© 1999 Rainer Glaser. All rights reserved.

The University of Missouri at Columbia
Chemistry 412 - Computational Organic Chemistry - Fall Semester 1999

Instructor Professor Rainer Glaser
Office 321 Chemistry Building
Telephone (573) 882-0331
E-Mail GlaserR@missouri.edu
Chemistry 412 Course Site http://www.missouri.edu/~chemrg/RG_T_FS99.html
Lecture MWF 9:00 - 9:50
Computer Laboratory 105 Schlundt Hall
Meet in 202 Schlundt Hall until 105 is ready.
First Lecture Monday, August 30
Office Hours MW 10:30-11:15 and by appointment
Review & Discussion Computer Laboratory in 105 Schlundt Hall on Wednesday evenings.
Course Content See Literature List

Course Materials I. Books and Model Sets.

Some of the content of this course is taken directly from the primary and secondary literature. You will be given reading lists for the various chapters containing the references to the literature discussed in this course. You will also be given a list of pertinent books on the various areas of computational chemistry. Many of these books are recent and up-to-date. Consult them for details, references, and later on in your own research. Three texts you might find useful to purchase for the course and for future reference are:

(1) REQUIRED Molecular Modelling. Principles and Applications. A. R. Leach; Longman, Singapore, 1996. ISBN 0-582-23933-8. Cost > US$ 50.

(2) RECOMMENDED Ab Initio Molecular Orbital Theory. W. J. Hehre, L. Radom, P. R. Schleyer, J. Pople John Wiley & Sons, New York, New York, 1986. ISBN 0-471-81241-2. Cost US$ 145.00.

(3) REQUIRED Exploring Chemistry with Electronic Structure Methods. J. B. Foresman, AEleen Frisch, 2nd ed.; Gaussian Inc.; Pittsburgh, PA, 1996. ISBN 0-9636769-3-8. Cost US$ 42.00 (softcover).

(4) REQUIRED Gaussian 98 User's Reference. AEleen Frisch, M. Frisch; Gaussian Inc.; Pittsburgh, PA, 1996. ISBN 0-9636769-7-0. Cost US$ 50.00.

Course Materials II. Webware & Software.

Inside and outside of the classroom, we will make use of the world wide web as a tool for instruction. Instructions will be posed in the section Exercises on the Chemistry 412 Course Web Site.

The course includes hands-on molecular modeling as a major part of the learning activities. The students will be working with word processing programs (WORD), spreadsheet programs (EXCEL), structure drawing software (ChemDraw), molecular modeling software (Chem3D), and electronic structure calculation software (Gaussian 98).

All required hardware and software are provided by the MU Department of Chemistry.


It is assumed that you are familiar with the concepts and principles covered in Chemistry 233, Physical Chemistry (Continuation of 231. Covers wave mechanics, bonding, molecular spectroscopy, and statistical mechanics.)


I. Lectures

It is important that you come to class well prepared! Do read the background material before it is covered in class. If primary or secondary literature will be discussed, make sure you have read the article(s) before the lecture. The lecture will be more beneficial to you if you do. One of the advantages of being well prepared is simply that you need to write less during the lecture and, instead, you will be able to follow the lecture intellectually. After the lecture, read the material again and test yourself, possibly in a small group setting. If uncertainties remain, review the material again or come to office hours.

II. Exercises - General, Specific and Online

General Exercises: Throughout the semester, we will read current articles on computational chemistry and discuss the items. Much of this discussion will occur on a discussion list. Written discussion will greatly improve your communication skills and your competency. Refer to the instructions concerning the organization of Paper of the Week Club.

Specific Exercises: I will select from various sources or generate and distribute (in hardcopy or electronic form) problems relating to specific topics discussed in lecture. Assignments will be posted on the Chemistry 412 Course Web Site. You are not required to return the answers. On occasion, we might discuss these problems in review & discussion sessions.

Online Exercises: There are quite a few useful computational chemistry related web sites on the WWW. We will make attempts to harvest whatever knowledge can be gained from such sources. Assignments will be posted on the Chemistry 412 Course Web Site. As the course progresses, there will be a little collection of interesting sites added to the Chemistry 412 Course Web Site. Feel free to inform me about sites you would like to have added.

III. (Group) Collaborative Semester Projects and Peer Review

Depending on enrollment, the semester projects will be pursued by individual students or by small groups. I favor group projects and groups of two or three would be ideal. We will have to see.

Case studies are the best way to exercise the concepts discussed in the lecture. The identification of an application of modern computational methods in the current literature and the creation of a problem assignment are the subject of Project #1.

