© 1998-9 Rainer Glaser. All rights reserved.
The University of Missouri at Columbia
Chemistry 412, Computational Organic Chemistry, FS99

Collaborative Learning
and Peer Review
in Chemical Learning Communities

Project #2: Project Proposal.



Purpose & Basic Idea

We will be dealing in this course with quite a variety of computational methods. In many instances we will only have time to concern ourselves with the important principles and some of the theoretical background. With the widespread availability of computers, the applications of the computational methods are so extensive in breath and depth that only a partial and subjective coverage is possible. Yet, it is the intelligent application of the methods to well formulated problems that determines the quality of computational studies in chemistry. Hence, the training of this aspect of computational chemistry is essential. There is a big difference between knowing about the principles of the theoretical methods and being able to employ these tools in a meaningful way. Chemical knowledge together with well developed deterministic as well as reflective judgments all are necessary ingredients to succeed at this level of complex analysis and synthesis. No budget is required as part of this project proposal. I want you to think freely at this stage of the game.


Assignment

(1) Read the current literature and identify a problem of general interest that has not been solved. Select an important problem. Select a difficult problem.

(2) Identify a specific problem that you will tackle. Be sure to select a key problem and make it understood why the problem you tackle is in fact a key problem.

(3) Describe in detail the project plan including methodology, scope, interpretation, feasibility and timeline.

(4) Posting the project proposal on the Chemistry 412 Course Web Site.

(5) Oral presentation and defense of the project proposal to the class.

(6) Project evaluation via peer review after the oral presentation.


Constraints on the Choice of Topic

You are not entirely free in the choice of the task. I would like you to select from the following methods. Ideally, there should only be one group developing a project in a certain area. There are circumstances, in which I will allow several groups to develop project based on similar methods.

	Hueckel Theory
	Extended Hueckel Theory
	Semi-empirical theories (CNDO, MNDO, SAM)
	Hartree Fock Theory (RHF, ROHF, UHF)
        Perturbation Theory (MP)
        Configuration Interaction Theories (CC, CI, QCI)
	High-Level Model Theories (G1, G2 and such)
	Properties (Populations, GVF, ELF, E-fields) 
	Molecular Modeling
	QSAR	

Project Proposal - Submission & Content

Your proposal needs to be emailed to the instructor as an attachment. Incomplete submissions will be returned by email with comments as to what additions and improvements are required. The write-ups can be prepared in either of two formats.

HTML Format. If you write HTML, then submit your report as an html file with the name "group_n_project2.html" where "n" is the number of your group. If you created any files that you want to link to the your project proposal page, start the names of all of these files with "group_n_" and include these files as attachments as well. For example, if your write-up contains GIF or JPEG images or molecules as PDB files, then these files all should be submitted along with the main page and relative path names should be used. Only such local and relative links are allowed to assure that the products will stay intact in the Chemistry 433 Course Web Site in future.

WORD Format. You can email a WORD file to me. This file will then be converted into a PDF files for posting on the Chemistry 433 Course Web Site. The submitted WORD file should be all-inclusive.


The write-up must contain the following information. Stick closely to the sequence. Review the peer review instructions for project #2 before you write your report. Your write-up is limited to (the equivalent of) 6 written pages of text with line spacing of 1.5 lines including text, references, art work and tables.

The project proposal title should describe what type of computational method is being used for what purpose. Leave one blank line after the headline and then provide the authorline. If the problem set was created by a group, then give the name of the group and the names of the students in the group in alphabetical order. Leave two blank lines after the authorline.

The introduction (not to exceed 1 page) should describe the context and should contain a very brief, concise, and clear synopsis of the general problem. The statements and claims made should be supported by a few references (about 5 - 10) to primary and secondary literature. State the general goals of current developments in this area and state what major problems need to be solved for significant progress to be made. As to the general problem, you have a choice: You can use a well-known standing problem (scholar projects) or you can try to formulate a new problem (inventor projects). There are merits to both approaches and you may pick according to personal preference. In particular, it is perfectly fine to select a topic that is directly related to your thesis research. Indeed, it is hoped that you will pursue such a topic and that the time spend in Chemistry 433 will initiate your own continued efforts!

The goals & objective section (not to exceed 1 page) should identify the specific problem you want to solve. Explain how this project would solve or bring closer to a general solution the larger challenge described in the introduction. Clearly isolate the problem that you want to take on and make clear statements as to what would be gained if such knowledge and/or understanding about this problem could be acquired. State clearly why such knowledge and/or understanding can only be gained from theory and computations or, at least, whey it would be advantageous to use theoretical rather then experimental approaches.

The proposed research section is the main body of project #2.
(a) Choice of Methodology. Describe in detail what methods you intend to use. Argue in favor of this choice as compared to other approaches.
(b) Scope of Project. Describe in detail what kinds of computations will be carried out and what kinds of key data will be obtained.
(c) Interpretation. Describe in detail how the data are to be interpreted. Be certain to separate fact and assumption.
(d) Facilities and Feasibility. Describe in detail the hardware that you intend to employ. For the purpose of this project proposal you are not limited by actual availability of hardware. Rather it is the intended that you show your ability to match the right kind of hardware (PC, workstation, minisupercomputer, Cray, 1024-PC-parallel net with Linda) to your problem.
(e) Timeline. Describe the planned timeline for the project. Use time estimates that are as realistic as possible.
Group Actions & Dynamics should also be described in addition if this project is carried out by a group. Supply this part in a separate file. This section should not exceed (the equivalent of) 1 written page with a line spacing 1.5 lines. Provide information about group meetings and about group dynamics. The description of the group meetings should include information as to how often and where the group has met to work on the Chemistry 412 Group Project #2 and should include accurate estimates of the time spend in each meeting. As to group dynamics, briefly describe experiences made while working on this project with the group. How useful was the group's brainstorming power in the quest to identify a suitable project? How many papers did you consider before you decided your selection? How many journals did you browse in the process? Mention advantages and be frank about problemes you encountered. Comment as to whether the collaborative learning went beyond working on the Chemistry 412 Group Project. Do you think you benefited on a personal level from the interactions you have had with your peers while working on this project? Conclude by stating whether you would want to engage in such group activities again.


Relevant Dates and Deadlines

Approval of Topic Selection. Friday, November 5, 1999.
Claim a topic and a computational method by sending a message to the Chemistry 412 mailing list stating your claim. Should similar claims be made, then the time on the email header decides priority. The instructor reserves the right to decide competing interests. Subsequently, you should meet with the instructor briefly to discuss the scenario and get it approved. It is the purpose of this approval to avoid weak proposals from the start.

Electronic Submission of Project Proposal to Instructor. Friday, November 26, 1999.

Posting of Project Proposals. Monday, November 29, 1999.

Presentation and Defense. Thursday, December 2, 1999.

Submission of Peer-Evaluations. Friday, December 3 (midnight), 1999.

Posting of Final Results of Group Project #2. Monday, December 6, 1999.




Absolument mon ami, l'excellence est une habitude.