CHEMISTRY 346
Winter 2012
Honors Organic Laboratory
Professor Paul Hopkins
Department of Chemistry
University of Washington
TABLE OF CONTENTS
Part I:
General Information
Syllabus
Laboratory Report Due Dates
1-3
4
Organic Chemistry Laboratory Safety
5-8
Working with Equipment & Glassware
9-10
Working with Chemicals
Waste Disposal
11-12
13
Chemistry Undergraduate Stockroom
14-16
Laboratory Notebook
17-18
Laboratory Report Format
19-20
Searching the Chemical Literature
21
Rotary Evaporator
22
NMR (DXP-200) Instructions
23-36
FT-IR Instructions
37-40
GC-MS Instructions
41-42
Part II: Experiments
1/3/2012
Experiment 1: Acid Base Extraction, Recrystallization, Melting Point
43-47
Experiment 2: Purification using TLC & Column Chromatography
48-51
Experiment 3: Reactivities of some Alkyl Halides
52-53
Experiment 4: Dehydration of 4-Methylcyclohexan-1-ol
54-55
Experiment 5: Diels-Alder Reaction
56-57
Experiment 6: Grignard Reaction
58-61
Experiment 7: Asymmetric Reduction of Ethyl Acetoacetate
62-71
Experiment 8: Multi-Step Tetraphenylnaphthalene Synthesis
72-75
Part III: Appendices
Experiment 4: 4-Methylcyclohexan-1-ol
A-2
Experiment 5: 3-Sulfolene
A-4
Maleic Anhydride
Experiment 6: Bromobenzene
2-Bromotoluene
Experiment 7: Ethyl acetoacetate
2-Methyoxyphenylacetic acid
Experiment 8: Benzaldehyde
1/3/2012
A-6
A-8
A-10
A-12
A-14
A-16
1,3-Diphenylacetone
A-19
Anthranilic acid
A-21
CHEMISTRY 346
Honors Organic Chemistry Laboratory
Winter 2012 Syllabus
Instructor:
Professor Paul B. Hopkins
Office: BAG 109H; Phone: 206.543.1613
Email: [email protected]
Office hours: Thursdays 2:00-3:00 pm or by appointment
Teaching
Assistants:
Simeon Andrews (Section AA—Lab meets Wed. & Fri., 1:30-4:20 pm, CHB 112)
Office: CHB 428; Phone: 206.616.4269
Email: [email protected]
Office hours: TBD in the Organic Study Center (BAG 331A)
Megan Duda (Section AB—Lab meets Wed. & Fri., 4:30-7:20 pm, CHB 112)
Office: CHB 418; Phone: 206.616.4267
Email: [email protected]
Office hours: TBD in the Organic Study Center (BAG 331A)
Lecture:
Tuesdays 10:30-11:20 am, BAG 261
Laboratory:
Wednesdays and Fridays, 1:30-4:20 pm (AA); 4:30-7:20 pm (AB), CHB 112
Required Text:
Introduction to Organic Laboratory Techniques, A Microscale Approach, Fourth
Edition, Pavia, Lampman, Kriz, and Engel (PLKE). Note: reading assignments
are listed in bold on the class schedule below.
Exams:
Midterm: Tuesday, February 14, 2012
Final: Monday, March 12, 2012, 10:30 am-12:20 pm
Grading:
8 lab reports
Midterm examination
Teaching assistant evaluation
Lab notebook
Final examination
Total Points
Class Schedule
3
January
4
6
10
11
13
17
18
20
24
25
1/3/2012
375
45
25
40
80
565
Lecture: Intro, Acid/Base Extraction (Techniques 1, 5, 6, 8, 10, 12, PLKE)
Lab Check-in
Acid-Base Extraction/Recrystallization/Melting Points (pp. 21-41, PLKE)
Lecture: Recrystallization, Melting Point (Techniques 2, 3, 9, 11, 19, 20, 22, PLKE)
Acid-Base Extraction/Recrystallization/Melting Points (continued)
Thin Layer Chromatography (TLC) and Column Chromatography (pp. 42-50, PLKE)
Lecture: Chromatography, NMR (Techniques 4, 13, 22, PLKE)
TLC and Flash Column Chromatography (continued)
Reactivities of Alkyl Halides (Exp. 20, PLKE)
Lecture: Reaction Methods, Distillation (Techniques 7, 14, 15, PLKE)
Dehydration of 4-Methylcyclohexan-1-ol (Exp. 25, PLKE)
1
February
March
27
31
1
3
7
8
10
14
15
17
21
22
24
28
29
2
6
7
9
12
Diels-Alder Reaction
Lecture: Grignard Reaction
Grignard Reaction
Grignard (continued)
Lecture: Asymmetric Reduction (Technique 25, PLKE)
Grignard (continued) and Asymmetric Reduction
Asymmetric Reduction (continued)
*Midterm Examination*
Asymmetric Reduction (continued)
Asymmetric Reduction (continued)
Lecture: Tetraphenylnapthalene Synthesis (Technique 26, PLKE)
Tetraphenylnaphthalene (Exp. 36A, 36B, 37, PLKE)
Tetraphenylnaphthalene (continued)
Lecture: Mass Spectrometry (Technique 28, PLKE)
Tetraphenylnaphthalene (continued)
Tetraphenylnaphthalene (continued)
Lecture: Miscellaneous
Tetraphenylnaphthalene (continued)
Lab Check-out
*Final Examination*
Course Objectives
1. Learn methods to synthesize, purify, and prove the structures of organic compounds.
2. Learn some of the experimental methods by which the principles of organic chemistry
discussed in CHEM 335, 336, and 337 were discovered, and remain useful, in current
research.
3. Improve your ability to communicate concisely and clearly in writing.
Pre-Lab Write-Up
Prior to beginning an experiment, you must complete a pre-lab write-up in your lab notebook.
A neatly-handwritten pre-lab is preferable to a typed version. A photocopy of the notebook page
containing this pre-lab should be handed in to your TA prior to the beginning of the lab.
The pre-lab should include, in your own words (not cut and pasted from other sources):
1. A statement of the purpose of the experiment;
2. A balanced equation describing any reaction you will conduct, which includes the
starting materials, expected products, reagents, and solvents;
3. Calculations of theoretical yield of the desired organic product (if applicable);
4. A table including relevant physical constants (mw, m.p., b.p., density, etc.) for starting
materials, with the quantity to be used in relevant units (g, mL, mmoL, etc.);
5. The procedure you hope to follow;
6. The answers to any pre-lab questions instructor has provided (these need not be included
in your lab notebook).
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2
Absences
If you are absent from a midterm examination through sickness or other valid unavoidable cause,
the weight of your final exam will be increased proportionately in calculating the course grade.
Examples of unavoidable causes include: illness, death or serious illness in the immediate
family, and, provided previous notification is given, observance of regularly scheduled religious
obligations and attendance at academic conferences or field trips, or participation in universitysponsored activities such as debating contests or athletic competition. Absences due to
participation in university-sponsored activities require PRIOR approval (please do this
during the first or second week of the quarter). Bring a letter from your coach/organizer with
your schedule for the quarter to Dr. Tracy Harvey in Bagley 303D.
Proper Procedures for Unavoidable Absences
1. Report your absence from an hourly examination within 72 hours to Dr. Tracy Harvey in
Bagley 303D ([email protected]), and
2. Bring proof of your emergency (a doctor's note (if appropriate), an accident report, a
memorial folder, or similar documentation). The documentation must include a contact
name and telephone number.
3. Dr. Harvey will notify the instructor of the status of your absence. If your absence does
not meet the above criteria, you will be given a zero for the exam.
Final Exam–Monday, March 12, 2012---10:30 am-12:20 pm (comprehensive)
Note: If you are absent from the final examination, and you are ineligible for an incomplete
according to UW regulations, then you will receive a course grade of 0.0. If an incomplete is
given, you must take the final exam for the same course in the next regular academic quarter in
which it is offered to remove the incomplete.
If you would like to request academic accommodations due to a disability, please contact Disabled Student Services,
448 Schmitz Hall, 206.543.8924 (V/TTY). If you have a letter from Disabled Student Services indicating you have a
disability that requires academic accommodations, please present the letter to me so we can discuss the
accommodations you might need for class.
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3
CHEMISTRY 346
Honors Organic Chemistry Laboratory
Winter 2012
Lab Report Due Dates
Report
Points
Due Date
1
Acid-Base Extraction, Recrystallization, Melting Point
50
January 20, 2012
2
Flash column chromatography
30
January 25, 2012
3
Reactivities of Alkyl Halides
20
January 27, 2012
4
Dehydration of 4-Methylcyclohexan-1-ol
25
February 1, 2012
5
Diels-Alder Reaction
25
February 3, 2012
*Midterm Examination*
45
February 14, 2012
6
Grignard Reaction
50
February 17, 2012
7
Asymmetric Reduction
75
February 24, 2012
100
March 12, 2012
80
March 12, 2012
8 Tetraphenylnaphthalene
*Final Examination*
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4
ORGANIC CHEMISTRY LABORATORY SAFETY
Non-compliance with the rules and guidelines listed below may result in the removal from
lab and/or a deduction of ‘lab safety/clean up’ points.
Safety in a chemical laboratory is mostly a matter of common sense coupled with knowledge of
the hazards associated with the materials used by you and your neighbors. A good perception of
your surroundings is also very important in a chemical laboratory. This state of mind requires
your full attention. If there is anything that is unfamiliar or doesn’t seem right, stop what you are
doing and ask your TA or the support staff for guidance. Don’t just plow ahead if anything looks
wrong. No one will be criticized for asking. It is, however, critical that you arrive prepared for
the laboratory, having worked out the procedures in your own mind and lab notebook so you
know what you’re going to do. Safety is an important aspect of this class and we want you to
think about safety as you read this lab manual and, especially, as you work in the lab.
Approach this course with a communal spirit. The success of a laboratory course of this size
depends on the cooperation of each individual. Take care of yourself and your neighbors.
Immediately warn your neighbor if you see him/her doing something dangerous. Accidents
happen, even if you are using common sense, someone else in the lab probably is not. An
example of good communal spirit would be if you see your neighbor looking at their reaction by
putting their head in the hood, remind them to take their head out of the hood and lower the sash
to watch their reaction through the glass. They would much rather hear this message from you
than teaching staff and lose safety points. Respect the fact that other students use the common
laboratory equipment, such as balances, melting point apparatuses, hoods, etc. Maintain your
work area in a reasonable state of neatness so other students will walk into a clean/organized
space just as you did. For example, the balances must be kept clean, hood bench tops wiped
down, and waste jugs emptied. Reagents must be capped and left in their proper place so that
fellow students do not waste time looking for them.
The most important safety rule is to THINK! Safety rules will be strictly enforced with the
possible consequences of removal from the lab and/or a deduction of safety points. What follows
is a detailed description of the safety rules for this class. For additional information on safety, see
your text, PLKE pp. 542-558.
SAFETY GOGGLES ARE TO BE PUT ON BEFORE ENTERING THE LAB AND
MUST BE WORN UNTIL YOU ARE OUT THE DOOR. State health regulations require the
wearing of soft goggles that shield the eyes from above, below, and both sides in the laboratory.
Eyes are too valuable to risk. Students will not be allowed to work in the laboratory without
approved standard laboratory goggles. Failure to observe this state health regulation may
result in removal from the laboratory and will result in a deduction of safety points.
Standard laboratory goggles that meet all state regulations may be purchased from the University
Bookstore and the Chemistry Undergraduate Stockroom in BAG 271. Safety glasses, goggles
that have the air vents removed, sports goggles, etc. are not acceptable. If you already have
goggles, stockroom personnel must first approve them before you can begin working. Because of
health regulations, goggles cannot be borrowed from the stockroom.
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DRESS APPROPRIATELY FOR THE LAB. A lab coat is required to be worn over your
street clothes before entering the lab and not removed until after leaving the lab. Lab coats
must be full length as they must extend to your mid-thigh. Short length lab jackets are not
acceptable. Lab coats may be purchased at the University Bookstore and the Chemistry
Undergraduate Stockroom (BAG 271).
You will not be allowed into lab if you are not dressed appropriately. All students in the
laboratory are required to have clothing coverage from neck to toe; there can be no exposure of
skin anywhere. Long pants, socks, and closed-toed shoes that cover the whole foot are
required. Long hair must be tied back (regardless of gender) when in the laboratory so that it
will not catch on fire or come into contact with chemicals.
The laboratory is not a good place to wear your favorite clothes. Do not wear clothing so loose or
bulky that it hampers your work and causes a safety hazard. Extra long jeans, while fashionable,
cannot drag on the ground. If your fashion sense is to have holes in your jeans, carry a roll of
duct tape because you will be asked to cover any holes. Do not wear hosiery or tight leggings as
they will “melt” upon contact with acid and some chemicals.
Closed-toed shoes (with socks) that cover the whole foot are the appropriate type of
laboratory footwear. Sandals, ballet flats, Mary Janes, shoes with open holes or without full
foot coverage, flip flops, etc., are not allowed in the lab. If you are wearing inappropriate shoes
for lab, you will be asked to go to the undergraduate stockroom to purchase yellow booties and
receive a deduction of lab safety points. If you commonly wear the shoes not allowed in lab, it’s
advisable to have a pair of sneakers in your locker to change into before the lab period begins.
Failure to remain safely dressed for the entire lab period (e.g., not wearing goggles correctly)
will result in a loss of safety lab points, and you will be sent out of lab to acquire the correct
clothing. If you do not return in time to complete your work, your absence will be unexcused.
GLOVES ARE AVAILABLE TO WEAR FOR ANY EXPERIMENT. Remember, gloves
are only a temporary barrier to chemical exposure, and should be replaced whenever they
become too contaminated. Experiments involving hazardous materials and requiring gloves are
usually noted in the manual. Gloves are not to be worn while using the computers in CHB 121.
This spreads hazardous chemicals into common areas and increases the risk of exposure.
IMPORTANT NOTE: Do not wear gloves outside of the lab; if you have to open a door
your gloves must be off! If you wear gloves outside of the lab you will have 10% deducted
from your lab grade for the day. This will be enforced by all TAs, instructors, lab techs,
stockroom personnel, and anyone else you encounter in the Department.
WASH HANDS OFTEN WHEN WORKING IN LAB AND THOROUGHLY BEFORE
LEAVING. Do not taste any chemicals. Do not put your hands, pens, or pencils in your mouth
while working in the lab. If you must leave the lab for any reason such as to use the restroom
during your scheduled time, please inform your TA, friend, or neighbor before leaving the lab.
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DO NOT EAT, DRINK, CHEW GUM, OR SMOKE IN THE LABORATORY. Do not even
bring these materials into the laboratory. Also, no make-up or lip balm is to be applied in the lab.
KEEP COATS, BACKPACKS AND OTHER NON-ESSENTIAL MATERIALS AWAY
FROM AREAS WHERE PEOPLE ARE WORKING. There are designated areas for the
storage of these items within the lab. If personal belongings are not stowed they become a
tripping hazard to your friends and colleagues. Additionally, with improper storage, hazardous
chemicals may come in contact with your belongings, increasing the risk of exposure outside of
the lab. Lockers are the best place for personal belongings that are not essential for lab.
Bagley Hall lockers (2nd and 3rd floor hallways): You may bring a lock from home and
claim an empty hall locker for use during the quarter. These are ideal for storing coats,
backpacks, and other bulky items during lab, and are the best place to store your goggles,
lab coats, and proper shoes when not in lab. Lockers must be emptied by the end of the
quarter; between quarters the locks will be cut off and the locker contents thrown away.
CELL PHONES AND HEADPHONES MAY NOT BE USED IN LAB. If you take your cell
phone out during lab it will be confiscated for the lab period and you will receive a deduction of
lab safety points. Cell phone use for any reason (including texting, internet surfing, timing
reactions or doing calculations) is not permitted. Protect your cell phone from chemicals by
leaving it in your backpack. Headphones are not allowed in the lab for any reason. If you don’t
remove your headphones, you will be removed from lab and receive a deduction in safety points.
DRUGS, ALCOHOL, OR MEDICATION THAT COULD IMPAIR NORMAL MENTAL
OR PHYSICAL FUNCTIONING ARE FORBIDDEN PRIOR TO OR IN THE ORGANIC
LAB. If you are taking prescription drugs that might fall in this category, please notify your TA
or Dr. Tracy Harvey before attempting any experiments. Anyone who displays questionable
behavior, in this or any other regard, will be removed immediately from the lab and subject to a
mandatory meeting with Dr. Tracy Harvey.
LEARN THE LOCATION AND OPERATION OF THE SAFETY SHOWERS,
EMERGENCY EYEWASHES, AND FIRE EXTINGUISHERS IN THE LABORATORY.
In case of a spill onto a person or clothing, IMMEDIATELY rinse with lots of water. Do not
hesitate to yell for help. Use the safety shower and/or eyewash and don’t worry about the
resulting mess. For non-emergencies, do not use the safety showers as they are designed to
deliver ~50 gallons of water before shutting off. Report all accidents to your TA, who will
submit an incident report with your assistance to the University. All instructors are certified
to administer first aid. If you are not familiar with operation of the fire extinguishers, ask your
instructor to show you. Only use fire extinguishers for real emergencies, as the chemicals they
contain can cause considerable damage. For any emergency that requires the fire
department, aid cars, or police, send someone to the stockroom (BAG 271) for assistance.
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LEARN THE EMERGENCY EVACUATION PROCEDURES AND KNOW ALL OF
THE EXITS FROM THE LABORATORY AND BUILDING. A repeating siren and flashing
of the FIRE indicator is the building evacuation signal. If this alarm goes off while you are in the
lab, turn off any open flames, grab your valuables if they are immediately accessible, and leave
the building as quickly as possible OR follow instructions being given by your TA. Assemble
with your lab section and TA by Drumheller Fountain (in front of Bagley Hall). Make sure you
check in with your TA when you arrive to the fountain as all TAs will be taking attendance. All
students must be accounted for at all times; DO NOT LEAVE WITHOUT CHECKING OUT
WITH YOUR TA. If you must leave while the evacuation is still in progress, you must check
out with your TA. Failure to check in for attendance at the fountain and leaving without checking
out will result in an automatic 10% deduction from your lab report.
SCHEDULED LAB TIME: You are not allowed to be in the lab before your lab section begins.
Even if the lab door is open and another TA is present you cannot enter unless your TA has
arrived. Students are allowed to work in the laboratory only during their scheduled sections and
under the supervision of their assigned TA. Removal from the lab and a deduction of safety
points will be a consequence to breaking this rule.
NEVER ATTEMPT ANY UNAUTHORIZED OR UNASSIGNED EXPERIMENTS.
Follow the experimental procedures explicitly, checking and double-checking the identity of all
reagents before you use them. There are potentially hazardous combinations of chemicals present
in the laboratory. If you have an idea for further investigation, discuss it with your instructor.
LAB CLEAN-UP: At the end of each lab period you should clean up your work area and the
areas assigned to you by your TA. In the back of each hood, there is a list stating the proper clean
up and hood shut down procedure. All equipment checked out from the stockroom must be
properly returned by the end of the period. Point deductions may be made if the lab clean up is
not done or is insufficient.
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WORKING WITH EQUIPMENT AND GLASSWARE
Fume Hoods: Do all experiments and keep all chemicals in the hood. The ventilation system
draws the fumes generated by an experiment away from the person working in the hood. The
walls of the hood enclose the experiment on five sides. Therefore, if on explosion or spill occurs,
the experiment can be contained. The sash should always be kept between the individual's
eyes and lowered as much as possible but with the ability to conduct the experiment. Set up
equipment at least six inches from the front edge of the hood. Close the sash when you are not
working in the hood. Never put your head inside the fume hood.
Do not leave Bunsen burners or other heated apparatus unattended. The person working
next to you may not know what is involved with your setup and may be working with a
flammable material. Turn off open flames if you must leave your area. Make sure the gas taps
are completely off whenever the Bunsen burner is not lit.
Hot plates, Bunsen burners & aluminum blocks are hot and pose a significant burn and/or
fire hazard! Do not use flammable liquids near open flames. Most organic liquids are
flammable. Diethyl ether is especially dangerous. Flammable vapors can ignite when exposed to
hot plates. Keep papers and all combustibles away from the hot plate/aluminum block/Bunsen
burner. Turn off hot plates when not in use. Hot plates and aluminum heating blocks will remain
hot for a long period of time after being turned off. Neither hot plates nor aluminum heating
blocks give any visual indication that they are hot, so check by holding your hand a couple of
inches away while “feeling” for heat. Only after checking this way should you attempt to pick up
the aluminum heating block or hot plate. If your hot plate or aluminum block is still cooling
down, put a hot sign on them to warn others. Hot signs are located under the prep hood in the
marked drawer.
Do not pick up hot objects with your bare hands. Be sure all apparatus is cool before picking
it up with your fingers. A hot glove is located in the red box within the lab if you need it.
Do not use cracked or chipped glassware. Examine your glassware for “star” cracks. Broken
glassware should be replaced immediately with new glassware from the stockroom. We can firepolish chipped glassware so it is usable, but we can’t fix cut hands. Never heat cracked, chipped
or severely etched glassware.
Do not adjust glass tubing connected to rubber stoppers. Severe cuts or puncture wounds
may result.
Lubricate rubber tubing. When slipping rubber tubing over connectors, such as filter flasks or
aspirators, lubricate with a drop of glycerin (balance area) or liquid soap (by the sinks in the lab).
Do not use mouth suction when filling pipettes with chemicals. Use a rubber suction bulb. Do
not force pipet bulbs onto pipets. Apply just enough pressure to maintain a seal between the
pipet and the pipet bulb. Forcing the bulbs may cause the pipet to slip and break, leading to
severe cuts or puncture wounds.
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Broken glassware, used pipets, melting point capillaries, and TLC capillaries are to be
disposed of in laboratory glass boxes only. In each lab there are two. One is located in front of
the pillar by the balances and for the pipets that have been used with “smelly” chemicals, dispose
of these in the laboratory glass box in the prep hood. Instrument rooms have melting point
capillary tube waste bins on the island with the Mel-Temps as well as a laboratory glass box in
the room. No glass goes into the regular trash. Custodial personnel can be injured by sharps
and will stop collecting trash if they find them in the trash cans.
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WORKING WITH CHEMICALS
General Chemical Safety: Horseplay and carelessness are not permitted. Add concentrated acid
to water. Waft fumes gently toward your face. Never point a heated test tube toward you or your
neighbor; the contents may erupt and cause serious burns. A separatory funnel must be used in a
hood, vented often, and pointed away from you and your neighbor. Don’t walk around shaking
separatory funnels, test tubes, or centrifuge tubes. Leave chemicals in your hood; if you need
advice from your TA, raise your hand or go to them, but leave the chemicals in the hood.
Proper chemical storage: The policy is that all chemicals need to be stored in the upright
position, clearly labeled, and capped, covered, or parafilmed. Beakers are a good tool to use to
keep vials in the upright position. Solids that are being dried until the next period need to be in a
labeled beaker loosely covered with a watch glass or parafilm. Random drawer checks may be
done and safety point deductions will be made for improperly store chemicals.
Reagents: Read the labels (contents and hazards) before using reagents. Take only as much
reagent as you need; they are expensive and time-consuming to prepare. When taking reagents,
transfer the amount you need to a clean beaker or other suitable container for taking the material
back to your desk. Replace the cap. Let your TA know if a reagent stock bottle is empty.
Never return unused reagents to their storage containers. If you accidentally take an excess
amount of a reagent, share it with a fellow student or dispose of the excess properly.
Clean up spills immediately. The next person to come along has no way of knowing if the clear
liquid or white powder on the lab bench is innocuous or hazardous. Neutralize acid spills with
sodium bicarbonate before cleaning them up.
Keep the dispensing areas clean and pick up any spills immediately. Return all chemical
bottles to the proper location when finished with them. Hand brooms and dustpans are on top of
the flammable cabinets in the lab. Brushes are supplied at each balance. Clean off chemical spills
and keep the common areas clean.
SUGGESTED PROCEDURES FOR CLEANING UP CHEMICAL SPILLS
Solid Reagents: Wipe up small spills with a damp paper towel; rinse the reagent out of the towel
with water, then dispose of the towel in the trash cans. Clean up large spills using the broom and
dustpan (located on top of the flame cabinet) and dispose of the reagent in an appropriate waste
container. If glass is present in the spill, separate the glass from the reagent before disposal. DO
NOT place solid chemicals in either the trash cans or the glass box. Spills on the balances should
be immediately brushed out using the camel’s hair brush provided; the reagent may then be
disposed as above.
Liquid Reagents (Non-organics of near-neutral pH): Wipe up the spill using a damp paper
towel or sponge; rinse the reagent out of the towel with water, then dispose of the towel in the
trash cans.
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Acids: Neutralize the acid by sprinkling solid sodium bicarbonate over the area of the spill.
Clean up the bicarbonate residue with either a damp towel or the broom and dustpan, depending
upon the amount used to neutralize the acid. Dispose of the bicarbonate in the solid waste.
Organic liquids: Wipe up the liquid with paper towels. Do not rinse the paper towels or place
them in the trash. Instead, place them in a hood. Allow the liquid to evaporate and then dispose
of the paper towels in the trash cans.
Mercury: Inform your TA of the spill and they will assist you with the clean up procedure.
Obtain a “mercury sponge” from the instrument room. Moisten the sponge with water and then
rub it over the area of the spill (metal side down). The mercury should quickly become
amalgamated with the metal. When finished, place the sponge back into the plastic bag and
return it to the designated white bucket in the waste hood within the instrument room. During a
mercury spill, small droplets may spatter a surprising distance from the area of the spill,
especially if the mercury falls from the bench to the floor. Be sure to check a wide area around
the spill to be sure that all the mercury has been located and notify others in the lab to avoid the
spill area. If you have a large spill, a special mercury vacuum may be necessary; ask for
assistance.
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WASTE DISPOSAL
Dispose of chemical reagents and other materials properly. The proper disposal of chemical
wastes is essential for the protection of our environment. Improper disposal of chemical waste
puts at risk the health and safety of the University and the surrounding community. Chemical
wastes must be managed and discarded in the most responsible and environmentally sound
methods available. UW and the Seattle Metro expect your cooperation in reducing any
environmental impact. Your laboratory manual will specify how to dispose of chemicals used
during the laboratory period, make note of these instructions in your lab notebook. Do not put
chemicals into glass boxes or wastebaskets. Waste containers for other materials will be
provided. If you are unsure of how to dispose of a particular material, ask your instructor.
Waste disposal in CHEM 220/241/242/346/347/462: In general, nothing can go down the drain
or into the trash! Use specific waste bottles (acetone, organic solvents, aqueous acid/base)
located in your hood for collecting waste during your lab period. Empty and rinse waste bottles
into the corresponding waste jugs located in the “Instrument Room Waste Hood.” On occasion,
there will be waste jugs designated for use with specific waste or for particular experiments.
When in doubt as to what you should do with your waste, ask your TA or any instructional staff.
Solid chemical waste has its own waste jug. This specific collection is for solid organic waste,
Drierite, and sodium/magnesium sulfates. DO NOT put tlc plates, paper towels, filter paper, etc.,
in this jug.
All non-chemical solid waste used in this class should go into the trash, unless otherwise noted.
Paper towels, matches, pH paper, etc. should NOT be placed in the sinks.
Dispose of broken glassware and other sharp objects in the cardboard glass disposal boxes
as mentioned above. Cleaning up broken glass is greatly facilitated by using the broom and
dustpan (located on top of the flammable cabinet). Custodial personnel will stop collecting trash
after they find broken glass in the trashcans!
