From pc1@pctc.chemie.uni-erlangen.de Tue Jun 8 13:34:09 1993 Date: Tue, 8 Jun 1993 11:34:09 +0200 From: pc1@pctc.chemie.uni-erlangen.de Message-Id: <9306080934.AA21805@pc1.chemie.uni-erlangen.de> To: sc18@nemomus.bitnet Subject: DOS on RS6000 Hello, To access a DOS-formatted disk from a RS6000 running AIX you can use the commands dosdir, doswrite, dosread. Have a look at the info-system on the RS6000. dosdir - prints directory information doswrite - Write a file from an AIX-directory on the DOS-disc dosread - Read a DOS-file The following batch-job allows the use of wildcards to write multiple ASCII files to a DOS-disc. ----------------------------------------- # /bin/ksh # Call this for example dw #set -x #set -v for FILE in $@ do # doswrite -a is used to copy ASCII-files (conversion of newline) doswrite -a $FILE $FILE done ----------------------------------------- To read multiple ASCII-files from a DOS-disc use the next command. ----------------------------------------- # /bin/ksh #set -x #set -v for FILE in $@ do dosread -a $FILE $FILE done ----------------------------------------- Peter Gedeck Inst. f. Physikalische Chemie I Egerlandstrasse 3 8520 Erlangen Germany Tel: ++9131 - 85 7335 Fax: ++9131 - 85 8307 E-Mail: gedeck@pctc.chemie.uni-erlangen.de From milfeld@hermes.chpc.utexas.edu Tue Jun 8 04:26:54 1993 From: milfeld@hermes.chpc.utexas.edu (Kent F. Milfeld) Message-Id: <9306081426.AA18053@hermes.chpc.utexas.edu> Subject: Southwest Theoretical Chemistry Conf. To: chemistry@ccl.net Date: Tue, 8 Jun 93 9:26:54 CDT ***************************************************** * * * Southwest Theoretical Chemistry Conference * * November 12 & 13, 1993 * * SwT * * \ * * C=C * * - Univ. of Texas System - * * Center for High Performance Computing * * * ***************************************************** FIRST ANNOUNCEMENT Mark your calendars! The annual Southwest Theoretical Chemistry Conference will be held at The University of Texas System Center for High Performance Computing (CHPC) on Friday and Saturday, November 12 and 13, 1993. We anticipate that the conference will last through Saturday morning or possibly early afternoon. All theoretical chemists are invited to participate. PROGRAM Friday and Saturday will consist of lectures and poster sessions. Lecture presentations will be 20-25 minutes in length, followed by 5-minute discussions. As usual, postdoctoral associates and graduate students are encouraged to present new and exciting research as well. The space to display posters will be 4'h x 8'w tack boards. Push pins will be provided for mounting. Please bring any other special materials you may need. The invited speaker is Professor Keiji Morokuma of Emory University. ABSTRACTS Lecture and poster abstracts must be received no later than October 27. Include the title, author's name and organization, and the abstract on a single page. Mail abstract text to "swtcc@chpc.utexas.edu" (e-mail -- preferred); or US mail to CHPC's address below; or fax it to 512-471-2445. E-mailed text will be imported into Microsoft Word and reformatted for the proceedings booklet. If you have equations or graphics in your abstract, please send a hard copy and e-mail the text. REGISTRATION AND ACTIVITY DETAILS The registration fee is $22.00 US and includes a reception on Thursday night, breaks, and dinner. The registration fee must be received by October 27, 1993. Thursday (5:30 pm - 7:30 pm) there will be a reception at CHPC in the Balcones Research Center (BRC). If you are interested in graphics, CHPC's visualization group will demonstrate and explain the steps, processes, and equipment used to animate scientific information. Staff will provide tours of CHPC during this time. Friday (6:15 pm) a chartered bus will transport you to the County Line On The Lake, a local bar-b-que restaurant, for an all-you-can-eat feast. HOTEL We have blocked rooms at the Holiday Inn Northwest Plaza, (512-343-0888). The room rate is $59 per night and will be held until October 22, 1993. You must make reservations directly with the hotel. Be sure to mention "UT - CHPC" when making your reservation or you will be charged a higher rate. If you plan to arrive after 6:00 pm, you will need to guarantee the first night lodging by credit card or advance deposit. Dr. Kent Milfeld, SwTCC Host UT System - CHPC Attn: Joyce Kokes (Registration) Attn: SwTCC Attn: Dr. Kent Milfeld (Abstracts) Balcones Research Center swtcc@chpc.utexas.edu 10100 Burnet Rd., CMS 1.154 (800) 262-2472 phone Austin TX 78758-4497 (512) 471-2445 fax cut here for registration form ============================================================================== SwT Southwest Theoretical Chemistry Conference \ November 12-13, 1993 C=C REGISTRATION FORM Mail, E-Mail or Fax Registration to: UT System - CHPC, Attn: SwTCC Balcones Research Center Please TYPE 10100 Burnet Rd., CMS 1.154, or PRINT Austin, TX 78758-4497 FAX (512) 471-2445 E-mail swtcc@chpc.utexas.edu For Information, call (800) 262-2472 Name (as it will appear on badge) Last:___________________________ First: _________________________ Organization (as it will appear on badge) _________________________________________ US Mailing Address: UT Austin ONLY: Campus Address ____________________________________ _________________________ ____________________________________ _________________________ ____________________________________ Campus Mail Code ____________ ____________________________________ City _____________________ State ________ Zip Code ______________ Telephone Number: (____)___________ Fax Number: (___)____________ Electronic mail address: ________________________________________ ____ Check here if you DO NOT want your name/address listed in the proceedings. ____ Check here for oral presentation. ____ Check here for poster presentation. Abstracts must be received no later than October 27, 1993. Title of POSTER or LECTURE (if available): _________________________________________________________________ -----------------------------ACTIVITY