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CHEMISTRY 346
Winter 2016
Honors Organic Laboratory
Professor Paul Hopkins
Department of Chemistry
University of Washington
TABLE OF CONTENTS
Part I: General Information
Syllabus
Laboratory Report Due Dates
Reading
1-3
4
5-6
Organic Chemistry Laboratory Safety
7-11
Working with Equipment & Glassware
12-13
Working with Chemicals
14-15
Waste Disposal
16
Chemistry Undergraduate Stockroom
17-19
Laboratory Notebook
20-21
Laboratory Report Format
22-23
Tips for Writing Lab Reports
24-26
Searching the Chemical Literature
27
Rotary Evaporator
28
NMR (DPX200) Instructions
NMR Data Retrieval
29-32
33
NMR (Nanalysis) Instructions
34-37
SpinWorks Instructions
38-48
FT-IR Instructions
49-51
GC-MS Instructions
52-46
Part II: Experiments
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Experiment 1: Acid Base Extraction, Recrystallization, Melting Point
57-64
Experiment 2: Purification using TLC & Column Chromatography
65-69
Experiment 3: Reactivities of some Alkyl Halides
70-72
Experiment 4: Dehydration of 4-Methylcyclohexan-1-ol
73-75
Experiment 5: Diels-Alder Reaction
76-78
Experiment 6: Grignard Reaction
79-83
Experiment 7: Asymmetric Reduction of Ethyl Acetoacetate
84-94
Experiment 8: Multi-Step Tetraphenylnaphthalene Synthesis
95-100
Part III: Appendix I
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
A-8
A-10
A-12
A-14
A-16
1,3-Diphenylacetone
A-19
Anthranilic acid
A-21
Table of 1H NMR Chemical Shifts of Residual Solvents
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A-6
A-24
CHEMISTRY 346
Honors Organic Chemistry Laboratory
Winter 2016 Syllabus
Instructor:
Professor Paul B. Hopkins
Office: BAG 303F; Phone: 206.543.0578
Email: [email protected]
Office hours: Thursdays 2:00-3:00 pm or by appointment
Teaching
Assistants:
Patrick Shelton (Section AA—Lab meets Wed. & Fri., 3:30-6:20 pm, CHB 112)
Office: BAG 152A; Phone: 206.616.1290
Office hours: Mondays 10:00-11:00 am in the Organic Study Center (BAG 331A)
Derek Church (Section AB—Lab meets Wed. & Fri., 6:30-9:20 pm, CHB 112)
Office: CHB 217; Phone: 206.616.8276
Office hours: Fridays 4:00-5:00 pm in the Organic Study Center (BAG 331A)
Lecture:
Tuesdays 10:30-11:20 am, BAG 260
Laboratory:
Wednesdays and Fridays, 3:30-6:20 pm (AA); 6:30-9:20 pm (AB), CHB 112
Required Text:
Introduction to Organic Laboratory Techniques, A Microscale Approach, Fifth
Edition, Pavia, Lampman, Kriz, and Engel (PLKE). Note: reading assignments are
listed following the Lab Report Due Dates.
Exams:
Midterm: In class, Tuesday, February 16, 2016
Final: Monday, March 14, 2016, 10:30 am-12:20 pm
Grading:
8 lab reports
Pop Quizzes (Up to 5 @ 10 pts. ea.)
Midterm examination
Teaching assistant evaluation
Lab notebook
Final examination
Total Points
Class Schedule
January 5
6
8
Week 2 12
13
15
Week 3 19
20
22
Week 4 26
27
0BU
325
0-50
75
25
40
100
565-615
Lecture: Intro, Acid/Base Extraction
Lab Check-in
Acid-Base Extraction/Recrystallization/Melting Points
Lecture: Recrystallization, Melting Point
Acid-Base Extraction/Recrystallization/Melting Points (continued)
Thin Layer Chromatography (TLC) and Column Chromatography
Lecture: Chromatography, Proton NMR
TLC and Flash Column Chromatography (continued)
Reactivities of Alkyl Halides
Lecture: Reaction Methods, Distillation
Dehydration of 4-Methylcyclohexan-1-ol
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Week 5
February
Week 6
Week 7
Week 8
2
Week 9
March
Week 10
29
Diels-Alder Reaction
2
3
5
9
10
12
16
17
19
23
24
26
Lecture: Grignard Reaction, Infrared Spectroscopy
Grignard Reaction
Grignard (continued)
Lecture: Asymmetric Reduction, Proton NMR (coupling)
Grignard (continued) and Asymmetric Reduction
Asymmetric Reduction (continued)
*Midterm Examination*
Asymmetric Reduction (continued)
Asymmetric Reduction (continued) and Tetraphenylnapthalene Synthesis
Lecture: Tetraphenylnapthalene Synthesis
Tetraphenylnaphthalene
Tetraphenylnaphthalene (continued)
1
2
4
8
9
11
14
Lecture: Mass Spectrometry
Lecture: Carbon NMR
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; these methods remain useful in
current research.
3. Improve your ability to communicate concisely and clearly in scientific writing.
3BU
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.
U
U
U
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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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. Paul Miller in Bagley 303D.
4BU
Proper Procedures for Unavoidable Absences
1. Report your absence from an hourly examination within 72 hours to Dr. Paul Miller in
Bagley 303D ([email protected]), and
5BU
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. Miller 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 14, 2016---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.
Access and Accommodations
If you experience barriers based on a disability or temporary health condition, please seek a
meeting with Disability Resources for Students (DRS) to discuss and address them (011 Mary
Gates Hall, 206.543.8924 (V/TTY), [email protected] or disability.uw.edu). If you have already
established accommodations with DRS, please communicate your approved accommodations to
me at your earliest convenience so that we can discuss your needs in this course.
Your experience in this class is important to us, and it is the policy and practice of the University
of Washington to create inclusive and accessible learning environments consistent with federal
and state law. Disability Resources for Students offers resources and coordinates reasonable
accommodations for students with disabilities and/or temporary health conditions. Reasonable
accommodations are established through an interactive process between you, your instructor(s)
and DRS. If you have not yet established services through DRS, but have a temporary health
condition or permanent disability that requires accommodations (this can include but not limited
to; mental health, attention-related, learning, vision, hearing, physical or health impacts), you are
welcome to contact DRS at 206.543.8924 (V/TTY), [email protected] or disability.uw.edu.
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CHEMISTRY 346
Winter 2016
Laboratory Report Due Dates
Report
1
Acid-Base Extraction, Recrystallization, Melting Point
2
Flash column chromatography
1
Acid-Base Extraction Regrade (optional)
3
Reactivities of Alkyl Halides
4
Dehydration of 4-Methylcyclohexan-1-ol
5
Diels-Alder Reaction
Grignard Reaction
7
Asymmetric Reduction
8
Tetraphenylnaphthalene
*Final Examination*
Jan 22, 2016
Jan 27
Jan 29, 2016
Feb 5
Feb 3, 2016
Feb 10
Feb 5, 2016
Feb 12
Feb 5, 2016
Feb 12
Feb 12, 2016
Feb 19
50
6B
30
7B
8B
20
9B
10B
25
13B
12B
25
13B
14B
15B
75
*Midterm Examination*
6
Due Date
Points
Graded
Report
Return Date
Feb 16, 2016
16B
50
17B
18B
19B
Feb 19, 2016
Feb 26
50
Feb 26, 2016
Mar 4
Mar 14, 2016
Mar 18
20B
75
2B
23B
100
Mar 14, 2016
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CHEMISTRY 346
Winter 2016
Reading
PART 6 of PLKE consists of 29 short chapters that provide useful, practical descriptions of
techniques of use in the organic laboratory. About two-thirds of these chapters, enumerated below,
are highly relevant to the experiments you will conduct in CHEM 346; you are responsible for the
full content of these chapters by the dates indicated below. But I recognize that there will be times
during the quarter when you might need to delay a full reading. For that reason, I have indicated
below selected pages in each chapter that contain the most important content. Read these sections
first if you are pressed for time. You are not excused from reading the remaining material;
questions on quizzes and exams may be drawn from any part of each chapter.
Jan 5
Jan 12
Jan 19
Assigned Chapter
1. Laboratory Safety
5. Measurement of Volume and Weight
8. Filtration
10. Solubility
12. Extractions
Read First:
1.1
Intro, 5.4, 5.6, 5.7, 5.8
Intro, 8.1, 8.3, 8.7
All
12.1, 12.2, 12.3, 12.7, 12.9, 12.11
2. The Laboratory Notebook
3. Laboratory Glassware: Care & Cleaning
9. Physical Constants of Solids: The
Melting Point
11. Crystallization: Purification of Solids
19. Column Chromatography
20. Thin Layer Chromatography
2.2 (pp. 593-595)
3.1, 3.3, 3.9
9.1, 9.2, 9.4, 9.5
4. How to Find Data for Compounds:
Handbooks & Catalogs
13. Physical Constants of Liquids: The
Boiling Point & Density
26. Nuclear Magnetic Resonance
Spectroscopy (Proton NMR)
Intro
Intro, 11.1, 11.2
Intro, 19.3, 19.4B, 19.7, 19.8
Intro, 20.1, 20.4, 20.5, 20.6
13.1
Intro, 26.5, 26.6, 26.9, 26.10, 26.16
[NOTE ON TECHNIQUE 26, NMR: PLKE use a definition of “chemical equivalence”
that is inconsistent with common usage in this discipline. Most chemists reserve the term
chemically equivalent to describe only homotopic protons. PLKE categorize enantiotopic
and diastereotopic protons as chemically equivalent. This leads PLKE to a superficial
treatment of magnetic non-equivalence (section 26.11), involving only examples of
diastereotopic protons that are not surprisingly also magnetically non-equivalent.
Homotopic protons can be magnetically non-equivalent; an example is shown in Figure
26.22.]
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Jan 26
6. Heating and Cooling Methods
7. Reaction Methods
14. Simple Distillation
15. Fractional Distillation
Feb 2
25. Infrared Spectroscopy
Mar 1
28. Mass Spectrometry
Mar 8
27. Carbon-13 NMR Spectroscopy
Intro, 6.1, 6.3, 6.4
Intro, 7.1, 7.2
Intro, 14.2, 14.4
Intro, 15.1, 15.2
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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. Attention to your
surroundings is also very important in a chemical laboratory. 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.
Stop if anything looks wrong. No one will be criticized for asking. 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.
The success of a laboratory course of this size depends on the cooperation of individuals with one
another. 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
because someone else in the lab might not be. 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 Technique 1.
It is important for you to understand that the organic chemistry laboratory can be a dangerous place
if you or others around you fail to heed safety procedures. Technique 1 in PLKE provides a
thorough discussion of hazards in the organic laboratory, and how we mitigate them. You must
study this section.
The greatest hazard in the organic laboratory is fire. Most organic chemicals are flammable, but
organic solvents, such as diethyl ether and hexane, present a special hazard. Organic solvents are
useful in part because they can be separated from higher molecular weight substances by
vaporization. Therein lies the danger: organic compounds in the vapor state, admixed with air, can
travel undetected, are highly flammable or even explosive, and can be ignited by a heat source
such as a hot plate. For these reasons, organic chemists are extremely careful to prevent solvent
vapors from accumulating, and when solvent vapors might be present, to eliminate neighboring
heat sources. A fire requires a fuel (a reductant), oxygen (an oxidant), and an initiator (heat). We