Hazard Identification: As part of the UW Laboratory Safety Manual, each laboratory has a
Chemical Hygiene Plan (CHP). This is available to all students in the lab at all times. As part of
the CHP, Material Safety Data Sheets (MSDS)** must be readily accessible to all students.
MSDS and chemical information are available at:
http://hazard.com/msds/index.php
www.fishersci.com – type compound name in "product search", then click on "MSDS" link
www.vwrsp.com/search – go to MSDS tab
http://www.sigmaaldrich.com/safety-center.html
The Merck Index - this reference book is located in the instrument room
**Material Safety Data Sheets: Material Safety Data Sheets (MSDS) are provided by the
manufacturer or vendor of a chemical. They contain information about physical properties of
the chemical and identify any hazards associated with the chemical.
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13
CHEMISTRY UNDERGRADUATE STOCKROOM
271 Bagley Hall, 206.543.1607 (vm) or 206.685.9761
CHEMISTRY STOCKROOM POLICY
1. All stockroom sales are final – NO REFUNDS OR RETURNS.
2. All items checked out from the Undergraduate Stockroom must be returned at the end of lab.
3. It is good practice to inspect all items borrowed before leaving the stockroom window and to
report any damage immediately.
4. After accepting an item from the stockroom, the student is responsible for returning it
undamaged, clean, and dry.
5. Replacement glassware can be purchased from the Chemistry Undergraduate Stockroom
using your Husky Card. If you do not have funds on your Husky Card, each student has a
charge account within the Chemistry Undergraduate Stockroom. They may charge on their
account and pay it off at a later date, using their Husky Card.
6. Each quarter, all charge accounts must be settled by the Friday before finals week. Accounts
not settled by the end of the quarter will incur a $20.00 late fee and a hold is placed on all
University records, including registration.
7. No stockroom privileges will be extended to students with delinquent Chemistry
Undergraduate Stockroom accounts (accounts not settled from a previous quarter).
8. There will be a $5.00 charge for all items returned late, without a yellow slip, and/or with the
wrong desk number. The fine will accumulate on a daily basis (i.e. $5.00 per day) until the
item is returned. Fines are assessed to encourage the prompt return of materials so that they
will be available for others who need them.
CHECK-IN PROCEDURES
1. Find your name and desk number on the class list posted outside the lab.
2. Go to your station and wait for your TA.
3. The TA will open your drawer and give you a card which lists the glassware and tools
contained within your drawer. Carefully verify the contents of your drawer against this list. If
anything is missing or broken, ask the TA to verify this by filling out a pink slip. Take the
pink slip to the Chemistry Undergraduate Stockroom and they will give you a replacement.
Check-in day is the only day the stockroom will replace items at no charge to you. Claims
made at a later date will not be honored.
4. Fill out the required information on the card, read and sign the statement on the reverse side
of the card. Take your card to the Chemistry Undergraduate Stockroom and they will collect
your card and give you a combination lock to put on your drawer. The small silver padlock
stays in your drawer through the duration of the quarter.
5. You are responsible for the contents of your drawer. If any items break or are missing, you
must purchase a replacement from the Chemistry Undergraduate Stockroom. The
Department cannot honor claims for replacement of stolen drawer materials. Use good
judgment and keep your drawer locked when not in use.
6. The Chemistry Undergraduate Stockroom can help facilitate early check-out, if you drop the
class and/or you need to check-out of your drawer before the scheduled date listed on your
syllabus. Failure to check-out of your drawer will result in a $20.00 fee, in addition to
charges for any items that are broken or missing, and a hold will be placed on all University
records, including registration. Check-out is not final until a signed desk card is returned to
the stockroom and all bills are paid.
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14
How to fill out a loan-return slip (yellow slip) in order to check out equipment/supplies from the
Undergraduate Stockroom (Bagley 271)
The stockroom requires a picture student ID or non-picture student ID
with driver’s license to check out equipment.
For quicker retrieval, yellow slips are filed
by this number, not by your name.
No. 10
Date __________ Station# _______________
Name __________________________________
CLAIM TICKET
Keep the top half of the slip. This
portion is given to the attendant
when returning items checked out.
No. 10
STOCKROOM COPY
Write down your charge number. It is posted
by your name on the bulletin board outside
your laboratory classroom.
Date __________ Station# _______________
Name _________________________________
Course __________ Section ______________
1.
2. List the items that you want
3. to check out on this half.
4.
1/3/2012
The bottom half is what we file. It will be
returned to you when you return the items you
have checked out. We use these slips to keep
track of items not returned. It is your
responsibility that you get this half of the
yellow slip back when you return all items.
15
ORGANIC CHEMISTRY GLASSWARE
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16
LABORATORY NOTEBOOK
Your laboratory notebook is a complete record of the scientific activities in which you have
invested many hours. When it is time to describe your scientific activities in a report, you will
discover that your notebooks are indispensable because the human mind simply cannot
remember every minute detail of so many experiments. It is not uncommon to attempt to
reinterpret experimental results years after the original observations were made; an accurate
record is thus critical. This handout is designed to aid you in establishing an efficient method of
recording your experiments and their results.
You must use a notebook with bound pages and with page numbers. The reason is that, in time,
pages in three-ring binders will rip loose.
Do not use water soluble ink or pencil for obvious reasons.
Handwriting must be legible!
Each bound notebook must have a Table of Contents at the beginning of the book (on the inside
of the front or back cover is acceptable). You should update the Table of Contents as you fill out
the notebook.
The recordings of each day of research should include the date.
Start the notebook entry for a new experiment with the pre-lab. Provide a sketch of each
apparatus if it seems helpful. For simple operations such as heating an Erlenmeyer flask on a
steam bath or filtration through a Buchner funnel, sketch the device the first time it is used. You
don’t have to sketch it again if you use the technique in a subsequent lab. For more complicated
set-ups, i.e. distillation, refluxing, etc., sketch the apparatus each time you use it.
You must record your observations within minutes of making them. If you are collecting
recorder output data, you can jot down some specifics about the experiment (i.e. how much
enzyme, inhibitor, chart speed, etc.) on the output, and you should assemble the data into your
notebook with a day or two after the experiment. The details of the design and components of the
experiment should be recorded in your notebook as you set-up the experiment.
All experiments, regardless of whether they "worked" or not, regardless of whether you
are pleased or displeased with the results, must be recorded. Often the details of failures turn
out to be informative, especially in hindsight, as you consider all of your data.
If you purify or dry solvents, be sure to write down how this was done (i.e. distilled from CaH2
under argon, distilled from P2O5 with the outlet of the device attached to a Drierite-filled tube).
For TLC, draw a picture of the stained plate in your notebook, indicate the solvent and stain
used, the color of the spots, and the measured Rf values.
List the physical state of the synthetic product. If solid, measure and record the melting point.
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17
Draw the structures of molecules, with correct stereochemistry, if they are not obvious.
NMR spectra should be labeled with the solvent and the assigned chemical shift of the reference
signal. Interpretation of NMR spectra should include, for each signal, its chemical shift (in ppm),
integration, multiplicity, and coupling constant (J values in Hz). IR spectra should list the matrix
(i.e. in chloroform, KBr mull), the calibration and a list of important or characteristic bands. GCMS chromatogram spectra should include GC conditions and retention time(s) of your sample.
On the corresponding MS, list the molecular ion (M+) and base peak.
For all chromatography, give the dimensions of the column, the packing material, the flow rate,
and the volume of the collected fractions.
NOTEBOOK GRADING
These are the following guidelines that your TA will use when grading your notebook:
1.
The first notebook page of each new day should have a date.
2.
The writing must be with water-insoluble ink.
3.
The writing must be legible.
4.
The structures and amounts used for all reagents must be stated.
5.
The protocol used should be described in the notebook along with a drawing of the
apparatus (e.g. distillation set-up). The detail and clarity should be such that someone with a
background in chemistry could reproduce the work.
6.
The structure of the reagents and compound(s) prepared must be shown as well as other data
pertaining to the experiment (i.e. reaction time, temperature, yield, mp, sketches of TLC
plates, IR data, etc.).
7.
There should be a discussion at the end including whether the experiment was successful
and any conclusions drawn from it. If there were problems, possible reasons and solutions
should be given.
For samples of notebook format see also PLKE (4th edition), Technique 2.
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LABORATORY REPORT FORMAT
All laboratory reports should use the following format and length criteria. A partial example is
attached. While you should strive to be complete in your report, you should also try to be
concise. It is a goal of the course that you demonstrate good judgment concerning what is and is
not important to include in the reports. Your TA has as little interest in reading an overly-long
lab report as you have in writing one.
I.
Purpose
In a sentence or two, state concisely the purpose of the experiment you undertook.
II. Description of Experimental Approach
In a sentence or two, state concisely the experimental approach you have taken in order to
attempt to accomplish the goal stated in item I.
III. Summary of Findings
In a sentence or two, state concisely the conclusion you reached, based upon the outcome of
your experiment.
IV. Data and Analysis
Include in this section the relevant data you collected, which will include some or all of the
following: melting point, boiling point, TLC Rf, NMR spectrum, IR spectrum, mass
spectrum, yield, etc. For spectra, you should devise a sensible method to communicate the
important features. For example, in the case of a proton NMR spectrum, a table could list
for each resonance (a) its chemical shift (in ppm), (b) the multiplicity of the signal (singlet,
doublet, triplet, etc.), (c) the intergral (how many H represented), and (d) your assignment
(for example, “CH3 groups of isopropyl substitutent”). Focus especially on reporting data
that help you to demonstrate that you accomplished the purpose of the experiment. For
example, if you have attempted to reduce a ketone to an alcohol, cite data that show the
ketone functional group is absent and the alcohol functional group is present.
If there are literature values or spectra with which to compare the data you collected, please
provide them. If there is an analysis that provides chemical insight (such as the assignment
of signals in various spectra), provide that analysis in this section. If there is a calculation
(such as a percentage yield), show the calculation.
V. Answers to Assigned Questions
If the instructors provide a set of post-lab questions, please provide answers at this point.
Sections I, II, and III together should occupy one page or less! Sections IV and V have no
page limits.
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Unless otherwise instructed, you will need to turn in to your TA substances you have
synthesized, purified, etc. Be sure these compounds are provided in a capped disposable vial that
is labeled at a minimum with your name and the chemical structure the compound(s) therein.
A sample report follows.
LABORATORY REPORT 0
Chemical Formula of Cyclohexane
I.
Purpose
The purpose of this experiment was to determine the molecular formula for the hydrocarbon
cyclohexane.
II. Description of Experimental Approach
The results of a mass spectrometric analysis, to determine the molecular weight, and
combustion analysis, to determine the relative amounts of carbon and hydrogen, were
combined to yield the molecular formula of cyclohexane.
III. Summary of Findings
Based upon the molecular weigh of 84 and relative amounts of carbon and hydrogen (a 1:2
molar ratio), the molecular formula of cyclohexane was determined to be C6H12.
IV. Data and Analysis
Prior to burning and measuring the mass spectrum of cyclohexane, I assessed its purity by
gas chromatography. The chromatogram is attached, and showed a single predominant peak
representing 99.5% of the total material in the chromatogram. I concluded that this material
is roughly 99.5% pure.
A 10.4 mg sample of cyclohexane was burned, and yielded 32.7 mg of carbon dioxide and
13.4 mg of water. [In a real lab report, this is the spot where you would show a calculation
that converts these weights of carbon dioxide and water into an empirical formula of C1H2.]
Mass spectrometric analysis revealed a molecular ion of m/e 84. The mass spectrum is
attached. Assuming that this represents an ion with a charge of +1, the molecular weight of
cyclohexane is thus 84. In turn, the chemical formula (formula weight 14, or one sixth of
84) is thus C1H2 × 6 = C6H12.
[Most of your lab reports this quarter will include spectra. You will need to attach a hard
copy of each spectrum, and include some analysis of these spectra.]
V. Answers to Assigned Questions
[Self explanatory]
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SEARCHING THE CHEMICAL LITERATURE
All of the substances that you work with or synthesize in this course have been reported many
times in the chemical literature. Modest effort expended to find literature values for melting
points, spectra, etc. will be very helpful to you in interpreting your data.
The following hard copy compendia can be found in many libraries:
The Aldrich Library of Infrared Spectra
The Aldrich Library of NMR Spectra
The Aldrich Library of 13C and 1H FT NMR Spectra
An online database that you may find useful is:
SciFinder Scholar
You can access SciFinder Scholar through the chemistry subject guide provided by UW
Libraries (http://guides.lib.washington.edu/chemistry).
You will want to take some time to experiment with and explore these databases. You can search
by molecular formula, chemical structure, or even substructure, all of which tend to be more
useful than searching by compound name. The database provides quick access to physical data
on compounds, spectra, methods of preparation, and chemical reactions.
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21
ROTARY EVAPORATOR
Many procedures call for the removal of solvent in order to isolate the high boiling product of a
reaction. In your lab, you will have access to a rotary evaporator which is used for rapid solvent
evaporation. This is achieved by the combination of reduced pressure, and maintenance of a high
liquid surface area. A picture of this device is shown below (what you will use in lab may look
slightly different). The unit is connected to a water aspirator in order to reduce the pressure in the
system while a water bath is used to heat the solvent. A general procedure for use of the rotary
evaporator is given below (your TA will also demonstrate this):
1.
2.
3.
4.
5.
6.
7.
Turn on the water aspirator to full.
Turn on the condenser water (just a trickle).
Place the solution in a round bottom flask and connect it to the trap (not shown). Secure the
flask with a plastic connecting clip.
Use the quick-release jack to lower the flask into the water bath.
Turn on the drive unit in order to rotate the evaporation flask. This will accelerate
evaporation and prevent bumping.
Close the pressure valve at the top of the condenser to apply a vacuum to the system. As the
evaporation proceeds, solvent will evaporate from the round bottom flask, condense, and
flow into the receiving flask.
