Chemistry 39, Organic Chemistry II
Summer 2006
Course Times: M/T/R/F, 8:00 a.m. – 9:15 a.m.
Course Location: 117 Thomas
Faculty in Charge:
Dr. Katie Masters
Director, Organic Chemistry Labs
Office: 218 Whitmore
Phone: 863-3319
E-mail: kmasters@psu.edu
Office Hours: Thursday, 3:00 p.m. – 5:00 p.m.
TA Information:
TA:
Office hours:
Location:
E-mail:
Keith Reber
Tuesday, 3:00 p.m. – 5:00 p.m.
211 Whitmore Lab
kpr120@psu.edu
Website: http://courses.chem.psu.edu/chem36, click on the Chem 39 link
Texts:
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J. McMurry, Organic Chemistry, 6th ed.
S. McMurry, Study Guide and Solutions Manual to Organic Chemistry,6th ed.
Other Materials:
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A molecular model kit is required.
Course Content
For the purpose of quizzes, the course content is defined by (a) the lectures, (b) the relevant chapters and
problems in the text, (c) lecture problems, and (d) problem sets. The outline and order of the topics covered is
presented at the end of this handout. Please note that not all chapters will be covered in the order they are in
the book. Some sections have been omitted. The sections that have been indicated as excluded will not be
covered in the lectures, and the material will not be a part of the tests. It is recommended that the excluded
sections be studied independently by students in pre-medicine, chemistry, or related programs.
Grades
Your course grade is based on the scores of 17 lecture problems (5 points each; 85 points total; 23% of final
grade), four problem sets (20 points each; 80 points total; 22% of final grade) and four quizzes (50 points
each; 200 points total; 55% of final grade). Final grades will most likely be based on a curve. After each quiz,
you will receive some feedback as to how your numerical scores might translate into letter grades. These
indications should be treated as rough estimates of your final grade. The average in the class corresponds to
C+/B– grade.
Lecture Problems (23% of Final Grade)
You are required to complete 17 lecture problems, which will be handed out the day before their due dates.
Each lecture problem is worth 5 points. The lecture problems may be taken from the textbook, an MCAT
sample exam, or created by the instructor. These problems will serve as good practice in understanding the
course material, preparing you for quizzes, and keeping you up-to-date with the lecture material. The lecture
problems are to be handed in at the beginning of lecture; their due dates are listed on the course schedule.
Problem Sets (22% of Final Grade)
You are required to complete four (4) problem sets, which will be handed out during class about one week
before they are due. Each problem set is worth 20 points. The problems from these sets will resemble the
kinds of problems that will be on the quizzes. The problem sets are to be handed in at the beginning of
lecture; the due dates for the problem sets are listed below and are also listed on the course schedule:
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Problem Set 1: Friday, June 23
Problem Set 2: Thursday, July 6
Problem Set 3: Thursday, July 20
Problem Set 4: Thursday, August 3
Quizzes (55% of Final Grade)
All quizzes will be offered during the class time (8:00 – 9:15 am) in 117 Osmond. The quizzes will mainly
include short-answer questions. They will be constructed in such a way as to emphasize active
understanding of the material. Each quiz is worth 50 points.
To take the quiz you will need pencils and your student I.D. card. You cannot use books, notes, calculators,
etc. You may, however, use a molecular model kit, providing it does not contain any written materials.
Practice questions in the form of old exams are provided on the course website. Questions on your quizzes
will be similar in style and level of difficulty to those offered on the course website. The quiz schedule is listed
below and is on the course schedule:
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Quiz 1: Monday, June 26th
Quiz 2: Friday, July 7th
Quiz 3: Friday, July 21st
Quiz 4: Friday, Aug 4th
Procedures
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One comprehensive make-up quiz will be provided near the end of the semester to students with
valid excuses (family emergency, illness, etc.) who have missed either of the first three quizzes. In
order to be permitted to take the make-up quiz, you must provide the instructor with a documented,
written explanation of your absence within one (1) week of the make-up quiz date (TBA). This
explanation must include a telephone number for a person who can corroborate the reasons for the
absence, but should not include any unnecessary private details. All students permitted to take this
quiz must sign up with the instructor one week before the quiz.
Late-drop students will receive WN designations on their transcripts. Students who have taken at
least two quizzes may request a WP designation, if their class average is higher than the final grade
line for a C. Requests for WP designation must be submitted in writing no later than the last day of
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class.
