Preparing a Thesis and the Thesis Exam
When the experimental work on your thesis project is getting close to being finished you will begin to seriously plan the details of your PhD thesis. At this stage you should prepare a comprehensive list of "loose ends" so you and your advisor can agree on what you will finish, what will maight be abandoned, and what should be passed to a later generation. It is also useful to prepare a list of all of the compounds you have worked with, and the spectral information you have on each, so that deficiencies in characterization can be remedied. This is also the time to set up your thesis committee, which shouild consist of the three members of your mentoring committee and two additional faculty. During this time you should give some thought as to the extra members should be, and contact your committee about tentative dates for the thesis exam. It is also worthwhile to read through the Graduate School guidelines for thesis preparation and filing. [Rules for thesis committee?]
Your thesis advisor may have requirements in addition to the general guidelines listed below. Make sure you understand these, and refer to the theses of recent graduates in your group for examples of preferred organization, presentation and format.
Writing your thesis.
Organization. A thesis will usually include the following sections:
Items 2-6 may be repeated several times if there are several chapters. It is permissible to combine the results and discussion sections.
Outline. The first step in writing a thesis is to prepare a detailed outline, and show it to your advisor. If your work has not been completely published, it can save a lot of work in writing papers when the thesis organization approximately follows the plans for publishing papers based on your work
Style. The style of presentation in theses is not rigidly specified, but it is a good idea to use standard ACS (JACS) format to the extent possible. Refer to previous thesis in the group. Remember that the graduate school enforces the page numbering, margins and type size rules outlined in the information provided by them.
Numbering. Figures, Tables, compound numbers and references must be numbered consecutively, either within each chapter, or within the entire thesis. If item numbering starts from 1 in each chapter, it helps if you use a system like Fig. 3-6 for the 6th Figure in Chapter 3.
References and Footnotes. You should minimize placement of text material within the references (use footnotes), since such comments are too easily overlooked by someone using your thesis later. It is desirable to include titles of articles referenced in the footnotes/endnotes.
Experimental. The experimental section is perhaps the most important part of the thesis, and great care should be taken to make sure all information is accurate and up to date. A complete experimental description of a preparation must include, in addition to the operations performed, the notebook reference, the source of the starting material, the measured quantities and molar quantities of all materials used, description (with drawing, if complex) of any special apparatus used, and the spectral characterization and purity of the product. If the procedure was taken from the literature, or is a minor modification of a literature procedure, the reference should be cited. All new compounds must be fully characterized. This includes at least 1H NMR, 13C NMR, MS and MS peak match, but might also contain IR spectra if there are Ir-active functional groups, NMR of other nuclei when pertinent, UV spectra as well as C&H analyses for key compounds. Known compounds should be cited.
Graphs and Numeric Data. All information that is presented in the form of graphs (kinetic plots, product ratios as a function of time or other experimental variables, activation parameters, equilibrium constant measurements, etc) should also be given in numeric form as a Table, probably in the experimental section. All of the information needed to reproduce the graph must be presented, as well as a notebook reference.
Spectra: It is important to remember that your thesis and published papers are the only permanent record of your research project. All ancillary material will eventually be either lost, discarded or buried in masses of other material. It is therefore important that the thesis itself contain all significant spectra, properly labeled with a description of the experiment, as well as notebook reference, solvent(s), temperature(s), concentrations, spectrometer frequency and observed nucleus. Spectra can be interspersed through the text as part of the Results section, or placed in the Appendix. All spectra files (FID and worked-up spectra) should be organized on a CD-ROM or other large capacity storage device, using the notebook page number as a primary index (folder name).
Submission of Thesis. Each member of the committee gets a copy of the thesis at least one week before the final exam. Some members of the committee may want to keep their copy. After final corrections which were identified by the readers or during the exam have been made, you submit one copy to the graduate school, one bound copy (in the proper format) and a second unbound copy to your advisor. Originals of all drawings that appeared in your thesis, as well as the text files, drawing files, and all spectra files should be submitted to your thesis advisor on a CD-ROM or other high capacity storage device.
The Thesis Examination
When the end seems in sight, you should set a firm date for your thesis defense, with a timetable such that you can provide the committee (5 members) with a copy of your thesis one week before the exam. You should also schedule a seminar room large enough for an audience of 20 or so for the public presentation. Allow at least two hours for the exam. The presentation should be no longer than 30 minutes, after which the closed portion of the exam will be held. You should bring the following documents to the exam.
1. Thesis title page for signatures
2. Graduate School form for signatures.
3. Chemistry Department record sheet.
Checking Out
The following tasks need to be completed before you can leave the department.
Chemical Samples. The compounds you have prepared represent a very valuable resource to the research group. All chemicals you leave behind should be labeled properly, and organized in such a way that individual compounds can be found. There should be a sample of each important compound that you have prepared, particularly all of the compounds that play a significant role in your thesis. Samples should be labeled with your name, notebook number and structure. Samples known to be decomposed, unimportant reaction mixtures or those of questionable origin should be disposed properly.
Spectra. You should have a Compound File on each important compound that played a role in your research project. If you carried out comprehensive spectroscopic studies on one or more compounds, you should have Experiment Files containing the data from such experiments.
Spectra of routine compounds (and the corresponding FIDs or worked up spectra files) that you obtained in the course of your work (simple starting materials, commercial compounds) should be submitted to your thesis advisor (and also, perhaps, copies to the instructor for Chemistry 605, for use in lectures, exercises or exams).
The remaining spectra, which document the day-to-day details of your research should be submitted in numerical order, for storage. The organization of spectra should be such that this latter group of spectra can eventually be discarded without compromising the experimental basis for your research project.
Research Notebooks. Turn in research notebooks and other research data.
Bench. Clean out your bench area, check refrigerators for leftovers and properly dispose of them.
Checkout. Get signatures from the various shops, the library, etc.
Filing your thesis. After you have passed your thesis exam, you must submit an unbound copy of your thesis, printed single sided on proper thesis paper, to the Graduate School. The filing date is your official Ph.D. degree date, and the end of your status as a graduate student at UW.
Keys. Turn in your keys at the Business Office.
Rev. 02-05/04-08-HJR