CHEMISTRY 242

Organic Chemistry
Laboratory

Laboratory Manual
2018-2019 Academic Year

Dr. Lawrence Goldman

Professor Tomi Sasaki
Department of Chemistry
University of Washington
Chemistry 242 2018-2019

TABLE OF CONTENTS
Organic Chemistry Laboratory Safety .......................................................................................................... 3
Equipment and Glassware ........................................................................................................................ 7
Suggestions for Cleaning Glassware ........................................................................................................ 8
Working with Chemicals .......................................................................................................................... 9
Waste Disposal ....................................................................................................................................... 10
Laboratory Notebooks ................................................................................................................................ 11
Chemistry Stockroom ................................................................................................................................. 14
Organic Chemistry Laboratory Glassware .................................................................................................. 16
General Chemistry Review Material........................................................................................................... 17
Check-in Exercise ....................................................................................................................................... 21
Lab 1: Azo Dyes ........................................................................................................................................ 22
Background information on color and UV absorption: .......................................................................... 23
Synthesis of Azo Dyes ............................................................................................................................ 26
Dyeing Fabric ......................................................................................................................................... 27
Lab 2: Three-Step Synthesis ...................................................................................................................... 28
Step #1: Nitric acid oxidation of Benzoin to Benzil: .............................................................................. 30
Step #2: Synthesis of tetraphenylcyclopentadienone – Aldol condensation .......................................... 32
Step #3: Preparation of 1,2,3,4-tetraphenylnapththalene – Diels-Alder reaction ................................... 33
Lab 3: Synthesis of Esters ........................................................................................................................... 35
Day 1: Esterification Procedure .............................................................................................................. 36
Day 2 Analysis........................................................................................................................................ 37
Spectroscopy Worksheet ............................................................................................................................. 38
Lab 4: Qualitative Analysis (PLKE 57) ...................................................................................................... 39
Spectroscopy unknown ........................................................................................................................... 44
Sagacious Advice For The Chemical Warrior ........................................................................................ 45
I. Supplementary Classification Tests and Derivatives .......................................................................... 46
II. Supplementary Derivative Procedures .............................................................................................. 47
Qualitative Analysis Chemical Locations .............................................................................................. 49
Appendix I: GC-MS data processing and analysis instructions ................................................................. 52
Appendix II: NMR Spectrometer Instructions ............................................................................................ 58
Appendix III: IR Sample Preparation and data acquisition instructions .................................................... 75
Appendix IV: Useful spectral Data Tables ................................................................................................. 79

2
Chemistry 242 Organic Chemistry Laboratory Safety 2018-2019

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, mixed 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.

3
Chemistry 242 Organic Chemistry Laboratory Safety 2018-2019
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.

Lab Safety: You may work in the laboratory only during your scheduled section and under the supervision
of your assigned TA. You are not allowed in the lab before your lab section begins. You are required by
state law to wear approved safety goggles in the lab at all times. Goggles are to be put on before entering
the lab and must be worn until you are out the door. Goggles that have the air vents removed are not
acceptable. Departmental policy states “students not wearing goggles will be dismissed from the laboratory
immediately. A second infraction may result in dismissal for the remainder of the quarter. No makes-up
labs will be permitted. Students who have contact lenses are strongly urged to wear regular glasses instead
during the lab. Fumes from many organic solvents can dissolve in tear film and cause major eye damage if
they get under contacts.

Appropriate Clothing: A lab coat is required to be worn over your street clothes. Long pants, socks and
closed-toed shoes are required. All students need to have clothing coverage from neck to toe with no
exposure of skin anywhere. Headphones and/or texting are not permitted in lab. Please check the course
manual and the departmental website for proper lab attire:
http://depts.washington.edu/chem/courses/LabAttire.html.

Arriving Late to Laboratory: Lab periods start with a safety and procedure overview from the TA. If you
are late, you miss that information and also make your lab partner wait for you unnecessarily. If you are
late more than 30 min for any reason you will not be admitted.

Lab Clean-up: At the end of lab, clean up your work area and any areas assigned by your TA. The
procedure for hood clean-up and shutdown is posted in each hood. Turn off all equipment and
water/gas/steam lines. All equipment checked out at the stockroom must be returned by the end of lab.
Used glass pipettes and broken glass should be deposited in the glass waste boxes. Pipettes contaminated
with noxious chemicals should be placed in special “stinky” waste containers in fume hoods. Non-
compliance with the rules above will result in deduction of points from your lab score.

4
Chemistry 242 Organic Chemistry Laboratory Safety 2018-2019
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.

Closed-toed shoes (with socks) that cover the whole foot are the appropriate type of laboratory
footwear. Sandals, ballet flats, Mary Janes, shoes with open holes or without full foot coverage, flip flops,
etc., are not allowed in the lab. If you are wearing inappropriate shoes for lab, you will be asked to go to
the undergraduate stockroom to purchase yellow booties and receive a deduction of lab safety points. If
you commonly wear the shoes not allowed in lab, it’s advisable to have a pair of sneakers in your locker to
change into before the lab period begins.

Failure to remain safely dressed for the entire lab period (e.g., not wearing goggles correctly) will result in
a loss of safety lab points, and you will be sent out of lab to acquire the correct clothing. If you do not return
in time to complete your work, your absence will be unexcused.

GLOVES ARE AVAILABLE FOR EVERY 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 any computers in the lab room or instrument room. 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 3 points deducted from that lab’s
grade. This will be enforced by all TAs, instructors, lab techs, stockroom personnel, and anyone else
you encounter in the Department.
5
Chemistry 242 Organic Chemistry Laboratory Safety 2018-2019
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 or before entering
the lab.

KEEP COATS, BACKPACKS, AND OTHER NON-ESSENTIAL MATERIALS AWAY FROM

AREAS WHERE PEOPLE ARE WORKING. There are designated areas for the storage of these items
within the lab. If personal belongings are not stowed they become a tripping hazard to your friends and
colleagues. Additionally, with improper storage, hazardous chemicals may come in contact with your
belongings, increasing the risk of exposure outside of the lab. Lockers are the best place for personal
belongings that are not essential for lab.

Bagley Hall lockers (2nd and 3rd floor hallways): You may bring a lock from home and claim an empty
hall locker for use during the quarter. These are ideal for storing coats, backpacks, and other bulky items
during lab, and are the best place to store your goggles, lab coats, and proper shoes when not in lab. Lockers
must be emptied by the end of the quarter; between quarters the locks will be cut off and the locker contents
thrown away.

CELL PHONES, OTHER ELECTRONIC DEVICES, AND HEADPHONES MAY NOT BE USED
IN LAB. If you take your cell phone out during lab it will be confiscated for the lab period and you will
receive a deduction of lab safety points. Cell phone use for any reason (including texting, internet surfing,
timing reactions or doing calculations) is not permitted. Protect your cell phone from chemicals by leaving
it in your backpack. Headphones are not allowed in the lab for any reason. If you don’t remove your
headphones, you will be removed from lab and receive a deduction in safety points.

DRUGS, ALCOHOL, OR MEDICATION THAT COULD IMPAIR NORMAL MENTAL OR

PHYSICAL FUNCTIONING ARE FORBIDDEN PRIOR TO OR IN THE ORGANIC LAB. If you
are taking prescription drugs that might fall in this category, please notify your TA or Eric Camp
([email protected]) 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
Eric Camp

LEARN THE LOCATION AND OPERATION OF THE SAFETY SHOWERS, EMERGENCY

EYEWASHES, AND FIRE EXTINGUISHERS IN THE LABORATORY. In case of a spill onto a
person or clothing, IMMEDIATELY rinse with lots of water. Do not hesitate to yell for help. Use the
safety shower and/or eyewash and don’t worry about the resulting mess. For non-emergencies, do not use
the safety showers as they are designed to deliver ~50 gallons of water before shutting off. Report all
accidents to your TA, who will submit an incident report with your assistance to the University. All
instructors are certified to administer first aid. If you are not familiar with operation of the fire extinguishers,
ask your instructor to show you. Only use fire extinguishers for real emergencies, as the chemicals they
contain can cause considerable damage. For any emergency that requires the fire department, aid cars,
or police, send someone to the stockroom (BAG 271) for assistance.

6
Chemistry 242 Organic Chemistry Laboratory Safety 2018-2019
LEARN THE EMERGENCY EVACUATION PROCEDURES AND KNOW ALL OF THE EXITS
FROM THE LABORATORY AND BUILDING. A repeating siren and flashing of the FIRE indicator
is the building evacuation signal. If this alarm goes off while you are in the lab, turn off any open flames,
grab your valuables if they are immediately accessible, and leave the building as quickly as possible OR
follow instructions being given by your TA. Assemble with your lab section and TA by Drumheller
Fountain (in front of Bagley Hall). Make sure you check in with your TA when you arrive to the fountain
as all TAs will be taking attendance. All students must be accounted for at all times; DO NOT LEAVE
WITHOUT CHECKING OUT WITH YOUR TA. If you must leave while the evacuation is still in
progress, you must check out with your TA. Failure to check in for attendance at the fountain and leaving
without checking out will result in an automatic 10% deduction from your lab report.

SCHEDULED LAB TIME: You are not allowed to be in the lab before your lab section begins. Even if
the lab door is open and another TA is present you cannot enter unless your TA has arrived. Students are
allowed to work in the laboratory only during their scheduled sections and under the supervision of their
assigned TA. Removal from the lab and a deduction of safety points will be a consequence to breaking this
rule.

NEVER ATTEMPT ANY UNAUTHORIZED OR UNASSIGNED EXPERIMENTS. Follow the

experimental procedures explicitly, checking and double-checking the identity of all reagents before you
use them. There are potentially hazardous combinations of chemicals present in the laboratory. If you have
an idea for further investigation, discuss it with your instructor.

LAB CLEAN-UP: At the end of each lab period you should clean up your work area and the areas assigned
to you by your TA. In the back of each hood, there is a list stating the proper clean up and hood shut down
procedure. All equipment checked out from the stockroom must be properly returned by the end of the
period. Point deductions may be made if the lab cleanup is not done or is insufficient.

EQUIPMENT AND GLASSWARE

Fume Hoods: Do all experiments and keep all chemicals in the hood. The ventilation system draws the
fumes generated by an experiment away from the person working in the hood. The walls of the hood enclose
the experiment on five sides. Therefore, if an explosion or spill occurs, the experiment can be contained.
The sash should always be kept in a position that is low enough to protect the individual's eyes; keep
the sash lowered as much as possible without impairing your 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 time after being turned off. Neither
apparatus gives 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
7
Chemistry 242 Organic Chemistry Laboratory Safety 2018-2019
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. An insulated glove for handling hot objects 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 fire-polish chipped
glassware so it is usable, but we can’t fix cut hands. Never heat or apply vacuum on 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.

Broken glassware, used pipettes, melting point capillaries, and TLC capillaries are to be disposed of
in laboratory glass boxes only. There are two in each lab. One is located in front of the pillar by the
balances and for the pipettes 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 on the floor. 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.

Use care when using glassware, glass pipettes, melting point capillaries, TLC capillaries, or anything
made of glass. Glass can crack or break presenting the possibility of you sustaining an injury.

SUGGESTIONS FOR CLEANING GLASSWARE

See PLKE Technique 3 for more details.

It is best to clean your glassware right away before residues have a chance to “set” on the glassware. It’s
the same principle as to why it’s better to clean your dishes immediately after dinner rather than waiting a
week.

First, try soapy water. You might need to use a bit of “elbow grease” and the provided brushes to remove
solid residues. If soapy water isn’t enough, then try rinsing your glassware with a small amount of acetone.

Once you are done washing the glassware, dry the outside with a paper towel. You can dry the inside by
using the compressed air line or by rinsing with 1-2 mL of acetone. Don’t just leave wet glassware in your
drawer to dry, because as the dirty water evaporates it will just deposit the dirt back onto your glassware.

8
Chemistry 242 Organic Chemistry Laboratory Safety 2018-2019
WORKING WITH CHEMICALS
General Chemical Safety: Horseplay and carelessness are not permitted. Add concentrated acid to water;
adding water to concentrated acid can release a lot of heat and cause splattering. Waft fumes gently toward
your face rather than “sniffing”. Never point a heated test tube toward you or your neighbor; the contents
may erupt (called “bumping”) and cause serious burns. A separatory funnel must be used in a hood, vented
often, and pointed away from you and your neighbor. Don’t walk around shaking separatory funnels, test
tubes, or centrifuge tubes. Leave chemicals in your hood; if you need advice from your TA, raise your hand
or go to them, but leave the chemicals in the hood.

Proper chemical storage: All chemicals need to be stored in the upright position, clearly labeled, and
capped, or covered (for example, using a piece of Parafilm®). Storing vials in beakers is a good way to keep
vials in the upright position. Solids that are being dried until the next period need to be in a labeled beaker
or flask loosely covered with a watch glass or Parafilm®. Random drawer checks may be done and safety
point deductions will be made for improperly store chemicals.

Reagents: Read the labels (contents and hazards) before using reagents. Take only as much reagent as you
need; they are expensive and time-consuming to prepare. When taking reagents, transfer the amount you
need to a clean beaker or other suitable container for taking the material back to your desk. Replace the
cap. Let your TA know if a reagent stock bottle is empty.

Never return unused reagents to their storage containers. If you accidentally take an excess amount of
a reagent, share it with a fellow student or dispose of the excess properly.

