SYLLABUS Organic Chemistry I CHEM253 Fall 2008

SYLLABUS Organic Chemistry I CHEM253
Fall 2008
Instructor: J. Brent Friesen
Office: 326 Parmer Hall
Phone: 524-6972
Email: jbfriesen@dom.edu
Webpage: http://domin.dom.edu/faculty/jbfriesen/
Class Format:
Lecture A: Monday, Wednesday, & Friday 10:30-11:20; Thursday 11:30-12:30
Lecture B: Monday, Wednesday, & Friday 11:30-12:20; Thursday 1:00-2:00
Lab I: Wednesday 1:30 – 4:30 in Parmer 331
Lab II: Thursday 8:30 – 11:30 in Parmer 331
Lab II: Wednesday 1:30 - 4:30 in Parmer 331
Attendance is MANDATORY at all class meetings
Required Materials:
Organic Chemistry 7 th ed. 2007
By John E. McMurry Brooks Cole
Duplicate Page Lab Notebook: Hayden-McNeil specialty products, Jones and Bartlett Publishers,
or W.H. Freeman.
Protective Safety Goggles. “Goggles” not “glasses.”
Many Handouts will be distributed in this course.
You will need a three-ring binder to organize them.
Optional Materials:
Molecular Model Kit. (Available in bookstore, online and from former Organic students.)
Supplemental Materials: (on reserve at the library)
Study Guide with Solutions Manual for McMurry's Organic Chemistry, 7 th ed
By John E. McMurry Brooks Cole
The Organic Chem Lab Survival Manual, by J.W. Zubrick,
John Wiley & Sons, Inc. (The 7 th edition is most recent but the 5 th and 6 th are also fine.)
Websites:
http://domin.dom.edu/faculty/jbfriesen/chem253.htm
http://blackboard.dom.edu

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Course Description:
Chemistry is often characterized as the "central" science because of the many connections
to other fields. Due to the relevance of chemistry in many disciplines, it is important that
people in most scientific fields have some understanding of chemistry. This course will
be the first semester of an overview of organic chemistry. Organic chemistry is the study
of compounds that originate in living systems; therefore, it is recognized as an essential
ingredient in the education of scientists in a wide range of fields, particularly the life
sciences. The major foci of the course are to:
1) understand the reactivity of organic compounds,
2) to appreciate the role of structure in chemical identity and
3) apply reactivity and structure to the understanding the of organic molecule function.
This course in challenging and fast-paced. This means that a lot of material will be
covered in a relatively short period of time. The crucial importance of organic chemistry
dictates the pace. This course involves cumulative, vertical learning. That which is
learned in the first and subsequent weeks is needed continuously, throughout the year,
even into the last week!
Course Objectives:
1) Think Molecular! Molecules are interesting and important. Molecular thinking helps
us understand how organisms function and helps us appreciate what is going on in the
world in which we live. From the lecture, text, lab and problems in this course, you
will be able to ask questions about natural phenomena and use models and metaphor
to describe what is going on at the molecular level.
2) Become acquainted with the language of organic chemistry. Every discipline has its
vocabulary and terminology associated with it. Organic chemistry has much
representational language in the form of functional groups, molecular structural
formulas and 3-D representations.
3) Familiarize yourself with mechanism-based chemical reactivity. Much of what we do
involves using electron movement to explain and predict chemical reactivity.
4) Synthesis and spectroscopy problem solving is a means of improving your problemsolving
skills relating to real-world problems in the chemical sciences.
5) Basic experimental techniques will be learned and practiced in the laboratory section.
Creativity requires the courage to let go of certainties.
Erich Fromm

