Fall 2004

Fall 2004
Instructors: David J. A. Schedler and Regina Arnold-Stanton
Text: BSC Lab Manual and “Techniques in Organic Chemistry” by Jerry Mohrig, et. al.
Laboratory Notebook
Keeping a lab notebook is an essential part of every laboratory course. You have to prepare an adequate record of your work. The notebook must be bound, not spiral. All writing should be in ink. Draw a line through incorrect entries and write the corrections above. Do not erase notes. It is imperative that you read the lab project before coming to the laboratory. The prelab exercise also should be completed before coming to the lab.
Safety
Protecting your eyes is of utmost importance. You must wear safety glasses or safety goggles in the laboratory. Many organic reagents and solvents are corrosive and/or flammable. Do not wear contact lenses in the lab. Dress sensibly for work in the laboratory. Long pants should be worn. Do not wear shorts. Proper footwear is necessary.
Do not wear sandals. Loose clothes, long hair or dangling jewelry can be hazardous and need to be confined. Don’t wear expensive clothes or sentimental items that might get damaged. Be aware of your surroundings. Know the location of the nearest exit, the safety shower, the eye wash, and the fire extinguisher. One objective of this course is to learn good safety habits by taking the precautions noted in each experiment. Failure to follow safe practices endangers your fellow students and could affect your grade.
Grading
A written laboratory report for each project will be prepared and turned in the week after the project is completed. The breakdown of points and due dates is given after the description of the report format found below. There is a prelab due each week worth 3 pts., 30 pts. total for the course. The prelab should be completed on a separate sheet of paper and turned in at the beginning of the lab period. Cleaning up is an integral part of your work in the laboratory. Benches, hoods, balances, and reagent bottles will be inspected. A penalty in the form of a loss of points can be applied to your lab write-up.
Schedule
Lab meets in SSC 317 . There are four sections: Tue (8-11am), Tue (1:30-4:30 pm),
Wed (1-4 pm), and Thurs (8-11 am). Please arrive on time for the prelab lecture .
It is imperative that you read the information on the whole lab project BEFORE you begin work in the lab. Failing to do so may prevent you from finishing in the allotted time.
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Students should read the background information in “Techniques in Organic
Chemistry” corresponding to each week’s experiment given as “TOC:” at the beginning of each project.
Laboratory Project
Project 1: “Separation, Purification, and Identification Techniques”
Week of
September 6 Extraction and Crystallization of Unknown Acidic Substance
September 13 Separation of Two Neutral Substances by Distillation
September 20 Identification of Acidic Unknown Using Melting Point and Thin-Layer Chromatography
October 1 Project 1 Due
Project 2: “Isolation of Caffeine Using Column and Thin-Layer Chromatography and
Analysis of Caffeine Content in Various Over-the-Counter Medications Using Gas
Chromatography”
September 27 Analysis of Caffeine Content of Various Over-the-Counter Medications
October 4 Column Chromatography
October 15 Project 2 Due
Project 3, Part 1: “ 13 C NMR Spectroscopy”
October 11 13 C NMR of Alkanes and Alkyl Halides
October 18 FALL BREAK
Project 3, Part 2: “S
N and Reaction Order”
2 and S
N
1 Mechanisms: Determination of Characteristics
October 25
November 1
S
N
2 and S
N
1 Reactions
Determining the Reaction Order of the Sodium Iodide Reaction
Synthesis of the Dibromide for Project 4
November 12 Project 3 Due
Project 4: “Elimination Reactions: Elimination of Brominated Trans-Cinnamic Acid ”
November 8 Elimination Reaction
November 15 Analysis of Products
November 22 THANKSGIVING BREAK
December 3 Project 4 Due
November 29 LAB FINAL
HONOR CODE: students may NOT look at old lab notebooks or reports
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Formal Reports
After the completion of each lab project, an individual formal write-up should be written and turned in the following week. The report should follow the guidelines outlined below. They should be word processed and stapled. Honor Code should be followed. In addition, you MAY NOT LOOK AT OLD LAB REPORTS.
I.
Title Sheet
This cover page should include a title, lab section, date, and names of the investigators involved.
II.
Abstract
Give a concise summary of the project in one single-spaced paragraph
(all other sections should be double-spaced). What were you trying to accomplish in this laboratory project?
What was the result?
III.
Introduction
Give an overview of the background information necessary for the reader’s understanding of the significance of the experiment (i.e. techniques and instrumentation). Describe the theory behind any method used in the experiment. You should cite the primary references used.
IV.
Experimental Procedure
Describe in detail the investigations you did with your lab partner(s).
This should be double-spaced and in paragraph form. Give the procedure you used, but not the results at this time. Give all materials and reagents used. If you perform a reaction, give a balanced equation.
An investigator should be able to duplicate your procedure from this description. This section should be a narrative of what you did in the lab. It should be written in the past tense and in passive voice.
V.
Results and Observations
This should give the results of your experiments and not be a discussion of why they occurred. For the investigations you did, you should detail your results and any observations or problems you encountered. You should include a table for all of the data collected (i.e. melting points and percent yields).
VI.
Discussion
In this section you will discuss your results. In addition, describe how you used the results from each week to design your protocols. Why was this procedure chosen and what advantages does it have over other procedures? Be as specific as possible about any assumptions you have made in your analysis of results.
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VII. Conclusion
How does all of the information presented above led you to meeting the outcome desired for the lab project.
Students should review the definition of plagiarism in the BSC Honor Code. If you are uncertain, ask for help at the writing center. Ignorance is not an excuse.
-Structures can be hand drawn neatly and inserted in the text.
-Any tables or graphs should have a meaningful title or caption and be clearly labeled.
The reader should be able to independently read the table or graph and get all the information needed without having to read the laboratory report.
-References should be presented in American Chemical Society format. You may use either endnotes or footnotes but indicate where the reference goes using a superscript in the text
1
. DO NOT USE WEBSITES AS REFERENCES. The internet can be used as a search engine to locate primary sources, but that is all. Also, your BSC lab manual is NOT a reference.
Books should use the format :
Author (Last name, Intials; separate with semicolon if more than 1). Title (in italics);
Publisher: City, year.
Example:
1 Anthony, S; Brauch, T. W.; Longley, E. J. What Should We Do About Global
Warming?
; Wiley: New York, 1998.