ATTENDANCE----------------------------- I WILL ATTEND THE FOLLOWING Please check appropriate response Reception, Thursday 5:30 pm - 7:30 pm _____YES _____NO Dinner, Friday evening _____YES _____NO Do you require transportation on Friday? _____YES _____NO Transportation to dinner is assigned on a first-come first-serve basis. Carpooling will be arranged at the conference if we cannot assign you a seat. -----------------------------PAYMENT INFORMATION----------------------------- **Registration - $22 on or before October 27, 1993 _____ Check enclosed (Make payable to UT SYSTEM - CHPC). _____ Check is in the mail. _____ IDT Information: (FOR UT AUSTIN ONLY) University Account Number _________________ University Account Title __________________ ___________________________________________ Authorized Signature Date ___________________________________________ (Please Print Signature Here) A separate registration form must be completed for each conference attendee. Maps and other information will be sent to registrants. This registration form is available from anonymous ftp: "ftp" to ftp.chpc.utexas.edu; use "anonymous" and your e-mail address for the account name and password, respectively; then "cd" to pub/swtcc and "get" regis. From JSCHELDE@STEEVAST.RUG.AC.BE Tue Jun 8 11:50:33 1993 Date: Tue, 8 Jun 93 15:09 N From: JSCHELDE%STEEVAST.RUG.AC.BE@OHSTVMA.ACS.OHIO-STATE.EDU Subject: Polygen or ...... To: chemistry@ccl.net Message-Id: <01GZ52HP0G2I000120@BGERUG51.BITNET> Hi all, I am looking for a MM/MD program .Therefore I would like to know more about the quality of different commercial packages from Polygen, Gromos ,Biosym,..... . I would really appreciate if experienced modelers could give their opinion(+ or -)on one or more of these packages. Jean-Luc ====================================================================== Verschelde Jean-Luc Dept for Mathematical Physics Dept for Biochemistry University of Ghent Krijgslaan 281 S9 B9000 Ghent Tel:091/644794 Email:jschelde@steevast.rug.ac.be Fax:091/644989 ====================================================================== From d3f012@pellucidar.pnl.gov Tue Jun 8 02:17:46 1993 Date: Tue, 8 Jun 93 09:17:46 -0700 From: d3f012@pellucidar.pnl.gov Subject: Water water everywhere but not a drop to drink To: chemistry@ccl.net Message-Id: <9306081617.AA28311@pellucidar.pnl.gov> I am curious about the way water is treated in the Discover code from Biosym. The Discover parameters below are from the Consistent Valence Force Field (CVFF) used by Discover. Biosym uses what appears to be some variant of SPC water. I give the relevant parameters below for comparison. For reference on SPC, I use the article by Jorgensen et. al. "Comparison of simple potential functions for simulating liquid water" J. Chem. Phys. 79 (1983) p. 926. SPC Discover (CVFF) ------------------------------------------------------ rigid water Yes No r(OH) Ang. 1.0 0.96 angle (HOH) deg. 109.47 104.5 Charge(O) -0.82 -0.82 Charge(H) 0.41 0.41 Ax10^-3, kcal A^12/mol 629.7 629.358 C kcal A^6/mol 625.5 625.5 The HOH angle of 109.47 for SPC water was required to fit the O-O radial distribution for liquid water, in particular the hump at ~4.5 angstroms (see above reference). The bond angle of 104.5, used in CVFF, is more in line with the gas-phase value. As well, SPC uses rigid water, while CVFF is a flexible water model with Morse potential for O-H and quadratic term for the HOH bond angle. My questions: Have there been any tests, published or nonpublished, to verify the modifications used by Biosym. Also, Discover, apparently does not implement SHAKE so that rigid water models could be used. Is the reason for this scientific or pragmatic? ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. ************************************************************************** From jstewart@fujitsu.fai.com Tue Jun 8 02:24:30 1993 Date: Tue, 8 Jun 93 09:24:30 PDT From: jstewart@fai.com (Dr. James Stewart) Message-Id: <9306081624.AA08852@fujitsu.fai.com> To: chemistry@ccl.net Subject: MOPAC 93 - Contents of MOPAC 93 (New Features) The main new features of MOPAC 93 are: ---------------------------------------------------------------------- David Danovich (Israel), Michael B. Coolidge, and James J. P. Stewart 1. Symmetry theory 1. All point groups up to order 8, except D8d, are supported. 2. Molecular symmetry is automatically recognized. 3. Molecular orbitals, normal modes, and States are labelled by symmetry. 4. Normal mode calculations are accelerated using symmetry. 5. Bloch functions in Brillouin Zones can be analyzed by symmetry 6. The Hessian matrix in normal mode calculations is symmetrized. ---------------------------------------------------------------------- Henry Kurtz, Prakashan Korambath (Memphis State University) 2. Non Linear Optics - quantities calculable: 1. Electrooptic Pockels Effect 2. Optical rectification 3. Second harmonic generation 4. Third Harmonic generation 5. DC-EFISHG 6. Frequency-dependent NLO ---------------------------------------------------------------------- James J. P. Stewart (USA) 3. Solid-state 1. Polymers, layer systems, and solids 2. Geometry optimization 3. Brillouin Zone calculation 4. Density calculation for 3-D systems ---------------------------------------------------------------------- George Medrano (USA) 4. Bond-order analysis 1. Coulson and Mulliken 2. `free valence' 3. Open shell bonding ---------------------------------------------------------------------- David Danovich (Israel) 5. Correction to Ionization Potentials using Green's Functions ---------------------------------------------------------------------- Andreas Klamt (Germany) 6. COSMO technique for modelling solvents 1. User-specified dielectric constant 2. General geometry optimization 3. Charged and uncharged systems supported 4. Dielectric of 1.0 reproduces gas-phase system ---------------------------------------------------------------------- MOPAC 93 (Improved Features) Frank Jensen (Denmark) . . . Much improved EigenFollowing routine Victor