Chem 112C Lab Book

Chem 112C Lab Manual Spring 2014

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Chem 112C

Organic Chemistry

Laboratory Manual

UC Riverside

Spring 2014


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CHEMISTRY 112C LABORATORY EXPERIMENTS Spring 2014 TEXTBOOKS "The Organic Chem Lab Survival Manual" Zubrick, 9th edition, John Wiley & Sons

Darling Model Kits (UCR Edition) Lab coat Student Lab Notebook: 100 Spiral

LABORATORY INSTRUCTOR Professor Richard Hooley Chemical Sciences 1, Room 444 (951)-827-4924 email: [email protected]

ACADEMIC COORDINATOR Dr. Rena Hayashi Science Laboratories 1, Room 103 (951) 827-3143, email: [email protected]

LECTURE INSTRUCTORS Professor Michael Pirrung Chemical Sciences 1, Room 448 (951)-827-2722 email: [email protected]

Professor Christopher Switzer Chemical Sciences 1, Room 436 (951)-827-2766 email: [email protected]

SPECIAL LABORATORY INFORMATION (1) It is not possible to get a passing grade for the course without completing the laboratory with a

passing grade.

(2) Academic dishonesty in any form will not be tolerated in this lab. In addition to the sanctions imposed on laboratory grades, all such incidents will be reported to the Office of Student Conduct for administrative review. Students found to be cheating will receive a zero grade for the experiment and may be subject to dismissal from the class with a failing grade. Cheating includes (but is not limited to) turning in a report without doing the experiment, interfering with another student's work, removing chemicals or glassware from the laboratory, or providing test questions or answers to other sections. All students enrolled in this class are also responsible for familiarizing themselves with the Student Code of Conduct. The general rules and student rights in that document apply to this lab.

(3) Attendance at your assigned laboratory meetings is mandatory. If you miss a laboratory you will not be able to make-up that laboratory. For one absence only, with a verifiable medical excuse accepted by Dr. Hayashi, your laboratory score will be pro-rated. You must contact Dr. Hayashi by telephone [(951) 827-3143] immediately upon learning you will miss a lab, leave a phone number where you can be reached, and provide a medical excuse (signed by a licensed medical doctor (M.D.)) to Dr. Hayashi as soon as you return to campus. Your TA may not alter this policy.

(4) Lab Preparation Write-ups (Pre-Labs) are due at the beginning of the lab period in which the experiment is to be done.

(5) Laboratory Reports are due at the beginning of the lab period following completion of the experiment.

(6) Enrollment questions concerning laboratory or lecture must be directed to Dr. Hayashi.

(7) Note on laboratory fees: Your laboratory fee will be paying for chemicals, glassware, hotplates, and other allowable teaching items and apparatus.

(8) Cellular Phones: For safety reasons cellular phones may not be operated in the laboratory. Make certain that your phone is in the off position before entering.

(9) Important: Be sure to record key information about this lab, including TA name, lab room, locker number, and combination, in a place that is secure and will be accessible to you during lab.


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CHEMISTRY 112 LABORATORY POLICIES on

SAFETY AND PERSONAL PROTECTIVE EQUIPMENT (PPE) INSTRUCTOR Professor Richard Hooley Chemical Sciences 1, Room 444 (951)-827-4924 email: [email protected]

ACADEMIC COORDINATOR Dr. Rena Hayashi Science Laboratories 1, Room 103 (951) 827-3143, email: [email protected]

This document establishes the safety policies for students enrolled in the Organic Chemistry teaching laboratory (Chem 112LA, 112LB and 112LC) and is incorporated by reference into the course syllabus. Students failing to comply with all safety rules herein as well as any safety direction from any course staff member (TA, Academic Coordinator, or the Instructors) are subject to a variety of sanctions, including dismissal from a particular laboratory session (resulting in a zero grade for the experiment), and may be subject to dismissal from the course.

Personal Protective Equipment a) Wear safety goggles at all times while in the laboratory.

b) Lab coats must be worn at all time while in the laboratory.

c) No exposed legs or arms are permitted in the laboratory – shorts or skirts may never be worn.

d) No sandals, open-toed or perforated shoes, or shoes with absorbent soles are allowed in the laboratory.

e) Nitrile gloves are supplied, and must be worn while performing all transformations. It should be noted that while gloves provide a barrier to chemicals coming into contact with skin, they do not provide perfect protection. Nitrile gloves are permeable to a number of organic liquids (especially chlorinated solvents and dimethylsulfoxide). If you spill chemicals on your gloves, remove and replace the gloves immediately. Good practices are to a) minimize spillage and other modes of contact with chemicals, and b) immediately wash your hands with soap and water after contact with any harmful reagent or solvent.

General Safety a) No hats, scarves, neckties, long unrestrained hair, or clothing with fringe or that is overly loose

are permitted.

b) Cellular phones may never be used in this laboratory. Make certain that your phone is turned off before entering.

c) No eating, drinking, or smoking in the laboratory. Food and drinks may never be present. This includes all visible water bottles or mugs, containers of water or flavored drinks, containers of ice intended for consumption, etc. A food or drink container may be present only if it is empty / unopened and out of sight, such as inside a backpack.

d) Bicycles, skateboards, in-line skates, roller-skates, and unicycles are not allowed in the laboratory. Their use is also not allowed inside the Science Laboratories building. If skateboards are brought into the building, they may not be placed on the floor.

Medical Conditions a) You should not work in the laboratory if you are pregnant or you might be pregnant. Contact

course staff in this situation. In addition, notify the Academic Coordinator if you have any other medical conditions (diabetes, allergies, etc.) that may require special precautions to be taken.


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Fire and Emergency

a) Make sure to know the locations of safety showers, eyewash fountains, fire extinguishers, emergency telephones, fire alarms and all exits. These are clearly marked in the laboratory.

b) FIRE: Immediately notify the supervising TA. A fire confined to a small flask or container can usually be extinguished by covering the flask with a large nonflammable container (e.g. beaker). Only attempt this is the fire can be easily contained: otherwise pull the fire alarm and exit the building. Go to the designated assembly area and do not use the elevator.

If a person's clothing is on fire, use the safety shower to put out the flames. If this is not possible, douse the person with water, cover them with a fire resistant coat and roll the person on the floor.

c) INJURY: Immediately report ANY injury to a TA, no matter how minor. The TA will initiate emergency procedures and arrange transportation to a medical facility.

If you are a member of the Campus Student Health Plan, then during normal business hours go to the Campus Health Center (for current business hours go to www.campushealth.ucr.edu).

After hours until 9 pm: go to Riverside Medical Clinic Urgent Care.

All other times: Riverside Community Hospital.

If you are NOT a member of the Campus Student Health Plan, then during normal business hours go to the Campus Health Center and inform them that you are not on the health plan but were injured while on campus. At all other times, obtain medical treatment through your personal health insurance coverage (i.e. HMO, PPO).

d) CHEMICAL SPILL: Chemical contact with eyes and skin must be washed immediately with water for at least 15 minutes (use the eye wash/safety shower). Remove contaminated clothing and immediately report the incident to a TA.

Other Laboratory Rules

• Do not put lab chemicals in your drawer, unless specifically instructed to do so by your TA. • NO ignition sources (matches, lighters, etc) are allowed in the laboratory. • There is absolutely no smoking allowed anywhere at any time in the Sciences Laboratories

building. • Do not pour chemicals into the sink or dispose into the trash: use the proper waste containers. • Dispose of chemical waste in the specified containers - some chemicals are dangerous if mixed. • Do not use unlabeled chemicals, and if you find any, report this to your TA • Do not drink from lab faucets or use the ice from lab ice machines to chill food. The water may

not be safe to drink. • NEVER mix chemical reagents unless instructed to do so by your TA as part of your lab

procedure. • NEVER taste or smell chemicals.


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Sunday Monday Tuesday Wednesday Thursday Friday Saturday

03/31 04/01 04/02 04/03 04/04 04/05 Lab Safety &

Check-in èèè

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04/06 04/07 04/08 04/09 04/10 04/11 04/12 Expt. 1: Synthesis

of Nylon èèè

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04/13 04/14 04/15 04/16 04/17 04/18 04/19 Expt. 2: Aldol

condensation

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04/20 04/21 04/22 04/23 04/24 04/25 04/26 Expt. 3: Claisen

Condesation

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04/27 04/28 04/29 04/30 05/01 05/02 05/03 Expt. 4: Unknown

Lab 1 - Esters

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05/05 Expt. 5: Unknown Lab 2 - Amines

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Expt. 6a/b: Azo Dye Synthesis or Case Study 3

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05/19 Expt.7: Saccharide Protection

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05/26 Academic Holiday

05/26 Exp. 8: Amino Acid Catalysis

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06/02 Expt. 8: Amino Acid Catalysis & Check-out Reports due

06/03 Check-out Reports due

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Schedule of Experiments - Chem 112C (Spring 2014) For each experiment, you should be familiar with the standard techniques taught in Chem 112A. These can be found in Zubrick: pp 1-37, 77-83 (clean and dry), 87-92 (melting point), pp 120-126 (recrystallization), 141-144 (liquid-liquid extraction), 195-199 (rotary evaporator), 222-233 (thin layer chromatography), 269-303 (IR spectroscopy). Experiment-specific reading is stated below.