Journal:
Author (same as above). Journal name(abbreviated and in italics) . Year (bold) , volume, page.
Example:
Porter, D. J.; Stewart, A. T.; Wigal, C. T. J. Chem. Educ . 1995 , 72, 1039.
Project write-up due by 10:40 am on :
Project 1: October 1 st
(30 pts.)
Project 2: October 15 th
(30 pts.)
Project 3: November 12 th
(30 pts.)
Project 4: December 3 (30 pts.)
Prelab exercises are worth 3 pts. each week for a total of 30 pts.
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Adapted from:
Extraction: “An Integrated Extraction/Crystallization/Distillation Experiment” Amsterdamsky, Claude.
J. Chem. Educ. 1998, 75 , 219-220.
Melting Point: “Identification of Unknowns by Melting Point and Thin-layer Cromatography in
Combination” Levine, S. G. J. Chem. Educ.
1990 , 67, 972.
TOC: pg 56-132 and 153-162
Objectives:
In this lab, you will separate the components of a mixture. The mixture contains an acidic and two neutral compounds. In the process, you will learn how to perform the following techniques:
1) acid-base extraction
2) distillation (simple and fractional)
3) crystallization
4) melting point determination
5) thin-layer chromatography (TLC).
Outcome:
At the end of this lab, you should have:
1) separated, regenerated, and purified the acidic component
2) separated the two neutral components using distillation
3) determined the melting point and R f
values of several standards
4) identified the acidic compound and another unknown using the information collected from the standards.
Introduction:
The basic laboratory techniques of extraction and distillation will be used to separate three substances from a mixture. An acidic substance will be separated from the two neutral components by an acid-base extraction. The two remaining substances will be separated by distillation. Crystallization will be used to purify the acidic component.
The mixture that you will separate contains:
COOH CH
3 the acid component 2,2,4- trimethylpentane toluene.
MW: 122.12 Density: 0.692 Density: 0.865
MW: 114.23 MW: 92.14
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How can extraction and crystallization be used to accomplish the goal of this project?
First, let's examine the principle that applies in acid-base extractions. Extractions involve the partitioning of substances between two different solvent layers. Usually one of the solvents is water (aqueous) and the other is organic. All three components are organic compounds and will dissolve in the organic layer, not the water layer. Therefore, to affect the separation, one substance must have its solubility altered, allowing it to be
"extracted" into the water layer. In this experiment, the acidic compound will be extracted using a base, sodium bicarbonate (NaHCO
3
), which neutralizes the acidic compound and produces two by-products. As a base, sodium bicarbonate will accept a proton, H
+
, from the acidic compound. The acidic substance forms the conjugate base, which is soluble in water. The insoluble acidic form of the conjugate base must be regenerated to complete the separation.
COOH
OH
COO
-
Na
+
+
C O
O
-
Na
+
+ 2 by-products
Acidic unknown NaHCO
3
conjugate base
The extraction process can be easily understood using a flow chart. Construct a flow chart that allows you to extract and regenerate the acidic compound from the mixture. While constructing the flow chart, you should also calculate the number of grams of sodium bicarbonate needed to form a 1:1 molar ratio to the 0.15 g of the acidic compound. Your sodium bicarbonate solution should be a 10% by mass sodium bicarbonate in water. (Density of water is 1 g/mL.)
FLOW CHART:
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Crystallization is a technique used to purify crude products. The steps of crystallization are choosing a solvent, dissolving the crude solute in a minimum of hot solvent, filtering out any solid impurities, crystallizing the solute, collecting and washing the crystals, and drying the crystals. The crude acidic compound obtained in the extraction will be dissolved in a minimum of hot solvent. The solvent used during crystallization should be similar in polarity to the solute, because like solvents dissolve like solutes. If any solid impurities are present in the hot, saturated solution, they can be removed by filtration. Crystallization is an efficient purification technique because soluble impurities remain in solution owing to the fact that they are not present in large enough concentrations to crystallize. The crude solute is present in large concentration and will readily crystallize out of solution, leaving behind any impurities. Crystallization must have a nucleus, any rough surface, on which crystal formation can begin. The nucleus can be a speck of dust, a scratch on the inside glass of the container, or a seed crystal. The crystals can be collected by vacuum filtration on a Hirsch funnel apparatus
(see figure in the experimental section for this project, week 1). Pipette filtration can also be used and, upon request, will be demonstrated by a TA. Washing the crystals with icecold solvent will remove any impurities from the surface of the crystals. The crystals are dried under vacuum while they are on the Hirsch funnel and can be dried further by squeezing them between sheets of paper towel.
Pre-lab Questions- Week 1:
1. How can the protonated acid be regenerated from the deprotonated product obtained from the extraction?
2. What is the purpose of the sodium bicarbonate in the extraction?
3. Look at the reaction using NaHCO
3
. What are the two by-products and how can you tell if the substrates are reacting?
4. Why is it necessary to crystallize the acidic compound after it has precipitated out of solution?
5. How many milliliters of boiling water are needed to dissolve 25g of the acid component? If the solution were cooled to 14 °C, how many grams of acid component would crystallize out? (Solubility of the acid in water is 69g/L at 100 ºC; 2.2g/L at 14°C)
Week 2
Distillation is a procedure used to separate substances with different boiling points. There are two types of distillation, simple and fractional (see figure in the experimental section, week 2). Simple distillation is a procedure used to determine a rough estimate of a substance's boiling point and to separate two compounds with substantially different boiling points. Fractional distillation involves a long column and a packing material (in our case, copper sponge), both of which allow for a larger surface
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area. In both methods, a liquid is heated until each component is converted to vapor.
The vapor travels through the apparatus and is condensed back into liquid form. As the surface area of the packing material increases, a heat exchange between the ascending vapor and the descending condensed liquid occurs and approaches equilibrium. In fractional distillations, the successive evaporations and condensations that occur when the vapor to liquid heat exchange is in equilibrium allow a better separation than in a simple distillation, but less material is often collected. To avoid heat loss and to maintain adiabatic conditions, the column should be insulated with glass wool.
Percent recovery allows you to obtain data on how much starting material you lost and how much you recovered during a separation or purification procedure.
Amount of Recovered Material