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Academic Integrity Policy
Students of the university must conduct themselves in accordance with the highest
standards of academic honesty and integrity. Failure to maintain academic integrity will
not be tolerated. The following definitions are provided for understanding and clarity.
Definitions of Plagiarism, Cheating and Academic Dishonesty
Student plagiarism is the deliberate presentation of the writing or thinking of another as
the student’s own. In written or oral work a student may make fair use of quotations,
ideas, images, etc., that appear in others’ work only if the student gives appropriate credit
to the original authors, thinkers, owners or creators of that work. This includes material
found on the internet and in electronic databases.
Cheating entails the use of unauthorized or prohibited aid in accomplishing assigned
academic tasks. Obtaining unauthorized help on examinations, using prohibited notes on
closed-note examinations, and depending on others for writing of essays or the creation
of other assigned work are all forms of cheating.
Academic dishonesty may also include other acts intended to misrepresent the authorship
of academic work. Deliberate acts threatening the integrity of library materials or the
smooth operation of laboratories are among possible acts of academic dishonesty.
Sanctions for Violations of Academic Integrity
If an instructor determines that a student has violated the academic integrity policy, the
instructor may choose to impose a sanction, ranging from refusal to accept a work
product to a grade “F” for the assignment to a grade “F” for the course. When a sanction
has been imposed, the instructor will inform the student in writing. The instructor must
also inform the student that she/he has the right to appeal this sanction, and refer the
student to the Academic Appeals Process described in the Bulletin of the Rosary College
of Arts and Sciences. The instructor will send a copy of this letter to the Dean of the
Rosary College of Arts and Sciences. The Dean will note whether a student has
committed multiple violations of the academic integrity policy over time, and in such
cases the Dean may institute a process leading to possible further sanctions, including
suspension or expulsion from the university…
“The ultimate goal in science education is no longer just amassing a body of
knowledge, but it’s also developing the skills to go about answering questions
independently. It is not possible for any one individual to learn that whole body of
knowledge. Perhaps equally important is to be able to generate ways of thinking
about questions that we have and how we might go about exploring those questions
on our own.” Dr. Anita Greenwood, University of Massachusetts - Lowell

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Tentative Course Calendar:
Date Topic Text Selection
8/27 Introduction/Overview 1.1 to 1.4
8/28 Bonding, & Hybridization, 1.5 to 1.8
8/29 Structural Formulas 1.9 to 1.12
9/01 Electronegativity & Formal Charges 2.1 to 2.3
9/03 Resonance 2.4 to 2.6
9/04 Acid/Base 2.7 to 2.10
9/05 Acid/Base 2.11 to 2.13
9/08 Functional Groups 3.1 to 3.3
9/10 Alkane Conformations 3.6 & 3.7
9/11 Alkane Classification & Nomenclature 3.4 & 3.5
9/12 Cycloalkanes 4.1 to 4.3
9/15 Cycloalkane Structure and Nomenclature 4.4 to 4.6
9/17 Cycloalkane conformations 4.7 to 4.9
9/18
9/19 EXAM I (Chapters 1, 2, 3, and 4)
9/22 Organic Reactions 5.1 to 5.4
9/24 Thermodynamics & Kinetics 5.5 to 5.8
9/25 Biological Reactions 5.9 to 5.11
9/26 Alkenes introduction and Naming 6.1 to 6.3
9/29 Alkene Stereochemistry 6.4 to 6.6
10/01 Alkene Reactivity 6.7 to 6.11
10/02 Preparation of Alkenes 7.1 to7.4
10/03 Alkene Reactions 7.5 to 7.8
10/06 Alkene Reactions 7.9 to 7.11
10/08 Alkynes introduction and Naming 8.1
10/09 Preparation of Alkynes 8.2 to 8.5
10/10 Alkyne Reactions 8.6 to 8.9
10/13
10/15
10/16 EXAM II ( Chapters 5, 6, 7, & 8)
10/17 LONG WEEKEND
10/20 Introduction to Stereochemistry 9.1 to 9.4
10/22 Absolute Stereochemistry 9.5 to 9.8

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Date Topic Text Selection
10/23 Diastereomers & Meso 9.9 to 9.11
10/24 Fischer Projections 9.12 to 9.14
10/27 Haloakane introduction and Naming 10.1 to 10.3
10/29 Preparation of Haloalkanes 10.4 to 10.6
10/30 Haloalkane Reactions 10.7 to 10.9
10/31 Substitution Reactions 11.1 to 11.3
11/03 S N 2 Reactions 11.4 to 11.6
11/05
11/06
11/07 EXAM III (Chapters 9, 10, & 11.1 to 11.6)
11/10 Elimination Reactions E2 11.7 to 11.9
11/12 Elimination Reactions E1 11.10 to 11.12
11/13 Summary of Substitution and Elimantion
11/14 Infrared Spectroscopy 12.5 & 12.6
11/17 Infrared Spectroscopy of Functional Groups 12.7 & 12.8
11/19 Nuclear Magnetic Resonance Spectroscopy 13.1 to 13.3
11/20
13 C NMR 13.4 to 13.7
11/21
1 H NMR proton equivalence & chemical shifts 13.8 & 13.9
11/24
1 H NMR integration & spin-spin splitting 13.10 & 13.11
11/26 THANKSGIVING HOLIDAYS
11/27 THANKSGIVING HOLIDAYS
11/28 THANKSGIVING HOLIDAYS
12/01 NMR problems 13.12 & 13.13
12/03
12/04 EXAM IV (Chapters 9 & 12a)
12/05
12/?? FINAL EXAM (Cumulative)
“We should never lose our zest for living, our excitement and enthusiasm, our curiosity,
our desire to know. The person who does is certainly blind to the world, its miracles and
possibilities, and one’s own possibilities.” Earl Nightingale

