From chiremv!andromeda!jeffb@uunet.UU.NET Fri Mar 27 02:07:29 1992 Date: Thu, 26 Mar 92 17:29:56 -0800 From: chiremv!andromeda!jeffb@uunet.UU.NET (Jeff Blaney) To: uunet!ccl.net!chemistry-request@uunet.UU.NET Subject: Re: Comp. Journal Status: R Although I also see no reason for the ACS to proliferate yet another journal in an area that already has plenty of publication possibilities, perhaps the ACS could be encouraged to make future modeling and structural (Xray/NMR) publications more useful by distributing 'Kinemages'. See the January issue of Protein Science for examples; Kinemage was described in a recent issue of C&E News. Jeff Blaney Chiron From marc@david.SACLAY.cea.fr Fri Mar 27 02:44:49 1992 Date: 27 Mar 92 08:40:58+0100 From: SBPM Marc GINGOLD To: jkl@ccl.net Subject: Re: New Journal of Molecular Modeling Status: R J. of Computer-aided Molecular Design: Volume5, Number6 December 1991 With a very good Computational Perspective by R.W.Counts (QCPE) Escom Scien Publishers B.V. P.O.Box 214,2300 AE Leiden The Netherlands. Salutations. From chemistry-request@ccl.net Fri Mar 27 12:11:12 1992 Date: Fri, 27 Mar 1992 10:19 CST From: Andy Holder Subject: Semiempirical references. To: CHEMISTRY@ccl.net Status: R Fellow Netters, Below is the compendium that I collected on the "success stories" on the application of semiempirical methods My focus was on commercial or "real world" applications, and I received quite a few entries that didn't fit into this categorization. I am surprised at the paucity of such data, but as I said in my original posting, a great deal of this is proprietary (I hope!). I would like to continue to expand this database so please pass along any further items you have. Thanks to all those who responded and to Clarke Earley here at UMKC for helping with the summaries. Enjoy... Andy =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || BITNET Addr: AHOLDER@UMKCVAX1 University of Missouri - Kansas City || Internet Addr: aholder@vax1.umkc.edu Spencer Chemistry, Room 502 || Phone Number: (816) 235-2293 Kansas City, Missouri 64110 || FAX Number: (816) 235-1717 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 1. Boyd, D. B.; Eigenbrot, C.; Indelicato, J. M.; Miller, M. J.; Pasini, C. E.; Woulfe, S. R. J. Med. Chem. 1987, 30, 528. In the search for new beta-lactam antibiotics (penicillins fall in this class of compounds), it was found that sulfur-based drugs (thiamazins) displayed no activity while the traditional oxygen-based drugs (oxamazins) were useful. The explanation of this surprising behavior was partially explained by semiempirical calculations, which indicated that the structure of the inactive drugs results in a poor fit with the "active site". These calculations (which utilized the AM1, MNDO, and MINDO/3 methods) were also able to show that several other factors were probably not important, which lowers the likelihood that potentially useful drugs will be eliminated without consideration. 2. Boyd, D. B. in Successes of Computer-Assisted Molecular Design; 1990; pp 362. Myclobutanil is a broad spectrum, agrochemical fungicide. After narrowing the possible types of compounds that appeared useful by field testing, differences between the activity of these molecules were correlated with a number of molecular properties, including an analysis of molecular charges calculated using the semiempirical MNDO method. The eventual development of myclobutanil was credited as a direct result of this analysis. 3. Earley, C. W. Inorg. Chem. 1992, in press. It is estimated that over 400,000 tons of zeolites are used annually, primarily in petroleum refining processes. Since these are solid state materials, both experimental and theoretical investigations are quite difficult. However, it has been shown that the results of quantum mechanical calculations on isolated molecules can be successfully applied to enhance understanding some of the properties of these solid-state materials. In this case, AM1 calculations on molecules containing as few as two or three silicon centers can be used to explain one of the basic structural features of these molecules, and semiempirical calculations on larger molecules have been used to determine the most acidic sites. 4. Holder, A. J.; Upadrashta, S. J. Pharm. Sci. 1992, in press. The antipsoriatic drug anthralin has been in use for over 60 years. This AM1 study explains some of the properties that make the drug active and suggests further directions for research. 