CHeM 2140 WS13 Advanced
Organic Chemistry Laboratory
Recitation/Lecture:
Fridays @ 2:00 pm in Schlundt 103.
Primary
Instructor Teaching
Assistants: NMR
Assistant
L. Phillip Silverman Pete
Punthasee ppxb5@mail.missouri.edu Eddie Pittman elpq63@mail.missouri.edu
Andrea
Cummings afh8k3@mail.missouri.edu
Room 123D Chemistry
(573) 882-1401
Office
Hours: Tuesday Thursday 2:00
– 3:00
Monday
1:30 – 2:30
Class
Philosophy and Goals: Welcome to CHEM 2140. This is a serious lab course,
unlike any other that you have taken thus far in the Chemistry Department here
at the University of Missouri – Columbia. We meet three times a week:
twice for lab and once for recitation. All this for 2 credit hours, so the
first point I need to make is simple:
NO WHINING!!
I
know that this is a lot of work for 2 credits and that the class is hard.
I’ve heard it all before and it gets you absolutely zero sympathy points
from me; in fact it will have the contrary effect. Chemistry is a discipline as
much as an art and I fully intend for this course to be both rigorous and
intense. Don’t worry so much about your overall grade; traditionally,
this course has resulted in mostly A’s and B’s. C’s can be
given out and D’s are not impossible to achieve. Your overall goal needs
to be achievement of understanding the basics of multi-step organic synthesis
and identification and interpretation of spectra of synthesized target
molecules and intermediates. These are hard tasks but achievable ones, if you
spend your time wisely and prepare ahead. Unlike other classes, most of the lab
work is SOLO, so you can’t lean on your partner. Gaff off the lab and it
will most surely blow you away!
REQUIRED TEXTS:
A carbonless lab notebook at least 50 pages
long. I recommend the 100 page lab notebook.
Introduction to Organic
Spectroscopy: by Laurence M. Harwood and Timothy D. W. Claridge [Oxford University Press; ISBN:
0-19-855755-8]
The other book is a GREAT READ: “Tales
of a Shaman's Apprentice: An Ethnobotanist Searches for New Medicines in the
Amazon Rain Forest” by Mark J. Plotkin [ISBN: 014012991X
]. This is inspiring stuff about natural products chemistry.
A book that might help is
“Spectrometric Identification of Organic Compounds” by Robert M. Silverstein
and Francis X. Webster Publisher: John Wiley & Sons; 6th edition (November
1997) ISBN: 0471134570. I wouldn’t make it a required text ($$$) but if
you are interested in ANYTHING to do with organic chemistry, this is a must-have textbook!
Do you HAVE to get these at the bookstore?
No. Go on-line from any of a number of retailers, if you desire! That is why
the ISBN was included.
Weekly recitation: Friday. Attendence will be taken EVERY
CLASS.
LAB SECTIONS:
We
are doing a blended teaching schedule:
Andrea
will teach Monday/Tuesday
Pete
will teach Wednesday/Thursday
The
course schedule for CHM 2140 will have each lab section meeting twice a week
for each section. Attendance is mandatory for all sections, however if you
cannot attend your own section, you may attend the other section providing you
have secured permission of the TA’s involved IN ADVANCE. Since these labs
build upon each other (precursor A is used to make B which in turn makes C),
missing a lab day can severely impact your ability to produce the target
compounds in the allotted time.
What
do I mean by an excused absence? There are 4 different categories of excused
absences: 1) medically excused, 2) death of someone close to you, 3) university
sponsored event, and, 4) “legally” excused. The definitions follow.
To
be medically excused, you SHALL get
written verification by a medical doctor stating both the time of visit and the
duration of the expected illness. No note, no excuse. If you are not sick
enough to go to the Student Health Center, go to lab/recitation. Death of someone close to you
isn’t something to use as an excuse unless it is legitimate. Obituaries
of people will suffice as an excused absence. If you are part of a University sponsored event, the letter
comes automatically from the program office (if you are presenting at a
conference, let me know!). Significant time away from lab and recitation can
impact your overall grade even though the absences would be excused. “Legally” excused absences
will involve subpoenas, court records, traffic tickets, or some other written
form of documentation stating that court or being arrested is where you were
(bring your bail agreement!). Also, all of the excused absences will need to
have a point of contact and a phone number that I can call to verify the claim.
