on IBM PCs or comparable machines. The software should be user friendly for a user with very little computer experience and very little theoretical background. The software should not cost too much because the money will come out of the person's own pockets. Of course, it should not be too slow. No one wants to wait for hours to get a response for a command. He wants to draw 2-D, 3-D molecular structures, do some energy estimation, conformational search, or molecule-molecule interactions(such as protein-ligand Anyway, he wants to get some information which an experimental chemist wants to know. Would someone recommend some software for him? And how can he get the software? Any suggestions will be welcome. Please send your e-mail to wei@hermes.chpc.utexas.edu or you can post it on the mailing list if you prefer to do so. Thank you very much for your help in advance, Tai-Guang Wei From rwoods@biop.ox.ac.uk Tue May 4 13:00:45 1993 Date: Tue, 04 May 1993 12:00:45 +0100 From: rwoods@biop.ox.ac.uk To: chemistry@ccl.net Message-Id: <0096BFFC.3563DFC0.21568@biop.ox.ac.uk> Subject: MNDO ESP-Charges Dear Netters, In reply to Joe Leonard's question regarding ESP-charges derived from an MNDO wavefunction, we have recently examined the use of such charges in a force field for carbohydrates. We looked at the ability of these charges to reproduce hydrogen bond energies and dipole moments. Scaled MNDO ESP- charges reproduced the HF/6-31G* hydrogen bond energies within about 0.5 kcal/mol. (Work submitted to JACS) Previously we found that HF/6-31G* ESP-charges could lead to an excellent reproduction of the SCF-dipole moment (J.Comput.Chem 11 (1990)297-310) so we had a look at the MNDO case. We and others (Breneman and Wiberg, J. Comput. Chem. 11 (1990) 361) have noted that charge convergence requires that the ESP should be sampled at a surprisingly high density of points. As far as where the points need to be located, we have found that as they should be between the VDW surface and about 3 angstroms of it. In our recent work with MNDO we modified the WILLIAMS surface in MOPAC_6.0 such that the default GRID spacing was decreased from 0.8 to 0.5 angstroms and extended the sampling shell from 1.2 to 2.8 angstroms. Such an arrangement produces about 750 points per atom. We also compared the results with a random point location method filling the same volume around the molecules with about 1500 points per atom (PDQC method). The extended high density grid seemed to be pretty good and was a bit faster. As far as dipole moments are concerned, with ab initio ESP-charges, excellent agreement between the SCF and ESP-charge-derived moments can be expected (differences of less than 0.01 Debye). We could not get anywhere near as good agreement from the MNDO wavefunction. The unscaled ESP-charges underestimated the MNDO SCF-dipole moment by about 0.3-0.4 Debye. The scaled ESP-charges underestimated the HF/6-31G* SCF-dipole by about 0.1 Debye. This feature was reported quite early (J. Comput. Chem. (1990), 11, 431) but has not been investigated fully. Hope this helps, Rob Woods Robert J. Woods Glycobiology Institute Department of Biochemistry University of Oxford South Parks Road Oxford, OX1 3QU From nystrom@ludwig.psc.edu Tue May 4 06:12:21 1993 From: nystrom@ludwig.psc.edu (N.A. Nystrom) Message-Id: <9305041412.AA13798@ludwig.psc.edu> Subject: Chemistry resources summarized on Gopher To: chemistry@ccl.net Date: Tue, 4 May 1993 10:12:21 -0400 (EDT) ============================================================= Announcement: Network-Accessible Chemistry Resources Summarized on Gopher ============================================================= As part of the InterNIC (Internet Network Information Center) project, the first list of chemistry-related resources accessible via the Internet has been posted on Gopher. This list includes ftp sites, mailing lists, email contacts, etc. The InterNIC chemistry database is located in the Chemistry section of the Gopher hierarchy: Remote Gopher Resources via Univ. of Minnesota Internet file server (ftp) sites InterNIC: Internet Network Information Center InterNIC Information Services (General Atomics) Internet Information for Everybody Things to Do on the Internet Chemistry Comments are welcome, as is information on other ftp sites, mailing lists, or other network-accessible chemistry-related resources. Please forward all replies to Nick Nystrom at nystrom@psc.edu. Nicholas A. Nystrom, Ph.D. Pittsburgh Supercomputing Center InterNIC Field Specialist in Chemistry nystrom@psc.edu From h.rzepa@ic.ac.uk Tue May 4 15:34:28 1993 Message-Id: <9305041434.AA00957@cscmgb.cc.ic.ac.uk> Date: Tue, 4 May 1993 15:34:28 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Videoconferencing We have tried some experiments in internet videoconferencing using a program called CU-SeeMe0.40, available via anonymous ftp from gated.cornell.edu in directory pub/video. The results are remarkable. All one needs to provide is an IP address, a videospigot card and a camera. It supports both two way and one way conferencing. Thus far, since I don't own the videospigot card, I have been the recipient rather than the sender! We would now like to try this out across the Atlantic! Does anyone have this configuration, and is willing to broadcast their image? I expect we will be configured suitably in the next week or two as well! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.3.1, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From DSMITH@uoft02.utoledo.edu Tue May 4 05:41:14 1993 Date: Tue, 04 May 1993 10:41:14 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: MNDO-ESP follow up question To: chemistry@ccl.net Message-Id: <01GXRW1X7PX4006T86@UOFT02.UTOLEDO.EDU> As a follow up to Joe Leonard's question, perhaps we could address an additional point which bothers me. I understand that the scaling of MNDO-ESP charges is what leads to good agreement with HF/6-31G* results, although it is still suprising to me that the correlation coefficient should be high and the deviations uniform. However, these charges are being calculated at the MNDO level at the MNDO geometry, which is quite often not particularly good. In our own experience with aromatic amines (e.g. aniline and others, J. Comput. Chem. 1992, 13(5), 640-650 and J. Mol. Struct. (THEOCHEM) 1991, 251, 283-96) MNDO gives very poor geometries compared to AM1, RHF calculations at a variety of basis sets, or experiment. So how can MNDO get the charges as good as it does? Is there some underlying systematic error or flaw in the MNDO formalism which leads to this result? And how can I really have faith in "correct" charges from "incorrect" geometries? Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From NEELY@DUCVAX.AUBURN.EDU Tue May 4 06:08:00 1993 Date: Tue, 4 May 1993 12:08 CST From: NEELY@DUCVAX.AUBURN.EDU Subject: Re: Hydrogen-bonding To: chemistry@ccl.net Message-Id: <01GXRZBAJI9S004X60@DUCVAX.AUBURN.EDU> A cheap way to check one's initial guess for H-bonded molecules is to use Fraga's program AMYR [computer Physics Communications, (1983), 29, 351-9]. It runs quickly, even on a PC, and isn't too hard to learn to use, although there are no bells & whistles. There are further references I could supply to interested people. Irene Newhouse From raman@bioc01.uthscsa.edu Tue May 4 08:43:44 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9305041843.AA10043@bioc01.uthscsa.edu> Subject: Re: Molecular Modeling software on PCs To: wei@hermes.chpc.utexas.edu (Tai-Guang Wei) Date: Tue, 4 May 1993 13:43:44 -0500 (CDT) The package that meets most of your requirements is HYPERCHEM, marketed by Autodesk Inc. I believe that the cost of the package with educational discount is $595; but, there are programs tailored towards educational and research institutions in mind and involve obtaining Hyperchem at no cost to the researcher. In return, the user must provide a detailed account of what he/she wants to do with the package. So, contact Autodesk for additional details about how the latter can be achieved. The program is quite easy to use and runs under a windows environment on a 486DX. The more memory you have the faster it runs. So, with about 8MB of RAM, one should be able to model and energy minimize small compounds with ease. Hope this helps! -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** All Science is either Physics or stamp collecting -E.Rutherford ****************************************************************************** From 100012.1163@compuserve.com Sat May 4 10:25:30 1993 Date: 04 May 93 14:25:30 EDT From: "100012.1163@compuserve.com Rainer Stumpe" <100012.1163@compuserve.com> To: Subject: Re: Molecular Modeling software on PCs Message-Id: <930504182529_100012.1163_BHB12-1@CompuServe.COM> To: >internet:CHEMISTRY@ccl.net Dear Fellow Netters, MOBY 1.5, a commercial program distributed by Springer-Verlag should do the job. It reads structures and alows to superimpose them - even displaying the distances of centers that do not match. It imports many file formats and also allows for defining new once - the only limitation is that all information related to a center has to be in one line. Output format from many standard programms can be read into MOBY. MOBY has a steep discount for multiple copy orders; if you order 10 copies the price per copy is equal to popular game software. MOBY has been written by a computational organic chemist - so it has everything one would look for. Here is a list of features (but words cannot substitute for the look and feel). MOBY is a molecular modelling program for IBM-PC-compatible personal computers. MOBY offers an extensive range of modelling functions: - Display of up to 2000 centers - Fast 3D graphics - Independent manipulation of freely-definable fragments - Structure comparison - Property comparison - Force field calculations on up to 150 centers interacting with up to 2000 other centers - Geometry optimization - Conformational analysis - Molecular dynamics simulation - Extensive tools for the energy analysis of structures - Quantum chemical calculations based on the semi-empirical MNDO and AM1 methods - Display of: - IR spectra and normal coordinates - UV/Visible spectra - Molecular orbitals - Isopotential surfaces for electrostatic potentials - Freely-definable format for reading non-MOBY geometry data - Library of important structures and their geometries - Construction and maintenance of an individual structure library - On-line help - PROTOCOL mode for recording a program session - DEMO mode for re-running a previously recorded program session This latest version, MOBY 1.5, is for IBM-PC-compatible personal computers with the following minimum specifications: - 640 kb errandom access memory (530 kb free) - 80x87 arithmetic coprocessor - graphics adapter: Hercules, EGA, or VGA (1024x768 maximum) - a mouse and - a hard disk are strongly recommended running under MS-DOS version 2.0 or later. Since MOBY requires 530 kB of random access memory to be free, MS-DOS Version 4.0 is not a good choice; MS-DOS 5.0 is strongly prefered. A free interactive demo availbale for download: >from our server. Just send the commands: get /chemistry/mobydemo.exe get /chemistry/manualps.exe to: SVSERV@DHDSPRI6-BITNET via FTP by the following procedure: ftp benny.bsc.mass.edu or ftp 134.241.41.5 anonymous your_email_address cd pub cd moby binary get mobyread.me get mobydemo.exe get manualps.exe quit For more information write to: In North America: Springer-Verlag New York Electronic Media Services c/o Ms. Raye Hazan 175, Fifth Avenue New York, NY 10010 USA Phone: (212) 460-1653 Fax: (212) 473-6272 InterNet: Hazan@SPINT.CompuServe.com elsewhere: Springer-Verlag Corporate Development c/o Dr. U. Hebgen TiergartenStr. 17 D(W)-6900 Heidelberg Germany Phone: +49-(0)6221-487 406 Fax: +49-(0)6221-487 288 InterNet:Griepke@SPINT.CompuServe.com Yours Sincerely Dr. Rainer Stumpe Chemistry Editorial Springer-Verlag Tiergartenstr. 17 D(W)-6900 Heidelberg Phone: +49-(0)6221-48 73 10 Fax: +49-(0)6221-41 39 82 INTERNET:stumpe@spint.compuserve.com From chm6@midway.uchicago.edu Tue May 4 11:27:39 1993 Date: Tue, 4 May 93 16:27:39 CDT From: "charles h martin" Message-Id: <9305042127.AA00297@midway.uchicago.edu> To: CHEMISTRY@ccl.net Subject: zmatrix -> cartesian coord. Dear Netters, Does anyone know of or have a simple program (source code perferably) which will convert Z-matrix input into cartesian coordinates ? Thanks Chuck Martin chm6@quads.uchicago.edu From ZOEBISCH@CRVAX.SRI.COM Tue May 4 09:08:43 1993 Date: Tue, 4 MAY 93 16:08:43 PDT From: ""Eve Zoebisch"" To: CHEMISTRY@ccl.net Subject: charges in semi-empirical methods Message-Id: <9879447.2237434688.ZOEBISCH@CRVAX.SRI.COM> In my experience, the charges in semi-empirical methods do not depend strongly on the geometry, but depend predominantly on the values of the one-electron integrals. The one-electron integrals in MNDO reproduce ab-initio results, hence the agreement noted by Dr. Smith. Eve Zoebisch From hogue@canada.den.mmc.com Tue May 4 12:21:33 1993 Date: Tue, 4 May 93 18:21:33 MDT From: hogue@canada.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9305050021.AA03470@canada.den.mmc.com> To: chemistry@ccl.net Subject: Dehalogenation Opinions are solicited on the possible mechanism for dehalogenation described below. Perfluoropolyethers (PFPEs) have been shown to react even at cryogenic temperatures with atomically clean aluminum and iron surfaces. PFPEs also react with (most probably) Lewis acid surface sites at elevated temperatures. In both cases AlF3 or FeF3 and carbonyl fluoride (COF2) is observed. There is also some evidence for ALF6-3 species. Is fluorine anion abstraction to Lewis acid site the initiating step? Or is atomic fluorine transferred instead? My AM1 model of the small polyether represented by F3COCF2OCF2CF2OCF2*CF2OCF2CF3 (where the asterisk represents the location of the Fluorine anion abstracted, it has the largest HOMO coefficient) indicates that these coefficients changed from a state of delocalization over the central portion of the molecule to a state where the coefficients are concentrated on the three terminal fluorines and oxygen at one end of the molecule. I propose that three fluorine atoms leave the terminal -O-CF3 group to form FeF3. I think the resulting carbon triradical can undergo rearrangement with oxygen to produce carbon monoxide (also reported by some workers). Any opinions? How about a second three atom transfer to form the hexavalent fluoride?