5. Kador, P. F.; Sharpless, N. E. Molec. Pharm. 1983, 24, 521. Clinical trials of an aldose reductase inhibitor suggests that these types of compounds can prevent certain eye problems (cataract formation and corneal re-epithelialization) in diabetic patients. Clinical studies indicate that no "universally potent" inhibitor exists, emphasizing the need to find new drugs of this type. Comparison of the activities of several of these drugs with results of quantum mechanical calculations (energies of lowest unoccupied molecular orbitals and atomic charges) showed strong correlations, which aided in prediction of the minimal requirements for an active drug. 6. Kehl, H.; Holder, A. J. J. Pharm. Sci. 1991, 80, 139. GABA (gamma-aminobutyric acid) is a mediator of the central nervous system and has been implicated as a contributor in chemically-induced depression. A theoretical study using the AM1 method on GABA and two derivatives of this compound was able to show that one of these derivatives is more closely related to the parent system than the second. This result is in agreement with the actual experimental results. 7. Ripka, W. C.; Sipio, W. J.; Blaney, J. M. Lect. Heterocyc. Chem. 1987, IX, S95. The Phospholiphase A2 enzyme is thought to be involved in the breakdown of phospholipids, important components in living systems. This study was undertaken to show that theoretical methods can be successfully applied to drug design. Analysis of the geometries of a number of proteins suggested one key structural component. Quantum mechanical calculations not only supported these findings, but were also able to offer a simple explanation for this phenomenon. 8. Szarek, W. A.; Smith, V. H.; Woods, R. J. J. Am. Chem. Soc. 1990, 112, 4732. Quantum mechanical calculations on a number of simple sugars provided an explanation of the relative sweetness of these compounds. Analysis of the structural features observed in the calculated geometries of these compounds suggests that a previously neglected feature of these molecules may be impor- tant in determining "sweetness". 9. Wasielewski, M. R.; Johnson, D. G.; Bradford, E. G.; Kispert, L. D. J. Chem. Phys. 1989, 91, 6691. Caroteniods are light-gathering agents in the pigments of eyes. In order to understand the efficiency of these compounds in transferring light energy, a theoretical study using the AM1 method was performed. The explanation for the high efficiency of this process obtained from these calculations was in agreement with the results of experimental studies. 10. Culberson, J. C.; Walters, D. E. 199th National Meeting of the American Chemical Society, 1990, 214. Muller, G. W.; Walters, D. E.; DuBois, G. E. J. Med. Chem. 1 992, 35, 740. Hallinan, E. A.; Walters, D. E.; DuBois, G. E.; Mazur, R. H.; Muller, G. W. J. Agric. Food. Chem. 1991, 39, 1836. These three references describe cxomputational work on defining the sweet receptor and investigating compounds to interact with it more advantageously. From chemistry-request@ccl.net Fri Mar 27 12:12:40 1992 Date: 03/27/92 08:10:24 From: ZJTG05@nap.amoco.COM To: chemistry%ccl.net@vnet04.trc.amoco.COM Status: R From: Joe Golab R&D Operations, NAPERVILLE C-6, x7878 Subject: NO SUBJECT PDN: chemistry%ccl.net@vnet04 For general information. Please send queries to the people listed in the posting as I no longer work@NCSA. Thanks. Joe Golab, Amoco Chemical Company C-6, P.O. Box 3011, Naperville, Il 60566 jtgolab@nap.amoco.com :Joe *** Forwarding note from SMTP --NAPVM 03/25/92 12:56 *** The National Center for Supercomputing Applications at The University Of Illinois Urbana/Champaign Announces: INTRODUCTION TO GAUSSIAN: THEORY AND PRACTICE June 23-26, 1992 The National Center for Supercomputing Applications is pleased to offer "Introduction to Gaussian: Theory and Practice." This workshop will be presented in conjunction with Gaussian, Inc., June 23-26 1992@NCSA. Gaussian 92 is a user-friendly set of programs for performing ab initio and semi-empirical molecular orbital calculations. This workshop provides an introduction to the underlying theory along with practical pointers. All of the ab initio methods available in Gaussian 92 will be covered along with discussion on choosing methods appropriate to the chemistry being studied. Additional topics will include estimating resource requirements and dealing with computational difficulties. Instructors: John A. Pople Carnegie Mellon University H. Bernard Schlegel Wayne State University Michael