I reserve the right to make the final call for all absences from lab and
recitation. Short and sweet: unless you are bleeding out of your eyes, show up.
I wouldn’t go down the road of “I get three strikes before I am in
trouble” philosophy; significant tardiness (more than 15 minutes) can
be considered as an unexcused absence.
Some
of the lab basics: come prepared to work. This means having good pre-lab
preparation: You need to state what the purpose of the experiment is in your
own words. You will have in your notebook a set of procedures that should allow
you to work without your lab
print-outs. Coming to lab without a properly prepared lab notebook or otherwise
being unprepared to work will result in points being taken from your final
grade: you need to have shoes that cover your toes, lab glasses that shall be
worn ALL period shall be brought to each lab meeting. These policies are in
keeping with EH&S policies concerning dress and conduct in lab. Also, it is
University of Missouri policy that there is no eating or drinking in lab. If
you come into lab with a water bottle, stash it in your backpack.
Arriving
late for lab (totally at the TA’s and my discretion) may result in you
not being allowed to attend the lab (3 hour blocks of time are pretty
unforgiving!) The TA and the website will give you more information about the
type of information you will need to include in a lab report. All observations
need to be recorded and your notebook shall be initialed by your TA before you
leave the lab.
The
notebooks you shall use for this class will utilize some type of direct
copying, either carbon or carbonless. Additionally, all work shall be
your own. If you are getting information from another source, annotate the
source! The line can get pretty blurred in lab courses, but you need to know
that from Day 1, I expect each person to work solo in this class on all graded
assignments with the exception of the chromatography section (groups of 3 or 4
depending upon class enrollment/number of bodies). You will be working on your experiments alone, so it behooves you
to be ready for lab.
Other
policy stuff: If you feel a grade is unfair, you need to take that grade up
with the TA who graded the experiment within 2 weeks of receipt of the grade. Past that point, the grade stands.
You need to resolve ALL conflicts at the lowest possible level. If you have an
issue with the TA, talk to the TA outside of class time. If you can’t get
past the issue after talking to the TA off line, come see me together.
If you come to me without the TA, I’ll send you back to the TA and we
will schedule a time when you both can come in and talk about the problem. The
only times you can come to me directly are about issues of “moral
turpitude” or lab safety.
Communications
with the instructor: sending me an email is usually not a problem. However,
when I receive email, I am not your “dog”, your
“proffie”, or your “bro”. Emails WILL be polite and
will use proper grammar, punctuation, and be professional in tone. Emails that
do not comply with these simple requirements will be ignored.
ADA Compliance:
If you need accommodations
because of a disability, if you have emergency medical information to share
with me, or if you need special arrangements in case the building must be
evacuated, please inform me immediately. Please see me privately after class,
or at my office. To request academic accommodations (for example, a notetaker),
students must also register with the Office of Disability
Services, (http://disabilityservices.missouri.edu),
S5 Memorial Union, 882-4696. It is the campus office responsible for reviewing
documentation provided by students requesting academic accommodations, and for
accommodations planning in cooperation with students and instructors, as needed
and consistent with course requirements. For other MU resources for students
with disabilities, click on "Disability Resources" on the MU
homepage.
Academic Integrity:
Academic integrity is
fundamental to the activities and principles of a university. All members of
the academic community must be confident that each person's work has been
responsibly and honorably acquired, developed, and presented. Any effort to
gain an advantage not given to all students is dishonest whether or not the
effort is successful. The academic community regards breaches of the academic
integrity rules as extremely serious matters. Sanctions for such a breach may
include academic sanctions from the instructor, including failing the course
for any violation, to disciplinary sanctions ranging from probation to
expulsion. When in doubt about plagiarism, paraphrasing, quoting,
collaboration, or any other form of cheating, consult the course instructor and
your TA .