General Considerations: Chemistry 39 is a continuation of Chemistry 38 and, as such, builds on the
foundations introduced in the first semester. If you did well in Chem 38, then you should be well prepared for
Chem 39. If you were below average, then the second semester may be somewhat difficult for the problems
are more mechanistic and a greater emphasis is placed on the synthetic aspects of organic chemistry. Owing
to the hierarchical nature of the material, it is important to not fall behind or leave studying for the exams until
the last few days. The material is not inherently difficult, but you must understand some concepts before you
can go on to new ones. Therefore, be sure to allow yourself sufficient time for absorbing the material.
Observations made over the past few years suggest some generally useful strategies that help to improve
student performance. These are summarized below.
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Read the chapter material before the lecture
Study everyday, do reviews bi-weekly
Solve as many end-of-chapter problems as possible (resort to answer book only after you have
attempted the problem)
Study with a friend; if you can explain a concept to your study mate, you understand it
Just reading and understanding the material (passive understanding) is insufficient; you should be
able to use the just learned concepts in situations not previously encountered, and make logical
connections with concepts learned previously (active understanding)
Constantly probe your understanding by asking (and answering) question "why?" in relation to
all statements and logical constructions
Do not fall behind in your study; especially when there is new material every day; it is virtually
impossible to prepare well for the quiz in just a couple of days before it
Academic Integrity: Instructors are now asked (Senate Rule 49-20) to provide at the beginning of a course a
statement to "clarify the application of academic integrity criteria to that course". The Senate Rule includes the
following:
Academic dishonesty includes, but is not limited to, cheating, plagiarizing, fabrication of
information or citations, facilitating acts of academic dishonesty by others, having unauthorized
possession of examinations, submitting work of another person or work previously used without
informing the instructor, or tampering with the academic work of other students.
(You should also be aware of the extensive parts of this Rule that describe procedures for handling alleged
instances of academic dishonesty.) Specific instances of academic dishonesty in this course would include
(but not limited to) copying or helping someone else copy during an examination, using unauthorized
materials during an examination, stealing or destroying course materials or another student's examination
paper, altering answers or grades on graded examinations, having someone take an examination for you, and
attempting to do any of the above. Such infractions are considered cause, at the least, for awarding a grade
of "0" on the exam in question (and not allowing the student to drop the class).
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Chemistry 39: Outline of Lectures
1. Structure Determination (7 lectures*): Chapters 12, 13, 14, 15
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Nuclear Magnetic Resonance (1H, 13C): Chapter 13
Infrared Spectroscopy: Chapter 12
Mass Spectrometry: Chapter 12
UV spectroscopy (review): Chapter 14
Sections covered:, 13.1 - 13.13, 12.1 - 12.9, 15.10, 14.9 - 14.11
Sections specifically excluded: none
Assigned Problems:
Chapter 13: 3, 5, 6, 8, 13, 14, 19-21, 43, 48, 49, 50, 51, 53, 56, 59 (5th ed: 27, 24, 31, 35, 40, 44, 46, 48,
50, 51, 53, 54, 55, 56)
Chapter 12: 5, 10, 11, 13, 20, 29, 34, 37, 38, 40, 43 (5th ed: 19, 27, 31, 32, 35, 36, 37, 41, 46, 47)
Chapter 15: 42-44 (5th ed: 42-44)
Chapter 14: 15, 46, 47 (5th ed: 15, 35)
2. Carboxylic Acids and Derivatives: Nucleophilic Acyl Substitution Reactions (4 lectures*):
Chapters 20 & 21
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Structure and acidity (pKa) of carboxylic acids
Preparation of carboxylic acids (oxidation, haloform reaction, Grignard carboxylation, nitrile
hydrolysis)
Preparation of carboxylic acid derivatives (acyl chlorides, anhydrides, esters, amides, nitriles)
Mechanism and relative reactivity of carboxylic acid derivatives in nucleophilic acyl substitution