Clean up spills immediately. The next person to come along has no way of knowing if a 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.

IMPORTANT NOTE: Do not bring contaminated material outside of the lab; if you bring glassware
or equipment back to the stockroom that still contains solvent or other reagents, that is a safety hazard
for all stockroom personnel along with anyone you walk by in the hallway. If you bring contaminated
material to the stockroom you will have 3 points deducted from that lab’s grade. This will be enforced
by all TAs, instructors, lab techs, stockroom personnel, and anyone else you encounter in the
Department.

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 yellow cabinet used to store flammable liquids) 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.

9
Chemistry 242 Organic Chemistry Laboratory Safety 2018-2019
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 they will assist you with the cleanup 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.

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 the health and
safety of the University and the surrounding community at risk and can have disastrous effects on the local
ecosystem. Chemical wastes must be managed and discarded in the most responsible and environmentally
sound methods available. UW and the Seattle Metro expect your cooperation in reducing any environmental
impact. Your laboratory manual will specify how to dispose of chemicals used during the laboratory period:
make note of these instructions in your lab notebook. Do not put chemicals into boxes of broken glass
or wastebaskets. Waste containers for other materials will be provided. If you are unsure of how to
dispose of a particular material, ask your instructor.

Waste disposal in CHEM 220/241/242/346/347/462: In general, nothing can go down the drain or into
the trash! Use specific waste bottles (acetone, organic solvents, and 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, or other non-powders
into this jug.

All non-chemical solid waste used in this class should go into the trash, unless otherwise noted. Assuming
that they are not heavily contaminated, paper towels, matches, pH paper, etc. should be placed in the trash,
NOT the sinks. Likewise water that has not been contaminated, for instance the water used in a water bath,
can simply be poured down the sink.

10
Chemistry 242 Laboratory Notebooks 2018-2019
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!

LABORATORY NOTEBOOKS
Use a carbonless copy notebook and a waterproof ballpoint pen with black or blue ink. Spiral notebooks and
pens with water-soluble ink are not acceptable. You can use the same notebook you used in Chem 241 as long
as there are at least 30 unused pages. Recording the details of each experiment is a crucial part of practicing
science. If you carry out an experiment without producing an easy-to-follow record of your experimental plan,
the materials used, and observations of the results, then what you have done simply cannot be called science.
Data can only be considered scientific evidence if it can be reproducibly obtained, and it is impossible for
someone else to attempt to reproduce your data if you don’t keep a good notebook. You will turn in some of
your notebook page copies with your pre-lab report, and the rest of the notebook page copies with your post-lab
report. Your notebook should have numbered pages and a table of contents, and should be written with ink, not
pencil. Here are some guidelines: (another sample notebook is provided on Canvas)

Parts of the notebook written before lab starts and turned in with your pre-lab report:
o Goals: The date, a title, and the purpose of the experiment – what are you trying to achieve? You
should be more specific than “Goal – to synthesize 2-heptanol”

o Safety: What are the major safety hazards in the experiment? You should include all reactants,
solvents, products, AND equipment. This can be included in your reaction table

o Reaction table: A table that includes data for all of your reactants, solvents, and products. Any
information that might be useful during the experiment should be included. For instance, solvent
density is relevant during extractions and solvent boiling point is relevant during recrystallizations.
Relevant information includes (but is not limited to):
o Name, including any abbreviations you are using
o Formula Weight (g/mol), density (for liquids), melting point (for solids), and boiling point
(for liquids)
o Amounts of each reagent you are using, in either grams or mL.
o Moles of all reactants (millimoles will usually be more convenient)
o Molar Equivalents (page 18)
o Theoretical yield, in both moles and mass, of your product
o For reactions where you don’t initially know your exact reactant, the prelab will explain
how you should write the initial reaction table. Generally you will write the table for a
specific reactant and/or amount. Then after you determine the identity of your unknown,
you can go back and change the numbers / calculate yield appropriately.
o Procedure: The procedure should NOT be a word for word copy of the lab manual. It should be
detailed enough for you to follow it without referring back to the lab manual.

o Diagrams: Drawings or diagrams for any complex apparatus or procedure. Examples of this might
include a picture of glassware for the first time you set up a distillation apparatus, or a flow chart
for a liquid-liquid extraction procedure.

11
Chemistry 242 Laboratory Notebooks 2018-2019
Parts of the notebook written during or after lab and turned in with your post-lab report:
o Any changes to your procedure, for instance a change to the reaction scale. Also, be specific about
what you did. If you ran a TLC, specify the eluent. If you dried your organic solvent, specify the
drying agent, etc.

o Observations, both quantitative AND qualitative, including the phase, color, and amount of
material isolated, percent yield where applicable, and any other important data like melting points,
spectral absorbances, Rf values from TLC, color changes, and unforeseen circumstances such as
spills or accidents. You should include qualitative observations for EVERY experiment since you
will always observe something.

o A brief conclusion of what the experiment accomplished (e.g. “The unknown ester was determined
to be methyl benzoate and it was synthesized in 58% yield”)

A sample notebook section is provided on the next page. Another sample notebook is provided separately
on Canvas.

12
Chemistry 242 Laboratory Notebooks 2018-2019
Example Notebook Page:

Experiment 5
7-Dec-2012 Literature reference: Vincent, S. P. Chem. Comm. 2011, 47, 1321.
Purpose To synthesize Pent-4-yn-1-yl pivalate
Balanced Equation

Materials
Chemical Name Safety Assessment Notes† FW (g/mol) Equiv Amount mmol Density
4-Pentyn-1-ol Irritant 84.12 1.0 1.4 mL 15.0 0.904 g/mL
Pivaloyl chloride Lachrymator 120.58 1.2 2.22 mL 18.0 0.979 g/mL
Pyridine Flammable, Affects CNS, 79.1 10.0 12.13 L 150.0 0.98 g/mL
Teratogen
Dimethylaminopyridine Toxic 122.17 0.1 180 mg 1.5
(Product) Pent-4-yn-1-yl Toxic 168.23 1.0 2.52 g 15.0
pivalate
(Product) Pyridinium Corrosive, Irritant 115.56 1.0 1.73 g 15.0
chloride
Procedure
Flame-dry a 25 mL flask then add (dimethylaminopyridine) and suspend in (pyridine). While stirring in an
ice bath, add (4-pentyn-1-ol), then add (pivaloyl chloride) slowly. Stir for 2 hours. When complete, filter
through a pad of celite with about 50 mL of diethyl ether, then concentrate under vacuum. (pent-4-yn-1-yl
pivalate) can be isolated by chromatography on silica gel. Characterize by 1H NMR.
Observations
After 2 h this was a white opaque mixture. At this time, TLC with 10% ethyl acetate in hexanes showed
completion. After chromatography, a clear, colorless liquid was isolated. Purity confirmed by NMR.
Yield
1.85 g of material recovered (11.0 mmol, 73% yield) [provide calculations]
Conclusion
Pent-4-yn-1-yl pivalate was synthesized in 73% yield. NMR confirmed the product had a purity of 42%.
Overall, the experiment was successful in producing a reasonable amount of product, although a more
effective purification would be helpful.
†REMEMBER: You need to review the MSDS for each chemical well before your lab. Writing Safety notes is
an important part of the work and you don’t want to lose points for not reviewing the MSDS and WRITING
DOWN the SAFETY NOTES in the appropriate column. If the lab does not involve a reaction, you still MUST
INCLUDE safety notes about materials you are working with.
Keep in mind that your notebook is not meant to be as verbose as your lab manual. It should be information-
dense. It’s not a bad idea to set a goal of fitting each experiment into two pages max while still being able
to conduct the experiment using your notebook as a reference instead of your lab manual. Consider that in
the real world, chemists don’t have lab manuals to go by – they follow experimental plans that were written
out in their notebooks prior to entering the lab.
Read PLKE Technique 2 for more information on Laboratory Notebooks.

13
Chemistry 242 Chemistry Stockroom 2018-2019
CHEMISTRY STOCKROOM
Bagley Hall 271 phone: 206-685-9761 & 206-543-1607 (vm)
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 up 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.

14
Chemistry 242 Chemistry Stockroom 2018-2019

How to fill out a loan-claim ticket in order to check out equipment/supplies from the 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 _________________________________
The bottom half is what we file. It will be
Course __________ Section ______________
returned to you when you return the items
you have checked out. We use these tickets
1. to keep track of items not returned. It is
2. List the items that you want your responsibility that you get this half of
3. to check out on this half. the claim ticket back when you return all
4. items.

15
Chemistry 242 Organic Chemistry Laboratory Glassware 2018-2019
ORGANIC CHEMISTRY LABORATORY GLASSWARE
Bring this sheet to the lab to help with check-in and check-out.

16
Chemistry 242 General Chemistry Review Material 2018-2019
GENERAL CHEMISTRY REVIEW MATERIAL
Below are some pieces of information from general chemistry lecture/lab that may be useful.

A: Molar Equivalences
Even though most organic reactions involve 1 molecule of each reactant, there are some cases where it is
practically useful to use an excess of 1 or more reactants. In this case, molar equivalences are used to
show the relative amount of each reactant. This allows the overall reaction to be scaled up as much or
little as desired. Compare this with a cookie recipe that might say “use 0.5 cups of sugar for each cup of
flour”.

Molar equivalences are generally not included for solvents, since they are not part of the reaction. Molar
equivalences are generally not included for solvents because they are regenerated at the end of the reaction
and the exact amount of catalyst isn’t important.

Example: To work well, the following reaction requires 1.5 equivalences of the alcohol. If 750 mg of the
product is desired, how much of each reactant should be used?

1 mol ester 1 mol carboxylic acid

0.75g ester ∗ ∗ = 0.0046 mol benzoic acid (4.6 mmol)
164.2 g ester 1 mol ester
122.1 g ben.
0.0046 mol benzoic acid ∗ = 𝟎. 𝟓𝟔 𝐠𝐫𝐚𝐦𝐬 𝐛𝐞𝐧𝐳𝐨𝐢𝐜 𝐚𝐜𝐢𝐝 (560 mg)
1 mol ben.
1.5 mol alcohol 60.1 g alc. 1 mL alc.
0.0046 mol benzoic acid ∗ ∗ ∗ = 𝟎. 𝟓𝟐 𝐦𝐋 𝐢𝐬𝐨𝐩𝐫𝐨𝐩𝐚𝐧𝐨𝐥
1 mol ben. 1 mol alc. 0.79g alc.
Note that we didn’t include equivalences for the sulfuric acid and diethyl ether since they are a catalyst
and a solvent, respectively.

B: Percent Recovery vs Percent Yield

Percent recovery applies when a chemical reaction has not occurred. If a compound is being purified,
then the theoretical recovery is the starting mass. Percent recovery should never be above 100%. If it is,
that usually indicates human error. For instance, not properly removing solvent or drying the product.

In contrast, percent yield applies when a chemical transformation is taking place. It refers to the relative
number of moles of product compared to the number of moles of reactant. It is calculated with
stoichiometry and must involve a conversion to moles rather than a direct comparison of reactant mass
with product mass. For many (but not all!) organic reactions, 1 reactant molecule leads to 1 product
molecule,. For instance, 1 molecule of propene + 1 molecule of HBr produces 1 molecule of 2-
bromopropane. Percent yield is calculated when a chemical reaction is occurring. Like percent recovery,
percent yield should never be above 100%

17
Chemistry 242 General Chemistry Review Material 2018-2019
Example: The following reaction is carried out. 0.34g of product is initially isolated. After purification,
0.24g of pure product is isolated. Calculate the % yield of the reaction and the % recovery for the
purification.

1 mol alkene
0.41g alkene ∗ = 0.0058 mol alkene used (5.8 mmol)(𝑙𝑖𝑚𝑖𝑡𝑖𝑛𝑔)
70.1 g alkene
1𝐿 2 mol bromine
3.2 mL bromine ∗ ∗ = 0.0064 mol bromine used (6.4 mmol)(𝑒𝑥𝑐𝑒𝑠𝑠)
1000 𝑚𝐿 1L bromine
1 mol product 230 𝑔 𝑝𝑟𝑜𝑑𝑢𝑐𝑡
0.0058 mol alkene ∗ ∗ = 1.35 grams product (theoretical yield)
1 mol alkene 1 𝑚𝑜𝑙 𝑝𝑟𝑜𝑑𝑢𝑐𝑡

Percent yield is based on the FINAL compound isolated.

0.24𝑔 𝑖𝑠𝑜𝑙𝑎𝑡𝑒𝑑
% 𝑦𝑖𝑒𝑙𝑑 = ∗ 100% = 𝟏𝟖% 𝐲𝐢𝐞𝐥𝐝
1.35 𝑔 𝑡ℎ𝑒𝑜𝑟𝑒𝑡𝑖𝑐𝑎𝑙
0.24𝑔 𝑝𝑢𝑟𝑒
% 𝑟𝑒𝑐𝑜𝑣𝑒𝑟𝑦 = ∗ 100% = 𝟕𝟏% 𝐫𝐞𝐜𝐨𝐯𝐞𝐫𝐲
0.34𝑔 𝑐𝑟𝑢𝑑𝑒
Comparing these tells us that the purification went pretty well, but it was the reaction that gave us such a
low final yield.