J. Frisch Gaussian, Inc. Douglas J. Fox Gaussian, Inc. Tentative Agenda Topics: Introduction to the NCSA Environment Building Gaussian Input Decks Model Chemistries (basis sets, level of theory) SCF Calculations (RHF/UHF/ROHF, GVB, MCSCF) Stability and Convergence of SCF Wavefunctions Geometry Optimization (Energy Derivatives, Minima, Transition States, Reaction Paths) Electron Correlation Methods Excited States via CI Singles Interpretation of Results and Molecular Properties Solvent Effects on Molecular Electronic Structure Guidelines for Choosing Algorithms and Estimating Resources Performance of Model Chemistries (Physical Chemistry, Thermochemistry) There will be hands-on sessions each day between the morning and afternoon lectures, as well as each evening from 5:00 - 8:00 p.m. Workshop participants will be provided with a class account of limited allocation for use during hands-on sessions. ------------------------------------------------------------------------------ APPLICATION PROCEDURE (Deadline for all materials: May 14, 1992) All applicants must submit the attached application form and a cover letter which briefly (one or two paragraphs) describes your current research and how participating in this workshop will enhance your research. The cover letter should also include one or two sentences indicating your level of experience with computers. Graduate and undergraduate students should submit a letter of recommendation from a faculty member. Faculty members, university staff and post-docs are asked to submit a curriculum vitae. The registration fee for academic participants is $125.00. Arrangements for corporate attendees can be made by contacting Gaussian workshop coordinator Martha Parish@(217) 244-4198. The registration fee is due upon your acceptance to the workshop. PLEASE DO NOT SEND THIS FEE WITH YOUR APPLICATION. Hotel and travel accommodations selections will be mailed to conference participants. Hotel and travel is@the expense of participants. Please return all materials to: Martha Parish, Gaussian Workshop Coordinator National Center for Supercomputing Applications 605 E. Springfield Ave Champaign, IL. 61820 Or FAX to: (217) 244-1987 ATTN: M. Parish For more information, contact: Martha Parish@ (217) 244-4198 mparish@ncsa.uiuc.edu Lyle Rigdon@(217) 244-3659 lrigdon@ncsa.uiuc.edu ------------------------------------------------------------------------------- APPLICATION FORM Name: Address: Telephone (home): (work) Affiliation: Citizenship: Social Security Number* E-Mail Address: Are you a current NCSA systems user? Machine and user Account #: Please indicate your Research Standing (check one): Faculty _______ Postdoctorate _______ Graduate Student ______ Undergraduate Student _______ University Research Staff _______ Industrial ______ University Non-Research Staff ______ Other ______ *Submission of Social Security Number is voluntary and will not affect application. From chemistry-request@ccl.net Fri Mar 27 14:06:32 1992 Date: 27 Mar 92 16:49:33 EDT From: "S. BADJOU" Subject: POSITION To: CHEMISTRY@ccl.net Status: R Dear Netters: I just want to to draw your attention and let those of you who are inter ested that I am lookig for a postion ( postdoctoral, teaching/research etc.) in areas related to physics ( physics, chemical physics, theoretic cal chemistry, interdisciplinary areas, etc.). I have a PhD in theoretic condensed matter, many body, and statistical physics (Northeastern University, Boston, USA) and I am currently completing postdoc research at the Institut de Recherches sur la Catalyse. My CV can be found in th list entitled "positions wanted". If interested please contact me at : Salah badjou CNRS-IRC 2, avenue Albert Einstein 69626 Villeurbanne France Tel: (33) 72 44 53 55 Fax: (33) 72 44 53 99 e-mail: UCOP038@FRORS31.bitnet From chemistry-request@ccl.net Fri Mar 27 18:59:45 1992 Date: Fri, 27 Mar 1992 17:46:52 EST From: Bill Winter To: chemistry@ccl.net Status: R Since several people asked for a summary to the list on my query about programs to calculate, display and plot molecular orbitals here is the original query and the responses. Thanks to all who took the trouble to respond:-) =========================================================================== ORIGINAL QUERY >>Date: Tue, 17 Mar 1992 00:32:43 EST >>From: Bill Winter >>Subject: MO Graphics >>To: "William T. Winter" >>An organic chemistry colleague inquired about software for a PC (DOS flavor >>preferably) to draw 