From chemistry-request@ccl.net Thu May 4 00:49:50 1995 Received: from postbox.acs.ohio-state.edu for chemistry-request@ccl.net by www.ccl.net (8.6.10/930601.1506) id AAA23257; Thu, 4 May 1995 00:49:49 -0400 Received: from www.ccl.net by postbox.acs.ohio-state.edu (8.6.9/5.901231) id AAA10869; Thu, 4 May 1995 00:50:01 -0400 Received: for chemistry-request@ccl.net by www.ccl.net (8.6.10/930601.1506) id UAA20627; Wed, 3 May 1995 20:50:40 -0400 Received: from bunyip.cc.uq.oz.au for wong@chem.chemistry.uq.oz.au by www.ccl.net (8.6.10/930601.1506) id UAA20579; Wed, 3 May 1995 20:46:40 -0400 Received: from chem.chemistry.uq.oz.au by bunyip.cc.uq.oz.au with SMTP (PP); Thu, 4 May 1995 10:46:25 +1000 Received: by chem.chemistry.uq.oz.au (5.65/DEC-Ultrix/4.3) id AA12073; Thu, 4 May 1995 10:45:42 +1000 Message-Id: <9505040045.AA12073@chem.chemistry.uq.oz.au> Date: Sun, 3 May 1998 23:03:19 +0900 To: chemistry@ccl.net From: wong@chem.chemistry.uq.oz.au (Richard Wong) Subject: CCL:summary (II): teaching material for computational chemistry Sender: Computational Chemistry List Errors-To: ccl@ccl.net Precedence: bulk Status: RO Content-Length: 18238 summary continue ..... -------------------------------------------------------------------- >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. ++~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~++ || __ |\ 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@chem.chemistry.uq.oz.au || ++~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~++ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: wong@chem.chemistry.uq.oz.au -- Original Sender From: Address: wong@chem.chemistry.uq.oz.au CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV