Information regarding Organic Research Proposals

An original research proposal is required of Ph. D. candidates in organic chemistry. Recognition and development of original and meaningful research problems is an important aspect of the work of a Ph.D. scientist. This requirement is intended to help you develop your skills in selecting a research problem and writing a research proposal. The proposal will be your property and should represent the best independent research idea that you have had to date. For this reason, to be acceptable, your proposal must not be closely related to, or an obvious extension of, current work at Wisconsin.

When and How to Submit Proposals

You should submit a proposal in the Fall semester of your third year of graduate work. Third-year students cannot delay submission of their proposal until the Spring semester without the consent of their major professor. Discuss this with your major professor.

A one-page summary providing the context for the scientific problem and the specific aims of the research is due two Mondays before Thanksgiving. The organic faculty will evaluate these summaries for approval.  If a revised written proposal is required, this may be submitted after these deadlines.  When your specific aims (Summary) have been accepted, you must provide a complete written proposal, which is due the Monday of exam week.   You may prepare and submit your proposal in advance of the deadlines to allow time for revision or replacement.

Completion of the Research Proposal is required for advancement to candidacy (the other requirements are the Research Preliminary Exam and 6 semesters in residence). It is therefore important to submit a proposal as early as possible. This will maximize your chances of successfully completing the proposal in time to qualify for candidacy and pay lower fees at the earliest possible time.

After review by the faculty, your proposal will either be accepted, returned for revision, or rejected. If your proposal is acceptable, it will be approved for oral defense. If it is returned for revision, your major professor will provide a summary of critical comments to help you in preparing a satisfactory version. If it is rejected, you will have to develop a new proposal. If there is time, corrected or new proposals may be submitted for the current round of oral exams, or they may be submitted for a subsequent round.Students who do not pass this requirement in the fall semester will have a second opportunity in the spring semester.  Timelines for spring:  deadline for the summary of three Mondays prior to the last week of classes; final due date for the written proposal on the Monday of the last week of classes.

Proposal Revision

A proposal revision must be accompanied by the letter you received from your advisor outlining the issues you need to consider, and a covering letter describing the changes that you have made in the write up and how you addressed the comments you received. A good format is to copy the comments into your letter, and describe your revisions below each comment. For example:

Criticism: "The synthesis of compound 4 in the original proposal is likely to fail because the proposed aryl bromide 7 contains an ester group that is unlikely to survive formation of a Grignard reagent."

Response: In the revised proposal a new synthesis of 4 is presented that avoids the problem pointed out in the review of the original proposal. In the revised synthesis, the Grignard reagent is formed from an aryl bromide that contains a protected primary alcohol. After the Grignard reaction, the primary alcohol is deprotected, oxidized to the acid and esterified.

Criticism: "The key proposed experiments require that nucleic acid analogues such as 9 form duplexes with natural DNA strands. How can we be confident that such hetero-duplexes will form?"

Response: The revised proposal contains references to the work of Jones et al. (refs. 4-6), who have shown that nucleic acid analogues very similar to 9 do indeed form duplexes with complementary DNA strands.

The Oral Examination

Only approved proposals may be defended orally in the first weeks of January. The examining committee consists of several faculty members including your major professor as an observer. The oral exam is typically 45 minutes and you should plan to present the essential aspects of your proposal in about 15-20 minutes, with only minimal background and introductory material. An informal chalkboard presentation is strongly preferred, although complicated structures or apparati can be presented in hard copy handouts or molecular models.

Research proposals are graded on a Pass/Conditional Pass/Fail basis. Conditional Pass requires additional work, specified by the examining committee, which may involve a written report or a repeat the oral examination at a later date.

Evaluation of Proposals

All faculty members will receive a copy of your proposal for evaluation in four categories as listed below.

Criteria for Evaluation:

   1. Presentation: Is the proposal understandable, does it comply with the required format in explicitly stating the Specific Aims and Hypotheses, does it clearly describe the significance of the problem and the proposed solution, does it include pertinent references to the literature?

