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 { *at * } 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).
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 { *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 { *at * } 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 { *at * } 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 { *at * } 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 { *at * } 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 { *at * } 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 { *at * } ibm.almaden.com (his name is Kevin
Johnson).
------------------------------------------------------------
From Pat Hogue(hogue { *at * } 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 { *at * } 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 { *at * } 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 { *at * } 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 { *at * } 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 { *at * } 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 { *at * } 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 { *at * } 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.