CHEMISTRY 191a,b
SENIOR EXERCISE IN CHEMISTRY
(September, 2007 Version)
FIRST MEETING PRESENTATION FALL 2007
The senior exercise in chemistry is designed to provide the student with an opportunity to examine a topic in depth and to communicate the results in both written and oral formats. Satisfying the graduation requirement for the senior exercise is achieved by successful completion of Chemistry 191a,b. There is one exception to this. Those with an interest in chemical engineering can satisfy the exercise by enrolling in the Engineering Clinic at HMC for two semesters if the project has a significant chemical component. Those selecting this option should make arrangements with the chemical engineering advisor and must in addition to the work required for HMC Engineering 112,113 also submit a written thesis to the department and give an oral presentation. Normally, the student enrolls in Chemistry 191a in the fall of the senior year and in 191b in the spring. In 191a, the student will be asked to submit short reports including an abstract of the work to be completed, an annotated bibliography, and a progress report on the work completed during the semester. In 191b, each student submits a written thesis and gives an oral presentation on the thesis.
The student can pursue either a literature thesis or an experimental thesis. A literature thesis involves drafting of a critical review of a topic on the frontier of chemistry. Further details on this option are provided in Appendix A. An experimental thesis involves a research project, normally in the laboratory of a member of the department or in the HMC Engineering Clinic. The research project could be entirely computational in nature. Students pursuing the experimental option often begin work on the project in the summer preceding the senior year. Those electing the literature thesis should establish at an early date a healthy habit of perusing the chemical literature (.e.g. by reading Science and C&E News) and are strongly encouraged to have a tentative selection of the topic before the start of the fall semester.
In any case, the student will select a thesis advisor and should meet periodically with him/her to discuss progress on the project. The thesis advisor will be the first reader on the thesis; the department will select the second reader for the thesis. Overall organization of the senior exercise is the responsibility of the senior thesis coordinator, the faculty member assigned to Chemistry 191. He/she will schedule periodic meetings and organize the oral presentations in the spring semester.
Each student will be asked as part of Chemistry 191a to submit his/her topic to the chemistry faculty for review. Approval of the topic is a prerequisite for a passing grade in 191a and registration in 191b. In the case of an experimental thesis in which a faculty member has selected a student to work in his/her laboratory, this approval is usually pro forma. However, feedback generated by other faculty in the approval process often can assist the execution of the project. Literature theses are examined more carefully. The student should expect anticipate a thorough review if he/she petitions the department for the option of completing the work under the auspices of another institution. With the exception of the HMC Engineering Clinic, a strong case will have to be given for work done elsewhere.
Chemistry 191a, the first semester of the Senior Thesis, is a half-course and is graded P/NC. The following schedule will be followed:
a) Preferably prior to the start of the semester, meet with faculty who are conducting research in an area that you find interesting. Information on faculty research can be found in the department Web page (www.chemistry.pomona.edu). It is your responsibility to make arrangements with the faculty member with whom you wish to work. If your thesis work is a continuation of work performed during the summer, this selection process was made when you were chosen for participation in our summer program. We shall assume that your summer research experience was positive. Continuing your summer research as your thesis project has benefits for both you and your faculty advisor.
If you prefer to elect the literature thesis, the selection of the topic is the most important step. The topic should be important, current, interesting to you, accessible to you, and represented by a reasonable body of papers. Finding a topic that meets all these criteria takes time. We encourage every student to browse on a regular basis periodicals such as Science, Nature, and C&E News. If you do this faithfully, you will inevitably stumble across suitable topics. Effort to define a thesis topic in a few days of concentrated library work usually yields an unsuitable topic. Once you have found a potential topic, discuss it with a faculty member with interests in the area or related area. The process of discussion will usually lead to defining a topic in a form that will be approved by the faculty.
