Sheryl A. Rummel, Kristin M. Beiswenger - Chemistry 213 Introductory Organic Chemistry Laboratory 2015-2016. Lab Guide-Hayden McNeil (2016)

1H 2H
·1 H
If an Accident Occurs
In case of accident notify the laboratory instructor and other students immediately with a
BURNING CLOTHING: Prevent the person from running and fanning the flames. Guide them
shower and hold the person under the shower until flames are extinguished and chemicals was
Remove contaminated clothing. Get prompt medical attention.
BURNING REAGENTS: Turn off any nearby Bunsen burner flames and carefully remove any
combustible material and solvents. Small fires in flasks and beakers can be extinguished by coverin •
container with a large beaker or a watch glass. Use a dry chemical or carbon dioxide fire extin1~is.t1er
directed at the base of the flames. Do not use water.
SKIN BURNS, either Thermal or Chemical: Flush the burned area with cold water for at least 15 min ··
Resume if pain returns. Wash off any chemicals with a mild detergent and water. Current practice
recommends that no neutralizing chemicals, unguents, creams, lotions, or salves be applied. Howev
the burn is mild, the stockroom has a topical analgesic that can be sprayed on the affected area.
If chemicals are spilled on a person over a large area quickly remove the contaminated clothing v ·
under the safety shower. Seconds count and time should not be wasted because of modesty. Get prom •
medical attention.
CHEMICALS IN THE EYE: Flush the eye with copious amounts of water for 15 minutes using the eye-
wash fountain at the end of the lab. Hold the eye open to wash behind the eyelids. After 15 minutes o
washing obtain prompt medical attention, regardless of the severity of the injury.
CUTS: Minor Cuts-This type of cut is most common in the organic laboratory and usually arises fro
broken glass or syringe needles. Wash the cut, remove any pieces of glass, and apply pressure to
stop the bleeding. Get medical attention.
Major Cuts - If blood is spurting place a pad directly on the wound, apply firm pressure, wrap e
injured to avoid shock, and get immediate medical attention. Never use a tourniquet.
POISONS: Obtain prompt medical assistance and call 1-800-521-6110 for the Poison Control Center in
Hershey, PA.
Adapted from Safety in Academic Chemistry Laboratories, prepared by the American Chemical Society C
tee on Chemical Safety, March 1974.
Lab Guide for CHEMISTRY 213W
Introductory Organic Chemistry

Laboratory
2015-2016
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Sheryl A. Rummel • Kristin M. Beiswenger
Department of Chemistry
Penn State
HAYDEN
1111
MCNEIL
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Copyright© 2016 by The Pennsylvania State University, Department of Chemistry

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Copyright© 2016 by Hayden-McNeil, LLC on illustrations provided
Photos provided by Hayden-McNeil, LLC are owned or used under license
Materials from Making the Connections 2: A How-To Guide for Organic Chemistry Lab
Techniques written by Anne B. Pad.fas, copyright© 2011 are reprinted with permission
of Dr. Padias
All rights reserved.
Permission in writing must be obtained from the publisher before any part of this
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Acknowledgements H Chemistry 213W
Acknowledgements
The materials in the Lab Guide for Chemistry 213W have been a collaborative effort
over the years. Special acknowledgements are given to the current editors, Sheryl
Kummel and Kristin Beiswenger, and writers of our previously published laboratory
manuals, including Bob Minard, Katherine Masters, Jackie Bortiatynski, Tracey Oris-
kovich Halmi, and Kenneth L. Williamson. The Department of Chemistry would also
like to recognize the support and contribut ions from our TAs, staff, and students.
Specific thanks to Ritobroto Sengupta for his contribution to the mechanism of the
ftuorene-to-ftuorenone reaction in the Column Chromatography chapter.
A separate and very special thanks to Kristin Beiswenger, Michael Banales, Luke Swid-
er, and Todd Pontius for the birth of Mr. Benzene. Additionally, your contributions
to this course have been invaluable; changing things for the better always requires
teamwork and great minds. You have been a BRILLIANT dream team. Things would
not be as they are now without you. To those of you that are moving on, know that
you will be greatly missed. You all will accomplish amazing things in life and those
amazing things are well deserved!
,1
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iii
Chemistry 213W II Introductory Organic Chemistry
iv
Table of Contents II Chemistry 213\V
Chemistry 213W
Table of Contents
1. Safety Firs t! .................................................................................................... . 1

2. Instrumental Analysis ................................................................................ 13
3. The Assignments ................ .......................................................................... 21
3.1 Prelab Assignments ........................................................................................ 23
3.2 Writing Procedures, Data, and Observations in Your Notebook ............... 31
3.3 Examples of Notebook Pages for an Experiment ........................................ 38
3.4 Notebook Pages Reports ...................................................................... .......... 41
3.5 Formal Final Reports ...................................................................................... 46
3.6 Example Formal Final Report ........................................................................ 55
4. Checking-In and Orientation ..................... .. ............................................. 67
5 . Extraction ........................................ ................... ... .............................. .......... 79
6. Thin-Layer Chromatography ................................................................... 119
7. Application of Thin-Layer Chromatography and Extraction:
Synthesis of Methyl Salicylate ................................................................ 143
8. Distillation .................................................................................................. 161
9. Recrystallization .. ........................ .. .................................... ... .... ....... .......... 189
10. Column Chromatography .............................................. ........................... 215
11. Synthetic/Isolation Experiments .............. ........ ......... ............................ 237
12. Optical Rotation, Refractive Index, and
Elemental Analysis .................................................................................... 2 43
13. Molecular Spectroscopy and Ultraviolet/Visible
Spectroscopy (UV/Vis) .............................................................................. 253
14. Nuclear Magnetic Resonance Spectroscopy (NMR) ............................ 267
15. Infrared Spectroscopy (IR) ...................................................................... 299
16. Mass Spectrometry (MS) .......................................................................... 313
17. Gas Chromatography (GC) ....................................................................... 323
\.~D CHAPTER 1
~~~~~~~~~~~~~~~~~~~~~~~~~~-
Safety First!
Our primary goal in the organic lab program at Penn State is to allow you to
experience organic chemistry as it is practiced in any modern synthetic organic
laboratory. The first portion of this course will be primarily devoted to learning
the techniques for purifying and characterizing organic compounds. Then, you
will use these techniques in a series of experiments involving synthesis or natu-
ral product isolation. Additionally, you will be using the types of sensitive and
analytical instruments used in modern research labs: NMR, IR, UVNis, and GC.
Please read the course syllabus and schedule for specific details about course poli-
cies regarding required materials, course assignments, determination of grades,
late policies, absences, academic dishonesty, and letters of recommendation.
1.1 Equipment Used in the Organic Laboratory

In the first lab period, you will check in to your assigned lab desk to make sure you
have all of the glassware you'll be using in this lab course. There are diagrams of
most pieces of the glassware on the Check-In sheets found at the end of this lab
guide. During the semester you'll become very familiar with the glassware utilized
in organic synthesis.
1.2 General Safety

Here to help us out with pointing out important safety rules and important experi-
mental details is Mr. Benzene! He'll be making appearances in all of our chapters.
Hey, everyone! I'm Mr. Benzene!
Safety is REALLY IMPORTANT so make sure you pay

attention when reading this chapter. Remember,
SAFETY FIRST!
1
ClerP1strv 213W : : Chapter 1
••
•• OTES
In organic lab, a majority of the reactions you'll be performing are considered to
be "small-scale." Small-scale organic experiments are much safer to conduct than
macroscale reactions (on a scale 10 to 100 times larger). However, on either a
microscale or a macroscale, it's still important to know what you're working with
so you can be safe while handling reagents AND how to properly dispose of the
chemical waste.
General Safety Rules

• Dress properly for work in the lab. Wear closed-toed shoes, not sandals. Avoid
wearing shorts and skirts. Long pants are mandatory!
Mr. Benzene says: Spilling chemicals on your bare

skin may result in a chemical burn. It's best to keep
everything covered and safe!
• Never eat, drink, or smoke in the laboratory. Eating and drinking in the lab
are not permitted due to the risk of inadvertent ingestion of chemicals.
• No iPods or music players with headphones are allowed. Cell phone usage is
also strictly forbidden.
• You may work in the laboratory only when your teaching assistant or a faculty
member is in the same lab.
• Confine long hair and loose clothes.
• Always take off gloves AND wash your hands before leaving the laboratory.
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Mr. Benzene says: Don't touch ANYTHING with
your gloves on except your chemistry; you don't
want to expose other people to the chemicals you
were handling!
0
• Know the locations of emergency eyewashes and safety showers.

• Report any accident immediately to your teaching assistant or to the faculty
member in charge and have your TA fill out an accident report, which can be
obtained from the stockroom.
• If a chemical gets on your skin or in your eye, rinse with water for at least
15 minutes.
2
Safety First! :: Chemistry 213W
eS\ in the Laboratory NOTES : :

• ~~ show up on time and be prepared for the day's work. Clean up and leave
irromptly at the end of the three-hour period.
• Cean your desktop, sink and hood before you leave the laboratory so these
areas will be ready for the next person who works at the same bench.
• Empty the organic waste that resides in your hood into the appropriate sate!-
.;~ waste accumulation area.
• _.fake sure you put all of your samples, glassware, etc., back in your locker at
the end of the lab period. Be certain that no items such as litmus papers or
Slrer papers collect in the sink. Dispose of all trash properly.
• ~·!hen you use other parts of the laboratory, such as the reagent shelves or
~alances, leave them clean. Please keep the electronic balances clean!
• Always replace the cap on a reagent bottle after use and return all
reagent and solvent bottles to their proper place or in the refrigera-
tor immediately! If you empty a bottle, take it to the stockroom for
refilling.
• Keep the Instrument Room clean and neat. Remove what you bring in and
properly store the instrument accessories in their proper containers or in
drawers. Throw away or recycle unwanted spectra and scraps of paper.
Information on Eye Protection

:C:ye protection is extremely important. The requirement that you wear approved
r.e protection in the laboratory is mandatory and is most effective in preventing
the largest number of potential accidents of serious consequence. For their own
;rrotection, those unwilling to comply with this rule will be excluded from the
::aboratory. Ordinary prescription eyeglasses do not offer adequate protection.
Safety glasses of some type must be worn at all times.
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Mr. Benzene says: Protect your peepers!
Contact lenses are allowed when working in the organic chemistry lab. However,
':"OU m ust wear some type of approved protective eyewear over your contact lenses
~en you are working in the lab, and you must identify yourself as a contact lens
~er in some manner to be designated by your instructor. This is to alert safety
personnel to the presence of your contact lenses in the unlikely event that your
eyes would need to be flushed while you are unconscious.
3
Chemistry 213W ;; Chapter 1
-
•• OTES Gloves
Be aware that "protective gloves" in the organic laboratory do not offer full protec-
tion from chemicals. Polyethylene and latex rubber gloves are very permeable t o
many organic liquids. An undetected pinhole can mean long-term contact with
reagents. Disposable polyvinyl chloride (PVC) gloves offer reasonable protection
from contact with aqueous solutions of acids, bases, and dyes, but no one type of
glove is useful as protection against all reagents. However, it is safer to wear gloves
and immediately wash your hands with soap and water after accidental contact
with any harmful reagent or solvent than to wear no gloves at all. If you spill a
chemical on a glove, that glove (or those gloves) should be discarded; over time,
the chemical can seep through the glove to your skin. Gloves can be obtained on
the common shelf located in your lab section.
Using the Laboratory Hood

Perhaps the most expensive and important piece of equipment in the organic
laboratory is the laboratory hood. Modern practice dictates that there should be
one exhaust hood for every two people in laboratories where workers spend most
of their time working with chemicals. All chemical manipulations and reac-
tions should be done in the hood. Air is drawn through the hood opening at
a velocity of 50 to 100 feet per minute, depending on how low the hood window
sash is closed. Virtually all vapors from chemicals in the hood are exhausted above
the roof of the building. All reactions should be at least 15 cm back from the hood
sash. Hoods are most effective if the sash is kept closed as far as possible, although
most operations can be carried out with the sash about halfway down. Each hood
bears a sticker that indicates the ideal sash level when working in the hood. Please
,.,
keep the sash at this level or lower.
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We don't want you huffing hazardous chemicals!
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Four "utilities" are provided by the hood: electricity, water, nitrogen, and vacuum.
Reactions that might be decomposed by atmospheric oxygen or moisture can be
run in an atmosphere of nitrogen. A stream of nitrogen can be used to speed up
evaporation of small amounts of volatile solvents such as dichloromethane or
hexanes. The pressure of the house supply nitrogen is 10 psi. The vacuum is used
to carry out suction filtration and to remove traces of solvents from solids. Be sure
to keep all three valves on your hood closed when not in use. Leaving a vacuum
valve open means that the vacuum will be poorer for everyone in the lab since you
are all connected to one vacuum pump.
Safety First! ;; Che mistry 213W
.3 \ \orking with Flammable, Hazardous, Corrosive, and NOTES ;;

Toxic Substances
~of the chemicals used in this course will not be familiar to you. Their prop-
ie:r:::!:es can be looked up in reference books and using online sources. If you do
;;:or h.ow the properties of a chemical you will be working with, it is wise to read
~.n: the potential hazards of all the reagents you use on Material Safety Data
:a.eets. You will be looking up safety information about all of the chemicals in each
lab as part of your Prelab Assignments. Because you may not have had previous
~ence working with organic chemicals, most of the experiments you will
carry out in this course will not involve the use of known carcinogens. You will,
D.owever, work routinely with flammable, corrosive, and toxic substances. A few
exp€riments involve the use of substances that are suspected of being carcinogenic,
such a s aniline. If you pay proper attention to the rules of safety, you should find
•a;orking with these substances no more hazardous than working with ammonia
or nitric acid. The single, short-duration exposure you might receive from a sus-
pected carcinogen, should an accident occur, would probably have no long-term
consequences. The reason for taking the precautions noted in each experiment
is to learn and implement good safety habits before beginning each experiment.
However, if an accident occurs and you spill any chemical on yourself, wash the
affected part immediately and thoroughly with soap and water, followed by a
thorough rinse (at least fifteen minutes with cool running water). Even if you are
not aware of any contact, you should always wash your hands thoroughly with
soap before leaving lab.
Mr. Benzene says: Be aware of the hazards of the

chemicals you're working w ith but not afraid of
them!
Flammable Substances
Flammable substances are the most common hazard of the organic laboratory.
Two factors can make this laboratory much safer: making the scale of the experi-
ments as small as possible and not using Bunsen burners. We will NEVER use an
open flame in the organic chemistry lab. Instead, we use heating mantles, sand
baths, hotplates, and hot water baths to heat reactions. Diethyl ether (hp 35°C),
the most flammable substance you will usually work with in this course, has an
ignition temperature of 160°C, which means that a hot plate at that temperature
will ignite ether vapors. For comparison, n-hexane (hp 69°C), a constituent of
gasoline, has an ignition temperature of 225°C. The flash points of these two
organic liquids, that is, the temperatures at which they will catch fire if exposed
to a flame or spark, are below 20°C. However, if you are careful, these flammable
5
Chemistry 213W H Chapter 1
H NOTES
liquids are not difficult to work with. Except for water, almost all the liquids you
will use in the laboratory will be flammable.
Hazardous Substances
Very rarely will you be instructed to work with explosive compounds in this
laboratory. However, it's still important to know a little bit about them. The chief
functional groups that render compounds explosive are peroxide, acetylide, azide,
diazonium, nitroso, nitro, and ozonide groups.
Ethers, especially cyclic ethers and those made from primary or secondary alcohols
(such as tetrahydrofuran, diethyl ether, and diisopropyl ether), form peroxides.
Other compounds that form peroxides are aldehydes, alkenes that have allylic hy-
drogen atoms (such as cyclohexene), compounds having benzylic hydrogens on a
tertiary carbon atom (such as isopropyl benzene), and vinyl compounds (such as
vinyl acetate). Peroxides are low-power explosives, but are extremely sensitive to
shock, sparks, light, heat, friction, and impact. Some peroxides are relatively safe.
For example, benzoyl peroxide is commonly used to treat acne. The biggest danger
from peroxide impurities comes when the peroxide-forming compound is distilled
The peroxide has a higher boiling point than the parent compound and remains
in the distilling flask as a residue that can become overheated and explode. This is
one reason why it is very dangerous to distill anything to dryness.
You may have occasion to use 303 hydrogen peroxide. This material causes severe
burns if it contacts the skin, and it decomposes violently if contaminated with
metals or their salts. Be particularly careful not to contaminate the reagent b ottle.
Materials like alumina and silica, while chemically inert, pose a hazard due to their
small particle sizes. The dust is an eye irritant and great care must be taken not
to breathe it into the lungs . Wet alumina and silica is relatively nonhazardous bu:
dry alumina and silica should only be handled in the hood.
Corrosive Substances
Handle strong acids, alkalis, dehydrating agents, and oxidizing ~gents care.fut:~
so as to avoid contact with the skin and eyes and to avoid breathing the corrosin:
vapors that attack the respiratory tract. All strong concentrated acids attack the
skin and eyes. Concentrated sulfuric acid is both a dehydrating agent and a str~g
acid that will cause very severe burns. Nitric acid and chromic acid (used in de~
solutions) also cause bad burns. Hydroft.uoric acid is especially harmful, causi:lg
deep, painful, and slow-healing wounds. It should be used only after thorm.:;...
instruction.
Sodium, potassium, and ammonium hydroxides are common bases you will encm=.-
ter. The first two are extremely damaging to the eye, and ammonium hydrox:-=-=
is a severe bronchial irritant. Like sulfuric acid, sodium hydroxide, phosphoro=s
6
Safety First ! : : Chemistrr 213\V
~;;:oiiC.e, and calcium oxide are powerful dehydrating agents. Their great affin- NOTES H
:nr water will cause burns to the skin. Because they release a great deal of heat
::.::=:i: they react with water, to avoid spattering, they should always be added to
11r....::er rather than water being added to them. That is, the more dense substance
shauld always be added to the less dense one so that rapid mixing results
as a consequence of the law of gravity.
Should one of these substances get on the skin or in the eyes, wash the affected
area ;..ith very large quantities of water by using the safety shower and/ or eye-
"a.Sh fountain. Do not attempt to neutralize the reagent chemically. Remove
contaminated clothing so that thorough washing can take place. Alert your TA
.!MEDIATELY that a corrosive substance has come into contact with your skin.
When you are using very small quantities of these reagents, no particular safety
equipment is needed except safety glasses. Take care not to let the reagents, such
as sulfuric acid, run down the outside of a bottle or flask and come in contact with
your fingers. Wipe up spills immediately with a very damp sponge, especially in
the area around the balances. Pellets of sodium and potassium hydroxide are very
hygroscopic and will dissolve in the water they pick up from the air; therefore, they
should be wiped up very quickly. Wear protective gloves when using acids or bases.
The corrosive vapors can be avoided by carrying out work in a good exhaust hood.
Toxic Substances
Many chemicals have very specific toxic effects. They interfere with the body's
metabolism in a known way. For example, the cyanide ion combines irreversibly
with hemoglobin to form cyanomethemoglobin, which can no longer carry oxygen.
Carcinogenic and mutagenic substances deserve special attention because of their
long-term insidious effects.
Women of child-bearing age should be careful when handling any substance of

unknown properties, and any woman who is pregnant, becomes pregnant, or
is actively seeking to become pregnant while working in any organic lab should
notify the instructor IMMEDIATELY. Certain substances are highly suspected
teratogens and will cause abnormalities in an embryo or fetus. Among these are
benzene, toluene, xylene, aniline, nitrobenzene, phenol, formaldehyde, dimethyl-
formamide (DMF), dimethyl sulfoxide (DMSO), polychlorinated biphenyls (PCBs),
estradiol, hydrogen sulfide, carbon disulfide, carbon monoxide, nitrites, nitrous
oxide, organolead and mercury compounds. Some of these substances will be used
in subsequent experiments.
It is impossible to avoid handling every known or suspected toxic substance, so

it is wise to know what measures should be taken. Because the eating of food or
the consumption of beverages in the laboratory is strictly forbidden, and because
one should never taste material in the laboratory, the possibility of poisoning by
mouth is remote.
7
••
•• OTES 1 .4 Waste Disposal
Handling of Waste
Chemicals are everywhere; they can be found in animals, plants, and water as well
as in many commercially available products including medicines, detergents, and
foods. Risks associated to exposure to a given chemical may be low, but is always
present. In order to keep the risk in the laboratory to a minimum, all chemical
waste must be disposed of properly. Not long ago, it was common practice to wash
all unwanted liquids from the organic laboratory down the drain and to place all
solid waste in the trash basket .
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Mr. Benzene says: It's NEVER a good idea to pour
organic chemicals down the drain or throw them in
the trash- thafs just not safe!
D
The following table breaks down the different waste categories for quick, easy
reference. Following the table, you will find m ore detailed explanations of the
waste categories.
8
Safety First! H Chemistry 213W
NOTES II
Inorganic acids (HCl, H3 P0 4 , H 2 S0 4),

D Drain inorganic bases (NaOH, NaHC0 3),
acetic acid
Ethyl acetate, diethyl ether, hexanes,

Nonhalogenated
NHO toluene, acetone, methanol, ethanol,
Organics
propanol
Halogenated Dichloromethane, chloroform,

HO
Organics deuterated-chloroform
HM Heavy Metals Compounds containing Pd, Cr, Zn
Biohazard
BW Bacteria, agar plates
Waste
SI Silica Waste Silica and alumina
Waste Chemicals That Can Be Flushed Down the Drain (D)

Inorganic Acids (such as hydrochloric, nitric, or sulfuric) and Inorganic Bases
(such as sodium or potassium hydroxide) that do not contain hazardous metals
(see the following page). If greater than 1 M and more than 5 mL in volume, these
should be neutralized with sodium bicarbonate or hydrochloric acid before flushing
down the drain with lots of water.
Solutions of Inorganic Alkali or Alkaline Earth Salts such as KBr, CaC12,

Na2 SO 4 , MgN0 3 , or Na2 HPO4 that do not contain hazardous metals. Small volumes
( <20 mL) of aqueous solutions of these salts can be flushed down the drain. Solids
of this type that are wet with organic solvents should be allowed to dry in a hood
before disposal in the trash bin.
Waste Chemicals That Must Be Collected

Nonhalogenated Organics (NHO) are water-insoluble organic liquids and
solids . These solvents can contain dissolved, solid, nonhazardous organic solids.
Nonhalogenated solid organic waste also should be placed in this container. The
solids will usually dissolve in the solvent present in the container. Nonhaloge-
nated organics that are very water soluble such as methanol, ethanol, propanol,
acetic acid, acetone, etc., which do not contain more than a few percent of water
insoluble organic materials, should not go down the drain. They should ALSO be
disposed of in the NHO waste. Each hood contains a labeled collection beaker for
---- ---- , - -
NHO waste. Make sure that at the end of the lab period, you or your hood-mate
: : NOTES
empties this waste into the larger waste receptacles located throughout the lab.
Acetone is used to rinse glassware. Acetone with a low percent of dissolved organic
residues should be placed in the appropriate Organics disposal beaker-Haloge-
nated or Nonhalogenated.
Halogenated Organics (HO) are halogenated organic liquids and solids. Sol-
vents, such as dichloromethane (CH 2Cl2), that contain Cl, Br, I, or F must go in
the halogenated organic container. This does not include inorganic materials such
as sodium chloride (NaCl), potassium bromide (KBr) , etc. Each hood contains a
labeled collection beaker for HO waste. Ultimately, this will go to a special incin-
erator equipped with a scrubber to remove HX from the combustion gases. Make
sure that at the end of the lab period, you or your hood-mate empties this waste
into the larger waste receptacles located in the front of the lab.
Heavy Metals (Hazardous Metals, HM) including Hg, Cr, Ce, Mn, Zn, Pd, Pt,
etc., in any form should be disposed of in special heavy metal collection containers
located near the waste accumulation area in the front of the lab. These cannot be
destroyed by burning and must go to a permanent secure waste storage area or
be recycled. Precious metals such as platinum, palladium, rhodium, and rhenium
are usually recycled as these are very expensive.
Silica and Alumina (SI) used for chromatography should NEVER be placed in
the general trash bins. The waste alumina and silica from chromatography columns
is disposed of in collection containers located near the waste accumulation area.
Other Miscellaneous Laboratory Waste

The Trash Bin (TB) can be used for nonhazardous solids such as sand, corks,
sodium sulfate, filter paper, paper towels, boiling stones, or sticks, etc. If free of
flammable organic solvents, they can then be thrown in the trash bin. One type of
hazardous waste is unique: a harmless solid that is damp with an organic solvent.
Sodium sulfate or calcium chloride used to dry organic solvents are 2 examples.
Being insoluble solids, they obviously can't go in the organic solvents container,
and being flammable when wet with organic solvent, they can't go in the non-
hazardous waste container. A solution to this problem is to spread the solid ou::
in the hood on a paper towel to let the solvent evaporate. You can then place the
solid in the trash.
Broken Glassware and Broken Pasteur Pipettes as well as unbroken useC.

pipettes should be disposed of in the bins marked "Disposable Lab Glass Onl;•-
located throughout the lab. Do not put broken glassware in the trash bins.
10
Safety First! II Chemistry 213W
S. a 'ks and Used Syringes should be disposed of in the "SHARPS" containers NOTES II
~ near tlle waste accumulation area in the front of the lab. These special
- -=-:.ers :nust be autoclaved before landfill disposal, a very expensive process .
..- e ::.Em-e, dispose of only needle and syringes in these containers. The "SHARPS"
-.....-------
~ers, should also be used for broken glassware contaminated with blood
Oeaning Chemical Spills
Mr. Benzene says: If you spill something, notify

your TA immediately! Don't try to clean it up on
your own.
Spilled solids should simply be swept up and placed in the appropriate waste
container. Spilled acids should be neutralized using solid sodium carbonate. For
eases, use solid sodium bisulfate (sodium hydrogen sulfate). If the spilled material
::.s very volatile, clear the area and let it evaporate, provided there is no chance of
::.gniting flammable vapors. Other liquids can be taken up into such absorbents as
""'ermiculite, diatomaceous earth, dry sand, or paper towels. Be particularly careful
ill wiping up spills with paper towels. If a strong oxidizer is present, the towels can
:.ater ignite. Bits of sodium metal also will cause paper towels to ignite. Sodium
metal is best destroyed with n-butyl alcohol. Wear gloves when using paper towels
or a sponge to remove the liquid.
Be Informed! For every experiment in Chem 213W you will be asked to fill out
a "Chemical Data Table" as part of a prelab assignment (details in Chapter 3). By
doing this, you will be informed about all reagents utilized in the lab, including
hazards and waste disposal. Remember, SAFETY FIRST!
11
G"lemistrY 21 JW : : Chapter 1
II NOTES
12
CHAPTER 2
Instrumental Analysis
Modern organic chemistry involves substantial use of spectroscopic and chromato-

graphic instruments to analyze the products synthesized or isolated from nature.
Hands-on experience with modem instruments is the best way for you to appreciate
how a modern organic chemist works. Unfortunately, most of these instruments
are fairly expensive ($20,000 to $100,000 or more) and we can't afford to have one
of each instrument for a TA's section of 16 students. For most product analyses,
we currently have two to three instruments of each type to serve the students in
each section of this course. Therefore, the Instrument Room is open and staffed by
undergraduate instrument room TAs, Chem 213W TAs, and Chem 203 TAs many
hours during the week so that you can sign up to use these instruments not only
during the lab period, but at other times as well.
The Instrument Room is an extension of the laboratory classroom and as such

we expect you to come prepared to obtain quality analytical data and to interpret
the results. When obtaining data using the NMR or IR, you are required to bring
the instrumental analysis checksheet that was completed as part of the Prelab
Assignment. The TAs in the Instrument Room may ask to see these checksheets
whenever you are using the NMR or IR. A TA can only assist you in obtaining your
data and guide you through the data analysis if you provide the relevant sample
information.
Instrumentation time is available by signing up on the appropriate sign-up sheets

located conveniently near an instrument or using the walk-on time (first come,
first served). Please be considerate of your colleagues by arriving promptly at the
time you signed up for and working efficiently.
To familiarize all students with the Instrument Room, an Instrument Room

Orientation Worksheet will be completed as part of orientation activities in
the fi.rst week of lab. Additionally, the last few chapters of this lab guide discuss
each of these analytical techniques in depth to give you a better understanding of
how the instrument works and how to interpret data.
13
Oiemistry 213W : : Chapter 2
..•• OTES 2.1 Instrument Room Policies

• The Instrument Room is open certain hours when TAs are on duty and sched-
uled to help you use the instruments. You can view the hours on the door of
the Instrument Room AND on ANGEL.
• Sign up for time on the appropriate instrument. Be on time or you might lose
your slot!
• If an instrument is dedicated for walk-on time, please put your name on the
waiting list and NO LINE CUTTING! Please be patient and respectful to TAs
and students while waiting.
• Remember to prepare your sample during your lab period. Label it clearly and
put it in your TA's basket/locker in the Instrument Room. You will NOT be
allowed back into the lab during another lab period!
• A TA must approve and sign your data before you leave!
• Be patient and treat other students, TAs, and instructors with respect.
• Inappropriate copying of analytical data will NOT be tolerated. You must obtain
your own analytical data on all compounds you make or isolate in Chem 213W
using the instrumentation provided in the Instrument Room. Fabrication of
data is an academic integrity violation; please review the course academic
dishonesty policies.
• Clean up after yourself!
• The TAs on duty will provide only limited help with lab reports and prelab as-
signments; there are separate office hours for that. Please see the "Resource
Room Schedule" for those hours.
2.2 Sample Preparation

Preparing NMR Samples
1. Each student is provided two NMR tubes to be used, cleaned, and then re-used
throughout the semester. An NMR sample requires a deuterated solvent; we
typically use deuterated chloroform (CDC13) .
'c
,.
......
~
8G I
c ....
D
Mr. Benzene says: Make sure you use the
appropriate DEUTERATED solvent! Otherwise your
NMR spectrum won't turn out well ...
2. For solid samples: To prepare a sample to be analyzed via NMR, weigh out
35-50 mg of your solid using a weigh boat. Transfer the solid to a 2 mL vial.
Using a clean pipette or syringe, measure out 1 mL of the appropriate deuter-
ated solvent (CDC13 and d 6-DMSO, which are available on the common shelf;
other solvents in stockroom) and dispense the solvent into the 2 mL vial. Cap
14
Instrumental Ana ~
and shake the vial to dissolve the solid. Transfer the solution using a glass
pipette to your NMR tube. Make sure NMR solvent in NMR tube is at LEAST
2 inches but no more than 2.5 inches in height.
Plastic cap
5 mm glass tube
Sample: -35 mg
2-2.5 in. deep
Figure 2.1. The NMR tube.
3. For liquid samples: There is no need to weigh the liquid. Place -0.25 inches
of your liquid sample in a NMR tube then fill to the proper height in the NMR
tube with the appropriate deuterated NMR solvent.
4. If you plan on visiting the instrument room outside of your lab period, make
sure that you label your NMR tube using an NMR tube tag (located on the
common shelf in the lab). Make sure you do NOT use tape to affix the label to
your tube! Place your sample in the Instrument Room inside the proper bin
with your TA's name on it. Remember that you will not be allowed back into
the lab outside of your scheduled lab period to retrieve prepared samples.
5. For 400 MHz NMR sample analysis: Prepare an NMR sample as instructed
above and then obtain a 1 H NMR on the 60 MHz Anasazi instrument. Print
out 2 copies of the processed NMR spectrum. Keep one copy for yourself. The
other copy will be submitted with a 400 MHz NMR request form. The form
is located in the Instrument Room. Make sure you completely fill out the
form, attach your NMR spectrum, and tape your NMR tube containing your
sample. Put the completed form and sample in the appropriate submission
bin. Your data will be run in a timely manner by an Instrument Room Super
TA, processed, and placed in the done bin.
,.,
; : NOTES 6. How to clean your NMR tubes:
'c c....... Mr. Benzene says: DON'T THROW YOUR NMR

,. t'.JG \ TUBES AWAY. That would be a rash decision.
You can clean them and re-use them the entire
~ D semester!
D
Dispose of your NMR sample into HALOGENATED ORGANIC WASTE; do not

dispose of your NMR sample down the drain. Rinse the NMR tube out with
acetone many times, taking care to dispose of the acetone rinses into the non-
halogenated organic waste. Avoid deaning the NMR tubes with water. Put the
NMR tube into a glassware oven for 20 to 30 mins to evaporate the acetone.
Preparing IR Samples
1. The IR can run both liquid AND solid samples. There is no sample prep neces-
sary except placing a bit of your sample in a shorty vial with a label to take to
the instrument room.
2. Cleaning out the 2 ml shorty vial: Don't throw away the vial. Dispose of the
compound in the appropriate organic waste. Rinse out the vial with acetone
and let it dry before you re-use it.
Preparing GC Samples
1. Place 1 drop of your liquid sample or 1 mg of solid sample into a 2 mL vial
Dissolve the sample in 2 mL of dichloromethane. DO NOT INJECT PURE
SAMPLE INTO THE GC. You must prepare your sample in this manner.
2. Cleaning out the 2 ml shorty vial: Don't throw away the vial. Dispose of the
sample in the halogenated organic waste. Rinse out the vial with acetone and
let it dry before you re-use it.
Preparing UVNis Samples for GC-MS Sample Analysis

1. Place 1 mg of your solid sample in a 20 mL vial. Dissolve your sample in 20
mL of ethanol OR the specified solvent for your compound. Label the vial to
take to the instrument room.
2. Cleaning out the 20 ml vial: Don't throw away the vial. Dispose of the com-
pound in the appropriate organic waste. Rinse out the vial with acetone and
let it dry before you re-use it.
16
Instrumental Analvs"s =: Ol~ ~ _
_..J nstrumentation ,oT£s •

·- --,...,.,.ar \iagnetic Resonance Spectroscopy (NMR)
learn the science behind how and why NMR works, please read Chapter 14. It
~ ,..ery helpful this semester; included in the chapter are example spectra and
be!?ful analysis of spectra using chemical shift NMR correlation charts, integra-
~ values, and splitting patterns.
Tuere are three Anasazi 60 MHz NMR instruments available for student use.
1, 'O of the instruments are designated as "walk-on" meaning "first come, first
served." Please put your name on the waiting list and a TA will call you up to use
rhe instrument in the order that you arrived. A third instrument is designated as
·sign-up" time only meaning you MUST have signed up for a timeslot in advance
to use that instrument. Instruction guides are provided for sample insertion and
running the appropriate programs. Your spectrum should be properly peak-picked
and integrated. The instruction guides can be viewed on ANGEL as well.
Figure 2.2. One of the 60 MHz NMR instruments.
Common problems that are often encountered when running the NMR: samples
not concentrated enough, no TMS standard, no deuterated solvent, sample not
depth gauged properly, and sample not spinning in the probe.
Infrared Spectroscopy (IR)

To learn the science behind how and why IR works, please read Chapter 15. It will
be very helpful this semester; included in the chapter are example spectra and
helpful analysis of spectra using IR correlation charts.
There are two Thermo Electron FT-IR instruments. They have a diamond ATR at-
tachment. You can run both solids and liquids with no sample prep needed when
using the diamond ATR. Both IRs are walk-on time. Walk-on time means first
Chemistry 213W : : Chapter 2
come, first served. If you come in to use the walk-on time, please put your name
H NOTES
on the wait-list so that there is no cutting in line. Please be patient and respectful
to the TAs and other students. Instruction guides are provided for using the IR
instruments both in the instrument room and on ANGEL.
Figure 2.3. One of the FT-IR instruments with a diamond ATR attachment.
Gas Chromatography (GC)

To learn the science behind how and why GC works, please read Chapter 17. It will
be very helpful this semester; included in the chapter are example chromatograms
and helpful analysis of data.
There are two Hewlett Packard GC instruments; you must sign up for a timeslot
to use them. You will need all 30 minutes of the signup time to run your sample
so come early/ on time. The most important thing to remember when using this
instrument is proper sample preparation. Samples cannot be too concentrated; an
improperly prepared sample can make the instrument unusable for an entire day!
Programming the GC with the proper temperatures is also important. Make sure
you know the proper initial temperature, final temperature, and rate of heating
before you inject your sample. Make sure you properly inject your sample: only
about 0.5 to 1 µLare needed! Ask a TA for help if you are unsure. A GC tutorial is
provided on a poster an on ANGEL to help you with these instruments.
18
Inst rumen tal Analysi s : : Chemistry 213W
NOTES II
Figure 2.4. The two GC instrume nts avai lable for use .
U traviolet/Visible Spectrophotometer (UVNis)

-~:earn the science behind how and why UV/Vis works, please read Chapter 13.
":: '1iil be very helpful this semester; included in the chapter are examples an d
E:.elpful analysis of spectra.
~are two Vernier UV/Vis spectrophotometers. There are NO sign-up books for
t:.e GV/Vis instruments; they are walk-on time only. This means first come, first
served so please be respectful and maintain order while waiting. Make sure that
turn on the instrument AND the LabQuest unit prior to use. The "on " switch
f:::rr the instrument is located on the back of the UV/Vis box in the lower left corner.
~ember t o run a "blank" using the provided instructions. The cuvettes you will
b: i.Sing are made of quartz and are expensive, so be careful and clean th em out
-roperly! Be aware that even though you only dissolved 1 mg of sample in 20 mL
: so~vent that you will MOST LIKELY need to dilute your sample to obtain useful
d.;;._:a_ .•fake sure that the absorbance units are less than or equal to 1 on the y-axis.
Pola rimetry
Pb!arimetery is used to measure the observed rotation of a chiral compound, and
&om that data you can calculate the specific rotation . Follow the sample prepara-
- ~ mstructions provided for your compound. When you make a solution of the
co=pound you are studying, you need to know its concentration in order to cal-
n::;a::e the specific rotation. The cell you will be using has polarized lenses at each
e.ci and is EXPENSIVE ($900!). Clean it out with the solvent you used to make
=r- solution, followed by METHANOL to avoid bacteria and mold growth inside.
__:-_re this instrument is not used often , it is walk-on only.
19
G"lefllistry 213W H Chapter 2
••
•• OTES
20
The assignments are designed to improve your ability to be prepared for experi-
ments, keep an excellent neat and organized notebook, and to write scientific
reports well. For each experiment, you will be required to submit the following:
1. Prelab Assignment: To be completed and handed in at the beginning of every

new technique experiment and synthetic experiment.
2. Notebook Pages Reports: Approximately 503 of the content of these pages will
be don e while in lab (recorded as Procedure, Data, and Observations); -503
will be completed outside of lab when the experiment is complete (as Discus-
sion and Conclusions) . To be handed in on specified dates on your schedule.
3. You will write a Formal Final Report for each of the synthetic experiments.
A detailed description of these assignments is given in this chapter.
Mr. Benzene says: Hand your assignments in on

time! If you don' t, there's a late penalty.*
First day late = 10% of the total possible points
Each additional day late =5 % of the total possible

points
*Lat e days include weekends and h olidays . This late policy applies to all Prelab
Assignments, Notebook Pages Reports, and Formal Final Reports.
'c
,,
......
~
8G \
c ....
D
Mr. Benzene says: You can't keep your graded work
in your possession! You'll need to give all prelabs,
reports, and quizzes back to your TA. You may
keep your graded Prelabs until you hand in your
report. You may keep your graded Reports until
the next lab period. Then you must turn all graded
work back to your TA. If ALL of your graded work
D
isn't accounted for, you will lose HALF of your
"Checkout points" at the end of the semester.
21
Oler:i istry 213W H Chapter3
Academic dishonesty is not limited to simply cheating on an exam or assignment.

II NOTES
The following is quoted directly from the "PSU Faculty Senate Policies for Students"
regarding academic integrity and academic dishonesty:
"Academic integrity is the pursuit of scholarly activity free from fraud and
deception and is an educational objective of this institution. Academic dis-
honesty includes, but is not limited to, cheating, plagiarizing, fabricating of
information or citations, facilitating acts of academic dishonesty by others,
having unauthorized possession of examinations, submitting work of another
person or work previously used without informing the instructor, or tampering
with the academic work of other students."
All University and Eberly College of Science policies regarding academic integrity/
academic dishonesty apply to this course and to the students enrolled in this
course. Refer to the following URL for further details on the academic integrity
policies of the Eberly College of Science: http:// www.science.psu.edu/academic/
Integrity/index.html.
Each student in this course is expected to work entirely on her/his own while
taking any exam, to complete assignments on her/his own effort without the
assistance of others unless directed otherwise by the instructor, and to abide by
University and Eberly College of Science policies about academic integrity and
academic dishonesty. Academic dishonesty can result in assignment of "F" by the
course instructors or "XF" by Judicial Affairs as the final grade for the student.
Academic dishonesty includes, but is not limited to, the following situations:
Giving your electronic file of your final report to another current student or
future student via e-mail, flash drive, etc.
Using someone else's data unless instructed to do so.
Not citing other students when instructed to collect other students' data.
Fabricating data. Fabrication of data includes, but is not limited to: handing
in the same data as another student and claiming it as your own, obtaining
data from an instrument outside of the Whitmore facilities, and printing of
internet data and submitting it in a report.
Using phrases or sentences directly from this lab guide or any other source
(book, journal, or Web site) and not referencing that source and not using
quotes.
Using phrases or sentences directly from this lab guide or any other source
(book, journal, or Web site), referencing that source, but not using quotes.
Using more than one sentence directly from or paraphrasing from the lab guide
or any other source (book, journal, or Web site) even if you reference it and
use quotes. You are required to have all your written work in your own words!
Submitting the same lab report, prelab, or quiz (word-for-word) as another
student.
22
The Assignments II Chemistry 213W
A note about the products you make: Any products from a reaction should not NOTES H
be declared waste and disposed of until the final grade for that experiment has been
cetermined. Your instructor will inform you whether products should be handed
m. Often, products are not handed in since you will usually present spectral or
chromatographic data proving product identity. However, if the analysis of your
product is done by melting point or MS (but not GC-MS), you may be asked by
";'OUT TA to turn in the product for verification. It is the student's responsibility to
keep products for verification. If there is any dispute about the results obtained,
vou must be able to turn in the product as proof. If products are turned in, the
following protocol should be followed:
SOLIDS: After thorough drying, taking a melting point, and obtaining any
other required data, you should put the remaining solid in a small 2- by 3-inch
ziplock bag (available on the common shelf). The ziplock bag should be sealed
tightly, labeled, and kept in your lab locker.
LIQUIDS: To prevent loss of liquid products by evaporation, you sh ould use

a small 2 mL "shorty" vial with a Teflon-lined screw cap (expensive, never
discard) from your desk. Transfer the liquid sample into this and screw the
cap on tightly. The "shorty" vial should then be labeled and placed in your lab
locker.
3.1 Prelab Assignments

The Prelab Assignments for each new technique experiment can be found on
ANGEL. You will also complete Prelab Assignments for each of your synthetic
experiments. You must complete this assignment BEFORE you begin the experi-
ment; your TA will collect it immediately after you take your Quiz for the technique
experiments or at the start of the lab on the due date for the synthetic experiments.
Prelab Assignments generally consist of the following sections*:
1. Chemical Data Tables

2. Prelab Exercises (Short-answer questions)
3. Chromatographic Features Comparison where appropriate
4. Balanced Chemical Reaction where appropriate
5. Electron-Pushing Mechanism where appropriate
6. IR and NMR Checksheets where appropriate
"Remember to print out the different Prelab Assignments for the different experi-
ments; the specific sections may differ depending on the activities associated with
that technique!
23
: : NOTES Details about Prelab Assignments
1. Chemical Data Table

For both safety and convenience, you must list and provide physical data:~
every chemical you will use in the lab. You can find all of the physical data o:::;;
Sigma Aldrich (www.sigmaaldrich.com) OR Chem Spider
(http://www.chemspider.com).
For this purpose, the blank Chemical Data Tables with carbonless copies a...~
located in your Organic Lab Notebook right before the blank notebook pages
Use these sheets for those chemicals (starting materials, solvents, catalys-..s
and products) that are unique to a particular experiment and that are NO:-
found on the solvents data table found earlier in your notebook. The origm.a:
copy of each experiment's unique Chemical Data Table must be turned in with
your Prelab Assignment for each experiment.
Mr. Benzene says: This table will be easy to fill out

if you use a Web site like ChemSpider! The MSDS
forms have all the info you need!
A sample Chemical Data Table is given on page 26. Entries should be made
according to these guidelines:
a. Chemical name and structure (or inorganic formula) for all chemicals or
reagents used in that particular experiment (starting materials, reactants,
solvents, catalysts, products, and by-products), including all possible un-
knowns for that experiment!
b. Physical State at room temperature and 1 atm pressure (normal laboratory
conditions). Enter ans for solid, 1for liquid, g for gas, and soln for solution
(most acids, bases, and salts are solutions).
c. Boiling Point (bp; For compounds that are liquids at room temperature;
if not 1 atm, give pressure in mm Hg or Torr) or Melting Point (mp; For
compounds that are solids at room temperature) .
d. Liquid Density (d) in g/mL for liquids that will be used (including com-
mon solvents). This information may be used to calculate the weight and
millimoles used and produced in your reactions and to determine which
layer (organic or aqueous) is on the top or bottom during extractions.
e. Quantity of material called for in grams (g), milligrams (mg), or milliliters
(mL). For synthetic products (start filling this out from Chapter 7
through the end of the semester), give the theoretical yield in mg
or g based on the limiting reagent and assuming a 100% conversion.
24
The Ass ignments :: Chemistry 213W
f. Molecular Weight (MW or formula weight, FW) of reactants, products, NOTES ::

but not solvents.
g. Millimoles (mmol) if actually consumed or produced in a synthetic reaction
(not solvents). For synthetic products (Chapter 7 and on), give the
theoretical yield in mmol or mol based on the limiting reagent and
assuming a 100% conversion. Again, for natural product isolation
experiments leave this blank.
h. Flammability State "yes" or "no." If data is available, give flash point temp.
(Fp) in °C.
i. Toxicity as defined by Aldrich MSDS sheets: www.sigmaaldrich.com and
www.msds.com. This is actual physical data: Putting a YES or NO is insuf-
ficient information!
j. Waste Category for each material, solvent included. Assume you have to
dispose of a few grams of each of the listed chemical substances. How
should this be done? In this column, enter the following codes according
to the correct channel for disposal:
NHO = Nonhalogenated Organics waste container (e.g., ether, ethyl acetate)
HO = Halogenated Organics waste container (e.g., dichloromethane,
chloroform)
HM = Heavy Metals waste container (e.g., palladium)
D =Drain disposal with lots of water (e.g., 53 HCl (aq) solution, NaHC03
(aq) soln)
TB= Trash Bin for dry, nonhazardous solids (e.g., NaCl, Na2 S04 , etc.)
Liquid unknowns can all be disposed of in the NHO container. Solid un-
knowns are to be disposed of in the trash bins, but leave them in their
snap-top containers. It should be noted that mistakes in this column will
lead to large point deductions! See Chapter 1 for more information on
waste categories .
k. Comments-Other noteworthy properties such as "hygroscopic"; "oxi-
dizer"; "moisture sensitive"; "corrosive"; "irritant"; "cancer suspect agent";
"lachrymator" (causing tears like tear gas); "explodes when heated"; color,
odor, or information such as supplier source (if unusual), etc.
25
~ 9
(I)
3
Chemical Data Table v;·
~
Name &njirn\o le.ne Desk No. 3A Experiment Name and No. SNb? ReacflOD - ::!:! 4- N
.....
w
~
Chemical
Name
Structure
Physical
State
BP(I) or
MP(s)
Liquid
Density
Quantity
MW
FW
mmol1 Flammability Toxicity
Waste
Cat.
Comments ••
••
()
~-h~drt>~'f N.0.;>. =:;-
s~\J.. -s ro ~cl rt ~'CJ. N-HD oro..n~

-
Ill
4-nitro ~~
~~~Tl - "O
N/A :>o\\ol
~
..,
I '!)
re,nw~
d-rndhoY.~
,...,-o
()(;H3
- ~}
- -....9 un~
o.5'v;.
~~ -HO 0\eo.y-
w
ben~il
bromide. &r--@J \~ - - 541~
Q
-qs0 b(_(gq
caurta1 # a1\
'1omss1dM rnp
'
-<O 1esJ s~\n +

