Chem 363Lab Syllabus Spring 2008 Chamberland

Chem 363 Lab, Organic Chemistry Laboratory II

Spring Quarter 2008, Sections 1 (TTh 9-12) and 3 (W 12-6), Science 202

Instructor: Dr. Stephen Chamberland

Phone: (509) 963-1126

E-mail: chambers@cwu.edu

Office: Science 310

Office Hours: Tuesday 1-2pm, Wednesday, 9-10am, Thursday 3-4pm, or by appointment.

Pre-Lab Lecture (Optional): Monday 4-5pm, Science 216, on April 7, 14, 21, and May 19

Teaching Assistants: Miss Doris Chen (TTh section and W 12-1), Office Hours: TBA

Miss Amanda Blackmore (W section 1-5), Office Hours: TBA

Course Website:

The course website can be found by navigating to the http://www.cwu.edu/~chem/courses/index.html website.

Course Content and Objectives: In Chemistry 363 Lab, students will build upon their foundation of organic chemistry knowledge and experimental techniques and tackle more challenging synthetic transformations. Students will be expected to display an advanced understanding of synthesis and mechanism in organic chemistry to rationalize the formation of the desired products of their synthetic undertakings as well as impurities that may form. Modern techniques for isolation (extraction, filtration), purification (crystallization, distillation, column chromatography), and spectroscopic characterization (¹H and ¹³C NMR, gas chromatography (GC), infrared (IR) spectroscopy, mass spectrometry (MS)) of organic molecules will be taught. In addition, experiments are designed to foster creative and independent problem-solving skills in the laboratory. Students will work independently and in small groups, and will be expected to develop hypotheses, effectively plan and trouble-shoot experiments, acquire, document, and present data, personally analyze their experimental results, and report results written and orally in a clear and concise fashion. Lastly, I realize this is not an English class, but you will also be expected to hone your written communication skills. Communication of experimental results is as important as the results themselves. Penmanship, spelling, and grammar are important aspects of an education in the chemical sciences, and will be treated accordingly. You are also responsible for the information contained within the Chemistry Department Lab Safety Rules on the first page of the green laboratory notebook. We will discuss this during the first lab session.

Course Materials:

· Texts: “Organic Chemistry Laboratory 2, CHEM 3631” (Green cover). This compilation contains important information for the lab experiments, but procedures will often be modified. Notification of any changes in the experiments will be given in advance (see below).

“The Organic Chem Lab Survival Manual” J. W. Zubrick, 6^th edition. This handy primer contains essential conceptual and technical information for the budding synthetic organic chemist.

Safety Glasses (must be worn in the lab at all times when anyone is working with chemicals)
Laboratory Notebook (with carbon copy pages – available in the bookstore)

Grading Procedure:

You will be striving to earn 300 points in five weekly experiments, quizzes, and a total synthesis project encompassing four weeks of laboratory time, with the following breakdown:

Quizzes (30, up to 50 points): There will be five quizzes given each of the first four weeks of lab designed to test your knowledge and preparation for experiments 1-3, 5, and 7. Each quiz will be worth six points, but will also contain two bonus questions worth potentially four additional points. Quiz questions will cover only the material pertinent to the experiment, while bonus questions can come from history, current events, popular culture, music, etc.

Lab Reports (120 points): Aldol Reaction (Exp 1): 20 pts.

Carbonyl Stretching Frequencies (Exp 7): 20 pts.

Diels-Alder Reaction (Exp 2): 20 pts.

Preparation of (E)-Stilbene (Exp 3): 40 pts.

Azo Dyes and Azo Couplings (Exp 5): 20 pts.

Total Synthesis Project (150 points)

*Your final letter grade will depend on the percentage of total points that you earn out of the 300 points available. If the average percentage for the class is less than a C (75%), grades may be curved up to this average. Also, if, over the course of the quarter, your performance improves or declines, I will take that into account in the determination of your final grade. There will not be a certain allotted number of each letter grade awarded; you will get the grade you earn.