C: Precision and Reporting Numbers

Unlike gen chem labs, we will not worry too much about accuracy, precision, and significant figures.
That being said, you should avoid reporting results to an level of precision that implies more confidence
than we have. Here are 2 examples:

1 - % yield calculations. Considering the human error associated with these techniques, you can report %
yield and % recovery to a whole number %. So in the example from section B, the % yield is 18% rather
than 17.8% or 17.8409% yield.

2 – melting points. We always report melting points as a range. Standard ranges for a pure compound are
2-3C. Since the range is more than 1C, there is no reason to include decimals. For instance, a melting
point range of 142.6-144.8C provides EXACTLY the same information as 143-145C, but the former
implies a level of confidence that we don’t actually have.

18
Chemistry 242 General Chemistry Review Material 2018-2019
D: Looking up Safety Information
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, Safety Data Sheets (SDS, formerly
called MSDS) are readily accessible to all students. They contain information about physical properties of
the chemical and identify any hazards associated with the chemical.

Safety information should be looked up in advance of each experiment and entered into your lab
notebook. One of the lab instructors recalls an incident from their undergraduate research days when they
were carrying out a reaction involving DDQ (dichlorodicyanobenzoquinone, an oxidizing agent). Had
they looked up its safety information, they would have seen that it can release cyanide if exposed to water
and reactions involving DDQ should be carried out in fully anhydrous solvents. Not knowing this, they
carried out the reaction in a solvent containing moderate amounts of water. During the reaction they got
dizzy and had to leave the lab. Further analysis showed they were suffering from a mild case of cyanide
poisoning. BE AWARE OF THE PRIMARY SAFETY HAZARDS FOR THE CHEMICALS YOU
ARE WORKING WITH!

Do note that SDSs are inherently general, so that our method of dealing with chemical hazards in lab
might differ slightly from the specific SDS you are referencing. SDSs 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

When reading an SDS, most of the core health safety information is in Section 3 - hazards
identification. Flammability information may be in Section 5 - fire data.

You may also look at the risk statements in section 15 - regulatory information. Risk statements are
numbered, for instance "R23: toxic by inhalation" or "R11: highly flammable".

**Specific note if you are using the UW catalog of SDSs

(https://cspc.admin.uw.edu/mychem/uwnetid/inventory/InvChemSearch.aspx, requires NetID). If you see
the line "Other Health Hazards - Including Carcinogens" in the fire code section, that does NOT mean the
compound is necessarily a carcinogen. It just means that firefighters treat it as potentially creating
carcinogens when it burns.

19
Chemistry 242 General Chemistry Review Material 2018-2019
E: pH, pKa, and Ionization
𝑏𝑎𝑠𝑒
Recall the Henderson-Hasselbalch equation. 𝑝𝐻 = 𝑝𝐾𝑎 + log( 𝑎𝑐𝑖𝑑 ) Without getting too much into
logarithms, what this equation tells us is:
When pH=pKa, we have equal amounts of acidic and basic forms
When pH > pKa, we have more basic form present than acidic form
When pH < pKa, we have more acidic form present than basic form

If the pH and pKa are more than 1 unit apart, we can assume that only 1 form is present.

For carboxylic acids and other acidic functional groups, the acidic formal is neutral and the basic form is a
negatively charged ion.

For amines and other basic functional groups, the basic form is neutral and the acidic form is a positively
charged ion.

Generally organic molecules are organic soluble if they are neutral, and they are water soluble if they are
charged.*

Example: Hexanoic acid has a pKa of 4.9 and hexylamine has a pKa of 10.2. At what pH values will
each of these be water soluble?

Hexanoic acid will be water soluble when it is ionized to hexanoate. That will be >1 pH unit above the
pKa. So hexanoic acid will be water soluble when pH > 5.9

Hexylamine will be water soluble when it is ionized to hexylammonium . That will be >1 pH unit below
the pKa. So hexylamine will be water soluble when pH < 9.2.

* Technically the neutral compounds still have a small water-solubility. In the case of hexanoic acid and
hexylamine, their water-solubility is approximately 1 gram / 100 mL. In the big picture, this is a relatively
small solubility and these neutral compounds will be considerably more soluble in organic solvents
compared to water. In contrast, sodium hexanoate and hexylammonium chloride will be much more soluble
in water than organic solvents.

20
Chemistry 242 Check-in Exercise 2018-2019

CHECK-IN EXERCISE
Prelab Checklist
□ Print out and carefully read the syllabus and course guidelines from the Canvas course site.
□ Print out and read the General Information section of the Lab Manual and bring it to lab.
Make sure you include the Organic Chemistry Glassware page (page 20) to expedite check-in.
□ Bring all required lab supplies (Approved safety goggles, lab coat, lab notebook, ball-point pen).
□ Wear lab-appropriate clothing (see General Information section for more information).
□ Before lab, read PLKE Technique 1 (Laboratory Safety) Techniques 3 and 4 (Laboratory Glassware & How
to Find Data for Compounds).
□ To prepare for the check-in exercise, review IR and NMR spectroscopy (Loudon Chapters 12/13 or McMurry
Chapter 13)
□ This exercise does not require a written prelab in your lab notebook, so copies of notebook pages need not be
turned in at the beginning of this lab period.
□ You will work in groups of 3-4.

21
Chemistry 242 Lab 1: Azo Dyes 2018-2019
LAB 1: AZO DYES
Scenario: You are working as an intern at a fabric company. The company is looking to design a new line
of clothing in a striking range of colors. They have turned to you and your fellow interns to synthesize new
organic dyes that have eye-catching colors. They’re giving you access to their chemical supplies to see
what interesting compound you can come up with. They also want you to see if your dye will lead to
dynamic clothing – clothing that changes color depending on the temperature or other physical conditions.

You decide to synthesize an azo dye since you are aware of some other azo dyes that people have used in
the past. Azo dyes are often intensely colored because of their high level of conjugation.

HO HO

N N
N N

CH3 CH3

CH3 N
N
Sudan II
CH3
 max = 493

Sudan IV
 max = 520
You remember that azo dyes can be synthesized by converting an primary aryl amine into a diazonium ion,
then reacting it with an activated aromatic compound. Each of you and your fellow interns will choose a
different primary amine and activated aromatic compound to synthesize a different azo dye. That way you
can see what range of colors can be produced.

You decide to also test some easily controlled physical conditions to see if that changes the color of your
dye. You will vary the pH, salinity, and temperature.

Lastly, you will need to check how well your dye successfully colors an assortment of fabrics and present
that to your boss to see if your dye will be chosen for the new clothing line.
X

X
acitvated aromatic
X= NH 2, OH, OR
NH2 NaNO2
+
N N N N
H3PO4
primary amine diazonium salt azo dye

22
Chemistry 242 Lab 1: Azo Dyes 2018-2019
BACKGROUND INFORMATION ON COLOR AND UV ABSORPTION: Dyes are
molecules that selectively absorb wavelengths of light within the visible range of the electromagnetic
spectrum (400-800 nm), the region to which the human eye responds. The white light we receive from the
sun contains all the wavelengths within the visible range; when white light passes through or is reflected
from a substance that selectively absorbs a particular wavelength, we see the wavelengths that remain, and
the object appears colored. Filtering orange light out of “white” light, for example, results in a blue-green
(cyan) hue. The hue resulting from the removal of a color from white light is that color’s complementary
color.

Complementary Colors

Color absorbed Wavelength absorbed (nm) Color observed

Red 647-700 Green
Orange 585-647 Cyan (green-blue)
Yellow 570-585 Blue
Green 491-570 Red
Blue 424-491 Yellow
Violet 400-424 Yellow-green

What determines which wavelengths of light a colored substance absorbs? The color in organic dyes is a
consequence of the presence of one or more chromophores. Chromophores in organic dyes are generally
large systems of conjugated double bonds (alternating double and single bonds). It is this delocalized
electron system that absorbs selected wavelengths from the light. The wavelength of light that is absorbed
is determined by the amount of energy required to promote an electron from the ground state to an excited
state. The relationship between the wavelength absorbed (λ) and the energy required to promote an electron
is the familiar equation E = hc/, where h is Planck’s constant and c is the speed of light. Thus, the larger
the energy difference between the ground and the excited state, the shorter the wavelength of the light
absorbed.

It is found experimentally, and it can be shown using molecular orbital calculations, that in general, the
more extensive the size of a delocalized π system (in other words, the larger the number of conjugated
double bonds present), the lower the energy gap between the ground and excited electronic states, and thus
the longer the wavelength of light absorbed.

Dyes also often contain auxochromes, substituents attached to a chromophore that modify the ability of that
chromophore to absorb light. The auxochrome may or may not be directly conjugated to the chromophore..
Auxochromes can influence the intensity of a dye, and they can also provide a site by which the dye can
chemically bond to a fabric. Auxochromes include alkyl groups, and O/N/S containing substituents.

23
Chemistry 242 Lab 1: Azo Dyes 2018-2019
In this lab, you will synthesize an organic dye that contains both aryl and azo functionality (see above). To
explore the impact of conjugation on the wavelength absorbed, consider two commercially-available azo
dyes:

HO HO

N N
N N

CH3 CH3

CH3 N
N
Sudan II
CH3
 max = 493

Sudan IV
 max = 520
Notice that Sudan IV has a more extensive system of conjugation and thus absorbs a longer wavelength of
light (lower energy).

The color we see is also dependent on the auxochrome, how the dye is bound to the fabric, the pH – the list
goes on. As part of this lab, you will look at the effect of a change in the pH on the color of the dye, and
sometimes it is quite dramatic. This is generally due to a change in the charge on the dye molecules or a
change in the degree of conjugation. Adding or subtracting auxochromes can also affect the electron
delocalization and thus change the color. Therefore, much of the work in discovering new dyes is “trial and
error”.

24
Chemistry 242 Lab 1: Azo Dyes 2018-2019
Choice of reactants:
You will choose two compounds from the list on this page according to the following rules:
1) Compound 1 must be a primary amine(R–NH2).
2) Compound 2 can be any compound, even the same as compound 1
3) No 2 students in a single section can choose the same 2 compounds in the same order
4) No more than 5 students in a single section can choose the same compound in any role.
To facilitate this, your TA will either assign compounds or have a sign-up sheet in lab.
Warning: Many Amines #2 #3 #4
are toxic compounds;
avoid skin contact.
#1

2-Amino-1,5- 6-Amino-2-
Aniline naphthalenedisulfonic acid 3,5-Dimethoxyaniline
naphthalenesulfonic acid
MW: 93 MW: 303 MW: 153
MW: 223
#5 #6 #7 #8

6-Amino-1- 3-Amino-1,5- N,N-Dimethyl-1-

8-Amino-1,5-
naphthalenesulfonic acid naphthalenedisulfonic acid naphthylamine
naphthalenedisulfonic acid
MW: 223 disodium salt MW: 171
monosodium salt
MW: 347
MW: 325
#9 #10 #11 #13

Sulfanilic acid sodium salt 4'-Aminoacetophenone p-Chloroaniline N,N-Dimethylaniline

MW: 195 MW: 135 MW: 127 MW: 121
#14 #15 #16 #17

2-Naphthol-6-sulfonic acid
8-Amino-1-Naphthol-5 7- sodium salt
2-Naphthol Vanillin
disulfonic acid monosodium salt MW: 246
MW: 144 MW: 152
MW: 341
#19 #20 #21

1-Nitroso-2-naphthol-3,6-
disulfonic acid disodium salt 4-Aminonaphthalenesulfonic o-Chloroaniline
MW: 377 acid MW: 223 MW: 127

25
Chemistry 242 Lab 1: Azo Dyes 2018-2019
SYNTHESIS OF AZO DYES

Safety Information:
Many amines are toxic, so avoid skin contact. Phosphoric acid can be corrosive. In the event of an
emergency in your hood (e.g. fire) close your hood sash, and alert your TA. In the event of a chemical spill
on your skin or clothing, or in the lab, immediately alert your TA. Because of the hazards associated with
the amines and azo dyes, there is a special waste container for this experiment.

Step 1. Formation of the diazonium salt. In a 5-mL conical vial with a spin vane, add 2 mL of water and
10 drops of concentrated (15M) phosphoric acid. Cool the solution in an ice-water bath and stir. Add 0.1
mmol of the amine that is to be converted into a diazonium salt. Note: if your amine is a liquid, you can
assume that one drop weighs about 0.015 g (15 mg). If the spin vane does not stir sufficiently, periodically
stir with your spatula to break up clumps. Let the solution stir at 0 ˚C for 10 minutes.

While the above solution is cooling, prepare a solution of 20 mg of sodium nitrite in 1 mL of water. Add
approx. 7 drops of the sodium nitrite solution to the conical vial (a color change may occur). Let this solution
stir at 0 ˚C for 10 minutes.

After 10 minutes, test the diazotization reaction solution for excess sodium nitrite using starch-iodide
paper*. If the paper immediately shows a dark blue/black spot (due to the formation of the starch-iodide
complex) then this means that there is an excess of nitrite, and all of the amine will have been converted to
the diazonium salt. If the paper does not turn black, add another 3-4 drops of sodium nitrite solution and
allow the mixture to stir for another 5 minutes. After 5 minutes of stirring, or as soon as a starch-iodide test
reveals excess nitrite, proceed to step 2.

*Dip a micro-capillary it into the reaction vial and then touch the capillary onto a piece of starch-iodide paper and let the solution
bleed onto it.