caib~~ ~C03 'iJ't>\\O. 891"C N/A
31-2r<lj ~ ~lo~ no ca.+. 0 e"e
i «i fu l"I t-
4
N,N-ciirnelh l Ji
-fucma.mk;l.Q -H N,rCllj ~~
bp
153'( 0.'144 l roL
0-
Q
- -fi~tt
1es!cat.4 ~es,
ca\-. NHO
cla~--
-Ham ~ 1 s~Vi
-t- i nna\C\ ~CJ\'j fl6 ' CK)
(OM~)
<¥)
c~ B/tnL t- 4 rev~duc,,ttv-e -ID'l< ici'-1
~~-~()~ NO.;> r-
Pe~i 1) 01'~-
4-ni*D ~\
Lo~
0Crl3 4'.J. - NIA ~\lrnj
<"O
~ 1.80 ~d cP>"'~
~
NttD
~\OUJ
$()\\Cl
-
t
berrt;a/deh'F- hr- ~
# mm ol (millimoles) are only calcu lated for starting mat erials and products in synthetic reactions.
The Assignments H Chemistry 213W
2. Pre/ab Exercise NOTES II

-{ou will be asked to answer a set of 2 or 3 questions that relate to the experi-
m ent you will be carrying out in lab. These questions can be found on your
Prelab Assignment handout for the techniques or on the Synthetic Handout
for the synthetic experiments.
3. Chromatographic Behavior Comparison (if Applicable)

If your experiment requires you to perform TLC or Column Chromatography,
then you will need to do a chromatographic behavior comparison of the re-
actants versus the products. Analyze the functional groups and compare the
overall polarities of the starting material(s) and product(s). Predict which
will have a lower or higher Rf value based on molecular structures and size.
(Rf value and polarities of functional groups are discussed in the TLC chapter.)
See the example below.
N02 N02
~ ~
OMe
Br~
o~
OMe
OH
I .&
H 0 H 0
1 2 3
aromatic ring aromatic ring two aromatic rings
nitro ether nitro
phenol bromine aldehyde
aldehyde two ethers
Order of overall polarities from most polar to least polar: 3 > 1 > 2
On a TLC plate, 3 will have the lowest Rt' 1 will have an intermediate Rt' and 2
will have the highest Rf If a column was run, 2 would elute first, followed by 1,
and 3 would elute last.
27
0.emistry 213W H Chapter 3
: : NOTES
4. Balanced Chemical Reaction (If Applicable)
Include the reagents above the arrow and the conditions (solvents, tempera-
ture, and time) below the arrow. Write the name of each chemical under its
structure, or if the name is long or complicated, assign it a number. Under-
neath the product's structure, write the theoretical yield calculation in grams
or milligrams. Here's an example:
~
OMe
Br~
"..:::::
K2C03
+
OH DMF
H 0
1 2 3
lmmoll lmmol3 287mg 3

3 00 mg 1 X 167 mg 1 X 1 mmol 1 X 1 mmol 3 = 516 mg 3
5. Reaction Mechanism (If Applicable)

If you are carrying out an experiment that requires a synthetic step, then you
are required to include a full electron-pushing react ion mechanism. If the
reaction mechanism cannot be found in your organic textbook, then the TA
or course instructor will provide you with the mechanism.
6. NMRllR Checksheets (If Applicable)

If you will be using either IR or NMR analysis or both on the products isolated
or synthesized in your experiment, then you will need to complete an IR or
NMR Checksheet or both. Please see the example on the next 2 pages.
Mr. Benzene says: If you need help with NMR or IR

theory, prediction, and interpretation, make sure
you look at Chapters 14 and 15!
28
The Assignments :: Chem istry 213W
NMR CHECKSHEET
Structure of starting matertal Structure of product
NO~ OCHS NO~ ('\

r-0;"
<A
e~oMb
g,,,4lc
t-~a
.
! ~\
~ 0Cti3
.Lhcl
e J /7f~e.
;--D (;f'\
ti<>. ~ @
Number ofchemicalfy distinct hydrogens: 5/ 5
Hr 0 O'
3 ·~
Number ofchemlcal(y distinct hydrogens: I0
Splitting Splitting
Hydrogen Predicted Hydrogen Predicted
Pattern Integral Pattern Integral
(label chemical (label chemical
(use the Value (use the Value
a,b,c) shift a,b,c) shift
n+1 rule) n+l rule)
1q q-JO 5 \ q 3.~~3.8 5 3
b 7-1~ s 1 b 3.~-3 . 8+ 5 ~
c <o.S-5 s l c 9~10 s l
d l\ d l cl {o.5-<Q cl l
e ll d l e \I t l
-- +. lJ t l
-
~a 3.~ ..3.8 s 3 ~ ii vi l
b ~.3-~.1 s ~ h II s 1
c <o.S-B d
4
l lI d \
. o\
d " t j I\ 1
e " t
H
f d
29
O.emistry 213W :: Chapter 3
IR CHECKSHEET
Structure of Starting Material Structure of Product
Fill out the following table based on the starting

Fill out the following table based on the product:
material·
Functional Group Predicted absorption Predicted absorption
Functional Group
frequency (cm-1) frequency (cm-1)
No~ ~ sso-14qo
0
R)~ co~ 1703
c=c ,11 3300-t>OOO
J(Q00 1 1S501
rD~ ) 560 1 l 4SO
C-0 JcilO-J~OO
ClV'\{ \
o-H
.phef\o\ 3S00
30
3.2 Writing Procedures, Data, and Observations in Your NOTES : :

otebook
_.;s a scientist, it is extremely important to keep accurate recordings of your labo-
ratory work. One goal of this course is to help you refine your notebook-keeping
s:O.Us as they will prove invaluable in your future endeavors.
General Items about Your Notebook

:. Number your Notebook Pages sequentially as you go.
2. Make sure you fill out your Table of Contents as you go; it will make things
easier to find as the semester goes on!
3. Record all entries in ink (not erasable ink!). Do not erase, obliterate with a big
inky mess, or white-out any entry in your notebook; cross out the erroneous
entries with a single line and initial next to the correction.
4. Record all data and observations directly into your notebook. Scraps of paper,
this lab guide, the back of your hand, paper towels, etc., are not appropriate
places for such information. You are not allowed to add observations outside of
lab. What you write in your notebook is legally binding so you are not allowed
to modify it, rip it out, or re-write it after you and your TA sign the Notebook
Pages!
5. Have your Notebook Pages signed at the end of each laboratory period by your
TA.
6. Notebook Pages MUST BE neat and legible. If you have poor handwriting, now
is the time to improve it. As a scientist in your future career, you will need to
take handwritten notes of your daily tasks. Thus, it is imperative to learn this
important tip now!
Sections of the Notebook Pages
I. Experiment Information
Fill in the empty boxes at the top of the Notebook Pages. Be sure to number the
notebook pages sequentially in the top or bottom right-hand corner of the page.
II. Procedure, Data, and Observations

As you are running the experiment, record the steps taken to complete the proce-
ri-.rre as well as data and observations of these steps. The information in this sec-
tion is to be kept very brief and should be in bullet statements. Remember you are
recording information that is vital to repeat the experiment, but you should avoid
cnnecessary and inconsequential details. For example, the weight of a reagent used
.=:ust be recorded, but there is no need to state that it was weighed on a balance (a
ireasonable assumption). The information should also be well-organized. If there
core than one procedure, then write each procedure separately: "Procedure 1:
.. tle for Procedure]" as a subheading, then follow it with "Procedure 2: [Title for
?:rocedure]" as another subheading. Procedures should be in the left-hand column
31
in bulleted format and observations in the right-hand column. The infonnatior.

••
•• OTES
should be recorded in the third-person passive tense. For example: "The reaction
was stirred for 30 minutes" not "I stirred the reaction for 30 minutes" or "Stir the
reaction for 30 minutes" (see the example on pages 39-40) .
.•.
'c
,.
~
8G \
c ,.....
D
Mr. Benzene says: If you can't repeat the lab from
your notes, you're not writing enough!
This section should be written in bullet form. Some experiments may require
that you draw a table of data. This section should include the following when ap-
propriate:
Record weights of glassware, all compounds
Volumes of solvents
Unknown letters or numbers
Solvents boiling
Solids dissolving
Melting points
Boiling points
Record reaction times
Describe the additions of chemicals (e.g., "over 5 min" or "all at once")
Color of solution and physical attributes of crystals (color, shape, size)
Note any color changes upon reaction
Note any gas evolution upon reaction (bubbles)
Record temperatures and varistat settings
Describe how samples were prepared for analysis
Precipitation of solids
How you monitored a reaction's progress
Tape TLC plates and litmus paper to these pages
Types of analysis used
Yield or recovery in mg or g
If you use an instrument, describe the settings used and the solvents and
concentrations employed.
For bioassays, note the appearance of bacterial growth inhibition and measure
the distance of the inhibition about the sample.
You must record each step you do and observe as you do each one. You should
not wait until the end of the lab period to begin writing in your notebook. Tue
observations are critical, so be as descriptive as possible.
32
The Assignments :I Chemistry 213W
'c,.1.
....
~
t)C!i I
c,
D
Mr. Benzene says: You must have your TA initial
and date each Notebook Page used during your
in-lab time. Once the page is signed, you cannot
add or subtract anything from that portion of your
NOTES H
D
notebook.
Ill. Calculations
~culations of percent yield, percent recovery, Rf values, and corrections for boil-
mg points are included in this section. Examples of molarity and yield calculations
follow:
A. Preparing Solutions
Often, you find that you need to prepare your own solutions. Example procedures
for some common instances are described as follows:
1. Volumetric Measurements
In column chromatography or TLC, you often need mixtures of organic solvents,
usually described by the ratio ofvolumes that can be measured using a graduated
cylinder. To prepare 25 mL of a 60:40 mixture of dichloromethane:hexane
solution, measure 15 mL of dichloromethane and 10 mL of hexane, mix, and
stir well. (Stirring is important-if the mixture is not homogeneous, then
its behavior during the course of a column chromatography experiment will
change, as the "top" of the solution has a different composition from the "bot-
tom.")
2. Preparations of Solutions ofAcids or Bases
To prepare 3.0 mL of 1 M HCZ from the Common Shelf concentrated HCZ, which is
12.0M:
First, calculate the moles of HCl that have to be present in the 3 mL of the
target 1 M solution:
1 Liter 1 mol
3.0 mL X lOOO mL X 1 Liter = 0.0030 moles of HCl needed
This HCl, of course, comes from a certain volume of the 12 M (cone.) hydro-
chloric acid that is supplied. How much is needed?
1 Liter
0.0030 moles of HO X
12 .0 mo1es
= 0.00025 Lor 0.25 mL of the cone. HCl
3. Dilutions
Another way to do this is to use V1 x M 1 = V2 x M2 where V are the volumes in
the same units and M the molarity of the stock solution and target solution.
33
Chemistry 213W :I Chapter 3
Here, we solve for V1' the volume of original 12 M Common Shelf hydrochloric
:: NOTES
acid:
V1 =
V2Mi
X Mi
_,. V1 = 3.012
mL X 1 M
.0 M :. V1 = 0.25 mL o f t h e stock so1utlon
·
In practice, the 0.25 mL (small volume best measured with a calibrated piperi.e)
is added to about 2.0 mL of distilled water in a 10 mL graduated cylinder, the
solution stirred well, and then the solution is diluted with additional distilled
water to a total volume of 3.0 mL, and mixed once more. Always remember to
add acid to water, NOT water to acid.
4. Preparation of Solutions from Solid Solutes

To prepare 10 mL of 3.0 M NaCl solution, first, calculate the number of moles
of NaCl needed and convert to mass:
10 0
L X 1 Liter X 3.0 moles NaCl X 58.45 g NaCl = 1 75 N Cl
· m 1000 mL 1 liter solution 1 mole NaCl · g a
Weigh out 1.75 g of NaCl, and dissolve the solid in about 8.0 mL of distilled
water in a small beaker with stirring. After the solid is completely dissolved
(the total volume at this point will be between 8 .0 and 10.0 mL), pour the
solution in a 10 mL graduated cylinder and add distilled water carefully until
,.,
the total volume is 10.0 mL. Pour back into the beaker and give a final stir.
'c c ........ Mr. Benzene says: The front pages of the Lab
.. t>G \ Notebook have some valuable conversion charts for
~ D
translating from weight percents to molarity, the
density of a variety of solutions, and the molarity of
D
some common acid and base solutions.
B. Calculating Yields and Recoveries

One of the most important considerations for the synthetic chemist is the yield
of a reaction. Success in the production of any commercial chemical, be it a poly-
mer or a pharmaceutical, depends on getting as much product as possible from
the starting materials, that is, a percent yield that is as close to 100% as possible.
In organic syntheses, yields are often less than 100% because:

1. many side reactions can occur to both starting material and product
2. it is sometimes difficult to get all of the starting material to react (for example,
in ester synthesis)
3. product is lost when transferring between glassware and during purification
steps such as distillation, extraction, etc.
34
In order to determine the percent yield, the chemist writes or calculates each of NOTES II
the following in the order given:
The Balanced Equation ... describes the chemical process of interest.
You need a balanced equation to deduce the mole-mole relation of reactants to

products, to determine the limiting reagent, and to calculate the theoretical yield.
In the two-step synthetic reaction shown, the balanced equation tells us that four
moles of acetone reacts with one mole of sodium borohydride, the product from
that reaction reacts with an excess of water to give four moles of 2-propanol and
one mole of sodium borate.
Sodium
borohydride
Acetone
OH
Na+B[OCH(CH3)2]4- + 3H 20
--- 4
H3C
/
I
CH
2-propanol
"' CH3
+ Na+H2B03-
Net Balanced Equation:
4
H3C
0
II
/ c"'
CH 3
+ Na+BH4 -
Sodium
+ 3H 20
-- 4
H3C
/
OH
I
CH
"' CH3
+ Na+H2B03-
Acetone borohydride 2-propanol
The Limiting Reagent ... determines the maximum yield obtainable. Most
"~en, in organic chemist ry, the organic starting material is the limiting
reagent, but you should check, nevertheless. If there are two or more or-
amc reagents, you have to figure out which one is the limiting reagent. The
c:.a.ss of the limiting reagent, converted to moles, determines the maximum
- es and from this, grams) of product that can be obtained from a reac-
assuming no losses due to side reactions or during purification. The
~um number of grams or theoretical yield of the desired product (see below)
c:a:ru:ated for each starting material in the reaction. In the example given be-
.s:: g is used for both starting materials, acetone and sodium borohydride,
w::n 5 mL (5 g) of water. The reagent that gives the lowest theoretical yield
~.--.rt is the limiting reagent.
35
;: NOTES The reaction above is used in the following sample calculations:
Theoretical yield based on acetone:

1 mole acetone 1 mole 2-propanol 60.10 g 2-propanol ~-------
0.500 g acetone X X X I0.517 g 2-propaDllil
58.08 g acetone 1 mole acetone 1 mole 2-propanol ·
Theoretical yield based on sodium borohydride:
1 mole NaBH, 4 mole 2-propanol 60.10 g 2-propanol ~------

0.500 g NaBH, X 37.83 g NaBH , X l mole Na BH, X l mol e 2-propano l = j3.17 g 2-propanol
Here, the theoretical yield of 2-propanol product is limited by the acetone, so

acetone is the limiting reagent. To be absolutely sure, one might check that the
water used in the second step is not a limiting reagent. However, it is generally
assumed that excess water is used.
'c
,.
......
~
8G I
c ....
D
Mr. Benzene says: Organic reactions often
employ catalysts in very small amounts, but
don't be tricked! Because they are (by definition)
regenerated during the course of the reaction, they
do not act as limiting reagents.
D
Theoretical Yield ... is the maximum amount of product that could be obtained,
determined from the mass of the limiting reagent used. From the previous example,
the theoretical yield of product, 2-propanol, would then be 0.517 g, based on the
limiting reagent, acetone. You could also calculate the theoretical yield of the inor-
ganic by-product, if that information were valuable to you, or the theoretical yield
(and therefore the volume) of a gaseous product that you might be synthesizing.
Crude Yield ... is the mass of product initially obtained from a reaction that often
contains some starting material or by-product impurities. It is calculated to compare
with the actual yield of the final purified product to determine the loss of yield during
purification or workup. For example, say an initial simple distillation were to give
0.480 g of impure product boiling from 78-88°C, the crude yield would be 0.480 g.
Actual Yield ... is the mass of the desired product obtained after purification. In
this example, if after a second careful fractional distillation, you collected 0.350 g
of product boiling from 80-84°C, then the actual yield would be 0.350 g.
36
The Assignments 11 Chemistry 213W
Percent Yield ... is the actual yield divided by the theoretical yield, multiplied NOTES II
:OO. Since 0.350 g of pure 2-propanol was obtained, then the percent yield is
0.350 g of 2-propanol
- -- - - - - x 100 = 68%
0.517 g of 2-propanol
Corrected Percent Yield .. .Sometimes (as in the column chromatography experi-

=ent), the percent yield is calculated by first correcting for unreacted reagent that
;.s isolated and quantified. In column chromatography, not all of the fiuorene reacts;
tlie unreacted fluorene is recovered (so you can calculate a percent recovery), and
";"OU assume that all unrecovered fiuorene reacts; therefore, the percent yield of
:luorenone is not based on the fiuorene that you started the reaction with, but
:ather, on the "missing fluorene" that is not recovered.
Percent Recovery ... is the ratio of the weight of substance isolated to the weight
of the original material. There are at least three instances where you are interested
m recoveries, rather than yields:
a. Isolation of a natural product from raw materials:

Natural product isolations do not involve a chemical reaction of a starting
material to a product. The product is only a component of a starting mixture
as complex as milk or hamburger and only needs to be separated and purified
from this mixture. Since you cannot calculate the number of moles of st art-
ing material, you cannot calculate a theoretical yield. Instead, a % recovery is
used. This is simply the weight % of material isolated from a given weight of
a natural material such as spinach, tomato paste, bark, tea leaves, hamburger,
etc. For example, ground cinnamon that you buy at the market is mostly water
and cellulose by weight. The main flavoring component is cinnamaldehyde. If
you isolate 0.0051 g of cinnamaldehyde from 2.23 g of ground cinnamon, the
% recovery would be
0.0051 g
2.23 g x 100 = 0.22%
b. Recovery of a starting material:

Many organic reactions are difficult to carry to 1003 completion or are only
allowed to react to a controlled extent (as in the column chromatography
experiment) and the starting material can be recovered. In this case, the %
recovery is the% of starting material recovered of the total amount of starting
::n.aterial you started with. In the case of the fiuorene oxidation to fiuorenone,
you start with 54 mg of fiuorene, and after column chromatography you get
~ck 9 mg. The % recovery would be
9mg
54 mg X 100 = 17%
37
Chemistf) 213W : : Chapter 3
c. Isolation of a component from a mixture when you know how much is really there:
H NOTES
You have a sample (0.400 g) mixture of two compounds and you KNOW the
mixture is 50% by mass (0.200 g) of each component. You separate and purify
the two compounds and in the process suffer losses due to materials sticking
to glassware, on filters, or evaporation so that you only get 0.170 g of A and
0.080 g of B. The percent recoveries would be
0.170 g 0.080 g
_ g X 100 = 85.0% recovery of A _ g X 100 = 40% recovery of B
0 200 0 200
3.3 Examples of Notebook Pages for an Experiment

Following are examples of Procedure, Data, and Observations. Please use these
as examples when you are keeping your own notebook throughout the semester.
38
Procedure 1- S~ntnesi s obser1a±)q<LS

• &:X)mq of d-h'fdr1>~~-4- •orao~e , CYlj~tlllline, sDliJ
ni+.rob~nialdeh~de: and
37.;)roq erf- porn55Jt.tfY"l • \Nhik.. pe>\NdeY"1anh'fdvtMS
cavbextlt k we.re added <Jfacie..
to a /O,rnl ruund~bofuxY'\ ------"-dried io over\ o'lexn~h-t
+-task. u
• 1.0 Ml of di f'f'eth'\ \WtMC-\ tn 1cle. • reacJic.n. r<fl~tufe. afe_eafS
N~s acld~d b~ s~v\n~eJ as o. bn3n ~ (eel 5USfleK1.'.:>l(A')
s-\i(f ed "'06\.lnJU.Sl~
• 541 Ml\ at: ~-l't1Cfuo~ • ,.._, l dYDf / sec

ben_t-'j1bYU(Y)\cJ..e wa_s
.s~nn~ccl in d~t~e..
• the re.~ct\O{' m\1' rufe
'Na5 bt'tJUAh l- fb SS. C
~hi le. s-ti Nir.113 co ntil)uous\'f
Mlfl .l hr
·-the reaction NO.S mwihl<ec\ . . . . . . . .-....-..-
b'i 1LC 3: 1 ace ooe/ hoanc:s •• ••
a~ mobi ~ ph(,(se. - 1tle..
Sf,>Dts N ue. vis ua \i Cd bi
• • • •
UV ~1Uh+-
• fue. reoc..tion reacned
• •
CC)(Y\pie-hc-n Qt-\>f d hOU(S
39
-
LAB PARTNER
· -tte. orqanic. ia~e~ 'f\/0.5

cl(o.1netv intD C\ ~at..ev
andc..anh~dVUI..{ ~ sod1u(Y) "
SUhvtle V'/<lS added - - - appro~. ~ &oep~ic'.l~'~\
3 scoops
0
f\1e O(C\C{l'1ic. \O.~er \J\JOS
d.ecani+e.Ci intD o. beater- - tare: I 0 ~. &i 3
•-the so\ve.nt- was ey(lQ'Jft\td
lf\Hfh ll s~ectf'Y1 of 1 - · - .
nitro3e() - ~elloV\I fesidue
\/\\e~ht ()f residue t ~tav:
/03.845
3.4 Notebook Pages Reports NOTES ::

You are required to handwrite reports in your notebook for each one of the tech-
""·que experiments. Remember that you will be tearing out the original perforated
pages from your notebook to hand in; the carbon copies stay in your notebook. Also
make sure you print out a grade sheet from ANGEL for each technique and attach
i~ to the front of your report. These reports will consist of the following sections,
IN THE ORDER THAT THEY SHOULD APPEAR IN YOUR REPORT:
1. Grade Sheet from ANGEL

2. Experimental Info and Name on the Top of Each Page
3. Purpose of the Overall Lab Technique/ Experiment
4. Procedure, Data, and Observations
5. Calculations
6. Experimental (if applicable)
7. Results, Discussion, and Conclusions
8. Spectral Data
9. References
10. Neatness/Grammar/Overall Organization
11. TA Evaluation of Your Technique Skills
Details about the Notebook Pages Reports
1. The Grade Sheets

The grade sheets for each specific technique experiment can be found on ANG EL.
Your TA will be using these grade sheets as a guideline for grading your reports.
Please make sure to double-check the sections of your report with the specific
grade sheet for that technique to make sure you left nothing out.
2. Experimental Info and Name on the Top of Each Page

See details in Section 3.2.
3. Purpose of the Overall Lab Technique/Experiment

This is a brief statement explaining the goal of the experiment, noting the
kinds of techniques and/ or analyses used. The purpose should also include
a sentence or two that conveys your understanding of why this technique or
this reaction or both are of value to the organic chemist. Avoid including any
experimental details in the purpose section. Write this on one page and make
sure it is stapled BEFORE your Observations section of your report.
Example:
The purpose of this experiment was to perform an SN2 reaction between a phenol
and a benzyl bromide to form an aryl ether. SN2 reactions are an efficient means of
creating larger molecules through nucleophilic substitution. The aryl ether produced
in this reaction will be purified by column chromatography and characterized by 1H
NMR and IR spectroscopy.
41
•• 4. Procedure, Data, and Observations

•• OTES
See details in Section 3.2 and example pages in Section 3.3.
5. Calculations
See details in Section 3.2.
6. Experimental
The Experimental is a very concise and compact description of the procedure,
namely how a compound was either synthesized from a reaction or isolated
from a natural source. This "bare-bones recipe" should only include the infor-
mation necessary for a trained chemist to obtain the same results; there is no
need to provide the level of detail used in the notebook pages. For example,
the glassware you used (unless it is some special piece designed specifically
for the experiment) is not included because this is a personal preference-the
reaction should work in any glassware that provides the necessary environ-
ment. The Experimental section also includes the characterization of the final
product in the form of a tabulated list of the spectral data of the compound.
Most students find that learning the appropriate amount of detail to include
in an Experimental to be the trickiest part of the reports; therefore, you will
be given the opportunity to practice writing Experimentals as part of each
Notebook Pages Report that involves a synthesis (Chapters 7, 8, 9, and 10).
The different approaches to writing a Procedure verses an Experimental can

be thought of in terms of the target audience. The Procedure section of the
notebook pages is written for a chemist-in-training, someone who will be using
the same exact laboratory as you. You can imagine that a fellow student who
has read the lab guide (but does not have the lab guide with him/her in the lab)
is using only your written procedure to attempt a technique for the first time.
Your procedure should be detailed enough so the fellow student can reproduce
your results (but your procedure should not attempt to teach the theory behind
the technique). The Experimental section is written for an audience of profes-
sional chemists who are already quite skilled in all of the techniques and only
need the key details to reproduce the results in any laboratory in the world.
Following you will see three examples of Experimentals. The first and second
examples are of compounds that were synthesized from a chemical reaction.
The third example is of a compound that was isolated from a natural source.
Note how each example is only a short paragraph, but contains all of the details
necessary for a trained chemist to complete the experiment.
Example 1: A Synthesized Compound, SN2 Reaction

2-((2-Methoxybenzyl)oxy-4-nitrobenzaldehyde). 2 -Methoxy-benzylbromide (541 mg, 2.69 mmol)
was added dropwise to a suspension of 2 -hydroxy-4-nitrobenzaldehyde (300 mg, 1.80 mmol) ano
potassium carbonate (372 mg, 2 .69 mmol), in dimethylformamide ( 1 .0 ml). The reaction mixture
was stir red at 55'C for 2 hours and monitored by TLC (30% acetone in hexanes). Upon completior.
42
the reaction mixture was partitioned in ethyl acetate (20 ml) and hydrochlor ic acid (1 M. 20 ml).
The organic layer was washed with saturated sodium chloride (2 x 20 ml) and dried over sodium
NOTES H
sulfate. The sodium sulfate was removed by vacuum filtration and the solvent was evaporated
~yield a yellow residue. Flash chromatography (30% acetone in hexanes) afforded a yellow solid
o
(460 mg, 89%) 1 H NMR (400 MHz. CDC13): 10.57 (s. 1H).8.06 (d, 1 H), 7.97 (d. 1 H), 7.85 (dd.
1 H), 7 .43 (d. 1 H). 7.34 (t. 1 H), 7.00 (t. 1 H), 6 .96 (d, 1 H), 5.35 (s, 2H), 3.92 (s. 3 H); IR (ATR)
Umax (cm- 1)3 1 13, 3009, 2885, 1685, 1532, 1289.
Example 2: A Synthesized Compound/ Oxidation

Citronella!. PCConalumina (1.5 g, 1.22 mmol),citronellol (120 mg.0.766mmol)and hexane (2 ml )
were combined and stirred for t hree hours. The reaction was monitored by TLC (100% dichloro-
methane). Upon completion, the alumina was removed by vacuum filtration and washed with ether
(3 x 2 ml ). The solvent was evaporated to yield a gummy oil. Flash column chromatography (1 :4
ethyl acetate:hexanes) afforded citronellaI as an amber solid (107 mg. 90%) mp 4 3-45°C; 1 H NMR
(60 MHz. CDC1 3 ) 8 (ppm) 9. 72 (t. 1 H). 5.20 (t, 1 H). 2.48 (m, 1 H), 2 .23 (m. 1 H). 1.82-2.Q1 (m.
6H). 1.70(s. 3 H). 1.54(q. 2 H),0.95 (d, 3 H); 13CNMR(15 MHz,CDCl3 ) 8 (ppm) 202.73, 131.60,
124.13, 51.01,37.00, 27.83, 25.70, 25.46, 19.88; IR(ATR) Umax(cm- 1 ) 2900, 1705, 1654;
GC (phenyl methylpolysiloxane, 250°C to 275°C at 2°C per min) RT 8.29 min; GC-MS (pheny l
methylpolysiloxane. 200°C to 275°C at 5°C per min) RT 10.32 min, m/z 154 .25.
Example 3: An Isolated Compound/ Chlorophyll A from Spinach Leaves

Chlorophyll A. Two spinach leaves (1.5 g) were ground with acetone (22 ml). hexanes (3 ml), and
calcium carbonate (0.5 g) with a mortar and pestle until the solution became highly colored. The
solution was diluted with hexanes (20 ml ). washed with saturated aqueous sodium chloride (4 x
5 ml), and washed with dist illed water (4 x 5 ml). The organic layer was filtered and concentrated
to 3 ml. The solution was purified by silica gel chromatography (30% acetone in hexanes); TLC was
used to monitor t he progress of the column. Chlorophyll A was isolated as a green-colored residue
(R,value = 0.45, 53 mg, 3 .5% recovery); UVNis A.max 625 nm.
7. Results/ Discussion, and Conclusions

This section is perhaps the most important section of any lab report. It ex-
presses to the reader your level of understanding of the experiment and how
the data and observations coincide with the expected results or goals for the
experiment. The easiest way to write this section of your lab report is to make
an outline on a separate sheet of paper, then translate this outline into your
notebook pages and fill in the holes with your data.
Your job is to analyze and discuss your results. For instance, you should
discuss how experimental parameters or physical and chemical properties
such as solubility, boiling point, purity, polarity, etc., affected the outcome
of the experiment. State how your specific data supports these ideas. Or if
you obtained deviations from expected results, you should be able to explain
the deviations. If you had to identify an unknown, please do so and support
your conclusion with the physical data. If you performed a reaction, justify
to the reader why you made your product by supporting your argument with
_fMR, IR, TLC, and melting point data. Compare your starting material to the
product. Attach your spectral data and make sure it is annotated!
43
••
•• OTES This section ends with a summary, namely conclusions. No new informatim:ns
presented here. You are to briefly summarize the success of the experim~~ c
the purpose was achieved, if expected results obtained, if the desired produa
was made, if the analysis supported/confirmed the predicted results.
Mr. Benzene says: See the end of each individual

technique chapter for details about what you
should include in your Discussion section.
8. Spectral Data
You are required to annotate each spectrum or chromatogram you acquire.
Draw out the product structure on the spectrum and give specific assignments
to important IR absorbances (e.g., -OH, C=O, N-H, C=C) on the spectrum, all
NMR peaks, or the five most intense mass peaks (point out the molecular ion
if present) directly on the mass spectrum. Attach/ staple the spectra (NMR,
IR, MS, or UVNis) to the report. Attach the gas chromatogram to the report
as well as a completed GC Conditions Sheet with the information required for
GC analysis. Again, the quality of your spectral data will be evaluated and will
count toward your grade. Don't forget to have the Instrument Room TA date
and sign your data.
Examples of Annotated Spectra Data: NMR, IR
!i
wiii il
11
CJ)
~
I-
Ha
<l>
,-. c:
0
Q)
(.)
He co
I l
10
44 Figure 3.1. Annotated 60 MHz 1 H NMR spectrum.

NOTES H
Figure 3.2. Annotated IR spectrum.
9. References
Reference the source of the experiment- either the lab guide or the handout
for synthetics. Please follow the format as used in the examples below when
listing your references.
During certain experiments, you will need to collect data from other students
in your lab section. When you do, you need to cite them as a reference.
Not ebook citation from a fellow student, general example: Student's last
name, first name. Chapter# Experiment, type of data collected (be concise
and specific), date collected.
Smith, John. Chapter 5, Fractional Distillation of Ethanol/Water Mixture

Data, February 20, 2000.
For books with editors, like your lab guide or organic lecture textbook, editors'
names can appear in either the author (first example) or the editor position
second example).
Richey, H. G., Ed. Grignard Reagents: New Developments; John Wiley &
Sons: Chichester, U.K., 2000.
Grignard Reagents: New Developments; Richey, H. G., Ed.; John Wiley &
Sons: Chichester, U.K., 2000.
45
Information obtained from an MSDS (melting point, color, etc.) should also
••
•• OTES
be referenced:
Example: Fluorenone; MSDS No. F1506; Sigma Aldrich. www.sigrnaalc:lricii..

corn (accessed 4/ 15/ 13).
10. Neatness/Grammar/Overall Organization

Make sure your Notebook Pages Reports are neat and arranged in the appro-
priate order. If your TA can't read your writing or if a page is forgotten, you
won't receive credit for it!
11. TA Evaluation of Your Technique Skills

Your TA is going to evaluate your lab t echnique throughout the semester,
and a portion of each lab report you hand in will be dependent upon how you
perform in lab.
3.5 Formal Final Reports

For each one of your synthetic experiments you are required to hand in a profes-
sional and typed Formal Final Report. The first part of the semester, you will
focus on developing good notebook-keeping skills and mastering the techniques
of organic chemistry synthesis. Once you master those skills, you will be required
to practice and improve your scientific writing skills. The ability to organize and
present complex ideas and support them with evidence in a concise report is an
important skill to master.
General Items about Formal Final Reports

1. Attach a grade sheet from ANGEL to your report!
2. Formal Final Reports are to be computer-generated: double-spaced, .75" mar-
gins, 12 point Times New Roman font, inserted page numbers.
3. Must use complete sentences in paragraph form. Grammar and spelling count!
Please proofread a few times and use spell check!
4. Style also count s . The tone should be scholarly and concise. The information
should flow with a logical progression of ideas using appropriate transitions
and varying sentence structure. Avoid "fluff" sentences, wordiness, and being
unnecessarily redundant.
5. Use scientific language, precise terms, and organic chemistry vocabulary
whenever possible.
6. Do not use the first-person narrative. Write "The reaction was stirred" rather
than "I stirred the reaction."
7. Do not use contractions. For example, use "could not" rather than "couldn't."
8. Use appropriate capitalization. Capitalize first words of sentences, proper
nouns, section headings, equipment named after people (e.g., Buchner funnel
and Hirsch funnel). Chemical names and techniques should not be capitalized NOTES H
unless they begin a sentence.
if you need to draw out chemical structures, do so very neatly by hand or use a
drawing program.
: n. Formal Final Reports will be read by someone who is familiar with the basic
organic chemistry techniques. Therefore, the information should be interest-
ing to your target audience (fellow chemists) and you should want to avoid
unnecessary details and "reteaching" the techniques.
:::... FFRs will be submitted electronically via Turnltln.
Policies Regarding Turnltln

Formal Final Reports will be submitted via www.turnitin.psu.edu to be checked
for plagiarism. The deadline for submission is 11:59 p.m. on the day that the
report is due as indicated on the Chem 213W assignment schedule.
In addition, paper copies must be handed in to your TA on the date indicated

on the schedule at the BEGINNING of the lab period.
Failure to upload your FFR report via Turnitin by 11:59 p.m. on the date it
is due will result in a 1-point deduction for each hour the report is submitted
late. Complete failure to upload your report means that your TA will NOT grade
your FFRand the grade will be recorded as a zero. You may NOT earn back the
Turnitin points when you do your corrections for FFR #1. These points are
free if you submit on time, so it's your responsibility!
Failure to turn in a paper copy of your FFR to your TA at the BEGINNING of

the lab period on the date it is due will result in a 10% points penalty on the
first day, and 5% for each subsequent day regardless of if you submitted your
FFR on the Turnitin Web site.
Please review Penn State's Academic Integrity Policies so you are aware of the
consequences of plagiarism.
Student Upload Instructions for Turnltln at Penn State
. log in to turnintin.psu.edu
a. Log in to http://turnitin.psu.edu. Enter your Penn State Access ID and
password as needed.
ib Select student from the drop-down list.
Note: If a user is both a student and faculty member, he/she will need to
change his/her user type (red tab at the top of the Turnitln screen) ac-
cordingly, depending on why he/she is using Turnitin at any given time.
c. Follow the instructions to create a new account.
47
Oremistrv 213W H Chapter 3
d. When prompted, enter the numeric class ID and enrollment password

H NOTES
provided by your instructor. I will send this to you as a PDF file so make
sure you check your ANGEL e-mail!
Note: If you have already used Turnltln for a course at Penn State, click
"Enroll in a Class" on your home page and enter the numeric class ID and
enrollment password there.
2. Access the class to submit a paper

Your Turnltln home page lists all your Turnltln classes. To access the location
to submit an assignment:
a. Select a class by clicking its name.
b. Submit a paper by clicking the Submit button next to the proper assign-
ment.
3. Upload your paper on the paper submission page

After selecting your Turnltln course and assignment:
a. Choose either the File Upload or Cut and Paste option.
File Upload allows you to upload a paper in Word, WordPerfect, Post-
script, PDF, HTML, RTF, or plain text format.
Cut and Paste allows you to copy and paste text directly onto the page.
b. Enter a title for the paper.
c. Click Browse to select a file to upload, or paste your text into the provided
box.
d. Click Submit to begin final submission.
e. The next page shows a preview of your submitted paper. Click Ye:;, Submit
to confirm the submission.
The next page is a digital receipt with a Paper ID that confirms your sub-
mission. The digital receipt will be sent to your e-mail account. IF YOU DO
NOT RECEIVE A DIGITAL RECEIPT, YOUR REPORT DID NOT UPLOAD
PROPERLY. Try again!
Additional Information for Students (http://tlt.its.psu.edu/turnitin/

students):
Penn State has made the plagiarism prevention resource Turnltln available to any
instructor at Penn State. Please note that any written work you produce for
any Penn State course could be checked for originality through the Turnltln.com
Web site.
Penn State takes violations of the University Code of Conduct related to Aca-
demic Integrity very seriously. As a result, procedures have been developed for
how allegations of academic dishonesty are to be handled including sanctioning.
Academic integrity is an essential component of any educational community.
Having academic integrity means being honest about where you get information
written assignments and giving credit for ideas and text that you copy. NOTES II
::;;.~policy requires faculty to include a statement in the syllabus for each
;;..!cressing academic integrity so you will know exactly what is expected
c each class.
mic Integrity Policy

~ G...""esome resources on Penn State academic integrity policy:
Senate Policy 43-00 (http://www.psu.edu/ ufs/ policies/ 43-00.html)
~ enn State's Academic Integrity Policy (http ://www.psu.edu/ dept/ ufs/
?Olicies/ 47-00.html" \l "49-20)
Statement from the Council of Academic Deans
'http://www.psu.edu/ provost/ integrity.htm)
Academic Integrity Procedures:
Academic Administrative Policies and Procedures Manual, G-9 (http://www.
psu.edu/ dept/ oue/ aappm/ G-9 .html)
Academic Integrity Statements (http://www.psu.edu/dus/handbook/integrity.
htr!_ll)
Learning to Avoid Plagiarism

~.....n important part of your education at Penn State involves learning to write, use
sources, and correctly cite the sources you use. In learning to use and cite sources,
r.-ou also need to know about copyright rules and what constitutes plagiarism.
Several Web sites have been created to provide this information.
iStudy for Success! Instructional module on Academic Integrity, Plagiarism,
and Copyright (http://istudy.psu.edu/ modules.html" \I "Integrity)
Penn State Libraries' plagiarism tutorial
(http://www.libraries.psu.edu/ psul/lls/ students/plagiarism_and_you.html)
Plagiarism Tutorial for Students at Penn State
(http://tlt.its.psu.edu/plagiarism/tutorial"\o "Plagiarism Tutorial for Stu-
dents)
Penn State page on copyright (http://www.psu.edu/ ur/copyright.html)
In addition to sites at Penn State, you should find Turnltln.com's FAQ on pla-
giarism and copyright useful. (http://www.turnitin.com/research_site/ e_faqs.
html)
Turnltln also has some useful information about citing sources. (http://www.
turnitin. com/research_site/ e_citation.html)
How Turnitin.com Works

Electronic versions of written works are submitted to Turnitin.com, which in
rum produces an "Originality Report." This report shows the instructor the results
of Tumitin. com's comparison of the written work to content on the Web, to
'furnitin.com's database of student writing, and to some databases of common
full-text journals. The quality of the report must still be evaluated independently
to determine if the parts identified by Turnitin.com that are similar or identical are
49
••
•• OTES actually plagiarized text or due to something else such as a properly cited quota-
tion. This is because all matches are shown, even those that were cited properly.
Similarly, instructors are aware thatif a paper is reported as "original"byTumitin.ar.:u..

that is not necessarily airtight evidence that the paper is original. Instead, it may
mean that the content was plagiarized from a work that is not available in the
Turnitin.com database.
When Plagiarism Is Suspected

If a faculty member believes you have committed plagiarism or another infraction
of the University's Code of Conduct related to Academic Dishonesty, they v.ill
schedule a time to meet with you to review the information that has led them to
believe a violation occurred, and will allow you the opportunity to respond to the
allegation.
If after this meeting the faculty member still believes you are responsible, that
faculty member will follow the guidelines that have been established for report-
ing a violation of the Academic Dishonesty section of the Code of Conduct. More
information on the Academic Integrity Policy procedures can be found at http://
www.psu.edu/dept/ oue/ aappm/ G-9.html or through your College.
Sections of the Formal Final Report

The sections of the final report are adapted from the format of articles published
in The Journal of Organic Chemistry, a reputable journal that contains cutting-
edge, novel organic chemistry research. These sections include Introduct!_on; Ex-
perimental; Results, Discussion, and Conclusions; References; and Supplemental
Information.
I. Introduction
The Introduction should contain three main parts. The first part should include
relevant background on the reaction or natural product under investigation. It
should also contain information about why the starting material and/ or product
is/ are important. The second part (if a reaction) should include the reaction mecha-
nism. You must draw out the mechanism and then verbalize it in the text of the
report. If an isolation experiment, include details about isolation technique. The
third and final part of the Introduction is the purpose of the experiment.
Mr. Benzene says: SciFinder Scholar is the single

most important search tool for chemists! Using it
will make writing your Intro a breeze!
50
To 5.nd relevant information on your molecule of interest, register for a SciFinder NOTES II
Sdiolar account (instructions on ANGEL). Search using the "structure search."
. nen the results pop up, find the molecule that you want and click on the struc-
~e. A whole bunch of relevant chemical information will appear BUT what you're
<:....~er are the references in the chart that are broken down by "uses," "relevance,"
·synthesis," etc. This will help you tremendously in finding information about the
s~ting material and/or product.
DO NOT include experimental, procedural detail in the Introduction! For

mstance, do not describe how you add a reagent to a flask or mention the size flask
"'TOU will use. Do not include specific measurements made. Save this procedural
detail for the Experimental section of your Formal Final Report.
II. Experimental
See details and examples provided in Section 3.4. Additional examples can be found
in the example Formal Final Report and on ANGEL.
Ill. Results, Discussion, and Conclusions

illi.s section is perhaps the most important section of any Formal Final Report.
It expresses to the reader your level of understanding of the experiment and how
the data and observations coincide with the expected results or goals for the
experiment.
Your job is to analyze and discuss your results. Start off with a short summary
::. to 2 sen tences) of what you did and why. Talk about the synthesis or isolation
and purification. Also discuss% yield,% recovery, or% composition. Discuss spec-
:ral data, justify WHY you think you made/isolated your compound. Remember:
This is more than just a typed-up summary of your data. It's an interpretation.
"\nenever possible, compare to NMR and IR of what the starting material would
look like. Justify the transformation. What else is in the literature?
Give a concise analysis and discussion of your data/results. This analysis may in-
C:ude comparing theoretical values to observed values, interpreting a graph or set
c: data, or giving a discussion on the interpretation of specific peaks in a spectrum
see the following list for guidance).
Discussion of analysis (whichever is applicable):

~.felting point and purity, boiling point and purity; compare your observed
results to the theoretical results
71.C: purity, progress of reaction, identification of compound, calculation of
R, values, compare Rf values (does the order of elution match your predic-
tion that you made in your Prelab?) and relate them to the structure and
polarity of the compounds
CC: success of separation; discuss the observed results from your TLC plates
51
H NOTES NMR: assignment of peaks, splitting patterns, integration, chemical st.:f::s.

identity of compound confirmed; discuss the actual values of chemi.:a:..
shifts
IR: analysis of functional group region, absence or presence of function.a:t
groups; discuss the actual wavenumbers.
UVNis: A.max' absorbance, molar absorptivity
RI: value-compare to expected value
Polarimetry: degree of rotation-compare to expected value
GC: labeled chromatogram (solvent and compounds), purity, retention times
tabulated, comparison of your chromatogram to that in the Compendiu:::::
(compare the relative retention times-relative to solvent), calculation of
%s of compounds in sample (from the % area values on chromatogram
Quality of spectral data counts! Be sure to have a TA sign and date all spectral data..
This section ends with a summary, namely conclusions. No new information is

presented here. You are to briefly summarize the success of the experiment: if
the purpose was achieved, if expected results obtained, if the desired product was
made, if the analysis supported/ confirmed the predicted results. It is appropriate
to include ideas for future improvements to the experiment if the desired results
were not obtained.
IV. References
All Formal Final Reports require three peer-reviewed journal article references. You
cannot use Wikipedia or a Web site as a reference. The reference must COIJle from
a published, peer-reviewed journal. If you include Web sites as references (the ex-
ceptions are: SigmaAldrich or MSDS for melting points and the Spectral Database
for Organic Compounds to reference spectral data), you will lose ALL of the points
associated with the References section. Textbooks may be used as a source but you
still need three journal articles in addition. Remember, the sources provided to
you in the synthetic handouts do not count towards the three sources you need.
Mr. Benzene says: Remember that Web sites aren't

peer-reviewed, meaning that other scientists
did NOT approve the content of that Web page.
Journals are a more reliable and vetted source of
accurate information!
If your article was found in an online journal, you should cite the print version
and include the DOI. Make sure that you format your references according to ACS
guidelines; see below on how to properly cite a source. Good databases to search
for relevant information about your compound or reaction include:
The Assignments :: Chemistr y 213W
Journal of Chemical Education: http://pubs.acs.org/journal/jceda8 NOTES : :