cannot eliminate oxygen in our laboratory, so we carefully monitor the other two components, fuel
and heat sources.
If your work area catches fire, step away from it, and let your instructor take care of it.
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As unpleasant as it may be to contemplate, you need a plan for what to do if you catch fire. Know
that your lab coat will burn poorly, and thus provides considerable protection (unless of course it
is splashed with a volatile organic liquid). But if you are on fire, your goal is to extinguish the fire
promptly. It costs almost no time to shout out to whoever is nearby that you are on fire and need
help, so do so. If the fire does not go out quickly, it is generally recommended that you either stop,
drop, and roll or get to and use an emergency shower. If the shower is not near to you, there is the
danger that moving rapidly to the shower will accelerate the fire. You will need to be the judge of
which of these two options to use.
If your neighbor catches fire, you should help to alert others, especially the instructor or staff, and
help the unfortunate neighbor to remember to stop, drop, and roll or proceed to the emergency
shower.
Many thousands of students annually complete an organic laboratory course without untoward
incident. You can, as well. Adherence to safety rules is the best way to stay safe.
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.
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. If you fail to wear appropriate lab apparel
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do not be surprised when the teaching assistants or lab techs ask you to purchase Tyvek leg
coverings at the Undergraduate Stockroom (BAG 271.)
Closed-toed shoes (with socks) that cover the whole foot are the appropriate type of
laboratory footwear. Sandals, ballet flats, Mary Janes, TOMS, or 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 is 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.
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.
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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), other than in the unlikely event you elect to call for help in an
emergency, 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 do use 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. Paul Miller 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. Paul Miller.
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 do not worry about the resulting
mess. For non-emergencies, do not use the safety showers as they are designed to deliver large
volumes (tens of gallons) of water rapidly. After completing use of a safety shower, please push
up on the handle to turn off the shower; it will NOT turn off automatically. 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.
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.
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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 as much of the time as is
possible. 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 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 pipette bulbs onto pipettes. Apply just enough pressure to maintain a seal between the
pipette and the pipette bulb. Forcing the bulbs may cause the pipette to slip and break, leading to
severe cuts or puncture wounds.
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Broken glassware, used pipettes, 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 rather than the opposite. Waft fumes gently toward your face. Never point the opening of
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 him/her, but
leave the chemicals in the hood.
Proper chemical storage: All solid or liquid chemicals need to be stored in the upright position,
clearly labeled, and capped, or covered (for example, using a piece of Parafilm®). 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 stored
chemicals.
Reagents: Read the labels (contents and hazards) before using reagents. Take only as much
reagent as you need; they are expensive and create waste. When taking reagents, transfer the
amount you need to a clean beaker or other suitable container for taking the material back to your
hood. Replace the cap (except on pump-type dispensers). 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.
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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.
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 he/she 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 planet. 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 minimizing 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 disposal 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 (except water) 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. Do note that MSDSs are
inherently general, so that our method of dealing with chemical hazards in lab might differ
slightly from the specific MSDS you are referencing.
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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 Chemistry Stockroom must be returned as soon as you are
done using them, no later than the end of the lab period.
3. It is a good practice to inspect all items borrowed before leaving the stockroom window and
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 Stockroom using your Husky
Card. If you do not have funds on your Husky Card, you may charge purchases to your
chemistry stockroom account (with your Husky Card) and pay off the charge at a later date.
6. All charge accounts must be settled by the Friday before finals week, each quarter. Accounts
not settled by the end of the quarter will incur a $20.00 late fee and a hold will be placed on all
University records, including registration.
7. No stockroom privileges will be extended to students with delinquent Chemistry accounts
(delinquent = charges from a previous quarter).
8. There will be a $5.00 charge for all items returned late, dirty or without a claim ticket. 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/Check-Out Procedures
1. Note the drawer number your TA gives you when walking into the lab for the first time. This
will be your drawer/fume hood space for the quarter.
2. 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, head to the Chemistry Stockroom (BAG 271) 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.
3. 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 Stockroom (BAG 271) 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.
4. The Stockroom attendant will ask you to write the combination on the top of your card in case
you forget your combination during the quarter.
5. You are responsible for all the contents of your drawer. If any items break or are missing, you
must purchase a replacement from the Chemistry Stockroom (BAG 271). The Department of
Chemistry cannot honor claims for replacement of stolen drawer materials. Use good
judgment and keep your drawer locked when not in use.
6. The Chemistry Stockroom (BAG 271) can help facilitate an early check-out, if you drop the
class and/or you need to check-out of your drawer before the scheduled check-out day listed
on your syllabus. ALL requests to check-out outside of the scheduled period MUST be
approved by the stockroom. 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 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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How to fill out a loan-claim ticket in order to check out equipment/supplies from the
7.
Undergraduate Stockroom
(Bagley 271)
The stockroom requires a picture student ID (Husky Card)
to check out equipment.
For quicker retrieval, claim tickets are filed by
this number, not by your name.
No. 10
Date __________
Station# _______________
Name __________________________________
CLAIM TICKET
Keep the top half of the ticket. This portion
is given to the attendant when returning
items checked out.
Write down your charge number. It is
your drawer number assigned in the lab.
No. 10
STOCKROOM COPY
Date __________ Station# _______________
Name _________________________________
Course __________ Section ______________
1.
2.
3.
4.
List the items that you want
to check out on this half.
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
tickets to keep track of items not returned.
It is your responsibility that you get this
half of the claim ticket back when you
return all items.
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Bring this sheet to the lab to help with check-in and check-out.
ORGANIC CHEMISTRY GLASSWARE
Beakers
Vacuum Tube
400mL
250mL
150mL
100mL
50mL
30mL
19/22 jt.
Craig Tube/
Recrystallization
tube
plunger
Erlenmeyer Flasks
Clasien Tube
125mL - qty 2
50mL
25mL
10mL
19/22 jt.
Round Bottom
Flask w/ 19/22 jt.
3-way Connecting
Tube
250mL - 2 neck
100mL
50mL
25mL
10mL-14/10 threaded top
19/22 jt.
Graduated Cylinder
Straight Tube
Adapter
Penney Head
Stopper
w/ rubber cap
19/22 jt - qty 2
100mL
10mL - qty 2
Stir Bar
Spin Vane
Crystatization Dish
100 x 50 mm
Filter Flask
Distillation Column
Conical Vial
125mL
19/22 jt.
5mL, 14/10 joint
3mL, 14/10 joint
Powder Funnel
West Condenser
plastic
19/22 jt.
Micro Air
Condenser
14/10, 7/10 joint
Short Stem Funnel
Drying Tube
Micro Drying Tube
pyrex
19/22 joints on
top & bottom of tube
7/10 inner joint
(no rubber stoppers)
Hirsh Funnel
porcelain
Separatory
Funnel
125mL
19/22 joints on
top & bottom of funnel
Thermometer
260˚ C
* non mercury
when available
Buchner funnel
43mm
Spatula
Centrifuge Tubes
NMR Tube
glass w/ cap - qty 2
& large test tube cover
plastic
Forcepts
Test Tubes
Watch Glass
side arm
100mm
75mm
16 x 125mm - qty 10
13 x 100mm - qty 6
Pinch Clamp
Test Tube Holder
Aspirator Bottle
Filter Adapter
Keck Clamp
Glass Stirring Rod
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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 CaH 2
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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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 pellet, nujol mull), the calibration and a list of important or characteristic
bands. GC-MS 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, Technique 2.
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LABORATORY REPORT FORMAT
All laboratory reports should use the following format and length criteria. 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.
Every report should be organized as in the outline below. The final page associated with each of
the eight experiments in this manual provides helpful suggestions concerning what to include in
each section of that report. An important element of becoming an independent scientist is the
development of a sense of what is and is not important and interesting to include in such a report.
For that reason, we purposely do not narrowly specify what to include and not to include in the
report. You will need to exercise and develop this judgment.
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.
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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.
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.
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TIPS FOR WRITING LAB REPORTS
General Tips
DO:



Use succinct language and simple sentence structure. Science writing is different than
writing you may have done in freshman English class. Subject, verb, object, maybe an
occasional clause; that’s all you need.
Type your reports using double-spaced formatting. Chemical structures may be included
using ChemDraw software, available through the University, or neatly hand-drawn into
your report.
Cite any outside sources you use to write your reports.
DON’T:


Write a novel. You should have no problem describing the results of the short
experiments in this course in 3-5 pages total. Even the reports describing the longest
experiments, such as Experiments 7 and 8, should not exceed fifteen double-spaced
pages.
Leave out important information, especially information that demonstrates your depth of
understanding of the material. Be thorough. What a conundrum, right? Say more with
fewer words. The challenge for you is to figure out what is important; improving your
judgment in this respect is an important learning goal.
Purpose
DO:



Describe the purpose using one or two complete sentences.
Consider what purpose(s) your professor believes this experiment serves in furthering
your education. Why was it included in the curriculum for this course? What laboratory
skills are you learning? What concepts from your organic chemistry lecture are being
reinforced?
If your experiment involves a chemical reaction, write the balanced reaction equation
here.
DON’T:

State only that “The purpose of this experiment was to synthesize compound A.” Chances
are the chemistry department has plenty of compound A already. Instead consider
whether there is some experimental technique you are learning or whether there is some
novel feature to the reaction you undertook.
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Experimental Approach
DO:



Keep this section brief.
Cite pages in your lab manual.
Mention how you characterized your product(s).
DON’T:

Rewrite the procedure in your lab manual.
Summary of Findings
DO:


Succinctly state the outcome of your experiment, whether it was the expected outcome or
not, using key data points to support your assessment.
Carefully consider which data support the apparent success or failure of the experiment.
Does the appearance or disappearance of a particular peak in your IR spectrum provide
evidence of the change in molecular structure you believe was achieved? Are there
signals in your NMR spectrum that through their chemical shift, multiplicity, or integral
support the proposed product structure? Cite these, e.g. “The appearance of a carbonyl
stretch at 1700 cm-1 and the disappearance of an alcohol stretch at 3300 cm-1 demonstrate
that oxidation of the alcohol to a ketone was successful.”
DON’T:


Write a qualitative assessment of the relative success of your experiment without
providing specific data that support your position, e.g. “My experiment was successful
because I made the compound in 73% yield.”
Discuss every peak in your IR or NMR spectrum.
Data and Analysis
DO:

Use an unambiguous system for labeling peaks and the structural features they represent.
o Label all major frequencies in an IR spectrum, e.g. C=O stretch, O-H stretch, C-H
bend, etc.
o For NMR spectra, draw the appropriate chemical structure on the spectrum, label
all protons, and annotate the corresponding peaks, including the solvent peak and
any impurities that may be present. See attached example.
o For GC-MS data, identify the parent ion and include possible structures for at
least the three most prevalent ion peaks. If you do a library search for a peak, print
the result and include it in your report.
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

o Melting point data should be reported as a range.
o For TLC data, include an Rf value for each spot and comment on how the plate
was visualized.
Analyze your data in terms of what you are expected to learn in this course. An example:
You should explain why a doublet of doublets is observed for a particular proton in your
NMR spectrum. Which structural features give rise to this splitting pattern?
Pay particular attention to how your data support the purpose of the experiment.
Comment on any techniques that you may have learned or concepts which were
reinforced through the execution of a particular experiment.
DON’T:

Present your data in an unorganized fashion or without an in-depth analysis.
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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
A useful spectral database that includes IR, NMR, and MS data can be found at:
http://sdbs.db.aist.go.jp
An online literature search engine 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). Help in learning to use SciFinder Scholar can be
obtained by the course TAs and from the natural sciences librarian who specializes in chemistry,
Ms. Susanne Redalje ([email protected]).
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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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.
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DPX200 NMR INSTRUCTIONS
(Version 16, 1/2014)
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.
I
c
o
n
B
a
r
P
u
llD
o
w
n
M
en
u
C
o
m
m
a
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dL
in
e
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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. Do not introduce uppercase letters, spaces or symbols, etc.
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).
o IMPORTANT NOTE: Please do not change the entry DIR. This will save your dataset in a
location that cannot be retrieved remotely, either in the Study Center or CHB121 computers.
After clicking ‘OK’, go to the ‘Sample’ tab and enter a description of the experiment.
U
U
U
U
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 SpinWorks.
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 the SpinWorks software.
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
Data workup
Data workup is done on the computers in CHB 121 during lab hours or in the Organic Study
Center, which allows the NMR machine to be free for other students to take spectra.
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NMR DATA RETRIEVAL
Downloading Data (Data must be copied off the server in order to edit/work up)
1. Double Click the “NMR Data” icon which can look like any of the following icons:
2. This will open up the data folder on the NMR DPX200 Server. Find your data by
navigating through the directories on the DPX200. If you do not see your file on the list,
press “F5” on the keyboard to refresh the data list

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”).

