Syllabus
Advanced Organic Chemistry (CHEM-405)
MWF 2:00 pm – 2:50 pm
Hayward 207
Spring 2010
Philadelphia University School of Science & Health
Professor: Dr. M. Milkevitch
Office: 304 Search Hall
Office phone: (215) 951-2779
Email: milkevitchm@philau.edu
Website: http://faculty.philau.edu/milkevitchm
NOTE: This syllabus is also available on my faculty website.
Office Hours: Formal office hours are MWF 9 am – 10 am. Otherwise, open door
policy. Other hours are also available by appointment.
Required Text: There is no required textbook for this course. You may use any current
Organic Chemistry textbook of your choice, including the one you used for Organic
Chemistry I & II. I will use “Organic Chemistry” 7th ed, by L.G. Wade, Jr., Prentice
Hall: New York, 2010 as a basis for some of the lectures, with other material coming
from other sources. If we cover topics not represented in your textbook, I will provide
you with textbook material (either photocopies or the book will be on reserve in the
library).
Course Pre-Requisite: Organic Chemistry I and II (CHEM 201 & 202)
Course Description: This course is a continuation of Organic Chemistry I and II, which
will include additional topics not covered in these courses as well as more advanced ones.
Overall, the subject of this course is the physical properties, reactivity and synthetic
transformations of organic compounds (mostly small molecules) containing a variety of
functional groups. The emphasis will be on aromatics, conjugated systems, functional
groups containing the carbonyl moiety, and amines. The reason for this emphasis is that
species within this group have some of the most interesting and useful chemistry within
the realm of organic chemistry. Conceptual, theoretical and mechanistic information as
they pertain to the specific functional group under discussion will be supplied. It is
assumed that the student has fundamental knowledge of basic organic chemistry concepts
such as nomenclature, conformational analysis, kinetics, and stereochemistry. Additional
review on these subjects (amongst others) will be given as needed. This course will be
taught in a mechanistic fashion, with and emphasis on whole molecule synthesis,
functional group transformation and retro-synthetic analysis. Special topics, such as
overviews of spectroscopic methods will also be covered.
Course Objectives:
1) To present a comprehensive overview of aromatic, aldehyde/ketone, carbonyl,
amine, and percyclic chemistry, with an emphasis on reactions of said compounds
and their use in organic synthesis
2) To introduce and use MO theory as a basis for explaining the reactivity of
organic compounds
3) To introduce special topics such as spectroscopy (various), retro-synthetic
analysis, protecting groups, and other specialized topics as they relate to organic
synthesis
4) To give the student experience/training on the formulation of a synthetic
strategy for whole molecule synthesis
5) To give the student experience/training on the use of retro-synthetic analysis as
a tool for whole molecule synthesis
6) To give the student experience with obtaining and searching the organic
chemistry literature
7) To provide training/experience in reading/assimilating the organic chemistry
literature and interpreting/presenting the main points of scientific papers to the
public
Exams and Grading:
Exams (3 total)
Problem sets
Student Literature Presentations
50%
35%
15%
Total
100%
Offical PhilaU Grading Scale:
A
AB+
B
BC+
C
C-
>94%
90 – 93%
86 – 89%
83 – 85%
79 – 82%
76 – 78%
73 – 75%
69 – 72%
D
F
59 – 68%
< 58%
Exam Distribution Dates: (Due dates will be indicated on the exam)
Exam 1: Feb 19, 2010
Exam 2: March 26, 2010
Exam 3: April 30, 2010
Performance Assessment:
1. Problem sets (35% of final grade): Problem sets will be distributed during the
course of the semester approximately every 1.5 -2 weeks. Typically, these
problem sets will be from 10-30 problems. Problem sets are due 1 week after
assigned. The intention of these assignments is to gauge student understanding of
course concepts.
2. Additional Assignments: Over the course of the semester, several additional
assignments will be offered. These assignments will be checked for accuracy but
will not be graded. The intention of these assignments is provide additional
student practice with course material. The format of these assignments may be of
various types.
3. Exams (50% of final grade): The emphasis of this course is organic synthesis,
and advanced concepts in this area will be presented. Due to the complex nature
of whole molecule synthesis, all exams in the course will be in a take-home
format. In this format, the following guidelines will be followed:
a. Exams will be provided at the end of the listed lecture day, and the due date
will be listed on the exam.
b. You may not consult your notes, any book or literature articles (other than
those which may be supplied specifically for this exam). Any deviation from
this will result in a Student Code of Conduct violation.
c. You may not consult one another or another party in the completion of the
exam. Any deviation from this will result in a Student Code of Conduct
violation.
d. The only person you may consult on the exam is me. However, I will only
provide minimal support, meaning I will be available to clarify a question and
so forth.
e. All work must be shown on the exam in order for you to receive credit for a
particular problem.
f. Due dates for the exams will be rigorously enforced.