Laboratory Topics and Sequence:

Week	Beginning	Experiment Number and Topic
Week 1	3/31	Introduction, Safety, Check-in, Aldol Reaction (Exp 1)
Week 2	4/7	Diels-Alder Reaction (Exp 2) and Carbonyl Stretching Frequencies (Exp 7)
Week 3	4/14	Preparation of (E)-Stilbene (Exp 3)
Week 4	4/21	Azo Dyes and Azo Couplings (Exp 5), Introduction to Total Synthesis Project
Week 5	4/28	Begin Total Synthesis Project
Week 6	5/5	Total Synthesis Project, continued
Week 7	5/12	Total Synthesis Project, continued
Week 8	5/19	Final Experiments and Analysis of Samples, Check-out
Week 9	5/26	Total Synthesis Project Oral Presentations (W and Th)
Week 10	6/2	Total Synthesis Project Report due by 5pm on your lab day (W or Th)

Laboratory Notebook: All of your work must be recorded in your lab notebook. Your lab notebook is your permanent record of your observations, data, the procedure you followed, and your results. Any data not contained in your lab notebook cannot be presented in your lab report. Record all changes in the experimental procedures, interesting or noteworthy observations, all data you collect, and all of the specifics needed to write a final experimental procedure (recipe). If something unexpected happened, note this as well because it will help you explain your results if they are better or worse than you expected. If you make a mistake, cross it out with a single line, and never use white out.

Laboratory Reports (Experiments 1–3, 5, 7):

Pre-Lab Reports: Prior to coming to lab each week, each person will have to write up a handwritten pre-lab report in your notebook. This report should contain the title of the experiment, the purpose of the experiment, and the detailed (step-by-step) procedure you will follow while carrying out the experiment in the laboratory. Your procedure should be written carefully and clearly so you could perform the experiment without using the course packet. Before performing any experiment, you need to have a good procedure, know the hazards associated with all the chemicals and equipment you will use, and visualize conducting the experiment. This pre-lab section, if done properly, will constitute one-fourth of your lab grade for each of the five experiments from the course packet. A comprehensive write-up will be required prior to the total synthesis project. Pre-lab reports must be submitted at the beginning of lab each week, and pages you write on during the lab must be turned in at the end of the lab.

Post-Lab Reports: Brief post-lab reports (no more than two pages) for each of the five experiments described in the course packet are to be handwritten (neatly and legibly) in your notebook, and you should append supporting data if necessary (e.g., IR spectra, GC traces, etc.). These reports are due at the beginning of the lab period following the week you performed the experiment. Late reports will be penalized five points per day. In the pre-lab report and during the experiment, you wrote the title, purpose, procedure, data, and observations. The post-lab report should contain all of the calculations you performed (e.g. percent yield, R_f, GC peak area, etc., show all work), a summary of your results (data analysis), a brief discussion of your results, and a very brief (one or two sentences) conclusion. The discussion section is where you would explain any significant findings, suggest changes/improvements you would make if you were to run the experiment again, and account for any unexpected data and results. Your comments should be clear and concise. You will be graded on your presentation and inclusion of all relevant experimental data, your presentation of the results, calculations, analysis (discussion), and conclusion.

Notes and Changes to the Experiments Described in the Laboratory Manual:

Aldol Reaction (Exp 1): Performed individually. The objective of the lab is to demonstrate proficiency in performing the aldol reaction; percent yield is important and should be reported. The experiment will be run on semimicroscale (10X scale, see page 8). Analyses include IR, a bromine test for unsaturation, and the 2,4-dinitrophenylhydrazine test (see Appendix 1). The ignition test will not be performed. A ¹H NMR spectrum of the desired product will be provided by the instructor, which must be analyzed in the report. Products must be submitted in a labeled vial with your name, course number, lab time and date, and a picture of the product.

Diels-Alder Reaction (Exp 2): Performed in teams of two. The objective of the experiment is to perform the reaction of anthracene and maleic anhydride, isolate and purify the product, determine percent yield, and demonstrate product purity. Percent yields will be graded. The ignition test will not be performed. The experiment will be run on a 5X scale (see page 12). Products must be submitted in a labeled vial and be characterized by ¹H NMR and GC/MS. A ¹³C NMR of the product will be provided.

Carbonyl Stretching Frequencies (Exp 7): Performed in teams of two. The objective is to carry out molecular modeling calculations of structure and compare the computational predictions with IR spectral data. IR spectra will be provided by the instructor. Each group will only do one of the four questions (groups/questions will be assigned during the lab period). A pre-lab report is not required for this experiment, but all data gathered, results of calculations, and a brief discussion answering the question must be submitted as a post-lab report.

Preparation of (E)-Stilbene (Exp 3): Performed in groups of four students (two teams of two). In one post-lab report per group, members will compare and contrast the synthetic, mechanistic, and experimental details (percent yields, purities, ease of performing the reaction, etc.) of the production of (E)-stilbene using the Wittig and Horner-Emmons synthetic methods. This experiment will be run on a 5X scale. The purity of products produced by both methods will be demonstrated by GC and TLC. The products will be analyzed by IR, NMR, and bromine tests. Percent yields are important. The products must be submitted in a labeled vial. Team participants must include a statement delineating their role in the laboratory and write-up portions of the experiment.