Samples ran 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. This was the number that you signed up for in class.
3. Right-click the folder you need and choose “Copy” and then Double Click on “My
Computer” and then the “D” drive. (Example below.)
4. Right-click in the white area and choose “Paste” this will put a copy of the data on the D:
drive that you can then use. (Example below.)
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INSTRUCTIONS FOR ACQUIRING DATA ON THE
NANALYSIS 60 MHZ SPECTROMETERS
1. Check that the ring around the NMR spectrometer is green. If it is blue or red, consult
your TA.
2. Carefully pull the tube in the spectrometer up, making sure the bottom of the tube clears
the hole. Then carefully insert your NMR tube.
3. If it isn’t already open, open the NMR software controller NanalysisRemote on the
attached PC.
4. On the startup screen, choose the room that you are in and click connect. Status changes
to “Connected”
5. Once the spectrometer Status says “connected”, click browse next to “Selected
Experiment”, then choose which experiment you’re working on. This is crucial to
ensuring the correct parameters are sent to the spectrometer. Status changes to
“Experiment Ready”
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6. Once you choose the experiment, the parameter boxes will automatically be filled.
Depending on the experiment, you may be able to choose your solvent, or it might be
preselected. If the solvent drop down box is clickable, make sure the correct solvent is
chosen.
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7. Click “Run Experiment. It will take 30-60 seconds for the spectrum to be acquired. Status
changes to “Running”.
8. Once the data is acquired, status changes to “Data Ready”, Experiment status changes to
“Success”, and a preview window will appear in the bottom half of the screen. Check that
the spectrum looks approximately correct. For instance, if your compound has a benzene
ring, do you see peaks between 7-8 ppm? Don’t worry about integration or if some of the
peaks are a bit crooked at this point, it’s only to see if the NMR spectrum is generally
good.
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9. Click “Email Data” and a small window will pop-up. Enter your UW email and
password, modify (if you want to) the email subject line to include your names, and then
click “Email Data”. That will send you the NMR spectrum as a .jdx file, which can be
opened by SpinWorks in CHB 121 or the organic study center. The file name will be the
same as the email subject. If you mistype your email/password, the program will alert
you.
10. The program will confirm the email was sent and ask if there are more people in your
group. If there are, click Yes, then they can enter their email and password.
IMPORTANT: If you click “No” the system will NOT let you send any more emails.
You would have to either retake the spectrum, or have the first person forward the email
to them.
11. Once you click “No”, the program will return to Step 6. A new spectrum can be taken, or
the experiment can be changed.
12. Carefully remove your NMR tube. The next group can insert their NMR tube at this
point.
13. (strongly recommended) Go to the separate computer in CHB 121, access your email,
and check that you received the data file. If the email failed for whatever reason, now is
the time to retake the NMR spectrum rather than in a week and possibly after you’ve
disposed of your sample.
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SPINWORKS INSTRUCTIONS
1. Introduction to 1-D NMR Data Processing with SpinWorks 4
The SpinWorks is a freely available program created by Dr. Kirk Marat at the University of
Manitoba. You can learn more about the program and how to download it at the NMR Wiki:
http://nmrwiki.org/wiki/index.php?title=SpinWorks
SpinWorks can do all of the routine NMR data processing needed for Chem 241 and 242. It is
also useful for routine research work in organic chemistry, but other free programs are available
(including programs for the Mac). If you are starting a research project, you should consult with
your research director before settling on a particular program.
This manual was adapted from the Reed College manual “SpinWorks3” for the University of
1
Washington’s version of SpinWorks4. It covers basic (“1-D”) data processing for H NMR
and guides you through a typical operating session.
2. What does an NMR spectrum look like?
The following spectrum is typical.
It contains several groups of signals separated by stretches of horizontal baseline. A chemist
can extract information about molecular structure by noticing where signals appear, and also
by noticing where they don't. Because ‘absence of signal’ is just as important as ‘signal’, it is
essential to record and print a “full” spectrum, one that runs from -0.5 to about 10 ppm.
Another typical thing: the spectrum is extremely hard to read and not useful in its present format.
We could correct this by:
 printing the spectrum on a larger piece of paper
o
 rotating the image 90 on this piece of paper
 zooming in on, or “expanding” selected regions of the spectrum. An example of this
appears on the next page:
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2. What does an NMR spectrum look like? (cont’d)
A complete “expansion” might show the shape of the signals, their chemical shifts (in ppm, red
scale beneath spectrum), integrals (rising green curves and green numerical values), and the
exact frequency of each peak (in Hz, red values above peaks).
This manual shows you how to print a “full” spectrum and then how to create expansions like
this one. To do this, you will need to:
 download and process your data to make a spectrum
 control which part of the spectrum is displayed (full vs. expansion)
 analyze the spectrum by integrating and “peak picking” (getting frequencies of
individual peaks)
 print the spectrum
The description of each set of operations starts on a separate page so you can quickly find a
desired set of instructions by flipping pages. The first time, however, you should go through the
full menu without skipping any pages.
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3. Opening Software and processing your data
1. Double-click the desktop icon for SpinWorks
. A reasonably complicated looking
window opens, but most of our work will involve the menus above the data area and the
buttons to the right.
2. Click File: Open and navigate to where you copied your file earlier.
3. Locate the folder and open the file with the extension .jdx (Nanalysis 60 MHz NMR –
all 241 and 242 labs EXCEPT 242 chiral reduction) or in your folder named fid (DPX200
autosampler – 242 chiral reduction only). Your raw data should look like the following
(this is a “free induction decay” or signal vs. time spectrum):
4. Click the
button. This applies a Fourier transformation (“FT”) to your data
changing it from signal vs. time to signal vs. frequency (chemical shift). The process also
phases the spectrum (phasing affects the rise and fall of the baseline on each side of your
signal). The result should look very much like a finished NMR spectra, but of course there's
more to do before you print and analyze your spectrum.
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4. Controlling the display
What you see in your display can be controlled by a variety of vertical and horizontal
adjustments. Try each of the adjustment tools listed below. Once you have tried them, restore the
full spectrum.
Adjust VERTICAL display

Click Expt: buttons

Press “up” and “down” arrows on keyboard

Roll mouse wheel
(upper right)
Adjust HORIZONTAL display

Slide horizontal scroll bar

Click H. Exp. (“horizontal expansion”) buttons

Left Click and drag across the region to be expanded.

ZOOM – This is a four step procedure. Hint: it helps to activate the “tracking
cursor,” a vertical line that follows the mouse, before attempting this. If necessary,
press “t” on keyboard or click View: Tracking Cursor.
1. Mentally identify region to be expanded
2. Left Click on left edge of this region
(Sample) Display after steps 3 and 4:
3. Left Click on right edge of this region
Selected region and edges look like this:
4. Click on
button
(upper right)
Expanded region now looks like this:
Restore FULL spectrum display

