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Simpson, Jeff, and Timothy F. Jamison, 5.46 Organic Structure Determination, Spring 2007. (Massachusetts Institute of Technology: MIT OpenCourseWare), (Accessed 09 Jul, 2010). License: Creative Commons BY-NC-SA

Organic Structure Determination

Spring 2007

Two-dimensional NMR spectrum (gCOSY) of a synthetic homoallylic alcohol. (Image by Prof. Timothy F. Jamison. Used with permission.)

Course Description

This course covers modern and advanced methods of elucidation of the structures of organic molecules, including NMR, MS, and IR (among others). The fundamental physical and chemical principles of each method will be discussed. The major emphasis of this course is on structure determination by way of interpreting the data (generally in the form of a spectrum or spectra) that each method provides.

*Some translations represent previous versions of courses.

 Outline and Overview of Topics

The following outline illustrates the major topics covered in the determination of organic structures.

I. Introduction: The tenets of assigning spectral features to molecular features

II. Features of the NMR spectrum

  1. A. Chemical shift
  2. B. Signal intensity
  3. C. Spin-spin coupling

III. NMR spectrum analysis

  1. A. Chemical shift prediction and interpretation
  2. B. Quantitation of signal strengths
  3. C. Deducing bond connectivity

IV. Advanced 1-D methods and concepts

  1. A. Spin gymnastics: APT and DEPT
  2. B. Selective decoupling
  3. C. Gated decoupling
  4. D. The Nuclear Overhauser Effect
  5. E. Fundamental limitations of 1-D methods

V. The second dimension

  1. A. Advantages associated with 2-D methods
  2. B. Caveats of 2-D

VI. Key 2-D experiments

  1. A. gCOSY
  3. C. HMBC
  4. D. NOESY and ROESY
  5. E. TOCSY

VII. Assignment strategies for a known compound

  1. A. Identification of entry points
  2. B. Good accounting practices
  3. C. Corroboration

VIII. Assignment strategies for an unknown compound

  1. A. Determination of molecular formula
  2. B. Identification of entry points
  3. C. Good accounting practices
  4. D. Parallel interpretations and Occam's razor


5.43 (Advanced Organic Chemistry) or permission of instructor.


None Required


Silverstein, R. M., F. X. Webster, and D. J. Kiemle. Spectrometric Identification of Organic Compounds. Hoboken, NJ: Wiley, 2005. ISBN: 9780471393627.


Pretsch, E., P. Bühlmann, and C. Affolter. Structure Determination of Organic Compounds: Tables of Spectral Data. Berlin; New York: Springer, 2000. ISBN: 9783540678151.

Problem Sets

Problem sets will be assigned each time the class meets and will be due the following lecture.

Grading and Assignments

Your grade in this subject will be determined by the following:

Five problem sets 15%
Two in-class exams 60%
Final project: Determination of the structure of an unknown 25%   Tell A Friend