b) Submit to the senior thesis coordinator and your thesis advisor an abstract with the following information: your name, the name of your advisor, the title for your thesis, the nature of the thesis (literature search or experimental thesis), a short description of what you are studying, and a short description of what you hope to learn. Please submit this Thursday September 20. (The first week of classes begins on a Tuesday.) The abstract will be reviewed by members of the department. We prefer that you submit the abstract electronically in Microsoft Word doc format as an Email attachment. Send it to Professor Garza. He will assemble all the abstracts received by Thursday 5pm and will distribute them together to each of the faculty members.
c) Professor Garza and Professor Taylor will organize a meetings to illustrate methods of searching the chemical literature. Prof. Taylor will be the key person for you to contact regarding EndNote. You will be notified via e-mail of times in which these Professor Taylor will do these demos.
d) Once your topic has been approved by your thesis advisor, begin work on your project. In the case of an experimental thesis, it is important that you reach an understanding with your advisor on his/her expectation of the amount time spent in the lab. All students should conduct a literature search. In the case of a literature thesis, the search is expected to be exhaustive.
e) Prepare an annotated bibliography of the material assembled in the search. Present a copy of the annotated bibliography to the senior thesis coordinator and to your advisor by the Wednesday following the fall break in October. A short example of an entry in an annotated bibliography follows. Note that it includes a full bibliographic citation with the title of the article and a précis of the content of the article.
Kohlmann, O.; Steinmetz, W. E.; Mao, X.-A.; Wuelfing, W. P.; Templeton, A. C.; Murray, R. W.; Johnson, C. S., Jr., "NMR Diffusion, Relaxation and Spectroscopic Studies of Water Soluble, Monolayer-Protected Gold Nanoclusters", J. Phys. Chem. B 2001, 105, 8801-8809. [The authors propose that gold nanoclusters complexed with the ligand tiopronin have gold cores with either octahedral or C5 symmetry and support this model with a variety of NMR measurements.]
f) Continue work on your project. At the end of the semester, submit a short progress report to the senior thesis coordinator and your advisor. The report should discuss what has been accomplished during the semester and set plans for work to be completed during the following semester. The report is due on the last day of classes (12 December in 2007). Send it electronically to Prof. O'Leary since I will be in Guatemala. I will be back on the 15th.
Chemistry 191b, the second semester of the senior exercise, is also a half course and must be taken for a letter grade. Satisfactory completion of Chemistry 191a is a prerequisite. The final grade in the course is based primarily on the grade on the written thesis. However, the grade on the oral presentation can have a subjective impact on the final grade and the recommendation of the department in awarding Latin honors, e.g. summa cum laude. Also, the evaluation of your oral presentation can be invaluable as an indication of where you have done well and where further learning is desirable. The following schedule applies to Chemistry 191b:
a) An orientation meeting will be held very early in the semester when concrete deadlines will be given.
b) Continue to analyze the literature and/or collect data in the laboratory.
c) Assemble the information into a coherent picture, identify holes, and attempt to fill them with further experimentation and searching of the literature.
d) Prepare your oral presentation and practice it before your friends. Discuss the format of your presentation with your thesis advisor. Most students prefer to use Microsoft PowerPoint. The following steps must be followed to avoid last-minute disasters. Users of PowerPoint must load their presentation onto a CD which can be loaded from a PC (not a Mac) at the time of delivery. Test your presentation on the PC in the auditorium before the day of the presentation. Do NOT depend on downloading your presentation from the network.
e) Submit to the senior thesis coordinator a one-page abstract of your work with the following information: your name, the title of your study, a summary of the work, and 2-3 relevant citations to the literature. The deadline is two weeks before the day of the thesis presentations. The abstracts will be collected in handout for the presentation. If you fail to meet the deadline, your entry in the collection will be a blank page containing your name and the title of your project. Also provide the name of the student who will introduce you. If you don't, the coordinator will find someone to perform a suitable introduction. Please provide the abstract electronically as an Email attachment in Microsoft Word doc format. Contact Lauri Bell for this.