Dates Experiment 03/31-04/04 Laboratory Safety & Check-in. You MUST make sure that you have all of the

necessary lab equipment and glassware in your assigned drawer before you leave. Read Zubrick, pp 1-37, 77-79 (clean and dry). Read Safety Handout.

04/07-04/11 Experiment 1: Synthesis of Nylon (30 pts). Lab Handout, p 9-77. Read McMurry 8th Ed pp 818-827 (nucleophilic acyl substitution), 847-850 (polymers).

04/14-04/18 Experiment 2: Aldol Condensation of Vanillin and Acetone (30 pts). Lab Handout, p 12-13. Read McMurry 8th Ed pp 904-915 (carbonyl condensation reactions).

04/21-04/25 Experiment 3: Solvent-Free Claisen Condensation Of Ethyl Phenylacetate (30 pts). Lab Handout, p 14-15. Read McMurry 8th Ed pp 915-921 (Claisen condensations).

04/28-05/02 Experiment 4: Unknown Lab Part 1 - Esterification via Acidic Resin (30 pts). Lab Handout, p 16-17. Read McMurry 8th Ed pp 824-826 (esterification), Lab book special section, p 29-41.

05/05-05/09 Experiment 5: Unknown Lab Part 2 - Reductive Amination (30 pts). Lab Handout, p 18-20. Read McMurry 8th Ed pp 958-960 (reductive amination), Lab book special section, p 29-41.

Note - 50% of the class will do Expt 6a and 50% will do Expt 6b. Your assignment will be posted after class starts. The grading scales will be identical, so there is NO difference between labs.

05/12-05/16 Experiment 6a: Synthesis of an Azo Dye (30 pts). Lab Handout, p 21-22. Read McMurry 8th Ed pp 968-972 (diazotization), p517-523 (UV/Vis spectroscopy).

05/12-05/16 Experiment 6b: Organic Chemistry Case Study 3 - "Targeted Pro-drugs for Cancer Treatment: A Case Study in Drug Discovery" (30 pts).

NOTE - this experiment will be handed to you by your TA (if you are assigned this experiment).

05/19-05/23 Experiment 7: Acetal Protection of Methylglucopyranoside (30 pts). Lab Handout, p 23-25. Read McMurry 8th Ed pp 742-746 (acetal formation), 1011-1018 (carbohydrate structure and reactions), Lab book special section, p 29-41.

05/27-05/30 Experiment 8: Amino Acids as Catalysts: Environmentally Benign Carbonyl Condensations (30 pts). Lab Handout, p 26-28. Read McMurry 8th Ed pp 736-740 (imine formation), 751-755 (conjugate addition).

Mon. May 26 Academic Holiday (*Monday sections will perform Expt. 8 on 06/02 followed by Check-Out)

06/02-06/06 Check-Out---Reports due.

Laboratory is worth a total of 240 points.


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FORMAT FOR LABORATORY NOTEBOOK REPORTS Keeping an accurate laboratory notebook is essential to your success in this class. Some guidelines are given below:

a) The laboratory notebook must not be loose leaf. Lab notebooks are available from the campus bookstore and are designed so that they permanantly contain the original pages of your Prelab and Postlab reports.

b) Use permanent blue or black ink only (ballpoint pen, NO red ink!)

c) Other textbooks, lab manuals, loose sheets of paper, iPads or cellphones are not allowed in the laboratory. The complete outline of procedures must be written in your laboratory notebook prior to performing the experiment.

d) Copies of your lab notebook pages are required for grading. The assigned notebooks are designed so that the carbon copies can be removed and handed in to your TA.

e) Your TA may periodically inspect your notebook.

YOUR LAB REPORT CONSISTS OF THREE (3) PARTS (30 pts) Part I - Prelab Report. A copy of your lab notebook pages containing the lab writeup and answers to

any prelab questions. This is due at the start of each experiment. Part II - Results. A copy of your notebook pages containing observations noted during the lab

experiment.

Part III - Postlab Report. A summary of results and answers to postlab questions. This can be written on separate loose-leaf paper.

I. PRELAB REPORT (10 pts) The initial part of your lab report must be written in your laboratory notebook. A copy of the original pages of this report will be collected prior to the experiment and will be returned to you after the whole lab is graded. It will consist of:

a) Your name, lab section and the name of your TA (on each page).

b) The title and number of the experiment.

c) Objectives. This should include hypotheses about the outcome of the lab, which you will test by experiment. It is your responsibility to propose what you expect to determine from each experiment. d) List of chemicals: masses or volumes. Look up molecular masses and calculate the material amount in moles (if appropriate), boiling/melting points (bp/mp) and density (if appropriate).

e) List of equipment (sketch complex apparatus).

f) Outline of procedure. This must be sufficiently detailed to allow you to perform the experiment. Make sure you note any necessary safety precautions.

g) Prelab question answers. These will always require an analysis of the hazards and risks associated with the experiment.

The carbon copy pages of this report must be handed in BEFORE you begin the experiment.


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II. RESULTS (3 pts) This section should be started on a fresh page of your notebook, after the prelab report. A combined copy of the Results/Postlab report will be stapled and turned in to your TA after the experiment is complete.

This section should be completed during the lab session and consists of:



c) Results: Date, times, measured masses and volumes used in the experiment (if you use different amounts from the procedure, note this), measured mp/bp of your products and any other observations (color changes, etc) recorded during the lab session.

d) Characterization materials: include copies of spectra, etc., recorded during the lab session.

Turn in your product(s) from the experiment in a suitably labeled vial to your TA at the end of the lab session.

III. POSTLAB REPORT (17 pts) This section does not need to be written in your lab notebook - it can be written on separate loose leaf sheets and stapled to your results copy pages. It is to be completed after the lab period at home, and consists of:



c) Analysis of results: In 5-10 sentences, comment on the outcome of your experiment, notably the quality of your results. Describe problems that may have occurred and possible solutions. How and why did the outcome differ from that predicted in your prelab report? What was learned from the experiment? Note - experiment 5 does not require this section. d) Answers to postlab questions.

Staple Parts II and III together and turn into your TA at the beginning of the next week's lab session. You should keep a copy of Part III for yourself.


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Experiment 1 - Synthesis of Nylon

Reading: McMurry 8th Ed pp 818-827 (nucleophilic acyl substitution), 847-850 (polymers). Introduction Nylon 6,6 is one of the most used polymers in everyday life. Approximately one billion tons of 1,6-hexanediamine are manufactured each year to satisfy the need for Nylon-based products. The procedure is quite simple, and is an excellent illustration of the applicability of nucleophilic acyl substitution reactions in the synthesis of materials used in everyday life. In this experiment, you will synthesize Nylon 6,6 by initially forming an acid chloride derivative of adipic acid and reacting it with 1,6-hexanediamine.

Prelab Questions 1) The Material Safety Data Sheets (MSDS) for all the chemicals involved in this lab are on iLearn. Read these and answer the following questions: a) Which chemical is the most dangerous in this lab? b) Explain why you chose your answer for part a), and the safety precautions you will take when handling this material.

2) Fill in the reaction table below. Make sure you correctly calculate the molar amounts of your reactive materials.

name formula mol.-eq. MW mmol amount

Adipic Acid 1.0 500 mg

Thionyl Chloride -- 0.75 mL Product 1 (Adipoyl chloride)

Recovered (step 1) -- -- N/A

Adipoyl chloride used (step 2) ~622 mg

1,6-Hexanediamine (5% aq.) 8 mL

cyclohexane -- -- -- -- 8 mL

product

(3) Explain why you need to use SOCl2 in this process. Why can you not just mix adipic acid, hexane-diamine and some mineral acid catalyst?

Figure 1. Reaction Scheme.


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(4) Explain why you form a polymer in this experiment, instead of a small molecule. Compare the reaction of adipoyl chloride and hexanediamine with the reaction of adipoyl chloride and 1-hexanamine.

Experiment 1. Reaction 1 - Synthesis of adipoyl chloride Set up a 10 mL round bottomed flask, a reflux condenser and a drying tube packed with cotton and alumina. Weigh 500 mg adipic acid and add to the flask, along with a magnetic stirrer. Add 0.75 mL thionyl chloride to the flask and transfer to a sand bath atop a magnetic stirrer.

Note - thionyl chloride is corrosive and toxic - all manipulations should be performed in the fumehood. Quickly attach the condenser and drying tube, and heat the reaction to 90 ºC. Continue stirring for 1 hour. 2. Reaction 2 - Synthesis of nylon-6,6. After 1 h of stirring, remove the flask from the hot plate and let the reaction mixture cool to room temperature (~10 min). Transfer the resulting clear solution of adipoyl chloride to a clean, dry 50 mL beaker via Pasteur pipette. Rinse the flask with 2 mL cyclohexane, and add the washings to the beaker, followed by an additional 6 mL cyclohexane.

