Computational Chemistry Final Project
One of the goals of the problems
sets I have assigned has been to give you a sense of the breadth of quantum
chemistry. We can predict geometries,
vibrational frequencies, NMR chemical shifts, relative stabilities of families
of isomers, activation energies, and reaction energies for organic, inorganic,
and organometallic systems. With
contemporary methods, we can generate reasonable predictions for literally any
small molecule or complex one could imagine.
This enables us to go well beyond what is known experimentally, and it
can guide future experimentation. Moreover,
if we use methods of sufficient rigor, we can predict properties as accurately,
or more accurately, than experimental measurements. This is especially true for short lived
and/or dangerous species. In short,
while we have not seen all that chemists do with computation nowadays, we have nonetheless
seen a lot.
We will spend the last half of
the semester working on projects of your own choosing. You are free to choose any subject to which the
quantum chemistry you have learned can be meaningfully applied. (So this does exclude studying systems like
enzymes or polymers.) Perhaps one of the
problem sets has inspired you to explore a topic in greater detail, or the
experimental research you or your classmates have done lend themselves to
computational exploration. I have some
suggested topics below.
Here are the parameters for your
project:
·
You must base your work on at
least one article from the primary chemical literature. The paper can be experimental or theoretical,
or both (combinations are common nowadays).
You are encouraged to try to reproduce theoretical results reported in
the article, but you must make new predictions as well, either by applying the
same method to new systems or new methods to the same systems. (When you write your paper and present your
talk, you must use at least two other references not counting web sites. See below for details.)
·
Every person must base his or her
work on a different article from the literature. (You are, of course, encouraged to help one
another with all aspects of the project.)
First come, first served: the first person to submit a proposal on a
particular paper lays claim to it.
·
At least one of your predictions
must be tested against experimental data.
However, do not be cramped by this!
It is common for computational studies to validate their methodology
against some experimental measurements, but then go on to make predictions that
may not be verified for years to come.
·
Do not worry about what specific
methods you should use. I will recommend
levels of theory and basis sets appropriate to the systems you wish to study.
·
In your talk and paper on your
work, you must provide at least some qualitative discussion of your computed
results. This could take the form of
discussing periodic trends, using Lewis structure, making simple molecular
orbital arguments, rationalizing systematic errors in your predictions as
compared to experiment, etc. What I want
you to avoid is merely tabulating numbers and calling it good! Chemistry—even computational chemistry—is not
just numbers!
Here are some suggested topics (admittedly biased by my personal scientific history):
Here are some key websites for searching the
chemical literature (on the Macalester network):
http://pubs.acs.org/index.html
This site gives you access to every article
published by the American Chemical Society since the 19th century! (This includes the five articles listed
above.) Moreover, the entire contents of
every article are fully searchable. This
is a very powerful resource.
This site lets you search all of the chemical
literature published since 1985. This includes
many journals for which Macalester does not have a subscription. However, you can request these articles via
interlibrary loan.
Project Timetable: What
you have to do, and when!
Paper Expectations
The
general format is the same followed for Physical Chemistry I lab reports. Here are the details: Your paper
should contain each of the following sections, in the order given: Title,
Abstract, Introduction, Procedure, Results and Discussion, Conclusions, Acknowledgment,
References, [optional Appendix].
The Title should be specific and descriptive, but not overly long.
The Abstract should, in fewer than 250 words, summarize the entire work: the purpose, procedure, key results, and their significance should all be briefly addressed in this essential part of your paper. The Abstract is not the place to introduce your calculations or describe the background in great detail. Stated in another way, the paper really begins with the Introduction, not the Abstract. Most scientists write the Abstract after they have written the rest of the paper, since it summarizes the work described. Never present material in the Abstract that you have not also presented somewhere in the main body of the paper.
The Introduction should present the scientific motivation and background for your project. At a minimum, you should discuss the article from the chemical literature that inspired your study, as well as insights gained from two other sources, not counting web sites. In this section you must also state clearly what the goals of your project were.
The Procedure should provide a concise description of the types of calculations you performed (e.g. locating transition structures by interpolation), what level(s) of theory you used (e.g. B3LYP) and what basis set(s) you used (e.g. 6-31G(d)). You should cite Gaussian 03 (see the raw output for citation information) and WebMO, but you do not need to cite any references for your methodology.