100 = Percent recovery
Amount of Starting Material
Pre-lab Questions- Week 2:
1. Predict in which order the two neutral components from week 1 will distill? Give reasons for your predictions?
2. Why is the collection flask immersed in an ice bath?
3. Refluxing is a common laboratory technique in which a reaction mixture is heated in an apparatus with an air- or water-cooled condenser. What purpose could this procedure serve?
4. Why does a fractional distillation of the same substance mixture take longer than a simple distillation?
5. What are the advantages and disadvantages of fractional versus simple distillation?
Week 3
Melting point is the temperature at which a crystalline substance melts into a liquid. Melting point determination is used in combination with other identification tools to properly identify an unknown substance. The temperature of the liquid formed by melting crystals does not change until all of the crystals have melted. This period of constant temperature is known as a phase change and is reported as the melting point.
The melting point of a substance is often reported as a temperature range. The first temperature is recorded at the point the initial liquid is observed, and the second temperature is recorded when all the solid has been converted to liquid. A smaller temperature range usually indicates a purer sample. Impurities on the crystals affect the melting point because they interfere with the melting process. When doing a melting
8

point determination, it is usually quicker if a rough melting point determination is done first. A rough melting point determination is achieved by heating the sample at a fast rate. This will provide you with a temperature range in which the melting occurred. You should then heat a new sample at a slower rate (4

C a minute) to determine a more accurate melting point.
Thin-layer chromatography (TLC) is a technique that is used to determine the purity of a solid. TLC requires plates or thin sheets that are coated with a thin layer of an adsorbent, most often silica gel. The adsorbent allows the solvent to migrate up the plate, along with the substance(s) contained in the sample. The silica gel serves as the stationary phase and is strongly polar and binds polar substances. The more polar a substance is, the slower it migrates along the plate. The mobile phase, the elution solvent, moves the substance(s) up the plate. The polarity of the solvent affects the migration of the substance upward along the plate, the more polar it is the farther the substance(s) move up the plate. Thin-layer chromatography can be used to obtain the R f value of a substance. This is the ratio of the distance the sample spot travels from the starting point to the distance that the solvent front travels from the starting point.
R f
=
distance compound spot travels
distance solvent front travels
Pre-lab Questions- Week 3
1. Why should you use melting point and TLC data in combination to identify an unknown?
2. Why would you get a melting point below or above the known standard for a substance?
3. If two substances, A and B, are in a TLC sample, with A being more polar than B, what is the relationship between their R f
values?
4. If a solvent is relatively polar, how will that affect the migration of a polar substance in comparison to the effect that a relatively non-polar solvent would have on the polar substance?
5. Why is an R f
value reported instead of the spot migration distance?
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Experimental:
Week 1:
Extraction and Crystallization of Unknown Acidic Substance:
Vacuum Filtration Apparatus:
H i r s c h F u n n e l
F i l t r a t i o n
F l a s k
T u b i n g
T o V a c u u m
Procedures:
You will be given 5mL of a mixture that contains an acidic substance (0.15 g) and two neutral substances. Place the 5mL of the mixture into a white-capped centrifuge tube, along with the appropriate amount of sodium bicarbonate solution. Use your flow chart and the information provided in the pre-lab to make up the sodium bicarbonate solution and to determine a protocol for the extraction of the acidic compound. During the extraction, invert the tube to thoroughly mix the solutions. Remember to vent the tube by removing the cap in between inversions. Allow the layers to separate, then remove the aqueous layer with a pipette and transfer it to an Erlenmeyer flask. Leave the organic layer in the centrifuge tube, add CaCl
2
pellets, then seal the tube and save for
Week 2. Carry out the regeneration procedure during which the acidic compound should precipitate out of solution and should be collected using a Hirsch funnel. To crystallize the acidic compound dissolve it in a minimum of hot water. A boiling stick should be used while heating the mixture to prevent superheating. A boiling stick is easier to remove before crystallization than a boiling chip. The mixture is then allowed to slowly cool to room temperature before being placed in an ice bath. The key to obtaining large, well-formed crystals is a slow cooling process. Crystals can be collected by vacuum
10

filtration using an apparatus that is composed of a Hirsch funnel and a filtration flask.
The crystalline product should be saved for identification in Week 3.
Week 2:
Separation of Two Neutral Substances by Distillation:
Simple Distillation Apparatus:
Procedures:
Working with a partner, combine your non-aqueous layer. Set up a simple distillation apparatus like the one shown above. Place 4 mL (or half – whichever is less) of your non-aqueous layer (measure and record the volume from Week 1) into a longnecked, round bottomed flask with a boiling chip. Devise a way to graph the temperature versus volume profile. A boiling chip should always be used when the substance is being heated to avoid superheating. The mixture should be heated using a sand bath. If the mixture begins to boil violently, it should be removed from the sand bath, or if it is heating too slowly, the sand should be stirred to evenly distribute the heat throughout the sand. Heat the solution in the sand bath and record the boiling points of the two liquids.
The temperature should remain constant at a substance's boiling point and then rise at a constant rate until the other substance's boiling point is attained. The collection flask should be surrounded by ice water in a beaker, and the thermometer bulb should be
11