Danilov (Ukraine) . . Improved description of MECI John Simmie (Ireland) . . . Manual reformatted in LaTeX James J. P. Stewart (USA) . Manual expanded to include more theory. Yoshihisa Inoue (Japan) . . Up-to-date fundamental constants used. James J. P. Stewart Tel: (719) 488-9416 FAX: (719) 488-9758 Email: jstewart@fai.com From tony@wucmd.wustl.edu Tue Jun 8 09:52:18 1993 Date: Tue, 8 Jun 93 14:52:18 -0500 From: tony@wucmd.wustl.edu (Tony Dueben) Message-Id: <9306081952.AA16035@wucmd> To: chemistry@ccl.net Subject: undergrad computational chem Netters: As promised, better late than never, summary of responses to my query about teaching computational chemistry at the undergraduate level. Thanks to all who responded by e-mail, phone, or letter. Anthony J. Duben (tony@wucmd.wustl.edu) Center for Molecular Design Washington University Campus Box 1099 One Brookings Drive St. Louis MO 63130-4899 314-935-4672 ------------------------------------------------------------- Henry Rzepa has been using Cache on a Mac and has developed a lot of material. He can be contacted -- Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.3, Tel:+44 71 225 8339, Fax:+44 71 589 3869. --------------------------------------------------------------- Volume 4 of REVIEWS IN COMPUTATIONAL CHEMISTRY has been published in the Spring of 1993. Not every library has a copy of it yet so you may not be aware of its contents. It contains a long article on the topic of teaching computational chemistry at the undergraduate level. "Computational Chemistry in the Undergraduate Curriculum" by Roger L. DeKock (Calvin College), Jeffry D. Madura (University of South Alabama), Frank Rioux (St. John's University), and Joseph Casanova (California State University at Los Angeles). REVIEWS IN COMPUTATIONAL CHEMISTRY is edited by K. B. Lipkowitz (IUPUI) and Donald B. Boyd (Lilly Research Laboratories). Information about Volume 4 (280 pp, ISBN 1-56081-620-1, 1993) can be obtained from VCH Publishers, Inc., 303 NW 12th Avenue, Deerfield Beach, Florida 33442. In the U.S., call 800-367-8249, FAX: 1-800-367-8247; in Europe, 49-6201-6060, FAX: 49-6201-606328. Price $79. With a standing order for the book series, the price is $65. ------------------------------------------------------------------ Greg Landrum at Cornell has used CaChe software and believes that it would be suitable in an instructional setting. -greg Landrum landrum@chemres.tn.cornell.edu ------------------------------------------------------------------ Ganesan Ravishanker (ravishan@swan.wesleyan.edu) will be teaching a modeling course here at Wesleyan in the Fall and will use Hyperchem on a 486PC running MS Windows. HyperChem is marketed by Autodesk. ------------------------------------------------------------------------ For the sake of reminding everyone of a complete set of notes at the graduate level, recall C. Cramer's earlier e-mail: Colleagues, Given the increased interest in computational chemistry courses taught at the undergraduate and graduate levels, I have provided the computational chemistry archive at the Ohio State Supercomputer Center with an ASCII ftp file containing the majority of the materials used in the teaching of Chemistry 8003 here at the University of Minnesota. All chemistry graduate students are required to take at least two of three core courses during their first two years, and Chemistry 8003 is one of these. This core program is new. Thus, this was the first time 8003 was taught. In this posting, I include only the general description (2nd below). The ftp file is roughly twenty pages long (Microsoft Word single spaced text only file). Jan has kindly provided me the foolproof instructions for getting this by either ftp or e-mail (1st below). If you access these materials, we would be VERY grateful to receive your comments. Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 cramer@staff.tc.umn.edu (612) 624-0859 ---------------------------------------------------------------- [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] You can obtain the materials (over 40kBytes file) via ftp or by e-mail: How to get it using FTP: ======================== ftp www.ccl.net (or ftp 128.146.36.48) Login: anonymous Password: Your_email_address ftp> cd pub/chemistry/comp-chem-courseware ftp> ascii ftp> get chem8003.txt ftp> quit How to get it using e-mail: =========================== Send the following message (exactly as written): send comp-chem-courseware/chem8003.txt from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET and the message containig the materials will be forwarded automatically to your electronic mailbox. ---------------------------------------------------------------- [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] Chemistry 8003 was a one quarter, four credit course. It met 30 times in ten weeks for one hour each class. The classroom included a Mac IIsi on the ethernet hooked to a large-screen projector for demos. The course was taught for the first time in the Winter Quarter of 1992. Attached are the course syllabus, outline, problem sets, handouts, and the final exam and final assigned paper. Literature articles were used heavily for discussion; the references are included in the course outline. The attached materials are not copyrighted, and we encourage their use by any organization or individual so inclined. Certain handouts did not lend themselves to ASCII reproduction, and are not included. The 39 students (and roughly 15 auditors) had access 12 hours per day to a microcomputer lab. The software used in the course included PCModel, running on IBM 386 clones and Macintosh IIci's (we preferred the latter), AMSOL v.3.0.1 and Gaussian92. The latter two program suites were run on an IBM RS/6000 model 560. Communication with the workstation used NCSA Telnet v.2.5 for Macintosh. Students also had access to Microsoft Word 5.0, ChemDraw 3.0 and Chem3D 3.1 all running on Macs. All software was obtained under the appropriate license agreements except AMSOL and NCSA Telnet, which are currently public domain. Problem sets were completed by groups of two, the final exam and critical analysis paper were individual projects. Some overall impressions were: 1) our syllabus was a bit ambitious given the time constraints -- we cut a few things down, although we still tried to cover all topics. 