PSU CHEM 408 - Guidelines for Final Projects

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CHEM 408 – Sp06 2/20/2006 1Guidelines for Final Projects What’s Required: Final projects should consist of computational and/or literature work on a topic related to molecular modeling that is of particular interest to you. You will present the results of your studies orally to the class via 20 minute presentations during the last two weeks of the semester and to me in the form of a short written report. Given that 25% of your grade in the course will be based on this project, you should expect to devote an amount of time equivalent to 3-4 homework assignments for its completion. Projects are to be done individually or in groups of up to 2, as in the case of problem assignments. However, unlike problem assignments, if you work with a partner, I will expect your project to have roughly twice the scope of a single-person project and to consist of two well-defined sub-areas that will define the responsibilities of each member of the partnership. Partners will be individually graded based on their contribution to the overall project. I’d like to leave you as much freedom as possible in the choice of projects, but I would like to be involved in the early stages of your thinking in order to help ensure its feasibility. I will also ultimately need to approve your choice of project. The main constraints are i) that it be on a topic of general interest to the class, ii) that it be of the appropriate scope to yield reasonable results within the time frame available. Use this opportunity to learn more about topics we’ve already covered or to explore areas we will not cover. Finding Topics: Because I’m going to ask you to choose topics soon, you will be partially constrained by the fact that we’ve thus far only covered molecular mechanics techniques. We will begin discussing electronic structure calculations this week, but it will take some time before you will develop a good idea of what might be possible with these latter methods. (We will also be covering some aspects of condensed-phase simulation at the very end of the course, but obviously you will not be able to base a project on these methods unless you have prior experience in the area.) I encourage you to think beyond what we have done thus far to also include projects related to electronic structure calculations. In doing so it will be helpful to talk to me about which sorts of calculations are feasible and which are not. I will be happy to provide individual help getting you started on projects. In addition to talking to me, there are a number of resources that could be useful in your search for topics. There are three computational chemistry workbooks: 1. M. L. Caffery, P. A. Dobosh, and D. M. Richardson, Laboratory Exercises using HyperChem (HyperCube Inc. 1998). - covers MM & QM problems that can be addressed with HyperChem - I have a copy & will get another for 207 Whitmore 2. J. Foresman and A. Frisch, Exploring Chemistry with Electronic Structure Methods (Gaussian Inc., Pittsburgh, 1995) - covers electronic structure calculations using (an older version) of the Gaussian03 program - on reserve in PMAS and copy in 207 Whitmore 3. W. J. Hehre, L. D. Burke, A. J. Shusterman, and W.J. Pietro, Experiments in Computational Organic Chemistry (Wavefunction Inc., 1993). - electronic structure calculations, not program specific I would not want to see you just do one or more of the exercises from one of these books and call it a project, but the exercises contained therein should help you think about what is feasible with different techniques and provide ideas for possible directions.CHEM 408 – Sp06 2/20/2006 2In addition to the course text, you might want to look at the other books on reserve for the course, especially the textbooks: A. K. Rappe and C. J. Casewit, Molecular Mechanics Across Chemistry (University Science Books, Sausalito, 1997). A. R. Leach, Molecular Modeling Principles and Applications, 2nd Ed. (Prentice Hall, 2001). F. Jensen, Introduction to Computational Chemistry (Wiley, New York, 1999). Finally, the review articles contained in the series Reviews in Computational Chemistry Vols. 1-21, K. Lipkowcz ed. provide helpful overviews of all aspects of computational chemistry and molecular modeling. These reviews are intended for the non-specialist and (at least some of them) should be suitable to your background. To give you some ideas about what I envision, a few potential topics / project ideas are listed below: • how molecular modeling is used in a specific area of chemistry • modeling of particular types of biomolecules • basic ideas of chemoinformatics • molecular modeling in drug design • QM/MM methods • exploring potential energy surfaces and reaction mechanisms • incorporating solvation effects into modeling • calculation of particular experimental observables: - NMR chemical shifts - vibrational spectra - thermochemistry - photoelectron spectra - ESR spectra • intermolecular forces and weakly bound species Due Dates: Mon. Feb. 27 – submit some half-baked ideas for comment Wed. March 15 – submit a short description of the topic and format of your project for approval Mon. April 3– submit a brief progress report to let me know how you are doing (and to ensure that you’ve worked on it before then) April 17-28 – oral presentations to the class Wed. May 3 – written reports


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