Click
button
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5. Phasing
SpinWorks attempts to make the phasing adjustment for you automatically when you initially
process your data, but you may need to make additional adjustments.
The following diagram shows the same set of signals with “bad” and “good” phasing. Notice
the difference in the rise and fall of the baselines. Ideally, none of your peaks should appear
slanted.
Inspect the baseline around each of the signals in your spectrum. If the baseline around all of the
peaks looks acceptable, proceed to 6. Calibrating on the next page. Otherwise, additional
phasing is required. Follow these steps:
1. Hint: Adjust VERTICAL display so that the noise in the baseline is fairly large, e.g.,.
2. Click
button. This opens a small “interactive phasing” window containing
four sliders, two for ph0 and two for ph1 (“zeroth-order” and “first-order” phase controls,
respectively). These sliders have very different
effects.
a. a. ph0 – These sliders affect the entire
spectrum in the same way. Adjust them so
that the baseline around the tallest signal
looks acceptable (a thick colored vertical bar
underneath the spectrum marks the location
of the tallest signal).
b. b. ph1 – These sliders have little or no effect
near the tallest signal, but their effect grows
with increasing distance from this signal. Adjust them so that the baseline looks
acceptable around signals that are far from the tallest signal.
3. Click
button in the interactive phasing window.
Troubleshooting
 Huge errors? If you feel like you have made some huge error, simply click
in
the interactive phasing window. This will undo any changes you had made and you can


start over by clicking on
.
Stuck slider? If you move the ph1 coarse slider to the end of its range and still can’t get
the adjustments you want, move it back to the middle of its range and click either
or
in the interactive phasing window.
Upside down signals? It’s tempting to fixate on the baseline’s shape to the point that you
overlook what is happening to the signals. Signals must point up, not down. Re-adjust the
sliders so that all signals point up.
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6. Calibrating
Chemists use the signal provided by TMS to calibrate the chemical shift (horizontal) scale of an
NMR spectrum. The TMS signal usually appears further right (upfield) than any other signal in
the spectrum. Note that depending on which solvent you used, and the concentration of your
sample, you may or may not see the TMS peak. The chemical shift of the TMS signal is
arbitrarily set to 0.0 ppm (parts per million). You can also calibrate the spectrum based on the
residual solvent signal since a small portion of the deuterated solvent will be the normal nondeuterated solvent that can be seen on the spectrum. If you chose the correct solvent when you
acquired your data, SpinWorks will have attempted to calibrate your chemical shift range, but
you can do it manually. Common solvent peaks include:
Deuterated Solvent
CDCl3
D2O
DMSO-d6
Acetone-d6
Normal Solvent
CHCl3
H2O
DMSO
(dimethylsulfoxide)
Acetone
Chemical Shift
7.26
4.75
2.50
2.05
1. Zoom in on the TMS signal or your solvent signal. You may need
to do this a couple of times so that the signal looks quite broad
(see image at right).
2. Move tracking cursor to top of signal and left click. This marks
the top of the signal (see image at right).
3. Click
window.
button. This opens a small “calibrate spectrum”
4. Click
or enter “0” in the F2(PPM) text box for TMS, or click 1H next to your
solvent.
5. Click
in the calibrate spectrum window and restore the full spectrum display.
6. Check that the chemical shifts look approximately correct. For instance, if you have
benzene peaks, are they ~7-8 ppm?
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7. Integrating
Integrating the spectrum means finding the area underneath the peaks that interest you. This
peak area, or integral, is proportional to the number of nuclei that create these signals. Therefore,
an integral is useful only in comparison to another integral. Furthermore, only the relative
integral size is meaningful; two integrals with values of 1 and 4 mean exactly the same thing as
two integrals with values of 0.2 and 0.8.
Remember, only integrate the signals that interest you. Do not integrate contaminants like TMS
or the signals produced by solvent(s). It is helpful, therefore, to have identified the signals of
important and to mark out mentally the extent of each hydrogen’s signal pattern. That being said,
it’s better to integrate unimportant peaks, than to not integrate peaks that turn out to be
important. So when in doubt, err on the side of integrating everything.
When integrating splitting patterns such as doublets, triplets, or quartets, you should integrate the
entire pattern in one integral rather than integrating each “spike” separately.
SpinWorks integration involves three steps:
1. Proper phasing. We will assume this has been done already.
2. Selecting integration regions. Generally, a region should contain all of the signals
produced by one type of hydrogen.
3. Calibrating the value of one integral (optional).
The detailed instructions, beginning with “selecting integration regions,” go like this:
1. Try to parse your spectrum by identifying signals that look like they come from a single
type of hydrogen. Pay attention only to those signals that might be produced by your
1
compound. Ignore contaminants like TMS, CHCl3, H2O.
2. Move the spectrum horizontally using the horizontal scroll bar so that the left-most
pattern of interest is in the middle of the window.
3. Expand the spectrum horizontally using the
buttons so that you can clearly
see where one hydrogen’s signal pattern ends and the next hydrogen’s pattern begins.
4. Click the
button. A small “integration dialog” window
will open.
5. Left Click the baseline on the left and right sides of the signal pattern.
This will produce an integration curve and the value of the integral
underneath this curve.
6. Move the spectrum horizontally to the left until you find the next
pattern and repeat step #5.
7. When all of the integrals have been marked, calibrate one integral (see
Troubleshooting section on next page) and click
in the
integration dialog window.
1
TMS appears at 0 ppm. CHCl3 is a singlet and appears near 7.2 ppm. The moist
Seattle environment often introduces water into samples. H2O usually appears as a broad singlet near 1.6
ppm in CDCl3. Water has a different chemical shift in each solvent, similar to how the chemical shift of
alcohols can be unpredictable. Water appears at 4.7 ppm in D2O, 3.3 ppm in DMSO-d6, and 2.8 ppm in
acetone-d6.
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7. Integrating cont’d
Troubleshooting
 Calibrate your integrals. All that counts with integrals are their relative values. Values of
0.634 and 1.902 have exactly the same meaning as values of 1.000 and 3.000. That said, the
latter are easier to use. You can set one integral to any value you want as follows: left click
on the integral curve (it will be marked by a vertical line), type the value you want to this
integral to have in the text box next to the
button in the integration dialog. Then
click the
button. The values of all integrals will be adjusted. You should calibrate
integrals based on a peak whose identity you are very confident about. Methyl peaks are
often good candidates because they are large, often have simple splitting patterns, and tend
to show up at ~1 ppm where not many other peaks are.
 Integral too narrow? The most common student mistake is to set the edges of the integral
on the sloping curve of the signal instead of the flat baseline. Examples of bad and good
settings are shown below. Notice that the bad integral starts and stops on the signal, not on
the baseline. The good integral runs from baseline to baseline. Not only that, it encompasses
enough baseline on each side of the signal so that the “flat” character of the baseline can be
verified. If you integral is too narrow, delete it (see next bullet) and mark it again. Note that
the entire triplet is being integrated at the same time.
bad integral
(integral region too narrow)
good integral
(region runs baseline to baseline)
 Bad integral? Too many integrals? Delete an unwanted integral curve by left clicking on
the curve (it will be marked by a vertical line) and clicking the
button underneath
Delete. If you are really ornery, you can click the
button, by why would you want to
delete all of the integral curves?
 Integral curves too tall or too short? You can change the vertical scale of all of the integral
curves by clicking the
and
buttons.
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8. Peak picking
The most reliable way to obtain coupling constants (J values) is to measure the distance between
signals (“peaks”) in PPM. Peak picking prints the frequencies of selected peaks above those
peaks. The tops of the peaks are marked with small vertical lines (see below). Peak picking is
applied only to the peaks that you pick:
1. Setting the peak pick units.
2. Bringing the signals of interest (and only these signals) into the window.
3. Repeating steps 2-3 for different signals of interest.
Steps 2-3 can be repeated as many times as you like. You can also delete values from the list of
picked peaks when the computer becomes overly ambitious. The detailed peak picking procedure
goes like this:
1. Select Peaks and Integrals: Units: PPM.
Peak Pick: Example
2. Adjust the horizontal scale so that only the peaks of interest are
visible in the window.
3. Right Click in the middle of the peak of interest with the green
vertical line.
4. If you need to pick more peaks, repeat steps 2-3.
Troubleshooting
 Too many picks or incorrect peak picking? You can remove
some or all of the picked peaks from the current list. To remove
some, bring these peaks (and only these peaks) into the window
and select Peaks and Integrals: Clear Peaks in Region. To
remove the entire list, select Peaks and Integrals: Clear Peak
List.