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Grading for Organic Chemistry : The grade for this course consists of both the lecture
grade as well as the laboratory grade. The distribution of the grades will be:
Quizzes (Best 40) Units of 5 points 20%
Homework Assignments (Best 5) 20 points each 10%
Laboratory 200 points total 20%
Midterm Exams (Best 3 of 4) 100 points each 30%
Final Exam 200 points 20%
Letter Grade Assignments:
100 > A > 92% 92 > A- > 90
90 > B+ > 88 88 > B > 84 84 > B- > 82
82 > C+ > 80 80 > C > 76 76 > C- > 74
74 > D > 65
Attendance:
Class attendance is an essential component of this course. If you are absent you cannot
receive the points designated for the class preparation or in-class quiz. You will lose 5
points for every 15 minutes that you are absent during regular class time. Consistently
missing class will not be tolerated. More than 8 missed class sessions will result in an “F”
grade for the course.
Why Should Students Attend Class?
1) Attending class allows you to be part of a learning community. Learning has a
personal and communal dimension, both of which are critical to the student.
2) Interaction with the instructor is another reason you should attend class. The
physical presence of an instructor has a holistic impact on each student that
cannot be duplicated or replaced by a book, video or electronic
communication.
3) The presence of students in the classroom is part of the course design. In order
to fulfill the purpose for which the course is offered, students must be present
in the classroom during class time.
4) The bottom line: you (and/or someone who loves you) paid for it!

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Lecture and Reading:
The lecture time will be spent introducing new concepts, solving sample problems and
going over problems areas that have been identified from graded homework and quizzes.
Preparation for lecture is essential. The current text is very organized and readable. Make
use of the many diagrams in the text, Organic Chemistry is a very visual discipline.
Follow the problems solved in the text. Reading the book before lecture will help you
assimilate new concepts easier and guide you to pose key questions about the material.
Bring all graded papers and work-in-progress to class. Do not hesitate to ask questions
about the worksheet you are currently doing.
Exams:
All examinations will be cumulative with the emphasis on the newest material. I will be
glad to schedule a review before any of the exams if the interest is there. Exams must be
taken the day they are offered. Any missed exams will be counted as a dropped score. No
make-up exams will be offered until finals week.
Quizzes:
There will be at least 40 five-point quizzes. The format of the quizzes will vary. Quizzes
may be given to prepare for the next class period. These are due at the beginning of the
class period for which they are assigned. Online quizzes will be completed before the
class period for which they are assigned. Quizzes given in class will be 5-10 minutes in
length. There are no make-up quizzes. Quizzes are designed 1) to help you keep you up
to date in the class, 2) to encourage you to do practice problems, and 3) to allow you to
become used to my style of questions. You will be allowed to drop quiz problems if more
than 40 are given.
Homework:
The only way to learn organic chemistry is to do problems. Thus, there will be homework
worksheets handed out regularly (about one for each chapter). Please do your homework
problems as they are covered in class. Be sure to raise pertinent questions in class about
homework problems. This effort should help you to keep up with the material and come
to class with questions about the material that is being covered. Be forewarned these
problems are a minimum requirement! You should attempt to solve many of the chapter
exercises, end-of-chapter problems, and web page exercises.
In the event that homework problems will be collected, hand your homework in at the
beginning of the class period the day it is due. Any homework handed in after it is due
will receive a two-point deduction. No homework will be accepted after the homework
has been graded and handed back. Extra credit will not be accepted on late work.
Consistently handing in late homework will not be tolerated. In addition to the above
penalties no more than two late assignments will be graded.