f) All the thesis presentations are given on one afternoon, usually the Friday before spring break. This is an occasion to shine and students normally do. Invite your parents and friends. Each speaker will be introduced and the introducer will also handle the short question period after the talk. Following the presentations, students and faculty will retire to a restarurant such as Bucco di Beppo for example, for an evening of frivolity.
g) At its first meeting after the break, the faculty will evaluate the presentations for form and content. Your thesis advisor will share the evaluation with you. The evaluation will provide direction for the final steps of your research and the preparation of the written thesis.
h) Address any deficiencies indicated by the evaluation of your oral presentation and write your senior thesis. Guidelines for the format of the thesis are included as Appendix B of this handout. Refer to J. S. Dodd, The ACS Style Guide, 2nd. ed. for recommendations on writing the thesis. Above all, consult with your thesis advisor on the format.
i) Submit two, unbound copies of your thesis (one to your thesis advisor and one to the second reader of your thesis) on the fourth Monday after the spring break (14 April in 2008). Treat the version that you submit as if it were the final version provided to the editor of a journal. It is not a rough draft.
j) The two readers will carefully read the thesis and provide you with their evaluations. Use their input to revise your thesis and submit one final, bound copy of the thesis as well as the two previously submitted copies with the readers' comments to the coordinator of the senior thesis on the sixth Monday after the spring break (28 April in 2008). This bound copy will become the permanent archival copy. It is considered a courtesy to provide your two readers with a bound copy of the final version.
Appendix A
Guidelines for a Literature Thesis
INTRODUCTION. The literature search option of the senior exercise in the Chemistry Department involves drafting a critical review of some chemical topic which is under active research investigation at the present time. The project consists of two parts: a written thesis and an oral presentation based on the thesis. Satisfactory performance on both parts is required although the written thesis is given greater weight in the determination of the final grade. The exercise provides an opportunity to explore a single subject in depth and tests your ability to analyze data using the principles and methodology of chemistry. This document, which is based on student and faculty experience, was drafted to give helpful information and ground rules for the exercise.
DEFINITION OF TERMS. A critical review is expected. A necessary component is an exhaustive review of the literature but the work must go well beyond this. The critical aspect of the project involves a careful reading of the papers, extracting the relevant material and organizing it, judging whether the claims made are valid, and suggesting further experiments to settle unanswered questions. Ask the following types of questions: What experimental evidence as opposed to conjecture actually supports the claims? Are the data valid (e.g. systematic error, controls, etc.)? Were the data analyzed correctly; do the data necessarily lead to the conclusions drawn in the paper or are alternate hypotheses also consistent with the data? The research on a well chosen topic may turn up two or more competing models. This is an ideal situation for a critical review which can have real value to the scientific community. The careful reviewer should marshal the evidence for each model and comment on the strengths and weaknesses of the models and the possible need for additional experiments. In separating the wheat from the chaff and in organizing the evidence, a reviewer can bring order and insight to a murky area. This type of review can be a stimulus to further progress in a particular field and a well written review on the right topic can be a research contribution as important as an experimental paper.
You should focus primarily on chemical ideas and information which are relatively new to all chemists rather than on empirical and theoretical elements of the established body of chemical knowledge. For example, a review of a new theoretical approach to the understanding of liquids would be acceptable; a compilation of partition coefficients of chlorinated hydrocarbons would not. Naturally, the specific project chosen may require more or less effort in reviewing, learning, and presenting "textbook" information, but a project that consisted of this alone would be another course, not the senior thesis. The majority of the papers in your bibliography should be recent (0-5 years old) although references to the older literature should be made when it is appropriate.
The Chemistry Department has given a broad definition to the term "chemical" so that students can work on topics that they find interesting. However, there are limits which the following examples should clarify. A proposal to review the chemical basis for the function of interferon was accepted but a suggestion to review the clinical use of interferon to combat tumors was turned down. A review that focuses more on the genetic than the biochemical aspects of oncology is more appropriate in the Biology Department. Recall that one goal of the senior exercise is to demonstrate a command of chemical principles.