SciFinder Scholar: www.scifinder.cas.org
Google Scholar: www.scholar.google.com
ACS Publications: www.pubs.acs.org
Science Direct: www.sciencedirect.com
The ACS Style Guide, 3rd ed., is the standard citation style for chemistry. This Quick
Guide includes the most common formats from that publication.
The ACS Style Guide: Effective Communication ofScientific Information, 3rd ed. Coghill,
A.M.; Garson, L.R., Eds. American Chemical Society: Washington, DC; Oxford
University Press: Oxford, U.K., New York, 2006.
Book with authors

Beall, H.; Trimbur, J. A Short Guide to Writing about Chemistry, 2nd ed.; Longman:
New York, 2001; pp 17-32.
Books With editors

Editors' names can appear in either the author (first example) or the editor posi-
tion (second example).
Richey, H. G., Ed. Grignard Reagents: New Developments; John Wiley & Sons:
Chichester, U.K., 2000.
Grignard Reagents: New Developments; Richey, H. G., Ed.; John Wiley & Sons:
Chichester, U.K., 2000.
Chapter in an edited book

McBrien, M. Selecting the Correct pH Value for HPLC. In HPLC Made to Measure:
A Practical Handbook for Optimization; Kromidas, S., Ed.; Wiley-VCH: Weinheim,
Germany, 2006; pp 89-103.
Print articles
_.;.:though nice, article titles from print journals are not normally included in the
citation.
Larabee, D. C.; Reynolds, T. Y.; Hochberg, R. B. Estradiol-16a.-carboxylic Acid Esters

.as Locally Active Estrogens. J. Med. Chem. 2001, 44, 1802-1814.
:.:.ara.oee, D. C.; Reynolds, T. Y.; Hochberg, R. B. J. Med. Chem. 2001, 44, 1802-1814.
'"Pri:::: articles that are viewed online are still cited as print articles.
53
••
•• OTES Online-only journal articles
The format for citing e-articles does include the article title.
Vandenabeele, P.; Edwards, H. G. M.; Moens, L. A Decade of Raman Spectroscopy

in Art and Archaeology. Chem. Rev. [Online] 2007, 107, 675-686. http:! / pubs.
acs .org/cgi-bin/article.cgi/ chreay/2007/ 107/i03/html/cr068036i.html (accessed.
Mar 19, 2007).
Early access articles

Padwa, A.; Bur, S. K. The Domino Way to Heterocycles . Tetrahedron [On-
line early access]. DOI: 10.1016/ j.tet.2007.03.158. Published Online: Apr 3.
2007. http://www.sciencedirect.com/ science? _ob= Publication URL&_tock
ey=%23TOC%235289%239999%23999999999%2399999%23FLA%23&_
cdi=5289&_pubType=J&view=c&_auth=y&_acct=C000014439&_version=l&_
urlVersion=O&_userid=209810&md5=5c2e57fa33fldOd201397bddOdd2a3c4 (ac-
cessed Apr 3, 2007) (accepted manuscript, has not undergone final copyediting,
typesetting, or proof review).
Material safety data sheets

Relevant section in ACS Style Guide on p 315. International Chemical Safety Cards
can also fit in this format.
Ethylene Glycol; MSDS No. E5125 [Online]; Mallenckrodt Baker: Phillipsburg, NJ,
Feb 25, 1999. http://www.jtbaker.com/ msds/ e5125.htm (accessed July 23, 2001).
Ethylene Glycol; ICSC No. 0270 (U.S. National Version) [Online]; National Institute
for Occupational Safety and Health, Centers for Disease Control and Prevention:
Atlanta, GA, 2001. http://www.cdc.gov/ niosh/ipcsneng/neng0270.html (accessed
July 23, 2001).
V. Supplemental Information
Your supplemental information needs to include the following:
Annotated Spectra (see examples in Section 3.4)
Notebook pages of Procedures and Observations
Notebook pages of Calculations
VI. Synthetic Mastery Evaluation by Your TA

Since organic chemistry lab is all about learning and applying techniques, a
portion of your grade for each synthetic will rely on how well you execute the
synthetic reaction assigned. Your TA will keep in mind how much help you
needed, how many times you had to repeat the reaction, if your reaction spectra
still show signs of starting material, and if your yields suffered because of poor
technique.
3.6 Example Formal Final Report NOTES : :

This last section is an example of a very good Chem 213W FFR. There is also an
example of a "typical" Formal Final Report on ANGEL; your TA has made com-
ments on this report to help you understand what he/ she is looking for in a FFR.
Each TA may have different expectations of how the intro and results/ discussions
sections are organized, so make sure you talk to your TA about this.
Mr. Benzene says: Your first FFR will be written in

two drafts to help you get used to this new style of
report. Your first draft will be graded harshly and
your TA will make tons of useful comments. You'll
be able to win back HALF of the points you lost by
doing corrections. Each subsequent report will be
easier to write after this process!
SS
Chem~stry 213W H Chapter 3
The Synthesis of 2-((2-Methoxybenzyl)oxy)-4-nitrobenzaldehyde via an Sx2 Reaction
Introduction
SN2 reactions are commonly used in organic chemistry because they directly join two
smaller molecules to form a larger molecule. The process is relatively straightforward - a
nucleophile attacks an electrophilic functional group, displacing a leaving group in a
simultaneous breaking and reforming of a bond - allowing a high-level of control when
synthesizing large and complex molecules. In addition, Sr..:2 reaction conditions can be quickly
optim ized by adjusting several factors including the nucleophile, the leaving group, the solvent,
and the concentration, allowing SN2 reactions to proceed relatively quickly and often in high
yields. 1
In this experiment, an SN2 reaction was used to synthesize the large, highly
functionalized molecule, 2-((2-methoxybenzyl)oxy)-4-nitrobenzaldehyde 3, from two smaller
molecules: a nucleophilic phenol, 2-hydroxy-4-nitrobenzaldehyde l, and an electrophilic benzyl
bromide, 2-methoxy-benzylbromide 2 (Figure I).
~
£
OCH3
OH
+ sru) K2C03
DMF, 55°C, 2 hrs
o~
0CH
3
H 0 H 0 h
2 3
Figure l. Synthesis of 2-((2-methoxybenzyl)oxy)-4-nitrobenzaldehyde 3 from 2-hydroxy-4-
nitrobenzaldehyde l and 2-methoxy-benzylbromide 2.
Zene 1
The product 3 is an important precursor to a type of molecule used as a monomer in the
synthesis of depolymerizable materials.2 Materials that can undergo controlled depolymerization
are a current focus of scientific research and are being developed for a wide range of applications
including drug delivering nanoparticles,3 self-powered pumps,4 self-healing materials,5 and
shape-changing plastic materials. 6
The mechanism for the formation of 3 begins when the potassium carbonate acts as a
base that deprotonates the phenol. The resulting phenoxide attacks the benzylic carbon of the
other starting material, simultaneously pushing out bromine to form the benzyl ether of the final
product.
~
2
roe aJ-6
H 0
(\ OMo
Scheme 1. SN2 mechanism to fom1 2-((2-methoxybenzyl)oxy)-4-nitrobenzaldehyde.
The purpose of this experiment was to use an SN2 reaction to synthesize the product 3
and purify it through flash chromatography. The product was then characterized by IR, 1H
NMR, and 13 C NMR analyses.
Experimental
2-((2-Methoxybenzyl)oxy)-4-nitrobenzaldehyde. 2-Methoxy-benzylbromide (541 mg, 2.69
mmol) was added dropwise to a suspension of 2-hydroxy-4-nitrobenzaldehyde (300 mg, l.80
mmol) and potassium carbonate (372 mg, 2.69 mmol), in dimethylfonnamide ( 1.0 mL). The
Zene 2
57
C:;a:Ustry :?13W H Chapter 3
reaction mixture was stirred at 55 °C for 2 hours and monitored by TLC (30% acetone in
hexanes). Upon completion, the reaction mixture was partitioned in ethyl acetate (20 mL) and
hydrochloric acid (IM, 20 ml). The organic layer was washed with saturated sodium chloride (2
x 20 mL) and dried over sodium sulfate. The sodium sulfate was removed by vacuum filtration
and the solvent was evaporated to yield a yellow residue. Flash chromatography (30% acetone in
hexanes) afforded a yellow solid (460 mg, 89%) 1H NMR (400 MHz, CDC'3): o (ppm) 10.57 (s,
1H), 8.06 (d, lH), 7.97 (d, lH), 7.85 (dd, lH), 7.43 (d, lH), 7.34 (t, lH), 7.00 (t, lH), 6.96 (d,
lH), 5.35 (s, 2H), 3.92 (s, 3H); 13

C NMR (100 MHz, CDCh) o (ppm) 188.49, 161.11 , 156.99,
152.08, 130.09, 129.24, 128.86, 122.89, 120.72, 115.47, 110.49, 108.94, 66.29, 55.41 ; IR (ATR)
Ymax (cm- 1) 3113, 3009, 2885, 1685, 1532, 1289.
Results and Discussion
In this experiment, the monomer precursor 3 was synthesized via an SN2 reaction
between a phenol and benzyl bromide. The product was purified by flash chromatography and
characterized by IR, 1H NMR, and 13C NMR analyses.
To synthesize product 3, an SN2 reaction was used to form the benzyl ether from a
phenoxide nucleophile and a bromine leaving group; the nitro, aldehyde, and metboxy functional
groups were stable and unreactive to the reaction conditions. Potassium carbonate was chosen
specifically because it acts as a non-nucleophilic base and is anhydrous. Care was taken to avoid
introducing moisture to the reaction as any water or hydroxide molecules present could compete
as a nucleophile and form unwanted byproducts. To promote the interaction of the two starting
molecules, a very high concentration reaction mixture was used. DMF was chosen as the solvent
for its high dielectric constant - a very polar solvent is necessary to support the highly charged
Zene 3
transition state of the SN2 mechanism. By monitoring the reaction with TLC, the reaction was
able to be quenched soon after the limiting reagent 1 had been consumed. An acid workup was
used to neutralize the basic mixture and remove the inorganic salts from the organic compounds
before the frnal purification.
From the information provided by the TLCs taken during the reaction, column
chromatography was chosen as the method to purify 3. Using a solvent mixture of 30% acetone
in hexanes, the starting material 2 eluted first, followed by the desired product. The polarities of
the remaining starting material and product were different enough to allow for complete
separation.
The product 3 was ultimately obtained as a yellow solid in a 89% yield. While there are
no direct comparisons for this compound, similar SN2 reactions have been shown to give yields
between 82% and 95%.1·8 In addition to the TLC plates used to monitor the progress of the
1 13
column separation, the product was also demonstrated to be pure from the IR, H NMR, and C
NMR characterization.
The IR analysis (Figure l, Supplemental Information) supports the formation of the pure
product 3. The aromatic and alkane carbon-hydrogen stretches appear at 3113, 3009, and 2885
cm· 1• The signal at 1685 cn1 1 corresponds to the carbonyl stretch of the aldehyde. The unique
signal at 1532 cm· 1 represents the nitro functional group, and the signal at 1289 cm·', despite
appearing in the fingerprint region, is most likely the carbon-oxygen bond of the benzyl ether.
While these signals would also be expected in the spectrum of the starting materials, the lack of a
phenol stretch around 3500 cm· 1 provides strong evidence that starting material 1 is not an
impurity in the sample.
Zene4
59
The 1H NMR (Figure 2, Supplemental Information) shows a singlet at l 0.57 ppm
indicative of the proton of the aldehyde. There are seven different signals in the aromatic region,
each integrating to one, that represent the seven aromatic hydrogens of the product. The singlet
at 5.34 ppm that integrates to two provides the strongest support that the benzyl ether had been
formed (the corresponding benzyl bromide signal would appear more upfield). The final signal
at 3. 92 ppm is a singlet that integrates to three and represents the protons of the methoxy group.
13
In the final spectral characterization, the C NMR (Figure 3, Supplemental Information)
further indicates the successful synthesis and purification of 3. The signal at 188.49 ppm
corresponds to the carbon of the aldehyde. The twelve unique carbons of the aromatic rings are
represented by signals between 161.11 and 108.94 ppm (the large signal at 128.86 ppm most
likely represents two very similar carbons). The two signals at 66.29 and 55.41 ppm represent
the two carbons bonded to an oxygen, the benzyl ether and the methoxy group, respectfully. The
lack of any other major signals in either NMR spectra demonstrates the overall purity of the final
product.
In conclusion, the SN2 synthesis successfully formed the desired molecule 3 in an overall
yield of 89%, and the IR, 1H NMR and 13

C NMR together indicate that it was of high purity.
Future experiments could aim to improve the yield by employing a benzyl iodine in place of the
benzyl bromide - a better leaving group could improve the overall conversion of the starting
materials to products. The ratios of starting materials could also be adjusted to minimize the
starting material remaining at the end of the reaction. If the starting material and other impurities
remained only in trace amounts, recrystallization (a generally faster and less expensive
purification method) could be attempted.
Zene 5
60
The Assign ments I: Chemistry 213W
References
(1) McMurry, J.; Organic Chemist1y, 8th ed.; Cengage Leaming: New York, 2011; pp 375-
407.
(2) Schmid, K. M.; Robbins, J. S., J. Org. Chem., 2013, 78, 3159-3169.
(3) DeWit, M.A.; Gillies, E.R.,J. Am. Chem. Soc., 2009, 131, 18327-18334.
(4) Zhang, H.; Yeung, K.; Robbins, J.S.; Pavlick, R.A.; Wu, M.; Liu, R.; Sen, A. ; Phill ips, S.
T., Angew. Chem. 1111. Ed., 2012, 51 , 2400-2404.
(5) Esser-Kahn, A. P. ; Sottos, N. R. ; White, S. R. ; Moore, J. S., J. Am. Chem. Soc., 2010,
132, 10266- 10268.
(6) Seo, W. ; Phillips, S. T., ./.Am. Chem. Soc. , 2010, 132, 9234-9235.
(7) Czeskis, B. A.; Clodfelter, D. K.; Wheeler, W. J., ./.Label Compd. Radiopharm. , 2002,
45, 1143- 1152.
(8) Chakraborti, A. K.; Chankeshwara, S. V.,J. Org. Chem., 2009, 74, 1367- 1370.
Zene 6
61
Chemistry 213W II Chapter 3
Supplemental Information:
(Note: The notebook pages with the handwritten procedure, data, observations, and calculations
sections are to be attached at the end.)
Figure l. FTlR of2-((2-methoxybenzyl)oxy)-4-nitrobenzaldehyde.
Figure 2. 400 MHz 1H NMR of2-((2-methoxybenzyl)oxy)-4-nitrobenzaldehyde.
Figure 3. l 00 MHz 13C NMR of 2-((2-methoxybenzyl)oxy)-4-nitrobenzaldehyde.

The Assignments
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:I NOTES
66
rII\.~D
I CHAPTER4
l_C_h_e_c_ki_n_g--1-n_a_n_d_O_ri-e-nt_a_ti_o_n_
Organic lab can be intimidating and seem like A LOT of work. This lab guide con-
tains a great deal of information, and the lab setting is both new and complicated.
To help you get situated with the course specifics and your new lab environment,
there will be two lab periods dedicated to getting you settled.
4.1 First Day of Lab: Lab Lecture and Checking-In
1. Lab Lecture
On the first day of lab during the first week of the semester, you will begin your
Chern 213W adventure by attending Lab Lecture in a designated classroom on
campus. Please check your e-mail and ANGEL to find out where you need to go.
At the Lab Lecture, the course instructor will explain the mechanics of the course,
report expectations, and other pertinent information.
2. Checking-In
After the Lab Lecture, all students will report to the second floor of Whitmore Lab.
Please find your assigned bench in the lab and wait patiently as the other students
in your section arrive. Once you meet your TA, he/she will give you instructions on
how to check in. Checking-in involves going through the glassware in your drawer,
accounting for each piece on a check-in sheet, replacing the missing items, and
cleaning EVERYTHING.
Check the contents of your locker against the Desk Equipment for Chemistry
213W checklist sheet found on the last few pages of the lab guide. Once you've
found the items on your checklist, go to the stockroom to obtain any MISSING
pieces. Then, wash your glassware. There is more to washing laboratory glassware
than simple soap and water! The detergent that you will use is in powder form
called Alconox. Rinse your glassware with water and fill with a solution of warm,
soapy water. Scrub with your brush using the soapy water then rinse thoroughly
with tap water. To ensure that your glassware dries swiftly, DO NOT USE PAPER
TOWELS as fibers will be left behind. Instead, rinse your freshly cleaned but wet
glassware 2 to 3 times with acetone. This used acetone is disposed of in the non-
halogenated waste containers found in each hood. Rinsing with acetone last will
67
Chem istry 213W II Chapter4
remove any water and it will evaporate quickly. You do NOT want wet glassware
: : NOTES
in organic chemistry .. .water is often the enemy of many reactions!
To help you identify the important pieces of equipment, here are pictures of the
important items and their most common uses:
Round-bottom flasks (5 sizes): 25 mL, 50 mL, 100 mL,

250 mL, 500 mL
Reactions are typically run in a round-bottom flask. The
bottom is round to give even heating or cooling and ef-
fective stirring. Usually, the round-bottom is clamped
in place above a stir/hot plate and the react ion mixture
inside is stirred with a magnetic stir-bar. When not
clamped in place, round-bottom flasks can be placed
inside the black rubber adapters so they don't tip over.
Erlenmeyer flasks (5 sizes): 10 mL, 25 mL, 50 mL, 125

mL, 250 mL
Containers for storing organic chemicals are normally
made of glass because many plastics dissolve in organic
solvents. Erlenmeyer flasks are used for storing both
solid and liquid compounds and can be sealed with a
septum and/ or Parafilm.
Beakers (5 sizes): 30 mL, 50 mL, 100 mL, 250 mL, 400

mL
Many of the solvents used in the organic lab have low
boiling points and evaporate readily. There will be a lot
of instances when you will be instructed to evaporate
solvent from a reaction work-up or column fractions.
Beakers are usually used in these situations because
the wide opening and larger surface area expedite the
evaporation process.
68
Checking-In and Orientation 11 Chemistry 213W
Graduated cylinders (2 sizes): 10 mL, 100 mL NOTES II

Liquids can be measured out by volume instead of weight
by using an appropriately sized graduated cylinder. To
measure out volumes less than 3 mL, syringes are avail-
able on the common shelf for greater accuracy.
TLC jars with lids

These jars are NOT meant to be used to store com-
pounds. They will be utilized during the TLC lab and
any other time you'll be monitoring reaction progress
via TLC. Make sure you keep these dean and dry.
Funnels (3 types, from left to right): long-stem funnel,

powder funnel, small plastic funnel
Long-stem funnels are useful to assist you when pouring
liquids into narrow openings, such as the opening of a
round-bottom flask. Powder funnels aid in the transfer
of solids through narrow openings. The smallest of the
funnels, made of plastic, is utilized to get solids into
reaction tubes AND is used to flash nitrogen through a
chromatography column.
69
Oiemistry 213W II Chapter 4
Vacuum flasks (2 sizes): 10 mL, 125 mL

I: NOTES
In this lab course, it is often necessary to separate solids
from a liquid. This is done using vacuum filtration. The
filter flask is the basis for the vacuum filtration setup;
the side arm of the flask can be attached to a vacuum line
with a thick-walled tubing. For smaller scale reactions,
the 10 mL vacuum flask is paired with a Hirsch funnel
(below). For larger scale reactions, the 125 mL filter flask
is paired with a Buchner funnel (below).
Vacuum funnels (2 types): Hirsch funnel, Buchner fun-

nel
The Hirsch funnel is made of plastic and is used when
isolating small amounts of material. On the inside, there
is a white frit. Make sure you always place a small filter
paper over the frit before use! If the frit is dirty or miss-
ing, a new one can be obtained on the common shelf.
The Buchner funnel is made of porcelain and is much
larger than the Hirsh. On the inside, there are many
tiny holes. A filter paper is needed to hold your crystals
in the funnel.
Rubber adapters for vacuum flasks

A "bumper" is needed to rest between the glass vacuum
flask and the vacuum funnel to create a good seal. Find
the appropriately sized rubber adapter and make sure
it's always placed BETWEEN the vacuum flask and the
funnel.
Watch glass
These curved discs are used after crystals are isolated
from vacuum filtration. Often crystals are spread out on
the watch glass to facilitate the drying process.
70
Checking-In and Orientat ion :: Chem istry 213W
Scoopers (2 types): rnicrospatula, scoopula NOTES H

The microspatula and scoopula are used to scoop re-
agents and solids. They can also be used to mix solutions.
A glass stir-rod is a better option if you need to stir a
solution or reaction by hand.
Reaction tubes
These test tubes have red markings on the outside that
measure approximate volumes. These will be the first
pieces of glassware you will use in the Extraction experi-
ment so clean them well!
Separatory funnel with stopper

The separat ory funnel is often used when working up
an organic reaction where a biphasic reaction mixture
is placed inside and shaken to mix. When the layers
separate, the bottom layer can be removed from the top
layer by turning the stopcock to open, and draining it
from the bottom. The separatory funnel can be secured
with an iron ring affixed to a ring stand (not the clamps).
71
: : NOTES Column for chromatography

On e of the bes t meth ods for purifying organic com-
pounds is via column chromatography (Chapter 10 . 1hls
column is made of glass and has a stopcock for allov.i."lg
solvents to be drained from t he bottom.
Drying tube with end-caps

If atmospheric moisture must be kept out of a reaction,
a drying tube filled with Drierite (anhydrous calcium
sulfate) is used . This maintains an open system; it allows
pressure to es cap e but the Drierite absorbs water vapor
from the air t hat diffuses into your reaction .
Distillation glassware: condensers, connectors, thermometer holder, fractional

distillation materials: There are a lot of glassware pieces that go into a distillation
set-up. See Figures 8.5 and 8.10 in the distillation chapter.
There are additional items that are located on the common shelf that you'll be
using every lab period. Make sure you make a not e of t hese important items in
your Scavenger Hunt!
3. Lab Tour and Instrument Room Tour

During the first lab period, your TA will give you a tour of the lab area. You can
fill out the Map of the Lab found on ANGEL during this time. Make note on
your map of the location of the following: your desk location, the com-
mon shelf, the synthetic chemicals, organic waste disposal, glass t rash,
eye wash, safety shower, first aid kit, fire extinguishers, safety blanket s,
nearest exit, balances, stir/hot plates, Mel-Temps, ice machine, distilled
water tap. Additionally, your TA may answer some of the questions found in your
"Scavenger Hunt" worksheet found on ANGEL.
72
Checking-In and Orientation II Chemistry 213W
Your TA will also give you a tour of the Instrument Room. You may complete the NOTES II
map of the instrument room found in the "Instrument Room Orientation Work-
sheet" on ANGEL at this time.
4. Scavenger Hunt
Please print out and answer the questions for the "Scavenger Hunt Worksheet"
that is found on ANGEL. Record the answers to these questions in your notebook!
Mr. Benzene says: Before you leave on Day 1

make sure that you find and fill out the "Organic
Lab Safety Agreement." It's located in your lab
notebook. Give it to your TA!
4.2 Second Day of Lab: Additional Orientation Activities

This is the first time you'll be writing/recording Procedure, Data, and Observa-
tions in your notebook so make sure that you follow the guidelines set forth in
Chapter 3. Your Orientation Assignment will be graded with this format in mind.
In addition, please look at/print out the gradesheet for the Orientation Activities
located on ANGEL so you don't forget anything when you hand in your completed
orientation assignment!
If you don't complete all of the Instrument Room Orientation activities during
lab, there will be TAs present in the Instrument Room outside of your lab hours so
that you can get it done. However, you must complete the Laboratory Orientation
Activities during this second lab period.
1. Laboratory Orientation Activities

Complete the following in-lab activities in ANY ORDER before your lab period is
over on the 2nd day of lab:
a. Melting Point Determination of an Unknown

You will learn to use the Mel-Temp Apparatus to obtain the melting
point of an unknown compound. Your unknown will be assigned to you
by your TA. Record your assigned unknown letter in your notebook! The
unknown compounds can be found on the Common Shelf in your area.
Use your microspatula tip to remove some of the solid from the jar and
place it on a clean watch glass. Use the tip of your spatula to grind up the
solid into a fine powder. Push the open end of a melting point capillary
tube into the crystals such that some solid is forced into the tube. Invert
the capillary and gently tap the closed end on your lab bench to help the
73
H Chapter4
solid fall down the tube. This can be facilitated by dropping it down a PVC
'-OTES
melting point tube (attached to your common shelf) onto a solid surface.
You should have no more than 1 cm of solid in the bottom of the capillary
tube. Insert the capillary tube into the Mel-Temp and slowly heat your
sample to obtain a melting point. Record the temperature when the first
crystal melts into a liquid and then record the temperature at which the
last bit of solid melts. Follow the procedure on pages 100- 111 to operate
the melting point apparatus .
'c
"
......
~
VG (
c ....
D
Mr. Benzene says: Record both your unknown
letter AND the melting point you observed in your
notebook and then consult your TA to check the
accuracy of your data!
D
b. Balance Training
When using the scales, make sure all scale doors are closed when pressing
the "tare" button and after you place anything on the balance pan. Air
currents will make the scale unstable and inaccurate if the doors are left
open!
You will determine the mass of a watch glass. Obtain the mass of a watch
glass two times and record these values in your notebook. The values of the
two trials for one balance should be reproducible within 1 % if you operate
the balance properly. Calculate the average of these masses. Now go to
another balance and repeat the same procedure. Do you see any difference
in the mass of the watch glass? What do the results suggest in terms of
your weighing of chemicals and products for your laboratory work? Record
your results in your notebook. Ask your TA to examine your results.
c. Thermometer Calibration
You will calibrate your thermometer with boiling water and an ice bath.
Boil water in a 100 mL beaker using a hot plate. Record the thermometer
temperature in your notebook. Allow the thermometer to cool to room
temperature and then obtain the temperature of an ice bath. Record the
observed temperature in your notebook. If the temperatures you observe
for the boiling and freezing point of water differ by more than 5 degrees
from their known values, please see the stockroom to obtain a new ther-
mometer.
74
Checking-In and Orientation 11 Chemistry 213W
d. Pipette Practice: Separation of a Mixture of Dyes NOTES II

New and clean pipette bulbs are found on the common shelf. Keep the
ones that you use in your locker; they can be re-used all semester as long
as you keep them clean. Do NOT put dirty pipette bulbs back on the com-
mon shelf. You should not draw any liquids up into the bulb itself so that
it does not become contaminated. Pipette bulbs are hard to clean once
they become dirty, and then could potentially contaminate your chemistry
later!
The glass Pasteur pipettes are also found on the common shelf. If you only
used them to transfer solvent, you can allow them to dry in your hood
or locker and reuse them; however, it is not worth it to try to clean them
out if they are quite dirty because the solvent used to clean them is more
expensive than the glass used to make them! Therefore, very dirty pipettes
are one-time-use and can be disposed of in the glass waste containers.
You will be using pipettes to transfer, mix, and separate liquids throughout
the semester, so this is your chance to practice good pipetting. For this
orientation activity you don't necessarily need to understand the chemistry
happening yet (you will learn it in Chapter 5, Extraction!); the goal here
is just to help you develop good "lab hands" -this means having steady
and precise technique (and obviously not spilling anything). You will be
separating three dyes via extraction to practice your pipette mixing:
HO
0
OH ~
N
Toluidine blue Bromocresol purple Quinoline yellow
Appears blue when in Appears purple when in Appears yellow when in

aqueous acidic solutions aqueous basic solutions neutral organic solutions
75
Chemistry 213W H Chapter4
Step 1:
II N OTES
Obtain three test tubes from the common shelf area. Labels are also
located on the common shelf; make three labels that say: Dye Mix, Blue
Dye, Purple Dye. Affix your labels to the different test tubes.
= =
Add 1 ml of 1.5 M HCI
4.5 4.5
4.0 2 Pipette mix 4.0
3.5 3.5
3 Remove upper blue layer.
3.0 Put into tube labeled "Blue Dye" 0
2.5 2.5
4 Repeat TWO more times
2.0 2.0
3 ml of blue dye
t5 1.5
CIHaydca-McNcil, LLC
Test tube containing Test tube labeled

1 ml of "Dye Mix" "Blue Dye"
With a 1 mL syringe (located on the common shelf), measure out 1.0 mL

of the dye mixture into a small test tube labeled "dye mix" which is a 1:1:1
mixture of toluidine blue, bromocresol purple, and quinoline yellow in
dichloromethane. Add 1 mL of l .5M hydrochloric acid (aq) to the test tube
and pipette mix the two layers. Pipette mixing is drawing up the liquid into
the pipette (but not the pipette bulb!) and then briskly squirting it back
into the tube. Do this 15 to 20 times to get effective mixing between the
two layers. Allow the two layers to separate and remove the aqueous (up-
per layer) with the pipette and place it in another test tube labeled "blue
dye." This is where you want to practice being precise! Can you transfer
the layer over without leaving a drop behind or taking a drop of the bot-
tom layer over? Using the same pipette, extract the organic layer with two
additional 1 mL portions of 1.5 M HCl and combine them with the first
in the "blue dye" tube.
76
Checking-In and Orientation H Chemistry 213W
Step 2: NOTES II
Add 1 ml of 1 M NaHC03
4.5 4.5
4.0 2 Pipette mix 4.0
3.5 3.5
3 Remove upper purple layer
3.0 Put into tube labeled "Purple Dye" ao
2.5 2.5
4 Repeat TWO more times
2.0 20
3 ml of purple dye
ts t5
CHaydcn·Mc.'Oc:il. UC
Test tube containing Test tube labeled

1 ml of "Dye Mix" "Purple Dye"
Now with a new, clean pipette, extract the remaining organic layer in the
"dye mixture" tube with 1M sodium bicarbonate in the same manner as
the previous separation into a new test tube labeled "purple dye."
After both separation steps, the yellow dye should be the only remain-
ing compound in the organic layer of the original "dye mixture" tube. At
this point, you should have 3 reaction tubes with 3 different colors. Do
they match the expected colors? If not, why? Record your procedure and
observations in your notebook.
,.1.
'c
,.
~
t)(j \
c ...
0
Mr. Benzene says: Never invert your pipette when
there is liquid inside! The back-pressure will force
the liquid to squirt out of the pipette. This can
be quite dangerous if there is acid or base in the
pipette!
D
e. Preparation of NMR and IR Samples

In addition to recording the melting point of your unknown sample, you
will also team up with a person in your section that was assigned the same
unknown to obtain NMR and IR data for your Instrument Room Orienta-
tion Worksheet. Make sure you prepare your NMR and IR samples before
you leave the lab. Instructions on sample prep can be found in Chapter 2
pages 14-16.
77
Chemistry 213W : : Chapter4
H NOTES 2. Instrument Room Orientation Activities

Complete the Instrument Room Orientation Worksheet found on ANGEL and
hand it in with your notebook pages on the date indicated on the schedule. You
will be required to take an NMR and IR of the Unknown sample assigned to you by
your TA with a partner. Make sure you prepare your NMR sample according to the
instructions in Chapter 2! ALSO MAKE SURE YOU FULLY ANNOTATE YOURNMR
AND IR DATA (look in Chapter 3 for instructions and examples on how to do this) .
3. Outside of Lab Orientation Activities

a. Plagiarism and Ethics Activity
Complete the plagiarism and ethics activity that you printed out from
ANGEL; hand it in with the rest of your orientation materials on the due
date.
b. Make Your List of Possible Unknowns Based on Melting Point AND