3. Student Literature Presentations (15% of final grade): An important part of a
professional scientist’s career is working with the scientific literature. Therefore,
students will be required to present (2) scientific papers during the course of the
semester. These papers must illustrate the synthesis and characterization of
organic molecules, however the student is free to choose a topic/reaction/total
synthesis of interest. Here are some guidelines for this course requirement:
1. All papers must be approved prior to presenting. Please provide me with a copy
of your paper and see me to discuss at least 1 week prior to your scheduled
presentation.
2. Presenting students must supply the class with copies of their paper at least 1
week prior to their scheduled presentation.
3. Student presentations will be a maximum of 20 minutes in length with 5 minutes
for questions.
4. Presentations will be scheduled every 2 weeks and will occur on Fridays.
5. A sign-up sheet will be circulated during the first week of class for scheduling
purposes.
6. Students are advised to choose a paper of suitable length. If the paper is too long
it will take more time/effort to present and remember you have a time constraint!
7. Scientific papers typically include a great deal of information. The student must
analyze the paper for the important information and only present that information.
8. The organic chemistry literature is huge and subject matter is very diverse. The
student is free to choose a topic/reaction that appeals to their individual interest.
9. A list of journals to consider for articles will be circulated the first week of class.
10. Be aware that our library at Phila U has very few organic chemistry journals.
Therefore, if you need to use interlibrary loan (ILL) to obtain a journal
article, be sure to do that well in advance because it typically takes 1-2 weeks
for you to receive a journal article by ILL.
11. Grading rubrics will be circulated on presentation days.
Tentative Lecture Schedule
Week
Jan 11
Jan 18
Topic(s)/ Text Chapter
Conjugated systems; concepts and
theoretical concerns, Diels-Alder
reactions (introduction to pericyclic
reactions), other reactions of conjugated
systems. MO theory will be reviewed as
needed. Special topic: Ultraviolet
spectroscopy (if time permits)
Conjugated systems, con’t.
Important Notes
Jan 18: MLK Day, No
Class
Jan 25
Feb 1
Feb 8
Feb 15
Aromaticity; concepts and theoretical
concerns (MO theory), aromatic ions,
heteroaromatics, fused ring aromatics and
other related topics
Aromaticity, con’t.
Reactions of aromatic compounds;
Electrophilic Aromatic Substitution,
directing groups, activating/deactivating
groups, Friedel-Crafts alkylation and
acylation, Nuclophilic Aromatic
Substitution, addition reactions, side-chain
reactions, reactions of phenols. Special
topic: retrosynthetic analysis
Reactions of aromatic compounds,
con’t.
Friday, Jan 29:
Student Presentations
Friday, Feb 12:
Student Presentations
Exam 1 distributed;
Feb 19
Feb 22
Reactions of aromatic compounds, con’t Friday, Feb 26:
(as needed).
Student Presentations
March 1
Aldehydes and Ketones; comprehensive
overview, nomenclature, synthesis of
aldehydes & ketones, reactions of
aldehydes & ketones (nucleophilic
addition, Wittig synthesis, hydration,
formation of cyanohydrins, formation of
imines, condensation reactions, acetal and
hemicacetal formation, oxidation and
reduction), advanced topics. Special
topic: protecting groups
Aldehydes and Ketones, con’t.
March 8
March 15
SPRING BREAK
March 22
Aldehydes and Ketones, con’t.
Friday, March 12:
Student Presentations
NO CLASS
Exam 2 distributed;
Friday March 26
Friday, March 26:
Student Presentations
March 29
Comprehensive Condensation
Reactions & Alpha Substitution
Reactions of Carbonyl Compounds;
keto-enol tautomerism, enamines and
enamine reactions, alpha halogenation of
ketones (haloform reactions), aldol
condensation, dehydration of aldols, aldol
cycliczations, Claisen condensation,
Dieckmann condensation, crossed
claisens, malonic ester syntheses,
acetoacetic ester syntheses, The Michael
Reaction, the Robinson Annulation
Condensation Reactions & Alpha
Substitution of Carbonyls, con’t.
Condensation Reactions & Alpha
Substitution of Carbonyls, con’t (as
needed)
Amines; overview, nomenclature, basicity
of amines, Aromatic Subtitution of
arylamines and pyridine, acylation of
amines, alkylation reactions,
sulfonamides, The Hofmann Elimination,
The Cope Elimination, Nitroso Amines,
reactions of arenediazonium salts,
syntheses utilizing amines
Amines, con’t.
April 5
April 12
April 19
April 26
Friday, April 9:
Student Presentations
Friday April 23:
Student Presentations
Exam 3 Distributed:
Friday April 30.