slightly below the distilling arm. Collect the liquids in three separate collection flasks, based on temperature, and save all of your fractions. Do not distill all the liquid from the flask in order to avoid accidents! If the temperature rises above 120°C, remove the flask from the sand bath. Determine the total percent recovery.
Fractional Distillation Apparatus:
Thermometer
Distilling Head
Copper
Sponge
Column
Short-necked
flask
Erlenmeyer flask
Beaker
Sand
Bath
Set up a fractional distillation apparatus like the one shown above. Place the remaining half of the non-aqueous layer from Week 1 into a short-necked, round-bottomed flask with a boiling chip. The column in fractional distillations can be insulated with glass wool to avoid heat loss and speed up the distillation process. Heat the solution in the sand bath and graph the temperature versus volume as you did in the simple distillation.
Collect the liquids in three separate flasks and determine the total percent recovery. Save all three fractions. Then use the volume versus temperature data from both distillations to determine which method gives a better separation, simple or fractional distillation.
Week 3:
Identification of Acidic Unknown Using Melting Point and Thin-Layer
Chromatography:
Procedures:
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Get into groups of four. Weigh out 10-15 mg of each of the following: biphenyl,
2,5-dimethylphenol, acenaphthene, mtoluamide, methyl 4-nitrobenzoate, benzoic acid, trans -stilbene, and succinimide. Perform melting points on each of these standards and your unknown acidic compound from week one. Record them in the provided table and in a table in your notebook. When obtaining a substance's melting point, a few crystals should be placed in a melting point tube and forced to the closed end of the tube by repeatedly tapping on a hard surface. A Mel-Temp apparatus is used in the melting point determination. The temperature should be increased in small increments by slowly turning up the knob so that an accurate melting point can be obtained. To observe the crystals melting, look through the lens piece and watch for the melting of the crystals.
Record the melting point range for each compound.
Dissolve the remainder of each standard in 1mL of dichloromethane and place a small amount onto the starting line of the silica gel plate using a capillary tube. Perform
TLC procedure, using 5% ethanol in hexane as the eluent, on all 8 standards and record the R f
values in the provided table and in a table in your notebook. The starting point should be marked before the sample is placed on the plate. The starting line is made by gently drawing a line about 2-3cm above the bottom of the plate with a pencil. Care should be taken when drawing the starting line to avoid scraping off the silica gel. The starting line should be above the solvent level in the TLC jar to avoid the spreading of the substances. The sample is placed on the silica plate using a capillary tube and should be placed directly on the starting line in as small a spot as possible. The plates should be placed in a TLC chamber one at a time, but each plate can have two labeled spots on it.
The TLC chamber should contain a piece of filter paper to ensure that the atmosphere is saturated with solvent vapors. The plate should be removed from the jar before the solvent front reaches the top of the silica plate, and after the plate is removed from the jar, the solvent front should be marked with a pencil before it disappears due to evaporation. The plate can then be placed under UV light and the spots of the different substances should be visible. Circle the spots with a pencil and measure their migration distance from the center of the spot to the starting line. Using the table you have constructed, determine the identity of each of the individual unknown crystals from Week
1 and the unknown provided by the T.A.
Silica Gel Plate Thin-Layer Chromatography Jar
Solvent front
Distance solvent front migrated
Distance spot migrated
Starting line
Solvent front
Solvent
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methyl 4-nitrobenzoate benzoic acid trans -stilbene
Succinimide
Unknown
Melting Point and TLC Table:
Biphenyl
2,5-dimethylphenol
Acenaphthene mtoluamide
Melting Point (°C) R f
Value
14

Adapted from:
GC: Yang, M. J.; Orton, M. L.; Pawliszyn, J. “Quantitative Determination of Caffeine in Beverages
Using a Combined SPME-GC/MS Method” J. Chem. Educ.
1997 , 74, 1130-1132.
CC: Taber, D. F.; Hoerrner, R. S. “Column Chromatography” J. Chem. Educ.
1991 , 68, 73.
TOC: 163-193
Objectives:
In this lab, you will be isolating and analyzing caffeine using the following techniques:
1) thin-layer chromatography
2) column chromatography
3) gas chromatography
Outcomes:
At the end of this lab, you should have isolated caffeine and determined its retention time. You also should have determined the relative amounts of caffeine in three over-the-counter medications.
Introduction:
In this lab, you will be using thin-layer and column chromatography to isolate caffeine from a sample. Gas chromatography will then be used to analyze the relative caffeine content of three over-the counter medications. Thin-layer chromatography has been described in the previous lab. The three major variables that must be considered in both TLC and column chromatography are the polarity of the solvent, the polarity of the solute, and the nature of the adsorbent. Column chromatography can be used to separate different fractions that are present in a mixture based on their polarities. The major difference is that column chromatography allows you to isolate components of a mixture
(preparative technique). As in TLC, the polarity of both the solutes and the solvents play a role in the separation of a mixture. If you are eluting the column with solvents that are increasingly polar, then the last fraction you collect will contain the most polar solute.
Gas chromatography (GC), also known as gas-liquid chromatography, is used to separate volatile organic substances. It is a quick and easy method to qualitatively and quantitatively analyze mixtures. The technique is very sensitive allowing the detection of even trace amounts of substances in complex mixtures. Because of this, very dilute solutions are used in the analysis. This quality makes them useful in arson investigations, because trace amounts of accelerants and flammables can be detected in or on materials from fire scenes. The same applies for detecting various drugs in urine analysis. In gasliquid chromatography the stationary phase is a non-volatile, high boiling liquid. The
15