Finish Instrument Room Orientation Worksheet
At home, in your Notebook Pages, give the name and draw the structures
for all compounds that have melting points within plus or minus S°C of
your Unknown's melting point you obtained in Day 2 Activity la. This list
can be found on ANGEL and in paper form in the Instrument Room. You
will have between 5 and 30 compounds. Structures can be found by using:
1) ChemExper (www.chemexper.com); 2) SigmaAldrich www.sigmaaldrich.
com); or 3) ChemSpider (www.chemspider.com).
'c
..
,.1.
tlG I
~
c ....
0
Mr. Benzene says: Looking up and drawing
structures of organic compounds may be tedious
but it's super helpful!!! Structures are much more
important than names because without them
you will not be able to interpret the NMR and IR
data you'll obtain during your Instrument Room
0 Orientation Activities.
78
Chemistry 21 3W H Chapter 5
: : NOTES Introduction to Synthetic Organic Chemistry

The first half of Chem 213W is dedicated to teaching you the basics of organic
chemistry; we call them techniques. The second half of Chem 213W is dedicated
to you APPLYING these techniques to three organic syntheses. Remember that
in this course, all work is done individually and all lab reports and prelabs
are to be written individually. Collaboration is encouraged when data and
ideas are shared; you will be instructed several times throughout the semester to
exchange analytical and/or observational data.
The techniques you are going to learn follow a logical progression based on how
organic chemists approach each and every organic reaction that they do. Each
chapter in the technique section of this lab guide will fall into this overall progres-
sion. Before you start mixing any chemicals together, you need to think about:
The Setup: things you need to know and prepare BEFORE you do a reaction.
Running the Reaction: how to start and end a reaction, what you need to do
in order to monitor the progress of the reaction (Thin-Layer Chromatography,
Chapter 6; Application with Methyl Salicylate, Chapter 7).
The Workup: the basics of quenching a reaction and how to isolate your
product from leftover starting materials and solvents (Extraction, Chapter 5).
Purification: what's the best method to purify what you made? (Distillation,
Chapter 8; Recrystallization, Chapter 9; Column Chromatography, Chapter 10)
Final Identification: using spectroscopy to characterize what you made
(NMR, IR, GC, GC-MS, UV/Vis).
Let's further investigate the above steps and talk about why approaching organic
chemistry this way is important.
A. TheSetup
Before you do ANY organic reaction, you need to think critically about what
you'll be doing, why you'll be doing it, along with the quantities, toxicities, and
states of the chemicals you'll be handling. In order to get you thinking about
these things, we have you complete the Prelab Assignment for each new activ-
ity as described in Chapter 3. There are additional things to think about that
are not directly included in the Prelab Assignments. I would recommend that
you make an outline of the activities for the day so that when you get into the
lab you have a clear picture of what needs to get done. Also think about how
you are going to measure out each reagent and the proper equipment to use.
It would also be helpful to note if you need any specialty glassware or special
preparation for a reaction. Sometimes (especially during the synthetics portion
of the semester) you'll encounter a water-sensitive reaction that will require
you to put glassware in an oven at least 24 hours before you plan to use it.
80
Extraction :: Chemistry 213W
B. Running the Reaction NOTES : :

1. Starting the reaction:
Often in organic chemistry, the order in which you add reagents to a reac-
tion is critically important. Weigh out or measure your starting materials
and add them to the appropriate reaction vessel in the appropriate order.
It's important the first time you do a reaction to follow the literature
procedure exactly as written.
2. How you know if your reaction is working (or how fast it's reacting):
In order to monitor the progress of your reaction, you will use one of your
organic techniques: Thin-Layer Chromatography (Chapter 6). Monitoring by
TLC is important because the prescribed amount of time for a reaction to
run is approximate: it could be done sooner OR it could take a lot longer!
3. Record all pertinent observations in your notebook as well as the exact
details of how you set up your reaction. Pointers for this can be found in
Chapter 3.
4. When your reaction is complete by TLC, you may need to quench (stop)
your reaction. This can involve pouring your reaction over water, cooling
the reaction mixture, or adding an acid or base. Sometimes quenching can
be exothermic so take care if gas evolution takes place!
C. The Workup
Working up a reaction is a process that involves the technique of Extraction
(Chapter 5) and is important for isolating your product from leftover starting
materials and/or solvents. Extraction workups often involve acid/base chem-
istry but also require you to recall knowledge about densities of solvents and
solubility of compounds. Neutral organic compounds are usually found in the
organic layer, which must be washed with aqueous acidic or basic solutions
to remove unwanted starting materials or products. It is important for you
to keep track of what compounds reside in which layers; you will learn this
in this current chapter! An important part of this whole process is to NEVER
discard any of your layers until you are sure that you isolated the right one!
D. Purification
Running an organic reaction is usually the easiest part of a synthesis. The
challenge comes in isolating and purifying the product from the reaction.
There are three main purification techniques (besides extraction) you will
master: Distillation (Chapter 8), Recrystallization (Chapter 9), or Column Chro-
matography (Chapter 10). Mastery means not just learning the motions, but
also understanding the underlying principles involved. Then you'll be able to
assess what purification technique or combination of techniques is optimal
for a given organic product.
81
Che mistry 213W ;; Chapt er 5
:I N OTES
E. Final Identification
You'll need to prove that you made or isolated your intended compound or
diagnose what went wrong if you didn't). Spectral methods available t o you
include NMR, IR, GC, GC- MS, and UVNis . Chapters 11 through 17 in this LaD
guide provide vital road maps to help you characterize your organic compounds.
Often it is helpful to compare your data t o a standard data set of the starting
material and/or the product.
Extraction Introduction
Liquid/liquid extraction is the first technique learned in this laboratory course
because it will be utilized in some form in all the remaining experiments. It is
one of those techniques that is used in concert with other isolation protocols and
proficiency can only be obtained with practice. You will need to be mindful of the
type of apparatus you select to carry out the separation whether that be a reaction
tube and pipette or a separatory funnel. It is also important to point out the sloppy
work will certainly influence your results so you will need to pay close attention
to detail and try to develop good bench technique. Once you have completed this
experiment you will be ready to proceed to the next technique and continue to
build your bench skills.
Extraction is the drawing or pulling out of something from something else. Chem-
ists extract compounds from solids or liquids using an aqueous or organic solvent.
Liquid/liquid extraction is often a major part of the workup steps in an organic
reaction to isolate a product. It is also often used in the isolation of natural products
from plant materials. This technique relies on the physical and chemical proper-
ties of organic molecules. The solubility and acid-base properties of compounds
play a major role in the way this extremely useful method is utilized in any science
laboratory experiment.
By far, the most universal and ancient form of extraction is the brewing of tea or
the making of coffee. Every pot of coffee or cup of tea involves solid/liquid extraction,
the extraction of organic compounds from solid ground beans or leaves using hot
water as the liquid extractant. The lower molecular weight polar molecules such as
caffeine dissolve in the hot water and are removed from the high molecular weight
water-insoluble cellulose, protein, and lipid materials . Over 200 compounds, some
in only trace quantities, are extracted from the solid into a cup of coffee or tea.
Decaffeinated coffee is also an excellent example of solid/liquid extraction. Coffee
manufacturers extract the caffeine from the coffee to provide modern society with
a decaffeinated version of an ancient drink.
82
Extraction II Chemistry 213W
Figure 5.1. The structure of caffeine.
Over the centuries, humans have carried out solid/liquid extraction by brewing just
about every common plant leaf, fruit, or root. In the process, they have isolated a
number of extracts with pharmacological activity.
Compounds extracted from plants or animals (i.e., from nature) are called natu-
ral products by chemists. Many are used for medicinal purposes. For example,
Sertiirner first extracted morphine from poppy seeds in 1805. This drug and several
derivatives, including codeine, are used as painkillers today. Unfortunately, other
derivatives such as heroin have become drugs of abuse.
0
II
CH3 CO
H
CH3 CO,-
ll H
0
Morphine Codeine Heroin
Figure 5.2. Legal and illegal drugs: morphine, codeine, and heroin.
The Importance of Extraction in Organic Reactions

· ·:bile s olid/liquid extraction is the most common technique used to brew bever-
ages and isolate natural products, liquid/liquid extraction is the most common
method used in the organic laboratory. Organic reactions often yield a number
b;-products, some inorganic, some organic. Also, since most reactions do not
: ~o 1003 completion, some starting material is often present at the end of an
crganic reaction. Again, the real "work" in organic chemistry is not running the
reaction, but rather in what is aptly called the "workup" of the reaction mixture,
............: JS, the separation and purification of the desired product from the mixture
by-products and residual starting material.
83
Chemistry 213W :: Chapter 5
:: NOTES
.•
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~
,
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D
Mr. Benzene says: Liquid/liquid extraction is often
used as the initial step in the workup of a reaction,
followed by final purification of the product either
by recrystallization, distillation, sublimation, or
chromatography.
D
A Workup Example
Throughout this lab guide we will be visiting the example reaction below to dem-
onstrate the thought processes behind the workup and purification steps in an
organic synthesis reaction.
OMe
+ arl) DMF
2 3
This reaction is a simple SN2 reaction of a phenol and benzyl bromide to form a
larger benzyl ether. The potassium carbonate base produces a phenoxide of com-
pound 1 which acts as a nucleophile, attacking the benzylic carbon of compound
2, causing the bromide to leave. Upon completion, the final reaction mixture is
comprised of the solvent dimethylformamide (DMF), excess base, the organic
product, inorganic bromine by-products, and probably some leftover, unreacted
starting materials. How does an organic chemist isolate the product from all of
this "stuff" in the reaction mixture?
First we want to quench the reaction mixture. Quenching is the addition of a

solution that deactivates the reagents involved in the reaction. This SN2 reaction
was run under basic conditions, so it will need to be neutralized with acid. This is
accomplished by adding aqueous acid until it reaches a neutral pH. This stops the
reaction by extinguishing the phenoxide nucleophile and neutralizing the base,
leaving us with a relatively safe neutral mixture to work with. The first step of the
workup-quenching- is complete!
Now we start isolating the product from everything else in the workup. The workup
usually involves several steps of extraction. First we add ethyl acetate to the
quenched reaction mixture. Since the acid water (from the quench) and ethyl acetate
are immiscible, we have two separate layers, the aqueous and the organic. Since
84
ethyl acetate is less dense than water, it will comprise the top layer. Your knowl- NOTES : :
edge of chemistry and the application of the general principle "like-dissolves-like"
should help you to guess that in the 2-phase ethyl acetate-water reaction mixture,
die ionic inorganic salts of bromine should want to be completely in the aqueous
layer, and the water-insoluble organic products and starting materials should want
to be in the organic, ethyl acetate layer. Also, the DMF used as the solvent in the
reaction (because of its very high dielectric constant- polar molecules support the
charged transition states of SN2 reactions) is so polar that it is largely partitioned
in the water layer. This is good because its high boiling point makes it difficult to
evaporate away. By simply separating these two layers, we can separate the
inorganic salts and small polar organic molecules from the larger organic
molecules, getting us closer to obtaining a pure product.
Ethyl acetate "organic"
r ~a~~~a:~:::~:::ct
J
(3)
•Starting materials (1 and 2)
• Organic byproducts
.::;;;;.~ W•te• "•q"~"'"

layer contains
• Inorganic salts
• Water-miscible
solvent (DM F)
Exploring the Specifics of Extraction: The Distribution Coefficient

In almost all cases, liquid/liquid extraction can be used to separate ionic or polar
low-molecular-weight substances into an aqueous phase and less polar, water-insol-
uble, organic substances into an immiscible liquid organic phase. This phenomenon
is governed by the distribution coefficient.
In the example of liquid/liquid extraction described on the previous page, the

