Syllabus as web page

Organic Chemistry II – NSC22, 4 credits                                                 Spring 2013

Instructor         Todd Smith

Location            Science 216

Days, Time        T, Th 11:30 – 12:50

Text                 Organic chemistry, 6e,  L.G. Wade

 The Emperor of scent: a story of perfume, obsession, and the last mystery of the senses, Chandler Burr


Course Description

Organic chemistry takes its name from the ancient idea that certain molecules – organic molecules – could only be made by living organisms. In second semester organic chemistry we will continue our study of different classes of organic compounds and their reactions. The first part of the semester will include material on important analytical techniques such as IR spectroscopy and Nuclear Magnetic Resonance. In the latter part of the semester we will turn to the original realm of organic chemistry – living systems. For example, we will examine properties and reactions of amines, carboxylic acids, carbohydrates, amino acids, and proteins. This semester will also include a special focus on the process of olfaction in humans.


Course Goals

  • Learn a vocabulary of organic chemistry facts and principles

  • Learn how central concepts in chemistry underly organic chemistry reaction mechanisms

  • Hone problem-solving skills

  • Understand connections between organic chemistry and biological processes

Readings & assignments

Chapters from text; homework assignments; read Emperor of Scent and write a book review; summaries of journal articles

Grading Policy

Students are expected to attend all lectures and to complete all reading assignments. There will be two 3-hour ‘take-home’ exams, weekly homework assignments, a book review, and a final exam. The one-hour exams are worth 150 points each, the homework 20 points each, the book review 100 points, and the final is worth 100 points. The grade received in the course will be the ratio of points earned over points possible: 90% & above = A, 80-89% = B, 70-79% = C, 60-69% = D. Diligent and conscientious participation in class and on assignments will boost borderline grades to the higher grade.

If extenuating circumstances will prevent you from taking an exam notify me as soon as possible so that we can make alternative arrangements for administering the exam.


Book review assignment

The process of olfaction is widely-thought to be based on molecular shape: an odorant molecule has a particular shape and this particular shape recognized by one of many olfactory receptors on the surface of cells. But there have been some challenges to this prevailing view. In The Emperor of scent you will read an engaging account of a scientist who champions a decidedly minority view: that olfaction is based on molecular vibration, not shape.

Your assignment is to write a review of this book. The goal of your review is to provide potential readers of the book with a preview of the book, as well as some critical analysis of the book’s organization and content, and the author’s writing style. Please include discussions of which aspects of the book you enjoyed or did not enjoy, and why. To repeat, this is a book review, not a book report.

For some ideas on how to go about preparing for and writing your review, take a look at Purdue University’s Online Writing Lab (OWL). On the left-hand menu, under the heading “Common writing assignments,” there is a link titled “Book Review.”

             Due in class on Tuesday, April 9, 2013


 Approximate schedule for the semester






Intro class (Wed, 1/23 @ 9:00 a.m.)




Alkyne structure and bonding




Structure and synthesis of alcohols;

The Grignard reagent creates new C-C bonds




Reactions of alcohols;

Biological oxidation of alcohols

Discussion of Emperor of Scent, part I



Spectroscopy:  Infra-red & mass spec;

Bond vibration & bond cleavage



12 & 13

Spectroscopy: Nuclear magnetic resonance;

Spin orientation of a hydrogen nucleus

Take-home Exam I on Friday 3/1



Spectroscopy continued


Discussion of Emperor of Scent, part II



Ethers & the Williamson ether synthesis


Spring Break







Conjugated systems, orbital symmetry, energy & color


Retinal:  tuning light-absorbing pigments


16 & 17

Aromatic compounds


Book reviews due Tuesday 4/9


16 & 17

Graphene – a new wonder material?


Take-home Exam 2 on Friday 4/19



Ketones & aldehydes








Carboxylic acids – why do they deprotonate?


23 & 24

Carbohydrates and the enzyme salivary amylase


5/9, 10

Reading days



5/11, 13, 14

Exam days






Last modified: Tuesday, January 22, 2013, 10:10 PM