Organic Chemistry Division

Research Group

            Graduate students are expected to choose a research advisor by the end of the first semester.  The organic divisions has faculty presentations to help students get started on this, although it is recommended that students talk to potential advisors one on one about research projects.   Attending group meetings is a valuable experience.  It allows students to check out the group dynamic, observe the communication between potential advisors and their students, and learn about the expectations that are placed on the students. 

Coursework

            Incoming organic chemistry students usually finish their coursework in the first year.  Typically, in the fall semester three 3-hour classes are taken: Advanced Synthetic Organic Chemistry I (CHEM 5311), Advanced Spectroscopy Techniques (NMR, CHEM 5331), and Advanced Physical Organic Chemistry (CHEM 5321).  In the spring semester two 3-hour classes are taken, usually Advanced Synthetic Organic Chemistry II (CHEM 5311) and special topic or an elective, such as biochemistry or inorganic chemistry.  Three credits of research are taken, and students are expected to start working in their advisor's lab to earn those credits.

How to Prepare

The following is a note from Professor Doug Gin, who taught this course in Fall 2003:

For my Phys Org (CHEM 5321) grad class, the students should review
the following topics before taking the class:

(1) Basic thermodynamics and free energy relationships
(2) Stereochemistry principles and prochirality
(3) Basic reaction kinetics and rate laws
(4) Diels-Alder and related rxns
(5) Drawing cyclohexane conformations

A note from Richard Shoemaker about his prerequisite expectations For CHEM 5331 (from Fall 2003):

1.) Students taking this class should come prepared with a good understanding (at the level of undergraduate organic chemistry) of basic interpretation of 1H and 13C NMR spectra, including chemical-shifts, J-coupling (spin-spin coupling), and the use of peak areas (integrals). No prior understanding of the mechanics of NMR spectroscopy is required.

2) Although this is not a mathematically intensive course (i.e. quantum mechanics based), basic algebraic manipulation of trigonometric functions and exponentials and logarithms is important. The ability to manipulate these functions, and (more importantly) to visualize the physical relevance of these functions will be expected.

3) Students will be expected to read and learn independently from texts and other supplied references. At the graduate level, students should be expected to read assigned materials, and subsequently learn and understand the information therein. Lectures in this course will be intended to supplement (not replace) written materials assigned for independent study.

Here is a note from Professor Andy Phillips about what you should know before taking his Fall 2003 Advanced Synthetic Organic Chemistry I course (CHEM 5311):

Although 5311 is fairly self-contained, a good understanding of undergraduate O-Chem II is expected. In particular, it is important to be able to do simple functional group interconversions, and to be able to think about mechanisms.

A worksheet/review that contains the simmered down basics from O-Chem II is available at:

spot.colorado.edu/~aphillip/chem5311/Undergrad FGIs.pdf

Working through this, with an emphasis on writing mechanism, should help with the step up to graduate synthesis.

Cumulative Examinations

            Graduate students are required to pass 6 cumes before 11 are failed.   During the first year cumes that are not passed only count as half a fail and halves are rounded down at the end of the first year.   Also, during the first year taking cume exams is optional though it is highly recommended.  All other years cumes are mandatory and count as a full fail if the cume is not taken.  Students are required to pass at least three cumes in the organic division.  In the organic division it is recommended that students take cumes during the first year and that 6 cumes are passed before oral examinations.  Here is some more information about cumes.

Oral Examinations

            Part 1:  Oral examinations occur during the spring of the second year.  Graduate students write a 5 to 8 page proposal on their thesis project.  Oral exams consist of the three-member committee that will ask the graduate student questions in two sections.  The first section is the thesis project and the second section is general questions.         

Part 2:  Graduate students will write a 5 to 10 page proposal on a unique research topic.  This unique research proposal needs to be approved by a two-member committee. After completion of oral exams the student becomes an official Ph.D. candidate. 

 Seminars

All organic division students (1st years included) are expected to attend the regular seminar sessions on Tuesdays 4-5 pm in Chemistry 142.  Organic graduate students will give one 20-minute seminar to the organic division in the third year on a literature topic.  In the fourth year, another 20-minute seminar is given which covers the student's research results up to that point.

 Thesis Defense 

            The defense consists of a public seminar-length presentation followed by a closed question session with the committee members.  The committee members consist of the student’s advisor as the chair, and four other members.  One of these members has to be from outside of the department of chemistry and biochemistry. The thesis must be approved by the student’s advisor and given to the committee members two weeks prior to the defense.