2) We converted about 5-10% of the class to computational chemistry, inspired another 25-30% to start using some modeling software in their experimental research, left another 50% with a demonstrably larger (and perhaps even appreciated) understanding of computational chemistry, and the remainder left with the same prejudices against theory with which they came in. 3) As a rule, physical chemists thought there wasn't enough theory, organic chemists thought there was far, far too much theory, inorganic chemists felt slighted that so few techniques existed to treat metals effectively , and biological chemists wondered who cared about small molecules anyway. 4) More workstation power would have been nice. 5) As far as the course text(s), Clark is very out of date at this point with regard to ab initio HF theory, fairly out of date with regard to semiempirical MO theory, but still quite reasonable for molecular mechanics and technical issues like Z-matrices, etc. Hehre, Radom, Pople and Schleyer was placed on reserve for the class, but deemed a bit too expensive and technical to be a required textbook. The same was true for the Reviews in Computational Chemistry series edited by Boyd and Lipkowitz. -- With the exception of the conversion to comp. chem. rate (which we never expected to be so high!), all of these things were about what we expected, and we were pleased with the initial offering of the course. Obviously, we hope to improve on this in future years. Christopher J. Cramer Steven R. Kass ------------------------------------------------------------- Rozeanne Stecker (steckler@sdsc.edu) has been teaching such a course for the past four years. ------------------------------------------------------------ Tom Cundari at Memphis State (cundarit@memstvx1.memst.edu0 has begun teaching such a course at the upper division undergrad/. lower division grad level. He has taken what may be an unorthodox approach in that he has used no texts, no handouts, tests or anything. He subdivides the students into groups and has them work on projects where the chemistry is of interest to them. As most of undergrads do research with the profs here at MSU, they have some feel for what they find interesting and what they would like to calculate (some feasible; some not). The only requirement is to write a paper in JACS format abut their project: successes, failures, what new chemistry the learned, what could be done (or avoided) for the future, etc. By taking the "learn by doing" approach it is more work (for students and prof), but he believes that the approach is more realistic than giving canned projects or just lecturing on the laws of quantum mechanics. The benefits are 1) the students are forced to work together as a team, crucial in modern research. 2) the students are given ample opportunity to screw up (no amount of lecturing can reinforce what one simple deletion of a full days work can!) and discover (e.g., why does MOPAC work for this and not that; what can be calcd. and what can't and why?), 3) being in the lab is just plain more fun than sitting in lecture! The main deficit in addition to the extra work is that the class will fail for students who are not self motivated. They have been fortunate in that this has not been a problem. Some of the projects have turned out to be quite neat. Perhaps the best thing from his point of view is that nearly all of the projects correlate with experimental research going on in the Chemistry Department at Memphis State (either that of the students taking the courses or their fellow students). Examples: "A Semi-empirical Study of Homoaromaticity in Nitrogen-Substituted Carbocycles;" "A Semi-empirical Study of the Synthesis of Potential Drugs and a Comparison of the Stabilities of Ene-amine and Imine Tautomers;" "Designing New Cyclopentadienyl Ligands with Chelating Substituents;" "A Computational Study of Spin-Density Patterns in Substituted Dihydropyrazine Cation Radicals;" "An Ab-initio Investigation of Transition and Lanthanide Metal Catalyzed Hydrogen Exchange in the Presence of an Electric Field;" "An Ab-initio Investigation of Metal-Sulfido Bonding;" Future modifications: First, introduce more cutting edge technology, in particular parallel computing access. Second, induce/force/coerce more of the computational students into taking the class, even though they know most of this already! This gives the exptl. folks an anchor for the first few weeks while learning the mechanics of the programs; it also forces the comp. chem. people to talk to exptlsts. (and vice versa) and gives everyone a better comprehension for the problems of each other and what it takes to solve these problems and get the job done. Hardware Resources: 3 RS-6000 550's; 2 VAX mainframes; a DECstation 3100, and attendant PCs and Macs to serve as front end GUIs and back end data analysis stations. Student Prerequisites: The students must have at least taken up to the first semester of P. Chem. All I really want is for them to have an open mind to the potential of comp. chem. to act as an aid to traditional experimental research. The class is taught in a fashion which resembles the running of a research group. The students stop by usually with a day or so notice and work for 3-5 hours at a clip. It is very informal and we have been lucky to have independent students who can handle this set up and who when they run into problem call me or get a book out and learn how to assign a point group, the diff. between ROHF and UHF, why MOPAC doesn't work for TMs, etc. and related discoveries. Since we have some very good comp chem grad students between Henry Kurtzand myself it has been like having full time TA's to get the exptl. folks up to