From wong $#at#$ chem.chemistry.uq.oz.au Wed May 3 20:52:44 1995 Received: from bunyip.cc.uq.oz.au for wong "at@at" chem.chemistry.uq.oz.au by www.ccl.net (8.6.10/930601.1506) id UAA20510; Wed, 3 May 1995 20:42:12 -0400 Received: from chem.chemistry.uq.oz.au by bunyip.cc.uq.oz.au with SMTP (PP); Thu, 4 May 1995 10:41:51 +1000 Received: by chem.chemistry.uq.oz.au (5.65/DEC-Ultrix/4.3) id AA12031; Thu, 4 May 1995 10:41:09 +1000 Message-Id: <9505040041.AA12031 -x- at -x- chem.chemistry.uq.oz.au> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sun, 3 May 1998 22:58:47 +0900 To: chemistry #*at*# ccl.net From: wong -AatT- chem.chemistry.uq.oz.au (Richard Wong) Subject: summary (I): teaching material for computational chemistry Dear netters, Last week I posted a question on the availability of teaching material in internet suitable for undergraduate courses in computational chemistry and molecular modeling. Many thanks to people who replied to my request. Appended below is the summary. Cheers! Richard From: savary "at@at" sc2a.unige.ch (Francois Savary) ____________________________________________ You can take a look at my WWW Document, it might interest you. It deals with Molecular Graphics and Rendering techniques. http://scsg9.unige.ch/eng/toc.html in English http://scsg9.unige.ch/tabmat.html in French hope it helps Francois From: b_duke(-(at)-)lacebark.ntu.edu.au (Brian Duke) _____________________________________________ We have a CAUT grant for doing exactly what you are asking. It is early days however. Point your browser to http://www.chem.swin.edu.au/CAUT.htnl and you will see where we are at. If you want any more information, mail me. I would be interested to hear what you you are planning. I have done a lot of Gaussian work with final level students here. Cheers, Brian. From: borkent' at \`camms1.caos.kun.nl (Hens Borkent) _______________________________________________ In reply to your question I would like to point to our www page at www.caos.kun.nl which contains links to html courses 'under development'. There is one on computational chemistry, albeit confined to the programs we offer. See under 'tutorials' on the home page, and 'watch the progress' of the compchem course. Comments are very welcome! Hens Borkent CAOS/CAMM Center From: jim (+ at +) volvo.wavefun.com (jim Parisi) ________________________________________ Have you tried "Experiments in Computational Organic Chemistry" by Hehre, Burke, Shusterman, and Pietro? If you are interested in a copy, please let me know. Thanks! Jim Parisi Marketing/Sales Coordinator From: "Jeffry D. Madura" _______________________________________________________ I am teaching such a course right now. I will be placing the lecture notes, course outline and homework assignments on Mosaic in the next few weeks. I will send a follow-up e0mail to you and the CCL list when I have this done. You may wish to look at Chapter 4 in vol 4 of Rev. Comp. Chem. where we discuss this topic. Best Regards, Jeffry D. Madura From: "Wayne Huang" _____________________________________________ Regarding your quest for teaching materials or media, we have developed some undergraduate computational chemistry materials over the time which might be related what you asked (1) Textbook: Warren Hehre, Lonnie Burke, Alan Shusterman & William Pietro, Experiments in Computational Organic Chemistry, wavefunction, 1993. (2) CD-Rom: Tom Hehre, Lonnie Burke, Wayne Huang & Warren Hehre, Chemistry Disk I, Wavefunction, 1995 (3) Warren Hehre, Wayne Huang, Chemistry with Computation, wavefunction, 1995. Currently we are working on a book "Computational Experiments in General Chemistry". We also offer three-day intensive workshops in Computational Chemistry which has been helpful for people interested in undergraduate education. For workshop info: workshop -8 at 8- wavefun.com For book info: sales ^at^ wavefun.com From: P8946019[ AT ]csdvax.csd.unsw.EDU.AU _____________________________________ I have written and put together a teaching package which can be used to illustrate the basic priciples of computational chemistry and quantum mechanics.If you are interested, send me an enote and I'll give you some further info. Try science (+ at +) uniserve.edu.au for other educational science progs. Hugh From: kcousins-0at0-wiley.csusb.edu (Kimberley Cousins) __________________________________________________ I posted this a while back. Hope it helps. Kimberley Cousins Date: Tue, 8 Jun 93 14:52:18 -0500 From: tony $#at#$ wucmd.wustl.edu (Tony Dueben) Subject: undergrad computational chem Sender: chemistry-request -x- at -x- ccl.net 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 -x- at -x- 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 #*at*# 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 %-% at %-% chemres.tn.cornell.edu ------------------------------------------------------------------ Ganesan Ravishanker (ravishan # - at - # 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.,at,.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;at;ccl.net or OSCPOST;at;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 (+ at +) sdsc.edu) has been teaching such a course for the past four years. ------------------------------------------------------------ Tom Cundari at Memphis State (cundarit %! at !% 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). Th e 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 at.at 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 -AatT- 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} ++~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~++ || __ |\ Dr. Ming Wah (Richard) Wong || || / |_| \ ----------------------------------------------|| || .' \ Department of Chemistry || || / *\ The University of Queensland || || \ __ / Brisbane, Qld 4072, Australia || || \_.-' \_ / Fax: +61 7 365 4299 | Phone: +61 7 365 3829 || || v email address: wong (- at -) chem.chemistry.uq.oz.au || ++~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~++