Spring 2016 Organic Chemistry 2P20

Course Outline
Instructor
Paul M. Zelisko, PhD
Office: CRN 520
Tel: ext. 4389
E-mail: pzelisko@brocku.ca
Web: www.brocku.ca/node/9904
Office Hours: Monday-Friday (1-2pm) or by appointment

Laboratory Coordinator

Fran Holland
Office: MC E223
Tel: ext. 4977
E-mail: fholland@brocku.ca

General Overview:
Organic chemistry is, in general, the study of molecules based on carbon and reactions
involving these molecules. This course will examine a wide variety of chemical reactions
and principles and will undertake a mechanistic approach to studying chemical reactions.
CHEM 2P20 will serve to provide students with a solid grounding in the guiding
principles of organic chemistry which can subsequently be applied to other chemistry
courses or courses in the physical or life sciences.

Students will note that the approach for this, and other organic chemistry courses, will
likely be different from other courses that they are taking or have taken in the past;
simply memorizing the material will not be sufficient for success. The material presented
in the lectures, weekly labs, and weekly tutorials will emphasize an understanding of

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basic concepts and the application of these concepts to a variety of problems. Students
are expected to keep up with the course material and to work through the problems in the
text. Since the material in organic chemistry builds upon the preceding topics students
are encouraged to seek assistance as soon as possible to clear up any areas of confusion if
they encounter difficulties.

It should be noted that students are expected to be active participants in their own
education with respect to CHEM 2P20 – they are to be active participants in the lectures,
they are to read the text and work through the problems contained therein, and to seek
assistance when they need it.

The lecture material will focus on topics/concepts from the textbook that historically
benefit from greater explanation; topics not covered in lecture but contained within the
Detailed Chapter Coverage (below) are the responsibility of the students. In the interest
of time, straightforward molecules will often be used to exemplify concepts in order to
save the time that would be required to draw more complex structures. Students should
ensure that they are comfortable translating the concepts illustrated by these simple
molecules to more complex structures.

Topics to be Covered:
Topic Chapter(s) in Text Lecture Date(s)
Functional Groups and Intermolecular Assumed
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Forces Knowledge
Review of Organic Chemistry Basics 1 Sept. 12-15
Organic Acids and Bases 3 Sept. 19-20
Alkanes and Cycloalkanes 4 Sept. 22-26
Alkenes 7, 8, 13 Sept. 27-Oct. 4
Aromatic Compounds 14, 15 Oct. 6-18
Free Radicals 10 Oct. 20-24
Stereochemistry 5 Oct. 25-31
Nucleophilic Substitution and Elimination
6 Nov. 1-7
Reactions
Alcohols, Diols, and Ethers 11, 12 Nov. 8-14
Macromolecular Chemistry 10 and notes Nov. 15-21
Infrared Spectroscopy 2 Nov. 22-24
Mass Spectrometry 9 Nov. 28
Nuclear Magnetic Resonance Spectroscopy 9 Nov. 29-Dec. 5

[Chapter references correspond to Solomons, Fryhle, and Snyder, Organic Chemistry,

12th Ed.]

Test 1: October 7, 2016 (6-7:30pm, TBD)

Test 2: November 11, 2016 (6-8pm, TBD)

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Final Exam: December 2016 (Scheduled by the Registrar’s Office)

Assignment 1: September 20, 2016 (Posted), September 27, 2016 (Due)

Assignment 2: October 24, 2016 (Posted), October 31, 2016 (Due)

Assignment 3: November 22, 2016 (Posted), November 29, 2016 (Due)

Laboratory Scheduling:
Each student registered in Chemistry 2P20 must attend one laboratory period (3 hours)
every week and one tutorial every week. Conflicts will be resolved during the first week
of labs. Labs will begin the week of September 12, 2016. Students MUST attend their
first lab slot to ensure their spot and to check-in. Following this first week students who
are missing glassware or incur breakages will have the replacement cost deducted from
their lab deposits. Lab deposits will be refunded by Financial Services at the end of the
school year. Failure to check out of the lab at the end of term will result in forfeiture of
the lab deposit. Laboratory material may appear on tests and the final exam.

Students should note that arbitrary switching between laboratory and tutorial
sections is not permitted.