speed as quickly as possible. I will be very interested to see how others have tackled the problems of teaching a comp chem class. [We have limited ourselves to the programs MOPAC (because of its relative ease of use and applicability to large organic systems) and GAMESS (because I am familiar with it and it forces the students to know how to assign point groups!).] ----------------------------------------------------------------- Brian Duke (B_DUKE@DARWIN.NTU.EDU.AU) and Brian O'Leary carried out a survey last year of what is going on in this area and there is quite a lot. Unfortunately both have massive teaching loads at present and analysing the results keeps getting postponed. They hope to write it up for J Chem Ed. Brian Duke teachs a final level course (or unit as we call them in Australia) here that includes comp chem, but mainly comp quantum chem - use of ab initio (GAUSSIAN), Huckel, EHM,etc. This goes down quite well. I would like to broaden the Comp Chem material, but it is also the only final year Phys Chem and it includes Stat Mech, Spectroscopy, general Quant Chem etc. --------------------------------------------------------------- From Jeffry Madura(madura@moe.chem.usouthal.edu): Attached below is a copy of my syllabus for the course I teach here at the Univ. of South Alabama. %% This document created by Scientific Word (R) \documentstyle[12pt,qqaalart]{article} \author{Jeffry D. Madura} \title{Computational Chemistry } \input tcilatex \begin{document} \maketitle The application of computational chemistry methods to solve problems in chemistry and biology will be discussed. Topics to be covered in the course include {\it ab initio}, density functional, semiempirical, and empirical methods, molecular modeling, and molecular and protein dynamics. Each of the above topics will be reinforced through the use of the latest software available on the ASN supercomputer and the IBM workstations located in the Chemistry Department. \medskip\ \TeXButton{Text} {\begin{tabular}{p{5.5in}} \centerline{{\bf Text}} \\ "A Computational Approach to Chemistry" David M. Hirst, Blackwell Scientific Publications, Oxford, 1990. \\ "A Handbook of Computational Chemistry: A Practical Guide to Chemical Structure and Energy Calculations" Tim Clark, Wiley-Interscience, 1985. \\ "Dynamics of Proteins and Nucleic Acids" J. A. McCammon and S. C. Harvey, Cambridge University Press, Cambridge, 1987. \\ "Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics" C. L. Brooks III, M. Karplus, and B. M. Pettitt, Wiley Interscience, 1988. \\ "Molecular Mechanics" U. Burkert and N. L. Allinger, American Chemical Society, 1982. \\ "Learning the UNIX Operating System" O'Reilly and Associates, Inc., 1987. \\ "Computational Chemistry Using the P.C." Donald W. Rogers, VCH, 1990. \\ "Computer Modeling of Chemical Reactions in Enzymes and Solutions", Arieh Warshel, Wiley, 1991. \\ "Molecular Dynamics Simulation: Elementary Methods" J. M. Haile, Wiley, 1992. \end{tabular} } \medskip\ \TeXButton{Programs} {\begin{tabular}{lp{3.25in}} \multicolumn{2}{c}{{\bf Software}} \\ HyperChem & Molecular modeling program that runs on the PC. \\ QUANTA/CHARMm & Molecular modeling program that runs on the IBM. \\ Gaussian 92 & {\it ab initio} program that runs on the ASN Cray. \\ SPARTAN 2.0 & {\it ab initio} program that runs on the IBM. \\ DMol 2.2 & Density Functrional program that runs on the IBM. \\ UHBD & Electrostatics and Brownian Dynamics program that runs on the IBM and ASN Cray. \\ MS Word & Word processing program that runs on a PC. \\ MS Excel 4.0 & Spreadsheet program that runs on a PC. \\ MS FORTRAN 5.1 & Programming language that runs on a PC. \\ \end{tabular} } \medskip\ \TeXButton{Syllabus} {\begin{tabular}{ll} \multicolumn{2}{c}{{\bf Material to be Covered}} \\ Topic & Laboratory Topic \\ \\ {\it ab initio} methods & {\it ab initio} experiment \\ & Gaussian 92 calculation or SPARTAN \\ \\ Density Functional methods & DFT experiment \\ & using DMol 2.2 \\ \\ Semiempirical methods & Semiempirical experiment \\ & MNDO and AM1 calculation \\ & using HyperChem or SPARTAN \\ \\ Empirical methods & Empirical application \\ & Extended H\"uckel calculation\\ & using HyperChem \\ \\ Molecular Mechanics & Energy minimization application \\ & using HyperChem or SPARTAN \\ \\ Molecular Dynamics & Molecular dynamics application \\ & using HyperChem or QUANTA \\ \\ Protein Dynamics & Protein dynamics application \\ & using HyperChem or QUANTA \\ \\ Electrostatics & Electrostatic calculation \\ & using in house program (UHBD) \\ \\ Brownian Dynamics & Calculate diffusion-controlled \\ & rate constant by writing a simple \\ & FORTRAN program \\ \end{tabular} } \bigskip\ \begin{center} {\bf Guidelines} \end{center} \medskip\ Since this is a ``Directed Studies'' type of course the following guidelines will be enforced. \begin{itemize} \item Eleven (11) laboratory units covering the topics outlined above must be completed within the quarter. It is suggestted that two units be completed each week and handed in within one week of finishing the laboratory. \item The laboratory report will have the following sections \begin{itemize} \item abstract \item introduction \item computatioanl method \item results \item discussion and conclusions \item references \item answer to questions \end{itemize} \item Each experiment should take 2-3 hours to execute on the computers. \item It is anticipated that each laboratory should take approximately 2 hours to write. \item Preparation time, i.e. becoming knowledgable about the topic, should take about 6-8 hours. \item Arrange a time in which I can sit down with you for about 1 hour to discuss any problems or explain what is going on. \end{itemize} \end{document} -------------------------------------------------------------------- From James Foresman (foresman@lorentzian.com) As regards your question about Computational Chem. in the undergraduate curricullum, I would like to inform you of the existence of two resources: 1. The MoleCVUE Consortium (Molecular Computation and Visualization in Undergraduate Education Consortium) This is a group of a dozen of so active undergraduate educators who are working together to build various experiences of comput. chem. into undergraduate curriculla (freshman-senior years). You may contact the organizer at: ranck@vax.etown.edu This is the email address of John Ranck of Elizabethtown College. If you desire, he can put you on the email list for distribution and information regarding the activities of the consortium. We welcome people who are interested in reviewing and/or adding to the things which we develop. 