Chemistry c34

CH S343 – Honors Organic Chemistry Laboratory

The honors organic chemistry laboratory and spectroscopy course, CH S343, is well suited for incorporation in to this semester’s theme of “Good Behavior/Bad Behavior.” In this course, we study methods for synthesizing small organic molecules, as well as methods for interpreting structures using spectroscopic methods. Many biologically active molecules and common medicines are small organic molecules, which can easily be studied spectroscopical y and/or in the laboratory setting. Each biologically relevant or medicinally important small organic molecule has its own intriguing story of how it was discovered or developed, and these molecules, while beneficial in their current states, often are derived from much less well-behaved compounds. Three examples of molecules displaying “Good Behavior/Bad Behavior” are listed below. These and other intriguing stories will be incorporated into our study of organic molecules throughout the semester through a mixture of lecture and laboratory activities. This course is taken by all chemistry majors at IU, and is therefore wel suited for incorporation into this year’s themester. These students have already indicated a natural affinity for chemistry, and will appreciate the histories and backstories of the molecules that they study.
Lidocaine is a topical analgesic (found in sunburn treatments that also often contain aloe), and its structure is derived from that of another very well known naturally-occurring pain reliever, cocaine. Medicinal chemists synthesized a variety of related molecules in order to exploit the pain- relieving properties (“good behavior”) of cocaine while reducing the addictive side-effects (“bad behavior”) by structurally modifying these molecules using known organic reactions. Another molecule in this structure class which came from the same screening process is procaine (Novocain). The students will synthesize lidocaine in the laboratory towards the end of the semester. In the introduction of their lab report for this experiment, the students will be asked to summarize and comment on the development and discovery of lidocaine and related molecules.
Aspirin (acetylsalicylic acid)
The bark of the willow tree has been used since the time of Hippocrates as a remedy for pain and inflammation, however the active compound (which was later determined to be salicylic acid) is irritating to the stomach and thus is not an ideal oral medicine. As with lidocaine, medicinal chemists synthesized a variety of derivatives of salicylic acid, hoping to keep its pain- and inflammation-relieving properties while lessening the side effect of stomach irritation, and came up with acetyl-salicylic acid which is commonly known as aspirin. The success of aspirin spurred the synthesis of thousands more related compounds over the years, leading to other successful analgesics including Aleve (naproxen). The structures of both salicylic acid and acetylsalicylic acid are simple enough that they will be used early on in the spectroscopy portion of the course as unknowns. The structure of naproxen is slightly more complex and will be used later in the semester. In addition, the students will study the chromatographic properties of aspirin and other For each molecule that is studied spectroscopically in the lecture portion of the course, the students will be asked to come prepared to discuss the history and development of the molecule.
Cytoxan (Cyclophosphamide)
Cytoxan is an anti-cancer therapeutic that is used to treat several types of cancer. This compound is in a class of compounds called nitrogen mustards, which were originally developed as chemical warfare agents (very “bad behavior”). The biological effects of these highly toxic molecules were studied during WWII, and their application in chemotherapy became readily appreciated closely following the war. The structure of Cytoxan is very well suited for a combined spectroscopy
Description of the course (The description is divided into two portions, spectroscopy (lecture)
and laboratory. Themester incorporations are in italics.)
I. Spectroscopy

A majority of the themester incorporation will be in the lecture, or spectroscopy, portion of the course, due to the obvious challenges that come along with having students work with biologically active molecules in a laboratory setting. In this portion of the course, the students spend time studying and interpreting spectroscopic data. We spend approximately two weeks on each of the following topics: Elemental Analysis, Mass Spectrometry, Nuclear Magnetic Resonance (this topic has 4 parts, and covers 8 weeks), and
II. Laboratory
Each week the students will complete a laboratory experiment, where they will explore new
organic chemistry techniques and reactions. Some representative examples of laboratory experiments include the total synthesis of lidocaine, extraction of the triglyceride trimiristin from nutmeg, hydroboration of an unsymmetrical alkene, and the stereochemistry of the Wittig reaction. Chemistry S343
Honors Organic Chemistry Laboratory
Fall 2011
Email: – include ‘S343’ in subject
Tues. and Thurs. 11:15 am – 12:05 pm, Swain West (SW) 220 Section 1: R 1:20 pm – 5:20 pm, Chemistry (CH) 145 Section 2: F 1:20 pm – 5:20 pm, Chemistry (CH) 145
Office Hours:

Course Website:
The website can be found on the Oncourse site.
Learning Objectives: S343 has two components: a laboratory and an introduction to spectroscopy. As
such, the semester will be spent developing a proficiency in laboratory techniques and skills, and
learning methods for data interpretation and structure elucidation.
Required Texts:
1. Gilbert & Martin, Experimental Organic Chemistry, 5th ed. 2. Pavia, D.; Lampman, G. M.; Kriz, G. S.; Vyvyan, J. R. Introduction to Spectroscopy (4th ed.)
Recommended Texts: You should refer to the textbooks that you used in your C/S341/342 lecture
series. If you no longer have these books, you wil find copies of the fol owing books on reserve in the
chemistry library:
Organic Chemistry: Brown, Foote, Iverson, Anslyn
Organic Chemistry: David Klein
Required supplies: approved safety goggles, lab notebook
A.I.s and Laboratory Sections: Your A.I.s are an important source of information, and can help you to
develop essential problem-solving skills and lab techniques. Plan to ask well-prepared questions during
lab and go to their office hours! Attendance at the section for which you enrolled is mandatory, and no
make-up times will be available.

The lecture portion of this class meets twice a week. During this time, we will cover various
spectroscopic methods and spectral interpretation, work on spectroscopy problems, introduce pertinent
laboratory techniques, review chemistry related to current lab projects, and take quizzes. Attendance at
these sections is extremely important. Tuesday lectures will generally be used to discuss the laboratory
techniques, theory, and experiments for the week, while Thursday lectures wil be dedicated to
spectroscopy and structure elucidation.
Lab Notebooks and Pre-Lab Requirements: Each student is required to maintain a lab notebook
throughout the semester. This notebook must be dedicated only to S343 experiments (not lecture
notes) and must have carbon-copy pages. The notebook must be fil ed out in pen only (no pencil) and
errors should be neatly crossed out with ink. The procedure must be written before the lab period
starts in order to enter the laboratory
(see below for details). The AI will collect the carbon copies
before the lab session ends.
The lab notebook is the foundation for all written assignments for the lab. It serves as a recording of all
data and observations made in lab with a few preliminary conclusions. To organize the notebook, save a
few pages at the beginning of the book for a table of contents. The lab notebook will be filled out before
and during lab in the following format:
Prior to lab:
1. Title 2. Statement of purpose or question 3. Main reaction/table of reagents (if applicable) 4. Experimental procedure During lab
Title: Each experiment or multipart experiment should start on a new page. At the top of the page, label the experiment with a short title that summarizes the work to be done in the experiment. Statement of purpose or hypothesis: After reading the lab background and procedure, write a statement of purpose or an experimental question to be addressed in your own words. Main reaction/table of reagents: In a synthetic lab, write the main reaction being performed including all reagents and products. Under the main reaction, write the quantitative data for each reagent, including molecular weight, density, gram amount, mole amount, and volume. For a non-synthetic lab, no main reaction is written, but a table of chemical data may be compiled. Procedure: Before the start of each new experiment, each student must come to lab with the procedure written out in his or her lab notebook. No text books, handouts, or lab manuals will be allowed into
the lab—only lab notebooks may be used
. No student wil be al owed to begin the lab until the
procedure is written out in the lab notebook. The procedure, however, should not be simply copied
from the lab manual. Rather, time should be taken to ensure that each step of the procedure is
understood so that each student knows exactly what to do when he or she enters lab.
Observations and results: Thoroughly record what happened during the experiment. Include final mass yields, tables of spectral data, times between changes, color changes, physical properties (mp, bp, etc.), evolution of gases, temperature changes, and anything else of interest that you note.
Lab Reports:
Because one of the major goals of this course is to learn effective communication skills in
the field of chemistry, the lab reports comprise a significant portion of the final grade. To communicate
chemical results and conclusions well, one needs first to be able to know what is important to
communicate and then be able to communicate in an effective style.
Lab reports serve two purposes. The first is to document for the professor and A.I. your results and your
interpretation of these results. The second is to provide you, the student, with the opportunity to spend
some time thinking about the results of your experiment, the chemistry that took place, and the reasons
for employing the various techniques use in the experiment. Lab reports must be done and turned in
reports wil be due at the beginning of the lab section one week after the lab has been completed. All
lab reports must be neatly typed. Reports must be submitted via the “Assignments 2” tab of the
oncourse website (details to follow) and as a hard copy. In order to save time, it is not necessary to type
your procedure. Some experiments will require a formal lab report (details are below); others will be
evaluated based on the answers to a series of questions (details will be given during lab lectures).
Missing or failing to turn in assignments for three or more labs will result in an F in the course.
Formal lab reports should include the fol owing sections:
1. Objective – This is a two or three sentence statement of the goal of the lab experiment.