When evaporation is complete: 1) turn off the drive unit to stop rotation; 2) open the
pressure valve in order to equilibrate the internal pressure with the surrounding atmosphere
(be sure to keep your hand on the evaporation flask to insure that it doesn’t drop off into the
water bath); and then 3) turn off the aspirator and condenser water sources.
1/3/2012
22
DPX-200 NMR INSTRUCTIONS
(Version 14, 2/09)
Wear your goggles! Eye protection is required in the instrument room.
No metal near the magnet! Credit cards and cell phones will be erased; keys and other
ferromagnetic items will stick to the magnet.
In what follows:
• things in “quotation marks” should be typed verbatim in the appropriate place.
• things in bold type are commands that you can type in on the command line.
• names in bold italics are those of pull-down menus.
• most actions using commands or pull-down menu entries can also be done via icons.
Logging in
Log in with the username “chemuser”, password “cmpnd463”. The NMR spectrometer software
called Topspin automatically opens.
The Topspin software graphical interface is shown below.
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Go to the pull-down menu entry File – New. The following window appears:
There are only two entries you need to type within this window:
NAME: enter a reasonable name that you can identify later. This will create a folder where your
data will be stored.
USER: chemXXX (where XXX is your course number) (type this exactly as shown; do not
introduce uppercase letters, spaces or symbols, etc.). Also, note these points below:
o The experiment number (EXPNO) will be “1” for your first spectrum. Increment the EXPNO
for each new NMR spectrum you take.
o The process number (PROCNO) will always be “1”.
o The entry USER is always your course number (all lowercase and no spaces).
After clicking ‘OK’, go to the ‘Sample’ tab and enter a description of the experiment.
Inserting your sample
You must first eject the sample that is currently in the machine (which will be a sample of D2O).
Type in ej and wait until the sample appears at the top of the magnet. Remove the sample and
place your sample in the holder and gauge for the correct height. IMPORTANT: the NMR tube
must be in the holder in order to avoid having it “free-fall” into the magnet, the consequences of
which would be dire!
Type in ij to lower your sample into position. Note that the solvent level in the NMR tube should
be between 1.5 and 3 inches. If there is too little or too much solvent it may affect the spectra.
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Preparing for Acquisition
There are two ways you can acquire your NMR data:
Automated method. The automatic method will do all the necessary steps and collect the FID
and store it. You can work up the FID file later using the MestReC software in CHB 121 or the
Organic Study Center.
Manual method. With the manual acquisition method, you initiate the actions in a step-by-step
manner, as given below. (Consult your TA as to which method is recommended for use in a
given experiment.)
AUTOMATED METHOD
To begin, type the command proton on the command line.
Wait for a pop-up window that announces that the acquisition has been completed.
Work up your data using MestReC in CHB 121 or the Organic Study Center.
MANUAL METHOD
Preparing the sample for Acquisition
• Enter protonprep on the command line to load the standard parameter set for your experiment
• To spin the sample, enter ro on on the command line
• Load the standard shim values by entering rsh stdbbo
• To lock on the correct solvent, enter: lock
o you will see a lock solvent list (see below)
o Select your solvent (usually CDCl3)
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Start the automatic shimming procedure by entering on the command line: shimf
o You will see the following message once the automatic shimming is complete:
Acquiring the data (for a standard 1D proton NMR)
Start acquisition by typing on the command line: xaua
o The FID that is being recorded will be automatically displayed, as shown here:
o
o
The above window will also display useful status parameters such as, number of scans
completed, type of nucleus observed.
Once the acquisition is complete the FID window shown above will disappear. You will see
the following message popup to tell you that Acquisition is complete
For all practical purposes, the above completes your proton NMR data acquisition. Although
you will work up these data with the MestReC software running on workstations in CHB 121 or
the Organic Study Center, it is still recommended that you do a quick automatic processing in
Topspin software itself, to check that your spectrum does not show any undesirable features, as
shown on the next page.
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Processing the FID that is acquired
Enter on the command line: efp
o The FID will be processed to show you a 1D proton NMR spectrum
This spectrum is not phased properly. That will be the next step.
To obtain the phase corrected spectrum enter: apk
o After the automatic phase correction, the spectrum shown above, will look like this:
o
Important: In the example spectrum shown above, there is no TMS peak, as the sample tube did
not contain TMS. But in the samples you prepare, usually TMS will be there as a standard
additive. The TMS peak marks the 0 ppm position, also called the 'reference' position. Once you
process the data you must check that the TMS peak is indeed displayed at 0 ppm. If this is not
the case, enter sref on the command line.
This will automatically identify the 0 ppm position of TMS peak. For this to work properly, you
must select the correct lock solvent during the preparation for Acquisition.
Data workup
Data workup is done on the computers in CHB 121 or in the Organic Study Center, which allows
the NMR machine to be free for other students to take spectra.
See the next page for MestReC instructions.
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NMR Analysis Instructions for MestReC
(Updated 1/2010)
The following directions are to be used with the workstations in either CHB 121 or the PCs in
Organic Chemistry Study Center. No explicit login is necessary on these computers and you can
simply start by accessing the MestReC icon on the desktop or in the program list.
There are six important stages in using the MestReC software and getting your NMR data
processed and printed out. These are:
1. Locating the Raw Data file
2. Opening the Raw Data file
3. Fourier Transformation and Spectrum Optimization
4. Integration
5. Spectrum annotation, saving data and printing
6. Close the software and exit.
1. Locating the Raw Data File (FID file). NOTE: Instructions must be followed exactly to be
able to use the software in the study center!!
In Microsoft Internet Explorer: Go to ftp://phoenix.chem.washington.edu/DPX200. View
this FTP site in Windows Explorer, click Page, then click Open FTP Site in Windows
Explorer.
Samples that have been run on the autosampler
Open tauser/nmr/<experiment classname labsection>/<your number>. You must identify the
correct section and data number used to collect your data (the number that you signed up for in
class). Copy the entire data file to my documents or a USB stick/thumb drive. Rename if desired.
Student-run samples
In this “dpx200” folder, you will see the NMR user directories that were created for different
courses in the NMR machine located in CHB 118. You must identify the correct user name that
was originally used to collect the data from this displayed list (unless otherwise instructed, this is
always in the form “chemXXX” with the XXX replaced by the course number, e.g. “chem347”).
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Double-click it, find the data set that you created, then save the whole data file to my documents
or a USB stick/thumb drive. Rename if desired.
2. Opening Raw Data File (FID file)
Locate the MestReC program in the program list to open the following startup screen:
Pull-down Menu
Icon Bar
Click on the File menu and Select the entry Import Spectra...
You will now see the following dialog box and can find your file by accessing the Look in: pulldown menu of this dialog box. Locate the correct folder where you saved the data in step one.
You can either double-click it or point the mouse and then click “Open”.
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Each dataset directory has several subfolders. You must descend into the tree structure and
access the file called “fid” for MestReC software to process your data. Select the file called
“fid” once you descended into the correct branch of the dataset tree.
Click on Open after
selecting fid.
MestReC displays the FID as shown here
3. Fourier Transform (FT) and Spectrum Optimization:
Select the FFT icon on the top right corner of the MestReC icon bar, as shown here:
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The transformed spectrum appears in the window but it may not be optimally phase corrected.
You should select the Automatic Phase Correction icon next to perform the phase correction:
The spectra before and after phase correction are shown below:
before
after
QUICK TIP! If you want to zoom into a certain portion of your spectrum, a helpful tool is the
Magnifying Glass. Click on the icon and then hold down the left-mouse button while dragging
the cursor across the area that you would like to see a bit closer. Clicking ‘Full’ will show the
entire spectrum again. The mouse wheel will enlarge or reduce the spectrum vertically.
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You have to reference this optimized spectrum so that the TMS peak is calibrated to 0 ppm.
Click on the Referencing icon:
You will be presented with a cross-hair icon “+” on the screen. Position this on the TMS Peak
(the right most peak in the spectrum) and click on it. The following dialog appears:
Simply select TMS from this list and click OK. If TMS is not listed, enter 0.000 for the value and
press OK. This completes your Fourier Transform and optimization.
4. Integration
To begin integration, click on the Integration icon
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You can now select a range of the peaks to integrate using the mouse. Simply click and drag the
mouse from the left side limit to the right side limit of a given peak group (see below). Be sure
to include some baseline to the left and right of the peak(s) of interest.
Once you release the mouse button after selecting a range, the integral will appear automatically:
o
o
You can select as many ranges as needed to integrate all the peaks
Optimize the integrals using Auto Adjust. You can access the Auto Adjust by two methods:
ƒ
Click the Right mouse button on the spectrum and a menu will appear. Choose the Auto
Adjust from this list :
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ƒ
OR click on the Down Arrow next to the Integration Icon and start the Auto Adjust:
The Integrals before and after the Auto Adjust are shown below
before
after
Other Helpful Integration Hints…
If you accidentally integrate the wrong area or want to start the integration over, right click in the
green integration box/integration number and select delete.
The integration manager can be accessed by either double clicking in the green box or right
clicking on the green box then selecting integration manager. This tool will allow you to finely
tune the width of the integration that you are working with or set the integration reference value.
1/3/2012
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5. Spectrum annotation, saving data and printing
Peak Picking is an option to enhance the data you are working up. This feature lets you pick a
peak and the software will display the exact ppm shift. To do this, choose the Peak Picking icon,
then left click and drag across the top of the peak.
You should attach a meaningful title to your spectrum so that you can recognize it at a later date.
Click on the Annotation icon on the icon menu
Enter the title in the dialog box that appears
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After you click OK, the title appears on top of the spectrum
To save the work done, select Save from the File pull down menu. If you want to come back to
this spectrum, you can save this in a unique filename of your choice, on a USB stick/thumb
drive.
You can now use the Print option in the File pull down menu to print the spectrum with the
integrals and other information. In the organic study center, you can print to the copier in the
chemistry study center if you have your husky card and the room is open.
6. Close MestReC and exit
Access the Exit button on the File pull down menu to exit MestReC.
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PERKIN-ELMER FT-IR INSTRUCTIONS
WARNING: Do not use gloves on the controls of this machine.
Press enter if the screen is blank.
For the scanning process below you will sometimes use the softkeys which are the top row of
grey keys on the key board. On the lower portion of the screen you will see the softkey label and
below the label is the corresponding softkey.
Scanning your sample:
Place your salt plate into the 'v-groove' holder. Be sure to close the door of the sample
compartment.
On the key pad press the green 'scan' key followed by the softkey '4'.
Wait for the scanning to finish after about 20 seconds – the display will read “Ready”. You will
see your spectrum on the screen.
Manipulating the data:
Moving the spectrum: use arrow keys
Enlarging/reducing: use “< >” “> <” keys
SHIFT functions: use the shift and arrow keys to access the following functions:
Rerange
maximizes the horizontal range
Rescale
sets the %T (y-axis) range from 0 to 100
Autex
sets the %T so that your spectrum fills the screen
Peakcur
brings up a vertical line to mark peaks; move with arrow keys
Mark
peaks marked will show the wavenumbers when printed
If your spectrum does not look as you would expect, use the following sequence of functions to
reset the range and fill screen with the spectrum:
Shift -> Rerange -> Shift -> Autex
Plotting your spectrum:
Press the plot key (not the print key) located in the lower portion of the keyboard.
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1600 FT-IR INSTRUCTIONS
NOTE: THIS MACHINE IS FOR SOLID SAMPLES ONLY!
Press enter if the screen is blank.
For the scanning process below you will sometimes use the softkeys which are the top row of
grey keys on the key board. On the lower portion of the screen you will see the softkey label and
below the label is the corresponding softkey.
1.
Preparing your solid sample: If your sample is extremely crystalline (like salt or sugar),
check out a mortar and pestle from the stockroom. Grind your sample into a fine power.
Your sample in now ready to place on the zinc selenide (ZnSe) plate. The zinc selenide plate
is the small 3 mm crystal located in the center of the circular metal plate
While avoiding contact of your spatula with the zinc selenide plate, cover the plate with
100-200 mg of your ground sample. Carefully lower the press onto the sample by using the
large circular knobs located on the side of the press. The teflon tip should be pressing your
compounds against the ZnSe plate.
2.
Scanning your sample: On the key pad press the green scan key followed by the softkey
'4'. Wait for the scanning to finish after about 20 seconds. On the screen you will see your
spectrum.
By using the white Autex key you can enhance peak intensities (bring the largest peak to the
bottom of the spectrum). “Rescale” will shrink the spectrum.
3.
Plotting your spectrum: Press the green plot key located in the lower portion of the key
board. This will activate the printer at then end of the bench.
4.
Sample Clean up: Using the brush located near the IR, sweep up your sample and dispose
of your solid in the solid waste jar in the hood. Do NOT leave chemicals in the staging area.
Using a cotton Q-tip doused in 2-propanol, wipe off residual compound from the ZeSe plate
– DO NOT USE A KIMWIPE (it is abrasive on the plate).
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INFRARED SAMPLE PREPARATION TECHNIQUES
Salt Plates, KBr pellet presses, and mortar and pestles are checked out from the stockroom.
Note: PLKE has excellent and more detailed instructions for the preparation of IR samples (see
Technique 25, Part A, pp.834-847).
FOR LIQUID SAMPLES
Thin film
The fastest sample preparation technique is simply to place a drop of liquid sample between two
salt plates (KBr) and squeeze gently. If this is done properly, the film has enough surface tension
to hold the plates together. Caution should be used to prevent air from getting back into the
sample after it has been compressed. If the spectrum is too concentrated (many peaks bottoming
out at 0 %T) try adding a much smaller volume of sample to the salt plate.