The Results and Discussion section presents the key numerical results, comparison to experimental measurements whenever possible, and your interpretation of the results. Present your results in tables or graphs as much as possible. I also encourage you to use Chem Draw both to show molecular structures and to construct diagrams. Three-dimensional renderings (in color) of molecules may also be appropriate, especially for your talk. It is appropriate here to discuss any problems you had in your calculations, and what you did to (try to) fix these problems. As I discuss above, it is essential that you provide some qualitative discussion of your numbers. You should draw on other references to help you interpret your data.
The Conclusions section should summarize what you have accomplished in your project. Unlike the Abstract, the conclusion need not recapitulate every part of the paper. This section also should contain reflections on what hypothetical future calculations would be useful or interesting.
The Acknowledgment section should thank every person who helped you with this project.
References: You must cite all sources you have used except for course handouts. Insert a superscript number the first time you cite a particular reference, and always use the same superscript number whenever you cite the same source in your report. Instead of using footnotes, collect all citations in this final section. Follow the American Chemical Society’s conventions:
Books without Editors: Author 1; Author 2; Author 3; Author 4. Book Title, number of ed.; Publisher:
Place of Publication, Year; Number of Chapter(s) Cited. For example,
Masterton,
W. L.; Slowinski, E. J.; Stanitski, C. L.
Chemical Principles, 5th ed.;
Saunders:
Books with Editors: Author 1; Author 2; Author 3; Author 4. Chapter Title. In Book Title, number of ed.; Editor
1; Editor 2, Eds.; Publisher: Place of Publication, Year; Number of Any
Specific Chapter(s) Cited. For example,
Articles:
Author 1; Author 2; Author 3. “Title of
Article.” Name of Journal Year,
Volume, Beginning – Ending Page.
For example,
Kuwata, K. T.; Erickson, R. I.; Doyle, J. R. “Improved
Interatomic Potentials for Copper and Aluminum Sputter Atom Transport
Simulations.” Nuclear Instruments and
Methods in Physics Research B 2003, 201, 566-570.
Software:
Author 1; Author 2; Author 3. Name of
Program; Publisher: City, Year. For
example,
Corchado, J. C.; Chuang, Y.-Y.; Coitiño, E. L.;
Truhlar, D. G. GAUSSRATE 9.1; Department of Chemistry and Supercomputer
Institute, University of Minnesota: Minneapolis, MN, 2003.
Web Sites: Cite their URL.
Also note the last day you accessed the site. For example,
http://bcs.whfreeman.com/qca/
(accessed
An Appendix is not
required, but it is a good place to place extra data that you should feel
should be presented, but is too unwieldy to fit into the Results and Discussion
section.
Finally, I have no absolute minimum or maximum
length, but somewhere between 1500 and 2500 words should make the paper
sufficiently detailed without being tedious.
Talk Expectations
Prepare a formal presentation using PowerPoint or
transparencies. Follow the same
structure that you use for your paper, except that you would not have an
abstract. Be prepared to answer
questions from me and from your classmates after the talk.
For your talk, I do have absolute time limits. It must be
between 15 and 20 minutes, not counting time for questions. Practicing the talk will enable you to fit it
into the required length.
Grading
Your work on this project will be graded out of 100 points, earned in the following ways:
|
|
Task |
|
10 |
Proposal |
|
5 |
Five-Minute Update |
|
20 |
First Draft of Paper |
|
25 |
Oral Presentation |
|
40 |
Final Paper |
As stated in the course syllabus, the final project is worth 30% of
your overall grade.
REVISED COURSE
SCHEDULE (including final project deadlines)
Day
|
Date
|
What’s Due |
What’s Happening
in Class
|
|
M |
3/5 |
PS 5
|
Lecture
on basis sets, introduction to final projects, start searching the literature
|
3/12 – 3/16 Spring Break (no classes)
|
|||
M
|
3/19
|
|
Lecture on levels of theory and highly accurate
methods, hand out and introduce Problem Set 6
|
W
|
3/21
|
Proposal |
Please e-mail to me; note that this is not due on
a Monday!
|
M
|
3/26
|
PS 6 |
Brief lecture on
solvation, introduce and discuss your proposals, start working on final project
calculations!
|
M
|
4/2
|
|
Continue final project calculations
|
|
M |
4/9 |
Update
|
Listen to and discuss updates, continue final project calculations
|
|
M |
4/16 |
|
Continue final project calculations
|
|
M |
4/23 |
First Draft |
Continue final project calculations
|
|
M |
4/30 |
Talk
|
Come ready to listen and ask questions of your colleagues!
|
|
F |
5/4 |
Paper
|
This is when your final exam is scheduled; deadline is not
negotiable!
|