Need to see an organized list of the peaks? If a list of peak is a
preferred supplement, Peaks and Integrals: List Peaks.
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9. Printing a full spectrum
A proton NMR spectrum will contain signals from every hydrogen-containing compound in
your sample. A full spectrum, one that displays chemical shifts (horizontal scale) from -0.5 and
10 ppm (12 ppm for spectra that contain carboxylic acids), will display all of these signals, both
the signals that you think your compound has produced and also the signals produced by
contaminants.
Organic chemists normally expect to “interpret” every signal in an NMR spectrum. Conversely,
they expect to find a signal for every hydrogen nucleus in their sample. The assignment of
signals to nuclei, and of nuclei to signals, means finding a satisfactory interpretation for every
signal’s chemical shift, integration, and coupling pattern. A full spectrum reveals all of the
signals and allows an unbiased observer to consider alternative interpretations of the NMR data.
Printing note: Although there is a printer in the General Chemistry study center, it is strongly
recommended that you print your spectra as PDF files, save these files in a secure location, and
then print these files on another printer.
1. Click
button to adjust horizontal display. If the chemical shift region is too
broad, select and expand the region from approximately -0.5 to 10 ppm.
2. Adjust the vertical scale (up/down arrows on keyboard) so that tallest signal fits on
screen. Hint: SpinWorks will add some text to the top of the spectrum so leave about an
inch of blank space above the tallest signal.
3. Select Edit: Plot Title and enter a descriptive title. Useful title components include: your
name, lab & Section, Lab Experiment, sample name, NMR solvent, and date. Click
to close “plot title” window.
4. Select File: Print. If necessary, find the printer named PDF Creator > Click OK > Enter
desired file name inside "Document Title" field > Click Save > A ‘Save as’ dialog box
opens up. Choose a path to save the file (either on the desktop to send it to yourself as an
email attachment or to a USB thumb drive) and click ‘Save’ to save it to the destination.
5. Find your PDF file and open it. Inspect the horizontal scale (-0.5 to 10 ppm?). Inspect the
vertical scale (Peaks large enough? Not too large?). Inspect the paper alignment
(Landscape mode?). If everything seems satisfactory, go to the next page. Otherwise,
make corrections and print your spectrum again.
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10. Printing expansions
Once you load up a spectrum with integrals and peak picks, you will want to print your data.
Unfortunately, a full spectrum will cram all of this information into a small space rendering it
unreadable in most cases (see pages 1-2 above). A better alternative is to expand regions of
interest so that the integrals and peak picks in these regions can be read clearly.
1. Zoom in on the chemical shift region of interest.
2. Adjust the vertical scale (up/down arrows on keyboard) so that tallest signal fits on
screen. Hint: peak pick data adds text to the top of the spectrum so leave about an inch of
blank space above the tallest signal.
3. Select Edit: Plot Title and enter a descriptive title. Useful title components include: your
name, lab & Section, Lab Experiment, sample name, NMR solvent, and date. Click
to close “plot title” window.
4. Select File: Print. If necessary, find the printer named PDF Creator > Click OK > Enter
desired file name inside "Document Title" field > Click Save > A ‘Save as’ dialog box
opens up. Choose a path to save the file (either on the desktop to send it to yourself as an
email attachment or to a USB thumb drive) and click ‘Save’ to save it to the destination.
5. Find your PDF file and open it. Inspect the horizontal scale (the region you intended?).
Inspect the vertical scale (Peaks large enough? Integral and peak pick data easy to read?).
Inspect the paper alignment (Landscape mode?). If everything seems satisfactory, expand
and print another region by repeating steps 1-5.
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PERKIN-ELMER FT-IR INSTRUCTIONS
For the scanning process below you will sometimes use the softkeys which are the top row of grey
keys on the keyboard. On the lower portion of the screen you will see the softkey label and below
the label is the corresponding softkey.
Taking an IR Spectrum of your sample:
1. Place your salt plate (or KBR minipress) into the 'v-groove' holder. Be sure to close the
door of the sample compartment. Press enter if the screen is blank
2. Ensure that the %T scale (vertical axis) is set at 0% and 100% by pressing the “Shift ->
Rescale” keys. Ensure the horizontal axis is set at 4000 cm-1 by pressing the “Shift ->
Rearrange” keys.
3. Press the green 'scan' key followed by the grey 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.
4. Press the “Shift -> Peakcur” keys. (A vertical cursor is displayed. The cursor data box is
at the bottom right of the screen reporting the wave number.)
5. Press the “Shift -> Mark” keys. A small vertical bar will be displayed on the screen. When
you plot the spectrum the marked peaks will display the wavenumber for that peak.
6. Press the “arrow keys” to move the cursor to the left or right. Mark all the significant
peaks in your spectrum.
7. Press the Plot key located in the lower portion of the keyboard to obtain a paper copy of
the spectrum.
If your spectrum does not show the full range from step 2 (you accidently hit the wrong
key), use the following sequence of functions to reset the range and fill screen with the
spectrum: Shift -> Rearange -> Shift ->Rescale
Important Note for Solid Samples using KBr pellets
Always ensure you have completed step 2 before you scan. This shows the %T scale (0 to
100%T). A KBr pellet is less transparent than a KBr salt plate, therefore the amount of light
reaching the detector (%T) will be diminished. After you scan, observe the amount of light
transmitted on the baseline (%T). If no light is transmitted (the KBr pellet is completely opaque)
a baseline of 0%T would be observed. If all the light is transmitted a baseline of 100%T would
be observed.
If your sample has at least 5%T, you will be able to obtain useful data. Use the IR function keys
to expand the spectra. Press Shift -> Autex, the spectrum will be expanded to fill the screen.
Useful Keys to Manipulate the data:
Moving the spectrum or cursor: 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
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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).
36B
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)
U
U
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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GC-MS DATA ANALYSIS
General Approach
Entering the GC-MS “Data Analysis” Program
The screen should be showing the “Enhanced Data Analysis” or “Data Analysis” program. (If
not, click on the “Data Analysis” icon the desktop).
Open your GC-MS data file from the local drive.
1. Go to ‘file’ and click on ‘load data’. Select the path where you saved your file (Data Retrieval
instructions suggest the D: drive). (Example below is with CA001).
2. Select the file that you pasted and click “ok” and your ‘Total Ion Chromatogram” (TIC) will
appear. In the upper left hand corner you should see “[2] TIC: ‘YourFileName’”. Check to
confirm that you brought up the correct file.
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Integrate the TIC spectrum:
3. To integrate the peaks, go to ‘Chromatogram’ and select ‘AutoIntegrate’. If ‘AutoIntegrate’
is not an option, click ‘Integrate’. Click ‘no’ on the message box. Now each peak on your
chromatogram will have an exact retention time listed.
4. Go back to ‘Chromatogram’ and select ‘Percent Report’. You will get a white window that
will show the Area Percent Report of your sample. This will show your peak numbers, retention
time of the peaks, area of the peaks and what the percentage of the sample each component is.
Right click in the white space, select print. In the popup dialog box, choose PDF Creator and
click OK. A new dialog box will open up and you enter a desired file name inside the field
“Document title” and click ‘Save’. A new ‘Save as’ dialog box opens up. You can save the PDF
file to your USB thumb drive or save the file on desktop and send it to yourself as email
attachment. Click the “×” on the ‘Area Percent Report’ window to close it.
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5. Go to ‘file’ and ‘print’. Select “TIC & Spectrum” and hit ok. Give a desired file name within
the field “Document title” and Click Save. A ‘Save as’ dialog box opens up. Choose a path to
save the file (either on the desktop to seed it as a PDF attachment to yourself via email or to your
USB thumb drive).
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.
Determine the identity of the peaks:
If you would like to zoom into your peaks, drag while holding the left mouse button loosely
around the peaks. To go back to the full chromatograph at any time, click the left mouse button
until you get to the point you want.
7. To select the correct database, go to ‘Spectrum’ and select ‘Select Library’. The selected
library that needs to be used is the NIST08.l, if it isn’t, click browse and find,
C:\DATABASE\NIST08.L, click ok.
8. Using the right mouse button, double click near the middle of the largest peak. Below will
now be the Mass Spectrum (MS) of this peak. Go to ‘file’ and print out the TIC and Spectrum.
9. To identify this peak, double click anywhere on the MS with the right mouse button.
 This will initiate a library search that will match your spectrum to Mass specs
contained in a large electronic library. The search results table will have selectable
choices with the top one being the highest quality match to your experimental mass
spectrum.
 Expect the highest quality match to be the proper identification, but not always. To
print the graphical spectrum comparison, select what you think the correct matched
compound name from the results table and click the ‘Print’ button. Click on ‘Done’
when finished with the search.
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You can locate the retention time at the top of the MS window (bottom one of the two). This