product was a fairly large organic molecule, which you would predict to be not very
soluble in water. On the other hand, if the product were a lower molecular weight
or "small" molecule, you would predict that it might be at least partially water-
soluble. Therefore, it might not completely "move" into the organic layer, but also
partially dissolve in the aqueous layer. For water-soluble organic materials, such
as DMF, acetic acid, and sugar, most of the solute will reside in the water phase. A
quantitative measure of how an organic compound will distribute between aqueous
and organic phases is called the distribution or partition coefficient. It is the ratio, K,
of the solubility of solute dissolved in the organic layer to the solubility of material
dissolved in the aqueous layer. (Note that K is independent of the actual amounts
of the two solvents mixed.)
85
K = distribution coefficient
: : NOTES
K= solubility of organic (g/100 mL)

~~~~~~~~~~~~~
solubility of water (g/100 mL)
The constant K is essentially the ratio of the concentrations of the solute in the
two different solvents once the system reaches equilibrium. At equilibrium, the
molecules largely distribute themselves in the solvent where they are more soluble.
Inorganic and water soluble materials will stay in the water layer and more organic
molecules will remain in the organic layer.
Since the distribution coefficient is a ratio, unless K is very large, not all of a solute
will reside in the organic layer in a single extraction. Usually two, three, or four
extractions of the aqueous layer with an organic solvent are carried out in sequence
in order to remove as much of the desired product from the aqueous layer as pos-
sible. The effectiveness of multiple small-volume extractions versus one large-
volume extraction can be demonstrated by a simple calculation. Imagine that one
extraction can recover 903 of the compound. A second extraction with the same
solvent may be able to pull out 903 of the remaining material. Effectively, 973 of
the compound would be recovered with two extractions. A single large extraction
would have only obtained the initial 903. Many smaller extractions are more ef-
ficient than one large extraction. This phenomenon can be proved mathematically,
but, in short, follows the equation:
1
fraction extracted into B = ( Vs )n
l+ VAnK
This equation provides the fraction of material extracted by solvent B where n is

the number of extractions performed, K is the distribution coefficient, VA is the
volume of solvent A, and V8 is the volume of solvent B.
Standard Workup Steps to Follow

Now that key concepts and underlying principles have been discussed regarding
extraction, there are practical procedures to contemplate in order to execute a
workup. Standard steps are usually followed as expounded upon in this section
and include: picking an organic solvent, using correct glassware, washing/extract-
ing the organic layer, using a salt water wash, drying the organic layer, decanting,
then evaporating the organic solvent.
1. Pick an organic solvent

The first and most important aspect when choosing a solvent system for extrac-
tion is to pick two immiscible solvents. Some common hquid/liquid extraction
solvent pairs are water-dichloromethane, water-ether, and water-hexane.
Notice that each combination includes water. Most extractions involve water
because it is highly polar and immiscible with most organic solvents . In ad-
86
Extraction :I Chemistry 213W
dition, the compound you are attempting to extract must be soluble in the NOTES II
organic solvent but insoluble in the water layer. An organic compound like
benzene is simple to extract from water because its solubility in water is very
low. However, solvents like ethanol and methanol will not separate very well
using liquid/liquid extraction techniques because they are soluble in both
organic solvents and water.
There are also practical concerns when choosing extraction solvents. As

mentioned previously, the two solvents must be immiscible. Cost, toxicity,
and flammability should be considered. The volatility of the organic solvent
is important. Solvents with low boiling points like ether are often used since
they readily evaporate to leave the desired organic compound. If ether (bp =
35°C) is used as the solvent, then evaporation and collection of the desired
compound is fast.
One common mistake when performing an extraction is to misidentify the

layers and discard the wrong one. The densities of the solvents will predict
the identities of the top and bottom layers. In general, the density of nonha-
logenated organic solvents are less than 1.0 g/mL and halogenated solvents
are greater than 1.0 g/mL. One common solvent pair is dichloromethane and
water. The density of dichloromethane is 1.325 g/mL and water is 1.000 g/mL.
Dichloromethane is more dense than water; therefore, dichloromethane will
be the bottom layer and water will be the top layer. Table 5.1 lists the densities
of some extraction organic solvents.
Table 5.1. Common extraction solvents listed by density.
Solvent Density (g/ml)

hexane 0.695
ether 0.708
toluene 0.867
water 1.000
dichloromethane 1.325
chloroform 1.492
For a complete list of physical properties of some common organic solvents,

please see the table located in the front of your laboratory notebook. Although
the density is the physical property that determines which layer is on top or
bottom, a very concentrated solute dissolved in either layer can reverse the
order. The best method to avoid making a mistake is a drop test. Add a few
drops of water to the layer in question and watch the drop very carefully. If
the layer is water, then the drop will mix with the solution. If the solvent is
87
the mistaken organic layer, then the water drop will create a second layer. In
••
•• OTES
general, this method can help determine the identity of the layer. However,
it is still best to keep ALL the layers until the extraction is complete
and your product has been isolated.
2. Decide what type of glassware is needed for the separation of the

organic and aqueous layers
Separatory funnel: Separatory funnels are often used in workups where 500
milligrams or more of a reactant was used in a reaction. You could separate
the aqueous layer from your chosen organic solvent layer by decanting the
less dense layer into a separate container. Decantation, however, is an inferior
separation method. Chemists often use a separatory funnel to achieve an ef-
ficient separation .
'c
..
.......
t!G \
~
c,
D
Mr. Benzene says: Make sure you always use an iron
ring attached to a ring stand for your separatory
funnel! A clamp won't be secure enough and you
don't want your reaction mixture to spill!
D
CHaydcn-McKcil. U..C
Figure 5.3. A separatory funnel.
Reaction tube/ test tube: For microscale separations Oess than 500 milligrams),
pipette layer separation is convenient and normally very little product loss
is incurred. Since the two solvents are already in a reaction tube, instead of
transferring the small volumes of solvent to another piece of glassware and
ultimately losing product, the solvents can be mixed and separated directly
from the reaction tubes . You can use a Pasteur pipette to gently mix the lay-
ers. This can easily be accomplished by drawing the liquid into the pipette and
88
Extraction H Chemistry 213W
squirting it back into the tube rapidly. Once the layers are thoroughly mixed, NOTES I:
let them separate and use the pipette to draw up the bottom layer as shown
in Figure 5.4.
l 1
i
Water layer
- Ether layer
Water layer
Figure 5.4. Microscale pipette extraction.
3. Wash and/or extract the organic layer to remove impurities

How much organic solvent and aqueous phase should there be? Typically, the
volume of the aqueous layer is one tenth to one half the volume of the organic
phase. It's best to complete a wash or extraction two or three times due to the
partition coefficient described previously.
If your reaction is acid catalyzed or base catalyzed, an acid wash (5-10% HCl)
is usually used to remove amines while a basic wash (sodium bicarbonate solu-
tion or 5-10% NaOH) is used to remove unwanted acids. In this manner, the
catalysts, acids, and/or bases used in the organic reaction can be removed into
the aqueous layer and your desired organic compound is left in the organic
layer.
Sometimes acid/base chemistry is used to actually EXTRACT an organic

compound into the aqueous phase as you will do in Procedure l; this will be
discussed further.
89
How does one actually use the separatory funnel? First, make sure the
: : NOTES
stopcock at the bottom of the funnel is closed (in the horizontal position).
The complete reaction mixture including both aqueous and organic layers can
now be poured into the separatory funnel.
Mr. Benzene says: Be careful adding the liquid

to the separatory funnel. Remember to dose the
stopcock!
Extraction and washing are not very effective unless the two layers are mixed
together vigorously to provide maximum surface contact between the two im-
miscible layers so that substances can be pulled or extracted from one into the
other. To do this, the separatory funnel is stoppered. With one hand gripping
the top of the funnel so that a finger holds in the stopcock, the separatory
funnel is tipped upside down (Figure 5.5). Gently shake or swirl the funnel
to mix the two layers. With the separatory funnel still upside down, open the
stopcock with your other hand to relieve pressure that usually builds up due
to the vapor pressure of ether or another solvent. Shake, then vent often and
point the funnel away from yourself and classmates while shaking and vent-
ing the separatory funnel. Since extraction solvents typically have a very high
vapor pressure Oow boiling point), considerable vapor pressure is created while
mixing the two layers. If you do not vent the pressure often, the separatory
funnel caps can pop off due to vapor pressure buildup.
Figure 5.5. The proper method to vent a separatory funnel.
Thorough mixing is very important because the two solutions must be in contact
with each other to allow the solute to be extracted into the secon d layer. Once
the immiscible layers have been thoroughly mixed, the separatory funnel can
90
Extraction 11 Chemistry 213W
~ Oac.k in the ring stand, with the top stopper removed and open to the NOTES II
.:---.::-_.>,:ere.. Each layer can be easily separated using this method. The lower
car;. nor be drained into a beaker or flask by opening the stopcock. Just as
_ i::::::er:ace between the two layers enters the stopcock, the stopcock is closed.
::.___ U>p ~yer can then be drained out of the separatory funnel into a separate
becker or flask. REMEMBER: Look at the density chart to keep track of which
-. =r :.Son the TOP and which layer is on the BOTTOM. The most common sol-
~~ ve will use in extraction in Chem 213W include ether and ethyl acetate
wL:. be the TOP layer) or dichloromethane (will be the BOTTOM layer).
Finish with a saturated salt water wash

Smee there are usually droplets of water containing inorganic salts clinging
-:o the walls of the separatory funnel or floating in the organic layer, chem-
:.sts often keep or place the organic layer in the separatory funnel and mix it
...;th a volume of pure distilled water. Removing traces of unwanted materials
this way is often called washing. Often a final washing of an organic layer is
accomplished with a saturated sodium chloride solution (also called "brine").
The bulk of water left behind in an organic layer can be removed in this man-
ner. Because the concentrated salt solution wants to become more dilute, it
is effective at pulling water molecules into the aqueous layer.
.:>. Dry the organic layer over sodium sulfate

One significant problem with liquid/liquid extraction is that no solvent is
COMPLETELY insoluble in another solvent. In practice, one additional step
is usually carried out before evaporating the organic solvent: drying over anhy-
drous sodium sulfate or another drying agent. Drying a liquid might seem like a
peculiar concept, since we normally think of all liquids as being wet. Drying an
organic liquid in the organic lab has a special meaning to chemists. It means
to remove all traces of water. Even water and hexane are slightly soluble in
each other. After separating the two solvents, residual water will remain in the
hexane or ether organic layer. The water will stick to the solid product even
after the removal of the more volatile solvent. Therefore, chemists remove the
water from the organic layer by adding an insoluble inorganic solid to the solu-
tion that will absorb the water, thus "drying" it. Granular anhydrous sodium
sulfate is the drying agent most often used although other drying agents are
also available. All of the inorganic solids work by reacting with the water to
form hydrates, which is the preferred form of inorganic solids.
Mr. Benzene says: Drying the solvent means to

remove water.
91
H NOTES Na2 S04 + H 2 0---+ Na2S04 •5H2 0

sodium sulfate
MgS04 + H 2 0 ---+ MgS04 ·7H 2 0

magnesium sulfate
CaC1 2 + H2 0---+ CaC~·6H 2 0

calcium chloride
2CaS04 + H2 0 ---+ [CaS0 4] 2 ·H 2 0

calcium sulfate "Drierite"
Figure 5.6. Hydrated complexes for some common drying agents.
These compounds will associate or hydrate themselves with water. Table 5.2 lists
some common drying agents along with their speed, capacity, and hydration.
Table 5.2. Common drying agents.
Drying Agent Formula Speed Capacity* Hydration**
Sodium Sulfate Na 2S04 Medium High 7-10

Magnesium Sulfate MgS0 4 Fast High 7
Calcium Chloride CaC12 Fast Low 2
Calcium Sulfate
(Drierite)
CaS04 Fast Low 1/2-2
I
*Capacity refers to the amount of water removed per given weight of drying agent.
**Hydration is the number of water molecules removed per molecule of drying agent.
These drying agents do not dissolve in the solvent they are "drying." They may
change somewhat-for example, sodium sulfate will clump together as it reacts
with water-but they will remain solids in normal extraction solvents. This makes
them easy to remove by decantation (pouring off) of the liquid or by gravity
filtration. Usually the organic solvent will go from cloudy to clear in the process
of being "dried." You should be careful to remove all of these solid drying agents
before solvent evaporation to not mistake them for your product. When you take
a melting point, and the product doesn't melt by 300°C, you have probably iso-
lated your drying agent. Sodium sulfate is a widely used drying agent and the one
predominantly used in this course. It is relatively inexpensive and works quickly
and efficiently.
It is recommended that the drying agent you choose be in a granular form since
it is easier to remove compared to powdered forms. Drying a solvent, however,
is not an exact science. An excess of drying agent should be used to ensure that
92
Extraction ;: Chemistry 213W
all the water is removed. If the water remains after the materials are collected, NOTES II
it could interfere with the analysis. The most common question in this course is
always "How much sodium sulfate should I use?!" Add enough drying agent
so that there is some drying agent remaining as a free-flowing solid, not
completely clumped or stuck to the sides of the ftask (this is the hydrate
form). The presence of undumped drying agent means that all of the trace
water has been taken up.
There are many other choices for drying agents including molecular sieves and
sodium metal. There are benefits and disadvantages to each one. Sodium, for
example, is an excellent drying agent; however, it violently decomposes in water
to create NaOH and H 2 gas and may ignite spontaneously. Therefore, it should be
used with caution and only when removing very small amounts of water. Many
times a particular drying agent will work better than others in a certain situation.
6. Decant or filter off the drying agent

You don't want the drying agent you use to remain behind when you isolate
your organic compound; it will only interfere with the purification. You can
use gravity filtration with your powder funnel, a folded/fluted filter paper, and
a beaker/ Erlenmeyer to remove the drying agent. Sometimes just decanting
works too!
7. Evaporate the organic solvent

In order to get to your organic compound of interest, the solvent needs to be
removed. In this lab, you will be using a stream of nitrogen and a warm water
bath to encourage the quick evaporation of s olvents.
Troubleshooting
One difficulty encountered during a workup is when an emulsion occurs. An emulsion
:s a suspension of tiny droplets of one solvent mixed in the other. Emulsions are
common in extraction. In Italian salad dressing, an emulsion is desired to keep the
water and oil mixed. Additives are added to the dressing in order to keep the two
normally immiscible solvents miscible. In a liquid/liquid or solid/liquid extraction,
however, an emulsion will lead to a poor separation. Gentle shaking and swirling
::he separatory funnel is the best technique to avoid emulsions. However, if an
emulsion occurs, there are several simple methods to destroy it. The first is time.
Over time the layers will eventually separate. However, you may not have enough
time during a three-hour lab period to wait. Another method is to add NaCl brine
or salt water to the mixture. Since ether is less soluble in a highly ionic solution
such as salt water, the ether and water will be forced to separate. This method
·orks well with small emulsions. If you have a more difficult emulsion, separate
the layers as much as possible and dry the organic layer with a drying agent such
as sodium sulfate. The water will be removed from the organic layer along with
:he drying agent. Subsequent extractions of the original solution should proceed
•vithout further trouble.
93
H NOTES
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~
c,
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Mr. Benzene says: Shake the mixture gently to avoid
emulsions. Use salt water to remove emulsions.
The second diffi.culty encountered during a workup is the confusion oflayers. Make sure
you save ALL of your layers just in case the wrong layer is kept. Using a drop test
with water will help you determine which layer is aqueous and which one is organic.
Acid/Base Extraction
Solid/liquid or liquid/liquid extractions rely on the solubility of the solute to be
extracted. In acid/base extraction, the molecule to be extracted is transformed
so that we impose a new solubility on the molecule. There are three special cases
of liquid/liquid extraction that are extremely useful for isolating and purifying
amines, carboxylic acids, and phenols . All three of these functional groups can be
interconverted from nonionic organic-soluble forms to water-soluble ionic forms
by changing the pH:
Amines: RNH 2 + H+ ~
RNH 3 + (pH> 7)
Strong base only
Phenols: PhOH +OH- ~
Pho-+ H 2 0 (pH< 7)
Strong or weak base
Carboxylic Acids: RCOOH + OH- ~
~ Rcoo- + H 2 o (pH< 7)
RCOOH + HC03 - ~ Rcoo- + co 2(g) + H 2 0 (pH< 7)
By changing the pH of the aqueous phase in a liquid/liquid extraction, the dis-

tribution coefficient is drastically changed, thus pulling molecules into either
an organic layer or aqueous layer. Carboxylic acids, phenols, and amines can be
easily separated from neutral components. However, molecules with other com-
mon functional groups (i.e., neutral components) are not affected by changes in
aqueous pH and so they will always distribute between layers as normal. Figure
5.7 details the reagents needed to separate benzoic acid (acidic), aniline (basic),
and phenol (acidic) .
'c
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.......
ti GI
~
C,
D
Mr. Benzene says: Changing the pH of the aqueous
phase changes the distribution coefficient
D
One specific example is benzoic add, an organic carboxylic acid. Benzoic acid is NOTES ::
soluble in most organic solvents, including dichloromethane and ether. However,
this acid can be easily deprotonated with base to give a charged ionic species that
is readily soluble in water:
( ' Y COOH
Base
v (NaOH)
Sodium salt of
Benzoic acid
benzoic acid
soluble in some organic soluble in H20; insoluble

solvents; H2 0 insoluble in organic solvents
By converting benzoic acid to the sodium salt of benzoic acid, the solubility has
drastically changed. Now the sodium salt is soluble in the water and will migrate
to the water layer. Because the solvents chosen are immiscible in each other, the
layers can be easily separated. To obtain the original compound, benzoic acid, the
salt must be protonated with a strong inorganic acid. Once the benzoic acid is
formed by adding acid to the aqueous layer, it will precipitate in the water layer to
provide a pure compound. This method works very well with mixtures of strong
organic acids, weak organic acids, bases, and neutral compounds. We can use the
acid/base functionality to our advantage .
.•.
'c
,. ~G\
~
C,
,..
D
Mr. Benzene says: Acid/base extraction is useful to
separate acidic, basic, and neutral components.
95
Chem istry 213W H Chapter 5
: : NOTES
v
~COOH
Benzoic acid
Weak base
Sodium salt of
benzoic acid
-
Acid
(HCI)
~COOH
v
Benzoic acid
(1)
Aniline
- Acid
(HCI)
Protonated aniline
Base
Aniline
UOH uO-Na• UOH

~
Phenol
Strong base
(NaOH)
Sodium salt
of phenol
-
Acid
(HCI) ~
Phenol
Water insoluble
(3)
Water soluble
Figure 5.7. Ac id/base extraction equat ions.
Acid/base extraction is on e of the more difficult principles in organic chemistry

to understand. The most straightforward approach to understanding th is subject
is to create a flowchart to follow which species has been created upon pH change
and in which layer (aqueous or organic) the species resides. If you can imagine
the molecule changing and moving to the appropriate layer, you will be able to
complete any acid/base separation very easily. Figure 5.8 is a detailed flowchart of
the separation of a strong organic acid, a weak organic acid, an organic base, and
a neutral component. If you can follow the steps involved in the flowchart, the
unknown extraction in this ch apter will be much easier to understand.
Mr. Benzene says: Building a flowchart can help

you understand the acid/base separation.
96
a COOH
Slightly acidic Acidic Basic
0Neutral
Dissolve all four compounds in organic solvent (ether or CH 2Clz)
Extract with Na HC03 (aq); a weaker base will react with

acidic component
Water
layer
I Separate Organic layer I
Conjugate base
of acid Three components remain
Extract with Na OH (aq); strong base

HCI will react with slightly acidic
component
Q COOH Organic
layer
Separate Water
layer
Acid
NaCl
Two components remain Conjugate base

of acidic phenol
Extract with HCI, will react

with basic component HCI
Organic Separate Water

layer layer
0 ()':NH,cr Phenol
+
Neutral remains Conjugate NaCl
acid ol base
Dry with drying agent
Evaporate organic solvent
Allow to dry
I NaOH
Base
Figure 5.8. Flowchart of an acid/base extraction.

97
: : NOTES An Extraction Example

Let's revist our example reaction from the beginning of this chapter. After the
initial work up steps of quenching the reaction and using liquid/liquid extrac-
tion to remove the small polar molecules and inorganic salts, we are left with a
mixture of our product 3 and both of the starting materials 1 and 2 dissolved in
ethyl acetate. Can we use any acid/base chemistry with liquid/liquid extraction
to purify our product more?
OMe
+ Brl)
2 3
We can! By washing the organic layer with a strong base like NaOH, we can turn
1, the neutral phenol, into the sodium salt of the phenol, which will move it to the
aqueous layer. Once the layers are separated, the salt can be reacidified back to the
neutral phenol, which will precipitate out of the water and be collected by filtration
(collecting unreacted starting material in its pure form can reduce chemical waste
and save money) .
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D
Mr. Benzene says: Draw these steps out in a
flowchart to check your understanding.
Now 3, our product, is in a mixture with only one other compound, 2. Can we use
acid/base chemistry with liquid/liquid extraction to further separate these com-
pounds? In this case, no, because both 2 and 3 are neutral molecules that contain
no acid/base reactive functional groups. The compounds will have to be separated
using another one of the other purification techniques that you will soon learn.
Melting Points
After an extraction, chemists often take the melting point of the resulting com-
pound to get an idea about the compound's identity and/or purity. The melting
point or freezing point of a compound is the physical state change from a solid
to a liquid or a liquid to a solid, respectively. Each pure organic compound has a
characteristic melting point or range. This determination can be used to correctly
identify and/or demonstrate the purity of the compound.
98
Solid organic compounds can melt from just above room temperature to about NOTES II
35C"C. Above 350°C, organic compounds decompose and char rather than melt.
So.!ids with normal melting behavior are in the molecular weight range from 59
g. :nol (e.g., acetamide CH3 CONH 2, mp 79-81°C) to roughly 1500 g/mol (e.g., the
c=.tibiotic bacitracin, C66H103 N170 18S, mp 221-225°C). Notice that while we talk
a.:xiut melting point and use the abbreviation mp for it, we almost always report
a. melting temperature range of a few degrees as seen in the examples just cited .
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Mr. Benzene says: Not all compounds melt! Some
will char and burn at higher temperatures instead!
In these situations, record a decomposition
temperature.
D
ill addition to traditional melting points, compounds can sometimes decompose

before actually melting. Instead of a solid clearly turning into a liquid, the solid
may turn gray, brown, or black at a certain temperature. This does not mean that
vou have obtained the wrong compound, just that this particular compound is
not stable at the observed temperatures. Saccharin, for example, does not melt
but decomposes at 229°C. This is symbolized as 229 d. This may happen to some
of the compounds you purify throughout the semester.
Adding impurities to organic compounds lowers their melting point. In addition

we observe that the melting range is broadened. Even small amounts of impuri-
ties, -1 %, will lower and broaden the melting temperature range. This behavior of
solids is consistent and can therefore be used as a test of whether we have a pure
compound or one mixed with impurities.
Why does this happen? When a compound contains soluble impurities, those
impurities disrupt the ordered, crystalline structure of the compound, and the
compound becomes amorphous. The attractive forces that hold the crystal lattice
have been weakened by the presence of the impurities. Weakening of the forces
means that not as much energy is needed to overcome them, thus a lowered melt-
ing point is observed. If an insoluble impurity is present in the sample, it will have
no effect on the melting point of the compound since insoluble impurities cannot
incorporate themselves into the crystal lattice of the compound and weaken the
forces that hold the lattice together. (If the impurity's melting point is higher
than the desired compound, you will see the solid mass in the capillary tube.) One
example of an insoluble impurity would be a piece of sand. The sand will not have
an effect on the melting point.
99
Thus, a melting point (really melting range) determination is a quick and simple
: : NOTES
test of a compound's purity. For example, the true melting poin t range for caffeine
is 234-237°C. If the caffeine is obtained directly from tea and is not purified, the
observed melting point is much lower. In fact, crude caffeine extracted from tea
bags melts as low 180- 220°C.
Figure 5.9 is a melting point composition diagram that shows how the melting
temperatures are affected in a two-component mixture. Either component may
be regarded as an impurity in the other component.
~in °CofpureA
MP in °C of pure B
Increasing
i
Melting
Temperature
- - - - Et
Mole percent of A 100 50 Ep 0

Mole percent of B 0 50 100
Figure 5.9. Melting point composition diagram of a two-component mi xture.
The left and right y-axes are marked with the known melting temperatures for pure
compound A and pure compound B, respectively. However, upon mixing A with B,
the melting temperature of the mixture is decreased. The amount the melting point
is depressed is a function of the molar percent of each component and can be read
directly from the diagram. There are two special points on this diagram. The first
is the Eutectic temperature, designated by Et. This is the lowest temperature at
which the mixture will begin to melt. The Eutectic point, Ep, is the mole percent-
age where the mixture of two compounds are dissolved equally in each other. At
this particular point, even though the mixture is not pure, it will appear to have a
sharp melting point. As discussed earlier, a sharp melting point indicates a pure
material. A broad melting point is normally an impure compound. The Eutectic
point is an exception to this rule and can lead to misidentification of the sample.
If you are determining the melting point of a known compound, the results can
be compared to literature values. Sigma Aldrich and ChemSpider have enormous
amounts of physical data for organic compounds including melting points. Use
these and other sources to verify your melting points. However, if the compound
100
is unknown or has been synthesized for the first time, the melting range may still NOTES II
help in determining the purity of the substance. The melting point range is the
temperature at which the solid begins to melt to the temperature when the solid
has completely been converted into a liquid. Note that powder solids may sinter
or dump together when heated before actually melting. Do not confuse sintering
·a/ith melting. Melting points should always be recorded as a range. As previously
mentioned, the purer the compound is, the narrower the melting point range. In
contrast, the more impure the compound is, the broader the melting point range.
Melting point ranges can vary, but a good range is typically 1-3°C. Poor ranges
can be as broad as 20°C.
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D
Mr. Benzene says: Solids must be free of solvent in
order to obtain an accurate melting point. When in
doubt, dry it out!
D
It is of utmost importance that any sample be thoroughly dry and free from all
traces of solvent before trying to determine its melting point. Otherwise, the
solvent, like any other impurity, will cause the melting point to be depressed, and
you won't obtain an accurate melting point. Normally, most solvents evaporate
completely from crystals in an open reaction tube in the two to five days between
-:abs, but higher boiling solvents such as water (hp 100°C) and toluene (hp 110°C)
may require drying on an open watch glass for a day. If your solid still seems wet
and sticky after this period of time, you may have to allow additional time for
drying by leaving it open in your locker for another few days, or you may have to
speed up the evaporation process by applying vacuum. Another common mistake
is to heat the sample too fast . In general it is best to heat the sample slowly, no
faster than 2°C per min in the range of the melting point.
One advantage of a melting point analysis is the very small amount of sample
::.eeded to obtain good results. Each machine uses glass capillary tubes to obtain
the melting point. To load the capillary, take a few milligrams of the material to
be analyzed and push the solid together on a watch glass or other clean surface.
:Jse the open end of the capillary tube (found in your desk equipment; not the
::.c spotting capillary tubes found in your kit) and push the open end onto the
?Ue of solid material. You only need - 1 cm of sample in the end of the tube. Too
much sample will lead to uneven melting and possibly increase the range of your
~elting point. Insert the tube, closed-end down, into the Mel-Temp, heat slowly,
and observe the melting point range.
101
H NOTES
Only 1 cm of
sample in mp
capillary
Mixed Melting Points

Although melting points can be used as an identification tool, there are many
compounds that have coincident melting points. There may be an occasion when
a sample contains two compounds that have the same melting point. A mixed-
melting point determination can verify whether they are the same compound or
two different compounds. Mix equal amounts of the two solids and determine the
melting point of this mixture. If the mixed-melting point is the same for both the
mixed materials and the individual compounds, they are the same compounds.
However, since mixtures of different materials melt at lower temperatures than
either compound (the combined melting point is depressed compared to the in-
dividual samples), then the materials are not the same.
102
EXPERIMENTAL PROCEDURES
NOTES==
Extraction Experiments
Procedure 1 demonstrates the Microscale Separation of Basic, Acidic, and
--eutral Substances by liquid/liquid extraction and Procedure 2 instructs you
on how to take the melting points and NMR of your extraction unknowns.
Students normally do Procedure 1 in the first lab and Procedure 2 in the sec-
ond lab. NMR and melting points can also be obtained during the catch-up
}ab AND outside of your lab period in the instrument room.
Reagents used in this technique:

Benzoic acid, 3-toluic acid, 4'-aminoacetophene, 3'-aminoacetophene, 1,4-di-
methoxybenzene, fluorenone, ether, 53 HCl solution, concentrated HCl, 103
NaHC0 3 solution, 503 K:iC0 3 solution, saturated NaCl solution, anhydrous
sodium sulfate
Glassware/eq uipment used in this technique:

In your drawer-Three reaction tubes (the test tubes with red volumetric
marks), test tube rack, two watch glasses, 10 mL filter flask, small rubber
bumper, Hirsch funnel with frit
Speciality items from the common shelf-Pasteur pipettes, pipette bulbs, small
filter paper (for Hirsch funnel), clamp, clamp holder, thick-walled vacuum
tubing, 2 mL vial ("shorty vial"), melting point capillary tubes, litmus paper
Mr. Benzene says: In this experiment you will be

using the REACTION TUBES located in your drawer.
Most volumes can be measured directly into the
reaction tube using the calibration marks on the
side of the tube as shown in Figure 5.10. Because of
this convenience, do not use a regular test tube!
2.0 ~
1.0
0.75
0.51
Figure 5.10. Reaction tube.
103
H NOTES
.......
Mr. Benzene says: It is extremely important that
you do not throw away any liquid extracts, both
aqueous and organic, or any solids isolated in
;c c.. this experiment until after the NMR spectra have
t'.JG been interpreted and the notebook pages have
~ been submitted for a grade. The biggest mistake
D you can make with this experiment is to throw
D away the wrong layer or any solids isolated in this
experiment. Keep everything until after you have
finalized all written analyses.
Procedure 1 : Microscale Separation of Basic, Acidic,

and Neutral Substances
A mixture of equal parts of an unknown carboxylic acid, an unknown amine, and
an unknown neutral compound is to be separated by the liquid/liquid extraction
technique. See Figure 5.10 for possible components. The carboxylic acid could
be benzoic acid or 3-toluic acid, the amine could be 4'-aminoacetophenone or
3'-aminoacetophenone, and the neutral compound could be 1,4-dimethoxy-
benzene, or ftuorenone. Carefully follow the detailed directions for component
extraction and isolation.
Mr. Benzene says: Ether is extremely flammable and

boils at a low temperature (your body temperature)!
Work in your hood!
Every hood will have its own bottle of ether located in the metal rack with the
acetone bottles. If the bottle is empty, full bottles of ether can be found at the
hooded shelves; tum in the empty bottle and pick up a full one. Keep the ether
in the hood and do the extraction in the hood. The amines are irritants. Wear
gloves when doing this experiment or wash your hands frequently, particularly
in the first step in which the amine is extracted.
104
Extraction ;; Chemistry 213W
, EXPERIMENTAL PROCEDURES
NOTES : :
Possible Carboxylic Acid components:
(i'oH
Benzoic acid 3-Toluic acid
m.p. 121-125-C m.p. 107-113 •c
Possible Amine components:
4'-Aminoacetophenone 3'-Aminoacetophenone
m.p. 103-107-C m.p. 94-98 •c
Possible Neutral components:
0
OR
do
1,4-Dimethoxybenzene Fluorenone
m.p. 54-56 oC m.p. 80-83 oC
Figure 5.11. Possible unknowns for acid/base extraction.
Procedure
Obtain an unknown from your TA and record its number in your lab notebook
immediately. In the event that the three unknowns may not be homoge-
neously mixed, you can use your microspatula to mix your solid unknown
before weighing out the amount required for extraction.
~'leigh out 300 mg of your 3-component unknown mixture. Dissolve the mix-
:ure in 2 mL of ether in a reaction tube, which should be labeled tube 1 (use a
• rax pencil). Sometimes the solid does not entirely dissolve even after mixing
with a stirring rod. If this situation occurs it is still suggested that you proceed
with the first extraction making sure the HCl solution comes in cont act with
rhe contents of the entire tube including any undissolved material.
105
Chem istry 213W ; : Chapter 5
II NOTES
1 A. Separation of the Basic Component (Amine) by
Extraction with Acid
1 Mix layers well

with pipette
2
2 Let layers separate
'·'
l
A)l_OH
0
A- NH2
R-H
- s% HCl(aq)
)
In ether
uo - {
3
4
Pipette Into tube 2
~~:;·· } - - - - - - -+
Extract with HCl(aq)
••
...co l 1.5 mL
..,. total
again
To tube 1, add 1.0 mL of 5% aqueous hydrochloric acid. Mix the two immis-
cible layers vigorously by drawing up as much liquid as possible into a Pasteur
pipette so that the pipette (but not the pipette bulb!) is completely filled and
then squirting it back into the reaction tube briskly. Do this between 15 and
20 times so that there is maximum mixing between the aqueous and organic
layers, thus allowing extractable material to move from one layer to the other.
Let the layers separate, draw off the lower layer using the pipette and place it
in the reaction tube labeled tube 2. Extract tube 1 with one 0.5 mL portion of
5 % H Cl, again using pipette mixing. After separation, draw off the lower water
layer and add it to tube 2. YOUR AMINE IS NOW IN TUBE 2. YOUR NEU-
TRAL COMPONENT AND CARBOXYLIC ACID STILL REMAIN IN TUBE 1.
1 B. Separation of the Acid Component (Carboxylic

Acid) by Extraction with Base
1 Mix layers
well with pipette
3
2 Let layers
separate
•.O
l 0
A)l_OH
A-
)
H
In ether
- j A- H f ln elher
3
4
Pipette into tube 3
Extract with
..."' ltSmL
O NaHC03 (aq) again
- R) lO_Na•(aq) ------~ "" total
106
A.dd 1 .0 mL of a saturated aqueous solution of sodium bicarbonate (approx. 10% NOTES II

~:aHC0 3) to tube 1. Pipette mix the layers thoroughly, allow the layers to
separate completely and then draw off the lower layer into the reaction tube
:abeled tube 3. Add 0.5 mL of sodium bicarbonate solution to tube 1, mix the
contents as before and add the lower layer to tube 3. YOUR CARBOXYLIC
ACID IS NOW IN TUBE 3. YOUR NEUTRAL COMPOUND REMAINS IN
TUBE1.
1 C. Isolation of the Neutral Component
1 Mix with pipette 2

2 Let layers separate ..•
3 Remove NaCl (aq) ..• 5 Seal with white septum;
3 .5 shake occasionally
4 Add Na2 S04 (anhyd)
for 5-10 min
3.0 Decant onto
tared watchglass
2.5
j R- H f 1n ether
2mltotal (
NaCl solution ether
To tube 1, add 1 mL of saturated NaCl solution, pipette mix, and remove the
aqueous layer. Put the lower aqueous layer in a beaker that you can then dis-
card later down the drain. If the volume of your ether layer has now dropped
below 1.5 mL, add enough et her to make the total volume about 2 mL. Now
add to this enough anhydrous sodium sulfate to fill the tube with solid up to
the 0.5 to 0.75 mL mark. DO NOT ADD TOO MUCH! Seal the tube with a
white septum from the common shelf and gently shake and vent every 10 to
20 seconds to avoid pressure buildup for about the first minute. Then let the
tube sit for a period of 5 to 10 min. This drying agent does not react with the
product, but only absorbs the water from the ether layer.
Mr. Benzene says: The white septa can be found on

the common shelf. Ask your TA to help you use the
septa correctly.
During the 10-minute drying time, you can work on steps D and E, then return to
dzis point.
107
Chemist ry 213W H Chapter 5
: : NOTES
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Mr. Benzene says: B~ careful not to get any drying
agent into the final ether solution. Otherwise the
salt will make a mess of things for you!
The neutral component is recovered by pipetting or decanting (carefully pour-

ing off) the ether solution from the solid drying agent onto a tared watch
glass. The drying agent in tube 1 is washed once or twice with additional small
amounts of ether to ensure complete transfer of the product; combine the
ether washes with the main ether extract on the watch glass . Do this carefully
so that no solid sodium sulfate is transferred onto the watch glass. The used so-
dium sulfate should be allowed to dry in the hood and discarded in the waste
bin. Set the watch glass in your locker and allow the ether to evaporate until
the next lab period.
......
Mr. Benzene says: Remember to record in your
notebook the tare of any glassware that will be
used to hold drying final products. The tare of a
container is its weight when empty. With the known
'c
..
, 8~ \
c ...
tare, the product can then be weighed without
~ removing it from the container (subtracting the tare
D gives only the weight of the compound within). This
D minimizes the loss of compounds that is inherent
when transferring products to and from weighing
paper.
After drying in your locker thoroughly until the following lab period,
determine the weight of the neutral compound. Determine the percent
recovery, prep your sample to take the melting point as instructed in
Procedure 2, and keep your neutral compound for 1 H NMR analysis.
108
1 D. Isolation of the Amine Component

NOTES II
1 Add 3 or 4 drops of
3 Vacuum filter
50% K2C03 (aq)
2 Seal with septum 4 Dry 2-5 days

I-.., and shake
R- NH3+ -
cr (aq)
- - - --
------~
uj Solid
R-NH 2
....
0.15
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c ...
D
Mr. Benzene says: Add base to precipitate the basic
component.
Make the contents of tube 2 basic by adding small amounts (3 or 4 drops)

of 50% potassium carbonate (aq). Mix with a glass stirring rod and test with
litmus paper for a slightly basic pH of 8 to 10 by dabbing the glass rod onto
the litmus paper. (Mix with a glass stirring rod thoroughly before testing the
litmus paper, since in the process of transferring a drop onto litmus paper,
you're really testing the pH of the top of the solution in the tube!) seal with a
white septum and shake for a minute. This will cause the amine to precipitate
out. Cool the tube in ice for a few minutes (5 to 10 minutes).
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...
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c,
D
Mr. Benzene says: Recheck the pH of your solution,
or else you may have to re-do the experiment!
Remove the solvent from the crystals using vacuum filtration. Since the amount
of crystals you will isolate is relatively small, utilize the small Hirsch funnel
and filter flask from your red kit.
The small Hirsch funnel is made of an inert plastic and is found in your red
kit. ~fake sure that your funnel has a frit in it. It's a hard whitish disk at the
very bottom of the funnel that snaps into place. If yours is dirty or is missing
109
:: NOTES the frit, a clean and new one is found on the common shelf. Pop the frit in
place. Next, a round piece of filter paper of a matching diameter is placed over
the frit. Keep the frit in the funnel until it gets really dirty; it can be re-used
many times! The very small filter papers are found on the common shelf. Tue
Hirsch funnel can now be put into a vacuum filter flask with a rubber adapter
in between to assure a vacuum-tight seal. The filter flask (also found in your
red kit) has a connecting tube, or "side arm," which is connected to the h ouse
vacuum using the THICK-WALLED tubing in your locker. Make sure you use a
clamp to secure the filtration apparatus to a ring stand so it doesn't fall over.
Wet the filter paper with a small amount of solvent to prohibit loss of product
under the filter paper. Once the vacuum is turned on, the wet filter paper is
sucked down on the plate so that it seals uniformly. The crystals and solution
are swirled or agitated and quickly poured onto the filter funnel. The vacuum
quickly draws the liquid (aka, the filtrate) through the filter paper disk, leav-
ing the crystals behind. Any crystals remaining behind in the test tube are
scraped out with a spatula and/ or washed out with some of the solution from
the filter flask or with a small amount of cold water.
~-Flat filter
paper
Rubber adapter
Thick-walled
tubing
Hirsch Funnel
Figure 5.12. Vacuum filtration apparatus using a Hirsch funnel. All parts are found in
your red microscale kit.
Once your crystals are on the filter paper, get tweezers out of your locker and
tare another watch glass. Take out the entire filter paper+ crystals (let the
frit alone!) and place it on the watch glass. Let your amine dry in your locker
before weighing it.
110
I EXPERIMENTAL PROCEDURES
After drying in your locker thoroughly until the next lab period, scrape NOTES ==
the dried crystals off of the filter paper and determine the weight of the
amine compound. Determine the percent recovery, prep your sample
to take the melting point as instructed in Procedure 2, and keep your
amine compound for 1 H NMR analysis.
1 E. Isolation of the Carboxylic Acid Component
•O
2 Vacuum filter
._. o 1 Add cone. HCI 0 2.5
z.o R) l o-Na•(aq) R) lOH ! 2.0
J ppct. in H2 0 ts
3 Dry 2-5 days
Jl Solid
L l .J)
075
R OH
050
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0
Mr. Benzene says: Add acid to precipitate the
acidic component.
By d~opwise addition of concentrated hydrochloric acid [not 5% HCl(aq)] ,

carry out the acidification. If you add the acid too quickly, the solution may
foam (carbon dioxide evolves during this neutralization!). Mix with a glass
stirring rod and test with litmus paper for an acidic pH of 4 or less by dabbing
the glass rod onto the litmus paper. (Mix with a glass stirring rod thoroughly
before testing the litmus paper, since in the process of transferring a drop
onto litmus paper, you're really testing the pH of the top of the solution in
the tube!) An excess of hydrochloric acid does no harm; you want your pH
paper to be red. This acidification must be carried out slowly because much
carbon dioxide bubbles off in the process. This step is where a lot of students
lose their carboxylic acid because the solution isn't mixed properly with a glass
stir rod during the acidification process and the carboxylic acid never crashes
out because the pH reading is not accurate.
111
H NOTES
Mr. Benzene says: Make sure you mix the solution

and after a few minutes mix it again and re-pH
test it to make sure that it's STILL acidic. If it's not
acidic then add more HCI.
Cool the tube in ice and remove the liquid by the Hirsch filtration method
(described previously) and discard the liquid. Dry the crystals by spreading
them out on a tared watch glass or other appropriate piece of glassware (like
in a small beaker) in your locker for a few days.
After drying in your locker thoroughly until the next lab period,
determine the weight of the carboxylic acid compound. Determine
the percent recovery, prep your sample to take the melting point as
instructed in Procedure 2, and keep your carboxylic acid compound
for 1 H NMR analysis.
Procedure 2: Melting Point Determinations and

NMR Analysis
In this experiment, you will determine the melting temperature ranges of all
three of your extraction components you separated in Procedure 1. You will
need to use the melting point capillary tubes (found in your locker and on the
common shelf) and one of the "Mel-Temp" electrically heated melting point
units found in the other "common shelf" areas near your lab section.
Mr. Benzene says: It is of utmost importance that

your samples be thoroughly dry and free from all
traces of solvent before trying to determine the
melting point.
Assuming your crystals are dry, proceed as follows: Remove a few mg of your
sample and place it on a watch glass. If it is lumpy, grind it into a fine powder
using the fiat end of a spatula. Push the crystals into a small pile and then
push the open end of a melting point capillary tube into the crystals such that
some solid is forced into the opening of the tube. The sample is then shaken
down into the closed end of the capillary either by: 1) wrapping the capillary
tube with a paper towel and tapping sharply onto a hard surface, or 2) drop-
ping it down a 2- to 3-foot length of 5- 10 mm I.D. tube onto a hard surface.
112
(There are a few of these tubes on the side shelves.) If necessary, push more NOTES H
crystals into the open end and pack it down into the closed end so that you
have no more than a 1 cm column of solid at the bottom of the melting point
capillary tube. Repeat this process for all of your samples you wish to take a
melting point of. Make sure you mark the MP capillaries so you don't get them
confused! You can use the white labels found on the common shelf to make
"flags" on the capillaries.
When a melting point apparatus is available, check that it has cooled to below
40°C. If the temperature is more than 40°C as read on the thermometer, wait
for it to cool below 40°C. Then you can insert three samples into the slots
located behind the guard on the Mel-Temp. Turn on the LabQuest unit to
observe the temperature. Turn the dial on the Mel-Temp unit to a reasonable
heating rate. You may need to adjust the heating rate control dial so that the
temperature does not rise too rapidly.
Record the temperature in your notebook when the first drop of liquid forms
and the temperature when all of the solid turns liquid; this will be your melt-
ing point range.
It is best to heat the samples slowly, no faster than 1°C per min. However, it is
possible to get reasonable melting points while heating at 2 to 3°C per minute,
which will expedite the use of the few mp units in the lab. Watch the samples.
When you start to see any one of them start to melt, record the starting tem-
perature. When the solid in a particular tube has completely melted, record
this ending temperature also (87-88°C, for example). Once your samples have
melted, you should have recorded melting ranges for each. Turn the heating
rate control dial to the blue fan setting so the unit can begin to cool down.
Mr. Benzene says: Melting points can be depressed

but can they be elevated? I wonder why THAT'S
important. ..
Spectral Analysis
Once you have separated and dried the unknown components, you are re-
quired to collect and interpret a 1 H NMR spectrum of two components. You
will choose two components for spectral analysis. It is suggested that you
examine your neutral component because it is the most likely candidate for
cross contamination; the contaminants, if any, are usually residual acid or base
components that were not completely extracted from the starting unknown.
113
II NOTES You will also want to analyze any component with a broad melting point range
because that is indicative of contamination by one or more of the unknowns.
You can take an NMR of all three components if you want to! Remember that
NMR doesn't lie: your melting points may be misleading so it's always best t o
prove structure with spectra!
To prep your NMR sample, follow the NMR prep instructions in Chapter 2. If
you don't have 35 mg, make your NMR sample with the amount that you have.
Mr. Benzene says: Remember to use the

DEUTERATED chloroform in the brown bottle and
NOT dichloromethane! Otherwise your NMR will
look pretty bad...
Make sure that there is a minimum of 2 inches of solvent in your tube

but no more than 3 inches. Now fill out an NMR tube label found on the
common shelf and punch your tube through t he label. Do not use tape. The
tape will gunk up your NMR tube and potentially mess up the instrument.
The melting point data you obtain for your unknowns should clue you in as
to the identity of the components. NMR spectroscopy will be used to confirm
the proposed identity. Therefore, you should anticipate the peaks you would
see in the spectrum. However, what if you see additional signals? Perhaps the
separation wasn't exactly perfect, and small amounts of the other components
remain with the neutral component (this would be likely if the melting point
data is depressed). No need to fret! Use the situation to your advantage. If
small amounts of the other components remain in the neutral sample, then
you can interpret these additional signals to confirm the identities of those
components. Take a look at the possible acidic, basic, and neutral components'
structures. There should be key signals that would differentiate the two possible
components from each other. Use the correlation charts in your notebook to
help with the interpretation of signals and annotate the signals (see Chapter 3
for an example annotation). Also view the example NMR spectra on the fol-
lowing page and compare your NMR to these standards to help you make an
identification:
114
NOTES II
-•
Amine Unknown 1 H NM Rs
Carboxylic Acid Unknown 1 H NMRs
~eutral Unknown 1 H NMRs
Data You Need

TMR data on TWO of the THREE components
.viP data on ALL THREE components
% recovery calculations for ALL THREE components
115
Chem istry 213W II Chapter 5
H NOTES NOTEBOOK PAGES REPORT
Your Notebook Pages Report should include:
I. Experiment Info
For Procedure 1, include the unknown number under the boxes at the top of
the page.
II. Purpose
On a separate notebook page (stapled first when you put your report together),
write a brief statement explaining the goal of the experiment, noting the
kinds of techniques and analyses used. Make sure your purpose conveys an
understanding of why this technique and/ or reaction are of value to organic
chemists. Always write the purpose AFTER you complete the experiment so
you have a better understanding of what you did and why!
Ill. Procedure, Data, and Observations

Include subsections in this section for each procedure; use subheadings, e.g.,
Procedure 1: Separation of Basic, Acidic, and Neutral Substances. Remember,
this section should be written in bullet form. It should be written as you
complete the steps of each procedure, making sure to include pertinent data
and observations (as the steps are performed). Nothing may be added to this
section after you leave the lab and your TA has signed the pages.
IV. Calculations
Be sure to include the following:
Calculate the 3 recovery of each component in your unknown mixture. As-
sume that each component is one-third of your total mixture's weight. That
is, if you weighed out 300 mg of the unknown mixture, assume that 100 mg
is the acidic component, 100 mg is the basic component, and 100 mg is the
neutral component. Be sure to include your unknown number.
V. Discussion and Conclusions

a. State your unknown number. Briefly describe the acid/base chemistry
involved in separating your three-component unknown.
b. Discuss each component separately (acid, base, neutral) : identity by
melting point, confirmation by NMR, 3 recovery, and explanations of
low/high recoveries. (Remember, you only need to have two NMRs but
if you can' t ID all three of your components definitively then NMR of
all three may be necessary!) If melting points are depressed, discuss
why. For NMR discussions make sure that you talk about chemical
shifts of the peaks, integration values, and splitting patterns that
116
NOTES ::
NOTEBOOK PAGES REPORT
led you to identify your product. Also discuss impurities seen in your
spectra (water, other components). Make sure you don't just justify
your data but prove WHY it's not the other choice. For 3 recovery, if
it's low, where did the rest of your material go? If it's high, why?
c. Conclusions: Summary of data, sources of error, improvements.
VI. Spectral Data

~fake sure that your NMR data is properly annotated and labeled as figures to
refer to in your discussion. For proper annotation, please refer to Chapter 3.
VI I. References
Please view the references formatting section of Chapter 3 to make sure you
do this properly (ACS style).
Submitting Your Notebook Pages Report for Chapter 5

1. Rip out the white, original Notebook Pages and attach your NMR spectra.
2. Download and attach the Chapter 5 grade sheet to the front of your as-
signments.
3. Hand in to your TA on the due date.
117
Chemistry 213W H C hapter S
H NOTES
~ l\ JD 6
rm : CHAPTER
~~~~~~~~~~~~~~~~~~~~~~~~~~
Thin-Layer Chromatography
'c
,.
......
~
t'.>G I
c ....
D
Mr. Benzene says: In this experiment you'll be
using TLC plates. To get the most out of the plates,
cutting them in half is ideal. Not all plates will be
used in this experiment; some will be needed in the
application lab, column chromatography lab, and
for your synthetic experiments.
D
Cut TLC plates in half
()Hayden-Mc1'cil, U.C
Prelab Assignment
Your Prelab Assignment (worksheet on ANG EL) must be completed before coming
to lab. You cannot start any experimental work until your TA collects your Prelab
Assignment at the beginning of the class period. You will also be assessed a 103
points penalty if you do not have it complete. There are no exceptions to this rule!
Before beginning the Prelab, read through the entire chapter. Pay close attention
to the introductory material AND the main activities of this experiment:
1. Determine a correct mobile phase to separate analgesics using TLC

2. Identify the analgesic active ingredient(s) in an over-the-counter medicine
Quiz for Chapter 6

Quiz 2 will test your preparedness for the activities in Chapter 6 and for the safety
considerations for this experiment. The quiz will also test your understanding of
119
the theory behind the experiment, and you may be asked to label equipment used
== NOTES
in the procedures. The quiz is worth 25 points.
Perhaps the best way to prepare for the quiz is to outline all of the main experi-
mental procedures of the main activities in the chapter's experiment. It will also
be beneficial to know the chemicals involved with the experiment; that is, their
safety considerations (flammability, toxicity, and other comments) and their waste
disposal, which is determined when you prepare the Chemical Data Table for the
Prelab. The Introduction section of the chapter will contain all pertinent theory
for the experiment.
Activity Breakdown
Day 1: Procedures 1, 2
Introduction
In the previous chapter, we saw how Extraction can be used to workup a reac-
tion and isolate a product from a reaction mixture. But, how exactly do we know
WHEN to quench the reaction? There is a way to monitor the progress of an or-
ganic reaction so we can see exactly what's in the reaction mixture: Thin-Layer
Chromatography (TLC).
Chromatography is the separation of two or more compounds or ions by the distri-

bution between two phases, one which is moving and the other which is station-
ary. These two phases can be solid- liquid, liquid-liquid, gas-solid, or gas-liquid.
Although there are many different variations of chromat ography, the principles
are essentially the same.
TLC is a solid-liquid form of chromatography where the stationary phase is

normally a polar solid adsorbent and the mobile phase can be a single solvent or
combination of solvents. TLC is a quick, inexpensive microscale technique that
can be used to:
determine the number of components in a mixture

verify a substance's identity
monitor the progress of a reaction
determine appropriate condition s for column chromatography
analyze the fractions obtained from column chromatography
You may have had a previous experience with chromatography in Chem 113. In
paper chromatography, the stationary phase is a specially manufactured porous
paper. The samples are added to one end of the sheet of paper and one edge is
dipped into the liquid or mobile phase. The solvent is drawn through the paper
120
Thin-Layer Chromatography :; Chemistry 213W
Er.- capillary action, and the molecules are distributed by partition between the NOTES ;:
mobile and stationary phases. The partition coefficient, k, similar to the distribu-
n.on coefficient for liquid/liquid extraction, is the equilibrium constant for the
distribution of molecules between the mobile phase and the stationary phase.
:t is this equilibrium that separates the components. Different inks and dyes,
depending on their molecular structures and interactions with the paper and
:nobile phase, will adhere t o the paper more or less than the other compounds
allowing an effective separation.
:-LC works on the same principles. In thin-layer chromatography, the station-

ary phase is a polar adsorbent, usually finely ground alumina [Al2 0 3]x or silica
:si02]x particles. This absorbent is coated on a glass slide or plastic sheet creating
a thin layer of the particular stationary phase. Almost all mixtures of solvents can
be used as the mobile phase, except for water and methanol, which can p artially
dissolve the stationary phases. By manipulating the mobile phase, organic com-
pounds can be separated.
Theory
To thoroughly understand the process of TLC, as well as all types of chromatog-
raphy, we must consider it at the molecular level. All forms of chromatography
involve a dynamic and rapid equilibrium of m olecules between the two phases. As
shown in Figure 6.1, there are two states:
1. free-completely dissolved in the liquid or gaseous mobile phase.