SELECTION OF THE TOPIC. The most important step in the completion of the senior exercise is the selection of a topic and sufficient time should be budgeted for this step. Ideas for past theses have come from several sources: a seminar talk, a topic mentioned in passing in a course, a journal article, or a suggestion made by a faculty member. In selecting a topic, you should consider the following factors. The topic should be sufficiently narrow so that a thorough analysis and discussion is possible. If the topic is too broad, there is barely enough time to assemble a bibliography; and a cut-and-paste job is usually the result. If the topic is too narrowly defined or if the literature is too recent, there is not enough material to write on. Such a topic may be fine for a short paper but not for the senior thesis. The selection of the topic may be limited by the number of core courses completed by the time of registration. It would be inappropriate to write on the molecular spectroscopy of gas phase ions if you have not yet taken physical chemistry. You should be interested in the topic. It is your thesis and you choose the topic. From the student's point of view, this is the advantage of the exercise. The student has a major role in defining the exercise and controlling its direction.
ROLE OF THE FACULTY. As mentioned above, one member of the faculty who assists you in the selection of your topic becomes your thesis advisor. He/she will also be available for discussion and advice during the development stage of the thesis. You are encouraged to discuss the planning of your oral presentation with your thesis advisor. Soon after your oral presentation, you should meet with your advisor who will discuss with you the faculty evaluation of your talk. The evaluation will be invaluable in directing the preparation of the written thesis. The faculty may require examining aspects of your topic that were not addressed in the oral presentation. Your advisor will also give you the comments on your written thesis and recommendations for revision.
Do not feel restrained to seek advice only from your advisor. Your advisor may refer you to other members of the faculty who have the expertise to answer particular questions more thoroughly. Professors emeriti/ae such as Professor Hansch have also been helpful. One member of the faculty has the responsibility for handling the mechanics of the senior exercise. He/she will schedule an information meeting early each semester and can also arrange sessions on effective use of the library. You can refer questions relating to writing mechanics or techniques of oral delivery to this person.
THE LIBRARY SEARCH. A careful literature search is to be made and should include monographs and other references as well as journal articles. Journals such as Science, Nature, and Angewandte Chemie and review journals such as Accounts of Chemical Research and Trends in Biochemical Science are useful in getting a start but the use of electronic bibliographic aids such as SciFinder Scholar, MedLine, and Web of Science are essential in getting a handle on the entire literature. As you read, you will gradually recognize which journals are likely to carry articles pertaining to your topic. As they arrive in the library, you should check new issues for papers of interest. Dealing with the enormous scientific literature is not an easy task and you may want to seek advice from the science librarians.
THE ORAL PRESENTATION. An appropriate selection of material from your thesis will be presented orally at a chemistry seminar. The dates for the seminars are set at a meeting early in the semester. Attendance at these talks is expected of all junior and senior Chemistry concentrators, irrespective of enrollment in Chemistry 191. When well prepared, these talks have been extremely valuable both to the listeners and to the student lecturers. They provide valuable speaking experience and an opportunity for evaluation of the work done at a time when significant revision is still possible.
In planning the talk, keep in mind that you are the expert. Your goal is to present in understandable terms an overview of your topic. The presentation should be addressed to the general scientifically literate audience. Avoid using jargon and acronyms. Include a brief discussion of concepts or techniques which are important to your discussion but are not necessarily known to the average chemist. Resist the temptation to mention every detail and every paper. The talk is an exercise in organizing and communicating a set of information, and it will necessary to omit parts of what you plan to include in your paper. You will probably have several examples to support each you that you want to make in the talk. Include one illustrative example for each point. The remaining information can be referred to as needed in the question-and-answer period and in your thesis. In planning your remarks, think of yourself as being in the audience and ask, "Would I really want to see or hear this?"
Careful planning will be necessary so that the essential material will be covered in the time provided. Clear exposition of complicated material requires considerable thought. Give an informal presentation. Don't read verbatim from a manuscript; such an approach is always deadly. However, effective use can be made of note cards or your PowerPoint presentation as an outline. The talk should include a short introduction which includes an account of the nature of the problem, done in a way which relates to the background and experience of the audience. Also leave time for a short summary at the end, followed by a question-and-answer period.