FOR SOLID SAMPLES
ATR (attenuated diffuse reflectance)
Please see your TA if you have not had instruction on this apparatus. Use the IR that is
designated "For Solid Samples Only”. Grind a small amount of your solid (~100 mg) in a mortar
& pestle. Carefully place this solid on top of the small zinc selenide crystal in the center of the
apparatus. Do not contact the crystal with metal (your spatula) or paper products (e.g. Kim
Wipes). Use a cotton Q-tip to maneuver your solid to fully cover the crystal. Once the solid is in
place gently lower the press onto your sample/crystal (rotate the two black circular knobs). Scan
the specta as you would for a liquid. For clean up, carefully sweep up your solid reside with the
brush and dispose of in the solid waste container. Finish cleaning the zinc selenide crystal using
a Q-Tip dipped in 2-propanol (not Kim Wipes)
Potassium bromide pellets (see PLKE, page 840)
In this method, a 1 mg solid sample is mixed with 80 mg of potassium bromide (located in the
oven) and pressed between two stainless steel bolts in a threaded barrel. The two materials are
ground to a find powder using a mortar and pestle. Screw one of the bolts into the barrel of the
KBr press leaving one to two turns left. Pour the mixture into the open end of the pellet press and
tap lightly on the benchtop to evenly distribute on the face of the bolt. The second bolt is then
carefully screwed in until it is finger tight. Place the head of the bolt into the hexagonal hole that
is attached to the benchtop. Using the torque wrench, making sure direction indicator on the head
of the wrench is pointed to the “R,” tighten the bolt system until the wrench makes a loud click
for the first time which is at 120 in/lb. Keep the bolts tight under pressure for approximately 60
seconds so that the crystals "settle". Be sure not to tighten the bolts too much–be firm, don't give
it too much muscle. If you heard the loud click, not the softer clicks of the ratchet mechanism,
you are done! Reverse the wrench by switching to “l” and rotating in the opposite direction.
Remove both bolts and place the cylindrical chamber containing your pellet into the sample
holder within the IR equipment. Some pellets will appear white. You may have used too much
sample. If the pellet is more than 1-2 mm thick, you probably should regrind and remake it with
less material. Your pellet could also have the freckled look. Tiny but distinct spots are apparent
throughout the pellet. This arises from insufficient grinding.
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Methylene chloride solution
Dissolve ~100mg of your solid in a small amount of methylene chloride (approximately 1 ml).
You may heat the solution to help it completely dissolve. Add 3-5 drops of this solution to a salt
plate and let the methylene chloride evaporate. Once evaporated, it should leave a thin film of
your solid on the plate that is ready to be analyzed.
Mineral oil (Nujol) mulls
A relatively simple sampling method for softer organic samples is a mull. The proper approach is
to use an agate mortar and pestle. Place a few milligrams of the sample into the mortar and grind
it until it looks like a thin film. At this point, add a drop of mineral oil and continue to grind. The
particle size must be reduced before the sample can be lubricated. Mineral oil has a considerable
spectrum of its own, being a hydrocarbon of high molecular weight. See the sample mineral oil
spectrum located by the IR.
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AGILENT 5973 GC-MASS SPECTROMETER
(Updated 1/2010)
DATA ACQUISITION
1. If the software isn’t running, select the Mass Spectrometry icon from the desktop. Two
programs will start labeled “GC/MS MSTop/Enhanced” and “GC – Mass Spec”. Note: These
programs should already be running.
IMPORTANT: If your sequence is already running, click on “Edit Sample Table,” add
your sample to the end of the list as detailed in step two, and click ‘OK’. If a sequence
table from a different class is running, your data may be saved to a different folder.
Always put your samples on the end of the list.
2. If no sequence is running: From MS TOP go to Sequence –> load and open sequence file
chem463.s (or chem346.s, etc). Return to sequence and select edit sample log table. Enter
the appropriate data for each vial to be analyzed. Use “repeat” and “cut” to add/delete entries.
Type – should always be ‘Sample’.
Vial number – corresponds to the numbered slots in the autosampler tray.
Method – There should be a method for your class: chem463, chem346 etc. Note – no
spaces or characters other than letters/numbers!
Data file – enter the designation for the sample. The data will be saved under this name.
If you use the same name your files will be overwritten. Any characters other than letters
and numbers will not save properly and possibly stop the sequence.
Press ‘OK’.
3. Make sure that the solvent vials A and B on the injector carousel are filled with solvent and
that the waste vials are emptied. The solvent vials usually contain methylene chloride (A)
and acetone (B).
4. Put your sample vials in the appropriate slots in the auto sampler tray. The samples should be
at least half-full. Go to Sequence –> Run sequence. Check that the data is being sent to
D:\MSData\undergrad\<yourclass>. Click on ‘Run sequence’.
5. To restart a run from the middle of the sequence, choose Sequence –> Position and Run.
You will be prompted for the entry at which to start the run.
DATA ANALYSIS
1. To analyze data from a run for which the acquisition is complete, select GC Data Analysis.
Click File –> Load and select the datafile that you want to look at. The data should be in
acropolis/MSDdata/Undergrad/ <your class>/<your datafile>. This drive should be available
in the drop down menu under either “m:” or “z:”.
2. The total ion chromatogram (TIC) from the acquisition will be displayed when the data file
has loaded. To zoom in on a selected area of the TIC, drag a box over the plot with the left
mouse button. Double click with the left mouse button to display the previously selected
region.
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3. To display a selected mass spectrum, double click with the right mouse on the TIC over the
desired scan. Drag the right mouse button over a retention time range on the TIC to display
the average of several scans.
4. To subtract the background from the spectrum, drag the right mouse button over the TIC
baseline adjacent to the peak displayed, and then select Subtract from the Spectrum menu.
5. To print a copy of the displayed spectrum select Print from the File menu, choose Selected
Window, then enter 1 as the window to print, or select TIC/Spectrum.
6. To generate a tabulated mass list of the displayed spectrum, select Tabulate from the
Spectrum menu. Select Print in the Tabulate window for a printed copy of the mass list, and
Done to clear the window.
7. Double right click in the lower pane (showing the mass spec) to do a library search of your
data. A new window will appear showing the spectrum that you took and the best match
found by the computer.
8. Click on File –> Print Autoreport to get a printout of your data and the best match.
9. Quit the Data Analysis window when you are done by selecting Exit from the File menu.
LIBRARY SEARCH
1. Return to the TIC window. The left mouse button can be used to draw a box around any
peaks of interest. This will enlarge this area. Using the right mouse button, draw a box
around a peak. Below will now be the mass spectrum (MS) of this peak. Go to ‘file’ and print
out the TIC and spectrum.
2. To identify this peak, double click anywhere on the MS (lower window) with the right mouse
button. This will initiate a library search that will match your MS to mass spectra contained
in a large electronic library. The results will be presented as several choices with the top one
being the most likely candidate. Look through the possibilities and select the most likely
possibility. On the right hand side there will be a structure of the compound you select. You
have the option of printing this out or recording the identity in your notebook. Click on
‘Done’ when finished with the search.
3. Go back to the TIC and make a box with the right mouse button around any smaller peaks to
generate its MS and subsequent library search.
4. When you are done you may leave the program where it is. Before you leave make sure you
have 1) a printout of the TIC and library results, and 2) a printout of the TIC-mass spectrum
of the largest peak.
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EXPERIMENT 1:
ACID BASE EXTRACTION, RECRYSTALLIZATION, MELTING POINT
Pre-Lab Questions:
1.
State what you would do if each of the following (unfortunate!) things were to happen to
you while in the CHEM 346 laboratory:
a.
b.
c.
d.
You were splashed in the eye with a chemical other than water.
Your laboratory coat caught fire.
You broke a 1 liter bottle of concentrated hydrochloric acid and the contents
thoroughly doused your clothing.
You cut yourself badly (blood, etc.).
2.
Write a balanced chemical equation for the reaction of a carboxylic acid with aqueous
sodium bicarbonate. Label the organic and inorganic products as soluble (mostly) in water
or organic solvent.
3.
Repeat question 2 for the reaction of an organic amine with dilute aqueous hydrochloric
acid.
4.
Why is the solubility of a neutral organic compound unaltered by exposure to aqueous acid
or base?
5.
What is the purpose of recrystallizing a solid organic substance you obtain following
evaporation of an organic layer acquired from a separatory funnel?
6.
Explain why the mixture melting point method is very useful to prove that samples of two
substances that exhibit identical sharp melting points (for example, 100-100.5 ˚C) are either
structurally identical or non-identical. In your answer, please refer either to PLKE Figure
9.1 (p. 628) or Figure 9.2 (p. 629).
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ACID BASE EXTRACTION, RECRYSTALLIZATION, MELTING POINT
The purpose of this lab is to use the influence of pH on the water solubility of certain organic
compounds to separate a mixture containing a carboxylic acid, an amine, and a neutral organic
compound. This macroscale experiment will use a separatory funnel for extractions.
This lab will also demonstrate the purification of solids by different methods of crystallization,
and the identification of unknown compounds by comparison of melting points to literature
values, including the use of the mixture melting point method, to prove the structural identity of
two samples.
Acid/Base Extraction
Most organic carboxylic acids (with more than 5 carbons) are not very soluble in neutral water.
Treatment of a carboxylic acid with dilute aqueous NaOH produces the corresponding sodium
carboxylate salt. Due to its ionic character, the sodium carboxylate salt is soluble in water but not
very soluble in organic solvents. If the basic aqueous solution is then made acidic by addition of
aqueous HCl, the sodium carboxylate salt will be converted back to the original carboxylic acid,
which is not water soluble.
NaOH
RCO2H
-
+
HCl
RCO2 Na
water insoluble
RCO2H + NaCl
water soluble
water insoluble
Likewise, most organic amines are not soluble in neutral water. Treatment of organic amines
with aqueous HCl produces the corresponding ammonium salt. The ammonium salt is soluble in
water but not very soluble in organic solvents. If the acidic aqueous solution is then made basic
by the addition of aqueous NaOH, the ammonium salt will be converted back to the original
amine, which is not water soluble.
HCl
RNH2
water insoluble
RNH3
+
Cl
-
water soluble
NaOH
RNH2 + NaCl
water insoluble
By taking advantage of these solubility properties, it is possible to separate a mixture containing
acidic, neutral, and basic components using acid and base extractions.
Before beginning, make sure that you are familiar with the proper techniques for using a
separatory funnel (Technique 12.7, p. 677). You should also make a flow chart that outlines the
separation (see p.687).
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Recrystallization
Once the acid, amine, and neutral compound have been separated using the extraction technique
described above, all three will be further purified by crystallization. The two methods of
crystallization will be: a) microscale using a Craig tube, and b) semi-microscale using the mixed
solvent method. Once recrystallized, the structure of each substance will be determined by its
melting point. For one of your purified compounds, you will prove its identity to an authentic
sample using the mixed melting point method. Read Techniques 8, 9, 10, and 11 in PLKE to
become familiar with the techniques and theory behind crystallization and melting points
(emphasize sections 8.3, 8.5, 8.6, 8.7, 9.1-9.5, 9.7, 11.1, 11.2, 11.4, 11.5, and 11.8-10).
You are to choose ONE of bottles #1-5, each of which contains a mixture of three compounds,
one acid, one amine, and one neutral component, all in equal amount by weight. The acid
component of your mixture will be benzoic acid or toluic acid. The amine will be ethyl 4aminobenzoate or 4-dimethyl aminobenzaldehyde. The neutral compound will be pdibromobenzene or benzophenone.
Br
CO 2 H
NH2
CO 2 CH 2 CH 3
Br
ethyl 4-aminobenzoate
benzoic acid
p-dibromobenzene
CO 2 H
CH3
o-toluic acid
O
H3 C
N
H3 C
O
H
4-(dimethylamino)benzaldehyde
benzophenone
PART I: SEPARATION
Extraction procedure. Dissolve 1 g of a mixture of an acid, base, and neutral (from bottles #15) in 15 mL of diethyl ether. Caution: Ether vapors are highly flammable! Keep ether solutions
in the hood whenever possible – this will help keep ether fumes from building up in the lab.
Transfer the ether solution to a separatory funnel and add 5 mL of 1 M HCl (Be sure to use 1 M
and not 6 M HCl, which will be used in a later step!). Gently shake the separatory funnel for
several minutes, venting it frequently to avoid the build up of pressure. Place the separatory
funnel in a ring stand and allow the ether and aqueous layers to separate. Uncap the funnel and
drain the lower aqueous layer into a flask. Repeat the extraction with another 5 mL of 1 M HCl.
Save the ether layer in the separatory funnel for later use. Combine (in a beaker) and cool the
acidic aqueous extracts in an ice-water bath. Add 6 M NaOH (≈ 2 mL) until the aqueous layer is
basic (use pH paper to confirm). Collect the precipitate on a Buchner funnel by vacuum filtration
(see Figure 8-5, PLKE p. 622). Wash the filtrate with cold water (≈ 2 mL) and allow it to air-dry
until the next period.
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Extract the saved ether solution sequentially with two 5-mL aliquots of 1 M NaOH. Again, save
the ether layer in the separatory funnel. Combine and cool the basic aqueous extracts in an icewater bath. Add 6 M HCl (≈ 2 mL) to the basic aqueous extracts until it is acidic. Collect the
precipitate on a Buchner funnel by vacuum filtration. Wash it with water (≈ 2 mL) and allow it to
air dry until the next period.
Add 10 mL of saturated aqueous sodium chloride solution to the ether remaining in the
separatory funnel and shake gently. Allow the layers to separate and discard the lower sodium
chloride layer. Pour the ether layer into a beaker containing 1 g of anhydrous Na2SO4 and allow
it to stand for about 15 minutes. Decant the ether into a 25-mL round bottom flask and evaporate
the ether by using the rotary evaporator (see your TA for instructions). Optional: you can also
evaporate the ether using a stream of air directed into a test tube containing the ether (connect
amber tubing to your air line and at the open end, insert a pipet as in figure 7.17A on p. 612 of
PLKE). When all of the ether has evaporated, weigh the remaining solid (note: if an oil forms
instead of a solid, just let it cool on ice until it solidifies).
PART II: RECRYSTALLIZATION
Recrystallization procedure. The solids from the three layers (acid, base, neutral) will now be
purified by recrystallization. None of these recystallizations will require a hot filtration step.