3-dimensional images (wire frame possibly) of molecular >>orbitals. As a modeler of fibrous biopolymers, I had to confess my ignorance >>and so I seek your assistance in locating such programs. Please reply >> to address in signature below. Thanks for your help. =====================RESPONSES FOLLOW ================================ >>Date: Wed, 18 Mar 92 9:33:57 GMT >>From: Barry Dean I have seen a package called Alchemy for ther PC, I don't know who produces it but at least it's a start for you! (it's for Messy-DOS) >From what I saw, it was very good. It was also fast even on a 386sx. Hope this helps. COMMENT (WTW) Alchemy (at least version 2)will not perform the requested function. It is a perfectly could PC or MAC prog for molecular graphics. ========================================================================= >>From: DLICHTEN@CCIT.ARIZONA.EDU >>Subject: orbital graphics on pc I would also be interested in what you learn about orbital graphics on a pc. In addition, what kind of hardcopy output can be obtained for publication purposes? Dennis Lichtenberger ========================================================================= >>From: jkl@ccl.net I am not sure about DOS, but there is a package for workstations in our archives: Dan Severence from Yale University has another present for us. The Molecular Orbital Plotting program - PSI88. Send your comments and thanks to: Dan Severance dan@rani.chem.yale.edu The headlines are: PSI/88 Version 1.0 Purpose: To plot wavefunctions in three dimensions from semi-empirical and most popular ab initio basis sets. Valence semi-empirical, STO-3G, 3-21++G(*) and 6-31++G(d,p) basis sets are implemented for atoms H-Ar. Language: FORTRAN 77 Tested on: Silicon Graphics, SUN, VMS, ULTRIX, CYBER 205, CRAY. Should be easily portable to others. Required: Any CALCOMP compatible graphics library - some are included in the distribution (e.g. PostScipt and HPGL) Memory: 200K Single precision 32bit words - PSI1, PSICON 400K Single precision 32bit words - PSI2 Authors: William L. Jorgensen Daniel L. Severance Department of Chemistry Yale University P.O. Box 6666 New Haven, CT 06511, USA. Phone (203) 432-6288 Fax (203) 432-6144 Internet: dan@rani.chem.yale.edu ========================================================================= How to get it ? (the total disk space required is about 400kBytes) If you have ftp: ================ ftp www.ccl.net (or ftp 128.146.36.48) Login: anonymous Password: Your_email_address ftp> cd pub/chemistry/psi88 ftp> ls -l ftp> binary ftp> get psi88.tar.Z ftp> quit then uncompress and untar psi88 as: zcat psi88.tar.Z | tar xvof - If you do not have ftp: ======================= You can only use this method if your mailer allows files as large as 140kB. Send following messages to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET send psi88/readme from chemistry send psi88/psi88.doc from chemistry send psi88/oscpostfile from chemistry Read "readme" and "psi88.doc" files when they arrive and decide what you need. Use your favorite editor to remove headers from "oscpostfile" and delete files which you need. Send "oscpostfile" to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET and patiently collect the incoming mail into appropriate files (which are given in the subject lines). It is a lot of work (as you can see after reading "readme" file) since before you can use these files, you have to carefully edit out the e-mail headers. Jan Labanowski Ohio Supercomputer Center jkl@ccl.net, JKL@OHSTPY.BITNET ===================================================================== Dr. S. Niketic (xpmfh01@yubsss21.bitnet) also pointed to PSI88 ========================================================================= >>From: "To help us serve you better, please take a number..." >> There is such a program in the QCPE : a modified version of Jorgensen's program by Seida and Francl (MOPC, Quantum Chemistry Program Exchange #QCPMC090). It runs under FORTRAN on the PC and compatibles. Michelle M. Francl Associate Professor Dept. of Chemistry Bryn Mawr College Bryn Mawr, PA 19010 Internet: mfrancl@cc.brynmawr.edu ========================================================================= >>From: FABY000 Bill; I know of two such systems: Desktop Molecular Modeller 2.0, Oxford Univ Press, 212 679-7300 MOBY, Springer, 800 777-4643 I cannot attest to the usefulness of these programs. A demo is available for MOBY. Roger Barry, Department of Chemistry, Northern Michigan Univ.