2. Introduction – The introduction should explain why the goal of the experiment is desirable, should
explain the chemistry underlying the experiment, should introduce the reader to all special equations that wil be used to analyze the data and the theory behind them, and should describe specific techniques that are going to play a role in the experiment. The introduction may be used to give a historical context to the experiment.
3. Experimental Procedure – The experimental procedure should include a list of all chemicals used
during the experiment, a list of other materials used, and a list of specialized equipment that is used in the lab. In the case of electronic instrumentation the make and model number of the device should be provided.
4. Results – This section includes tables or graphical representations of data, sample calculations and
always includes a written section, in paragraph, form of the results and observations of the experiment. Every table of data, graph, or calculation presented in the result section should be talked about in the written section, but you do not try to interpret the results in this section.
5. Discussion – In this section you interpret your results, evaluate the relevance of your results, analyze
the sources of error in your experiment, and place your results in context of previous results found in the literature.
6. Conclusion – Three to four sentences relating the results and discussion to the objective of the

7. References – The ACS style should always be used for references.

Grades for the course will consist of three parts: labs, exams, and quizzes (summarized
A total of 1050 points is possible for the class. You must pass both the laboratory and spectroscopy
portions of S343 in order to earn a passing grade in the course.
Total Points

Grading Scale: The anticipated grading scale is tentative: A = 90-100%, B = 80-89%, C = 70-79%, D = 60-
69 %, F = 0-59 %. Please note that I reserve the right to adjust the grade requirements to slightly lower
numbers depending on class averages. Plus/minus grades wil be awarded.
Lab Assignments: Each of the 15 labs (including the ChemDraw assignment and the unknown analysis
project) will be worth 50 points (for a total of 750 points). Grades wil be determined by examination of
lab reports, lab skills (as observed by your A.I.), and experimental accuracy. The lab assignments from
both sections will be graded by one AI on a rotating basis, using a rubric provided by the instructor.
Therefore all lab sections will be graded equally. The unknowns lab will be graded by Dr. Brown.
Exams: Two 100 point exams (for a total of 200 points) wil be given during the semester on Tuesday,
February 28th (7:15-9:15 pm) and Thursday, May 3rd (2:45 – 4:45 PM). These exams wil cover topics
from both lecture and lab.
Quizzes: There wil be six quizzes throughout the semester, given during class (see syl abus). These
quizzes wil be worth 20 points each, and the lowest score wil be dropped (100 points total). If one quiz
is missed, it wil be counted as the dropped quiz score. Quizzes will be given during the first fifteen
minutes of class on Tuesdays.

Policy on Cheating: Any student caught cheating wil be dealt with according to the Code of Academic
Ethics described in the Schedule of Classes. The standard minimum for cheating is a grade of 0 on the
assignment or an F in the entire course. CHEATING WILL NOT BE TOLERATED!
Missed and Late Assignments: There will be no makeup labs, exams, or quizzes – NO EXCEPTIONS!!!
it is unavoidable to miss a lab or an exam due to illness, personal conflict, etc, written documentation
(for example, a doctor’s note) must be provided to Dr. Brown PRIOR to the absence to avoid a failing
grade. If a quiz is missed, it wil count as the dropped quiz. Additional missed quizzes wil be counted as
zeros. Missing or failing to turn in assignments for three or more labs will result in an F in the course.
Late assignments wil be penalized 10% per day (starting on the due date – a report turned in after lab
instead of before will be penalized). Remember that a report must be submitted online at through the
“assignments2” tab of the OnCourse website by the due date to be considered on time.
Tentative Lecture Schedule:
This schedule may be changed by the instructor to better meet the needs of the class.

Week Date
MS section of organic textbook Klein: 15.8-15.13 Quiz 1 – MS and molecular formula
Pavia 2.1-2.3, 2.6-2.9, 2.10-2.21* IR section of organic textbook Klein: 15.2-15.7 Quiz 2 – IR and MS
NMR section of organic textbook Klein: 16.1-16.10 Quiz 3 – intro to 1H NMR
Exam 1 (7:15-9:15 PM, location TBA)
Quiz 4 – advanced 1H NMR
Quiz 5 – 13C NMR
Quiz 6 – 2D NMR
Final Exam - Thursday, May 3, 2:45-4:45 PM
* These sections are more detailed than required for this course. The relevant material from these sections will be covered in the lecture notes, but the book should be used as a reference. Tentative Lab Schedule
This schedule may be changed by the instructor to better meet the needs of the class.
Week Date
Tentative Lab Assignment
(Results and Discussion)
due in class on 4/19
(objective, introduction and results) + discussion questions Partial Lab Report (experimental, results, and discussion) + questions (Introduction and Experimental) + discussion questions Part 1: p 770-772 parts A&C, and 1st two discovery experiments on p 772; Part 2: p 780-782 miniscale 4/19-20 Chemiluminescence & G&M Chapter 20 p 693-695 assignments are due this week! Work ahead!)


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