reactions
Sections covered: 20.1 - 20.8, 20.10, 21.1 - 21.7, 21.10
Sections specifically excluded: 20.9, 21.8, 21.9
Assigned Problems:
Chapter 20: 25, 26, 33, 34, 35, 45 (5th ed: 22, 23, 29, 30, 31, 38)
Chapter 21: 36, 37, 41, 42, 45, 50 (5th ed: 40, 41, 42, 47, 52, 53)
3. Aldehydes and Ketones: Nucleophilic Addition Reactions (2-3 lectures*): Chapter 19
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Overview of chemistry of carbonyl compounds (molecular orbital description of the carbonyl
group, nucleophilic addition/substitution reactions, -substitution, enolates, condensations)
Preparation (oxidation of alcohols, ozonolysis, functional-group interconversions)
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Nucleophilic addition (irreversible: hydride, organometallic reagents, Wittig; reversible: HCN,
alcohols, amines)
Conjugate addition (HCN, cuprates)
Sections covered: pp. 672-681; 19.1 - 19.12, 19.14, 19.16
Sections specifically excluded: 19.13, 19.15
Assigned Problems:
Chapter 19: 32-34, 37, 41, 45, 49, 63, 65, 67 (5th ed: 29, 31, 32, 35, 39, 43, 44, 47, 61, 63, 65)
4. Carbonyl -Substitution Reactions (1-2 lectures*): Chapter 22
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Enols/enolates, (pKa of carbonyl compounds)
Reactions with electrophiles (halogens, alkylations)
Sections covered: 22.1 - 22.8
Sections specifically excluded: none
Assigned Problems:
Chapter 22: 22, 24, 25, 29, 31, 40, 41, 44, 45, 47, 48 (5th ed: 20, 23, 26, 27, 30, 38, 39, 42, 43, 45, 46)
5. Carbonyl Condensation Reactions (1-2 lectures*): Chapter 23
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Aldol reaction
Claisen condensation
Michael reaction (and Stork enamine reaction)
Sections covered: 23.1 - 23.12
Sections specifically excluded: 23.13-23.14
Assigned Problems:
Chapter 23: 28, 35-37, 39, 40, 42, 44, 47, 48, 57 (5th ed: 26, 33, 34, 35, 37, 38, 41, 42, 45, 46, 54)
6. Amines (1.5-2 lectures*): Chapter 24
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Amine basicity
Synthesis of amines
Reactions of amines
Sections covered: 24.1 - 24.7, 24.9
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Sections specifically excluded: 24.8, 24.10
Assigned Problems:
Chapter 24: 25, 31, 36, 38, 39, 40, 45, 63, 66 (5th ed: 20, 29, 33, 35, 36, 37, 43, 60, 63)
7. Carbohydrates (2 lectures*): Chapter 25
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Structure of carbohydrates
Reactions of monosaccharides
Di- and polysaccharides
Sections covered: 25.1 – 25.7, 25.9 – 25.12
Sections specifically excluded: 25.8
Assigned Problems:
Chapter 25: 32-34, 39, 43, 44 (5th ed: 29 - 31, 34, 36, 38, 39)
8. Amino Acids, Peptides and Proteins (2.5 lectures*): Chapter 26
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Structures, properties and synthesis of amino acids
Peptide synthesis and sequencing
Protein structure
Sections covered: 26.1 – 26.3, 26.5 – 26.7, 26.10, 26.12 – 26.16
Sections specifically excluded: 26.4, 26.8, 26.9, 26.11
Assigned Problems:
Chapter 26: 30, 34-36, 44 (5th ed: 30, 31, 35-38, 43)
9. Lipids (2 lectures*): Chapter 27
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Structure of waxes, fats, oils
Prostaglandins, terpenes and steroids
Sections covered: 27.1 - 27.8
Sections specifically excluded: 27.9
Assigned Problems:
Chapter 27: 15, 16, 19, 24, 30, 42 (5th ed: 13, 14, 17, 22, 25, 37)
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10. Heterocycles and Nucleic Acids (1 lecture*): Chapter 28
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Heterocycle examples
DNA structure (nucleotide, double helix forms)
Central dogma of molecular biology: Replication, Transcription, Translation
Sections covered: 28.7 – 28.14
Sections specifically excluded: 28.1 – 28.6, 28.15 – 28.17
Assigned Problems:
Chapter 28: 35, 42, 44 (5th ed: 36, 43, 45)
11. Pericyclic Reactions (2 lectures*): Chapter 30
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Molecular Orbitals
Electrocyclic Reactions
Cycloaddition Reactions
Sections covered: 30.1 - 30.7
Sections specifically excluded: 30.8 - 30.10
Assigned Problems:
Chapter 30: 15, 23, 27 (5th ed: 15, 23, 27)
-----------------------------------------------------------------------------------------------------------------* The number of lectures is only approximate; adjustments may be made as necessary.
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