May 3, Last Day of
Class and Final
Student Presentations
Course Policies:
1) Attendance:
a. Your regular attendance is vital to this course. There is a direct correlation
to performance in this class and regular class attendance.
b. Skipping classes will put you behind in the course material and very likely
result in a lower grade for the course. Therefore, don’t miss class.
c. Get the most out of your investment…don’t miss class.
2) Late Work:
a. The due date for all problem sets/assignments/exams will be listed on
the assignment.
b. All assignments and problem sets must be completed by the indicated due
date and turned in at the beginning of class.
c. Any assignment submitted by email will NOT be accepted.
d. The only acceptable excuse for a missed problem set/assignment/exam is
an illness/acute familial crisis/court date. If something like this comes
up, you must follow the following procdure:





Inform me (via email, phone call, contact through the SSH
departmental office) within 48 hours of the due date listed
on the assignment.
Documentation (doctor’s note, letter from attorney, etc)
will then be required and must be submitted to me for
consideration.
If these requirements are followed accommodation will be
granted and a makeup/additional assignment time will be
decided upon.
Again, you must inform me within 48 h for an excuse to be
considered. If I am informed after 48 hours then no excuse
will be considered and the result shown in part e (below)
will come into effect.
Also, if you fail to provide adequate documentation for the
excuse to be considered, no consideration will be given and
the result in part e (below) will come into effect.
e. If this procedure is not followed (I am not informed within 48 h,
improper or no documentation supplied), no accommodation will be
given and you will suffer a 20% daily grade penalty for the late
assignment.
f. These procedures will be rigorously enforced.
g. The best way to avoid any of this is to turn your assignments in on time.
Also, if you feel that you may be absent from a class where an assignment
is due, you may turn the assignment in early or arrange for a classmate to
turn it in on time.
3) Missed Exams/Presentations:
a. Exams/presentations must not be missed.
b. The only acceptable excuses for a missed exam/presentation are the same
excuses listed in section #2 above.
c. In this case, the same procedure for an excused absence (as shown in
section #2 above) must be followed. In the case of a missed presentation,
if the procedure is followed and the excuse is acceptable, then your
presentation will be rescheduled.
d. Again, if this procedure (shown in section #2 above) is not followed,
no accommodation will be given and you will suffer a 20% daily grade
penalty for the missed/late exam. For the missed presentation, you
will suffer a 25% penalty and you must see me to reschedule the
presentation.
e. These procedures will be rigorously enforced.
f. The best way to avoid any of this is to turn your assignments in and do
your presentations on time. Also, if you feel that you may be absent from
a class where an assignment is due, you may turn the assignment in early
or arrange for a classmate to turn it in on time.
4) Tardiness:
a. Being late to class disrupts the lecture and will not be tolerated.
b. Be respectful of your fellow students and me: show up on time.
5) Email Etiquette:
a. I’m not your facebook friend or the like. If you wish to correspond with
me using email, you must use the appropriate, professional style. In
addition, when you enter the workforce this will be expected.
b. Example style:
Dr. Milkevitch:
Could I make an appointment with you for some extra help with
stereochemistry? I am available on TR from 1-3:30 pm. Please let me know.
Thank you,
Jane Doe
c. If you do not use the appropriate style, then your email will be deleted and
not responded to.
5) Student Code of Conduct: The faculty of Philadelphia University takes academic
integrity seriously. Instances of academic dishonesty will not be tolerated, and
students violating the University’s Academic Integrity Policy will be subject to
appropriate sanctions. Plagiarism on any written assignments will not be tolerated.
You may turn in only your own work and homework assignments (unless otherwise
informed), and any references that you use must be documented appropriately.
Cheating on exams will not be tolerated and will result in a failing grade and will be
reported. The student is highly advised to read the Student Code of Conduct as it
appears in the Student Handbook for Philadelphia University, or visit the website
www.philau.edu/learning
Academic Support Services:
Gutman Library (www.philau.edu/library)
The home page of the Gutman Library provides students with a variety of information
resources, including databases and research guides. Librarians are available online and in
person at the information desk to help students with research.
The Learning and Advising Center ( www.philau.edu/learning)
The Learning and Advising Center provides one-on-one tutoring assistance for writing,
study strategies, test taking, and specific Philadelphia University courses*. To make a
tutoring appointment, students should stop by the Learning and Advising Center in
Haggar Hall or call (215) 951-2799. Academic resources, including information on
citation and documentation, note taking, and study strategies are available on the Center’s
website.
Technology assistance (http://www.philau.edu/OIT/)
For assistance with technology issues, students should contact the Technology Help Desk
at (215) 951-4648 or send an email to helpdesk@philau.edu. General purpose computing
facilities are available in Search Hall and Gutman Library.