Slowly add 8 mL of a 5% aqueous solution of 1,6-hexanediamine (containing 8 drops 25% NaOH: this solution will be provided to you) to the beaker.

3. Isolation of nylon-6,6. You will observe a "film" of nylon polymer in the center of the beaker, where you added the diamine solution. Using a copper wire with the end bent into a small hook, hook this film and slowly draw the nylon fiber from the interface. If you pull the polymer from the solution slowly and steadily, you will be able to obtain long strands of nylon polymer (be careful not to pull to quickly, or you will break the strand). Wash the fibers in a beaker of water before handling them.

Post Lab Questions (1) Draw the arrow-pushing mechanism for step 1. You can write the mechanism for the reaction of propionic acid with SOCl2 to avoid repetition.

(2) Draw the arrow-pushing mechanism for step 2. You can write the mechanism for the reaction of propionyl chloride with butylamine to avoid repetition.

(3) You used dry glassware for the first step. Explain why you must keep the reaction free from water.

(4) Based on your mechanism from Q2, explain why you add the diamine in the presence of NaOH.

(5) You might think that you could make a similar polymer to Nylon-6,6 by reacting 1-aminohexanoic acid with SOCl2, but this doesn't work. Explain why this route will fail to make a polymer.


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(6) Polyesters are also useful polymers, notably for clothing purposes. The polyester equivalent of Nylon-6,6 is a weaker polymer, and is more easily biodegradable. Explain why.


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Experiment 2 - Aldol Condensation of Vanillin and Acetone Reading: McMurry 8th Ed pp 904-915 (carbonyl condensation reactions) Introduction Species containing a nucleophilic carbon are of considerable use to synthetic chemists for making carbon-carbon bonds, and building molecular backbones. In a previous laboratory experiment, we have utilized a phosphorus ylide reagent to generate double bonds via a Wittig reaction. In lectures, you have discussed the reaction of nucleophilic carbon in the form of Grignard reagents, alkynylides and cyanide. In this lab, we will utilize another form of nucleophilic carbon – an enolate anion.

In this lab, we will generate an enolate by removing the α-hydrogen of acetone, and react the enolate with 4-hydroxy-3-methoxybenzaldehyde (vanillin). The aldol condensation product undergoes elimination under the reaction conditions to generate 4-(4-hydroxy-3-methoxyphenyl)-3-buten-2-one.




Vanillin 1.0 1.25g

Acetone -- -- -- 7.5 mL

10% Aqueous NaOH -- -- -- 6.5 mL

6 M Aqueous HCl -- -- -- 3 mL

product

3) Calculate the Theoretical Yield of your product, i.e. the mass you would expect to recover (assuming 100% conversion to product).

4) Draw the product of reaction of acetone with a strong base. Make sure to draw all possible resonance structures of this anionic species.

5) IR analysis of the products A and B is little tricky - explain the differences and similarities that you would expect to see in the corresponding IR spectra. Which functional groups are the same, and which are different?



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Experiment 1. Reaction Setup Combine 1.25 g of vanillin and 6.5 mL of 10% aqueous NaOH solution in a 50 mL round bottom flask containing a stir bar. Add 7.5 mL of acetone, equip the flask with a reflux condenser, then heat under reflux conditions (acetone has a boiling point of 56 °C) for 60 min. 2. Isolation of Product After heating is completed, allow the solution to cool to room temperature, then pour it into 100 mL of water in a 400 mL beaker or Erlenmeyer flask, and cool the resulting mixture in an ice bath. Add 6M HCl solution dropwise with swirling until the pH of the solution is acidic (this will probably require approximately 3 mL of HCl solution). Isolate the precipitate formed by vacuum filtration, and wash it with a small amount of ice-cold water.

3. Purification by Recrystallization Recrystallize the material from a mixture of ethanol and water (1:1 ratio), then isolate the crystals by vacuum filtration, wash with a small amount of ice-cold water, and allow the product to dry.

4. Analysis of your product Weigh your purified product and determine the yield. Obtain an IR spectrum of your product and determine a melting point range. Your TA will give you a 1H NMR spectrum of your product. Hand this in with your postlab report. Post Lab Questions (1) Draw the mechanism of the first reaction (to make the initial aldol product A), making sure you account for all steps in the mechanism.

(2) Draw the mechanism of the second reaction (to generate 4-(4-hydroxy-3-methoxyphenyl)-3-buten-2-one B), making sure you account for all steps in the mechanism.

(3) You have been given a 1H NMR spectrum of your product. Fully assign this spectrum (i.e. determine which peaks in the 1H NMR correspond to which hydrogens in the product). The peaks have been labeled 1-8 on the spectrum, and the relevant hydrogens Ha-Hh below.

(4) Explain how you distinguished between Hb, Hc and Hd (the aromatic protons) in the NMR spectrum of molecule B. Determining the coupling patterns and coupling constants will be useful.

(5) Calculate the coupling constant between He and Hf. Explain how can this can help determine the stereochemistry (i.e. cis vs. trans) of the double bond.

(6) UV spectroscopy is a useful method of analyzing products A and B. Based on your knowledge of UV/Vis spectroscopy from 112B (McMurry p517-522) which species (A or B) will have the longest wavelength of absorption in the UV? Explain your choice.

(7) Acetone is a symmetrical molecule, so there are two positions that can react. Draw the product you would expect to obtain if you used two molar equivalents of vanillin rather than one.


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Experiment 3 - Solvent-Free Claisen Condensation Of Ethyl Phenylacetate Reading: McMurry 8th Ed pp 915-921 (Claisen condensations). Introduction Carbonyl condensation reactions play an extremely important role in organic synthetic transformations. However, due to the long reaction times generally required for the reactions to reach equilibrium, they are seldom studied as part of the standard organic laboratory. Recent improvements in solvent-free reaction methods have greatly reduced reaction times necessary for reasonable conversions in Claisen condensations. Recently, there has been a major push in the chemical field towards “green chemistry”, which involves an effort to reduce or eliminate the use or generation of hazardous substances during the manufacture and use of chemical products and processes.




Ethylphenylacetate 0.500 mL

Potassium tert-butoxide 246 mg

1 M Aqueous HCl -- -- -- ~1.5 mL

product

3) Calculate the Theoretical Yield of your product, i.e. the mass you would expect to recover (assuming 100% conversion to product). 4) Explain the benefits of performing a "solvent free" reaction, as opposed to one that requires an organic solvent. 5) Explain why we perform a "self-condensation" here. What would happen if we used one molar equivalent of ethylphenylacetate and one molar equivalent of methylphenylacetate?

Experiment 1. Reaction Setup In a 10 mL round-bottomed flask equipped with a magnetic stirrer and air condenser, thoroughly mix 0.246 g of potassium tert-butoxide and 0.500 mL of ethyl phenylacetate. Attach a reflux condenser and



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heat the reaction at 100 ºC for 30 min. Cool to room temperature and then carefully neutralize the reaction mixture by the dropwise addition (~1.5 mL) of 1 M HCl. Test the solution periodically with litmus paper to ensure complete neutralization.

2. Isolation of Product Extract the residue in 2 x 15 mL of ether. Dry the organic extract with sodium sulfate, gravity filter, and remove the ether by rotary evaporation. Triturate the residue with 7 mL of cold petroleum ether (35-50) in an ice bath for 10 minutes and filter off the solid white product.

3. Purification by Recrystallization Dissolve your product in a minimum amount of hot hexanes and allow to cool to room temperature slowly. Once recrystallization is complete, isolate the product by vacuum filtration.

4. Analysis of your product Weigh your purified product and determine the yield. Obtain an IR spectrum of your product and determine a melting point range. Your TA will give you a 1H NMR spectrum of your product. Hand this in with your postlab report. Post Lab Questions (1) Draw the mechanism of the reaction, making sure you account for all steps in the mechanism.

(2) Why does the added base only remove the H atom on the CH2 group adjacent to the benzene ring?

(3) Why does the potassium tert-butoxide not attack the C=O group directly?

(4) If you use excess sodium methoxide (NaOCH3) as a base, a different product is observed. What is it?

(5) You have been given a 1H NMR spectrum of your product. Assign the aliphatic region of this spectrum (i.e. determine which peaks in the 1H NMR correspond to which hydrogens in the product, not including the benzene rings). The peaks have been labeled 1-4 on the spectrum, and the relevant hydrogens Ha-Hf below. NOTE - you can't distinguish between Ha and Hb or Hd and He - assign those protons as Ha/b or Hd/e. (6) Ha/Hb and Hd/He show unusual coupling patterns because the protons are diastereotopic (i.e. chemically inequivalent). Explain why Ha/Hb and Hd/He are chemically inequivalent.