You will want to make one or two dry runs of your talk before a friend who will give you an honest evaluation of your performance. This will allow you to locate the rough spots. Your friend should note your pace and voice control. A moderately paced delivery with good breath support increases the effectiveness of the presentation. If you tend to take off like a race horse, take a deep breath and count to five before you start. If you are using audio-visual aids, you or your friend should also check for blind spots in the room.
Appendix B
Suggestions for Writing the Thesis.
Don't limit your paper to the coverage needed for the seminar. A long paper is neither expected nor encouraged, but a thorough coverage of your topic is. The expected length for papers is 20-30 pages, exclusive of tables, diagrams, bibliography, etc. Lengthy papers in most cases reflect either an inadequacy in writing style or a poor choice of a topic. Remember that you are not writing the definitive monograph on your topic. Rather, your paper should be critical, selective, and in sufficient depth to be scientifically informative and illustrative of your ability to analyze, understand, and communicate chemical information. Also, do not make your thesis an annotated bibliography, i.e. a paper consisting merely of accounts of what was done, by whom, and when. In all cases you should try to discern the connections implicit in the collected works, suggest resolutions of conflicting data or theories, and project the direction of future work.
Each thesis should have the following components: a title page, a table of contents, an abstract, a table of symbols, and acronyms used in the thesis, the body of the paper, and a bibliography. A suggested form for the paper is that used for articles in Chemical Reviews. For other acceptable formats, refer to the "Instructions to Authors" section in selected issues in most review journals in the library. A detailed discussion of scientific writing is J. S. Dodd, The ACS Style Guide. Refer to this monograph when in doubt. The Faculty Regulation on English applies to the senior exercise and students are expected to use English that is grammatically correct and logically sound. Additional examples of the thesis format are provided by the senior theses of former students. These care kept on file in the departmental office and you may borrow one of them if you feel that would be useful. Many of the theses on file are excessive in length so don't feel that the opera maxima have to be matched in length. These theses may not be taken out of the chemistry building and should be returned to the office as soon as possible.
Authors have found that carefully prepared tables and figures can be very effective aids in communicating complex information. A good figure always has a figure caption and can be understood without extensive reading of the text. If you borrow a figure from another source, you must indicate its source in the figure caption.
The bibliography serves two major functions: to provide the reader access to the literature and to give credit where credit is due. Special conventions are used in scientific writing to keep costs down. Refer to journals in the library for examples. The references section and the bibliography sections are combined in a references section at the end of the paper. Each paper cited is given a unique citation number and is only listed once in the references section. In other words, Ibid. is rarely used. The papers are numbered in the order of appearance in the paper. If a paper is cited more than once, refer to the same footnote even though different sections of the paper may be cited. Be sure to give references for all tables and figures which appear in your thesis. Avoid paraphrasing large sections from articles or books. If you quote directly, be sure to use quotation marks. If you quote a reference you have not actually read but have seen referred to, it may be listed but should be indicated as "...as referenced in..."
Several citation formats are used in the chemical literature and any format found in a research journal is acceptable with the following qualifications. Follow the format used in a journal whose style you choose to follow. Provide more than just the last name, e.g. C. H. Hansch and R. N. Smith instead of Hansch and Smith. The use of et al. is never permitted in the bibliography but is allowed in the text. (Note the abbreviation is et al., a Latin abbreviation for and others, and not et. al. Readers with classical training will also object to the use of data and spectra as singular nouns. Data and spectra are the plural forms of datum and spectrum.) A complete set of abbreviations as well as a list of libraries subscribing to obscure journals can be found in the Chemical Abstracts bibliographic aid Chemical Abstracts Source Index (CASSI). We also ask you to include the full title of each article as part of each citation.
seniorthesis.doc, 10 September 2006, RAGL (revised)
seniorthesis.doc, 16 September 2007, RAGL (revised)