As this is a graduate class, it is assumed that everyone is in the class because they are highly motivated to truly master all of the fundamentals of organic chemistry by consolidating all of their previous coursework in the area, learning a few new reactions and concepts, and applying this knowledge in an integrated way to new chemical problems. It is the prime objective of this class that students emerge from it with several indispensable skills, including the ability to:

• recognize most modern synthetic reagents and illustrate their common use(s) with sample reactions of their devising.
• read, comprehend, and summarize articles in journals such as the Journal of Organic Chemistry, Synthesis, Tetrahedron Letters, Organic Letters, etc.
• understand and illustrate the mechanisms for all reactions to which they are exposed.
• locate accurate literature precedent for any transformation they wish to suggest, and to cite it the correct format.
• design an original synthesis for any molecule presented to them (within reason), complete with accurate, appropriate literature references for all non-trivial steps.

Class Structure & Comments on the Textbooks     The two texts for this course were chosen for very specific reasons.  We will loosely follow the organizational format of Carey & Sundberg, but we won't just take each chapter as it comes along.  For instance, we'll spend some time in Chapter One (Alkylation of Nucleophilic Carbon Intermediates), since not only does it address the formation and uses of enolate anions and their equivalents, but the concepts of kinetic vs. thermodynamic control of certain reaction parameters are introduced and applied.  Conversely, Chapter Four (Electrophilic Additions to Carbon-Carbon Multiple Bonds) and Chapter 11 (Aromatic Substitution Reactions) will probably merit only one class meeting each, as the material therein is covered in undergraduate courses.

    As we go, I will often use papers from the current literature to illustrate a topic or concept we've just discussed.  Occasionally, I'll make a homework assignment out of something in the literature - finding an article where a certain reaction type is utilized, writing a short (<1 pg.) analysis of a reaction in a current paper (e.g., why this reaction was used and not a common alternative, explain a stereochemical result, etc.).  Also, I'll suggest certain end-of-chapter problems each time we begin a new chapter.  C&S has great problems, and their solutions are all provided via references to the primary literature.

    I suggest that you read the text (C&S) carefully, with a pad of paper nearby.  The text is very readable, but many structures/ mechanisms/ figures are interspersed throughout, and jotting down any mechanisms or figures that aren't immediately obvious to you is a great way to learn and conceptualize the material..  The material is also very well referenced, and you're encouraged to consult primary papers for material which is challenging for you.

    The other book (March) is much less readable, in the way that C&S is.  The first nine of its 19 chapters constitute Part One, which is an introduction to the reactions covered in Part Two.  Part One covers topics like stereochemistry, reactive intermediates, mechanisms, etc.; Part Two's chapters have very general names, like Aliphatic Nucleophilic Substitution, Addition to Carbon-Hetero Multiple Bonds, and the like.  March is where you go to find leading references to something, along with a terse, accurate summary of the topic; the book is over 2,000 pages containing 40,000 references to the primary literature.  I leave it completely up to you when and how often to consult this amazing reference work.

Grading and Class Policies

    There will be three literature assignments; their specific topics and due dates will be announced in class. For the first two, you will be asked to find an organic synthetic reaction (or several) in the very recent literature that accurately illustrate(s) an important concept being discussed in class; detailed handouts will be supplied for each assignment that explain what is expected. You will then analyze the literature example, comparing and contrasting it with other, similar strategies for effecting the same transformation. These projects will be worth 50 points each.

    For the third literature project, you will locate a very recent (published in 2002) total synthesis of a complex molecule (again, specifics will be provided at the time the assignment is formally distributed). You will then find an earlier synthesis of the exact same molecule that utilizes a completely different synthetic approach. Your assignment will be to perform a comparative analysis of the two methods, pointing out differences and similarities in both synthetic tactics and strategies. In addition to the written report, you will also deliver a 20-minute oral presentation to the class, utilizing overhead transparencies or PowerPoint⁷, in a seminar format. This final literature project is worth 100 points.