(7) Peak 2 is complex - using your assignment and the structure above (don't bother looking at the peak itself), describe what you expect the coupling pattern to be.

(8) You can analyze peak 3 in more detail. It is not a quartet, but two doublets. Calculate the coupling constant of the two doublets. Read p33-35 of the special section and explain the appearance of peak(s) 3 - why does it look like it does?

O

O

O

CH3(f)Ha Hb

HcHeHd


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Experiment 4: Unknown Lab Part 1 - Esterification via Acidic Resin Reading: McMurry 8th Ed pp 426-432 (mass spectrometry), 824-826 (esterification), Lab book special section, p29-41.

Introduction In this experiment, you will synthesize an ester from acetic acid and an unknown alcohol, then determine the structure by Mass spectrometry, NMR and IR spectroscopy. You will be familiar with the classical Fischer esterification from class, which uses aqueous acid (HCl, H2SO4) and the promoter of the reaction. In this experiment we will use an acidic resin, Nafion 417, as the acid catalyst to make the synthesis and product isolation a little more straightforward. The focus will be on determining the structure of your unknown ester product (and by extension your alcohol reactant) by a combination of IR, NMR and mass spectral techniques.

Prelab Questions 1) The Material Safety Data Sheets (MSDS) for some of the chemicals involved in this lab are on iLearn. Ethanol has been added as a surrogate for your unknown alcohols. a) Which chemical is the most dangerous in this lab? b) Explain why you chose your answer for part a), and the safety precautions you will take when handling this material.

2) Why do you require an acid catalyst to make an ester? Why not just mix acid and alcohol?

3) Describe an alternate method of making an ester that doesn't involve an acid catalyst (for a hint, see expt 1…).

4) Describe how to distinguish between an alcohol and an ester by IR spectroscopy.

5) Describe how to distinguish between a carboxylic acid and an ester by IR spectroscopy.

Experiment


Unknown Alcohol ???? -- -- -- 1.0 mL

Nafion Resin 417 -- -- -- -- 1 strip

Glacial Acetic Acid -- -- -- 700 µL

product

You will be assigned an unknown alcohol, labeled A, B, C, D or E. Your task will be to convert the alcohol into an ester derivative with acetic acid, and determine the structure of this ester by NMR and MS analysis, and by extension the structure of the alcohol.

1. Reaction Setup Place 1.0 mL of your designated alcohol (A, B, C, D or E. - note which alcohol you were given in your notebook) into a 10 mL round-bottomed flask containing a magnetic spinbar. Add a strip of Nafion 417



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resin to the flask and, followed by 700 µL glacial acetic acid. Equip with an air condenser and transfer the flask to a sand bath on a magnetic stirrer. NOTE: Glacial Acetic Acid is corrosive and toxic - all manipulations should be performed in the fumehood. Heat the reaction to 170 ºC for 30 mins, then remove the reaction from the sand bath and allow to cool to room temperature.

2. Isolation of Product Remove the Nafion strip and spinbar (with tweezers), and carefully rinse them (into the reaction flask) with 1 mL deionized water. Carefully add 3 mL 5% NaHCO3 solution to the flask (add dropwise to avoid foaming) and swirl to mix the phases.

Transfer to a separatory funnel and add 20 mL diethyl ether. Separate the aqueous phase and place it in a 50 mL Erlenmeyer flask (keep the organic layer in the separatory funnel). Wash the organic layer with 2 x 5 mL portions of NaHCO3, followed by 2 x 10 mL deionized water, combining the aqueous washes in the Erlenmeyer. Transfer the organic layer to a second Erlenmeyer flask, add anhydrous sodium sulfate and leave to dry for 5 mins. Remove the sodium sulfate via gravity filtration. Discard the solid and transfer the solution to a 50mL round-bottomed flask, then remove the solvent via rotary evaporation.

Obtain an IR spectrum of your liquid product and you alcohol starting material.

3. Analysis of your product Your TA will give you a 1H and 13C NMR and EI Mass spectrum of your product. Hand these in with your postlab report. Post Lab Questions In your lab report, MAKE SURE to identify which alcohol you were assigned (A-E). (1) Draw the arrow-pushing mechanism of a generic esterification reaction:

(2) From the spectral data (NMR, IR, MS) you were given, identify the structure of your ester product. (3) Based on your answer to Q2, what is the structure of your starting alcohol?

(4) Assign the major peaks in the IR spectrum of your product.

(5) Fully assign the 1H NMR spectrum of your product (i.e. determine which peaks in the 1H NMR correspond to which hydrogens in the product). You will not receive full marks for determination of the unknown unless you assign the 1H NMR spectrum completely. (6) You will notice that we gave you the m/z value of the M+ ion of your product on the EI (electron impact) mass spectrum, but the actual peak on the spectrum is very small (or even non-existent). Read McMurry p426-432 (especially p431) and explain why the M+ peak is so small.


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Experiment 5: Unknown Lab Part 2 - Reductive Amination Reading: McMurry 8th Ed pp 958-960 (reductive amination), Lab book special section, p29-41. Introduction In this experiment, you will synthesize a secondary amine by a reductive amination reaction between a primary amine, an aldehyde and a reducing agent, sodium triacetoxyborohydride. You will then determine the structure of the product (and by extension, the reactants) by Mass spectrometry, NMR and IR spectroscopy.

Prelab Questions 1) The Material Safety Data Sheets (MSDS) for some of the chemicals involved in this lab are on iLearn. Read the MSDS sheets for sodium triacetoxyborohydride and dichloromethane and explain the safety precautions you will take when handling these materials. 2) Read the special section (p29-41) and explain why protons attached to nitrogen (i.e. N-H) show broad peaks in the 1H NMR and do not couple to other protons. 3) If the reaction doesn't go to completion, you will have aldehyde starting material present. How would you identify this impurity most easily by 1H NMR? 4) How would you identify an aldehyde by IR spectroscopy?

Experiment


Unknown Aldehyde ???? -- -- 0.7 mmol See below

Unknown Amine ???? -- -- 0.74 mmol See below Sodium

Triacetoxyborohydride NaBH(OCOCH3)3 -- -- 0.77 mmol 163 mg

Dichloromethane CH2Cl2 -- -- -- 2 mL

product

You will be assigned two starting materials - the aldehydes are numbered 1-5, the amines are numbered A-F (your assignment will be something like A1, B1, C3, etc). Write down your assignment and make sure you are given the correct spectral data of your product! You will take an IR spectrum of your product, but the NMR and MS spectra will be given to you. You will perform the reaction on a 0.7 mmol scale: the amounts of the unknown amine/aldehyde are shown below. Make sure you weigh out the correct amounts for your specific reaction! Amounts for each unknown: Unknown Amine A: 73 uL (54 mg) Unknown Amine B: 73 uL (54 mg) Unknown Amine C: 77 uL (54 mg) Unknown Amine D: 126 mg Unknown Amine E: 79 mg Unknown Amine F: 91 mg

Unknown Aldehyde 1: 74 uL (60 mg) Unknown Aldehyde 2: 76 uL (60 mg) Unknown Aldehyde 3: 130 mg Unknown Aldehyde 4: 83 uL (85 mg) Unknown Aldehyde 5: 85 uL (95 mg)



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To make the assignment a little easier, your amines and aldehydes come from this list. Not all of these reactants will be used…

1. Reaction Setup Add your unknown aldehyde (see above for mass/volume), amine (see above for mass/volume), sodium triacetoxyborohydride (163 mg), and methylene chloride (2 mL) (in that order) to a dry 10 mL round bottomed flask equipped with a magnetic stir bar. Transfer the flask to a stirplate and stir the reaction for 2 h.

During the 2h stir time, you can begin to analyze your NMR spectra and determine the structure of your unknown. Use this time to confer with your TA and your labmates about anything you don't understand in assigning your NMR spectrum. The more you do in this time, the less you have to do at home… 2. Isolation of Product. NOTE: Perform this extraction in a fumehood. After 2h, quench with saturated. aq. sodium bicarbonate solution (5 mL) and transfer to a separatory funnel. Add 10 mL dichloromethane to the separatory funnel to make the separation easier. Separate the aqueous phase and place it in a 50 mL Erlenmeyer flask (return the organic (lower) layer to the separatory funnel).

Separate the layers and transfer the organic (lower) layer to a 25 mL Erlenmeyer flask. Wash the aqueous layer with methylene chloride (5 mL). Combine the organic layers and wash with sat. aq. sodium bicarbonate (5 mL), then brine (5 mL). Transfer the organic layers to the Erlenmeyer and dry over sodium sulfate.


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Remove the sodium sulfate via gravity filtration. Discard the solid and transfer the solution to a 50mL round-bottomed flask, then remove the solvent via rotary evaporation. Obtain an IR spectrum of your product.

