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SYLLABUS FOR CHEM 365 – 2007-2008 academic year (subject to change)
Prof. Rob Scarrow
office INSC E214A
610 896 1218; home 215 793 9673 [except in emergency, please call before 9:30 pm]
From Haverford College Catalog: “Topics include synthesis, spectroscopic and kinetic studies of metalloproteins and inorganic coordination compounds. Prerequisite: Consent of instructor.”
Students normally enroll in Chemistry 365 for both semesters of their senior year, and I generally give a separate grade at the end of each semester.
Subject of the bioinorganic chemistry research at Haverford. For the last several years, students in Chem 365 and I have been studying the usefulness of urea and guanidinyl substitutents within metal complexes that might act as oxidation catalysts. More recently, I’ve become interested in additional substituents that, like urea and guanidine, combine nearby Lewis base sites (that can bind to a metal ion) and hydrogen atoms with partial positive charges (that can act as hydrogen bond donors).
Modeling shows that such an arrangement could stabilize O2 binding to an iron(II) or cobalt(II), since these MII-O2 complexes have an important MIII-O2- (superoxide ligand) resonance structure, and the nearby hydrogen bond should help to stabilize the negative change on the superoxide. It remains to be seen whether this initial stabilization of O2 bound to the metal will result in a reversible dioxygen carrier, or whether the O-O bond will break to form a MIV or MV oxo species, but the latter scenario is exciting because such high-valent metal oxo species are reactive with organic species (such as with olefins to yield epoxides) and could lead to the development of new oxidation catalysts.
I will work with each student who enrolls in Chem 365 to craft their own area of contribution to the research project.
The importance of Research Groups in Chemistry. Research in chemistry (and the natural sciences in general) requires considerable resources (i.e. money), and these are usually obtained through a peer-reviewed grant funding process. Because the time from proposal submission to funding can take up to a year (even if the proposal is funded on the first submission, which is usually not the case), research must be planned months or years before it is actually performed. For this reason, it is impractical for students to independently design and carry out chemical research projects. This is true not only of undergraduate research, but also of graduate research leading to Masters or Ph.D. degrees.
Thus, both at Haverford College and colleges and universities around the world, students of chemistry join “research groups” that study a particular topic (or a set of related topics). Each research group is headed by a faculty member who has primary responsibility for the long-term planning of the research and for obtaining research funding. The student members of the research group are each responsible for a particular aspect of the research and need to work out the details of how the experiments are carried out and the results interpreted. Ideally, members of the research group are cooperative and supportive of each other and work together to carry out the research and understand the results. As students gain experience and expertise, they often work together with the faculty member to help craft proposals to fund future research (even though the funding often doesn’t arrive until after the students have left the research group).
Research groups generally have weekly meetings at which members alternate to give progress reports to the other members of the group, and/or to brainstorm with other members of the group about ways around problems that have been encountered and future directions of the research. Published papers usually include contributions from several members of the research group as well as the faculty member who heads the research group.
The bioinorganic chemistry research group at Haverford College consists of me (Rob Scarrow) and (usually) two or three students.
Expectations. I expect that each student enrolled in Chem 365 for a full credit each semester will dedicate at least six to eight hours a week to work in the laboratory. These 6-8 hours can be 2 days of 3-4 hours, or some other combination, but should involve work done during weekdays when other students and faculty are around. In addition to this, you will need to spend at least four hours a week doing literature background reading, and working on presentations or the paper. We will have a scheduled weekly group meeting and I also schedule a weekly individual meeting with each student.
Over the course of the year, students will write their senior thesis. You will also prepared a Powerpoint presentation on your research plans and early progress during late fall or early spring, and prepare a final poster based on your research which will highlight the significant findings of your research. Your presentation of the latter two assignments will influence your seminar grade, but your preparation of the PowerPoint and printed poster will be graded as part of Chem 365. (i.e. it will count for both courses, which since Chem 399 is a half credit course for the whole year, seems fair).
In writing your senior thesis, you should consult and follow the departmental writing guidelines (from the Chem Department web site under departmental resources). Various parts of the senior thesis are due as follows:
November 2: Introduction to thesis due. This should include results of literature searching and should explain the experiments you plan to do and what you hope to learn. You will probably want to revise the introduction again in the spring, but don’t view the initial submission as a rough draft. This introduction to your thesis can serve as a guide for your fall semester seminar presentation.
December 21: Fall semester progress report due. This should include all the experimental section from the fall semester experiments, as well as results and discussion of the results, as well as a plan for how to continue the experiments in the spring semester.
April 18: Rough draft of thesis due. You should aim to make this draft as finished as possible, but it may be rough in formatting details (hand-drawn structures and figures, footnote references not in final form [OK to repeat the same reference multiple times in the rough draft and fix this in the final draft], and it’s OK to include a FEW (not many!) instances of “????” to indicate a melting point or spectral data that you still need to get, reference you need to look up, or result you need to interpret better.
The final draft of the thesis will be due during finals week in Spring 2007. You will need to turn it in by the date announced by the department if you wish consideration for honors. This may be as early as May 2. Otherwise, you may turn it in on May 10, the deadline for submission of senior work.