Evaluation: The final grade for the course will be determined on the basis of the
following weighting:

Course Component Mark Value

Assignments (x3) 5%
Tutorials 5%
Test #1 10%
Test #2 15%
Class Participation 5%
Laboratories 20%
Final Exam 40%

A MINIMUM of 8 out of the 9 experiments must be completed and the corresponding

report submitted for marking in order to meet the course requirements; students who do
not complete the required labs will not pass the course. A medical note from a physician
is required for a missed lab. The material from the labs will appear on the tests and on
the exam. Late assignments WILL NOT be accepted and will receive a mark of zero. If
an assignment or term test is missed the student must submit the “Student Medical
Certificate” (located on the Sakai homepage) to the course instructor, and the value of the

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final exam will be increased accordingly to compensate. Any piece of work submitted
for remarking will be remarked in its entirety to correct any and all marking errors and
the grade will be adjusted accordingly. A minimum mark of 30% MUST be achieved on
the final exam in order to pass the course, irrespective of the student’s other grades (if a
grade of at least 30% is achieved on the final exam the student’s other marks in the
course and the exam mark must add up to a passing grade before credit in CHEM 2P20
will be given.

NOTE: You are responsible for material covered in class, including any announcements,
changes to the syllabus, changes to due dates, etc., whether you are there or not.

Detailed Chapter Coverage:

The following list outlines the sections of each chapter that will be responsible for.
Please note that the instructor may supplement the course with material/topics that are not
covered in the text.

Chapter and Topic Sections

Chapter 1 – Electronic Structure and 1.1 – 1.17
Bonding
Chapter 3 – Introduction to Organic 3.1 – 3.16
Reactions (Acids and Bases)
Chapter 4 – Alkanes and Cycloalkanes 4.1 – 4.14, 4.17, 4.18
Chapter 7 – Alkenes I 7.1 – 7.18
Chapter 8 – Alkenes II 8.1 – 8.13, 8.15 – 8.20,
Chapter 14 – Aromatic Compounds 13.1 - 13.10, 14.1 – 14.11
Chapter 15 – Reactions of Aromatic 15.1 – 15.12
Compounds
Radical Chemistry 10.1 – 10.10
Chapter 5 – Stereochemistry 5.1 – 5.12, 5.14 – 5.18
Chapter 6 – Ionic Reactions 6.1 – 6.14
Chapter 11 – Alcohols, Ethers, and 11.1 – 11.17
Epoxides
Macromolecular Chemistry 10.11, 10.12
Chapter 2 – Infrared Spectroscopy 2.15 –2.16
Chapter 9 – Mass Spectrometry 9.10 – 9.16
Chapter 9 – Nuclear Magnetic Resonance 9.1 – 9.8
Spectroscopy

Learning Objectives:
At the completion of CHEM 2P20 students will have an appreciation for the diverse
nature of organic chemistry and its applications. Students will understand how to draw
chemical reactions and how to properly illustrate molecules. They will understand the

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principles of chemical bonding and how polarity affects chemical reactions and the
stability of molecules. Students will be able to extrapolate/apply concepts from rather
simple molecules to more complex organic structures.

The learning objectives for each topic to be covered in CHEM 2P20 are listed below. It
should be noted that it is the responsibility of the course instructor to present the
information in each topic and that it is the responsibility of the students to ensure that
they are meeting these learning objectives and to seek assistance when necessary.

Electronic Structure and Bonding

Upon completion of this section students should be competent with the following:

• Understanding what atoms typically comprise organic molecules

• The principles that determine how the atoms in organic molecules are bonded
together
• How to best depict organic molecules
• Using the periodic table to determine the number of valence electrons in a neutral
atom and/or its ionic state
• The concept of electronegativity and how to determine differences in
electronegativity
• Formal charges and how to calculate them
• Drawing Lewis structures
• The concept of resonance and how to draw resonance structures
• Determining a molecules three dimensional structure using valence shell electron
pair repulsion (VESPR) theory and molecular orbital (MO) theory

Organic Acids and Bases

Upon completion of this section students should be competent with the following:

• Classifying molecular domains in terms of their relative acidity/basicity

• Identifying various domains in a molecule and classifying them as electron-rich or
electron-deficient regions
• Depicting the movement of electrons in chemical reactions using the appropriate
arrow notations
• Brønsted-Lowry and Lewis acid/base chemistry and their application to organic
reactions

Alkanes and Cycloalkanes

Upon completion of this section students should be competent with the following:

• The IUPAC nomenclature of linear, cyclic, and bicyclic organic molecules

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 • The flexible, three dimensional nature of organic molecules including free
rotation around bonds in linear structures and ring flips and related conformations
in cyclic systems
• Drawing Newman projections for a compound and comparing their relative
energies

Alkenes
Upon completion of this section students should be competent with the following:

• The properties of alkenes and their nomenclature

• Planning the synthesis of an organic compound including retrosynthetic analysis
• The synthesis of alkenes
• The factors influencing the regiochemistry of addition reactions of alkenes
• Reactions that can add molecules of water, halogens, carbon, and other functional
groups to alkenes
• The chemical cleavage of C=C bonds and the resulting products
• The mechanisms of the reactions associated with alkene-centred reactions