3. Analysis of your product Weigh your product: when you have determined the structure of your unknowns, you will be able to calculate a yield (you started with 0.70 mmol of reactant). Your TA will give you 1H, 13C NMR and EI Mass spectra of your product, as well as 1H NMR spectra of the starting materials you used. Hand these in with your postlab report. Post Lab Questions Note that no analysis section is required in this postlab - your structure determination and spectroscopic analysis will be used instead. In your lab report, MAKE SURE to identify which amine (A-F) and which aldehyde (1-5) you were assigned. (1) The reaction you actually perform in this experiment has some complexity in the mechanism, but you can analyze a more simple two step version that is described on p598 of McMurry. Draw the arrow-pushing mechanism of the first step of this mechanism to form an imine.

(2) Draw the arrow-pushing mechanism of the second step of this mechanism to convert the imine to an amine using sodium borohydride.

NOTE - in the 1H spectra, the peak for the NH proton in your product is often very broad and may be unobservable. If you don't see it, assume it's there (for an explanation as to why, see p34 and your prelab). (3) From the spectral data (1H, 13C NMR, IR, MS) you were given, identify the structure of your product. Explain why you chose your particular product based on the spectroscopic data. You will not receive full marks for determination of the unknown unless you explain why. (4) Fully assign the 1H NMR spectrum of your product (i.e. determine which peaks in the 1H NMR correspond to which hydrogens in the product). You will not receive full marks for determination of the unknown unless you assign the 1H NMR spectrum completely. When performing your assignment, p37 of the lab handout will be indispensable… (5) Now work backwards (or consult the NMR spectra of the two reactants that your TA gave you) and determine the structure of the two unknown reactants.


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Experiment 6a - Synthesis of an Azo Dye Reading: McMurry 8th Ed pp 968-972 (diazotization), p517-523 (UV/Vis spectroscopy).

Introduction Azo dyes have long been used in the fabric industry to color clothing and other materials. Their synthesis is relatively straightforward, and uses classical aromatic substitution chemistry. In the experiment, you will make a simple azo dye from some aromatic starting materials and analyze the product using UV/Vis spectroscopy.




p-Nitroaniline 1.0 350 mg

HCl (6M) -- -- -- -- 3 mL

Sodium nitrite (NaNO2) 190 mg

2-Naphthol 320 mg

Sodium Hydroxide (2.5 M) -- -- -- -- 15 mL

product


4) Read p517-523 of McMurry and describe what molecular characteristics allow a molecule to absorb Ultraviolet light (and be observed by UV spectroscopy). What causes an absorption at increased wavelength?

Experiment: 1. Reaction Setup/Diazotization Combine 350 mg p-Nitroaniline and 190 mg NaNO2 in a test tube with 5 mL H2O. Stir until the p-nitroaniline is thoroughly suspended, and then place in an ice bath. Meanwhile, add 3 mL of aqueous



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HCl (6 M) to a 50 mL Erlenmeyer flask equipped with a spin bar. Place that flask into the ice bath also, and allow to cool. Once both flasks are cooled, add the p-nitroaniline suspension to the Erlenmeyer in portions (approximately 1 mL each) over 5 minutes. It is imperative that the solution remain cooled during this period. Once complete, use cold water to rinse the majority of residual p-nitroaniline into the 50 mL Erlenmeyer flask. Stir for 10 mins. 2. Azo Dye Formation While this solution is stirring, add 320 mg of 2-naphthol to 15 mL NaOH solution (2.5 M) in a 125 mL Erlenmeyer flask. Stir for 2mins, and cool in an ice bath. After the acidic solution (in the 50 mL Erlenmeyer, step 1) has been stirred for at least 10 minutes, remove the stir bar from that solution and place into the 2-naphthol-containing 125 mL Erlenmeyer. Fit this 125 mL Erlenmeyer with a short stem funnel with filter paper. Pour the acidic solution through the filter in portions (to prevent warming). Once the addition is complete, stir the reaction mixture for an additional 5 minutes. 3. Isolation of Product Treat the solution with 3M aqueous HCl until the reaction mixture tests acidic to Litmus. Add 0.5 mL of saturated brine, and heat the reaction to a gentle reflux for 5 minutes. Cool to room temperature and place into an ice bath. A precipitate should form on cooling: isolate the solid via filtration using a Hirsch funnel. rinse the solid with 5 mL of deionized water, and dry on the filter. 4. Characterization Weigh your dry, purified product to determine the yield and obtain a melting point. Compare your observed melting point to the literature value. Your TA will give you UV/Vis spectra of your product and starting material. Hand these in with your postlab report. Post Lab Questions (read p517-523, UV/Vis spectroscopy) (1) Draw the arrow-pushing mechanism for step 1, making sure you account for all steps in the mechanism.

(2) Draw the arrow-pushing mechanism for step 2, making sure you account for all steps in the mechanism.

(3) Draw three resonance structures of phenol. Is the OH group a donor or acceptor? Is phenol activated towards electrophilic aromatic substitution or deactivated?

(4) Based on your answers to Q3, explain why 2-naphthol reacts with the diazonium salt at only one position.

(5) Which molecule, phenol or 2-naphthol, will display an absorbance at longest wavelength in the UV/Vis spectrum? Why?

(6) Based on your answer to Q5, would you expect your product to absorb at a longer or shorter wavelength than the 2-naphthol starting material? Explain why.

(7) Is the visible region of the electromagnetic spectrum at a longer or shorter wavelength than the ultraviolet region?

(8) Based on your answer to Q6 and Q7, explain why your product acts as a "dye".

OH OHphenol 2-naphthol


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Experiment 7 - Protection of a Carbohydrate: Acetal formation from α-Methylglucopyra-noside Reading: McMurry 8th Ed pp 742-746 (acetal formation), 1011-1018 (carbohydrate structure and reactions).

Introduction Carbohydrates are a vital part of natural processes: many cellular receptors involve multiple carbohydrates appended to proteins and other biomacromolecules. Synthesizing sugar derivatives is therefore a tremendously important research area in organic chemistry. The problem with sugar chemistry is that all the basic carbohydrates have multiple different alcohol groups, as well as multiple conformations and structures. Experimental techniques that allow selective protection of alcohols in sugar derivatives are an important first step in complex syntheses of polysaccharides. Here, you will perform one of these protections: a selective acetalization of a glucopyranose derivative.




α-Methylglucopyranoside 1.0 500 mg Benzaldehyde dimethylacetal 700 µL

p-Toluenesulfonic acid 25 mg

Acetonitrile -- -- -- 10 mL

Triethylamine -- -- 2 drops

product


4) How many stereocenters are there in the sugar starting material? How many in the product?

5) Why do we use benzaldehyde dimethylacetal for the reaction, rather than benzaldehyde itself? (think back to 112B…)



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Experiment: 1. Reaction Setup

In a 50 mL round bottom flask equipped with a magnetic spin bar add 500 mg of methyl-α-D-glucopyranoside and 10 mL of acetonitrile. Place on the hot plate and stir vigorously. To this solution add 0.7 mL benzaldehydedimethylacetal and 25 mg p-toluenesulfonic acid while stirring. Attach an air condenser and turn the hot plate on to reflux the solution at 85 ºC for 30 min. After 30 min, turn the hot plate off and let the reaction cool to room temperature.

2. Isolation of Product Once the reaction is cooled, neutralize the reaction mixture by adding 2 drops of triethylamine. Pour the reaction mixture in to a separatory funnel and add 50 mL ethyl acetate to the funnel. Wash three times with 15 mL water and once with brine. Dry the organic layer with Na2SO4. Filter off the Na2SO4 and remove the solvent by rotary evaporation.

3. Purification by Recrystallization At this point your product is mostly pure but contains some slight impurities. Purify your product by recrystallization. Dissolve your crude product in about 10 mL dichloromethane and crystallize your product by slow addition of hexanes (~75 mL). Make sure to stir the contents of the flask. Collect your product by vacuum filtration. Your product may have a gel-like consistency. If this occurs, just allow it to fully dry on the vacuum and it will eventually become a solid.

4. Characterization Weigh your purified product to determine the yield and obtain a melting point. Compare your observed melting point to the literature value. Your TA will give you a 1H NMR spectrum of your product. Hand this in with your postlab report. Post Lab Questions (1) Draw the mechanism of the reaction, making sure you account for all steps in the mechanism.

(2) Only one product is observed in the reaction - draw the other possible stereoisomer that could conceivably be formed by this process (HINT - the stereocenters in the sugar are unaffected by the reaction). (3) Why is this other stereoisomeric product not formed?

(4) A different possibility is the formation of a constitutional isomer by reaction with different OH groups. Draw the acetal product that would be formed by reaction of benzaldehyde dimethyl acetal with hydroxyl groups 3 and 4 in the structure below. Explain why this species is not favored in this reaction.

(5) The 1H NMR spectrum of the product is quite complex, but you can assign some of it. I have labeled some of the peaks on the spectrum as 1-5. Now look at the product structure below. Ha and Hf are both near two O atoms, so will have the highest chemical shift (ignoring the aromatic ring). Assign peaks Ha and Hf, and explain how you distinguished between them.