Step 2. Addition of the activated aromatic compound. To the diazotization reaction, add 0.1 mmol of the
aromatic amine, phenol, or naphthol to which you are coupling your diazonium salt. Stir at 0 oC for 5 minutes
(there may be a color change). If the solid does not mix well by the spin vane action, stir with your spatula
or periodically cap the vial and shake gently for 10 seconds. After 5 minutes let the solution stir at room
temperature for 30 minutes. If necessary, periodically shake gently to help mixing. The solutions should
slowly develop color. If time permits you may want to let the reaction stir longer in order to insure more
dye formation.

Step 3. Dye color dependence on pH. While you are waiting for the completion of Step 2, prepare four
test tubes as described below:

To test tube 1, add 1 mL of 1 M aqueous NaOH; this is your basic solution.

To test tube 2, add 1 mL of distilled water; this will be acidic once you add your dye solutions.
To test tube 3, add 1 mL of 1M NaCl
To test tube 4, add 1 mL of distilled water, then chill the test tube in an ice bath.

After your dye synthesis reaction has stirred at room temperature, add approximately 5 drops of the reaction
mixture to each of the test tubes you just prepared. Note the resulting colors, which may be different in each
tube.

26
Chemistry 242 Lab 1: Azo Dyes 2018-2019
DYEING FABRIC
Introduction. In the last part of the experiment, you will use your synthesized dye to color a special swatch
of fabric. The swatch is woven such that it contains bands of some of the more common fibers used in
making clothing. The fibers included are both natural and synthetic. Here you will explore how the
interaction of the dyes with the fiber affects the colors.

The fibers contained in the swatch are shown below.

Fabric type (starting at end with black thread)

Filament Acetate
Bleached cotton
Spun polyamide
Spun polyester
Spun polyacrylic
Spun silk
Spun Viscose
Worsted Wool

Procedure. Select one of the base- or water-containing test tubes containing your dye whose color you like
the best. Dilute with ~10 mL of distilled water. Obtain a piece of multi-banded fabric. Submerge a piece of
the fabric into the diluted dye solution and gently heat on a hot plate in an aluminum block or beaker of hot
water for 10-15 minutes. If you want to increase the concentration of your dye, you may add the residue
from the original reaction vial.

Once you are done heating, remove the fabric from the dye solution, rinse with water, and leave the fabric
sample in your drawer to dry. In some cases, the dye color and intensity will change once the fabric has
dried out.

Your azo dye may be a skin irritant. While the dye is wet, it will bind to organic materials including
your skin and clothing. Keep the fabric swatch in a plastic bag until it is dry. Once the fabric is dry, you
can keep it as a souvenir. You should show the fabric to your TA, but it isn’t necessary to physically hand
it in to your TA or to upload pictures onto Gradescope.

You are also responsible for entering the colors of your dye in different conditions onto Canvas by the
deadline indicated in the course calendar, generally the same day that the azo dye report is due.

There is a known limitation to Canvas where by 2 students in the same section cannot enter data
simultaneously. 1 – if you get a warning that the data page has changed while you are editing it, you should
cancel and reload the page. 2 – each student is responsible for ensuring that their data remains on the page
by the deadline. It is highly suggested you check back 10-15 minutes later to make sure your data is still
there, and if need be re-enter it.

27
Chemistry 242 Lab 2: Three-Step Synthesis 2018-2019

LAB 2: THREE-STEP SYNTHESIS

Scenario: Your boss at the chemical company calls you into their office saying, “We urgently need a
bunch of 1,2,3,4-tetraphenylnaphthalene for our experiments. The problem is our usual supplier ran out
of stock and won’t get more for another 3 months. That’s not acceptable since we need it by next week.
You will have to make some. Design a synthesis of the target compound using reagents that we already
have in our stockroom.

You do some looking in the chemical literature and see that 1,2,3,4-tetraphenylnaphthalene can be
synthesized from anthranilic acid and tetraphenylcyclopentadienone.

You show this to your boss who shakes their head. “We have anthranilic acid, but not the ketone. So
you’ll have to make some of that too. Next time, check our inventory before you propose a synthetic
route.”

You go back to the literature and see that tetraphenylcyclopentadienone can be synthesized from benzil
and 1,3-diphenylacetone using an aldol condensation.

The company has diphenylacetone, but not benzil. But benzil can be made by oxidizing benzoin, which is
also in stock.

28
Chemistry 242 Lab 2: Three-Step Synthesis 2018-2019

You triumphantly present your 3-step synthesis of 1,2,3,4-tetraphenylnaphthalene starting from benzoin.
Your boss looks it over and says, “This looks like a good route. It’s quite efficient since you’re building
several C-C bonds at a time to build up a more complex structure. Try to synthesize about half a gram of
the target compound by next week so we can get to work on these studies. You’ll need to be careful,
because any product you lose in earlier steps will reduce your yield in subsequent steps.”

Notebook notes: You will write separate pre-lab notebook pages for step 1 and combined steps 2-3.
Turn in each set with the appropriate pre-lab. Your notebook must have all safety data and a reaction
table for those step(s). The initial reaction table for steps 2-3 will be an estimate which you will adjust
once you determine your exact yield.

General note: You should take a melting point for the crude product in each step to compare it with
the crystallized final material. Make sure to save your material between steps and ensure that all containers
are clearly labelled.

29
Chemistry 242 Lab 2: Three-Step Synthesis 2018-2019
STEP #1: NITRIC ACID OXIDATION OF BENZOIN TO BENZIL:
Use PLKE Expt 34B for background information. You will run the reaction procedure below on the same
scale as Expt 34B, starting with 0.300 g of benzoin.

Safety Information:
You are required to wear gloves as nitric acid will burn the skin upon contact. Keep hood sashes
down as much as possible as considerable amounts of noxious nitrogen oxide gases are evolved. You
should avoid breathing any of the red nitrogen oxide gas that forms during the reaction.

Always use dispensers slowly; they may splatter if too much pressure is placed on them. If you spill or
splash any of the chemicals used in this experiment on you, immediately remove any layers that contacted
the chemical, wash your skin with lots of water and soap, and alert your TA. There is a special waste
container for all nitric acid waste.

Procedure (modified PLKE#34B):

Reaction Mixture
Place 0.30 g of benzoin into a 5-mL conical vial and add 1.5 mL of concentrated nitric acid. Add a
magnetic spin vane and attach a micro water condenser. In a hood, place an aluminum heating block on
the hot plate stirrer with a thermometer. Pre-heat the aluminum block until the temperature reaches to 60
~ 70 °C. Place the reaction vial in the heating block, and heat the reaction mixture at 70 °C for 1 hr with
stirring. Make sure cold water is running through the micro water condenser. Avoid heating the mixture
above 70 °C to reduce the possibility of forming a byproduct. During the 1 hour heating period, nitrogen
oxide gasses (red) will evolve. During the reaction, you will do TLC to monitor the reaction at 30 and
50 minutes. There will be standards of benzoin and benzil to compare with. Let your TLC plate sit for 5
minutes after spotting it to allow the nitric acid solvent to evaporate. It may help to gently blow a
stream of air on the plate to speed up drying TLC plates will be eluted using methylene chloride in a
beaker covered with a watch glass. The spots will be visible by UV light. If it appears that gasses are
still evolving after 1 hour, continue heating for another 15 minutes but then discontinue heating after
that time.
Isolation of Crude Benzil
Cool the mixture for a few minutes then detach the water condenser. Pour the reaction mixture to a
beaker containing 3-5 mL of ice-cold water. Rinse the conical vial and spin vane with a small amount of
water (~1 mL) and add this to the reaction mixture. Cool the mixture in an ice bath until crystals have
formed. If the material oils out rather than crystallizes, scratch the oil vigorously with spatula until it
does crystallize completely. Collect the crude product on a Hirsch or Buchner funnel under vacuum.
Wash it well with cold water (about 5 mL) to remove the nitric acid. Ensure that your product is dry,
then weigh it and take a melting point.

30
Chemistry 242 Lab 2: Three-Step Synthesis 2018-2019
Crystallization of Product

Oiling out is what happens when a compound becomes insoluble, but is too hot to freeze into a
solid. Instead, the compound “precipitates out” as an oil. This is a problem because while crystals
would selectively avoid trapping impurities, the oil acts as an alternate solvent layer that can easily trap
impurities. Avoid melting (rather than dissolving) the benzil by occasionally picking up the Erlenmeyer
flask and swirling it. BE CAREFUL not to burn yourself when doing this.

You will need to recrystallize your product in 95% ethanol. See the procedure in PLKE #34B for more
details. You may get better quality crystals by adding a little extra solvent after all of the crude benzil
dissolves. To prevent the solution from becoming supersaturated, you can do the following: Dip a
spatula into the solution, then lift the spatula out and wait for the ethanol to evaporate off the spatula.
Once that is done, there should be some solid material on the spatula. Dip the spatula with solid product
back into the flask to act as a seed to encourage slow but steady crystal formation. Once you have
vacuum filtered the pure benzil, weigh it, determine the % yield, and take the melting point of BOTH
crude and recrystallized materials. You do NOT need to record the IR spectra of the product.

Special waste disposal

Aqueous solutions with nitric acid go into separate nitric acid waste jugs in waste hood. Solid chemical
waste can go in the solids waste jug. Note: Do NOT put filter paper, weigh paper, cotton, etc. in the
solid waste jugs; they should go in the trash.

31
Chemistry 242 Lab 2: Three-Step Synthesis 2018-2019
STEP #2: SYNTHESIS OF TETRAPHENYLCYCLOPENTADIENONE – ALDOL
CONDENSATION

Notes for days 2 & 3 on choosing glassware

Choose the appropriate glassware for your reaction based on the yield of benzil from day #1. A general
guide is:
o Under 100 mg: 5 mL conical vial
o Between 100 mg & 200 mg: 10 mL round bottom flask
o Over 200 mg: 25 mL round bottom flask

You need to calculate the amount of materials needed for days 2 & 3 based on your yield from the
previous day. You can save time by writing up a reaction table / procedure assuming 100 mg of benzil.
Then adjust your numbers based on the amount of benzil you actually have.
Procedure:
These are the amounts needed to set up the reaction:
*Benzil (amount from step 1)
*1,3-diphenylacetone (1.0 molar equivalent)
*Absolute ethanol – 200 proof (8 mL per gram of benzil)
*Potassium hydroxide solution in ethanol [density: 70 drops/mL, 0.1g KOH/mL solution] (0.5 molar
equivalents)

Mix the benzil, 1,3-diphenylacetone, and ethanol in a conical vial or round bottom flask along with a stir
bar / spin vane (depending on scale). Place a Drierite-filled drying tube on top of the reflux condenser.
Heat the mixture with a warm water bath until all the solid dissolves.
Continue to heat the contents of the round bottom flask to just below the boiling point of ethanol and
slowly add potassium hydroxide solution in ethanol. The mixture should immediately turn a deep purple
color. Allow the mixture to reflux for 15 minutes with gentle stirring. Cool the mixture in an ice water
bath. Collect the crystals and wash them with 95% ethanol and allow them to dry on the funnel for
several minutes. Weigh your product, determine a percent yield and take a melting point of the crude
product. Recrystallize the pure product using a 1:1 mixture of 95% ethanol and toluene. The crystals
dissolve slowly so let them heat for a minute between additions of solvent. Otherwise, too much solvent
may be added, resulting in a low or zero yield of crystals (you can always boil off excess solvent if
you've added too much). Ensure that the crystals are dry and determine the mass, melting point, and %
yield of your product.

32
Chemistry 242 Lab 2: Three-Step Synthesis 2018-2019
STEP #3: PREPARATION OF 1,2,3,4-TETRAPHENYLNAPTHTHALENE – DIELS-
ALDER REACTION
In this reaction 1,2,3,4-tetraphenylnaphthylene is synthesized by reacting the
tetraphenylcyclopentadienone from the previous step with benzyne in a Diels-Alder reaction. Benzyne is
a highly reactive molecule that is generated in situ using anthranilic acid and isopentyl nitrite. The Diels-
Alder reaction makes an unstable intermediate which, after loss of CO, gives the desired product.

Safety Information:
Isopentyl nitrite, used below, is a vasodilator (it expands blood vessels, lowering blood pressure).
Avoid breathing the vapors, said to smell like “old socks or dirty feet”. For this reason, prepare the
solution of isopentyl nitrite in 1,2-dimethoxyethane described below in a fume hood, and transport it to
your work area in a closed vessel (e.g. screw top vial or capped conical vial). Symptoms of exposure
(increased heart rate, dizziness, flushing of face) set in within seconds and disappear within minutes. If
you experience any of these, tell your neighbor and TA, and get some fresh air. Leaving open bottles is
a safety hazard, not only as an inhalation hazard but also as a spill hazard. You are required to wear
gloves during this part of the experiment and keep your hood sash down as far as possible at all
times.

Because of how hazardous isopentyl nitrite is, do NOT dispense more of it than you will need.

33
Chemistry 242 Lab 2: Three-Step Synthesis 2018-2019

As in step 2, this procedure is written for ~100 mg of tetraphenylcyclopentadienone. Scale the

amounts of all reagents, solvents, and glassware based on how much
tetraphenylcyclopentadienone you have. If you have more than 100 mg, use a larger round
bottom flask.