mobile phase is an inert gas like nitrogen or helium. The instrument you will be using is equipped with a capillary column. In this capillary column, a thin layer of fused silica on the inside of the column is coated with a high boiling liquid that serves as the stationary phase. Three main variables affect the separation: the column temperature, the nature of the stationary phase, and the nitrogen flow rate. When conducting a GC analysis, a syringe is used to deliver the sample into the injector, which is at high temperature, quickly vaporizing the sample. The carrier gas (nitrogen) moves the sample through the column, which is kept at a preset temperature in a thermostated oven. The components of the sample mixture condense and vaporize as they move through the column. In this process they are partitioned between the gas and liquid phase. The substances continue this pattern until they reach the flame-ionization detector (FID). The detector has a flame, which uses air and hydrogen gas as fuel, which burns the components as they exit the column. When the substances are burned, they produce ions, which can be detected.
The integrator records the peaks and retention time of each substance onto a graph. The retention time is the time it took the substance to travel through the column. A component should have the same retention time for every run provided that the settings of the instrument are not changed. The integrator also determines the relative concentrations
(peak areas) of each substance in the sample. The peak area is proportional to the amount of that substance in the sample.
Caffeine is a component of food, drinks, and analgesics. It is a stimulant that increases respiration, heart rate, and affects the central nervous system. The effects of this on the body may cause nervousness, insomnia, and addiction. Caffeine is also a diuretic, a substance that increases the excretion of water and results in frequent urination. Pure caffeine in large quantities is toxic. Caffeine is an alkaloid, a class of compounds that also includes cocaine, morphine, and strychnine.
Caffeine:
O
CH
3
CH
3
N
N
O
N
N
CH
3
Pre-lab Questions- Week 4:
1. How does increased oven temperature affect how quickly a substance moves through the GC column. How does that affect the efficiency of separation?
2. Why would you want to avoid air pockets in the adsorbent in column chromatography?
3. Based on its structure, do you believe caffeine is relatively polar or non-polar?
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Experimental:
Week 4:
Analysis of Caffeine Content of Various Over-the-Counter Medications:
Procedures:
Students, in groups of four, should obtain the pills and, if necessary, remove the plastic coating from the capsules. The samples should then be ground up into a fine powder using a mortar and pestle. 10 mg of each powdered sample should be dissolved in 2 mL of dichloromethane. If there is any undissolved solid, filter before proceeding.
When you are using the gas chromatograph, the samples should be extremely dilute due to the sensitivity of the instrument. The remainder of each sample should be saved in a closed container. A gas chromatographic analysis should be done on each sample. The syringes are fragile and should be inserted and removed carefully. The needle of the syringe will usually hold enough of the sample to obtain an adequate reading. The sample should be drawn into the syringe and expelled a few times. The needle is inserted into the injector port and left for about five seconds, during which time the sample is vaporized due to the high temperature of the injector. Be sure that you do not touch the surfaces near the injector because they are very hot. The sample is carried by nitrogen gas through the column. The fractions reach the detector at different times. The peaks on the chart represent the different components and a retention time is recorded for each.
The area under a peak represents the relative concentration of that component in the sample.
A TLC should be performed on the medication sample labeled C using 75% ethyl acetate/25% dichloromethane as the eluent. Students should begin discussing a protocol to determine which peak on the chromatogram is caffeine and which sample contains the greatest amount of caffeine.
Pre-lab Questions-Week 5:
1. Devise a method to determine which peak on the GC chart (chromatogram) was caffeine.
2. Devise a way to separate the major components of one of the over-the-counter medications you will obtain from the TA. What techniques might you use to identify which component is caffeine?
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Week 5:
Procedure:
Inform your T.A. of the protocol your group designed from your pre-lab exercise.
If your protocol is feasible, you will be given a handout of the procedure. Which sample,
A or B, contains the most caffeine? What is the retention time of caffeine?
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13
Adapted from:
“Reeves, P. C.; Chaney, C. P. "A Strategy for Incorporating 13 C NMR into the Organic
Chemistry Lecture and Laboratory Courses." J. Chem. Educ.
, 1998 , 75 , 1006.
TOC: 224-232 and 270-277
Objective:
In this lab, you will learn how to run an NMR experiment, analyze NMR spectra, make predictions about NMR spectra, and match compounds with their spectra.
Outcome:
At the end of this lab, you should have:
1) made predictions about the fourteen
13
C NMR spectra
2) obtained and processed the
13
C NMR spectra of the samples
3) matched the actual fourteen spectra with the given structures
4) compared your predictions with the actual spectra.
Introduction:
In lab, you will use 13 C nuclear magnetic resonance (NMR) spectroscopy to identify different alkanes and alkyl halides.
13
C NMR spectroscopy allows you to determine the kind, location, and number of non-equivalent carbon atoms in a molecule.
NMR spectrometers detect nuclei that generate a magnetic field when they spin. The spinning nuclei behave like a bar magnet, and when placed in the presence of an external field, a super-conducting magnet, they will align with (parallel) or against (antiparallel) the external field. The parallel orientation is lower in energy than the antiparallel orientation by an amount that depends on the strength of the external magnetic field. The
13
C nucleus has the ability to generate a magnetic field when it spins;
12
C nuclei do not.
13
C isotopes occur at an abundance of about 1 in every 100 (1.1%) in an organic sample.
The 13 C nucleus will spin-flip when exposed to a radio wave frequency that is equal to the energy needed to flip the nucleus from the alpha (parallel) to the beta (antiparallel) spin. When a nucleus spin-flips it is said to be in resonance. The amount of energy released when the nucleus returns to the alpha state is recorded by the instrument.
The chemical environment of a nucleus plays a major role in determining when a nucleus will come into resonance. The denser the electron cloud around a nucleus, the less the nucleus feels the applied force of the magnet because the electrons shield the nucleus from the applied field. The electrons’ shielding effect can be thought of as H local
, the field applied to the nucleus as H applied
, and the field felt by the nucleus as H effective
as shown in the equation below.
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H effective
= H applied
- H local
The chemical shift of the carbon resonance depends on how the atoms around it affect the density of its electron cloud. If the
13
C is in the presence of electronegative atoms, its electron cloud is less dense, or its nucleus is deshielded. Deshielding of the nucleus occurs because the electronegative atoms pull the electron density away from the
13
C nucleus. The more deshielded a nucleus is the more downfield its resonance will occur. The density of the electron cloud is also affected by the number of carbons attached to the
13
C nucleus. If there is only one carbon attached to the
13
C nucleus then it is called a methyl carbon. If there are two carbon atoms and two hydrogen atoms attached to the
13
C nucleus, then it is referred to as a methylene carbon, and if there are three carbons and one hydrogen attached to the 13 C nucleus, it is called a methine carbon.
A methine carbon nucleus is more deshielded than a methylene carbon nucleus because carbon atoms are more electronegative than hydrogen atoms. The electron cloud is also affected by the hybridization of the atom. If the atom is sp 2 or sp hybridized, the electron cloud is less dense because the electrons are being shared in the bonds. The calibration peak is the resonance signal for the solvent, and will occur at 77.16 ppm for your solvent, d-chloroform (CDCl
3
).
You will be performing a DEPT
13
C NMR experiment, which allows you to distinguish between methyl carbons, methylene carbons, and methine carbons.
Quarternary carbon atoms, which have four other carbons attached to them do not show up in this experiment. The methyl carbon and methine carbon resonances are located above the baseline, and the methylene carbon resonances are located below the baseline.
If an atom is not sp
3
hybridized, its resonance will occur above the baseline regardless of the number of hydrogens attached.
20