Step 1. The solid isolated from the base extraction (the second extraction of this lab) will be
recrystallized using the Craig tube. This is the microscale method and you can follow the
procedure below. For this method you will only recrystallize 60 mg of the material, as
microscale is not effective for amounts above 100 mg. The solvent of choice is water.
Place 60 mg of the solid in a Craig tube with about 0.5 mL of hot water. (You will want to
maintain a container of boiling solvent, which will be added later). Dissolve the sample by
heating the mixture on a sand bath or aluminum heating block (two students can share one hot
plate). Stir the mixture with a spatula using a twirling motion to prevent bumping. Add small
portions of boiling solvent until all the soluble material dissolves.
After all the soluble material has dissolved, place the Craig tube in a beaker of warm water.
Insert the Teflon plug and allow the system cool to room temperature. The warm water in the
beaker will insure slow cooling and increase the chances of growth of pure crystals. When the
water in the beaker reaches room temperature, cool the Craig tube in an ice bath. Crystals should
be forming at this point.
When your visual inspections suggest crystal formation is complete, remove the solvent from the
Craig tube using the following procedure. Place the Craig tube assembly in a plastic centrifuge
tube (glass centrifuge tubes may break in the centrifuge) as shown in Figure 8.11 on p. 626 of
PLKE. Be sure to use thin copper wire for the Craig tube assembly, as thick wire will not fit.
Make sure that the Craig tube is resting at the bottom of the centrifuge tube. Counterbalance the
centrifuge, and spin for 30 seconds. Stop the centrifuge and remove the Craig tube from the
mother liquor in the centrifuge tube using the copper wire. Disassemble the Craig tube and
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collect the crystals by scrapping off the Teflon plug and the inside of the tube onto a piece of
pre-weighed, clean filter paper.
Step 2. For the solid isolated from the acid extraction (the first extraction of this procedure,
containing the amine) you will carry out a semi-microscale recrystallization using the mixed
solvent method as described on p. 667 of PLKE. Use ethanol and water as the solvents. You will
use an Erlenmeyer flask (see Figure 11.4 on p. 651 of PLKE) to carry out this procedure.
Step 3. Recrystallize the solid isolated from the ether layer (the neutral compound) using hexane.
You may use the microscale method (using the Craig tube) or semi-microscale method (using an
Erlenmeyer flask). If you choose the latter, the following procedure may be helpful to you:
Place your solid in a 10-mL Erlenmeyer flask. Add the minimum amount of hot hexane (heating
on a steam bath) required to dissolve the solid. This is achieved by adding hexane drop-wise
until all of the solid dissolves. Once the solid is dissolved, set the solution aside and allow to cool
to room temperature. Next, cool the solution using an ice bath until crystal formation appears to
the eye to be complete. Filter the crystals on a Buchner funnel and wash with cold hexane
(approximately 0.5 mL).
PART III: MELTING POINT DETERMINATION
Weigh and take melting points for the three recrystallized compounds. If the compounds are not
yet solvent free, melting points can be taken during the next lab period.
The melting point values from the literature are:
Benzoic acid: 122 ˚C
4-(Dimethylamino)benzaldehyde: 74 ˚C
Dibromobenzene: 89 ˚C
Toluic acid: 110 ˚C
Ethyl 4-aminobenzoate: 94 ˚C
Benzophenone: 50 ˚C
For at least one of your recrystallized compounds, use the mixture melting points method (PLKE
p. 630-631), to prove the identity of your sample to an authentic sample provided by your TA.
For example, if you believe your acid is benzoic acid, prepare and melt a 1:1 mixture of your
recrystallized sample with an authentic sample of benzoic acid and prepare and melt a 1:1
mixture of your recrystallized sample with o-toluic acid. Be sure to explain the results in your lab
report.
Turn in purified samples of your acid, base, and neutral compounds in capped vials to your TA.
Be sure to label each with the chemical structure and your name.
Waste Disposal: All aqueous acid and basic waste goes into the Aqueous Acid/Basic Waste jug
located in the hood. Ether goes into the Organic Solvent Waste jug (do not put aqueous
solutions in this container!). There is also a jug for Solid Waste (sodium sulfate & organic
solids). Do not put filter paper, cotton, etc. into the solid waste jug – the trash is fine.
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EXPERIMENT 2:
PURIFICATION OF A FERROCENE MIXTURE USING
THIN-LAYER CHROMATOGRAPHY & COLUMN CHROMATOGRAPHY
Pre-Lab Questions:
1.
TLC and column chromatography are examples of a “solid-liquid” partitioning technique.
What is meant by this? What is the solid? What is the liquid?
2.
Explain why organic compounds containing more polar functional groups migrate more
slowly on silica gel. (Reference to PLKE Figure 19.2 might be helpful.)
3.
Explain why increasing the polarity of the mobile phase increases the mobility of organic
compounds on silica gel. (Again, reference to PLKE Figure 19.2 might be helpful.)
4.
How would you modify the ratio of hexane:acetone if it was your goal to reduce the Rf of a
ferrocene using this eluent, for example, if a 70/30 hexane/acetone mixture was initially
used?
5.
Describe three methods to visualize colorless organic compounds on a TLC plate.
6.
An orange compound was added to the top of a chromatography column. Solvent was added
immediately, with the result that the entire volume of solvent in the solvent reservoir turned
orange. No separation could be obtained from the chromatography experiment. What went
wrong?
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PURIFICATION OF A FERROCENE MIXTURE USING
THIN-LAYER CHROMATOGRAPHY & COLUMN CHROMATOGRAPHY
In CHEM 165 laboratory, you performed a Friedel-Crafts acylation of ferrocene, creating a
mixture of the starting compound and its mono- and di-acetylated forms. In this experiment, you
will separate, by column chromatography, this mixture of organometallic ferrocenes. This
mixture contains ferrocene, monoacetylated ferrocene, and/or diacetylated ferrocene (see
structures below).
Initially, during the NMR and thin-layer chromatography (TLC) lab, you will assess the
composition of the ferrocene mixture using thin-layer chromatography (TLC). (PLKE Technique
20 gives an in-depth description of TLC; read sections 20.1, 20.2, 20.4, 20.5, 20.6, 20.9, and
20.10). You will use TLC on a regular basis throughout the quarter so it will be important to get
a thorough understanding of TLC and its many uses.
From TLC analysis, you should be able to determine the contents of the mixture (which
ferrocenes are present) and what will be the most appropriate solvent system for the column
chromatography purification of the mixture. Column chromatography will take place during the
next lab period. (Read PLKE Technique 19 for a full explanation of column chromatography).
Ferrocene is a compound that contains an iron (II) ion sandwiched between two flat
cyclopentadienyl anions. Ferrocene and the mono- and di-acetylated derivatives are also shown
below.
O
O
-
-
Fe++
Fe++
Fe++
-
-
-
Ferrocene
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-
CH 3
Acetylferrocene
CH 3
O
CH 3
1,1'-Diacetylferrocene
49
Thin layer chromatography (TLC). Commercial TLC plates and micropipets will be provided
in this lab.
Procedure. Prepare a solution of the ferrocene mixture by dissolving 5-10 mg of the mixture in
2-3 mL of methylene chloride or use the premade solution provided. You will spot this solution
on a TLC plate and develop it using 70/30 hexane/acetone as the solvent. (See PLKE Technique
20.4. Your TA will also give a demonstration of proper TLC spotting.) You should practice
making very small spots (~1-2 mm diameter) by very briefly touching the capillary to the plate.
There will also be individual standards of ferrocene and mono- and di-acetylated ferrocene
(dissolved in methylene chloride) to spot along side your mixture.
Once you have developed your TLC plate using the 70/30 hexane/acetone mixture you will then
run TLCs using various proportions of hexane/acetone as developing solvent. By noting the
various distances the ferrocenes travel (Rf values) you will determine which will be the best
solvent system to purify your product mixture using column chromatography (see PLKE pp.
761-762 for more details). The solvent system that best separates the spots and gives Rf values
between 0.2 and 0.5 is the system of choice for column chromatography*.
* Columns tend to "run" faster than TLC plates so we recommend that you reduce the percentage of polar solvent
by about 10% (e.g., if you found that the best solvent system for TLC was 60/40 hexane/acetone, then use 70/30
hexane/acetone for your column).
Column Chromatography. In this lab you will separate 100 mg of the ferrocene mixture into its
individual components using a silica gel column. Columns can be checked out at the stockroom.
Procedure. Prepare approximately 50 mL of your solvent system of choice (determined above).
To the column add a cotton plug followed by 0.5 cm of sand, and finally 15 mL of your solvent
system. You are now ready to prepare your silica adsorbent. You will use the "slurry" method.
Please read section 19.7 in PLKE for a more complete explication of the following procedure.
In an Erlenmeyer flask, slowly add 5 g of silica gel to 30 mL of your solvent system. Heat may
be liberated as you add the silica; any solvent that evaporates can be replenished. Swirl the
solution a couple of minutes to ensure that slurry is free of trapped air bubbles. Place a beaker
below the column, open the stopcock, and add in portions the slurry to the column, making sure
to swirl the slurry before each addition. As you add, and until the silica has settled, tap on the
side of the column with a pencil (the wooden part) to aid in the packing of your adsorbent. Note:
Always keep the solvent level above the adsorbent – add extra solvent when needed.
Once the adsorbent has settled in the column and a well-defined top has formed, add solvent
from the collecting beaker to your column and let it run through two or three more times to
ensure a tight pack. The column should not contain any air pockets at this point. Finally, add 0.5
cm of sand to the top of the silica and adjust the solvent level so that it is just above the silica (12 mm).
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The next step is to apply your sample to your column. Dissolve 100 mg of ferrocene mixture in
approximately 1 mL of methylene chloride. With a pipet, add this solution down the sides of the
column as to not disturb the surface of the silica (the sand acts as a protective layer). Carefully
open the stopcock to allow the solution to absorb onto the silica – be sure not to let the solvent
fall below the silica surface but to keep it at the same level as the silica surface. Now add 1 mL
of hexane down the sides of the column and again drain until the surface of the silica is just at the
same level as the solvent. Repeat this procedure two more times. At this point, all of your
compound should be bound on the silica in a tight band. Now carefully fill the column with
solvent (the first few mLs should be pipetted in as to avoid disturbing the silica surface). Once
the column is filled, you may begin your elution. Collect only the colored fractions and add
solvent as needed. You may recycle the solvent in fractions that are colorless. Try to achieve a
flow rate of 1-2 mL per minute. If the flow rate is too slow you can push the solvent through
using air from your air line*.
* This is done by placing a rubber thermometer adapter at the top of your column and then inserting a pipet that is
connected by amber tubing to an airline, into the thermometer adapter. When using this system be sure that the
pipet is not too tightly inserted into the adapter as it needs to be easily pushed out if the air pressure gets too high.
Collect the colored fractions in separate, tared Erlenmeyer flasks. You may leave these in your
drawer to evaporate or, if time permits, evaporate using the rotary evaporator. To remove silica
gel from you column when are done, attach amber tubing to the tip or the column and push it out
with air pressure (hook it up to your hoods airline). Any small amount of silica sticking to the
sides of the column can be washed out with tap water and rinsed down the drain. Do this in your
own hood and not out by the waste hood. Put spent silica in the silica waste jug.
Weigh, determine the yield, and record melting points of the separated compounds. The
following melting points have been reported in the literature:
ferrocene
acetylferrocene
1,1'-diacetylferrocene
mp 173-175 ˚C
mp 81-83 ˚C
mp 125-127 ˚C
Your TA will divide the class into groups of three students to learn to use the NMR
spectrometer. Your group members should each contribute one NMR sample, so that your group
acquires a spectrum of each of the three ferrocenes. Be sure to interpret all three proton NMR
spectra in your lab report.
Be sure to turn in your purified samples of the three purified compounds, each in a capped vial
labeled with the chemical structure and your name, to your TA.
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EXPERIMENT 3:
REACTIVITIES OF SOME ALKYL HALIDES
Pre-Lab Questions:
1.
In both parts of this lab, you use the rate of appearance of a precipitate (NaCl, NaBr, AgCl,
or AgBr) as a measure of the rate of a nucleophilic substitution reaction. Using chemical
equations like these on PLKE p. 176, explain why for this to work it is important that the
precipitation reactions (for example Na+ + Cl- → NaCl (solid) or Ag+ + Cl- → AgCl (solid)
are fast relative to the nucleophilic substitution. (It might help you to imagine what would
happen if this were NOT true.)
2.
Suggest a reason that Part A calls for a “dry” test tube. How might the results differ if the
acetone were very wet (Hint: water is a very polar solvent)?
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REACTIVITIES OF SOME ALKYL HALIDES
In this experiment, you will determine the order of rates of reactivity of some alkyl halides
toward nucleophilic substitution. In Part I, you will use the rates of appearance of precipitated
NaCl or NaBr as an indicator of the rate at which alkyl halides react with iodide ion (I-) in
acetone. In Part II, you will use the rate of appearance of precipitated AgCl or AgBr as an
indicator of the rate at which alkyl halides react with ethanol, a polar solvent.
The experiment is conducted as described in PLKE Experiment 20, pp. 176-178.
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EXPERIMENT 4:
DEHYDRATION OF 4-METHYLCYCLOHEXAN-1-OL
Pre-Lab Questions:
1.
Write a step-by-step mechanism for this reaction.
2.
What controls the temperature of the distilling head as the product distills?
3.
Why is it very important to leave the distillation apparatus open to the atmosphere (rather
than sealed)?
4.
What is the purpose of the condenser?
5.
What is the purpose of the sodium sulfate?
6.
Describe at least one specific spectroscopic feature in all three of the IR, 1H NMR, and GCMS spectra that will distinguish the starting alcohol from the product alkene.
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DEHYDRATION OF 4-METHYLCYCLOHEXAN-1-OL
In this experiment, you will prepare an alkene by acid catalyzed dehydration of a secondary
alcohol. The chemical reaction is similar to that described in PLKE, pp. 211-217, except on four
times the scale of experiment 25B (PLKE, pp. 214-216). The experiment demonstrates
distillation of a low boiling reaction product from a higher-boiling starting material.
Assemble a macroscale fractional distillation apparatus as shown on p. 724 of PLKE, Figure
14.11. Using a graduated cylinder, transfer 16.0 mL of a cis/trans mixture of 4methylcyclohexan-1-ol to a 50-mL distilling flask. Add a magnetic stir bar or boiling stone.
When everything else is ready to go (and your apparatus is fully assembled) use a disposable
pipette and graduated cylinder to add 4.0 mL of 85% phosphoric acid (H3PO4) to the alcohol in
the flask. Promptly swirl the contents to mix the liquids, and connect the distilling flask to the
apparatus.
Circulate cooling water through the condenser. Heat the mixture until it boils then begins to
distill. The products should distill over the range of 100-105 ˚C. The distilling head temperature
should begin to fall when the reaction is complete. A few milliliters of undistilled liquid should
remain in the distilling flask. Discontinue heating.
Remove and cap the receiving flask. Using a disposable pipette, add about 4 ml of saturated
aqueous sodium chloride. Cap and (holding cap in place) gently shake. Vent. Allow layers to
separate. Remove lower (aqueous) layer with a disposable pipette. Add anhydrous sodium sulfate
to remove residual water and swirl. Recap flask. Swirl occasionally for 5-10 minutes. The
distillate will be clear, not cloudy, when it is dry. Transfer the dry distillate to a tared vial with
cap. Weigh the product and calculate the yield.
Determine the IR and 1H NMR spectra of your product. (As noted in PLKE, because of the high
vapor pressure of the product, you must “work quickly” to obtain an IR spectrum before the
sample evaporates.) Note that IR spectra for the starting material and product appear on pp. 215216 of PLKE.
Measure the molecular weight of your product using the GC-MS. See GC-MS operating
instructions earlier in the manual.
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EXPERIMENT 5:
DIELS-ALDER REACTION
Pre-Lab Questions:
1.
Suggest a reason that an excess of sulfolene is used in this reaction. (Hint: Look up the
boiling point of 1, 3-butadiene.)
2.
What is the purpose of the reflux condenser?
3.
Suggest a reason that xylenes are used as the solvent for this reaction. Do you think toluene,
benzene, or pentanes might work equally well?
4.
What is the purpose of the activated charcoal?
5.
Why used cold rather than room temperature hexanes to wash the solid product?
6.
Name at least one spectroscopic feature you will look for to distinguish the product from:
a. sulfolene
b. 1, 3-butadiene
c. maleic anhydride
d. a 1:1 mixture of 1,3-butadiene and maleic anhydride
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DIELS-ALDER REACTION
This experiment demonstrates a reaction run under reflux. A somewhat challenging to handle
gas, 1, 3-butadiene, is generated and consumed in situ.
3-sulfolene
maleic anhydride
To a 50-mL round-bottom flask equipped with a reflux condenser (see PLKE p. 601, Fig. 7.6B)
sequentially add 25.0 mmol 3-sulfolene, 19 mmol of maleic anhydride, and 5 mL of xylenes.
Swirl the mixture for about 5 minutes to facilitate dissolution of the solids, then add a boiling
chip. Heat the mixture to gentle reflux for 30 minutes. Avoid overheating!
Cool the reaction mixture for a few minutes. Add 20 mL toluene, then ~0.5 g activated charcoal.
Heat the mixture on a steam bath until the product dissolves. Filter the hot mixture through fluted
filter paper (see PLKE p. 619) into an Erlenmeyer flask. Heat the filtrate on a steam bath until
the product dissolves, then add hexanes just until the solution becomes turbid. Cool the solution
on ice, and then collect the solid product by vacuum filtration (see PLKE pp. 621-623). Wash the
solid product with a small volume of cold hexanes.
Allow product to air dry until next lab period. Determine yield, m.p., IR (nujol mull) and 1H
NMR (CDCl3).
Turn your product, in a capped vial, in to your TA. Be sure to label with the chemical structure,
weight of material, m.p., and your name.
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EXPERIMENT 6:
GRIGNARD REACTION
Pre-Lab Questions:
1.
Write balanced chemical equations for the three main steps in the Grignard synthesis of a
carboxylic acid (Grignard reagent formation, C-to-C bond formation, neutralization of
halomagnesium salt of carboxylic acid).
2.
Write a balanced equation for the reaction of a Grignard reagent with H2O.
3.
Why is it important for Bunsen burners to be off before ether is used?
4.
What is the purpose of the CaCl2 filled tubes (Hint: CaCl2 is also called “Drierite”)?
5.
Describe specifically how an IR spectrum can easily distinguish the starting bromoarene
from the carboxylic acid product.
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GRIGNARD REACTION
This experiment demonstrates how to conduct a reaction that includes an air- and water-sensitive
intermediate substance, a Grignard reagent. You will prepare a Grignard reagent (an
organomagnesium compound) and to convert it to a carboxylic acid by reaction with carbon
dioxide. A Grignard reagent is formed by reaction of an alkyl or aryl halide with magnesium
metal in diethyl ether.
Mg
RX
δ-– δ+
behaves like: R····MgX
RMgX
Et2O
The alkyl group of the Grignard reagent has partial ionic characteristics and behaves like a
carbanion. A Grignard reagent is a strong base. It will be protonated by water, alcohols, or
carboxylic acids to afford the corresponding hydrocarbon.
H2O
RMgX
RH + MgXOH
Grignard reagents react with and are destroyed by the oxygen in air. This reaction is not
generally preparatively useful. A Grignard reagent also behaves as a strong nucleophile. It will
add to the carbonyl group of aldehydes or ketones to give the alkoxide of an alcohol. It also will
react with carbon dioxide to give the salt of a carboxylic acid. In both cases, the resulting
magnesium salts may be hydrolyzed by addition of dilute aqueous acid.
RMgX
OMg X
R
R' '
R'
O
+
R''
R'
H 3O +
OH
R
R' '
R'
Because the Grignard reagent reacts with water and oxygen, it must be protected from air and
moisture. The reaction apparatus and the ether must be dry. During the reaction, the flask is thus
protected by a CaCl2 drying tube. Oxygen is excluded by allowing the ether to reflux and form a
blanket of solvent vapor above the surface of the reaction mixture.
In this experiment, bromobenzene or a bromotoluene isomer will be converted to the
corresponding Grignard reagents. Reaction of the Grignard reagent with carbon dioxide followed
by neutralization with aqueous acid will afford a carboxylic acid.
O
Br
Mg
Mg Br
CO2
OMg Br H3O+
CO2 H
Ether
Biphenyl is the main by-product in this experiment.
biphenyl
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Notes:
1. The description below does not include a purification procedure. You must decide how to
purify the reaction product and to obtain pure carboxylic acid using techniques that you have
learned so far. Discuss your proposed purification procedure with your TA before you begin.
2. Initiation of the reaction which forms the Grignard reagent is unpredictable for reasons that
no one understands. Some suggestions are included below that you can try if your reaction
does not spontaneously initiate. There is a chance that this reaction may not work on your
first attempt. If this is the case, repeat the reaction during the next lab session.
Procedure. This experiment must be completed through the reaction of the Grignard reagent
with dry ice in one lab period. It is not possible for you to store the Grignard reagent between lab
sessions. The hydrolysis and purification may be conducted in a second lab period. Check-out a
drying tube packed with Drierite from the undergraduate stockroom.
Caution! Diethyl ether is extremely flammable. NO FLAMES will be allowed once diethyl ether
is in use. Everyone in the lab must complete the operations described in this paragraph before the
TA will distribute the diethyl ether. Assemble a clean, dry 250-mL round-bottom two-necked
flask with a dry reflux condenser and addition funnel. Also prepare a drying tube filled with
Drierite similar to the one you checked out at the stockroom. You may lightly grease the ground
glass joints of your apparatus – this helps prevent moisture from entering the system. Place
drying tubes on both the addition funnel and the condenser (see figure on next page). Add 0.7 g
of magnesium turnings and the stir bar and gently flame-dry the apparatus. Let the apparatus cool
to room temperature. Attach water hoses to the condenser and turn on the cooling water.
After everyone has completed the above procedure and put away their Bunsen burners, the TA
will distribute the diethyl ether.
Have an ice bath and a steam line ready to control the rate of reaction. Dissolve 0.025 moles of
bromobenzene or bromotoluene in 25 mL of anhydrous diethyl ether. Make sure to close the
addition funnel stopcock. Place this solution in the addition funnel and replace the drying tube.
Add approximately 5 mL of this solution to the flask by briefly opening the stopcock. Stir the
mixture and observe whether any reaction begins to occur as evidenced by the formation of
cloudy material or a brown solution. If there is no reaction, heat the flask gently with a trickle of
steam from the steam line. Only a small amount of steam is needed to bring the ether to reflux. If
there is still no reaction, add a small crystal of iodine to clean the surface of the magnesium. As a
last resort, with permission of your TA, you may add about 1 mL of a successfully formed
Grignard reagent from a lab mate to your reaction mixture.
When the reaction has started, add the remaining ether solution to the reaction flask at a rate of 1
to 3 drops per second. The rate of addition should be controlled such that the reaction mixture
refluxes gently. If the reflux ring goes above the lower third of the condenser, slow the addition.
Heating should not be necessary since the reaction is exothermic. If the reaction becomes too
vigorous, it can be slowed by cooling with an ice bath. When all the ether solution has been
added, gently reflux the mixture with steam for 15 minutes. The mixture is now ready to be
added to dry ice.
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Crush 10 g (~1 pellet) of dry ice and place it in a beaker. Use the dry ice immediately after
crushing to avoid the condensation of water on the surface. Remove the condenser and addition
funnel from the reaction flask and pour the entire contents slowly over the dry ice. Allow the
excess dry ice to sublime and stir the viscous, glassy mass. If the mass is too viscous, add 15 mL
of diethyl ether.
If time permits, you can continue with the workup. If you cannot finish the experiment during
this period, cover your beaker with a watch glass, label it with your name, and give it to your TA
for safe-keeping until the next lab.
Hydrolysis procedure. If you are continuing your reaction from a previous lab period, add 20
mL of ether to the solid in your beaker and stir. Add to this a mixture of 15 g of crushed ice and
5 mL of 6 M hydrochloric acid. At this point it is up to you to devise and carry out a proper
purification procedure – both the purity and yield of your product will be considered in
determining your grade. Try to obtain a highly purified crystalline compound. Characterize your
product by IR, 1H NMR, and m.p. Discuss your proposed purification procedure with your TA
before you begin. Turn in your product to your TA, and be sure to label the container with your
name, the structure and weight of the isolated final product, the percentage yield, and the m.p.
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EXPERIMENT 7:
ASYMMETRIC REDUCTION OF ETHYL ACETOACETATE
Pre-Lab Questions:
1.
State specifically how an IR spectrum will distinguish ethyl acetoacetate from ethyl 3hydroxybutyrate.
2.
The goal of this experiment is to determine the ratio of the R- and S-enantiomers of ethyl 3hydroxybutyrate produced by a baker’s yeast reduction.
a) State why you cannot use 1H NMR directly to measure the ratio of these two alcohol
products.
b) State why 1H NMR can be used to measure the ratio of the two esters that result from
the coupling of the mixture of alcohols with one enantiomer of 2-methoxyphenylacetic
acid.
c) Would the method work if the opposite enantiomer of 2-methoxyphenylacetic acid
were used?
d) Would the method work if benzoic acid were substituted for 2-methoxyphenylacetic
acid?
e) Would the method work if racemic 2-methoxyphenylacetic acid were use?
3.
We assume without proof that the efficiencies with which the R- and S-enantiomers of ethyl
3-hydroxybutyrate are converted to the corresponding esters are identical. How would it
impact the analysis if this were NOT true?
4.
Assign the spectra of the two pure samples of each diastereoisomer (see following pages).
(Though a detailed analysis of the proton NMR splitting patterns of the two
diastereoisomeric esters is not necessary to interpret your data, working this example will
provide to you a deeper understanding of slightly more complex spectra.) Present your
assignment in a table modeled on the example below. Caution: The two protons on all
methylene (CH2) groups are diastereotopic. They thus can have distinct chemical shifts, and
distinct coupling constants with neighboring protons and with each other.
CH3-CH2-OH
A B C
A
B
C
Shift (δ)
Multiplicity
Coupling (Hz)
1.23
3.69
2.61
t
dq
t
JAB = 7
JAB = 7, JBC = 5
JBC = 5
(Note: s = singlet; d = doublet; t = triplet; q = quartet)
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ASYMMETRIC REDUCTION OF ETHYL ACETOACETATE
This experiment uses common baker's yeast as an asymmetric reducing agent to transform an
achiral starting material, ethyl acetoacetate, into a mixture of two enantiomeric ethyl
3-hydroxybutanoates in unequal amounts.
O
HO
Bakers' yeast
O
O
O
O
sucrose aq
ethyl acetoacetate
ethyl 3-hydroxybutanoate
(R and S isomers possible)
Once you have isolated the alcohol products you will ascertain the ratio of the R and S isomers
by esterifying the alcohol mixture with enantiomerically pure (S)-methoxyphenylacetic acid.
This reaction will yield a diastereomeric pair of esters (S,S and S,R). The relative amounts of the
starting R and S alcohols can then be derived by 1H NMR analysis of the ester products by
assuming that the ratio of S,S to S,R isomers is identical to the ratio of S to R isomers in the
original alcohol mixture.
O
Ph
OH
OH
+
H3CO H
(S)-methoxyphenylacetic acid
H 3C
*
O
DCC
CH3
O
Ph
OCH2CH3
O
*
O
OCH2CH3
H3CO H
R,S mixture of chiral
reduction products
+ DCU
Diastereomeric pair of esters
(S,S and S,R)
Procedure for Day 1. Yeast reduction of a ketone. At the beginning of the period you will
need to check out a 500-mL Erlenmeyer flask. To the Erlenmeyer flask, add 150 mL of water.