2. The book, "Exploring Chemistry Through Computational Methods: A Guide to using Gaussian," J.B. Foresman and AE. Frisch, 1993. Is available from Gaussian Inc. A copy comes free with the purchase of Gaussian or it may be obtained for $35 by contacting Gaussian Inc 4415 Fifth Ave Pittsburgh, PA 15213 voice: 412-621-2050 fax: 412-621-3563 This is a work which I co-authored with AEleen Frisch Which was intending to be used as a special topics course or as a part of a physical chemistry course. Let me know if I can comment further on either of these resources. --------------------------------------------------------------- From Bill DeSimone: You might want to call Warren Hehre of Wavefunction, Inc. (SPARTAN). He is interested in this market and has done some prelimary work. Warren doesn't use e-mail, but you may get through to him through Joe Leonard. Anyway, his phone number is 714-955-2120. [I talked with Warren Hehre and he graciously sent me a lab manual of projects that he has developed. His approach is a practical one that seeks to develop judgment about the capabilities of various kinds of software.] --------------------------------------------------------------- From Ken Fountain (sc18@NEMOMUS): He has put together such a course in a pair of lab manuals he wrote around the old AEON coprocessor boards running MOPAC. The course is being totally revised this summer around HYPERCHEM and some more standard computer engines. -------------------------------------------------------------- From Dan Thomas (CHMTHOM@vm.uoguelph.ca ) Last fall I attempted such a course. Briefly, it was very difficult but quite rewarding. I hope to give it another try or two and see if it is possible. The reasoning behind this attempt was rather obvious. In looking in the offices of my various colleagues in the department, it became clear that the individuals who were most regularly using "quantum mechanics" were not the physical chemists but rather the organic and inorganic chemists, who with their commerical molecular modeling programs were daily looking at structures and assessing stabilities of molecules. The theoretician in the department was naturally the power user, but the people, some of whom admitted to never having had a course in quantum mechanics, who really "used" quantum mechanics were from this other group. With the advent of more and more software, it is only to be expected that our students will be utilizing these tools upon graduation. It is requisite upon us to make sure that we generate students with sufficient knowledge to be able to critically evaluate the results from these commercial programs, for we all know the multiplicity of dangers which lurk behind the blind acceptance of the results from these programs (we used Hyperchem from AutoDesk). Hence I approached this course from the idea that this might be the last P. Chem. course the students would take and that it would prepare them to intelligently use the upcoming software tools. I hoped to get the students to the point where they could appreciate the significance of the various semi-empirical techniques, starting with Extended Huckel and going through CNDO, MINDO/3, NNDO, to AM1. They also need to understand the various molecular modeling procedures like MM2 or MM3. As well, a number of programs employ routines for biochemically important species with different forcefields such as AMBER or CHARMM. Most chemists only employ these kinds of calculations, leaving ab initio techniques to the real quantum chemists, but an appreciation of what is involved in running a progam such as GAUSSIAN 92 would not be inappropriate for these people. Such were the objectives of the course. So, what happened. The course had previously been given as a third year, one semester course in quantum mechanics. The students had previously only had about 5 weeks of quantum based physical chemistry in second year. I determined that it would be important to start from the beginning, review vector and matrix algebra and then briefly demonstrate the correlation between functional analysis and vector analysis. This, of course, justifies the mixed usage of the terms "wavevector" or "wavefunction". We also discussed eigenvalue problems. We spent some time with simple models (free particle, tunneling through a barrier, particle in a box, particle on a ring, particle on a sphere, particle in a sphere), showing how to apply these ideas rigorously. We quickly got into Dirac notation, emphasizing that we will let others solve these problems from first principles, but that we will simply use the known results. From there, we needed to touch on spin and atomic spectroscopy. This lead to the theory of bonding and molecular orbital theory. At this point one can start to discuss the various semiempirical techniques. As you can see, this is an horrific amount of material and it was my downfall. There were 14 students in the course. 