2. adsorbed-stuck on the surface of the solid stationary phase.
A
free (
B
liquid or gas
mobile phase
Figure 6.1. Mixture of A and B free in mobile phase and adsorbed on the stationary phase.
Molecules are continuously moving back and forth between the free and adsorbed
states with millions of molecules adsorbing and millions of other molecules desorb-
ing each second. The equilibrium between the free and adsorbed states depends on
three factors:
the polarity of the molecule's groups and the size of the molecule
the polarity of the stationary phase
the polarity of the solvent
121
Chemistry 213W II Chapte r 6
Thus, there are three different variables to consider when trying to separate
II NOTES
compounds using chromatography. The polarity of the molecules is determined
by their structures, so by selecting different stationary and mobile phases, one
can change the equilibrium between the free and adsorbed states to separate just
about any mixture of molecules.
Different molecules partition differently between the free and adsorbed state. In
Figure 6.2, molecule A is weakly adsorbed; its equilibrium lies in the direction of
the free state and there is a higher concentration in the mobile phase. Molecule B,
on the other hand, is strongly adsorbed; its equilibrium lies in the direction of the
adsorbed state, and has a higher concentration on the stationary phase.
Liquidorgas ~~~B'-----.il.A ~B ........__

containing ~ :/1 ,)/ -------. Mobile
phase
mixtureof _____... B A /'~ ell' ~ flow
A and B ~
--==--~ A ~
~A-----
/'A
~ AB~
~B
Figure 6.2. Dynamic equilibrium between A and B and the mobile and stationary phase.
For separation to happen, the mobile phase must flow past the stationary phase
as depicted in Figure 6.2. Since molecules A spend more time in the mobile phase,
they will be carried through the stationary phase faster and move farther in a
given amount of time. Since B is adsorbed to the stationary phase more than A,
B molecules spend less time in the mobile phase and therefore move through
the stationary phase more slowly. The B molecules don't move as far in the same
amount of time.
The consequences of this flowing mobile phase is that A is gradually separated from
B by moving ahead in the flow. This separation process is depicted in Figure 6.3.
122
Thin-Layer Chromatography :I Chemistry 213W
II
A NOTES
lV\_
B
Mobile B B
phase B
::+ Be
B
B
AA
A A
Figure 6 .3. Mixture of A and B separated over time by a moving mobile phase while
being adsorbed on the stationary phase.
'.'.7hat does this look like on an actual TLC plate? Molecules A and B will actually
appear as "spots" on the plate and are able to be visualized using various methods:
Remove from
TLC chamber,
"
J
~
D
evaporat_e so~vent, - ~
then visualize ;::
spots. F;
The Stationary Phase

In nc, the stationary ph ase is typically alumina CA1203•XH20)n or silica gel
S102 •xH20)n. The covalent network of these adsorbents creates very polar ma-
terials. The structure of silica is shown on the next page.
123
H NOTES
Silica
Silica
surface
hydrated
Figure 6.4. Structure of silica (Si0 2 • xH 20 )n.
The electropositive character of the aluminum or silicon and the electronegative

oxygen create a very polar stationary phase. Therefore, the more polar molecules
to be separated will have a stronger attraction to the stationary phase. Nonpolar
groups of molecules will have a lower affinity for the stationary phase and will travel
more with the moving solvent. This is essentially how the partitioning separates
the molecules. The equilibrium governs the separation, but each component's at-
traction to the stationary phase determines the equilibrium. In general, the more
polar the component, the stronger the interaction with the stationary phase and
the more slowly the molecule will move up the plate. In an extreme situation, the
molecules will not move at all. This problem can be overcome by increasing the
polarity of the mobile phase so that the equilibrium between the free and adsorbed
state is shifted toward the free.
The ability of a molecule to hydrogen-bond with a polar stationary phase is one

of the most important factors in determining its equilibrium. Figure 6.5 shows
how butylamine interacts with silica gel. Note the charge separation that exists
between the C-N bond (as indicated by the partial positive and partial negative),
and how these charges are attracted to charges of the Si-0 bond of the silica gel
stationary phase. The 8+Si is attracted to the 8- N, and the 8+C is attracted to
the 8- 0. Also, the hydrogen of the N- H bond can hydrogen-bond to an oxygen of
silica gel (indicated by dashed lines). A molecule like pentane (C5 H12) is not polar
(no significant charge separation between bonds) and will therefore not interact
as strongly with the silica.
Figure 6.5. Interaction of butyl amine w ith sil ica gel; dashed lines indicate the attractive forces .
124
Thin-Layer Chromatography H Chemistry 21 3W
Although alumina and silica are the most common stationary phases used for NOTES ::
71.C, there are many different types. They range from paper to charcoal, nonpolar
:o polar, and reverse phase to normal phase. Several different types of stationary
phases are listed according to polarity in Figure 6.6.
Chromatography Stationary Phase Polarities

Reverse Phase (hydrocarbon-coated silica, e.g., C-18)
Paper
~
·~ Cellulose
0
a.
Starch
Cl
c
Calcium sulfate
.Ci)
co Silica (silica gel)
(!? Florisil (magnesium silicate)
0
c:
Magnesium oxide
Alumina (aluminum oxide; acidic, basic, or neutral)
Activated carbon (charcoal; Norit pellets)
Figure 6.6. Common stationary phases listed by increasing polarity.
Determining Molecule Polarity

Now that we understand how the stationary phase operates, and assuming we
are using a polar absorbent, how can we determine the elution sequence for our
particular mixture? The elution order is determined by the relative polarity of each
molecule, and the overall polarity of a molecule depends on five factors where the
higher rules tend to have a larger effect than the lower rules:
1 Ability to hydrogen bond

Ratio of electronegative atoms to carbon/hydrogens
3. Polarizability of the atoms
~- Dipole moment
5 Overall size of the molecule
.?rom these we can make a list that roughly ranks the elution order for common
functional groups from silica or alumina.
Alkanes will travel the farthest up the plate because they are the least polar. They
cannot hydrogen bond, have no electronegative atoms or much polarizability, and
• e ::iet dipole moment is small.
Alke:n.es are similar to alkanes except the large p-orbitals give some polarizabil-
=aking them a little more polar than alkanes. More conjugated alkenes and
~:::::i.atic compounds have more p orbitals, and therefore will have higher polarity
tt.;c.::. :ess conjugated compounds .
125
Ethers and Alkyl Halides are more polar than alkanes and alkenes because of
II NOTES
the introduction of a polar atom.
Aldehydes, Ketones, and Esters have a large dipole moment due to the carbonyl
They are considered hydrogen-bond acceptors. Along with the electronegative
oxygens, this makes them more polar than an ether or alkyl halide.
Amines and Alcohols have the ability to hydrogen bond, the most important
factor. When other factors are similar, an alcohol is usually more polar than an
amine because an oxygen atom is more electronegative than a nitrogen atom.
Carboxylic Acids and Amides are the most polar functional group because they
can hydrogen bond extensively, and they have a dipole moment and two electro-
negative atoms. Carboxylic acids tend to be a little more polar than amides, again
because oxygen atoms are more electronegative than nitrogen atoms.
It is important to understand the factors governing polarity so that you will not
have to memorize the order of elution. You should be able to easily recognize the
functional groups of a molecule (even less common ones not ranked above) and
quickly determine which one is more polar than another. However, it should be
noted that chromatography predictions are not an exact science. These factors
should only be used to help predict the order of elution, but only performing the
experiment will give the answer.
In general, the more polar functional groups in a molecule, the more at-
tracted that molecule will be to the stationary phase; this results in the
molecule moving slowly on the TLC plate.
Mobile Phase Polarity

As mentioned earlier, the mobile phase polarity can also be varied to affect the
chromatographic separation. Figure 6.7 lists some common mobile phases accord-
ing to increasing polarity.
126
- - -- - - - -
Thin-Layer Chromatography H Chemistry 213W
NOTES I;
Chromatography Mobile Phase Polarities
Less Polar
Petroleum ether (pentanes)
Hexanes
Cyclohexane
Carbon tetrachloride•
Toluene
Chloroform·
Dichloromethane (methylene chloride)
t-Butyl methyl ether
Diethyl ether
Ethyl acetate
Acetone
2-Propanol
Pyridine
Ethanol
Methanol
Water
Acetic acid
More Polar
•suspected carcinogens.
Figure 6.7. Common mobile phases listed by increasing polarity.
Finding a good solvent system is usually the most difficult part of TLC. If the mobile
phase has not been previously determined, start with a nonpolar solvent such as
hexanes and observe the separation. If the mixture's components do not move
very far, try adding a polar solvent such as ether or ethyl acetate to the hexanes.
Compare the separation to the previous plate. In most cases, a combination of two
solvents is the best solution. If the spots stay at the bottom of the plate, add more
of the polar solvent. If they run with the solvent front (go to the top too fast) then
add a more nonpolar solvent. Unfortunately, rules are not foolproof and some trial
and error is involved in determining the best solvent system.
On the molecular level, why do polar solvents move both the polar AND non-polar
compounds up a TLC plate faster? Remember that molecules exist in an equilib-
rium between the free and adsorbed state on a TLC plate. Polar molecules spend
more time in the adsorbed state whereas non-polar molecules spend more time in
the free state. A polar solvent floods the TLC plate with polar solvent molecules.
Therefore, the compounds one is analyzing spend less time on the polar station-
ary (adsorbed) phase because they are out-competed by the polar solvent. Thus,
they travel farther!
127
II NOTES
Mr. Benzene says: Be aware that a polar mobile
phase will make both polar and nonpolar spots
travel quickly (assuming a polar stationary phase is
used).
Steps for Running TLC
1. Spotting the TLC Plate

One advantage that TLC has over other separation methods is it is truly a rnicroscale
technique. One needs to dissolve only a few milligrams of material in a few mil-
liliters of a volatile solvent (-0.1 % solution) and then spot a tiny fraction of this
onto a TLC plate since one can detect a few micrograms of the solute on a TLC
plate. Choose a volatile solvent that completely dissolves the sample. However,
even if it is partially soluble, you will normally be able to observe the compound
since only low concentrations are needed.
'c.....
,,. tiG I
~
c..,
0
Mr. Benzene says: Bigger isn't ALWAYS better. In
TLC, smaller spots are the best!
Once the sample is prepared, a spotting capillary must be used to add the sample
to the plate. The spotting capillaries must be extremely small. In fact, the opening
at the end of a regular Pasteur pipette is too big for spotting a TLC plate. Your TLC
spotting capillaries can be found in a baggie in your locker. Both ends are open
and they have a very small internal diameter. Make sure you don't get these tubes
confused with the melting point capillaries. The solution can be drawn up the tube
by capillary action (hence the name) and spotted on the plate at the origin mark
drawn in pencil as shown in Figure 6.8. Since a TLC plate can run three, if not
four mixtures at one time, it is very important to properly label the plate. Notice
that pencil is always used to mark a TLC plate since the graphite carbon is inert
to the mobile phase solvents. If organic ink is used to mark the plate, it will chro-
matograph just as any other organic compound and interfere with your results.
128
Thin-Layer Chromatography 11 Chemistry 213W
A B C - Lanes (properly marked) NOTES ==
- TLC Plate (coating side up)
Level of Solvent ~
Figure 6.8. TLC plate marked and ready to be spotted with three samples.
Mr. Benzene says: When in doubt, pencils out! If

you use a pen, you won't again!
7o spot the plate, briefly and lightly touch the end of the capillary tube to the silica
side of the plate. The solvent should evaporate quickly leaving your mixture behind
on the plate. You may have to spot the plate a couple of times to ensure sufficient
material is present, but do not spot too much sample as this will lead to a poor
separation. Overloading leads to smearing, smudging, and spots that overlap,
:::iaking identification of separated components difficult.
Some compounds may h ave very similar Rf values, and their spots may look
identical. One way to determine whether the spots with similar Rf values are of
the same compound or are of two different compounds is to do a co-spot. To do
a. co-spot, do the following (assuming your sample is dissolved in a solvent): (1)
on the origin line, spot the first compound and let the solvent dry; (2) spot the
second compound on top of the first compound and allow the solvent to dry; (3)
de-7elop the plate in the TLC jar/chamber; (4) visualize the spots. If Rf values are
sril.. too close to make a call, change your solvent system! Then repeat steps 1-4.
.: rwo spots show up from the co-spot, then the spots are two different com-
pounds. If only one spot shows up, then the first and second spots are of the same
cnmpound.
129
: : NOTES 2. Development
Once the dilute solution of the mixture has been spotted on the plate, the next
step is the development. Just like paper chromatography, the solvent must be in
contact with the stationary phase. Figure 6.9 shows a wide-mouth bottle commonly
used to develop TLC plates.
CHayden-).fcNeil. lLC
Figure 6.9. Placing a TLC plate into development jar.
The bottle is filled with a small amount of the mobile phase and capped. Remember
to keep the solvent level below the origin line on the TLC plate. In addition, a piece
of filter paper is put in the bottle to help create an atmosphere saturated with sol-
vent. Use your tweezers to place the plate in the development chamber; oils from
your fingers can sometimes smear or ruin a TLC plate. Also, make sure the origin
spots are not below the solvent level in the chamber. If the spots are submerged
in the solvent, they are washed off the plate and lost. Once the solvent has run
within a centimeter of the top of the plate, remove it with tweezers. Using a pen-
cil, immediately draw a line across the plate where the solvent front can be seen.
The proper location of this solvent front line will be important for Rf calculations.
Mr. Benzene says: Remember to cap your TLC

chamber! Otherwise your solvent will evaporate
off of your plate faster than it runs up your plate!
3. Visualization
If you are fortunate enough to be separating organic molecules that are colored such
as dyes, inks, or indicators, then visualizing the separated spots is easy. However,
since most organic compounds are colorless, this method does not often work. In
most cases observing the separated spots by UV light works well. TLC adsorbents
are often doped with a fluorescent indicator, which makes the TLC plate glow green
under UV light of wavelength 254 nm. Compounds that absorb UV light at this
130
Th in-Layer Chromatography II Chemistry 213W
;a'":"elength will quench the green fluorescence yielding dark purple or bluish spots NOTES II
c= the plate. Simply put the plate under a UV lamp, and the compounds become
Vl.Sihle to the naked eye. Lightly circle the spots with a pencil, so that you will have
a permanent record of their location for later calculations.
Figure 6.10. UV lamp used to visualize spots.
Another useful visualizing technique is an iodine (I 2) chamber. Iodine sublimes and

· rill absorb to organic molecules in the vapor phase. The organic spots on the plate
will turn brown and can be easily identified. Circle these observed spots since the
:rrown color will eventually fade from the plate. Sometimes, a combination of both
a. UV lamp and iodine is needed to observe all the spots. Many compounds such
as alkanes, alcohols, and ethers, are not "UV active," that is, they do not absorb
..:ght at the wavelength of 254 nm. Using both methods will ensure location of all
:.."le spots on the TLC plate.
Another way to visualize organic compounds is by using a variety of TLC stains.

:.n general, a TLC plate is dipped into a stain solution, allowed to dry, and then
~e TLC plate is heated until the compound spots show up as a different color
25ciinst the stain background. Typically these stains are actually mini-reactions on
me TLC plate where specific functional groups react with the stain components.
Fer example, a Ninhydrin stain is particularly good for detecting amino acids and
a-i•ne-containing compounds whereas potassium permanganate stain is good for
ee~g compounds that have functional groups that can be readily oxidized.
4. R, Values
Ir. addition to qualitative results, TLC can also provide a chromatographic mea-
sm-ement known as an Rf value. The Rf value is the "retardation factor" or the
ra::io-ro-front" value expressed as a decimal fraction.
::=e R: value can be calculated as:

distance spot travels from origin
R, - ~~~~~~~~~~~~~
- distance solvent travels from origin
131
: : NOTES Note: Rf is unitless and will always be <l.
Figure 6.11 shows a diagram of a typical TLC plate and how the distances are
measured to calculate the Rf value.
x y z
--+----·
. - - Solvent front
R1 =~ for substance X
D
D R1 = _.§.. for substance Y

D
R1 = ~ for substance Z
D
.--Origin
Figure 6.11. Calculation of R, values for three compounds.
This number essentially describes the distance t raveled by the individual com-
ponents. If two spots travel the same distance or have the same Rf value then it
might be concluded that the two components are t he same molecule. For Rf value
comparisons to be valid, however, TLC plates must be run under the same exact
conditions. These conditions include the stationary phase, mobile ph ase, and tem-
perature. Just as many organic molecules have the same melting point and color,
many can have the same Rf value, so identical Rf values doesn't necessarily mean
identical compounds. Additional information, such as Rf values measured using a
different stationary and mobile phase must be obtained before this conclusion can
be made. It is important to restate that this number is only signifiant when the same
chromatographic conditions are used. This is why including the standards on the
same TLC plate as the sample being analyzed gives the most reliable information
132
Th in-Layer Chromatography 11 Chemistry 213W
Table 6.1. Terminology of thin-layer chromatography, TLC technical terms. NOTES II

Scientific Term Definition Example
aspirin, ibuprofen, caffeine,
Mixture Any number of substances.
fl.uorene/ fluorenone
A fixed material that
Stationary alumina, silica gel,
adsorbs (attracts)
Phase paper
substances.
A moving phase that
h exanes, CH 2 Cl2,
Mobile Phase carries the substances
ethyl acetate
along.
The strength of attraction
London, H-bonding,
Adsorption between the substances
dipole-dipole
and the stationary phase.
A measurement of the
Separation speed of movement of a Rf(TLC)
substance.
A Case Study of TLC: Our SN2 Reaction

Let's return to our example reaction and determine the order of elution of the
three compounds involved in the reaction using polarity arguments, their order
on a TLC plate, and how to calculate their Rf values.
OMe
+Br~
2 3
Compound 1 contains an aldehyde, phenol, and nitro functional group on an
aromatic ring. Compound 2 contains a bromine and ether functional group also
on an aromatic ring. The product 3 contains an aldehyde, nitro, and two ether
functional groups spread over two aromatic rings. To compare the polarities of
these molecules, use the rules outlined earlier in this chapter. Based purely on
the number of electronegative atoms/ functional groups, 2 is the LEAST polar out
of the three molecules. Let's now compare 1 and 3. Compound 1 has three polar
functional groups AND has hydrogen-bonding capabilities. However, compound
3 has four polar functional groups AND is larger overall compared to compound
1. It can be concluded that 3 will be retained more strongly on a polar stationary
phase and move a smaller distance compared to 2.
133
Therefore, the overall order of the compounds by INCREASING Rf value would be:
:I NOTES
3 < 1 < 2. A TLC plate comparing their relative positions would look like the following:
"E c
Q)
>
·-
C\I
u
0 ..
"'~
0 c:
- ro
~ ]!
• .~
lO
=
Q) -
'O
.~ .....
...: .~4·
"'
ro c:
o ~
lO
cc .:: c:i
1 2 3
Figure 6.12. TLC plate of SN2 reaction.
Remember that the Rf value is the distance the spot travelled divided by the dis-
tance from the baseline to the solvent front. The Rf values would be as follows:
Compound 1: 1 inch/2 inches= 0.5

Compound 2: 1.75 inches/2 inches= 0.88
Compound 3: 0.5 inches/2 inches = 0.25
Predicting the relative positions of compounds involved in a reaction on a TLC

plate is very important for monitoring the progress of the reaction of interest,
and we will revisit this in Chapter 7, Application of Thin-Layer Chromatography
and Extraction.
In this chapter, you will learn how to properly perform TLC using a variety of an-
algesic compounds. Your newly found skills will be utilized to identify the active
components of an over-the-counter analgesic tablet by comparing Rf values after
you run a few TLC plates.
134
Thin-Layer Chromatography II Chemistry 213W
TLC Separation of Analgesics NOTES H

Analgesics are substances that relieve pain. The most common of these is aspi-
rin, a component of more than 100 nonprescription drugs. In this experiment,
analgesic tablets will be analyzed by thin-layer chromatography to determine
which analgesics they contain.
acetylsalicylic acid 4-acetamidophenol

(Aspirin) (Acetaminophen)
O CH3
H3c,N)(_N
;__ __ jl J
0 N N
I
CH3
2-(4-isobutylphenyl) propanoic acid 1,3,7-trimethylxanthine

(Ibuprofen) (Caffeine)
Figure 6.13. Some common ingredients in commercially available painkillers.
To identify an unknown by TLC, the usual strategy is to find a stationary

phase/mobile phase combination that will separate all the compounds in a
mixture. In this experiment, you will not vary the stationary phase (silica gel),
but you will vary the polarity of the mobile phase by using differing ratios of
the solvents hexane (nonpolar) and ethyl acetate (polar) to develop TLC plates
spotted with standard solutions of all four compounds. Once you and your
lab mates determine the optimal mobile phase that g~ves the best separation
of these, you will use this composition to run TLC of an unknown painkiller
tablet versus the known standards. If the unknown has one or more spots
that correspond to spots with the same Rf values as the standards, then those
substances are probably present in the tablet.

Aspirin, acetaminophen, ibuprofen, caffeine, ethyl acetate, hexanes, acetic acid
Glassware/equipment used in this technique:

In your drawer - TLC jars, TLC plates
Speciality items from the common shelf - TLC capillary spotting tubes
135
-------~ -
== NOTES
Procedure 1: Choosing a TLC Mobile Phase
You will work in a group with three other students. Each of you will be given
two different hexane/ ethyl acetate compositions to test depending on the as-
signment of solvents systems by your TA. You'll work together to fill in the Rf
values in the table below. Copy this table into your notebook.
Mobile Phase
Mixture % Ethyl % Rf R, R, R,
Composition Acetate Hexanes Acetam'n Aspirin Caffeine Ibuprofen
Number
1 100 0 I
2 90 10
3 80 20
4 70 30
s so so
6 30 70
7 20 80 I
8 10 90
I
Label the lids of your two TLC jars with the mixture composition numbers
assigned to you by your TA. Use a 10 mL graduated cylinder to prepare S mL
of each of the two compositions assigned. Working in the hood, pour each S
mL mixture into the corresponding wide-mouth jar. Also add 1 DROP ofacetic
acid to your TLC solvent mixture: this will help with streaking that could potentially
occur. Swirl to mix. Insert a piece of filter paper into each jar so that it wraps
around the inside wall of the jar and dips into the liquid. This creates a satu-
rated vapor atmosphere that improves spot shape and reproducibility. Students
typically find that the TLC plate often falls over inside of the jar so to prevent
this, one of two things can be done. The first is getting the smallest circular
filter paper from the common shelf that fits perfectly on the bottom of the
TLC jar, creating an even surface to place your TLC plate on at the bottom of
the jar. The second is getting a boiling stick from the common shelf. Cutting
it in half and placing the halves inside the TLC jar in an "X" fashion creates a
support system to lean your plate up against. When done, cap both jars.
Using a lead pencil (not a pen) and a ruler, mark two plates as shown below.
First, draw a light pencil line across the plate about 1 cm from the bottom of
two TLC plates. It is easy to scratch the solid phase off the surface of the plate
so be careful when making the pencil line. Make four equally spaced vertical
136
dashes on this line. The dashes should be about 5 mm from the edge and 5 NOTES ==
mm apart. Then label the lanes at the top of the plate.
Ac As C I
Acetaminophen
spot
Aspirin spot
Caffeine spot
Ibuprofen spot
Depth of __
solvent
Figure 6.14. An example of a properly spotted TLC plate.
In a shorty vial, obtain a small amount of dichloromethane from the common

shelf. Using a TLC spotting capillary tube from your desk, practice spotting on
one of your TLC plates, using pure dichloromethane. After filling the capillary
by dipping it in the liquid, touch it quickly to the TLC plate so that the spot is no
larger than 1 to 2 mm diameter. The smaller the spot, the better the final TLC
analysis. After the solvent evaporates, you can apply more material in the same
spot by, again, quickly touching the capillary to the surface at the same place.
Now each person in your group of four should obtain just a few drops of one of
the 13 or 23 solutions of the four standard analgesics: aspirin, acetaminophen,
ibuprofen, and caffeine in shorty vials, properly labeled. Each should get a dif-
ferent one and share it with the others. Spot both of your plates with each of
these four standards, placing the spot at the origin mark corresponding to each.
Examine the plate under the UV light to see that enough of the compound has
been applied by observing a visible dark purple dot; if not visible, spot more.
Of the four standards, the ibuprofen spots the lightest so spotting it 5 or 6
times to get the proper intensity under the UV light is normal and encouraged.
Using forceps, gently place one in each TLC bottle, being careful not to splash
solvent up the plate (see Figure 6.9). Be sure that the spots are not below the
solvent level or they will wash away into the solvent. Allow each plate to de-
velop until the solvent front is approximately 1 cm from the top of the plate.
Using forceps, remove the TLC plate and quickly mark the solvent front with
a pencil. Allow the plates to dry in the hood.
137
; ; NOTES Examine the plate under the UV lamp to see the components as dark spots
against a bright green background. Outline the spots with a pencil. The spots
can also be visualized by putting the plate in an iodine chamber that can be
found on the side shelf. After a few minutes sitting inside the closed bottle,
compound spots turn brown. Calculate the Rf value for the center of each spot
as shown in Figure 6.11 and enter in Table 6.2. Tape the properly labeled TLC
plates in your notebook using the wide sticky tape available on the side shelf.
Cover the whole plate with tape after showing the results to your TA.
Obtain Rf values for the other mobile phase compositions from the other
students in your group and enter them in Table 6.2 also . As a group, decide
which composition gives the best separation, in other words: (1) it does not
allow any of the compounds to remain on the baseline, (2) it does not allow
any of the compounds to travel with the solvent front, and (3) it provides the
greatest differences in the Rf values for the compounds to be separated.
For the whole group, make up 50 mL of this % ethyl acetate/hexanes compo-

sition in a clean, dry 125 mL Erlenmeyer flask, making sure to mix the two
solvents together thoroughly. Replace the developing solvent in every group
member's TLC jars with 5 mL of this composition.
Additionally, find another student who had the same mobile phase and ex-
change Rf data with him/her. You will need this data to discuss Rf reliability
and reproducability in your report.
Procedure 2: Identifying the Compounds in an

Analgesic Tablet
Choose one of the commercially available analgesics located on the common
shelf (DO NOT USE ASPIRIN) and prepare a sample by crushing 1/4 of a
tablet; crush the tablet by putting it between two pieces of weighing paper and
roll the bottom of a TLC chamber over the covered tablet (do not tap or bang
the TLC jar). If a half of a pill is provided, crush the half of a pill and use only
half of the crushed pill powder. Place this powder into a shorty vial along with
0.75 mL of ethanol and 0. 75 mL of dichloromethane, and then mix the suspen-
sion. Not all of the tablet will dissolve, but enough will go into solution to spot
the plate. The binder, starch or silica, will not dissolve. It may be necessary to
use a pipette filtration through a plug of cotton to remove the binders from
your solution in order to use the TLC spotter effectively. Your TA will demon-
strate how to do this. Mark two plates as shown on the next page.
138
NOTES II
As Un I C Un Ac
lbupr~~e0~~
,.----+-- Caffeine spot
Unknown spot + Unknown spot

Pencil line 1 cm
Aspirin spot / from bottom ~ Acetaminophen
spot
i--·•·, - ..
·~-...';...__. Depth of 1--_ __ ..._--1
~solvent~
Now spot each of the plates on the middle vertical dash with your unknown
tablet extract and on the outside with two standards as shown. Again, try to
make each spot as small as possible.
Check under the UV light to see that enough of the compound has been ap-
plied; if not, spot more (especially the ibuprofen lane). If the spot is too big, it
may streak on the plate; if it is, use a new plate and dilute your sample before
spotting.
Develop your spotted TLC plates in the selected mobile phase. After develop-
ment, dry the plates, mark the spots, calculate their Rf values, and tape the
plates in your notebook as before.
You are looking to see what components are in your tablet. This is done by
comparing the Rf values of your tablet with the Rf values of the analgesics and
caffeine. For example, your tablet may contain acetaminophen and caffeine.
Thus, the TLC plates should look like this:
As Un I C Un Ac
• • • • •
I
• I
:he tablet or unknown's lane contains two spots: one that matches up with
caffeine's spot and the other that matches up with acetaminophen's spot. Now
:he identities are complete.
139
H NOTES
'c
...
......
~
t) GI
c ...
D
Mr. Benzene says: Streaky plates? Do your lanes
look like a big smear? Add a few drops of acetic
acid to your mobile phase, dilute your samples,
make smaller spots, and stay positive!
D
If it is difficult to identify for certain which spots match, remember that you
can perform a co-spot. A co-spot is described in the background material.
Cleaning Up
Do not dispose of the spotting capillaries; they are reusable! They may
be cleaned by dipping the ends into acetone and blotting the ends with a paper
towel several times. Store them safely in the baggie labeled for TLC spotting
capillary storage in your drawer for use in other experiments.
Used and mixed solvents should be placed in the appropriate organics waste
container in your hood.
Data You Need

For TLC of analgesics:
Rf data from other students in Procedure 1 to complete the chart
Rf data from another student who was assigned the SAME mobile phase as
you in Procedure 1
Identity of the components of your chosen analgesic in Procedure 2
140
Thin-Layer Chromatography II Chemistry 213W
NOTEBOOK PAGES REPORT NOTES •.•.
I. Experiment Info
II. Purpose
write a brief statement explaining the goal of the experiment, noting the kinds
of techniques and analyses used. Make sure your purpose conveys an under-
standing of why this technique and/or reaction are of value to organic chemists.