Warm the water to 35 ˚C using a hot plate set on low. Once the temperature is stabilized at 35 ˚C,
add 7 g of sucrose and 7 g of baker’s yeast. Incubate this solution for 15 minutes at 35 ˚C.
Dissolve 3 g of ethyl acetoacetate in 8 mL of hexane. Add this solution to your yeast mixture
along with a stir bar and begin stirring. At the end of the period, turn your hot plate off but
continue stirring. Label the Erlenmeyer flask with your name, as your flask will be stored until
the next lab period.
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Procedure for Day 2. Isolation of the alcohol product. Check out a 250-mL separatory funnel,
a large Buchner funnel and a filter flask. Add 5 g of Celite to the yeast solution and stir for 1
minute. Let the solid settle as much as possible (wait about 5 minutes). While the solution is
settling, set up a vacuum filtration apparatus with trap using the large Buchner funnel. Add one
sheet of filter paper and wet. Obtain a square of cheese cloth and fold it two times to make a
3”×3” square. Wet it and place it on top of the filter paper. You are now ready to filter your
solution. First, decant and filter as much of the clear supernatant liquid as possible before adding
the Celite slurry. Wash the Celite residue with 20 mL of water (the Celite and cheesecloth waste
can go in the trash). Finally, filter the solution one more time using the plastic steri-cup filtration
apparatus (pick one up from your TA).
To the filtered solution, add 20 g of sodium chloride and swirl the solution until it dissolves.
Now extract the aqueous solution twice with two 35-mL aliquots of diethyl ether using a 250-mL
separatory funnel. If you form an emulsion, drain off the lower aqueous layer up to the emulsion.
By gently stirring the emulsion with a stirring rod you may help break it up. If necessary, you
may also transfer the emulsified portions to your glass centrifuge tubes and centrifuge the
mixture in order to separate it.
Collect the ether extracts in an Erlenmeyer flask. Dry the extracts over 1 g of anhydrous
magnesium sulfate for 5 minutes – you will analyze this solution using GC-MS (see “GC-MS”
below for prep). Decant the liquid to a tared round bottomed flask and remove solvent using the
rotary evaporator until the volume of liquid remains constant (approximately 1-2 mL). This is
your final product, the mixture of two enantiomeric ethyl 3-hydroxybutanoates (the reduced
ketones). Weigh and record the amount recovered.
IR spectroscopy. Obtain an IR spectrum of your isolated product. Look for presence of an
alcohol group (O-H stretch) and compare with the spectrum of the starting ketone (C=O stretch).
GC-MS. Dissolve 10 drops of the drying ether solution in 1.5 mL of methylene chloride and add
this to a capped vial.
NMR. Prepare an NMR sample of your product by dissolving your sample in CDCl3.
Procedure for Day 2 or 3. Esterification of the alcohol products with an enantiopure acid.
In a 5-mL conical vial, equipped with an air condenser, prepare a solution containing 3 mL of
methylene chloride, 65 mg of (S)-(+)-α-methoxyphenylacetic acid (0.4 mmol), 4 drops of ethyl
3-hydroxybutanoate (50 mg, 0.4 mmol, d 1.017 g/mL). Cool this solution to 0 ˚C and then add
0.44 mL of the provided 1.0 M solution of N,N-dicyclohexylcarbodiimide** (DCC, MW 206,
0.44 mmol) and ~2 mg 4-(N,N-dimethylamino)-pyridine (~0.02 mmol). Caution: DCC and 4(N,N-dimethylamino)-pyridine are highly toxic–wear gloves and avoid skin contact!
NCN
**dicyclohexylcarbodiimide (DCC)
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Allow the mixture to stir at 0 ˚C for 30 minutes. During this time dicyclohexylurea (DCU) will
precipitate. At the end of the reaction time, filter off the DCU precipitate using a Hirsh funnel.
Add 2 mL more of methylene chloride to the solution after it has been filtered. Using your
centrifuge tube with a cap, extract the methylene chloride solution twice with 2 mL of 5% acetic
acid solution and then twice with 2 mL of 5% sodium bicarbonate solution. (Methylene chloride
will be the bottom layer in these extractions.)
Prepare a microcolumn for filtration by placing a small piece of cotton at the constriction of a
pipet and then filling the pipet with 0.5 g of sodium sulfate followed by 0.2 g of silica gel. Clamp
the column upright and carefully add 1 mL of methylene chloride onto the column (do not
disturb the surface) and let it drain to where the solvent level just approaches the surface of the
silica gel. Just the before the solvent reaches the surface of the silica gel add the methylene
chloride solution from above and collect the eluent in a tared test tube. Once the solution has
drained to the top of the silica add another 2 mL of methylene chloride to rinse off any product
that remains on the column.
Remove the methylene chloride solvent using an air stream. Weigh the test tube after
evaporation and record the weight of the recovered product.
NMR. Prepare an NMR sample of your product by dissolving your sample in CDCl3 as solvent.
Since the S,R and S,S isomers are diastereoisomers, their chemical and physical properties (such
as NMR spectra) will be different. The proton NMR spectra of the pure S,R and S,S isomers are
shown on the following two pages. On the right hand side of each spectrum is shown the
expanded 1.1 to 1.3 ppm region. This region contains the signals for two methyl groups of
interest (labeled ‘a’ and ‘b’ on the S,R spectra). Note that the ‘a’ and ‘b’ methyl groups of the
S,S disateromer have slightly different chemical shifts from that of the S,R methyl groups.
Because of these differences we can ultimately, by integration of these signals, measure the
relative amounts of S,S and S,R in a mixture containing both.
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EXPERIMENT 8:
MULTI-STEP TETRAPHENYLNAPHTHALENE SYNTHESIS
Pre-Lab Questions:
1.
If you begin with 50 mmol of benzaldehyde, and all 4 steps in your synthesis proceed in
100% yield and you were to use all of the product of each step in the next, what would be
the yield of final product in grams? What if each step proceeds in 75% yield? 50%? 25%?
10%? Why is it especially important to obtain high yields in each step of a multi-step
synthesis?
2.
Step 3 is an example of a double aldol-dehydration reaction. Identify in the product which
carbons are derived from dibenzylacetone and which are from benzil.
3.
Identify the eight chemically distinct hydrogen types in the final product. [Hint: In the
present case, hydrogens are not chemically distinct if they are not interchanged by: a)
rotation about a C-C single bond, b) rotation about an axis of symmetry, or c) reflection
through a mirror plane of symmetry.]
4.
How can IR easily distinguish:
a. benzaldehyde from benzoin
b. benzoin from benzil
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MULTI-STEP TETRAPHENYLNAPHTHALENE SYNTHESIS
In this experiment you will carry out four consecutive organic transformations with the goal of
preparing at least a few milligrams of 1,2,3,4- tetraphenylnapthalene.
CHO
OH
Catalyst
O
Benzoin
Note: You are to conduct the first step of this sequence on the scale indicated below (50 mmol of
benzaldehyde). You will need to plan the scale of each subsequent step in the synthesis to be sure
you have enough of each of the three intermediates, not only to prepare some of the final
product, but also to be sure you have enough of each of these to characterize by TLC, m.p., IR,
1
H NMR, and have at least a few milligrams to turn in to your TA. You should either go to a
library or refer to online databases to find literature values for the melting points and IR and 1H
NMR spectra. Be sure to account for any significant differences between your data and the
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literature values. In addition to the procedures that follow, you may find it helpful to consult
PLKE experiments 36A, 36B, and 37.
Step 1. Coenzyme synthesis of benzoin from benzaldehyde. (Note: see PLKE Experiment 36A
(p. 303 ff) for background information of this reaction.)
In a 100-mL round bottom flask, dissolve 1.7 g (0.005 mol) of thiamine hydrochloride (Vitamin
B1; thiamine chloride hydrochloride) in 4 mL of distilled water. Add 15 mL of 95% ethanol and
cool the resulting solution using an ice/water bath. While you continue to cool the solution,
slowly add 3 mL of cold 3 M aqueous sodium hydroxide solution over a 7-10 minute period
(prepare the 3 M solution from a 6 M NaOH solution). Gently swirl the solution during addition
to insure thorough mixing. The solution will become yellow.
Add 5 mL (5.2 g, 0.049 mol) of fresh benzaldehyde (note the almondy smell) to the solution with
swirling. Attach a reflux condenser to the flask (see fig 7.6B on p. 601) and heat the mixture
gently over a water bath for about 90 minutes (60 ˚C recommended). Monitor the reaction by
TLC every 20-30 minutes using CH2Cl2 as eluent and UV as visualization. Allow the mixture to
cool to room temperature and then cool further in an ice/water bath. The benzoin should
crystallize out of solution during this cooling process. If the product separates as an oil, reheat
the solution and then let it cool down again slowly, scratching the flask with a glass rod if
necessary. The oil is probably a mixture of benaldehyde and benzoin. Analyze your crude
product via TLC.
Collect the solid product by vacuum filtration. Wash the crystals with cold water on the funnel.
Recrystallize from ethanol. As with all intermediates and the final product, calculate a yield,
determine the Rf, determine the melting point, measure IR and 1H NMR, and be sure to save
some of the pure product to turn in to your TA.
Step 2. Nitric acid oxidation of benzoin to benzil. (Note: see PLKE Experiment 36B (p. 309 ff)
for more information. Note that we are using nitric acid for the oxidation.)
To a round-bottom flask, add 12.5 mL of a 3:2 volume ratio of concentrated nitric acid (70%
HNO3) and glacial acetic acid per gram of benzoin (i.e., 1 g benzoin gets 7.5 mL HNO3 and 5
mL AcOH). Add your benzoin from Step 1. Heat the mixture on a steam bath in the hood. Stir
the reaction vigorously and note that the red nitrogen oxide gases will be evolved most heavily
while the benzoin oxidation is proceeding. You may follow the reaction by TLC using CH2Cl2 as
eluent and UV for visualization.
When the reaction is complete by TLC or an hour has passed, whichever comes first, pour the
reaction mixture into 100 mL of cooled distilled water in a 250-mL Erlenmeyer flask (don't
forget to rinse your flask) and stir vigorously until the oil crystallizes as a yellow solid. Collect
the crude benzil and wash it well with cold water.
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Recrystallize the product from ethanol. Scratch the flask with a stirring rod if needed to initiate
crystallization as it cools. Cool to room temperature and collect the crystals. Weigh the product
and calculate a percentage yield. Fully characterize your product as above, and save some to turn
in to your TA.
Step 3. Synthesis of tetraphenylcyclopentadienone. Place benzil, 1.0 mole dibenzyl ketone
(1,3-diphenylacetone) per mole of benzil, and absolute ethanol (anhydrous) (8 mL per gram of
benzil) in a round bottomed flask equipped with a reflux condenser and a stir bar. To the top of
the reflux condenser add a Drierite-filled drying tube. Heat the mixture (with a steam or water
bath) until all the solid dissolves. In a test tube, dissolve 0.5 mole of potassium hydroxide per
mole of benzil in absolute ethanol (10 mL/g KOH). Carefully crush the pieces with a spatula,
heating if necessary, to dissolve the KOH. Continue to heat the contents of the round bottomed
flask to just below the boiling point and slowly add the solution of potassium hydroxide through
an addition funnel (rinse the funnel with a few mLs of EtOH after the addition is complete). The
mixture should immediately turn a deep purple color (the color of the product). Allow the
mixture to reflux for 15 minutes with gently stirring. Cool the mixture in an ice water bath.
Collect the crystals, wash them with 95% ethanol, and allow them to dry for several minutes.
Weigh your product, determine a percentage yield. Fully characterize your product, as above,
and save some to turn in to your TA.
Step 4. Preparation of 1,2,3,4-tetraphenylnapththalene. (DANGER: Isopentyl nitrite is a
powerful heart stimulant and is dangerous. DO NOT breathe the vapors directly! Handle the
solution with care.)
Place tetraphenylcyclopentadienone and 1,2-dimethoxyethane (DME, glyme) (1000 mL
DME/mol dienone) into a round-bottom flask. Add 1.1 mole of anthranilic acid per mole
dienonein 1,2-dimethoxyethane (5 mL per g anthranilic acid) to the solution. Add a reflux
condenser with a drying tube, and reflux the solution using a sand bath.
Prepare a solution of 1.5 mole isopentyl nitrite per mole anthranilic acid in 1,2-dimethoxyethane
(5 mL per mL nitrite) in a graduated cylinder. Add the isopentyl nitrite solution drop-wise
through the top of the condenser over a 45-60 second period. Reflux for an additional 15 minutes
after the addition is complete. The solution should change from a deep purple color to a yelloworange color as the reaction nears completion.
After cooling the flask to room temperature, transfer the solution to a beaker containing 4:1
(volume:volume) mixture of water and methanol (about 5-10 mL of this mixture/mL of final
reaction volume). Stir the mixture to break up the precipitate. Filter and wash the precipitate with
cold methanol to remove any impurities.
Recrystallize the product from 2-propanol. Because the product is only sparingly soluble even in
hot 2-propanol, we recommend you recrystallize only about 20-30 mg of your product (to keep
solvent volumes reasonable). This should provide enough pure material to fully characterize your
product. If you have too little, record the data in this order: m.p., 1H NMR, IR, TLC, and a
sample for TA. The product can exist in two crystalline forms, one with a melting point of 196199 ˚C, the other with a melting point of 203-205 ˚C.
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CHEMISTRY 346
Lab Manual Appendix I
Infrared and Proton Nuclear Magnetic Resonance Spectra (200 MHz) for organic
starting materials used in this course.
Experiment 4: 4-Methylcyclohexan-1-ol
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Experiment 5: 3-Sulfolene
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Maleic Anhydride
Experiment 6: Bromobenzene
2-Bromotoluene
Experiment 7: Ethyl acetoacetate
2-Methyoxyphenylacetic acid
Experiment 8: Benzaldehyde
Appendix I
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1,3-Diphenylacetone
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Anthranilic acid
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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Appendix I
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