1 had not had any quantum before, 3 were physics students who had 2 full courses of quantum before, 1 was a mathematics student with lots of math but no chemistry, and the rest were mainstream chemistry students with the background I was expecting. The spectrum of preparation was too broad. We spent about 5 hours a week in classes and it was grueling. At the end, we were all glad we did it. The physics students regularly expressed appreciation for the physical descriptions given for the equations employed - they had been taught how to use the mathematics but had never received an explanation for what they meant. The other students were pushed far beyond what they thought they could do. (Near the end, they reported incidents of where they were able to assist friends with problems in the physics quantum courses). We are learned a lot, but it was not a pedagogically sound course. It should take at least a full year to cover this material. We used the text "Elementary Quantum Chemistry" by Pilar (McGraw-Hill). I chose it because it was the only one I found which had extensive sections on the semiempirical and ab initio techniques (about half the book). It did start from the beginning and it was a good development, but it was more appropriate for a grad course or at least to be covered in a full year. I am worried that the answer needs to be something like: We can either teach non-physical chemists how to use these programs and to give them an appreciation of the procedures so that they can start to critically evaluate the results OR we can teach quantum chemistry to physical chemists. I would like to think we could do both, but I'm afraid that the two may be mutually exclusive if one or two semesters is all that is available. I want to try it again and I would appreciate any feedback you may have from your own experiences. I have a colleague who may be trying to start this kind of program at a small college (Goucher in Baltimore) this coming year. He is currently at IBM Almaden but would equally be interested in any comments or suggestions. If you have information or more questions you might try communicating with him at johnson@ibm.almaden.com (his name is Kevin Johnson). ------------------------------------------------------------ From Pat Hogue(hogue@canada.den.mmc.com) As a graduate student using a MOPAC-type program (GEOMOS QCPE #584) I think undergraduates would benefit especially if a graphical output is used. I learened a lot just by modelling molecules like HF an O2 etc. The little graphical demo from CaCHE can teach a lot about the quantum mechanical basis for thermodynamics.God bless your efforts. =---------------------------------------------------------------- From: ranck@albert.etown.edu (John P. Ranck) Welcome to the MoleCVUE Consortium e-mail list. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PURPOSE ======= The MoleCVUE [Molecular Computation and Visualization in Undergraduate Education] consortium was formed by faculty in undergraduate chemistry departments (principally members of MAALACT): to focus and stimulate cooperative development, testing, sharing, and promulgation of ideas, systems, and pedagogical materials for teaching and using computationally-aided molecular structure and reactivity tools in the undergraduate curriculum; to develop and distribute instructional materials freely; to influence commercial developments supportive of these activities; to serve as a model for cooperative curricular development among faculty at geographically dispersed institutions working via the Internet and to stimulate the formation of other such groups in other fields of chemistry. MEMBERSHIP & COMMUNICATIONS =========================== We are currently fifteen active members from Pennsylvania, Maryland, Virginia, North Carolina, New York, Missouri, and South Dakota and approximately thirty "listeners" from a much wider geographic region. We are trying to make this an open consortium. All interested parties are invited to listen to and/or join in the electronic discussions and to become "active" members by attending our workshops or otherwise participating in the work. E-MAIL: ------- Messages posted to: MOLECVUE@VAX.ETOWN.EDU will be forwarded to all known participants -- by email if you have email, otherwise by U.S. Mail periodically until things get out of hand. Members may of course communicate directly among themselves as it serves their purposes. FTP: ---- I will maintain an ftp site Host: VAX.ETOWN.EDU (I.P.Address: 192.146.186.2) Username: MOLECVUE Password: MOLECVUE I will maintain several files and directories in this "library" MEMBERS : A current list of names, addresses, phone numbers, etc. A member will be identified as "active" if he/she has participated in one or more of the activities of the consortium until is is apparent that he/she is no longer active. Others on the distribution list will be identified as "listeners" until they choose to participate. Commercial "listeners" will be identified separately. INTERESTS : A directory containing a text file submitted by each member who cares to contribute -- stating his/her interests and/or (ESPECIALLY) current projects. Please post an entry for yourself to MOLECVUE@VAX.ETOWN.EDU This posting will be automatically distributed to all and I will update your entry in the ftp library. New members will be able to find out who is doing what by reading this library. You are free to "roam" the library and "get" anything of interest or to create directories in which you may "put" files others may be interested in. Please use descriptive names for your directories and files, include some obvious .DOC or README file to describe what is there, and announce your contribution to all by posting a message to everybody (via the MOLECVUE@VAX.ETOWN.EDU address). PLEASE BE CAREFUL AND TRY NOT TO CREATE HEADACHES FOR ME OR FOR THE SYSTEM ADMINISTRATORS. Contact me if you need any assistance getting anything in or out of the ftp library. CURRENT ACTIVITIES ================== The consortium meets two or three times yearly for several days to examine and learn new software and techniques and to plan cooperative projects. The next such workshop is planned for early summer 1993, probably at Elizabethtown College. Currently, each member is exploring a variety of instructional tools and techniques by developing one or more instructional units from his/her own pedagogical perspective. These units are to be completed by May 1, 1993 and shared with other participants for criticism (via