Organic Chemistry II

Course Info

Course Number/Code: 5.13 (Fall 2006)
Course Title: Organic Chemistry II
Course Level: Undergraduate
Offered By: Massachusetts Institute of Technology (MIT)
Department: Chemistry
Course Instructor(s): Prof. Timothy Jamison
Dr. Kimberly Berkowski
Course Introduction:
Syllabus Help support MIT OpenCourseWare by shopping at! MIT OpenCourseWare offers direct links to to purchase the books cited in this course. Click on the Amazon logo to the left of any citation and purchase the book from, and MIT OpenCourseWare will receive up to 10% of all purchases you make. Your support will enable MIT to continue offering open access to MIT courses.Overview

This intermediate organic chemistry course focuses on the methods used to identify the structure of organic molecules, advanced principles of organic stereochemistry, organic reaction mechanisms, and methods used for the synthesis of organic compounds. Topics include spectroscopy, spectrometry, and structure elucidation with an emphasis on the application of infrared and nuclear magnetic resonance spectroscopy. Additional specific topics include:

Molecular Orbital Theory and Pericyclic Reactions Modern Concepts of Bonding and AromaticityThe Woodward-Hoffmann RulesMechanism of Pericyclic Reactions and Applications in SynthesisChemistry of Functional Groups Ethers, Epoxides, Amines and Carboxylic AcidsEnols, EnolatesChemistry of Reactive Intermediates Carbocations, RadicalsRequired Text

McMurry, John. Fundamentals of Organic Chemistry. 6th ed. Pacific Grove, CA: Thomson-Brooks/Cole, 2006. ISBN: 9780495012030.

Additional Texts

McMurry, Susan. Study Guide and Student Solutions Manual for John McMurry's Organic Chemistry. 6th ed. Belmont, CA: Thomson-Brooks/Cole, 2003. ISBN: 9780534409340.

Wade, L. G., Jr. Organic Chemistry. 5th ed. Upper Saddle River, NJ: Prentice Hall, 2002. ISBN: 9780130338327.

Clayden, J., et al. Organic Chemistry. Oxford, England: Oxford University Press, 2000. ISBN: 9780198503460.

Molecular Models

Several units in 5.13 will emphasize stereochemical aspects of organic reactions and molecules. To help you visualize stereochemical concepts, we recommend that you purchase the WH Freeman HSG Molecular Structure Model SetTM . Note that you will be permitted to bring model sets to the hour exams and the final.

Problem Sets

Eight problem sets will be required throughout the semester and are worth 10% of your final grade. These problem sets should be handed in to your recitation instructor at the beginning of lecture on the dates announced (or earlier). No late work will be accepted.

Written solutions are given for each problem set in the assignments section. In addition, "drill problems" will be assigned approximately every week in conjunction with the weekly reading assignments.


There will be four exams in addition to the final. These exams will be held during the class lecture time. Review sessions will be scheduled prior to each exam. Please notify course instructors and the Chemistry Education Office of any conflicts or concerns regarding taking exams at the scheduled time. Conflict exams generally will be scheduled for the same day as the regular exam.

Absolutely no make-up exams will be given for a missed exam. To accommodate unexpected illnesses, family emergencies, and other conflicts, one of the 50-minute exams will be dropped when calculating your final grade. The purpose of the dropped exam is to relieve extra stress and pressure during a particularly difficult time in the semester. Use this option with caution because you cannot predict if a serious emergency will arise later in the semester.

Regrade Policy

You may submit a graded 50-minute exam to your TA for a regrade up to one week after it is returned to you. Oral or late requests for regarding will not be accepted. Include a justification for the basis of your regrade. Please note: We will regrade the entire exam and photocopy it for our records.


The 50-minute exam with the lowest score will be dropped.

Grading criteria.ACTIVITIESPERCENTAGESRemaining Three 50-Minute Exams (300 pts)60%Final Exam (150 pts)30%Problem Sets (50 pts)10%Academic Integrity

Students will not turn in assignments that are the result of copying the work of another student or by using the work or solutions from this course given in previous years. However, discussing the homework problems is permitted and encouraged after attempting to work the problems independently. During an examination, a student will not:

Accept or use information of any kind from other students.Represent the work of another student as his or her own.Use aids to memory other than those expressly permitted by the examiner.

Following an examination, a student will not try to deceive instructors or graders by mispresenting or altering his or her previous work. In advance of an exam, a student will not knowingly obtain access to the exam questions.

The following excerpt was taken from section 10.2 of MIT's Policies and Procedures, "MIT assumes that all students come to the Institute for a serious purpose and expects them to be responsible individuals who demand of themselves high standards of honesty and personal conduct. Cheating, plagiarism, unauthorized collaboration, deliberate interference with the integrity of the work of others, fabrication or falsification of data, and other forms of academic dishonesty are considered serious offenses for which disciplinary penalties can be imposed." Thus, any infraction of academic integrity will be dealt with as outlined in section 10.2 of MIT Policies and Procedures and could result in disciplinary penalties, including suspension and expulsion.