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Hc

OOHO

OOH

CH3

O

HaHb

Hd

He

Hf

H

H

Large J(~12 Hz)

H

HSmall J(~5 Hz)

(6) Everything else you need to know is in the above diagram. If two H are both axial, they have a large coupling constant (~12 Hz). If one is axial and one equatorial, they have a small (J ~5 Hz) coupling constant. Look at the structure of your product and determine which pairs of protons have diaxial (large) coupling constants and which have small (equatorial-axial) coupling constants.

(7) You can now assign some more of the spectrum. The peak labeled 4 is a triplet with J = 12 Hz (i.e. coupled to 2 different H both with large coupling constants). This can correspond to one of two hydrogens from Ha-Hf. Which is it? Can you discriminate between the two possibilities easily?

(8) Measure the coupling constants for peaks 2 and 3. Which peak is 2 coupled to? Based on that assignment, your answer to Q5 and the structure shown above, assign (from Ha-Hf) peak 3.


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Experiment 8 - Amino Acids as Catalysts: Proline-catalyzed Condensation Reading: McMurry 8th Ed pp 736-740 (imine formation), 751-755 (conjugate addition).

Introduction Green chemistry is the design of chemical products and processes that reduce or eliminate the use and generation of hazardous substances. Often referred to as a form of molecular-level pollution prevention, green chemistry relies on a set of twelve principles that can be used to design or re-design molecules, materials and chemical transformations to be safer for human health and the environment. Volatile organic solvents (VOCs) are used in the manufacturing and processing of almost all commercially available products. VOCs are typically small organic molecules which are flammable and often toxic in nature. Studies have shown that use of large quantities of VOCs has led to a significant destruction of the protective ozone layer. With an increasing emphasis on employing safer and more environmentally friendly compounds in the chemical industry, there has been keen interest in finding alternative solvents to VOCs. PEG-400 (below) can be considered as a useful option in this regard.

In today’s experiment, PEG-400 is used as a recyclable solvent for the catalyzed condensation reaction between 4-nitrobenzaldehyde and 5,5-dimethylcyclohexane-1,3-dione (dimedone). Racemic proline (an amino acid) acts as an organocatalyst under these conditions to form a tetraketone product that exists in its dienol form shown below.




p-Nitrobenzaldehyde 1.0 151 mg

Dimedone 280 mg

(±)-Proline 57 mg

PEG-400 -- -- -- -- 2.0 mL

product



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4) We use racemic proline for this reaction, mainly for cost reasons - single enantiomers are more difficult to isolate and are more expensive than racemic mixtures. Does this matter for the reaction? Would you expect any difference in the reaction if we used pure (S)-proline?

Experiment: 1. Reaction Setup

IN A FUMEHOOD, place the following in a 50-mL round-bottomed flask:4-nitrobenzaldehyde (151 mg); 5,5-dimethylcyclohexane-1,3-dione (Dimedone, 280 mg); (±)-proline (57 mg) and PEG-400 (2 mL – use an automatic delivery pipette). Introduce a small stir bar and stir VIGOROUSLY at room temperature using a magnetic stirring plate.

After 30 minutes, perform TLC on the reaction solution (stationary phase, silica gel; eluent, 2:1 hexanes:ethyl acetate). Be sure to include the following three spots on the TLC plate (left lane: 4-nitrobenzaldehyde; centre lane: 5,5-dimethylcyclohexane-1,3-dione; right lane: product mixture) and visualize the spots using ultra-violet light. Perform TLC again after one hour of reaction time. Remove the flask from the magnetic stirring plate and add ice-cold water to the reaction flask (10 mL). Return the flask to the stirrer/hotplate and stir for 10 minutes (a white precipitate will form).

2. Isolation of Product Collect the crude product by vacuum filtration using a Hirsch funnel, rinsing any residual product from the reaction flask with no more than 5 mL of ice-cold water. Leave the solid under vacuum on the filter funnel until it is reasonably dry. Be sure to re-filter any solid that passes through the filter paper into the vacuum filtration flask. Pour the filtrate from the vacuum filtration flask into a 50-mL round-bottomed flask and evaporate the water using a rotary evaporator.

3. Purification by Recrystallization Recrystallize the crude solid product from a MINIMUM amount of absolute ethanol and rinse the solid with a small amount of ice-cold solvent (2 mL). Be sure to re-filter any solid that passes through the filter paper into the vacuum filtration flask.

4. Characterization Record the mass, percentage yield and melting point of your dried product. Obtain an IR spectrum of the product. Post Lab Questions (1) The mechanism of this reaction is a little complex, so we'll go step by step. The key to this reaction is the formation of a reactive "iminium" species with proline - draw the mechanism for the transformation below:

(2) Why is enol formation in dimedone more favorable than in cyclohexanone?

(3) This enol reacts with the intermediate iminium to give an addition product. Draw the mechanism.


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(4) The final step involves recovery of the proline catalyst via an acid-catalyzed elimination followed by a conjugate addition to form the product - draw the mechanism of those steps.

(5) We use PEG-400 as an recoverable, "environmentally friendly" solvent. Water is environmentally friendly, but we don't use that. Give two reasons why we cannot use water as solvent in this reaction.


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Special Section - NMR Spectroscopy NMR Basics: Chemical Shift, etc. For NMR basics, please read McMurry 8th Ed Ch 13, p 456-484. This section assumes you are familiar with the basics of 1H NMR, notably chemical shift (δ). 1) Equivalence Before we commence the discussion of coupling constants, it is important to establish the concept of equivalence of nuclei. Generally we speak of two types of equivalence in NMR – chemical and magnetic equivalence. Only systems that are chemically equivalent will be covered here; magnetic equivalence is a far more complex matter and is beyond this course.

Nuclei are chemically equivalent when they experience identical chemical environments. Chemically equivalent nuclei have the same resonance frequencies (i.e. appear at the same chemical shift). Also chemically equivalent nuclei DO NOT couple to EACH OTHER (they CAN couple to other nuclei, however, just not to each other). This may be achieved in a number of ways:

Symmetry: if a molecule is symmetric, then nuclei will have the same chemical shifts as their symmetry counterparts.

The two CH2 in chloropropane are termed "enantiotopic" protons. Read McMurry p471-473 for a full definition, but what it means here is that the two protons in the CH2 group are identical and have the same chemical shift. This only applies if there are no chiral centers in the molecule! Free rotation: free rotation is particularly important for alkyl groups. We may perform a conformational analysis of an alkyl group and find that the chemical environment is slightly different for each nucleus. However, the barrier to rotation between the rotamers is very small – at room temperature, we may consider the rotation about the C-C bond to be effectively barrierless (free rotation). The rate of rotation (fs to ps) is very much faster than can be resolved at the timescale of an NMR experiment (ms to s), so the signal will average out – we will see a single peak. This type of phenomenon requires discussion of


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a term seen often in NMR experiments – the NMR timescale. As stated above, this timescale is of the order of ms to s. Any type of change in the molecule which occurs at a timescale lower than this will lead to an average signal, rather than multiple distinct signals. Stereocenters: If there is a chiral center anywhere in the molecule, ALL protons in CH2 groups are different, and have different chemical shifts. These protons are termed diastereotopic (McMurry p473), and they couple to each other (see section 4). This does not apply to CH3 groups - the three H in CH3 groups are always identical.

2) Peak Integration The intensity of an NMR peak is proportional to the number of protons that resonate at a given frequency. If we integrate the resonance peaks, we find that the ratio of the peak integrals is equivalent to the ratio of protons resonating to generate that peak. Consider 1-chloropropane:

This compound will give rise to three distinct signals, each signal with a different chemical shift, due to a different type of hydrogen atom in the molecule. Integration of each of the signals gives peak integrals with ratios of 2:2:3, consistent with the number of each type of atom. The peak integral corresponds to the area under the peak, and so cannot be determined by just looking at the spectrum. It is usually represented by a curve above the peaks:

How to determine an integral: To determine the integral, measure the height of this curve (with a ruler!). You will obtain a ratio of heights, for example 1.2cm:1.2cm:1.8cm. You have to convert this ratio so that the sum corresponds to the total #H in your molecule. In chloropropane, there are 7 total H - multiply all your heights by 4/3 and


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you get a ratio of 2:2:3 - two 2H peaks, and one 3H peak. The ratio can also be given to you (the numbers beneath the peaks), but it isn't always! Make sure you understand what an integral is.

Also note - all protons must be present in a 1H NMR spectrum. If your ratio doesn't add up to the total #H in the molecule, you've added wrong…

Other points about integrals: The simple description above holds quite well, but it is important to note that the size of the integral is not simply a function of the number of protons corresponding to a resonance peak. There are a number of factors that can cause errors in the integral. Be flexible when interpreting integration if the ratio is 1.05:1, it doesn't mean there are 1.05 protons in your molecule! Some factors are:

• Relaxation time: most NMR spectrometers acquire spectra using multiple radiofrequency pulses. If the temporal (time) spacing between the two pulses is not sufficiently large, then the system will not be allowed to relax back to its starting state – the signal for the next pulse is correspondingly smaller. We usually set a spectrometer delay time that is much larger than the relaxation time of the slowest signal: for a proton NMR this is usually 5 seconds.