The structures of the fourteen compounds you will be using are shown below:
Cl
Cl
CH
3
Cl
CH
3
CH
3
1-chlorobutane 2-chlorobutane 2-chloro-2-methylpropane
Br
Br
CH
3
Br
CH
3 CH
3
1-bromobutane 2-bromobutane 2-bromo-2-methylpropane heptane 2-methylhexane 3-methylhexane
2,2-dimethylpentane 2,3-dimethylpentane 2,4-dimethylpentane
3,3-dimethylpentane 2,2,3-trimethylbutane
21

Pre-lab Questions-Week 6
1. Look at the structure and the DEPT 135 13 C spectrum shown below and match, the best you can, each resonance with a carbon in the given structure. Identify the solvent peak.
Experimental:
Week 6:
Analysis of
13
C Spectra:
Each lab section must complete this exercise as a group. In groups of two, prepare and run the spectra such that section as a whole will obtain the data. As a group, you must decide how to divide up the samples. After the spectra are obtained, the section should assign the identity of each sample based on the predictions and the experimental 13 C
NMR results.
You will obtain the samples from the TA’s.
22

Procedures:

Login window: Login - organic Password - $organic

Toolbar: single click the blue delta symbol with orbiting electron, this should open the control window

Control Window: single click on the magnet icon that is just to the left of the question mark icon, this should open the spectrometer control window

Spectrometer Control Window: wait for the instrument to connect automatically and then single click the Auto button, this should open the automation window

Automation Window:
Filename : Enter the filename (which cannot include spaces, hyphens, or
backslashes)
Comment : Enter a comment (can include anything)
Slot : Enter the slot number that your sample is in
Export to : Enter your BSC webmail address
-Single click on the appropriate experiment (for this lab- Carbon and DEPT
135)

To access your spectra, login to your BSC webmail account
-Save your spectra to the Organic lab folder on the network that corresponds to your lab section

To manipulate the spectra using the Delta software on the computer:
-Go to the organic lab data folder for your section on the Network, highlight the desired files, right click using the mouse and then choose copy from the menu that appears
-Open the organic lab data folder for your section on the desktop and right click and choose paste from the menu that appears
-Open the Delta software and select the heading Processors and then choose
the subheading Process 1D, and a new 1D window should appear
23

-From the new window click File , then Open Clear , and another new window
should appear on the screen
-In the white box, located below the Favorites box, click on the double dots
and continue to click on the double dots until Desktop appears as a choice listed
beneath the dots
-Click on Desktop and then choose the organic lab data desktop folder for
your section
-Select the desired spectra file and choose OK, then the window should close and
the 1D Processor window will display the desired FID
-In order to process the spectra, select the icon of a floppy disk with an arrow
pointing towards the process button, then select either carbon or proton
from the new window and press OK , then click the Process button, located in
the top right hand corner of the window

Your processed spectrum should then appear and you can manipulate it, as needed using the Delta software. The following are a few tools you can use.
-
-
-
Zoom: ( allows you to zoom in on desired area or peak)
Integration: ( located under the Integral category)
Peak Pick: (allows you to determine the exact location of a peak)
Y Gain: (increases peak height)
-
Print: (a print icon is located in the top row of icons and each time it is pressed one spectra is printed without an OK window appearing)
To obtain a digital copy of the spectra for use in your report, use the Print option
24

N
N
adapted from: Williamson, K.L. Macroscale and Microscale Organic Experiments, Houghton Mifflin Co.,
Boston, 1999.
TOC: none
Objective:
The objective of this lab is to facilitate your understanding of the mechanisms and characteristics of the S
N
2 and S
N
1 reaction. You will also experimentally determine the reaction order for one of the mechanisms.
Outcome:
During this lab, you will observe substitution reactions that vary in their mechanism and order. You will use the information that you gather and the NMR data from last week’s lab to:
1) determine how degree of substitution and nature of the leaving group affect the rate of the two substitution reactions
2) determine the reaction order of one of the substitution reactions mechanisms.
3) match the structures of the substrates A-F with their 13 C NMR spectra.
The substrates you will be using are:
Br
Br
Br
1-bromobutane 2-bromobutane 2-bromo-2-methylpropane
Cl
Cl
Cl
1-chlorobutane 2-chlorobutane 2-chloro-2-methylpropane
The substrates react at different rates based on degree of substitution and the nature of the leaving group.
25

