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One of the more challenging aspects of graduate school is the shift in testing from writing (exams, essays) to oral evaluation by a committee including your supervisor.  The format switch can leave students a little in the lurch, so I’ve done what I can below to demystify the tests and help with preparation.

Quals/Prelims/Candidacy Preparation

Breadth, not depth, is the hallmark of this exam. Positioned either at the end of formal classwork, the rough midpoint of a PhD program, or just prior to thesis writing, the exam of many names is designed to ensure that students are familiar with their field as a whole, not just their own research. This generally means understanding the mechanism of every reaction that you have performed, key work from related labs (in synthesis heavy programs this encompasses most named reactions), and the theoretical underpinnings of the techniques you practice. At best the experience is like a single-contestant version of Jeopardy, at worst it’s two hours of hospital rounds, just for you.

Sample questions:

Please draw pulse sequence for the 1H proton and 2D COSY NMR experiments on the board/Draw all the 4f orbitals/Draw and name all five-member heterocycles containing oxygen, nitrogen or sulfur.

Given line broadening in an HPLC trace, walk us through the steps you would take to improve resolution, assuming multiple causative factors.

Draw the mechanism of the Wittig reaction and explain why unstabilized Wittig reagents give cis-alkenes.  Which three alkene-forming reactions give predominantly trans alkenes?

How are ethyl acetate, acetonitrile and N-methylpyrolidone produced on an industrial scale? (Evil)



To handle the basic theory questions run through a couple of your sub-field’s intermediate level textbooks–the sort generally used by good 3rd or 4th year undergraduate [1]. Once you feel comfortable describing the inner workings of named reactions and NMRs, read up on your committee members’ research. Most of their questions are going to come from their field of interest, so if you’re familiar with a few of their recent papers and the basics of their sub-field you’ll have quite the edge.

Once the essentials are covered spend a day or two thinking up potential questions. If you have supportive labmates, ask them to quiz you en mass, to mimic the rapid switching between topics.  Bring a water bottle to the exam, and get plenty of sleep the night before.

Expect lots and lots of sketching during the candidacy.

Expect lots and lots of sketching during the candidacy.

I can guarantee that during the exam there will be questions asked that you can’t answer (including a few that have no known answer).  When this happens tell the committee that you’re uncertain, but offer your best guess and a follow-up experiment [2].  You don’t have to be right every time, but do your best not to be wrong.

The Thesis Defence

There is only one expert in your research, and that’s you.  In a small lab your advisor is probably steeped in the planning and execution of your work, but even their knowledge pales in comparison to what you’ve learned over years of dedicated study.  As a result, don’t expect your committee to dive into the minutiae of your work, looking for flaws in the experimental design and conclusions.  They know less than you (and are well aware of that fact), and generally aren’t eager for their ignorance to be exposed.

Outside of a few warm-up questions, most of the defence falls into one of two streams:

1) Back to the Fundamentals

The committee may not be comfortable in a back and forth on the fine details of your research, but they’re quite at home chipping away at the edges. Your thesis will be used as a springboard to broader questions on experiment design, troubleshooting, and basic chemical principles [3].

Sample questions:

The purity of your compounds was assessed via NMR, HPLC and HRMS. How did you quantify the concentration of various non-fluorescent salts, like sodium trifluoroacetate?

You state on page 173 of your thesis that compound 87 did not bind to the enzyme of interest. How was this determined? (Followup) How could you have assessed binding in the absence of fluorescence/ITC/NMR measurements? (Followup) What other means of assessing binding could you use?

How accurate are your yields? What would be required for statistical significance? (Evil)

2) What’s the impact?

Being a research scientist is (unfortunately) as much about promoting your research as doing it.  Regardless of whether your career lies in industry or academia a good committee will probe your ability to defend your work against attack, as well as see the see the larger picture of how it can benefit others and change our understanding of the world.

Sample questions:

How does your synthesis of everestane compare to previously published work? In which ways have you improved our access to this compound?

As the foremost expert in your research, how does it affect our understanding of the cell/environment/”Famous-name” process?

What is the most important next step for this project?

Explain your research to us using only non-scientific words (a common question long before up goer five became famous).


Depending on the dedication of your committee you are likely to see a bias in questions stemming from the first few chapters of your thesis. If you have received feedback on your thesis, the comments they have made there are also likely to reoccur during the defence. My preparation focused on brushing up on the basic chemistry (ie. mechanisms for every interesting reaction), reviewing comments made by the committee at earlier stages in the PhD, and brainstorming potential questions.

Get plenty of sleep for 2-3 days before the defence.  Don’t try to cram every last factoid in the hours before the defence, and instead focus on getting plenty of sleep for at least 2-3 days beforehand.  Common sense and proactive problemsolving will get you through many of the more difficult questions, but like the candidacy expect to be faced with the unanswerable. A defence is meant to determine the limits of your knowledge, and the only true way to assess that is to stretch you to the breaking point.

Good luck.


[1] Clayden is good for most programs, though synthesis heavy subfields may require Carey/Sundberg or March. Most books are too big to actually read in their entirety, so focus your attention on likely chapters and skim the rest.

[2] Ex. Q: What is the acid stability of allylic epoxides?

A: I’m not certain, but I believe that the alkene would increase acid susceptibility.  To verify this a diene could be reacted with stoichiometric mCPBA, then run on a 2D TLC.  The epoxide of an equivalent alkene could be used as a standard, and off diagonal spotting would clearly demonstrate acid-based decomposition.

[2] If you are at all uncertain about devising reaction mechanisms from scratch read “The Art of Writing Reasonable Organic Reaction Mechanisms.”  It’s the basic, 2nd year stuff that will trip you up.