example shows, “[1] Scan 70 (3.799 min): AA010.D\data.ms” Your samples would say, “[1]
Scan XXX (your retention time): YourSection0#.D\data.ms”
10. Go back to the TIC and double click with the right mouse button on other peaks to generate
its MS and subsequent library search.
11. Quit the Data Analysis window when you are done by selecting Exit from the File menu.
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GC-MS DATA RETRIEVAL
Downloading Data (Data must be copied off the server in order to edit/work up):
Double Click the icon for which your data was collected, “GC-MS PC” icon:
This will open up the data folder on the GC-MS Data Server
Find your data in “Undergrad” -> “your class” -> “your folder, experiment, or data file” ->
“Your data file” If you do not see your file on the list, press “F5” on the keyboard to refresh the
data list.
Right-Click the folder you need and choose “Copy” and then Double Click on “My Computer”
and then the “D” drive. (Example below.)
Right Click in the white area and choose “Paste” this will put a copy of the data on the D: drive
that you can then use. (Example below.)
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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 are the solubility properties of a neutral (e.g. no acidic or basic functional groups)
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 was historically 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 or Figure 9.2. [Today a scientist would use spectra to demonstrate the
identity or non-identity of two samples.]
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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
38B
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
HCl
-
+
RCO2H
RCO2 Na
RCO2H + NaCl
water insoluble
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
NaOH
+
Cl
-
RNH2
RNH3
water insoluble
water soluble
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 (Techniques 12.7, 12.8, and 12.9, pp. 708-720). You should also make a flow chart that
outlines the separation (see p. 719).
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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.
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 4-aminobenzoate or 4dimethyl aminobenzaldehyde. The neutral compound will be p-dibromobenzene or benzophenone.
Br
CO 2 H
NH2
CO 2 CH 2 CH 3
eth y l 4 - am in o b en zo ate
b en zo ic acid
Br
p -d ib ro m o b en zen e
O
CO 2 H
H3 C
O
N
CH3
o -to lu ic acid
H3 C
H
4 -( d im eth y lam in o ) b en zald eh y d e
be nzophe none
PART I: SEPARATION
Extraction procedure. Dissolve 1 g of a mixture of an acid, base, and neutral (from bottles #1-5)
in 25 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 buildup 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. 654).
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 airline and at the open end, insert a pipet as in Figure 7.17A on p. 644 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.
U
U
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. 658 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 collect the
U
U
U
U
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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 in Sec. 11.10 on p. 697 of PLKE. Use ethanol and water as the
solvents. You will use an Erlenmeyer flask (see Figure 11.4 on p. 682 of PLKE) to carry out this
procedure.
U
U
U
U
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,
sec 9.4, p. 662), 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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LAB REPORT SUGGESTIONS
I.
PURPOSE
The title of this experiment should be helpful. What will you accomplish using these techniques?
II.
DESCRIPTION OF EXPERIMENTAL APPROACH
Again, the title should help you to concisely describe the three stages of this experiment.
III.
SUMMARY OF FINDINGS
What did you achieve and what specific observations support your conclusion?
IV.
DATA AND ANALYSIS
In this section, focus on your observations concerning the organic matter you manipulated. What
amount of the mixture did you start with? What amounts of matter emerged from the steps expected
to yield each of the acidic, basic, and neutral components prior to recrystallization? After
recrystallization? What physical property did you measure to identify these substances? What
values did you observe for these physical properties? How do these compare to the known physical
properties for authentic samples of the pure compounds? What do these data lead you to conclude
concerning the identity of the three substances in your mixture? Are there any anomalies in your
data? If so, you should discuss their possible origins, how you might avoid such anomalies, and if
you had the opportunity to repeat the experiment.
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EXPERIMENT 1: EXERCISE
“IS MY PRODUCT IN THE AQUEOUS OR ORGANIC LAYER?”
To answer this question it is helpful to know the pKa of your product. You can then adjust the pH
of the aqueous layer in your separatory funnel in order to cause your product to be present in
whichever of these two layers you desire.
Electrically neutral organic substances with few polar functional groups tend to be soluble in the
organic layer.
Charged organic substances (anions or cations) tend to be soluble in the aqueous layer.
Thus a charge-neutral organic carboxylic acid will usually be found in the organic layer, whereas
the conjugate base, the carboxylate anion, will be found in the aqueous layer:
You can control which layer most of your product is found in by adjusting the pH of the aqueous
layer, because this will shift the position of the above equilibrium. A low pH (a high
concentration of H+) will shift the equilibrium to the left, and the carboxylic acid product to the
organic layer. A high pH (a low concentration of H+) will shift the equilibrium to the right, and
the carboxylic acid (as its conjugate, anionic base), to the aqueous layer.
We can use your knowledge of acid-base equilibria as a guide to tell us just how high or low we
need to adjust the pH to move most of the organic compound to either the organic or aqueous
layer.
A-  H +
[H + ][A - ]
Ka 
[HA]
HA
K a [A - ]
=
[H + ] [HA]
 Ka 
[A - ]
log10  +   log10
[HA]
 [H ] 
log10 K a  log10 [H + ]  log10
[A- ]
[HA]
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pK a  pH  log10
pH  pK a  log10
10(pH pKa ) 
[A - ]
[HA]
[A - ]
[HA]
[A - ]
[HA]
The final equation, above, illustrates why it is sufficient to adjust the pH of the aqueous layer to
ca. 3 pH units above or below the pKa of the acid whose solubility is being manipulated. For
example, in an aqueous solution of pH 8, an acid with a pKa of 5 will be 99.9% A- and only 0.1%
HA.
10(85)  1000 
99.9
0.1
And in an aqueous solution at pH 2, an acid with a pKa of 5 would be 0.1% A- and 99.9% HA.
10(25)  0.001 
0.1
99.9
EXERCISE:
Develop a similar equation for the ionization of an organic base:
Answer:
10(pH-pKa ) =
[B]
[HB+ ]
Why in this case does a low pH (high H+ concentration) drive the organic base to the aqueous
layer (as opposed to the organic layer as was the case with an organic acid)?
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EXPERIMENT 2:
25BU
PURIFICATION OF A FERROCENE MIXTURE USING
THIN-LAYER CHROMATOGRAPHY & COLUMN CHROMATOGRAPHY
26BU
27BU
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 R f 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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28BU
29BU
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
-
-
-
CH3
Fe++
Fe++
Fe++
-
-
-
Ferrocene
Acetylferrocene
CH3
O
CH3
1,1'-Diacetylferrocene
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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 23 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 alongside 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 sec. 19.4B 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.
U
U
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 (1-2 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
airline*.
* 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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I.
PURPOSE
The title provides a strong clue as to the general technique you demonstrated and the specific
problem you solved.
II.
In somewhat more specific detail than in the preceding section, state what specific problem you
solved and how you solved it.
III.
SUMMARY OF FINDINGS
Did the separation go as expected? What specific observations indicated whether you did or did
not achieve the desired separation? What observations indicate what specific organic compounds
were present in each fraction?
IV.
DATA AND ANALYSIS
Focus on your observations concerning the organic matter you manipulated. What amount of the
mixture did you start with? What amounts of matter emerged from each chromatographic band?
What colors were these bands? What physical properties did you measure to identify these
substances? What values did you observe? How do these compare to the known physical properties
for authentic samples? Which resonances in the NMR spectra correspond to which structural
features of the molecules? Are all of your data consistent with one another? If not, can you explain
the anomalies in some rational way?
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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 those in PLKE Experiment 21, 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)?
3.
Discuss the complications you foresee, if any, that would be caused by:
a. The presence of an organic halide that is substitution-inert as an impurity in a highly
reactive organic halide being tested.
b. The presence of an organic halide that is highly substitution-reactive as an impurity
in a substitution-inert organic halide being tested.
c. Can you imagine a way to distinguish a pure highly reactive organic halide from an
unreactive organic halide contaminated with 5 mole-% of highly reactive organic
halide?
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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 21.
The most common mistake students make in this experiment appears to result from failure to keep
track of which organic halide is in which test tube! We urge you to take steps to prevent this.
It is difficult to obtain very highly pure organic halides. As you make observations and interpret