Aromatic Compounds
Upon completion of this section students should be competent with the following:

• Conjugated systems
• The electronic structure/molecular orbitals of butadiene and related conjugated
systems
• Reactions of conjugated systems, especially the Diels-Alder reaction
• The structural characteristics that classify a molecule as aromatic, anti-aromatic,
or non-aromatic and Hückel’s rules for the classification of molecules into one of
these categories
• The challenges associated with the initial assignment of benzene’s structure
• The general parameters that permit for substitution reactions of benzene and
related compounds
• How existing substituents affect the addition of subsequent groups to the aromatic
ring
• A variety of reactions that install functional groups or organic units onto aromatic
ring systems and their associated mechanisms

Radical Chemistry
Upon completion of this section students should be competent with the following:

• The properties of radicals, their formation, and their reactivity

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 • Significant radical-based reactions in nature that include, but are not limited to,
the depletion of the ozone layer
• The application of radical reactions in synthetic chemistry and the associated
regiochemical implications
• The unique types of arrows associated with mechanistic depictions of radical
reactions
• The difference between homolytic and heterolytic bond cleavage
• A series of radical initiators and why they need to be used

Stereochemistry
Upon completion of this section students should be competent with the following:

• The identification of chiral centres

• The identification, classification, and naming of chiral molecules
• Understanding how chirality can affect the chemical and biochemical behaviour
of organic compounds
• The implications of increasing numbers of chiral groups on the number of
possible stereoisomers
• The application of stereochemistry to both linear and cyclic organic molecules
• Techniques/strategies for resolving chiral molecules
• The properties of enantiomers, diasteriomers, and meso compounds and how to
identify them
• The importance of mirror planes and symmetry in relation to chiral and achiral
molecules
• The Cahn-Ingold-Prelog system for assigning stereochemistry

Substitution and Elimination Reactions

Upon completion of this section students should be competent with the following:

• What groups in a molecule can be replaced or substituted

• The various mechanisms by which substitution and elimination reactions occur
• The conditions that promote substitution and/or elimination reactions
• The relationship between substitution reactions and stereochemistry
• The relationship between nucleophiles, electrophilies, Lewis acids, and Lewis
bases

Alcohols, Diols, and Ethers

Upon completion of this section students should be competent with the following:

• The structures, properties, and nomenclature of common alcohols, ethers, and

epoxides

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 • The identification of alcohols, ethers, and epoxides as components of larger
molecules
• The synthesis and reactivity of alcohols, ethers, and epoxides and the
mechanisms associated with these reactions

Macromolecular Chemistry
Upon completion of this section students should be competent with the following:

• Different mechanisms associated with polymer synthesis

• The different classes of polymers
• The difference between step-growth and chain-growth polymers
• Applications of various polymers
• The terminology associated with macromolecular chemistry

Infrared Spectroscopy
Upon completion of this section students should be competent with the following:

• The theoretical aspects with generating an infrared spectrum and how bonds are
affected by IR radiation
• The limitations of infrared spectroscopy and molecules that are and are not IR
active
• The interpretation and assignment of IR spectra
• The locations of signals associated with major functional groups in organic
chemistry in an IR spectrum
• The reporting of data in an IR spectrum
• What information IR spectroscopy provides for organic chemists
• How IR spectroscopy integrates with mass spectrometry and NMR spectroscopy
in structure elucidation

Mass Spectrometry
Upon completion of this section students should be competent with the following:

• The fundamental theory behind mass spectrometry

• Fragmentation patterns and mechanisms in mass spectrometry
• The assignment/interpretation of mass spectra
• The identification of characteristic peaks in a mass spectrum and the fragments
that they represent
• How mass spectrometry integrates with IR spectroscopy and NMR spectroscopy
in structure elucidation

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Nuclear Magnetic Resonance Spectroscopy
Upon completion of this section students should be competent with the following:

• The fundamental theory behind NMR spectroscopy

• How NMR spectroscopy can be used to identify functional groups in a molecule
and aid in the determination of connections between atoms in molecules
• The concepts of resonance, resonance frequency, chemical shifts, splitting
patterns, relaxation, etc.
• The different types of magnetic fields employed in NMR spectroscopy
• The interpretation and assignment of 1D 1H and 13C NMR spectroscopy
• Predicting the NMR spectrum of a given molecule
• Structure elucidation using NMR spectroscopy
• How NMR spectroscopy integrates with IR spectroscopy and mass spectrometry
in structure elucidation

Academic Integrity:
Students are expected to conduct themselves in accordance with the Brock University
Academic Integrity Policy (Code of Student Academic Conduct) with respect to all
aspects of the course.