Procedure:
These are the amounts needed to set up the reaction:
*Tetraphenylcyclopentadienone (amount from step 2)
*Anthranilic acid (1.25 molar equivalents)
*1,2-dimethoxyethane for the above two reactants (12 mL per gram of tetraphenylcyclopentadienone)
*Isopentyl nitrite [density: 0.872 g/mL, 75 drops/mL] (2.0 molar equivalents)
*1,2-dimethoxyethane for the isopentyl nitrite (5 mL per gram of tetraphenylcyclopentadienone)
Dissolve the tetraphenylcyclopentadienone and anthranilic acid in 1,2-dimethoxyethanein a 5 mL
conical vial with a water jacketed condenser. In a 3 mL conical vial dissolve the isopentylnitrite in 1,2-
dimethoxyethane

To prevent any hazardous and volatile liquids from escaping, do NOT remove the reflux condenser
to add liquids to your reaction. Instead, pipette them into the top of the reflux condense.

Reflux the mixture of tetraphenylcyclopentadienone and anthranilic acid. Add the isopentyl nitrite
solution dropwise through the top of the water condenser over 30 seconds. Rinse the 3 mL conical
vial with a minimum of DME and add it dropwise to the reaction mixture. Stir the reaction under reflux
until the solution changes color from deep purple to yellow-orange. If there is no color change after 15
minutes, add two drops of pure isopentyl nitrite to the reaction every 2 minutes until you see a color
change. Regardless of whether there is a color change or not, do NOT add more than 6 additional drops
of isopentyl nitrite in total.

After you observe the color change, precipitate out the product by transferring the reaction mixture into
a mixture of 5 mL water and 2 mL of methanol. Cool the mixture in an ice bath and stir it well to break
up the precipitate and encourage further precipitation. Filter the product and rinse with a small amount
of cold methanol. Dry the product and weigh it. Use the yield of this crude product as the yield for the
reaction. Melting points may vary based on the purity of the crude product. Due to the insoluble nature
of the final product, it is too difficult to recrystallize in the time you have to do the lab.

A quick note on yield calculations for multistep syntheses

The normal way to calculate yield is (moles of product)/(moles of limiting reactant). So for the 3 step
synthesis, this could be (moles tetraphenylnaphthalene)/(moles benzoin). However, this method is
ONLY valid if you did not receive any supplemental material along the way. If your TA did supplement
your material, you’ll need to calculate yield differently, as shown below.

In the reaction ABCD, we can define the yield as:

𝑚𝑜𝑙 𝐷 𝑚𝑜𝑙 𝐵 𝑚𝑜𝑙 𝐶 𝑚𝑜𝑙 𝐷

𝑌𝑖𝑒𝑙𝑑 = = = (% 𝑦𝑖𝑒𝑙𝑑 𝑟𝑒𝑎𝑐𝑡𝑖𝑜𝑛 1) ∗ (% 𝑦𝑖𝑒𝑙𝑑 2) ∗ (% 𝑦𝑖𝑒𝑙𝑑 3)
𝑚𝑜𝑙 𝐴 𝑚𝑜𝑙 𝐴 𝑚𝑜𝑙 𝐵 𝑚𝑜𝑙 𝐶
So you would calculate the % yield for each individual step and multiply them together.
34
Chemistry 242 Lab 3: Synthesis of Esters 2018-2019
LAB 3: SYNTHESIS OF ESTERS
Scenario: You have been hired as a consultant for a perfume company. They are trying to develop
some perfume additives that will add a more floral essence to their premium line. Unfortunately they
don’t have a chemistry background, so they don’t know what sort of compounds tend to have a
floral/fruity scent to them. For some bizarre reason, one of the executives thought that since vinegar has
such as a sharp odor, it would be a great perfume additive. So they bought hundreds of gallons of acetic
acid. But it seems that their focus groups participants don’t particularly want to smell like salad
dressing. So if at all possible, they would like you to find a more practical use for all of their unused
acetic acid.

You recall that of the major functional groups, esters and amines tend to have the strongest smells.
While amines tend to smell “fishy” and unpleasant, esters tend to have more of a fruity odor. So it
seems like an ester would be the best candidate. You further recall that esters can be synthesized from
carboxylic acids with the Fischer esterification. The reaction is usually catalyzed by a strong acid such
as sulfuric acid which you’re confident the perfume company will have.

One limitation of the Fischer esterification is that the equilibrium usually favors both the carboxylic acid
and the ester evenly. Instead, you can force the equilibrium through two actions. First, one of the
reactants can be used in excess. Since the company has an abundance of acetic acid, that can be used as
the solvent. And second, you can use a drying tube to remove the product water from the reaction
mixture, which will also drive the reaction forward.

All that’s left to do is to choose a suitable alcohol. You request that the executive shows you their
selection of alcohols so that you can design an ester that will have a pleasant smell suitable for the
perfume base. Imagine your surprise when 5 unmarked jars are delivered to your lab. You ask the
executive what they are and they respond, “You said you wanted our alcohols so I just poured them into
these jars”. You naturally ask which alcohol is in each jar. “To be honest, I don’t remember exactly
which is which. But I do remember what the 5 bottles were. They were the following alcohols:

35
Chemistry 242 Lab 3: Synthesis of Esters 2018-2019
It looks like you will just have to pick 1 of the 5 mystery alcohol jars and see what ester is made from it.
Since both the reactant alcohol and the product ester are relatively small molecules with relatively low
boiling points, they will likely be liquids. So melting point cannot be used to identify the product ester.
Instead both Infrared (IR) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy will be
used to determine the unknown. It also means that care must be taken to avoid your product
evaporating in between days 1 and 2 of the lab!

Safety Information:
In this experiment you will use glacial acetic acid and sulfuric acid. Both of these reagents are
corrosive, and sulfuric acid is especially nasty. Avoid contact with these materials: take appropriate
precautions including wearing gloves and all normal lab safety equipment (goggles, lab coat, etc.). If
you do get some of these acids on your skin, immediately wash that area with lots of cold water.

DAY 1: ESTERIFICATION PROCEDURE: Assemble the apparatus depicted below using a 25

mL round-bottom flask, water-jacketed condenser (also known as a West condenser), and drying tube.
The entire apparatus should be on a lab jack. Clamp the round bottom flask, use a heating mantle for
heating and add a boiling stone to prevent bumping. Use a thin film of grease on the ground glass joints
and pack the drying tube with Drierite.

Record the weight of an empty 10 mL graduated cylinder. Place approximately 5 mL of your unknown
alcohol into the graduated cylinder and reweigh it to determine the exact mass of your alcohol.
Disconnect the round-bottom flask from the apparatus that you assembled above and transfer your
alcohol from the graduated cylinder to the round-bottom flask. Do not clean or wash the graduated
cylinder. Add approximately 7 mL of glacial acetic acid (MW = 60.1, density = 1.06 g/mL) to the
graduated cylinder (in the hood) and add it to the alcohol already in the flask. This order of operations
ensures that a known amount of the unknown alcohol was added to the reaction, which allows you to
perform an accurate percent yield calculation. Add 1.0 mL of concentrated sulfuric acid to the reaction
mixture and swirl the flask to mix the contents. Reconnect the round-bottom flask to the reflux
apparatus.
36
Chemistry 242 Lab 3: Synthesis of Esters 2018-2019
A good initial setting for most VariAC outlets is 30-40, but you may need to increase this if your
reaction mixture does not boil. Reflux the mixture for 60 to 75 minutes. While your mixture is
refluxing, acquire an infrared (IR) spectrum of your unknown alcohol (see appendix III for more
instructions). Once the reflux has stopped, remove your reaction mixture from the heat and allow it to
cool to room temperature.

Isolation of the Product: Once the reaction mixture has cooled to room temperature, disassemble the
apparatus and transfer the reaction mixture to a separatory funnel. Leave the boiling stone in the round-
bottom flask. Wash the reaction mixture sequentially with 8-12 mL of water, then 4-6 mL of 5%
aqueous sodium bicarbonate, and finally with 4-6 mL of saturated aqueous sodium chloride.
Transfer the remaining organic layer (your crude ester) to a 25 mL Erlenmeyer flask and dry it by
adding approximately 0.8-1.2 g of anhydrous sodium sulfate. Once the solution is dry, determine the
yield of your product liquid. Also rinse off your boiling stone and return it to the container.
Prepare a GC/MS sample of your product. Add 2 drops of your product to a dram vial. Add about 5 mL
of methylene chloride to the vial. Take approximately 1.5 mL of this solution and transfer it to a GC/MS
vial provided by your TA. Make sure to write your section and sample number on the vial, and to record
your sample number from the sign up sheet! If time permits, you can take your NMR spectrum at the
end of Day 1 (see below).

Make sure to save your product until the next lab day! You should put your product in a sealed vial
or else it will evaporate.

DAY 2 ANALYSIS: Work on identifying your unknown with NMR and IR spectra & GC-MS analysis
in CHB 121.

IR Spectroscopy: Take an IR spectrum of your product ester. Also make sure that you took an IR of your
starting alcohol. Compare the 2 spectra for signs that a chemical reaction occurred.

GC-MS (Gas Chromatography-Mass Spec) Analysis: Your GC-MS sample will be analyzed and TAs
will be notified when your section is complete. It will be up to you to properly print out your data on the
computers in room CHB121 or the Organic Study Center. CHB121 is only available during your lab
section. The instructions for analysis and printing of your data are located on Canvas. Your sample will
be run on 1 of 2 different GC-MS instruments, so while the relative retention times will be the same, the
absolute retention times might differ.

NMR Spectroscopy: You will work in pairs for the NMR spectroscopy just like for the reaction itself.
Prepare an NMR tube by dissolving 7-8 drops of your product in 0.6 mL CDCl3. Acquire an NMR
spectrum, send it to both lab partners, and process it to determine which ester you synthesized, hence
which alcohol you started with. Make sure that all peaks in the NMR spectrum are identified

Spectroscopy Worksheet – During Day 2, work in groups of 3-4 to complete the spectroscopy worksheet
that will be handed out by your TA.

37
Chemistry 242 Spectroscopy Worksheet 2018-2019
SPECTROSCOPY WORKSHEET
□ Before lab read PLKE techniques 25 (IR) and 26 (NMR) and/or Loudon 7th, 8th or 9th editions 12.2-12.4,
13.3-13.5, 13.7 or McMurry 13.6-13.12.
□ Read the document on Canvas about using degrees of unsaturation to determine molecular structure
□ You will work in groups of 3-4 to identify an unknown chemical based on IR and 1H NMR spectra. Identify
the molecule and annotate the IR bands and NMR signals that match your proposed structure. Don’t
forget that there are useful data tables for analyzing IR and NMR data in appendix IV.
□ There is no prelab for this lab. You will receive the spectroscopy exercise in lab and complete it in groups
of 3-4. You will turn in the report as a group by the end of the lab period.

38
Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019
LAB 4: QUALITATIVE ANALYSIS (PLKE 57)
Scenario: You are a forensic scientist working for the Central City police department. Your coworker
has been taking a lot of time off after being struck by lightning. At first you were sympathetic, but it’s
been happening for several months at this point, so you’re mainly getting annoyed about the extra
workload being piled on you.
Today, you’re called to the scene of a robbery at the abandoned former site of the ACME chemical
factory. ACME recently moved to a larger facility across town and alleges that there was nothing of
value at their old factory. But based on the wreckage, it does appear that some materials were taken.
What is ACME hiding? You see some white powder and an oily residue on the floor near the broken
window. Your task is to identify what those compounds are and to determine if they were some of the
compounds stolen from the supposedly abandoned ACME facility. You also want to know if ACME
was carrying out some sort of illegal experimentation.

You will be issued two qualitative unknown substances and one spectroscopy unknown. Your qualitative
unknowns will consist of one solid and one liquid. Unknowns may be alcohols, aldehydes, amines,
carboxylic acids, esters, ketones, or phenols. Your unknown may also contain one or more "secondary"
functional groups, such as nitro groups, aromatic rings, or halogens. It is also possible for your unknown
to contain more than one primary functional group, i.e. a ketone and carboxylic acid in the same molecule.

PLKE experiment 57, "Identification of Unknowns" contains much of the information you will need
to identify your unknowns. You should bring the book/chapter with you to lab. Your 2 qualitative
unknowns will contain at least 1 of the following functional groups: aldehyde, ketone, ester, carboxylic
acid, amine, alcohol, phenol. The spectroscopy unknown may contain ANY functional group, not just the
above list.

IMPORTANT NOTE: Tollens’ reagent, and 2,4-dinitrophenylhydrazine are particularly toxic and
incompatible with aqueous and organic waste streams. Because of this, they both have separate
waste containers. DO NOT put any of these test solutions in the general aqueous or organic wastes!

You will run the different classification tests on some known compounds first. Do NOT record the IR
spectrum of known compounds. When you have completed the classification tests listed below, you may
pick up your unknowns (#1 and #2) from your TA. Begin your analysis by using the classification tests
on your unknowns to prepare the preliminary report.

DAY #1: The first day of qualitative analysis will give you a chance to familiarize yourself with the
different functional group classification tests using known compounds listed below. Run each test listed
below using the designated known compounds.

You will not be given your unknown compounds until you complete the Day 1 tests on known
controls. For due dates, it is entirely up to you whether you consider the liquid to be “unknown 1”
or “unknown 2” and likewise for the solid.

Be sure to record all experimental results in your notebook – write down what you observe, not just
that it was a positive or negative test.

39
Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019
From PLKE chapter 57:
57D 2,4-dinitrophenylhydrazine Controls: Acetone, sec-butanol (aka 2-butanol), benzophenone
57A Solubility Test (in water, 1M HCl, 5% NaHCO3, 1M NaOH) Controls: 2-naphthol,
benzoic acid, n-propanol (aka 1-propanol)

Note that some compounds may dissolve in water slowly, so be patient with the solubility tests.
DO NOT use sulfuric acid for the solubility tests.

