The University of Missouri at Columbia
Chemistry 433 - Computational Chemistry - Fall Semester 2002


Professor Dr. 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 11:00 - 11:50
MW in 209 Schlundt Hall, Classroom
F in 105 Schlundt Hall, Computer Laboratory
First Lecture Wednesday, August 28
Office Hours F 1:00-3:00 and by appointment


Course Goals

Applications of electronic structure theory have become a standard and powerful tool in chemistry research. It is the goal of this course to teach students the abilities to

develop clear conceptual ideas and quantitative knowledge about methods of electronic structure theory,

read the contemporary research literature with an understanding of applications of electronic structure theory,

identify a problem in their current research that is amenable to study with electronic structure theory,

write a proposal on the application of electronic structure theory on a problem specific to the student's doctoral research,

access research computing facilities and execute electronic structure computations with knowledge about input and output,

understand the culture of the field of computational chemistry and judge your own work and the work by others in that context.




Course Materials I. Books.

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 Essentials of Computational Chemistry, Theories and Models. Christopher J. Cramer, John Wiley & Sons, Chichester, UK, 2002. ISBN 0-471 48552 7 (paperback).

(2) 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$ 30.00 (softcover) plus $1 for shipping (group order earl.y in FS02).

(3) RECOMMENDED Gaussian 98 User's Reference. AEleen Frisch, M. Frisch; Gaussian Inc.; Pittsburgh, PA, 1996. ISBN 0-9636769-7-0. Cost US$ 50.00 plus $1 for shipping (group order early in FS02).



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 provides in the section Educational Materials on the Chemistry 433 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.


Prerequisites

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.)




Activities

I. Lectures

Most Monday and Wednesday meetings times will be used for lectures in the classroom. It is important that you come to class well prepared. 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. Hand-On Computer Laboratory Instruction

Most of the Friday meetings of Chemistry 433 will be scheduled in the Computer Laboratory in 105 Schlundt Hall.


III. Exercises

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. You are not required to return the answers.

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. As the course progresses, a collection of interesting sites will be added to the Chemistry 433 Course Web Site. Suggestions of sources are welcome.


IV. Collaborative Semester Projects and Peer Review

The semester projects will be pursued by individual students or by groups of two students. Both students working in a group will receive the same grade for their project irrespective of their individual contributions.

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.

The most difficult aspect of computational chemistry relates to the selection of the topic and the identification of the most appropriate computational tool. The Project #2 is designed to address this issue.

Both (Collaborative) Semester Projects will be evaluated via public peer review (from every enrolled student in the course). 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.



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 studied in exercises and during hands-on computer instructions.

Grading involves 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 %.

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 433 Schedule. Unless there exists a good reason, submissions received after the deadline will not be graded and automatically receive a score of zero points.

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 student's 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