Perhaps the most difficult aspect of computational chemistry relates to the identification of the right tool for the job. The Project #2 is designed to address this issue.

Both (Collaborative) Semester Projects will be evaluated via peer review. Aside from learning content, you will be learning how to judge / be judged via peer review. Your ability to prevail in peer review will, certainly no less than content knowledge, affect your success in future.

IV. Review & Discussion Sessions and Hands-On Computer Instruction

Review & discussion sessions will be scheduled in the evening on Thursdays. These sessions are intended to serve several purposes: First, further discussion of the more difficult topics presented in class, secondly, discussions of problems, and - most importantly - general Q&A and problem solving strategies. Furthermore, a large part of the hands-on instructions will occur in these sessions. For dates and topics of review & discussion sessions, see reviews & discussion.

V. Discussion List - Asynchronous, anytime, anywhere, on anything!

To encourage discussions amongst yourselves, you will be subscribed to an electronic discussion list. The discussion list will be employed for informal discussions as well as for the formal discussions associated with the Paper of the Week Club activities.

Details about the discussion lists will be given in lecture. See also the links to showme accounts and discussion list.

Examinations and Grading

The Greek philosopher Socrates argued that the unexamined life is not worth living. Accordingly, there will be two 1-hour-examinations (100 points each), two quizzes (50 points each), two term projects (100 points each assigned by peer review), and a comprehensive final (200 points) for a total of 700 points.

Quizzes are limited to inquiring facts dealt with in the lecture or in homework. Tests will assess your level of understanding of the material covered in the lecture. The tests will contain but are not limited to lecture and homework material. In tests you are expected to abstract from the latter and apply your knowledge to different scenarios. Tests will also include the materials studies in the online exercises, during hands-on computer instructions, and the materials associated with the Paper of the Week Club.

In the past, performance was assessed based on a relative grading scheme. No grades were assigned to individual tests, quizzes and projects. After each examination the students were given a graph representing the performance of the class so that an assessment of the student's relative performance was possxible. Grades were assigned on the basis of the average and the distribution width of the normed course performance diagram (frequency of score versus scores) such as to realize a grade point average of about 1.6 or 1.7. You may take a look at the instructor's Chemistry 433 WS98 site to find previous implementations of this grading scheme.

Beginning with WS99, the instructor has changed to an absolute grading scheme. Grading is now based on competency rather than competition. The following cuts will be used: Grade A above 85 %, grade B above 70 %, grade C above 55 %, and grade D above 40 %.

Deadlines for submissions of semester projects and for the submission of peer reviews are specified on the assignments and also can be found on the Chemistry 412 Schedule. Unless there exists a good reason, submissions received after the deadline will not be graded and automatically receive a score of zero points. Deadlines will be strictly enforced!

In concert with the policy of the Department of Chemistry, there will be no make-up exams. If a test is missed for a legitimate reason (sickness and the like with some type of acceptable written proof), a score will be determined for this missed test that is based on your average overall performance. If you know in advance, that you will not be able to take an exam for a certain reason, talk to the instructor before the date of that test. If you do miss a test without a legitimate reason, you will receive a score of zero points for that test.

Time and date of the final examination are determined by Article V of the Academic Regulations which are designed to protect students from irregularities in the administration of final examinations. The following two excerpts from Article V are relevant to this graduate class. (1) No teacher will hold an examination during any time other than the regular meeting time of the class or the time as approved by the Registrar for both final and multi-section examinations. The only exception is that examinations in courses numbered 400 and above may be conducted at any time agreeable to both the teacher and the students. (2) No examination may be held during Stop Day.

Academic Honesty

Academic honesty is fundamental to activities and principles of a university. All members of the academic community must be confident that each person's work has been responsibly and honorably acquired, developed, and presented. Any effort to gain an advantage not given to all students is dishonest whether or not the effort is successful. The academic community regards academic dishonesty as an extremely serious matter, with serious consequences that range from probation to expulsion. When in doubt about plagiarism, paraphrasing, quoting, or collaboration, consult the course instructor. Proven academic dishonesty will be reported to the Provost for Academic Affairs and the studentŐs Dean.

Compliance with the Americans with Disabilities Act

If you have special needs as addressed by the Americans with Disabilities Act (ADA) and need accommodations (for example, extended testing time, note takers, large print materials), please inform your instructor privately as soon as possible. In most circumstances, students with disabilities seeking academic accommodations should also register with the Access Office, A048 Brady Commons, 882-4696. As necessary, the Access Office will review documentation about your disability and about the need for accommodations you are requesting. The Access office will then assist in planning for any necessary accommodations.

Excellence is a Habit