   2. Scientific Merit: Is the proposal worth doing, does it lead to new and nontrivial results, does it overlap excessively with work under way at Wisconsin?

   3. Practicality: Does the proposal constitute a research problem (desirable) or a research program (undesirable); would an advanced student or postdoctoral fellow be expected to make substantial progress in a reasonable amount of time?

   4. Technical Competence: Will it work? Are theoretical arguments sound, will the experiments lead to conclusive and observable results, has the student overlooked reasonable alternatives, will synthetic steps work, are the analogies appropriate?

Proposals Involving Asymmetric Synthesis

Proposals involving asymmetric synthesis often contain no testable hypothesis - either the reaction works or it doesn't. The entire proposal boils down to a question of estimating small energy differences between diastereomeric transition states. One can speculate about the geometries and energies of the transition states, but, fundamentally, there is no hypothesis to be tested.

Developing asymmetric reactions often involves an Edisonian approach of trial and error. The ultimate goal is extremely important, but the pathway to achieving that goal involves a series of successes and failures that can only be rationalized after the fact. Even though the results of the proposal would be publishable if the project was successful, the lack of a compelling scientific hypothesis makes the proposal a poor subject for an oral exam.

If you wish to submit a proposal involving asymmetric synthesis, you should first discuss the matter with your research advisor.

Format of the Proposal

Formulate your proposal using the following outline.

A. Specific Aims

  1. Specific Research. State the specific research that the proposal is intended to accomplish. (This should require only a couple of sentences, not a paragraph.)
  2. Hypotheses. State the hypotheses to be tested. Keep in mind that a hypothesis is not simply a question for which there is an answer. A scientific hypothesis poses a testable postulate in a context that carries scientific insight.
    • Ask clear specific questions
    • If more than one hypothesis, state each hypothesis individually

    Understand the difference between

    • broad, long-term objectives e.g., "understand factors governing protein folding" (hard to quantify progress in achieving this objective)
    • specific aims e.g., "study the influence of intramolecular hydrogen bonding on the solution conformation of diamide X" (easy to quantify progress in achieving this objective). The specific aims comprise a list of items needed to pursue the broad, long-term objectives.

B. Background and Significance

C. Experimental Design and Methods

In this section, you should outline the experimental design and procedures you will use to accomplish the Specific Aims of the project. The experimental approach should be outlined clearly and in sufficient detail that the plan can be evaluated by the reviewers (faculty members).

The Experimental Design and Methods section is an important part of the Research Plan. You have said in the Specific Aims what you propose to do; now you are telling the reviewers how you propose to do it. Explain why the particular approach that you describe was chosen to attack the problem that you plan to research. Convince the reviewers that you can do what you propose.

Try to convince the reviewer that you have not merely gone to the library but that you really understand and know how to carry out the research and are familiar with the techniques and their shortcomings.

D. Notes and References

Be thorough, relevant, and current.

Use JACS format followed by the title of the article.

Choose wisely what you will include. Your choice of citations tells the reviewer about your quality as a scientist - your ability to evaluate the work of others and to distinguish the important from the mundane.

Format of the Proposal

Planning the Research Proposal

Before you begin to write your research proposal, you should be able to write down satisfactory answers to the following questions:

Writing the Research Proposal

Here are some questions the reviewers will be asking as they read your proposal:


Be Accurate

Be Clear: Use a logical sequence of presentation.

Be Consistent

Be Brief (Concise but Complete). In expository writing, the reader wants the maximum information in the minimum number of words. AVOID REDUNDANCY AND UNNECESSARY WORDS.

Think About Style and Tone

For further tips on writing research proposals and grant applications, see:

Checklist for Research Proposals

  1. Cover page giving name, title, submission date and research advisor.
  2. Pages numbered
  3. No more than 5 pages long (excluding references)
  4. Compounds numbered and compound cross references checked
  5. Titles of papers cited
  6. Graphics and text font size reasonable (>= 10 pt)
  7. Minimal use of R, L, M, X and Y groups

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Rev: 8/2014