This is a topic that I hope I will not have to
discuss again this semester. Any incidents of dishonesty with regard to this
course (e.g. cheating on an exam, turning in someone else's work as your own,
etc.) will result in a failing grade (a "0") on the exam where the
cheating takes place. In addition, I will report the incident to the Provosts
Office for possible disciplinary action; consequences of such action are severe
(read the M-Book for more details!)
Intellectual
Pluralism
The University community
welcomes intellectual diversity and respects student rights. Students who
have questions or concerns regarding the atmosphere in this class (including
respect for diverse opinions) may contact the Departmental Chair or Divisional
Director; the Director of the Office of Students Rights and Responsibilities (http://osrr.missouri.edu/) or the MU Equity Office (equity@missouri.edu; http://equity.missouri.edu/) All students will have the opportunity to
submit an anonymous evaluation of the instructor(s) at the end of the course.
If
you have any questions about academic integrity or intellectual pluralism,
please feel free to contact Associate Vice Provost
Michael Prewitt (882-1422) who oversees the Office of Student Rights and
Responsibilities (http://osrr.missouri.edu/).
Grades:
Assignment Points percent
|
Lab 1 |
50 |
6.67 |
|
Lab 2 |
50 |
6.67 |
|
Lab 3 |
50 |
6.67 |
|
Lab 4 |
50 |
6.67 |
|
Lab 5 |
50 |
6.67 |
|
Lab 6 |
50 |
6.67 |
|
Lab 7 |
50 |
6.67 |
|
Lab 8 |
100 |
13.33 |
|
Lab 9 |
100 |
13.33 |
|
Presentations |
100 |
13.33 |
|
Final
Exam |
100 |
13.33 |
|
|
750 |
100.0 |
A few of the labs from the first part of the course were derived
from the website of Dr. Jennifer Muzyka (http://web.centre.edu/muzyka/).
I gratefully acknowledge her efforts in adapting these experiments for use in
her Organic 341 class. We have made some modifications to the experiments from
her website but I would be entirely remiss without acknowledging her efforts
for adapting good labs from the sources cited within each experiment. These
labs are both useful and challenging!
|
Week |
Date |
Experiment |
Friday lecture topic |
||
|
1 |
JAN 22
– JAN 25 |
None: This is the week for everyone to check out the website
and learn about the expectations for the class. Also, recitation is MANDATORY
on Jan 25, 2010 and on all Fridays this semester. |
JAN 25 INTRODUCTION: Create a reagents table, use MSDS, lab reports,
safety rules |
||
|
2 |
JAN 28
– FEB 1 |
Mon/Tues: LAB
CHECK IN: you have to attend, otherwise it is an
unexcused absence |
Wed/Thur: SYN 1 |
FEB 01 LAB REPORTS: how to do, 1H nmr usage (TA’s
present info), what do we mean when we say to characterize
the product? |
|
|
3 |
FEB 04
- FEB 08 |
Mon/Tues: SYN 1 Run the
column and submit nmr |
Wed/Thur: SYN 2 Peptide
Coupling – READ! A method will be prepared and available. |
FEB 08 Proton nmr interpretation (read Chapter 4 of Harwood and Claridge) |
|
|
4 |
FEB
11 – FEB 15 |
Mon/Tues: SYN 2 Peptide Coupling |
Web/Thur: |
FEB 15 NMR: how it works and what we can do with it http://www.cis.rit.edu/htbooks/nmr/inside.htm http://www.chem.uni-potsdam.de/tools/index.html Problems from the Smith Website; Smith workbook |