• Peak broadness: Most spectrometers identify the beginnings and ends of peaks by sharp changes in the slope of the obtained spectrum (deviations from baseline), and integrate between these points. Broad and noisy peaks will often not be well defined for integration purposes.

• Sample dilution: dilute samples will have lower S/N ratios, and integration of noisy peaks will often be unsatisfactory.

3) Spin-Spin Coupling (McMurry p477-481) We know that the localized magnetic field around a nucleus may be affected by the presence of electron density (with its associated magnetic moment) and by the presence of other magnetic nuclei. Consider 1,1-dichloroethane, and let us consider the possible localized magnetic field acting on the single proton in the presence of a free rotating methyl group. We may do this by considering the possible spin states for the hydrogens in the methyl group:

Possible Nuclear Spin Configurations for the CH3 group:

We will have our signal split into four components, with relative signal intensities (and integrals) of 1:3:3:1 – a quartet. This fine structure is produced by spin-spin coupling. If we work the other way, and consider the effect of the C-H proton on the resonant frequencies of the methyl group, we find that we generate a coupling fine structure that is a doublet – two peaks with relative intensities 1:1.


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Three other points need to be made:

• The resonance frequencies are evenly spaced – the spacing between the peaks is the coupling constant, J, and is defined by:

J = Δδ (ppm) x νinstrument (MHz)

where Δδ is the spacing between peaks of the multiplet in ppm and νinstrument is the frequency of the NMR spectrometer (i.e. 300, 400 MHZ, etc.)

• Since the coupling constant is measured in a unit of frequency (Hz), its magnitude is independent of the strength of the magnetic field.

• The coupling constant for the splitting of the C-H resonance signal and the resonance signal for the methyl group must be equal in magnitude, i.e. peaks that couple to each other must have the same coupling constant (J).

The multiplicity of a coupled peak is determined by the (2S+1) rule: each individual proton attached to adjacent carbon atoms contributes a spin S of ½. Peak intensities of multiplets may be determined by referring to Pascal’s triangle (binomial distribution function):

# H on Adjacent C

Relative Intensity of Multiplet Multiplicity

0 1 Singlet

1 1 1 Doublet

2 1 2 1 Triplet

3 1 3 3 1 Quartet

4 1 4 6 4 1 Quintet

5 1 5 10 10 5 1 Sextet

Vicinal and Geminal Protons How far away can the coupling protons be? Generally, there are two types of coupling observed, vicinal and geminal coupling. We will use the words "vicinal" and "geminal" constantly, so remember what they mean:

Longer range coupling is possible (for example coupling between meta H on an aromatic ring), but those coupling constants are small and we won't discuss them here. Simply put, the further away (through bond) the protons are, the lower the coupling constant between them. Coupling constants smaller than 1 Hz are generally not observed with a common 300 or 400 MHz instrument. How to measure a coupling constant The picture below is of the upfield region of chloropropane (i.e. just showing the CH2 and CH3 groups). We will use this to illustrate how to calculate a coupling constant. The two resonances are a sextet and a triplet - six peaks for the CH2, and three for the CH3.


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To determine a coupling constant, you need two things - the exact chemical shift of each peak, and the frequency of the spectrophotometer. This will allow you to calculate the J value in Hertz (not ppm!).

This spectrum was taken on a 300 MHz instrument, and the exact position of each peak (the "peak pick") is shown above each peak:

Think about how you get a triplet - the original peak is split by coupling to two H, each with the same constant. Therefore, the J value is the space between each peak (i.e. between the left peak at 1.0465ppm and the center peak at 1.0222 ppm, or between the center peak at 1.0222 ppm and the right peak at 0.9977ppm - both those spaces are the same). To calculate the J value for the triplet, calculate the spacing between the peaks in ppm, i.e. subtract one value from the other.

1.0465 ppm - 1.0222 ppm = 0.0235 ppm.

To convert to Hz, multiply this by the magnet frequency (300 MHz in this case - remember that ppm just means 106 and is unitless - multiply ppm by MHz and you get Hz):

0.0235 ppm x 300 MHz = 7.35 Hz, i.e. J = 7.35 Hz Repeat with the sextet - we'll use the rightmost peaks (the spacings are all the same, so it doesn't matter which you pick).

1.7656 ppm - 1.7421 ppm = 0.0235 ppm

0.0235 ppm x 300 MHz = 7.35 Hz, i.e. J = 7.35 Hz Note that the two J values must be the same - peaks that couple to each other have the same coupling constant by definition. 4) Complex Spin-Spin Coupling (McMurry p482-484) Coupling Constants are not all the same! The "simple" spin-spin coupling described above refers to vicinal protons that all have the same coupling constant. This usually applies to substituted alkanes - there is free rotation about all C-C bond and the distance between the H atoms averages out. As a rule, the vicinal coupling constant in a substituted alkane will be 7 Hz. Hence in chloropropane (see above), three signals are observed: 3H triplet (Ha), 2H sextet (Hb - vicinal to CH3 and CH2), and a 2H triplet (2H sextet (Hd - vicinal to CH2 only) - all the coupling constants are the same, so the Pascal's Triangle rule applies.


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What happens if the molecule isn't an alkane? Coupling constant magnitude relies on three things - distance, angle and rigidity. Consider a simple alkene, 2,2-dimethylbutene. We won't consider the tert-butyl group (a 9H singlet at 0.9 ppm), just the alkene. The alkene region of the NMR spectrum is shown below.

The alkene group has three protons on it, Ha, Hb, Hc, and there are three corresponding peaks in the NMR spectrum. The relationship between Ha, Hb and Hc is different to that displayed by a normal alkane - there is no rotation around the C=C, and so all three H are different, and couple to each other with different coupling constants. Resonance Ha (δ 5.85 ppm) shows four peaks – this comes from coupling to 2 protons with DIFFERENT coupling constants. As an exercise, think about what happens when you couple a proton to 2H with the SAME coupling constant. We can use the following diagram, which gives us a triplet, as we expect:

However, if the coupling constants are different, then the diagram looks like this:


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Hence Ha shows four lines with the same area (a 1:1:1:1 ratio) - it couples to both Hb and Hc, but with different J values.

Measuring Coupling constants in a Doublet of Doublets. This is the same procedure as described above. You just need to know on which peaks to perform the subtraction. Look at the doublet of doublets from our alkene example:

Now consider how we determined the coupling pattern:

Measuring the small J is easy - just subtract the shift of peak 2 from that of peak 1. This also works for 3/4 - they're the same! Unfortunately, there is no peak at the position of the "1st coupling" lines. What you do to determine the Ja is subtract the shift of peak 3 from that of peak 1 (or 4 from 2 - again, they're the same.

For the alkene example (which was taken on a 400 MHz machine), the two coupling constants are:

Jb = [δ (peak 1) - δ (peak 2)] x 400 MHz = [5.891 - 5.864] x 400 MHz = 0.027 ppm x 400 MHz = 10.8 Hz Ja = [δ (peak 1) - δ (peak 3)] x 400 MHz = [5.891 - 5.847] x 400 MHz = 0.044 ppm x 400 MHz = 17.6 Hz

The two coupling constants of 10.8 Hz and 17.6 Hz correspond to the cis (Ha - Hc) and trans (Ha - Hb) couplings, respectively.

Second Order Effects - "Why are my peaks of different height?" We won't go into this in detail, but coupling effects are more complex than the simple Pascal's Triangle rules we discuss in lecture. The easiest effect to use in analyzing 1H NMR spectra is called "leaning" or "roofing". If two protons are coupled to each other, the inner peaks are often higher than the outer ones: you can think of this as either "leaning" towards each other, or forming a "roof" shape (thank the Germans for that one…). An example of this is shown below:


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This effect generally occurs when the two peaks are close in chemical shift, and varies with magnet strength. Most "real" spectra exhibit this to some degree, so don't expect your doublets and triplets to be exactly level. The good thing is that this helps you determine which peaks couple to each other: if the peaks lean towards each other, then they can be coupling. If not, they're coupling to other protons.

Exchange Sometimes expected signals may disappear from the 1H NMR spectrum: this may occur for the following types of compounds: carboxylic acids, phenols, alcohols, amines, etc. The reason for this is that many NMR solvents (particularly CDCl3) have a small amount of D2O or DCl in them. If the compound contains labile protons (eg. a carboxylic acid), then proton/deuterium exchange may occur.

This process may be used to our advantage: if we have a compound that we suspect contains a labile proton, we can add D2O to the NMR tube and shake it: the disappearance of an NMR signal is usually good evidence for the presence of a labile group such as those listed above.