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Some Reflections On Teaching and Learning:
My job is to identify and develop the major conceptual issues for the course and then to
show how those concepts are used in understanding chemical reactivity. In addition, I
hope to articulate the connections between concepts in this class, lab, and other classes
that you are taking. I would also like to share with you some of the exciting modern
advances in organic chemistry and the applications. In order to accomplish these goals, I
would like to have an interactive classroom with feedback from you. This possibility
means less lecturing and more discussion with a focus on problem solving and conceptual
understanding. Hopefully, we can create an environment where it is possible to ask
questions, take risks and even fail. Listed below are some suggestions which will help
you to learn organic chemistry and will also help set up an interactive, constructive
environment.
1. Come to class. Regular attendance is expected. You are responsible for all
information disseminated at all class meetings. If you are not there, you will miss the
flow of events, the questions and discussion of your peers, and information given in
the lecture.
2. Work problems. Work all of the problems in the text and at the end of the chapter.
Try to work the problems in a reflective manner. Test your understanding of
concepts. Don't jump to the solutions manual if the answer is not immediately
apparent. As the exams and quizzes will test your ability to apply the material to new
situations and problems, it is critical that you understand the concepts. There are also
be problems and exercises on-line at the Organic Chemistry Companion Page. If you
are having difficulties, this might be a place to find extra insight.
3. Read the chapter ahead of time. This suggestion does not have to be an intensive
effort. A look at which functional groups are involved, the topic headings, and the
type of reaction will give you some sense of where we are headed.
4. Study diagrams and tables. They are more than pretty pictures. They can pull together
what is being described in the text in a very vivid way.
5. Explore the on-line supplementary materials. The animations are awesome and show
chemical structure and reactivity in a very dramatic way.
6. It is absolutely essential that you learn the vocabulary of organic chemistry. Important
words and terms must be memorized. The textbook puts key terms in boldface and
includes them in the "Key Terms" section at end of each chapter.
7. If you are in trouble, ask for help. I have posted office hours at which time I will be
available to answer questions. I will also be glad to make an appointment for other
times. If you have a quick question, feel free to contact me by email. In addition, I
will organize help sessions if a group of students are having difficulty with a
particular topic or if the class requests a review session before an exam. Remember,
in the end, you are responsible for learning.

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What do I need to remember from General Chemistry?
There are several concepts from General Chemistry that we will assume you have learned
and learned well. While we will review all of them in class, the reviews will be rather
brief. It is absolutely essential that you have a solid understanding of these concepts. If
you don’t, you had best go back and review them.
1. Atomic structure and Periodic Trends
You should know about atomic orbitals and electron configurations. In Organic
Chemistry we will be playing “Where’s the electron?” from beginning to the end. It is
important to have a basic understanding of electrons of atoms in order to understand
electrons of molecules. Periodic trends especially that of electronegativity, are useful to
remember.
2. Bonding and Molecular Geometry
The principles of covalent bonding, ionic bonding, hybrid atomic orbitals and molecular
geometries (Valence Shell Electron Repulsion Theory) are absolutely essential to
understanding the behavior of organic molecules. It is very important to be able to draw
the Lewis Structure, complete with non-bonding electrons and formal charges, of every
molecule you come across.
3. Electronegativity and Molecular Polarity
Combining electronegativities of atoms in a molecule with its molecular geometry allows
one to predict the overall molecular polarity, which is an essential step in predicting
physical and chemical properties of organic molecules.
4. Acid-Base Concepts
Almost every single reaction in organic chemistry can be described in terms of an acidbase
reaction, either by the Bronstead definition or by the Lewis definition. (The latter
being far more common and important.) Also important is the concept of conjugate acids
and bases and their relative strengths (weaker acid means stronger conjugate base, etc…)
Know these concepts like the back of your hand!
5. Equilibrium, Kinetics and Thermodynamics
To understand organic reactions and mechanisms, we make extensive use of the
principles of equilibrium (Including Le Chatelier’s principle), thermodynamics and
kinetics. Unlike General Chemistry, though, we do very little mathematics in Organic
Chemistry. Rather, we are more often concerned with qualitative relationships between
these principles, and we make extensive use of reaction coordinate diagrams to describe
them. Be able to read, interpret, and draw reaction coordinate diagrams (also called
potential energy diagrams).