S
N
2 Reaction:
Rate = k [Nucleophile] [Substrate]
S
N
2 and S
N
1 reactions are both substitution reactions that involve a nucleophile attacking a substrate, but they have different characteristics. S
N
2 reactions are second order. The rate of an S
N
2 reaction is dependent on the concentrations of both the nucleophile and the substrate. An S
N
2 reaction undergoes an inversion of configuration since the nucleophile always attacks on the opposite side of the leaving group. It always produces an inverted product because it has no intermediate. S
N
2 reactions are favored on substrates with less substitution, polar aprotic solvents, leaving groups that are capable of stabilizing a negative charge (weak bases), and good nucleophiles. The solvent can greatly affect the rate of an S
N
2 reaction. A protic solvent can form a solvent cage around the nucleophile thereby decreasing its nucleophilicity by sterically hindering its approach to the substrate. In contrast, a polar aprotic solvent will not impede the attack of the nucleophile. The solvent in this case forms a cage around the nucleophile’s counter ion making the nucleophile more reactive.
S
N
1 Reaction:
Rate = k [substrate]
26

S
N
1 reactions occur in two steps. They are first order reactions because the rate of the reaction only depends on the concentration of the substrate. The nucleophile has no effect on the rate of an S
N
1 reaction since it is not involved in the rate-determining step.
The spontaneous formation of a planar carbocation is the rate-determining step. In order for the carbocation to form, the leaving group must be able to stabilize a negative charge.
In S
N
1 reactions, rearrangements may occur in order to form the most stable carbocation intermediate. S
N
1 reactions favor more highly substituted substrates, polar protic solvents, and leaving groups that can easily stabilize a negative charge (weak base).
Polar protic solvents increase the rate of an S
N
1 reaction by stabilizing the carbocation intermediate, which decreases the activation energy of the reaction. S
N
1 reactions can undergo both inversion and retention of the substrate’s stereochemistry. This leads to two possible products, with the inverted form usually being slightly more favored. The S
N
1 reaction that you will perform will only consist of the rate-determining step.
Be Sure To Bring A Stop Watch or A Watch With a Second Hand To Lab With
You.
Pre-lab Questions- Week 7:
1. Why can S
N
1 reactions undergo rearrangements but S
N
2 reactions cannot?
2. Why does the nucleophile have no effect on the rate of an S
N
1 reaction?
3. Why is the inverted product usually the slightly favored (major) product in S
N
1 reactions?
4. Which is a better leaving group, Br or Cl - ?
27

Experimental:
Week 7:
S
N
1 and S
N
2 Reactions:
Silver Nitrate Reaction:
Ag
+
NO
3
-
+ R X
R
+
+ AgX
Sodium Iodide Reaction:
Na
+
I
-
+ R X R I + NaX
Procedures:
Students should work in groups of two, and each group should place 5 drops of substrates A-F into separate reaction tubes. Substrates A-C have bromide leaving groups, and substrates D-F have chloride leaving groups. Add 1.0 mL of 1 % silver nitrate
(AgNO
3
) in ethanol solution to each tube, and watch for the reaction to occur, which is indicated by the precipitation of the silver salt. Repeat the procedure with 0.5 mL of each substrate in separate tubes using a saturated solution of 18 % sodium iodide (NaI) in acetone in place of the AgNO
3
solution. (Hint: It is easier to obtain more accurate data if you do one reaction at a time.) You should assume that a reaction has occurred when a precipitate is observed. Color changes do not indicate that a reaction has occurred but increased cloudiness does. Record the time it takes for the first change to appear. Watch for the first sign of precipitation and record the time. If no change occurs within one minute, place the reaction tube in a 40 ºC to 45 ºC water bath (hot water from the tap is about 45 ºC). It is important that you do not allow your water bath temperature to rise above 45ºC. Acetone boils just above this temperature causing the NaI to precipitate out, producing a false positive.
28

Pre-lab Question- Week 8:
1) Devise a way to determine the reaction order with the sodium iodide reagent.
2) Devise a way to determine the identity of substrates A-F using the data collected.
Week 8:
Determining the Order of the Sodium Iodide Reaction:
Procedures:
In this lab, you should gather enough evidence using your protocol to determine the reaction order with the sodium iodide reagent. After you have determined the order of the reaction, you should use your NMR data from Week 6 and your data from this project to match the substrate structures with the corresponding letter A-F. You should use your NMR spectra to determine whether there is a correlation between the electronegativity of the leaving group and its reactivity towards nucleophilic substitution.
Your written report should discuss this topic.
Procedures- Bromination of Cinnamic Acid :
Students should work in groups of two for this lab. Each group should obtain the
10 M bromine/chloroform solution from the T.A. and should place it under the hood.
Bromine is highly toxic, so students should wear gloves and use the hoods when handling bromine and bromine solutions.
Place 1.25 g of trans -cinnamic acid and a magnetic stir bar in a 25 mL Erlenmeyer flask, and then place the flask in a hot water bath on a magnetic hot-plate (set heat to about 1 and stir to about 2.) The trans -cinnamic acid should be dissolved in a minimum of chloroform, which is slowly added to the flask.
After the trans -cinnamic acid is completely dissolved, the flask should be removed from the water bath, and 0.9 mL of the bromine solution should be added slowly to the flask.
(If a solid begins to appear in the trans -cinnamic acid/chloroform solution as soon as it is removed from the heat, more chloroform should be added or if crystals form before the bromine solution is added, the flask should be heated slightly to dissolve the crystals and more chloroform should be added.) The bromine color should slowly disappear, and a white solid should begin to form. The solution should be stirred for 10-15 minutes (on a cool stir-plate) at room temperature during which time more white solid should appear.
Next, the flask should be placed in an ice-salt bath until crystallization is complete (about
5 minutes.) The resulting dibromide should be filtered using a Hirsch funnel, washed
29

with a few milliliters of pre-cooled chloroform, and dried for 5-7 minutes. If you wish to confirm that you have the correct starting material for the next reactions, you may run a
1 H-NMR (the T.A. will have a copy of what the spectra should look like) and/or determine the melting point of the product (the melting point should be around 204