Internet). At the Summer 1993 meeting, we expect to select the best tools and methods, select appropriate curricular writing projects, assign teams, and begin work in earnest with definite deadlines. A substantial amount of our current activities and development are related to the molecular modeling program HyperChem by Autodesk, Inc. COMPUTERS ========= An essential requirement in our efforts is that the hardware and software be affordable by any undergraduate chemistry department. Currently, we are examining computational systems and tools running on Intel 386 based systems under Microsoft Windows 3.1. There is some interest in low-end unix systems. We have had little discussion and made no decisions regarding MacIntoshes. FINANCIAL ========= We are pledged to distributing all materials as freely as possible and have no expectation of individual financial rewards. (We are also actively attempting to influence commercial software developers and vendors to provide software for undergraduate instruction at affordable prices.) CONTACT ======= John P. Ranck Internet: RANCK@VAX.ETOWN.EDU Department of Chemistry Voice: 717-361-1315 Elizabethtown College FAX: 717-361-1207 Elizabethtown, PA 17022-2298 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From: C.S.Raman(raman@bioc01.uthscsa.edu): 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. ------------------------------------------------------------------- from: Fred Brouwer Laboratory of Organic Chemistry , University of Amsterdam Nieuwe Achtergracht 129 , 1018 WS AMSTERDAM , The Netherlands phone 31 20 5255491, fax 20 31 5255670 I am running an undergraduate course on Molecular Modeling (molecular mechanics, dynamics, quantum chemistry) for third year chemistry students. We use Sybyl and Spartan on SGI and IBM workstations and PCModel on an IBM PC and a Macintosh. The approach is mainly to give hands-on experience. It turns out that these young people have very little computer experience, and dealing with the programs is a major effort. The theoretical part of the course is rather superficial. Most students are oriented towards organic chemistry (unfortunately primarily identified with synthesis in this lab, as in many other places) or inorganic chemistry (which in our department happens to be organometallic chemistry), and most of them hate everything that looks like an equation. In any case I hope they learn that they can use MM as a practical tool in their research, if only to help to look more closely to their molecules. After the course (3 credit points = 3 weeks of full-time work) they have some idea of Molecular Mechanics, are deeply aware of the multiple conformation problem, and know which systems they can and cannot submit to quantum chemical calculation. The course material is still in a primitive state, I don't dare to show it to anyone outside. ----------------------------------------------------------------------- I received from Lee Wilson (LWILSON@polaris.lasierra.edu) a copy of the syllabus used at LaSierra University in the mail. There is too much for me to retype here. Please contact Dr. Wilson directly if you would like a copy of the syllabus. From MARYJO@northeastern.edu Sat Jun 8 11:02:21 1993 Date: 08 Jun 1993 16:02:21 -0500 (EST) From: MARYJO@northeastern.edu Subject: polyethylene glycol? To: chemistry@ccl.net Message-Id: <01GZ53BWHHEW94GS3X@northeastern.edu> Hello netters. A colleague of mine is interested in polyethylene glycol (PEG) modified proteins. Is anyone aware of any modelling studies or other studies which might give information about the structure of PEG, or PEG-modified proteins? I will be grateful for any references or advice. Mary Jo Ondrechen From raman@bioc01.uthscsa.edu Tue Jun 8 14:44:56 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9306090044.AA07394@bioc01.uthscsa.edu> Subject: Re: polyethylene glycol To: MARYJO@northeastern.edu Date: Tue, 8 Jun 1993 19:44:56 -0500 (CDT) Hi > A colleague of mine is interested in polyethylene glycol > (PEG) modified proteins. Is anyone aware of any modelling > studies or other studies which might give information about > the structure of PEG, or PEG-modified proteins? Well, Plenum publishing corporation came out with a book last year called "POLY(ETHYLEN GLYCOL) CHEMISTRY: Biotechnical and Biomedical Applications" ed. J. Milton Harris, 1992; ISBN: 0-306-44078-4 which discussed in detail most of what is known about PEG and its structural implications. I also had quite a few chapters on PEG-modified proteins. You might want to obtain a copy of the same! Some related facts: 1. There is considerable interest at the moment in what is known as "macromolecular crowding", reactions by themselves slow but can be accelerated to the diffusion controlled limit in the presence of polymers like PEG (cf. see papers by P.-H.von Hippel and by Zimmerman as well) [Proc. Natl. Acad. Sci. USA 84, 1871 (1987)] 2. There has been numerous studies on the effect of PEG on protein stability by Timasheff's group (Brandeis) and Jim Lee (UTMB, Galveston) and these are good papers to read (see Biochemistry 26, 7813 [1987] and references therein. 3. Jan Hermans wrote an article back in 1982, that explicitly discussed modelling polymer-protein interactions: see J. Chem. Phys. 77, 2193 . 4. Polysciences Inc. (215-343-6484) is the leading manufacturer and supplier of PEG for medical applications and their tech. support might have additional information that may be of help to you. 5. A series of papers appeared recently on "Protein-surface interactions in the presence of PEG" in J. Colloid and Interface Sci. cf. 142, 159 [1991]. PEG is extremely interesting to those interested in protein structure since it not only can be used in assisting the folding process, but also be used in crystallization. Hope you find these citations helpful! Cheers -raman -- 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 UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ******************************************************************************