DAY #2: Boiling point determination of known and unknown compounds. On the second day of
qualitative analysis, you must determine the boiling point of a known and an unknown compound. The
Beilstein test & ignition test will also be done on this day as well. This is the only day that these tests
will be allowed. Bunsen burners will no longer be available after the designated “Bunsen Burner
Day".

From PLKE EXPERIMENT 57:

Semimicroscale boiling point (Semimicroscale Inverted Capillary method) PLKE, p. 748
Attempt on either isoamyl acetate (aka isopentyl acetate) or benzaldehyde, then your liquid unknown
57B Beilstein Test only Benzoic acid, bromobenzene & unknowns
57C Ignition Test only Benzoic acid, 1-octadecanol, & unknowns

Safety Information:
While any student has a Bunsen burner out, NO STUDENT is allowed to use any flammable materials.
The only additional activities that can be done are water solubility tests and melting point . No IR, NMR,
chemical tests, or derivatives can be done on Day 2. Your Bunsen burner flame should be compact and
blue, not large and yellow.

GOOD! BAD!
For the Beilstein test, make sure you hold the compound in the flame for less than 10 seconds to prevent
yourself from being burned on the metal. DO NOT heat your unknown higher than 200 °C. If your
unknown compound still has not boiled by this point, inform your TA. DO NOT immerse rubber bands in
heating oil!

40
Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019

Helpful hints: For the ignition test on your solid, you might try melting the solid before putting it into
the flame. You MUST have an accurate boiling point for your liquid unknown (within 6 °C) before the
end of Day 2 so be sure to check your measured boiling point with your TA.

Notebook Guidelines
You should maintain your notebook as a record of what you are doing. Please keep separate notebook
pages for each unknown. While you won’t know what your compound is until the end, you should
include: all procedures you are carrying out, safety information, partial reaction tables (mainly amounts),
observations, data, and conclusions. You DO NOT need to upload any notebook pages with your
spectroscopy unknown. You DO need to upload notebook pages with your solid and liquid unknowns.

Preliminary Report
After the second day, you will be ready to complete the preliminary report. A copy of the report form is
attached at the end of the manual and is also available from the Chem 242 Canvas page. You will
complete TWO preliminary reports, one for each of your qualitative unknowns. Your TA will provide
feedback on what functional groups you have identified. The TA will indicate in a timely fashion any
results that you should re-check before proceeding.

NMR Data
You will take the NMR for both of your qualitative unknowns AND your spectroscopy unknown. This
can be done at any time other than the Bunsen burner day.

Helpful hint: There will likely be a rush on students wanting to take NMR spectra. Waiting in a
long line is pretty much the least productive use of your time. Before committing to a 20 minute wait,
ask yourself if there is anything else you could be doing instead.

Solubility tests: You must choose an appropriate NMR solvent for each of your 3 unknowns. Not all
of your compounds will be soluble in CDCl3. Because of how expensive deuterated solvents are, you
will do the solubility tests using non-deuterated solvents. Test the solvents in the following order. Once
you find a suitable solvent, you can stop and don’t need to test the rest of the solvents on the list. Use
the same amounts as the water solubility tests (PLKE 57A).

1: Methylene chloride – if soluble you will use CDCl3

2: Water – if soluble you will use D2O
3: DMSO (dimethylsulfoxide) – if soluble you will use DMSO-d6
4: Acetone – if soluble you will use acetone-d6

If your compound is not soluble in any of those solvents, consult your TA. Prepare you NMR tube with
8 drops of a liquid or 70-80 mg of a solid in 0.6 mL of the appropriate NMR solvent. Take your NMR
spectrum and email yourself the data to be processed later. Once you are happy with your NMR
spectrum, you should rinse out your NMR tube with acetone and let it dry for either 20-30 minutes in the
oven, or overnight in your lab drawer.

41
Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019
IR Data
You will take the IR for both of your qualitative unknowns AND your spectroscopy unknown. The
infrared spectrum will provide important evidence for the presence of various functional groups (see
approach summarized in technique 25.13 of PLKE). The teaching assistant will demonstrate preparing
samples for IR spectroscopy in the laboratory, but see also Appendix 3 and PLKE Technique 25. In
your analysis you should assign as many of the significant peaks as possible, especially the ones that
appear above the fingerprint region. Focus on peaks that can provide you with key structural
information rather than trying to identify all the peaks in your spectrum.

To manage workflow, the stockroom will manage checking out salt plates and KBr presses. Each
lab room will have a sign-up sheet and you will claim a 1 hour checkout window sometime between
Days 3-6. DO NOT choose the same timeslot for both the salt plate and the KBr press, If you will be
absent during your assigned timeslots, it is your responsibility to trade times with another student. Keep
in mind the due dates for the various unknowns when planning how you will use the IR equipment.
After every student in your section has had a chance to check-out both the KBr presses and salt plates,
then the system will switch to first-come-first-served.
There are multiple ways to take an IR spectrum of a solid compound. Each has advantages and
disadvantages. Procedures for all 3 are given in Appendix 3. When deciding which technique to try,
you should consider (among other factors) whether the compound is soluble in methylene chloride, the
time you have available, when your check-out window is for salt plates and the KBr press, and which
compound(s) you intend to acquire IR data for at that time.
Technique Advantages Disadvantages
Methylene Relatively quick to do. Done Requires compound be soluble in methylene
chloride solution using salt plates. chloride. Methylene chloride IR peaks (3050,
2980, 1430 cm-1) may obscure sample peaks.
KBr pellet Works on practically every Time-intensive. Requires special KBr press.
solid compound. KBr doesn’t
have any IR peaks.
Nujol (mineral Works on many solid Nujol IR peaks (2930 [strong], 2850 [strong],
oil) mull compounds. Done using salt 1460, 1380 cm-1) may obscure sample peaks.
plates.

42
Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019
Identification of the Unknown
Once you have completed the preliminary report, continue your analysis with experiments suggested by
the preliminary report. The full list of possible compounds will be posted on the course website and a
hardcopy will be in the labs. The "Identification Report" form is included in this lab manual.
Solubility tests as described in PLKE 57A should enable you to narrow down the list of possible
functional groups for your unknown (see diagram on p 462 of PLKE but ignore the sulfuric acid
section).
Using the information you have gathered from the preliminary tests, solubility tests and the IR spectrum,
classification tests should be selected from procedures 57D through 57I, as appropriate for the
functionality(s) you suspect. It is always a good idea to run positive and negative controls when
conducting classification tests. You MUST do at least 1 supplemental chemical classification test for
each unknown.
The classification tests should enable you to decide what main functional group is present in your
unknown. Unknowns suspected of containing more than one primary functional group should be
checked under all suspected functional groups.
Finally, preparation of derivatives (PLKE Appendix 2) and the determination of their melting points
should enable you to positively identify your unknown. You are required to prepare a derivative for all
unknowns. Titrations can substitute for a carboxylic acid derivative. Esters require 2 derivatives. You
are strongly encouraged to take a melting point of your crude derivatives in case you have difficulty
with your recrystallization.
A list of supplementary classification tests and derivatives is provided in page 46 of this manual and in
PLKE.

Unknown Report Forms

Once you have identified your unknown you will fill out and turn in the "Unknown Report" and
"Preliminary Report" forms together, which are available on the course website. There is also one copy
of each report in the lab manual. You will submit one report for EACH of your two qualitative
unknown compounds. You must submit with your report a small sample of the derivative(s) you
prepared.

It is entirely up to you which of your two unknowns are “Unknown 1” and “Unknown 2”. Budget
your time in lab wisely so that at least 1 of your unknowns is completed in time for the first due date.
You should have ample material to carry out all of the necessary chemical tests and derivatizations. In
some cases, you might need to scale down the derivative reactions if you run low on material. If you run
out of material and need a replacement from your TA, there will be a 10 point penalty.

43
Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019
Suggested Strategy for Unknowns (Your approach may not be this linear!)

Cleanup
Once you are done with your unknown, you should clean out your sample vial and return it your TA.
Rinse the vial out thoroughly with acetone and ensure that no materials are left in your lab drawer. All
solid derivatives should be submitted to your TA in vials. If your unknown is an ester, and your
saponified carboxylic acid derivative is a liquid, you don’t need to submit it.

SPECTROSCOPY UNKNOWN
The structure of this unknown will be determined by only spectroscopic methods. You will take IR and
1
H NMR spectra in class and you will be given the mass spectrum of your unknown. Between these
three pieces of data you will determine the structure of the unknown. Since it does not require wet
chemistry, the spectroscopy unknown will be due first (see the lab schedule for exact due dates)

Unlike the 2 qualitative unknowns, the spectroscopy unknown may or may not be on the unknown
list. It could also contain any functional groups, not just the 7 core groups on the unknown list.

44
Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019
SAGACIOUS ADVICE FOR THE CHEMICAL WARRIOR
-Have a touch of cynicism on all tests - results aren't always as you interpret them to be. Patience and
scrutiny are your best allies.
For safety, instead of heating ether to boil it away, you should evaporate the ether using an air line.-
Dispense solutions from where you find them. Do not take reagents back to your hood because someone
else may be looking for them.
-When the book says "use 1 mmole of your unknown..." assume this to be about 100 mg.
-When the book says "use xx grams of a liquid" assume that the density of most liquids is about 1 g/mL.
-When running low on material don't feel obligated to use the amounts listed in the text, scale down
accordingly.
-All solutions are already made except for ferrous ammonium sulfate.
-When in doubt of a result of a test, run both positive and negative controls to compare.
-Use an aluminum block when heating a water sensitive reaction. Do not use a steam or water bath. (some
water sensitive reagents include: thionyl chloride, isocyanates, acyl chlorides.)
-When making 2,4-DNP derivative use only 2 mL of solution instead of the 10 mL that older editions of
the book recommend.
-To dry a "wet" sample, dissolve the material in ether, dry over a small amount of sodium sulfate for 15
minutes, decant, then evaporate the solvent. For specific guidance about drying DNP derivatives, see page
47.
-Consider that your unknown may actually have multiple functional groups. For instance, if your
unknown turns out to be benzoin, it will show positive tests for both ketone and alcohol tests, and you
will potentially have twice as many derivatives you could make.
-If you are drying crystals under the heat lamp, keep an eye on them to make sure they don’t burn or melt.

-If you fail on 3 successive attempts in synthesizing a derivative, it is best to go outside (after ensuring
that all of your equipment is turned off!) and have a stroll through the herb garden or gaze at Mt. Rainier
for a bit before continuing on once again (if it’s cloudy or there’s too many bees flying around the
garden, go get a latte instead). You should also confirm that you’re trying to make the correct
derivative. For instance, a phenol and an alcohol may both show a positive cerium test, but a
bromination derivative is destined to fail for the latter. If you’re confident about the functional group,
consider what might have gone wrong experimentally (e.g. a water sensitive reagent getting
hydrolyzed). That way you can improve your experimental technique on the 2nd try.

45
Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019
I. SUPPLEMENTARY CLASSIFICATION TESTS AND DERIVATIVES

Alcohols and Phenols:

Lucas test. See PLKE 57H.

Ferric chloride test (phenols). See PLKE 57F

Ceric nitrate test. Alcohols and phenols can form complex cerate anions with ceric nitrate reagent.
These complexes are colored but the ceric nitrate solution is yellow. Alcohols and phenols having no
more than ten carbon atoms give a positive test. Alcohols give a red solution while phenols give a
brown to greenish brown precipitate in aqueous solution. Aromatic amines may be oxidized by the
reagent and give a color indicating a positive test.

(NH4)2Ce(NO3)6 + ROH (NH4)2Ce(OR)(NO3)5 + HNO3

(yellow) (Red)

Experimental: Dissolve about 20 mg of a solid or 1 drop of a liquid unknown in 1-2 mL of water and
add 0.5 mL of the ceric ammonium nitrate reagent, shake and note the color. If the unknown is
insoluble in water, dissolve it in 1 mL of dioxane and add 0.5 mL of the reagent.

Aldehydes and Ketones:

Tollens’ test (for aldehydes). See PLKE 57D. Note that Tollens’ solution A is 5% silver nitrate while
Tollens’ solution B is 10% NaOH.

Iodoform test. This test allows you to detect an acetyl group in your unknown. See PLKE 57D.

Amines:

Nitrous acid test. See PLKE 57G.

Carboxylic acids:

Sodium bicarbonate test. See PLKE 57E

Esters:

Ferric hydroxamate test. See PLKE 57I

46
Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019
II. SUPPLEMENTARY DERIVATIVE PROCEDURES
General note: Whenever PLKE suggests doing the mixed-solvent method of recrystallization using water
and either methanol or ethanol, a simpler approach is to just make a 50:50 mixture of water and the alcohol
and follow the normal recrystallization procedure.
Alcohols and Phenols:
3,5-Dinitrobenzoate. See PLKE Appendix 2

Phenylurethanes and naphthyl urethanes. See PLKE Appendix 2

Bromo derivatives (phenols only). See PLKE Appendix 2

Aldehydes and Ketones:

2,4-Dinitrophenylhydrazones and Semicarbazones. See PLKE Appendix 2

Special note for DNP derivatives - carry out the reaction in a test tube or centrifuge tube as
indicated in PLKE. When the reaction is over, centrifuge the reaction mixture to collect the product.
Carefully remove the supernatant by using a pipette. The crystals at the bottom of the centrifuge tube
are then washed sequentially with water, ethanol, hexanes, and ether. The centrifuge tube is left
standing at room temperature to dry the crystals. Alternatively, the crystals can be collected and washed
using vacuum filtration. DO NOT put DNP derivatives under the heat lamp to dry, they will smoke!
Oximes.