Why are OH/NH peaks broad? This is a complex subject, but the general answer is either chemical exchange (as described above), or variable hydrogen bonding. In solution, protons attached to electronegative atoms (such as alcohol O-H, amide N-H, etc) are capable of H-bonding to other H-bond acceptors in solution (i.e. anything with a lone pair, even solvents such as CDCl3). In a solution, these molecules move around rapidly, FASTER than the NMR timescale. The H-bond strength is variable in the solution - some molecules have strong contacts and some have weak contacts, but they are all moving around rapidly.

H-bonding changes the amount of electron density on the H atom, i.e. changes the chemical shift. What you see in an NMR spectrum (and a solution-phase IR, for that matter) is an average of the H-bonding in the solution, i.e. an average of the chemical shifts. Hence the peak is not sharp and at a single δ, but is broad. An additional result of this is that the OH does not couple to adjacent CH protons. An example is shown to the right, for 1-hydroxy-4-pentanone:

Note the 1H peak at δ 3.65 - this is the OH peak, and is broad. The 2H triplet at δ 3.50 belongs to the CH2 adjacent to the OH, and only couples to its adjacent CH2, not the OH.

As we mentioned above, this is a complex area, and there are many exceptions. For this course, however, you can assume that OH peaks will be broad (and easy to identify) and will not couple to adjacent protons.


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5) Chemical Shift Determination in Aromatic Rings The major difference between aromatic rings and aliphatic chains in chemical shift determination is the π electron cloud that resides above and below the benzene ring (McMurry p552). This causes deshielding of the protons attached to the ring, and so the protons on benzene display a chemical shift δ = 7.30 ppm. We will be comparing all chemical shifts to that of benzene, so remember that number!

When considering substituted benzene rings, the nature of the substituted group can be determined by the change in chemical shift for the protons on the ring. This is easiest to explain for electron donating groups (e.g. OH) and electron withdrawing groups (e.g. NO2).

The result of all this is that aromatic rings with ortho/para directing, activating groups (e.g. OH, OR, NH2, CH3, etc) have protons with δ<7.30 ppm. The protons ortho and para are shifted further upfield than the meta protons, but they are all shifted upfield from 7.30 ppm.

Aromatic rings with meta directing, deactivating groups (e.g. NO2, CN, COOH, CHO, etc) have protons with δ>7.30 ppm. The protons ortho and para are shifted further upfield than the meta protons, but they are all shifted upfield from 7.30 ppm.

Other groups can be a little complex, especially halides, and we won't discuss them in depth here. The exact amount of shift from that of benzene depends on the strength of the activating/deactivating group: stronger donors shift the protons more, etc. Numerical examples:

6) Coupling Patterns in Aromatic Rings You can assign the structure of a substituted benzene ring by looking at the coupling pattern. As the aromatic ring is flat and there are no angle changes to worry about, the coupling constants in different benzene rings are quite consistent, no matter the nature of the substituent. Coupling constants between protons that are ortho to each other are usually 8 Hz, coupling constants between protons that are meta to each other are usually 2 Hz, and coupling constants between protons that are para to each other are <1 Hz, and generally cannot be seen. Some examples of coupling patterns in multisubstituted aromatic


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rings are shown below, where A, B and C are functional groups. NOTE - these patterns have nothing to do with chemical shift - that depends on the nature of the group. Coupling is essentially independent of that, although there are always exceptions.

Isotopes In Mass Spectrometry Mass spectrometry detects the m/z (mass:charge ratio) of each INDIVIDUAL molecule that strikes the detector. All atoms have multiple isotopes – i.e. same number of protons, but different number of neutrons in the nucleus. These have different masses! “Atomic Mass” is the number found in your Periodic Table. This is used for WEIGHING bulk amounts of chemicals. It is the AVERAGE of all known isotopes. i.e.: Mass of 12C = 12.0000, mass of 13C = 13.0034. 13C has an abundance of 1.1% (i.e. 1.1% of all carbon atoms are 13C), so the average mass of carbon atoms is 12.011. This is the atomic mass of “carbon”. The atomic mass is NOT used in mass spectrometry. EACH isotope is detected, so for a mass spectrum of carbon, you will see TWO peaks – one for 12C, one for 13C. The INTENSITY of the peaks is proportional to the abundance. So – a mass spectrum of methane (CH4, m/z = 16) looks like this:

R

elat

ive

Abu

ndan

ce /

% 100 (M)

1.1 (M+1)

m/z 14 16 18 20 22

M is the Molecular Ion – i.e. CH4

+, the mass of your target molecule. M+1 is the label given to a peak one mass unit larger than the molecular ion.


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More than one Carbon? Propane (CH3CH2CH3) has three carbons. The possible isotopes are: Mass = 44: 12CH3

12CH212CH3

Mass = 45: 13CH312CH2

12CH3 OR 12CH3

13CH212CH3 OR 12CH3

12CH213CH3.

The probability of ONE 13C is 1.1%, but there are three carbons that can be 13C in propane, and all have the same mass – the intensity of the M+1 (m/z = 45) peak is 3.3% (i.e. 1.1% x 3). Note that the probability of two 13C being present is (1.1%)2 = 0.012%, so can be ignored. This means that the intensity of the M+1 peak tells you how many carbons are present:

(M+1 intensity) = 1.1% x #C

Propane (C3H6): intensity (M+1) = 3.3% Pentane (C5H12): intensity (M+1) = 5.5% Dodecane (C12H24): intensity (M+1) = 13.2% What if M is not the base peak? The BASE PEAK is the most intense peak in the spectrum and ALWAYS has a relative abundance of 100%. The base peak does NOT have to be the molecular ion (and often isn’t). 2-pentanol can fragment in the mass spectrometer, losing a CH3 group. You therefore get a large peak at m/z = 75 as well as the molecular ion at 88:

Rel

ativ

e A

bund

ance

/ %

100 (BASE) 40 (M) 2.2 (M+1)

m/z 74 76 78 80 82 84 86 88 90

The intensity of the M+1 peak is ALWAYS relative to the intensity of M.

(M+1 intensity) = 1.1% x #C x (M intensity) So for 2-pentanol, the base peak is m/z = 75, intensity 100%. M (the molecular ion, m/z = 88) has an intensity of 40% and so M+1 = 40 x 0.011 x 5 (# of C) = 2.2%.

What if other atoms are present? The natural abundance of isotopes of H, N, O, F or I is negligible – these can be ignored. The important atoms are Cl and Br. These have two isotopes each, 35Cl / 37Cl and 79Br / 81Br

NOTE that the mass difference is 2 amu!

Ratio (35Cl / 37Cl) = 75:25 = 100:30 ~ 3:1

Ratio (79Br / 81Br) = 100:98 = 50:49 ~ 1:1

OH OH+ CH3

m/z = 88 m/z = 75


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Therefore, if a molecule contains ONE Chlorine atom (e.g. CH3Cl), you will see an M+2 peak with intensity = 1/3 x M. If a molecule contains ONE Bromine atom (e.g. CH3Br), you will see an M+2 peak with intensity = M.

Examples (NOTE – the peak heights are not exact, just representations):

CH3Cl (mass = 50)

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% 100 (M)

32 (M+2) 1.1 (M+1) 0.33 (M+3)

m/z 50 51 52 53

REMEMBER – there are 13C isotopes in this molecule too. So M = 12CH335Cl, M+1 = 13CH3

35Cl, M+2 = 12CH3

37Cl and M+3 = 13CH337Cl.

CH3Br (mass = 94)

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% 100 (M) 98 (M+2)

1.1 (M+1) 1.1 (M+3)

m/z 94 95 96 97

Finally, a molecule with a Cl and more than one C: CH3CH2CH2CH2Cl (mass = 92)

R

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Abu

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% 100 (M)

32 (M+2) 4.4 (M+1) 1.4 (M+3)

m/z 92 93 94 95


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Table of Elemental Masses

Element Isotope Unit Mass (a.m.u.)

Isotopic Mass (a.m.u.)

“Atomic Mass”

Hydrogen 1H 1 1.00783 1.0079

Carbon 12C 12 12.0000 12.011 13C 13 13.0034

Nitrogen 14N 14 14.0031 14.0067

Oxygen 16O 16 15.9949 15.9994

Fluorine 19F 19 18.9984 18.9984

Chlorine 35Cl 35 34.9688 35.4527 37Cl 37 36.9659

Bromine 79Br 79 78.9183 79.904 81Br 81 80.9163

Iodine 127I 127 126.9045 126.904 “Atomic Mass” is the number found in your Periodic Table. This is used for WEIGHING bulk amounts of chemicals. It is the AVERAGE of all known isotopes. It is NOT used in mass spectrometry. In mass spectrometry, you are looking at ONE ISOTOPE. Use the Isotopic Mass!

DO NOT USE ATOMIC MASS WHEN ANALYZING MASS SPECTRA!!!!

Chem 112C Lab Book

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