|
|
5 |
FEB 18
– 22 |
Mon/Tues: Anti-convulsant PART 2 |
Wed/Thur: SYN 3: Anti-convulsant PART 3 (CATCH-UP AND Purification DAY
for Dilantin) |
FEB 22 Problems from the Smith Website; Smith workbook (reread Chapter 4
of Harwood and Claridge) Lesson from
Smith for Interpretation |
|
|
6 |
FEB 25
– MAR 01 |
Mon/Tues: |
Wed/Thur: SYN 4: Sulfanilamide PART 2 |
MAR 01 C13 nmr / DEPT and other techniques Problems from the Smith Website; (read Chapter 5 of Harwood and Claridge) |
|
|
7 |
MAR 04
– MAR 08 |
Mon/Tues: |
Wed/Thur: SYN 4: Sulfanilamide PART 2 |
MAR 08 Tougher problems from Smith |
|
|
8 |
MAR 11
– MAR 15 |
Mon/Tues: Proton estimation for
Intermediate for EXPT 4
|
Wed/Thur: Proton estimation for Final
product for EXPT 4
|
MAR 15 IR and UV VIS and FGI (functional group identification) (read Chapters 2 and 3 of Harwood and Claridge) Spin Spin Splitting (what about protons on alkenes) |
|
|
9 |
MAR 18
– MAR 22 |
Mon/Tues: SYN 7: Competition |
Wed/Thur: SYN 7: Competition |
MAR 22 By the way, go to the PAPER versions of this journal!!! QH1.L94 in
Ellis. |
|
|
10 |
MAR 23
– MAR 31 |
SPRING BREAK |
|||
|
11 |
APR 01
– APR 05 |
Mon/Tues: SYN 7: Competition |
Wed/Thur: Catch-up Day for ALL Synthesis |
APR 05 CHROMATOGRAPHY: PREP TLC AND COLUMN TECHNIQUES NOTE: THERE
WILL BE RECITATION THIS WEEK!! Phytochemical and Ethnobotanical
Databases, Mayapple, mayapple photo 1, mayapple photo 2, Poisonous Plants:
Podophyllum peltatum, Why play with something so
nasty? |
|
|
12 |
APR 08
– APR 12 |
Mon/Tues: CHROMATOGRAPHY PART 1 |
Wed/Thur: CHROMATOGRAPHY PART 2 |
APR 12 SPECTROSCOPY:
MASS SPEC: (read
Chapter 6 of Harwood and
Claridge) GUEST LECTURER FOR TODAY! |
|
|
13 |
APR 15
– APR 19 |
Mon/Tues: CHROMATOGRAPHY PART 3 |
Wed/Thur: CHROMATOGRAPHY PART 4 |
APR 19 Organic classification tests
Useful stuff for unknown
identification; acid base separations (don’t do
the experimental part: just read for background!!) |
|
|
14 |
APR 22
– APR 26 |
Mon/Tues: UNKNOWN IDENTIFICATION PART 1 |
Wed/Thur: UNKNOWN IDENTIFICATION PART 2 |
APR 26 NOTE: LOCATION OF CLASS
WILL BE CHEM 125 MAIN CONFERENCE ROOM This class will run considerably past the 3:00 p.m.
(closer to 5:30 p.m. but I’ll have doughnuts/pastry!) Sample reports from past years’ classes: |
|
|
15 |
APR
29 – MAY 03 |
Mon/Tues: check-out
and lab clean-up |
Wed/Thur: check-out
and lab clean-up |
MAY 03 CLASS EXAM (Friday 03 MAY @ 2pm) |
|
|
16 |
MAY 03
– 04 |
Mon/Tues: last labs
due |
|
|
|
|
** Used with the permission of the University
of Maryland – College Park
Chemistry Department |
|||||
|
USEFUL WEBSITES WE WILL USE THROUGHOUT THE SEMESTER |
WHEN/WHY WE WILL USE THIS SITE |
|
good named reaction site |
|
|
vital IDOC site:
HOMEWORK will come from here! |
|
|
nmr |
|
|
Good general site: lots of links! |
|
|
GREAT MSDS SITE |
|
|
http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/cre_index.cgi?lang=eng -SDBS |
searchable spectroscopy site |
|
http://www.chem.wisc.edu/areas/reich/handouts/nmr/NMR-Biblio.htm |
stupid amounts of nmr gouge |
|
mass spectrum generators |
|
|
mass spectrum generators |
|
|
IDOC course from KY website |
|
|
carbon nmr |
|
|
natural products |
|
|
name reactions |