Experimental: About 0.5 g of hydroxylamine hydrochloride is dissolved in 3 mL of water, 2 mL of

10% sodium hydroxide solution and 0.2 g of the aldehyde or ketone are then added. If the carbonyl
compound is water-insoluble, just enough ethanol is added to the mixture to give a clear solution. The
mixture is warmed on a water bath for 10 minutes and then cooled in an ice bath. In order to hasten
crystallization, the sides of the flask are scratched with a glass rod. The addition of a few mL of water
will also assist in causing the oxime to precipitate.
Amines:
Acetamides and Benzamides. See PLKE 57G (no picric acid derivatives are allowed) and PLKE
Appendix 2.

(PLKE clarification for benzamides) When the reaction is over you should adjust the pH to 7-8.
This may require either HCl or NaOH depending on the pH of your solution.

Titration. See PLKE 57G. Note that this tells you the ratio of MW/(# of amine groups) By titrating
the amine with a known concentration of HCl, you can calculate exactly how much HCl is required to
neutralize the amine. But a diamine (e.g. ethylenediamine, MW 60 g/mol) will require twice as much
HCl as a monoamine with the same molecular weight (e.g. propylamine, MW 59 g/mol). Thymol blue

47
Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019
will change from yellow to red at the end of the titration. If it is blue at the start of the titration, ignore
that as it will change from blue to yellow in the middle of the titration.
Carboxylic acids:
Anilides and Toluidides. See PLKE 57E and Appendix 2.

Alternate procedure for anilides and p-toluidide: Place 0.5 g of the acid and 1 g of aniline or p-toluidine
in a 5 mL conical vial. This mixture will liquefy once it’s heated. Attach an air condenser and heat the
mixture at 140-160 oC for 1-2 hours. Caution should be used to avoid heating the mixture too
vigorously, thus causing loss of the acid by distillation or sublimation. At the end of the reaction time,
cool the mixture and dissolve it in an appropriate water insoluble solvent (ether, methylene chloride)
and wash the solution with 1M HCl and then with 5% sodium bicarbonate. Evaporate the solvent and
collect the precipitated derivative.

Amides. See PLKE 57E and Appendix 2.

Titration. See PLKE 57E. Note that this tells you the ratio of MW/(# of carboxylic acid groups) By
titrating the carboxylic acid with a known concentration of NaOH, you can calculate exactly how much
NaOH is required to neutralize the carboxylic acid. But a dicarboxylic acid (e.g. oxalic acid, MW 90
g/mol) will require twice as much NaOH as a monocarboxylic acid with the same molecular weight
(e.g. lactic acid, MW 90 g/mol).

Esters:

Esters require 2 derivatives, one derivative for the carboxylic acid half, and another derivative for the
alcohol half.

[Derivative of the alcohol portion] 3,5-Dinitrobenzoates. See PLKE 57I and Appendix 2. Follow
this procedure for both solid and liquid esters. If you have a solid ester, it will melt during the heating.
DO NOT put ether on a hot plate.

(PLKE typo) If your ester’s bp is below 150C, reflux it, if your ester’s bp is above 150C, heat at
150C.

[Derivative of the carboxylic acid portion] Saponification. See PLKE 57I. Hydrolyze the ester
under basic conditions and then isolate the free carboxylic acid. If the carboxylic acid is a solid, take
a melting point. If the carboxylic acid is a liquid, see if it has the familiar odor of vinegar (acetic acid).
Even if the carboxylic acid portion is an undetermined liquid carboxylic acid, you will have eliminated
most possibilities.

48
 Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019
QUALITATIVE ANALYSIS CHEMICAL LOCATIONS
Note: Please do not take chemicals back to your desk or hood to dispense.
This list will also be posted in the laboratory on the column by glass waste and the gloves.
Reagent Used in Lab Location
(Bis) Ethoxy Ethyl Ether...di(ethylene glycol) diethyl ether…has 2,4-DNP Test & Deriv Flammable
lots of names
1,2-Dimethoxyethane Br2 in DCM, Bromo Deriv, KMnO4 Test Flammable
(Baeyer), Iodoform Test, Cerium (IV)
Test (Text), 2,4-DNP Test & Deriv,
2,4 Dinitrophenyl Hydrazine (2,4 DNP) 2,4-DNP Test & Deriv Balance Area
2-Naphthol...β-Naphthol Solubility Tests, Nitrous Acid Test Known Box
2-Nitrotoluene Ferrous Hydroxide Test Known Box
3,5 Dinitrobenzoic Acid 3,5-dinitrobenzoate Deriv Balance Area
3,5 Dinitrobenzoyl Chloride 3,5-dinitrobenzoate Deriv Balance Area
Acetic Anhydride Acetamides Deriv Prep Hood
Acetone Reagent 2,4-DNP, NMR Solvent Testing Prep Hood
Acetone-d6 NMR Prep Hood
Acetyl Chloride Acetyl Chloride Test Prep Hood
Ammonium Hydroxide, 10% Tollens Prep Hood
Ammonium Hydroxide, Concentrated Amides Deriv Prep Hood
Aniline Anilides Deriv Prep Hood
Benzaldehyde Flame Day Known Box
Benzoic Acid Solubility Tests, Flame Day Known Box
Benzophenone 57D (2,4-DNP) Known Box
Benzoyl Chloride Benzamides Deriv Prep Hood
Boiling Stones Balance Area
Brominating Solution Bromo Deriv Prep Hood
Bromine (2%) In Methylene Chloride Bromine in DCM Test Prep Hood
Bromine Water Bromine Water Test Prep Hood
Bromobenzene Flame Day Known Box
Calcium Chloride, Anhydrous Carboxylic Acid Deriv Balance Area
CDCl3 NMR Prep Hood
Cerium Nitrate Solution, Aqueous…Cerium (IV) Test Manual: Ceric Nitrate Test & Text : Balance Area
Cerium (IV) Test
Cyclohexene Neutralizes Bromine Reagents, Control Prep Hood
Test
D2O NMR Prep Hood
Dimethyl sulfoxide…DMSO NMR Solvent Testing Prep Hood
Dioxane Ceric Nitrate Test (manual) Flammable
DMSO-d6 NMR Prep Hood
Drierite Drying agent Balance Area
Ethanol, 95% Solvent Prep Hood
Ether...Diethyl Ether Basic Hydrolysis,3,5-dinitrobenzoates, Flammable
Solvent
Ferric Chloride, 2.5% solution Ferric Chloride Test Balance Area
Ferric Chloride, 5% solution Ferric Hydroxamate Test Balance Area
Ferrous Ammonium Sulfate Ferrous Hydroxide Test Balance Area
HCl, 0.1 M Standardized For Titrations Titration Instrument Room
HCl, 1 M Solubility, Ferric Hydroxamate Test, Instrument Room
Anilides & Toluidides Deriv

49
 Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019
Reagent Used in Lab Location
HCl, 5%...Use 1 M HCl instead Anilides, Acetamides, Benzamides, & Instrument Room
Toluidides Deriv
HCl, 6 M Instrument Room
Hexanes Solvent Prep Hood
Hydroxylamine HCl Oximes Deriv Balance Area
Hydroxylamine HCl 0.5M in Ethanol Ferric Hydroxamate Test Balance Area
Iodine-potassium iodide solution...Iodine (10%) in Potassium Iodide 20% Iodoform Test Balance Area
Isoamyl acetate…isopentyl acetate Flame Day Known Box
KBr in Oven IR Instrument Room or if
in CHB 127, oven in the
room
Lucas Reagent Lucas Test Instrument Room
Magnesium Sulfate 3,5-dinitrobenzoates Balance Area
Methanol Semicarbazones Deriv, Bromo Deriv, Flammable
Acetamides
Methylene Chloride…DCM...Dichloromethane General Solvent Prep Hood
NaI in Acetone, 15% solution Sodium Iodide in Acetone Test Balance Area
NaOH, 0.1M Standard For Titrations Titration Instrument Room
NaOH, 1 M Solubility Instrument Room
NaOH, 10%...Also used as Tollens B Tollens B, Iodoform Test, Sodium Instrument Room
Hydroxide Test, Nitrous Acid Test,
Oximes, Benzamides Deriv
NaOH, 25%...Use 6 M NaOH instead Basic Hydrolysis Instrument Room
NaOH, 5%...Use 1 M NaOH instead Anilides & Toluidides Deriv Instrument Room
NaOH, 6 M Ferric Hydroxamate Test, Basic Instrument Room
Hydrolysis
Napthyl Isocyanate, alpha Naphthylurethanes Prep Hood
n-Butanol Lucas Test Control Known Box
Nitric Acid, 5% Silver Nitrate Test Prep Hood
n-Propanol Solubility Known Box
NuJol Mineral Oil (Shelf above KBr Presses in CHB 118) IR Instrument Room
Octadecanol Flame Day Known Box
Phenol, 4% aqueous solution Sodium Hydroxide Solution Balance Area
Phenolphthalein Solution Titration Instrument Room
Phenyl Isocyanate Phenylurethanes Prep Hood
Potassium Hydroxide 2M in Methanol Ferrous Hydroxide Test Balance Area
Potassium Permanganate, 1% aqueous solution KMnO4 Test (Baeyer) Balance Area
P-Toluidine p-Toluidides Deriv Balance Area
Pyridine Semicarbazones Deriv, Phenylurethane Prep Hood
Deriv, Acetamides, Benzamides, 3,5-
dinitrobenzoate Deriv,
Sec-Butyl Alcohol...2-Butanol 57D (2,4-DNP) Known Box
Semicarbazide HCl Semicarbazones Deriv Balance Area
Semicarbazide HCl, 2M aqueous solution Semicarbazones Deriv Balance Area
Silica Gel Balance Area
Silicone Oil Thiele Tube Refill Instrument Room
Silver Nitrate, 2% in Ethanol…2% Ethanolic Silver Nitrate Silver Nitrate Test Balance Area
Solution
Sodium Acetate Semicarbazones Deriv Balance Area
Sodium Bicarbonate Balance Area

50
Chemistry 242 Lab 4: Qualitative Analysis (PLKE 57) 2018-2019
Reagent Used in Lab Location
Sodium Bicarbonate, 5% aqueous solution Solubility, Sodium Bicarb Test, Anilides Instrument Room
& Toluidides Deriv
Sodium Bicarbonate, saturated solution Instrument Room
Sodium Carbonate Balance Area
Sodium Carbonate, 5%...Dilute 10% Benzamides Deriv, 3,5-dinitrobenzoate Instrument Room
Deriv
Sodium Chloride Balance Area
Sodium Chloride, saturated solution Instrument Room
Sodium Nitrite, 10% aqueous solution Nitrous Acid Test Balance Area
Sodium Sulfate Basic Hydrolysis, Drying Agent Balance Area
Sulfuric Acid, 2 M Ferrous Hydroxide Test Instrument Room
Sulfuric Acid, 5% Acetamides Deriv Instrument Room
Sulfuric Acid, Concentrated Nitrous Acid Test, 3,5-dinitrobenzoates Prep Hood
t-Butanol…tert-butanol Lucas Test Known Box
Thionyl Chloride Carboxylic Acid Deriv Prep Hood
Thymol Blue Titration Instrument Room
Tollens A Tollens A Instrument Room
Tollens B...NaOH, 10% Tollens B, Oximes Instrument Room
Toluene Benzamides Deriv Flammable

51
Chemistry 242 Appendix I: GC-MS data processing and analysis instructions 2018-2019
APPENDIX I: GC-MS DATA PROCESSING AND ANALYSIS INSTRUCTIONS
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)

GC-MS Analysis

52
Chemistry 242 Appendix I: GC-MS data processing and analysis instructions 2018-2019
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).

Retrieve your GC-MS data:

1. Go to ‘file’ and click on ‘load data’. Select the path where you saved your file (instructions suggest the
D: drive).

2. Select the file that you pasted and click “ok” and your ‘Total Ion Chromatogram” (TIC) will appear (see
next page). In the upper left hand corner you should see “[2] TIC: ‘YourSection0#’”. Check to confirm that
you brought up the correct file.

53
Chemistry 242 Appendix I: GC-MS data processing and analysis instructions 2018-2019
Integrate the TIC spectrum:
3. Go to ‘Chromatogram’ and select ‘Select Integrator’. Click on “RTE Integrator” and “ok” on the
window that pops up. Go back to ‘Chromatogram’ and select ‘Integrate’. Now each peak on your
chromatogram will have an exact retention time listed. (Note that this retention time might not match the
exact time given in the Canvasinstructions depending on which instrument your sample was run on).

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 #s, 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.

54
 Chemistry 242 Appendix I: GC-MS data processing and analysis instructions 2018-2019
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).

Determine the identity of the peaks:

On the TIC you will probably see 2-5 peaks between 13 and 16 minutes. 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.

6. 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.

7. Right clicking on the peaks will bring up the mass spec of each molecule. Using the right mouse button, double
click on the largest peak. Below will now be the Mass Spectrum (MS) of this peak. Go to ‘file’ and print out the TIC
and Spectrum.