Azo Dyes and Azo Couplings (Exp 5): Performed in teams of two. The objectives of the lab are to become familiar with azo dyes and the synthetic method (diazonium ion coupling) used to make them. Percent yields of the three products are important and the classification of the dyes will be performed as per the experimental protocol. Products must be submitted in labeled vials.

Total Synthesis Project:

Overview: This ambitious, multi-step synthesis project is taken right out of the primary literature – from the journal Organic Syntheses. Undertaking this project will demonstrate what most chemists actually do in their work: write grant proposals to fund and plan research, do the experiments, collect and analyze data, write up and publish results in journals, and orally present the work at local, national, and/or international meetings and conferences.

You will work in teams of two, but since there are only five procedures, two teams of two may work on the same procedure. When this occurs, an effort has been made to ensure that each group can prepare a different molecule using the same basic procedure. The yield and results may vary slightly, but you will have entirely different data to present and analyze. Teams working on the same basic procedure may consult with each other.

Objectives:

1. Each team must product 250 mg of the final product. Failure to produce the desired quantity of material will result in a loss of points. The final product must be submitted in a labeled vial, and will be checked for weight and purity. If your first run does not provide the desired amount, you may repeat the synthesis to make more.

2. The purity of the final product must be demonstrated by at least two distinct methods (e.g., ¹H NMR, ¹³C NMR, mp, IR), but collect as much data as you can.

3. The final product, as well as the intermediates prepared on the way to the final product, must be analyzed by the methods specified in the page of supplementary instructions. All ¹H NMR and ¹³C NMR signals, key IR absorptions (indicating key functional groups), and any MS fragments that support your structure should be identified in the report.

4. Each team of two will submit a formal report. This report should be typed, double-spaced, and enlist a standard, easy-to-read 12-point font. The report should describe the reaction sequence followed and should propose a reasonable reaction mechanism for each transformation, describe in detail the experimental procedure that was followed, note all observations and data that were recorded, provide an analysis of the results, and end with a conclusion affirming the success or failure of the experiment.

5. Each team will present their results orally.

Point Distribution: Proposal (20 pts); Final Product Produced (50 pts: purity (10 pts), all necessary characterization data (10 pts), percent yield (10 pts), producing the required amount (250 mg) of final product (20 pts)); Formal Report (50 points); Oral Presentation (30 points).

Proposal: Each team will plan every detail of the synthesis (handwritten) in their notebook before beginning the synthesis and have their plan approved by the instructor prior to beginning any experiments. You will use the procedure written in the Organic Syntheses article as a template to write a procedure that is easy for you to follow. If there are words you don’t understand, techniques you’ve never heard of, or if any other confusion arises, please ask. You must include the synthetic scheme, write the quantity of each substance you will need to use, draw a diagram of each apparatus you will need to assemble, discuss the hazards and anticipate any problems that my arise, outline the data you will need to collect for every compound you make, and draw up a reasonable time-line for completing the synthesis. Consultation of the “Survival Guide,” other chemical literature, MSDS information, and the TA and the instructor may be necessary to complete the plan. Explicit approval of the plan must be obtained from the instructor before doing any experiments in the laboratory. Approval consists of a separate meeting of the group with the instructor where the complete written plan will be discussed.

Analyses: Samples that you wish to analyze by GC/MS or NMR spectroscopy should be submitted to your TA. Spectra may possibly be available that same day. However, our goal is to have all spectra available by the next lab period. Please plan accordingly.

Recording and Reporting: All data and observations must be recorded in the lab notebook. Any supporting spectroscopic data should be clearly marked and included in your formal report as appendices. Team members must be identified and a description of each member’s contributions to the work must be presented in the report. Special attention should be paid to the discussion of any analytical and spectroscopic data supporting purity and identity of the synthetic intermediate(s) and the final product.

Formal Report: This will be essentially a typed, combined pre- and post-lab report. Each team will submit one report. More details will follow (pre-lab lecture on Monday 4/21).

Oral Presentation: Using Microsoft PowerPoint, each pair will present their experimental background, goals, data, and results in a presentation lasting between ten and fifteen minutes. You will be graded on the effectiveness and clarity of your graphics, your oral presentation of the material, and time management (do you stay within the allotted time). As a class, we will offer some constructive feedback to help you improve your next presentation.

The instructor reserves the right to change any part of this syllabus if necessary; any changes will be announced in class.