    Three one-hour exams (100 points each) will be evenly spaced over the term; the dates are given below.     The exams will all be in two parts: an out-of-class portion and an in-class section; each will be worth 50 points. The out-of-class part will be distributed one week prior to the in-class exam date and will be due at the start of that class period. The in-class part will require about 50 minutes to complete. If you are going to miss an hour exam (for an extremely good, documented reason), be sure and let me know ahead of time, or, at the latest, before the graded exam is returned to the class. There is no provision for making up an exam.
 

Exam Schedule

Exam Number	Out of Class Part  Distributed	Out of Class Part Due, In-Class Occurs
I	Sept. 23	Sept. 30
II	Oct. 21	Oct. 28
III	Nov. 15	Nov. 22
FINAL	MON., DEC 9	WED., DEC. 18 - 2:45pm

    The final examination (200 points) will also consist of two parts, and will be handled exactly like the hour exams. You will have two weeks for the take-home part, in which you will prepare a proposal for the total synthesis of a complex molecule. The in-class portion will be comprehensive, covering all topics discussed during the term. Thus, the total points available for the course equal 700 (two literature assignments at 50 pts each; one at 100 pts; three exams at 100 pts each; one final at 200 pts).

    Grades will be assigned based on a curve related to class performance; thus, individual literature assignments and exams will not receive a letter grade. The curve will be updated throughout the semester after every hour exam and presented to the class when the graded exam is returned, but you are encouraged to stop in my office at any time to see where you stand. After the last hour exam, the curve for the semester will be unequivocally set (i.e., will not be changed as a result of class performance on the final). That way, you will know, several weeks in advance, the exact score you will need on the final exam to earn a given letter grade for the semester.

Academic Integrity

    As noted above, all exams, including the final, feature an out-of-class section in addition to the in-class portion. In formulating your answers to the take-home section, you may use any sources of information you can think of except another person; this includes faculty and students. Anyone found to be in violation of this injunction will, at the least, receive a zero for the exam; receiving an F for the course is actually more likely, depending on circumstances.

    Regardless of the consequence, the Judicial Board will definitely be involved, and the incident will become a part of your permanent record.  Please, DO NOT violate this policy the consequences are most definitely not worth it, and it defeats the whole purpose of the exercise.  And yes, this kind of academic misconduct can be easily proven.

Note: It is possible that this injunction against consulting another person will be waived for the out-of-class portion of the final exam. You will be advised, in class, of whether or not this is the case when we get close to the end of the semester.

Literature Citations

    The correct citation of literature precedent is a very important skill in any science. You will get considerable practice in this class, so please pay close attention to the guidelines presented. Incorrect citations will result in point deductions, regardless of the assignment.

    When citing a literature reference, do not plagiarize the article. You should be able to explain, in your own words, the concepts/principles the article covers. It is easier to detect scientific plagiarism than you may think, and, of course, proving it is trivial once the copied article is found. If you are discovered to have plagiarized an article, including sentences or phrases from it, you will receive a zero for the assignment.

    Many assignments in this class, as well as any proposals you may write in your own career, require literature precedent for chemical transformations you are suggesting. When citing literature reactions, you must provide not only the correct citation, but also the exact reaction from the paper being claimed as precedent.

    Lets suppose you want to ozonize a tetrasubstituted double bond to form two ketone functionalities.  An appropriate, correctly presented citation follows.  Note the ACS style of citation, as well as the structure numbers from the original article (the numbers help find the reaction in the article, should I decide to look it up).

1. Mori, M.; Hori, M.; Sato, Y. J. Org. Chem. 1998, 63, 4832.

    It is best to try to find precedent reactions that involve molecules structurally similar to your own. This is particularly important to support proposed chemoselectivity (the selective reaction of one functional group in the presence of others that might logically be expected to also react under the conditions).

    For instance, if you are proposing the reduction of a double bond via catalytic hydrogenation, and the molecule also contains a nitro group which you are claiming is not reduced under the reaction conditions, your precedent reaction should illustrate this selectivity on an alkene that has a nitro group somewhere on the molecule that is not reduced. In a sense, your precedent reaction is proving that the selectivity you claim is, in fact, feasible. Without such support, a reviewer (or professor!) is going to ask why you think that the nitro group will not be reduced simultaneously with the alkene bond.