your data, it is worth considering how the presence of traces of substitution-reactive or
substitution-inert impurities might impact your results.
If time permits, you have the option to repeat some or all assays.
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I.
PURPOSE
Expand upon the title.
II.
Describe the chemical processes that are used to reveal the rates of reaction of alkyl halides.
Chemical equations will probably be helpful.
III.
SUMMARY OF FINDINGS
What reactivity trend did you observe for each of the two reaction types you studied? How are
these consistent with what you were taught about relative reactivity of alkyl halides in CHEM
335/336? Did you observe any anomalies? If so, can you offer possible explanations?
IV.
DATA AND ANALYSIS
A concise summary of what chemicals you combined, under what conditions (e.g. temp), what you
observed, and what conclusions you drew (perhaps with reference back to section II, above) seems
useful here.
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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.
7.
Suggest one or more mechanisms to account for the presence of traces of 3-methylcyclohex1-ene and 1-methylcyclohex-l-ene in the product.
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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, except on four times the scale
of experiment 24B. 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. 758 of PLKE, Figure 15.11.
Using a graduated cylinder, transfer 16.0 mL of a cis/trans mixture of 4-methylcyclohexan-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. 213-214 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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I.
PURPOSE
What important and general separation technique that you’ve not encountered previously in this
course was used? What general chemical reaction type is demonstrated? What specific chemical
reaction did you attempt/achieve?
II.
Which apparatus did you use? Which chemicals were combined? What was the limiting reagent?
What was the theoretical yield? How did you assess how long to run the reaction? Which
separation/purification technique did you use to isolate the desired organic product? How did you
characterize (in other words, obtain information about) the structure of the organic product?
III.
SUMMARY OF FINDINGS
State whether or not you succeeded in achieving the intended chemical transformation, and in what
actual yield. State concisely what evidence indicates that the structural change (alcohol to alkene)
was achieved. I suggest you save the details for section IV.
IV.
DATA AND ANALYSIS
This would be a fine place to expand upon most of the points in section II. Be sure to report the
actual yield, and an interpretation of all spectra, focusing especially on spectral features of both
starting materials and products that are characteristic of relevant structural features (alcohol,
alkene…). If you obtained any by-products, what were the structures, and can you offer a
mechanistic interpretation for their origin?
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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 rather than a lower
boiling point solvent. Why do toluene, benzene, or pentanes not 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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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. 632, 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 sec. 8.3). 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). (Note: No two protons in the final product are homotopic. As a result, the splitting pattern
cannot be interpreted without the help of a computer.)
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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30BU
NOTE: Reports 4-8 all involve one or more chemical transformations. The form and content of
these reports will be quite similar to one another. Rather than repeat the lab report suggestions for
each of these experiments, I recommend you refer to the suggestions for Report 4 (Dehydration of
4-methylcyclohexan-1-ol). You may wish to prepare a “checklist” of items to consider for
inclusion in this and subsequent reports.
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EXPERIMENT 6:
GRIGNARD REACTION
31BU
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 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.
δ-– δ+
behaves like: R····MgX
Mg
RX
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'
H3O+
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 Br
Mg
CO2
OMg Br H3O+
CO2 H
Ether
Biphenyl is the main by-product in this experiment.
Br
Mg Br
+
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, your TA may be able to provide to you some pre-made Grignard
reagent that can be substituted.
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.
U
U
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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GRIGNARD REACTION
31BU
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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
Shift (δ)
Multiplicity
Coupling (Hz)
1.23
3.69
2.61
t
dq
t
JAB = 7
JAB = 7, JBC = 5
JBC = 5
U
A
B
C
(Note: s = singlet; d = doublet; t = triplet; q = quartet)
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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
O
HO
Bakers' yeast
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 with water and place it on top of the filter paper. Uniformly spread a layer of about
5 g of Celite to cover the cheesecloth. 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 5 drops of this ethereal solution using GC-MS
(see “GC-MS” below for prep) to assess the extent of reduction of ketone to alcohol. 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. Dilute 5 drops of the dried ether solution reserved above in 1.5 mL of methylene chloride
and add this to a capped vial. Analyze the sample by GC-MS.
NMR. Prepare an NMR sample of your product by dissolving your sample in CDCl3, and record
the proton NMR spectrum.
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 3hydroxybutanoate (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,Ndimethylamino)-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 a gentle air stream. You may need to provide gentle
warming of the solution (a warm water bath or your hand) to speed the evaporation and to prevent
water condensation from the air. Weigh the test tube after evaporation of the methylene chloride
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
32BU
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 or b) rotation about an axis of symmetry.
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4.
How can IR easily distinguish:
a. benzaldehyde from benzoin
b. benzoin from benzyl
5.
The final step of this synthesis includes some mechanistic steps involving reactive
intermediates you have not previously encountered. Armed with the hint that anthranilic
acid and isopentyl nitrite react with one another to produce benzyne (look up this last
substance in your lecture course text), show how a Diels-Alder reaction, followed by a retroDiels-Alder like reaction (involving extrusion of CO) can produce the final product.
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3BU
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.
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, 1H 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 literature values. In
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addition to the procedures that follow, you may find it helpful to consult PLKE experiments 32A
and 32B.
Step 1. Coenzyme synthesis of benzoin from benzaldehyde. (Note: see PLKE Experiment 32A
for background information of this reaction.) Two procedural options are presented below. Option
1 is to allow the reaction mixture to stand at room temperature for two days. If you are in a hurry,
you will need to use Option 2, which calls for heating the reaction mixture at 60 ˚C for 90 minutes.
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. If you are in a hurry, proceed to Option 2 below, otherwise use Option 1, and skip
Option 2.
Option 1. Stopper the yellow solution and allow it to stand in the dark for two days or more at
room temperature. If crystals have not precipitated at the end of this time, try gently scratching the
inside of the glass container with a glass rod. If the product separates as an oil, proceed as instructed
in Option 2 below. Cool the reaction mixture in an ice/water bath before collecting the product.
Option 2. 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.
After completing Option 1 or Option 2, 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
1
H 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 32B 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.
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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.
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 (1,3diphenylacetone) 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 dienone in 1,2dimethoxyethane (5 mL per g anthranilic acid) to the solution. Add a reflux condenser with a
drying tube, and heat the solution to reflux using a heating mantle.
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 yellow-orange
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.
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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 196-199 ˚C,
the other with a melting point of 203-205 ˚C.
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32BU
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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
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
A-8
A-10
A-12
A-14
A-16
1,3-Diphenylacetone
A-19
Anthranilic acid
A-21
Table of 1H NMR Chemical Shifts of Residual Solvents
Appendix I
A-6
A-24
A-1
Appendix I
A-2
Appendix I
A-3
Appendix I
A-4
Appendix I
A-5
Appendix I
A-6
Appendix I
A-7
Appendix I
A-8
Appendix I
A-9
Appendix I
A-10
Appendix I
A-11
Appendix I
A-12
Appendix I
A-13
Appendix I
A-14
Appendix I
A-15
Appendix I
A-16
Appendix I
A-17
Appendix I
A-18
Appendix I
A-19
Appendix I
A-20
Appendix I
A-21
Appendix I
A-22
Appendix I
A-23
Appendix I
A-24
Appendix I
A-25

- Catalyst - University of Washington

Transcription

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