C.)
Save the crystals in an appropriate container until next week.
30

TOC: none
Objectives:
In this lab, you will be carrying out elimination reactions in order to determine the structure of the major and minor products of the reactions.
Using the background information:
1) predict the product(s) and ratio based on the mechanisms
2) match to the experimental resuts
Outcomes:
At the end of this lab, you should have completed the following:
1) made a prediction about the major and minor products of the reactions
2) analyzed the product(s) using the NMR spectrometer and GC
3) determined what the product(s) of the reactions are and major/minor products if applicable
Introduction:
In this lab, you will be performing elimination reactions on brominated trans cinnamic acid and predicting the product of both reactions. You will confirm your predictions using GC analysis of your product.
COOH
Trans-Cinnamic Acid
E2 reactions have three necessary components: a Lewis base, a substrate with a carbon bearing a leaving group, and an adjacent carbon bearing a hydrogen atom. E2 reactions are one-step reactions that exhibit second order kinetics. Polar aprotic solvents and more substituted alkene transition states are favored in E2 reactions. The E2 reaction is stereo-specific requiring that the leaving group and the proton being removed have anti-periplanar stereochemistry. The alkene product of the reaction is usually determined by the degree of alkene stability: Saytzeff’s rule states that the more highly substituted alkene is usually the major product. The base used in the reaction affects the product
31

that is formed. If the base is bulky or the proton to be removed is sterically hindered, then the less substituted alkene could possibly be formed. The base is directly involved in the rate-determining step; it initiates the reaction by removing the proton antiperiplanar to the leaving group. The reaction rate can be manipulated by changing either the strength or the concentration of the base.
B
H
R R
R R
X
E2 reaction anti-periplanar stereochemistry
E1 reactions are favored in polar protic solvents, in the absence of a strong base or a good nucleophile, and good leaving groups. If a strong base and a good nucleophile are present, then a S
N
2 reaction or an E2 reaction will occur. S
N
1 and E1 reactions both exhibit first order kinetics and go through the same rate-limiting transition state; therefore, S
N
1 and E1 reactions occur simultaneously. During the transition state, a carbocation forms from the spontaneous cleavage of a leaving group. Due to the carbocation intermediate, S
N
1and E1 reactions favor molecules that have a higher degree of substitution (tertiary>secondary>primary.) The rate of an E1 reaction is determined by the events that take place in the rate-determining step. The spontaneous cleavage of the leaving group is the only event that occurs during the rate-determining step, and therefore the better the leaving group, the faster the reaction. The rate of the reaction can also be manipulated by changing the degree of substitution of the carbocation intermediate. The more stable the carbocation intermediate is, the easier it forms, and the faster the E1 reaction will be. The base/nucleophile is not involved in the rate-determining step, so changing it has no affect on the rate of the reaction (although, increasing the strength of the base makes an E2 reaction more likely.) The carbocation intermediate can undergo rearrangements to achieve the most substituted and stable configuration. The mechanisms of a S
N
1 reaction and an E1 reaction are identical up to the formation of the carbocation intermediate; afterwards the reactions undergo different mechanisms. In the E1 reaction, a base removes a proton bonded to a carbon adjacent to the positively charged carbon (a proton that is beta to the leaving group), which forms a double bond. Due to the
32

reactivity of the carbocation species, a base/nucleophile can remove the beta hydrogen in the E1 reaction. An S
N
1and E1 mechanism is shown on the next page.
E1/ S
N
1 Mechanism
B
-
H
+
+
BH
E
1
Mechanism
H
Br
+
Carbocation
Intermediate
H
+
B
-
H
B
Sn
1
Mechanism
When a double bond is added to a molecule, the molecule can no longer rotate freely about that particular bond. The rotational hindrance creates geometrical isomers known as E and Z. The substituents at each carbon of the double bond are ordered according to priority according to atomic number. The Z isomer is analogous to a cis - isomer in that both of the high priority substituents are located on the same side of the double bond. The E isomer, being analogous to a trans - isomer, has the two high priority substituents on opposite sides of the double bond.
33

Pre-lab Questions - Week 9:
1) Write a balanced equation for the bromination of trans -cinnamic acid.
2) What observation(s) confirm(s) that bromine reacted with the starting material?
Experiment:
Week 9:
Decarboxylative Elimination:
Each group should perform the elimination reaction in both butanone and then water.
Elimination in Butanone-
Place 3.75 mL of butanone in a long-necked round-bottomed flask, add 0.25 g of anhydrous potassium carbonate and 0.25 g of the crystalline dibromide product. The solution should be refluxed and magnetically stirred for 1.5 hours and then cooled. The cooled solution should be poured into 2.5 mL of water, extracted with ether (2 x 3.75 mL), and the combined organic layers should be dried using anhydrous magnesium sulfate. The dried solution should then be filtered using a Hirsch funnel ( Do not use a vacuum because it will pull the MgSO
4
into the filtrate ) and the organic solvents should be evaporated. (Hint: The best way to evaporate the organic solvent is to leave the solution in the filter flask and pull the vacuum over it until the ether completely evaporates.) The final product should be a colorless or yellowish oil.
Elimination in Water -
Place 1.0 g of the crystalline dibromide product in a short-necked round- bottomed-flask with several boiling chips and 4.0 mL water and 1 pellet of potassium hydroxide. The mixture should be refluxed for 30 minutes and cooled to room temperature. Extract the yellowish oil from the aqueous layer.
34

Pre-lab Question Week 10
1) Give structures for the two possible geometrical isomers that can be formed in the eliminations.
2) Draw a Newman projection for the brominated trans -cinnamic acid.
Analysis of Products:
Each group should analyze each product using gas chromatography. Based on the
GC chromatogram, determine which reaction was E1 and which was E2. The remaining products should be placed in a reaction tube and dissolved in deuterated chloroform. If the mixture becomes cloudy, add calcium chloride pellets until the solution becomes clear (you may have to mix the solution for a few minutes before it becomes completely clear). Analyze the clear solution using
1
H NMR and determine the structure of each of the products. It is possible to use the NMR sample for the GC analysis also.
35