8. 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 results will be presented as choices with the top one being the most likely candidate.
 You have the option of printing this out or recording the identity in your notebook. To print it, select a compound
from the list of options and select Print. Click on ‘Done’ when finished with the search.

55
Chemistry 242 Appendix I: GC-MS data processing and analysis instructions 2018-2019

You can locate the retention time at the top of the MS window (bottom one of the two). This example shows,
“[1] Scan 2060 (15.183 min): AE001.D\data.ms” Your samples would say, “[1] Scan XXX (your retention
time): YourSection0#.D\data.ms”

9. Go back to the TIC and double click with the right mouse button on other peaks to generate its MS and
subsequent library search.

10. Next, go to ‘Spectrum’ and ‘tabulate’, then click ‘print’

Before you leave, make sure that you have everything asked for by the “Labelling GC-MS Files”
guide on Canvas

Quit the Data Analysis window when you are done by selecting Exit from the File menu.

MANUAL
To print GC profile/MS spectrum: INTEGRATION
GC-MS Analysis
Go to File > Print > Choose TIC & Spectrum > PDF Creator > Enter desired file name
inside "Document Title" and click 'Save'. You may save the PDF file to your USB
thumb drive or save it on the desktop then send it to yourself as email attachment.

56
Chemistry 242 Appendix I: GC-MS data processing and analysis instructions 2018-2019
Manual Integration:
1. These instructions are to manually integrate small peaks that are not automatically integrated by the GC-
MS
software during normal data analysis.
2. Integrate as many peaks as possible using the standard instructions
3. Go to Tools>Options and click ‘Manual Integration’.
4. Zoom into the desired peak using the left mouse button. This is done by drawing a box around the peak
while
holding down the left mouse button.
5. Right click mouse button and hold to draw an integration line from one side of the base of the peak to the
other.
6. Release button. The retention time of this peak will appear on top of the peak. Repeat if there are other
peaks
that need manual integration.
7. View Results (Chromatogram>Integration Results).
8. Deselect manual integration (Tools>Options).

57
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
APPENDIX II: NMR SPECTROMETER INSTRUCTIONS
A) NMR SAMPLE PREPARATION TECHNIQUES (NOT FOR CHIRAL REDUCTION)
You should have 2 NMR tubes in your drawer. They are expensive, so treat them gently.

Note: PLKE has excellent and more detailed instructions for the preparation of NMR samples (see
Technique 26, Part A, pp.916-919).

Make sure that your NMR tube is clean and dry. You should rinse your NMR tube out with acetone at
least 1 lab period before you intend to use it, otherwise you will see a large acetone peak at ~2.2 ppm in
your spectrum that possibly overshadows all of the important peaks from your compound.

For liquids, add 8 drops of your sample to the NMR tube. For solids, weigh out approximately 70-80 mg
of your sample into the NMR tube. Then add 0.6 mL of your NMR solvent – usually CDCl3 (with 1%
TMS), but possibly D2O, DMSO-d6, or acetone-d6 in the unknowns lab. The total liquid height should be
approximately 3 “fingers” high.

58
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
B) ACQUIRING THE NMR SPECTRUM

1. Check that the ring around the NMR spectrometer is not red. If it is red, consult your TA.
2. If it isn’t already open, open the NMR software controller NanalysisRemote on the attached PC.
3. If the “standby” icon is checked, uncheck it.
4. On the startup screen, click connect. Status changes to “Connected”
5. If there are error messages in the box in the bottom-right corner, inform your TA.

6. Carefully pull the tube in the spectrometer up, making sure the bottom of the tube clears the hole.
Then carefully insert your NMR tube.
7. (Begin here if you are using the instrument immediately after someone else who did not close the
software) 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”

59
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
8. 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.

9. Click “Run Experiment. Experiment status changes to “Running”.

10. Once the data is acquired (30-60 seconds), 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. If there is no sign of
any of your peaks, then you should consider making a new NMR sample or consulting with your TA.

60
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019

11. 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 (only
during your lab time) or either study center. The file name will be the same as the email subject. If
you mistype your email/password, the program will alert you.

12. 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.

13. Once you click “No”, the program will return to Step 7. A new spectrum can be taken, or the
experiment can be changed.
14. Carefully remove your NMR tube.
15. Regardless if other students are waiting to use the NMR, insert the blue-tipped standard tube back
into the NMR spectrometer and click “Standby” to put the NMR into standby mode. The ring will
turn from green to blue.

61
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019

16. (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.

C) PROCESSING THE NMR SPECTRUM – SPINWORKS SOFTWARE

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 Washington’s version
of SpinWorks4. It covers basic (“1-D”) data processing for 1H NMR and guides you through a typical operating
session.

2. What does an NMR spectrum look like?

The following spectra are typical. You will be using a 60 MHz NMR spectrometer so your spectrum will look more like
the top spectrum, however the processing is the same regardless of the spectrometer.

62
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019

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
63
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
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
 rotating the image 90o on this piece of paper
 zooming in on, or “expanding” selected regions of the spectrum. An example of this appears on
the next page:

64
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
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.

65
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
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.

66
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
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 (upper right)

 Press “up” and “down” arrows on keyboard

 Roll mouse wheel

Adjust HORIZONTAL display

 Slide horizontal scroll bar

 Click H. Exp. (“horizontal expansion”) buttons (upper right)

 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 Expanded region now looks like this:

Restore FULL spectrum display

 Click button

67
 Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
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 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.

68
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
6. Calibrating

Chemists use the signal provided by TMS to calibrate the chemical shift (horizontal) scale of an NMR spectrum.1 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 non-deuterated 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 Normal Solvent Chemical Shift

CDCl3 CHCl3 7.26
D 2O H2O 4.75
DMSO-d6 DMSO (dimethylsulfoxide) 2.50
Acetone-d6 Acetone 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 button. This opens a small “calibrate spectrum”

window.

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?

69
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
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 compound. Ignore contaminants like TMS,
CHCl3, water.3
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.
TMS appears at 0 ppm. CHCl3 is a singlet and appears near 7.26 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.

70
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
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 good integral
(integral region too narrow) (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.

71
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
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
preferred, then select Peaks and Integrals: List Peaks.

72
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
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.

73
Chemistry 242 Appendix II: NMR Spectrometer Instructions 2018-2019
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.

Before you leave, make sure that you have everything asked for by the “Labelling NMR Files” guide
on Canvas

74
Chemistry 242 Appendix III: IR Sample Preparation and data acquisition instructions 2018-2019
APPENDIX III: IR SAMPLE PREPARATION AND DATA ACQUISITION
INSTRUCTIONS
INFRARED SAMPLE PREPARATION TECHNIQUES
Salt Plates, KBr pellet presses, and mortar & 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.881-892).

Liquid Samples
Thin film
The fastest sample preparation technique is simply to place ONE 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% transmittance) try
adding a much smaller volume of sample to the salt plate.

Solid Samples

As discussed in the unknowns lab section, there are multiple techniques for acquiring the IR spectrum for
a solid compound, each with its own pros and cons. It’s up to you to decide which technique(s) to use.

Methylene chloride solution – requires that your compound be soluble in methylene chloride
Dissolve ~50 mg 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.

If you can still see liquid flowing on your salt plate, the methylene chloride has not fully evaporated.
If you can’t see the film, then there is nothing for the IR spectrometer to analyze.

75
Chemistry 242 Appendix III: IR Sample Preparation and data acquisition instructions 2018-2019
Potassium bromide pellets (see PLKE, page 886 and video on Canvas)
In this method, about 1 mg of solid sample is mixed with about 75 mg of dry potassium bromide and
pressed between two stainless steel bolts in a minipress die.

Steps in Preparing a KBr Pellet using a Minipress

1. Weigh out 0.5 – 1.5 mg of solid compound. Transfer the solid to an agate mortar and pestle and
grind until it is an exceedingly fine powder.
2. Add 70 – 80 mg of dry potassium bromide (stored in the oven) to the mortar. Thoroughly grind
and mix the KBr with the solid compound. It is critical to obtain tiny uniform crystals for best
results. Return KBr to oven to keep in dry.
3. Thread one bolt halfway into the minipress die (see diagram above).
4. Transfer all of the KBr mixture into the barrel of the minipress die (a piece of weighing paper may
aid in the transfer). Tap the side of the minipress to encourage all of the solid mixture to fall to
the bottom of the die. The bottom of the die should have a thin and even coating of the mixture.
5. Place the minipress die (the bottom bolt) into the “bench socket” (the permanent socket or
hexagonal hole that is attached to the benchtop).
6. Thread the top bolt into the minipress “clockwise” by hand as far as it will go.
7. Using the torque wrench (set at 240 in*lb.), continue to tighten the bolt clockwise into the
minipress die until the wrench makes a “soft click” sound (or you feel a “give” in the wrench).
Do not tighten beyond this point (the “soft click”), you will rip off the bolt head and ruin the
minipress!
8. Wait approximately 60 seconds. The KBr needs time to transform into a translucent crystal.
9. Place the manual wrench (NOT THE TORQUE WRENCH), on the top bolt and using both
hands, turn the bolt “counterclockwise” a turn or two. At this point, at least one of the bolts should
be loose from the minipress. If necessary, you may need to use the large hand wrench to loosen
the second bolt. Place the large hand wrench around the barrel of the minipress with the tight bolt
in the “bench socket” and turn to loosen.
10. When both bolts are loose, hold the barrel of the minipress horizontally and carefully remove the
two bolts by hand.
11. You should observe a clear or translucent KBr pellet in the center of the barrel. Even if the pellet
is not transparent, you should be able to obtain a satisfactory spectrum as long as light passes
through the pellet (greater than 5% transmission on the %T scale).
12. Place the minipress die containing the KBr pellet onto the IR sample holder just as you would a
salt plate when running a liquid IR.

76
Chemistry 242 Appendix III: IR Sample Preparation and data acquisition instructions 2018-2019
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.

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 key board. 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', then press scan again. 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. Pressing
“ShiftVcursor” allows for smooth scrolling between peaks; otherwise the cursor “jumps”
between peaks.

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.

77
Chemistry 242 Appendix III: IR Sample Preparation and data acquisition instructions 2018-2019
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.

The IR spectrometer doesn’t save data, so make sure that what you print is useful – that all important
peaks are labelled and that the spectrum is neither too zoomed-out nor too zoomed-in.

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

78
Chemistry 242 Appendix IV: Useful spectral Data Tables 2018-2019
APPENDIX IV: USEFUL SPECTRAL DATA TABLES
(IR and NMR tables should only be used as a guideline. Variations exceeding the given range may be possible.)
List of common IR frequencies NMR chemical shifts
Functional Bond (stretch Characteristic Type of proton Structure , ppm
Group unless noted) Absorption Cyclopropane C3H6 0.2
(cm-1) Primary alkane R-CH3 0.9
Alkane C-H 2950-2850 Secondary alkane R2-CH2 1.2-1.4
C-H 3100-3010 Tertiary alkane R3C-H 1.4-1.7
Alkene
C=C 1680-1620 Vinylic C=C-H 4.6-5.9
Alkyne
C-H ~3300 Acetylenic C≡C-H 2-3
C≡C 2260-2100 Aromatic Ar-H 6-8.5
C-H ~3030 Benzylic Ar-C-H 2.2-3
Benzene C-H bend 860-680 Allylic C=C-C-H 1.7-2
C=C 1700-1500 Halides H-C-X 2-4.5
O-H 3550-3200 H-C-OH 3.4-4
Alcohol/Phenol Alcohols
(broad, s) R-C-O-H 1-5.5 (b, v)
O-H 3400-2500 Phenols Ar-O-H 4-12 (b, v)
Carboxylic acid (broad, v) Ethers H-C-OR 3.3-4
C=O 1780-1710 (s) Thiols, sulfides, H-C-SR 2-3
Amine N-H 3500-3300 amines H-C-NR2
Nitrile C≡N 2260-2220 R-NH2, R-SH 1-5 (b, v)
C-H ~2720 RC(O)O-C-H 3.7-4.1
Aldehyde Esters
C=O 1740-1690 (s) H-C-C(O)O-R 2-2.2
Ketone C=O 1750-1680 (s) H-C-C(O)-OH 2-2.6
Ester C=O 1750-1735 (s) Carboxylic Acids
R-C(O)O-H 10-12 (b,v)
Amide
N-H 3700-3500 -Carbonyls H-C-C=O 2-2.7
C=O 1690-1630 (s) Aldehydic R-C(O)-H 9-10
N-O, N=O ~1530 and Enolic C=C-O-H 15-17
Nitro
~1350 (s) Amides R-C(O)-NH-R 5-9 (b, v)
(s=strong peak, v=variable intensity) (b=broad peak, v=variable position)

NMR Impurities CDCl3 D2O DMSO-d6 Acetone-d6

Residual solvent peak 7.2 (s) 4.8 (s) 2.5 (p) 2.1 (p)
Water 1.6 (s) 4.8 (s) 3.3 (s) 2.8 (might be s or t)
Acetone 2.2 (s) 2.2 (s) 2.1 (s) 2.1 (s)
Diethyl ether 1.2 (t), 3.5 (q) 1.2 (t), 3.6 (q) 1.1 (t), 3.4 (q) 1.1 (t), 3.4 (q)
Methylene chloride 5.3 (s) Not soluble 5.8 (s) 5.6 (s)

79