Procedure 1: Choosing a TLC Mobile Phase. Remember, this section should be
written in bullet form. It should be written as you complete the steps of each
procedure, making sure to include pertinent data and observations (as the steps
are performed) . Tabulate Rf values from Procedure 1 and Procedure 2. Tape
your TLC plates onto your notebook pages; cover the entire plate with tape.
IV. Calculations
Include one sample Rf calculation from Procedure 1.
V. Discussion and Conclusions

Include the following when writing this section:
a. A short summary of the technique of TLC as it applies to identifying
components in a mixture.
b. Discuss the results of Procedure 1: What mobile phase did you choose and
why? Why were the other mobile phases NOT ideal? Are Rf values repro-
ducible? Find one other student who had your assigned mobile phase and
compare your Rf values to his/hers to answer this question.
c. Discuss the results of Procedure 2: What pill was chosen? What's its com-
mercial name? What components are supposed to be in the pill? What were
your results and are they consistent with what is supposed to be in the pill?
d.. Discuss the predicted vs. observed elution orders of all compounds. Are
the observed relative Rf values the same as what you predicted for these
compounds in your prelab assignment? (Consider the structures and po-
larities of these compounds when answering this question.) Did the order
of elution of the compounds change when the mobile phase polarity was
increased? (Relate this to the molecular-level theory introduced in the
chapter.)
e_ Conclusion: Utility of TLC for this application, sources of error.
141
Che mistry 213W :I Chapter 6
:I NOTES NOTEBOOK PAGES REPORT
VI. References
Be sure to also include a reference of your lab mates (for shared data).

1. Rip out the white, original Notebook Pages.
2. Download and attach the TLC grade sheet to the front of your assignments.
142
mo CHAPTER7
~~~~~~~~~~~~~~~~~~~~~~~~~
II ~
Application of Thin-Layer
Chromatography and
Extraction: Synthesis of
Methyl Salicylate
1.1.
'c
.. t)(j \
~
c..
D
Mr. Benzene says: You'll be using TLC plates again in
this experiment! Cutting them in half saves money.
Not all plates will be used in this experiment; some
will be needed in the column chromatography lab
and for your synthetic experiments.
D
OHaydco-McNc:il. LLC
Prelab Assignment
Your Prelab Assignment (worksheet on ANG EL) must be completed before coming
Assignment at the beginning of the class period. You will also be assessed a 10%
1. Extraction of aspirin from commercial OTC aspirin tablets.

2. Synthesis of methyl salicylate from aspirin and monitoring the reaction by
TLC.
3. Using extraction to work up the reaction with a separatory funnel.
Quiz for Chapter 7

Quiz 3 will test your preparedness for the activities in Chapter 7 and for the safety con-
siderations for this experiment. The quiz will also test your understanding of the the-
ory behind the experiment. Since this chapter is an application of the previous
143
, j - 1 1 : ' 1 [1111 \ ' ' l ' I O
two techniques, you are also responsible for the content in Chapters 5 and 6.
:: NOTES
The questions you will be asked will mainly be application questions, analyzing a
reaction and how to monitor it by TLC and how t o work it up. The quiz is worth
25 points.
Mr. Benzene says: You are NOT expected to

memorize the mechanism of action of aspirin for
this class; that's just silly!
mental procedures of the main activities in the chapter's experiment. It will also be
beneficial to know the chemicals involved with the experiment; that is, their safety
considerations (flammability, toxicity, and other comments) and their waste dis-
posal, which is determined when you prepare the Chemical Data Table for the Prelab.
Activity Breakdown
Day 1: Procedure 1
Day 2: Procedures 2 and 3
Introduction
In the extraction and TLC chapters you learned the basics of performing these tech-
niques. Now you are going to combine your knowledge and apply it to a synthesis.
TLC is particularly useful for monitoring the progress of a reaction. By pulling just
a tiny amount of the ongoing reaction mixture out of the flask and running it on a
TLC plate, you can obtain an instant snapshot of which molecules have been con-
sumed and what new molecules may have formed. Without this, chemists would
not know if a reaction could be stopped after 30 minutes, or if it would take many
hours to reach completion or equilibrium. Allowing reactions to continue longer
than they need to increases the chance of unwanted by-products forming or the
product itself decomposing.
Let's re-visit the SN2 reaction that's been discussed in the previous two chapters
to discuss the utility of TLC for monitoring the progress of a reaction.
~ ~ol)
OMe
+Br~
~
K2C03
~ OMe
OH DMF
H 0 H 0 °
144 1 2 3
Application of Thin-Layer Chromatography and Extraction: Synthesis of Methyl Salicylate :: Chemistry 213W
Remember from the analysis of the relative polarities of these molecules that their NOTES ::
::l,. values in increasing order are: 3 < 1 < 2. How can we track the progress of this
reaction? At regular intervals of 30 minutes, the reaction can be spotted onto a
~C plate that also has standard lanes for the two starting materials. We can de-
velop and visualize the plates and compare what we see in the starting material
:.anes to the reaction lane.
Let's look at some TLC plates from our SN2 reaction and practice assessing the
information they provide us. Lane 1 is the starting material standard 1. Lane 2 is
Lhe starting material 2. Lane 3 is the reaction lane. Each plate was developed at
30-minute intervals: Plate A at time 0 minutes, Plate B at time 30 minutes, Plate
Cat time 60 minutes, Plate D at time 90 minutes, Plate Eat time 120 minutes.
•• •• •• •• •
• • • • • • • •
l
• • •
____ J. _____ J____ _
2 3
_____J______ 1______l_ __ _
1 2 3
.....L ......l.•••••L....
123
. ..••l ••.....l.••••• J.....
123
. ... ..l.•••••..l.•••••..l.••••
123
Plate A Plate B Plate C Plate D Plate E
Plate A at zero minutes shows only the starting materials, as expected; the spots in
the reaction Lane 3 match the starting material standards in Lanes 1and2. Plate B
at 30 minutes shows that partial conversion of starting material to product has
happened in Lane 3 as evidenced by the new spot of a lower Rf value. But how
far has the reaction proceeded at this point? You need to compare the relative
intensities of the observed spots in Lane 3 (realize that the relative intensities
of the standards don't give us any information). The starting material spots are
darker than the product spot by about 753, indicating that the reaction has gone
,.,
-253 of the way to completion after 30 minutes.
'c c... Mr. Benzene says: Make sure you always make
.. 8G\ note of the relative intensities of the spots IN THE
SAME LANE! This is the only way to know how far a
~ 0 reaction has gone to completion via TLC.
0
145
111·''''~11
II NOTES
When 60 minutes has passed in Plate C, the spots in Lane 3 are of equal intensity,
indicating that the reaction has gone -50% of the way to completion. By the time
120 minutes has passed (Plate E), the reaction has reached completion because
no starting material 1 is seen in the reaction Lane 3. Since starting material 2
was added in excess, it remains as part of the reaction mixture regardless of how
long we run the reaction. If any by-products had started to form we would have
known that another compound was present in our mixture because a spot would
have appeared that did not match the Rf of the starting materials or products
(for example, any water in the reaction flask would have turned 2 into a benzyl
alcohol). Please note that without a standard to compare to, we are assuming the
new spot is our product 3.
In this chapter, you will be converting aspirin to methyl salicylate in a 1-pot, 2-step
reaction. The progress of the reaction will be monitored by TLC and the reaction
workup will be accomplished using extraction. Let's take a look at the importance
of aspirin and methyl salicylate as some background knowledge.
Aspirin and Its Mechanism of Action

Many drug therapies currently exist to treat pain; of these therapies, aspirin and
other non-steroidal anti-inflammatory drugs (NSAIDs) are among the most widely
used agents for daily pain relief of everyday pain symptoms. One of the earliest
painkillers identified was willow bark extract, in which the active component was
characterized as salicin (Figure 7.1). Salicin is metabolized in the body into its
active form, salicylate. A more palatable form of salicylate, acetylsalicylic acid,
was developed in 1875. This drug, called aspirin, was one of a number of non-
steroidal anti-inflammatory drugs being developed at that time; others include
acetaminophen, ibuprofen, and naproxen. Unfortunately, it was observed that
prolonged and extensive use of NSAIDs could have serious side effects including
stomach bleeding, kidney failure and sometimes death. 1 Little else was known
about these drugs until 1971 when the prostaglandin pathway was proposed as
the mechanism of action of these NSAIDs.
The proposal that aspirin and other NSAIDs block prostaglandin production led to
the elucidation of the prostaglandin pathway (Figure 7.2). Prostaglandins are part
of the eicosanoid family: very potent, short-range biological signaling molecules
acting only on cells near their point of origin instead of being transported via the
blood to act on cells in other tissues. Prostaglandins regulate many physiological
processes including pain, inflammation, and the secretion of mucins that protect
the gastric mucosa from acid and proteolytic enzymes in the stomach.
1 Vane, J. R. Inhibition of prostaglandin synthesis as a mechanism of action fo r aspirin-like drugs.

Na t N ew Biol. 1971, 231, 232-235.
146
I
I' f ' '
I
~ ~.
I
Application of Thin-Layer Chromatography and Extraction: Synthesis of Methyl Salicylate 11 Chemistry 213W
n NOTES H
-0QO~OH
HO
OcrOH
HO
-;;:? OH
~'
0
HO OH
Salicin Salicylate Ibuprofen
Hoxo/oyo ~OH
)LN~
u Me H
Acetylsalicylic acid Acetaminophen Naproxen
Figure 7.1. Structures of known NSAlDs .
.;a eicosanoids are derived from arachidonic acid, released from cell membrane
phospholipids by the enzyme phospholipase A2 in response to extracellular stimuli.
•"Uachidonic acid is subsequently metabolized by different pathways to form ei-
ther prostaglandins, thromboxanes, which regulate platelet function and blood
pressure, or leukotrienes, which stimulate contraction of smooth muscle in the
:ntestines and pulmonary airways.
It was demonstrated in several laboratories that aspirin and other aspirin-like

drugs blocked the conversion of arachidonic acid to prostaglandins through the
inhibition of COX, preventing downstream effects of prostaglandins thereby giv-
:ng rise to their anti-inflammatory properties. Aspirin is able to acetylate COX
:sozymes in addition to several other targets which explains its known effects .
•;spirin has been shown to have at least two other modes of action including the
;,mcoupling of oxidative phosphorylation in mitochondria2 and modulation of
signaling through NF-kB, a transcription factor complex that plays a role in central
biological processes including inflammation. 3 Aspirin is metabolized into salicylic
acid, which also is known to have anti-inflammatory and analgesic properties. It
has been recently suggested that the activation of adenosine monophosphate-
a.ctivated protein kinase (AMPK), a central regulator of cell growth and metabolism,
b-;> salicylic acid could explain some of the observed effects. 4
2 Somasundaram, S. et al. Uncoupling of intestinal mitochondrial oxidative phosphorylation and

inhibition of cyclooxygenase are required for the development of NSAID-enteropathy in the
rat. Aliment Pharmacol. Ther. 2000, 14, 639-650.
3 McCarty, M. F.; Block, K. I. Preadministration of high-dose salicylates, suppressors ofNF-kappaB
activation, may increase the chemosensitivity of many cancers: an example of proapoptotic
signal modulation therapy. Integr Cancer Ther. 2006, 5, 252-268.
..., Hawley et al. The ancient drug salicylate directly activates amp-activated protein kinase. Science
2012, 336, 918- 922.
147
II NOTES O
Membrane
phospholipid
I
Polar head Mitogens, cytokines,
group Phospholipase A2 --- other stimuli
Arachidonic - -- - Leukotriene
acid synthesis
NSAIDs, COX-2
inhibitors
0 111,,.
I.!!;;~·~x
OOH
.••••~~coo-
P"""'''"d'" H,L~
OH
Thromboxane
synthesis
Figure 7.2. The prostaglandin pathway.
Methyl Salicylate and Essential Oils

Methyl salicylate is also known as "oil of wintergreen" and is considered an es-
sential oil, a hydrophobic liquid that contains the volatile compounds from plants
responsible for their aroma. These oils are "essential" due to the fact that they com-
prise the distinctive scent or "essence" of the plant from which they are extracted.
148
Application of Thin-Layer Chromatography and Extraction: Synthesis of Methyl Salicylate :: Chemistry 213W
Other well-known essential oils include eucalyptus oil, rose oil, and lavender oil. NOTES ::
~umerous plant species called "wintergreen plants" produce significant quantities
of methyl salicylate naturally including eastern tea berry (Gaultheria procumbens),
sweet birch (Betula lenta), and meadowsweets (Spiraea rosaceae). It is produced
mainly as an anti-herbivore defense mechanism againstinsects.5 Steam distillation,
cold-pressing, and extraction using hexanes or supercritical carbon dioxide are
common methods used to obtain essential oils. They have been used medicinally
in history but claims as to their efficacy are under scrutiny. More common uses for
essential oils include cosmetics, perfumes, soaps, and incense. Specifically, methyl
salicylate is used to treat joint and muscular pain in products such as Bengay. In
concentrations less than 0.043, methyl salicylate is used as a flavoring agent.
Higher concentrations are toxic and often lethal due to its metabolism to salicylic
acid in the body. Common products that use low concentrations of methyl salicylate
as flavoring include wintergreen Life Savers and Listerine.
Conversion of Aspirin to Methyl Salicylate

The ester functional group has been widely studied in the field of organic chemistry.
Low molecular weight esters often have a pleasant smell reminiscent of fruit, candy,
and spice. The flavor and fragrance industries utilize this ester characteristic as
food and fragrance additives. Esters can be synthesized by reacting an acid chloride
or anhydride with an alcohol. An alternative and widely used synthesis of esters
is the Fischer esterification, where an alcohol is reacted with a carboxylic acid in
the presence of an acid catalyst like HCl or H 2SO4 . Methyl salicylate is tradition-
ally synthesized from salicylic acid and methanol using an acid catalyst, but it can
also be synthesized directly from aspirin in a one-pot, two-step reaction. In this
application, you will be using TLC to monitor a single-pot synthesis to prepare
methyl salicylate from aspirin tablets via a tandem transesterification-Fischer
esterification reaction.
~OH
0
~O_,,CH3
+
uo Heat
O~CH
UOH
3
Aspirin Wintergreen oil

MW: 180.16 g/mol MW: 152.15 g/mol
mp 134-136 •c bp 222 ·c
Figure 7.3. Synthesis of oil of wintergreen from aspirin tablets.
5 James, D. G. and Price, T. S. Field-Testing of Methyl Salicylate for Recruitment and Retention
of Beneficial Insects in Grapes and Hops. Journal of Chemical Ecology 2004, 30, 1613- 1628.
149
II NOTES
In this reaction, the transesterification reaction takes place first. The mechanism
(Figure 7.4) begins with activation of the ester's carbonyl carbon by the acid cata-
lyst. The weakly nucleophilic methanol then attacks the carbonyl carbon, forming a
positively charged tetrahedral intermediate which is followed by a proton transfer.
Re-formation of the carbonyl forces off the leaving group (salicylic acid). The acid
catalyst is then re-formed by removal of the proton to give methyl acetate. This
first transesterification step occurs very quickly. The salicylic acid now undergoes
a Fischer esterification reaction to form methyl salicylate, which is the rate-
limiting step of this reaction and occurs at a much slower pace. The mechanism
for the Fischer esterification portion of this reaction is virtually identical to the
transesterification mechanism seen below (and it can be found in your organic
chemistry textbook!).
1 Proton
~ transfer
1
~OH
lA"/H-
_....._
Salicylic acid
(intermediate)
Figure 7 .4. Transesterification mechanism.
150
., - ~~;
11 I
Application ofThin-Layer Chromatography and Extraction: Synthesis of Methyl Salicylate II Chemistry 213W
Reagents used in this technique: NOTES II

Aspirin tablets, methyl salicylate, methanol, concentrated sulfuric acid, aspirin
and methyl salicylate standard solutions, 10% NaHC03 solution, dichlorometh-
ane, saturated NaCl solution, anhydrous sodium sulfate, ethyl acetate, hexanes

In your drawer-25 mL round-bottom fl.ask, large beaker, condenser, separa-
tory funnel, TLC jar, TLC plates, Erlenmeyer fl.asks, beaker
Speciality items from the common shelf-large test-tube, small magnetic
stir-bar, stir/hot plate, heating mantle, clamp holder, clamp, small iron ring,
thin-walled tubing (for water), TLC capillary spotting tubes, rubber septa
Procedure 1: Extraction of Aspirin from Commercial

Tablets-A Demonstration of Solid-Liquid Extraction
Mr. Benzene says: In the Extraction chapter,

liquid-liquid extraction was demonstrated by the
separation of a three-component unknown mixture
using acid/base chemistry. In this portion of your
lab activity, you will be using solid-liquid extraction
to isolate aspirin from commercial tablets.
Binders are used to hold tablets together. These binders can be lactose, sucrose,
starch, cellulose, or modified cellulose, all of which are pharmacologically inac-
tive substances. These binders break apart in the stomach, releasing the active
ingredient to be absorbed into the body's bloodstream. Aspirin tablets can be
crushed and the acetylsalicylic acid can be extracted from the binders using
an organic solvent. The binders are insoluble in the polar organic solvent and
are left behind while acetylsalicylic acid dissolves in the methanol. The solid
aspirin is now extracted into the liquid organic solvent.
Procedure
Using a mortar and pestle, grind up four aspirin tablets. Each aspirin tablet
contains 325 mg of acetylsalicylic acid. Place the resulting powder into your
large test tube and add 10 mL of methanol. Cap the tube with a red septum
(located on the common shelf) and shake the mixture vigorously for at least one
minute (remember to vent!). Using vacuum filtration, filter the slightly cloudy
suspension through your Buchner or Hirsch funnel to separate the unwanted
solids (pill binders) from the liquid containing the acetylsalicylic acid. Wash the
151
illlll..J1 ·-1....-H•-·-·--·--- -~-- - ~

Chemistry 213W I: Chapter 7
H NOTES solids with an additional 2 to 5 mL of methanol. The solid binders left behind
on your filter may be discarded in the trash. Pour the methanol solution into
a tared 25 mL round-bottom fl.ask and evaporate the methanol with a stream
of nitrogen. To expedite the process, place a larger beaker of water on a hot
plate at a low setting to warm the water. Then suspend your round bottom
containing the methanol and aspirin in the warm water. Continue to evapo-
rate with a stream of nitrogen until dryness. Then put the isolated aspirin in
your locker to let it further dry until the next lab period. DO NOT CAP OR
PARAFILM THE BEAKER! You want any remaining methanol to evaporate .
'c
...
......
~
VG I
c ....
D
Mr. Benzene says: You must manually evaporate
the methanol this lab period. If you leave it in your
locker without doing this step, the methanol will
not evaporate by the next lab period!
D
By the next lab period, all of the residual methanol from the extraction of the
commercial tablets will have evaporated and left the aspirin residue behind.
Weigh your flask that contains the aspirin residue .
'c
...
......
~
VG\
c ....
D
Mr. Benzene says: Calculate the % recovery of the
aspirin you extracted, keeping in mind that you
extracted 4 tablets that contain 325 mg of aspirin in
each tablet.
D
Procedure 2: Monitoring the Synthesis of Methyl

Salicylate by TLC
'c
...
......
~
VG I
c ....
D
Mr. Benzene says: In this synthesis, you will be
refluxing a reaction. Reflux is a technique that
involves the condensation of vapors from a boiling
reaction vessel and the return of this condensate to
the system from which it originated.
D
152
m'' -- - "'
11' 1
1 1
111
! . 1111
Application ofThin-Layer Chromatography and Extraction: Synthesis of Methyl Salicylate H Chemistry 213W
Set up a TLC chamber with 25% ethyl acetate/75% hexanes as the mobile NOTES H
phase. Set up your TLC plates with 3 lanes: Lane 1 is the aspirin standard, Lane
2 is the methyl salicylate standard, and Lane 3 is the reaction mixture. TLC
standards of aspirin and methyl salicylate are available on the common shelf.
_____ J _____ J _____ -L-----

AS MS Rxn
Set up your heating mantle, round-bottom flask containing dry aspirin, and
condenser like the following diagram (Figure 7.5). Affix your heating mantle
so it rests on your stir plate; plug the heating mantle into your Varistat on
the side of your hood and then plug the Varistat into the wall. If your heating
mantle has exposed coils on the bottom, put a small amount of sand in to
cover them. (NOTE: Place your used sand BACK into the silver bowl on the
front shelf, NOT in the garbage!) Next, damp your round-bottom flask so it
rests inside your heating mantle. For the condenser, use the skinny one from
your blue kit. The condenser has two layers of glass; the outside jacket is en-
closed and the water will flow from thin-walled rubber hoses you affix into
the bottom and out of the top. Put a small amount of silicone grease (found
on the common shelf) on the male joint of the condenser and place it into the
round-bottom to form a nice seal.
153
~ • .!lliiillill. I
II NOTES
- water OUT
- Ring stand
- - w ater IN
Voltage controller Use thin-walled hose.
or "Varistat"
Heating mantle
Stir plate
Figure 7.5. Reflux condenser.
To start your reaction, remove the condenser and add 5 mL of methanol to the
round-bottom fl.ask containing your extracted aspirin. Place your micro stir
bar in the round-bottom. At this point you might want to make a TLC plate
at time zero to compare to later TLCs since the aspirin starting material can
be consumed rather quickly. Finally, add 0.5 mL of CONCENTRATED sulfuric
acid (make sure you use the correct acid!). Attach the condenser to the round-
bottom. Tum your Varistat to -50 in order to make the heating mantle hot
and heat the mixture to boiling using your heating mantle on a stir plate for
-90 minutes (the reaction may take a shorter time OR longer time-this is
why monitoring with TLC is important!). Make sure you stir your reaction.
Monitor the progress of the reaction every 30 minutes by TLC.
154
.\pplication of Thin-Layer Chromatography and Extraction: Synthesis of Methyl Salicylate 11 Chemistry 213W
I EXPERIMENTAL PROCEDURES
NOTES II
Mr. Benzene says: This reaction proceeds through
the salicylic acid intermediate. A spot will show up
on your TLC plate that has an R value in between
the aspirin starting material and the product methyl
salicylate. It is imperative that you compare your
reaction to the standards as described!
Over time, you will notice the spots changing in intensity in your reaction
lane; your aspirin spot may be completely gone from your reaction lane after
the first 30 minutes. The intensity of the spots on your TLC plate can tell you
how far the reaction has gone to completion (make sure that you include
observations of the relative intensities in your lab notebook since
these cannot be directly observed after the TLC plates are taped in!).
After the reaction has reached completion as indicated by your TLC plates (no
more aspirin left and mostly/all methyl salicylate), allow it to cool to room
temperature. Even after 90 minutes there most likely will still be a middle spot
on your TLC plate but as long as you have SOME methyl salicylate, proceed
to the workup below.
'c
,
......
~
t>G I
c ...
D
Mr. Benzene says: You need to work up your
reaction in the SAME lab period that you run
your reaction in. Otherwise the sulfuric acid will
decompose the organic materials. And that's bad.
D
Procedure 3: Workup of the Reaction Using Extraction
In your extraction activity you utilized acid/base chemistry and pipette extrac-
tion to separate components. In this reaction workup, you will be using your
separatory funnel. To refresh your memory on the fundamentals of using your
separatory funnel, re-read the introduction in the Extraction chapter.
In this workup, you will use 10% aqueous sodium bicarbonate as your aqueous
:.ayer and dichloromethane as your organic layer. Make sure you refer to the
density chart found in your lab notebook to keep track of your layers.
Let's talk about WHY you are using a weakly basic aqueous solution in this
workup. It's for two reasons. The first is because this reaction is catalyzed
by concentrated sulfuric acid. It will need to be neutralized with a base. The
H NOTES second is because the aspirin starting material and the intermediate salicylic
acid are both carboxylic acids (weak acids) but the product methyl salicylate
has a phenol (an even weaker acid). Using the acid/base chemistry you used in
Chapter 5, the carboxylic acid is the stronger of the two weak acid functional
groups. The carboxylic acid will be deprotonated by the weak base, and both
the intermediate AND the starting material will be pulled into the aqueous
layer, leaving your product in the organic layer.
Procedure
Place your separatory funnel in your iron ring that you affix to a ring stand .
'c.......
.... t)G \
~
C,
D
Mr. Benzene says: Make sure your stopcock is in
the CLOSED position before adding your reaction
mixture!
D
Transfer the contents of the reaction vessel into a separatory funnel and slowly
add 10 mL of saturated (10%) aqueous sodium bicarbonate .
.......
;c
t) G
~
c ..
D
Mr. Benzene says: Use caution here! Fizzing
will occur as co2 will be released as the base
neutralizes the sulfuric acid!
D
Wait until the fizzing has ended. Add 10 mL of dichloromethane, thoroughly

mix the two layers in the separatory funnel, and drain off the lower organic
layer into a labeled "organic layer" Erlenmeyer fl.ask (you WANT TO KEEP the
lower layer). Keep the aqueous solution in your separatory funnel, and repeat
this process two more times, each time adding 10 mL of dichloromethane,
mixing the layers, then draining the lower organic layer into the "organic layer"
fl.ask. You are extracting the methyl salicylate product out of the aqueous layer
and into the organic layer; any starting material and intermediate should be in
the basic aqueous layer. After you've extracted the aqueous reaction mixture
three times with dichloromethane, drain the aqueous layer into a separate
beaker or flask.
Now, place the dichloromethane layer (-30 mL worth) from the three extrac-
tions back into the separatory funnel. Add 10 mL of saturated (10%) aqueous
sodium bicarbonate and mix the layers well. Drain the lower organic layer
into your organic fl.ask and then drain the remaining aqueous layer into your
156
Application of Thin-Layer Chromatography and Extraction: Synthesis of Methyl Salicylate ;; Chemistry 213W
NOTES : ;
aqueous waste flask. Pour your organic layer back into the separatory funnel
again, and repeat the wash but this time with 10 mL of saturated sodium
chloride solution. Drain the lower organic layer into an Erlenmeyer flask and
add a small amount of anhydrous sodium sulfate to dry the solution. Decant
the solution off of the sodium sulfate into a preweighed beaker or Erlenmeyer
fl.ask and evaporate the dichloromethane with a stream of nitrogen. A warm
water bath will expedite the evaporation process, just like what you did
in Procedure 1, but be careful not to burn or evaporate away the product.
When the volume of the contents is no longer changing, the evaporation of
the solvent is complete. Alternatively, you may seal your flask and evaporate
the solvent in the next lab period if you run out of time.
The product is a viscous oily liquid. Weigh the flask+ contents and calculate
your% yield. Waft the product. What does it smell like?
Mr. Benzene says: Make sure you smell... NOT taste!
Calculate the% yield of your product using the amount of aspirin you isolated
from your extraction. Analyze your product by IR and NMR. When analyzing
your NMR, make sure you look to see if there is any leftover starting material
(acetylsalicylic acid) or intermediate (salicylic acid) present. To help you with
this, compare your NMR t o the 60 MHz NMR spectrum of methyl salicylate:
Figure 7.6. NMR of methyl salicylate.
157
== NOTES Data Needed

% recovery from the aspirin extraction
NMR and IR of methyl salicylate
% yield of methyl salicylate
158
Application of Thin-Layer Chromatography and Extraction: Synthesis of Methyl Salicylate 11 Chemistry 213W
NOTEBOOK PAGES REPORT NOTES H
I. Experiment Info
II. Purpose

Include subsections in this section for each procedure; use subheadings for all
activities done in this chapter.
IV. Calculations
a. % recovery of aspirin.
b. Re-calculation of theoretical yield of methyl salicylate based on how much
aspirin you isolated in Procedure 1.
c. % yield of methyl salicylate using your re-calculated theoretical yield.
V. Experimental
Experimentals are very important in organic chemistry papers since they
are a short and concise way of telling the reader how the reaction was set up,
monitored, worked up, purified, and characterized. Write an experimental for
this synthesis following the examples set forth in Chapter 3.
VI. Discussion and Conclusions

a. First mention the chemistry of this reaction, why it is important. Make
this a very short and concise introduction.
b. Discussion of the extraction of aspirin from the commercial tablets. Was
the extraction effective? What was your% recovery?
c. Talk about the synthesis and monitoring by TLC. Was TLC effective at
telling you what was happening in the reaction? Why or why not? Did
your reaction go to completion? What did your TLC plates tell you?
d. How was extraction used in the workup? What was the purpose of using
the sodium bicarbonate? Was extraction effective at removing the inter-
mediate and/or starting material?
159
II NOTES NOTEBOOK PAGES REPORT
e. Finally, prove you made your product. Make sure you discuss appearance,
scent, IR data (specific peaks seen and what they mean), and NMR data
(chemical shift, integration, splitting pattern, impurities).
f. Conclusion: overall success, take home message, improvements, sources
of error.
VII. Spectral Data

Make sure your NMR data and IR data are fully annotated and labeled as fig-
ures. Make sure you attach them to your report!
VII I. References

2. Download and attach the TLC grade sheet to the front of your assignments.
160
......
I :I
~~JD CHAPTER 8
~~~~~~~~~~~~~~~~~~~~~~~~~~-
Disti11 at ion
Prelab Assignment
Your Prelab Assignment (worksheet on ANGEL) must be completed before coming
1. Synthesis of methylcyclohexenes from methylcyclohexanols

2. Purification of methylcyclohexenes
Quiz for Chapter 8

mental procedures of the main activities in the ch apter's experiment. It will also
be beneficial to know the chemicals involved with th e experiment; that is, their
for the experiment.
Activity Breakdown
Day 1: Procedure 1
Day 2: Procedure 2
161
: : NOTES Introduction
Purification Techniques of Organic Compounds and Distillation

Usefulness
The first three chapters/techniques taught you how to set up a reaction, monitor
its progress by TLC, and work up a reaction using liquid-liquid extraction. We
also used acid-base chemistry with liquid-liquid extraction to purify our methyl
salicylate product in Chapter 7, but that was a rare case. Both solids and liquids
can be separated by liquid- liquid extraction but it's limited by the unique acid-
base reactive functional groups of the molecule(s). These next three chapters will
inform you of the other three main techniques organic chemists use to purify a
crude product: distillation, recrystallization, and column chromatography. The
technique of column chromatography can be applied to both solid AND liquid
products, recrystallization can only be used for solid products, and distillation
can only be used for liquid products.
Table 8.1. Summary of the usefulness of the main purification techniques used in organic
chemistry.
Liq-Liq Column
Distillation Recrystallization
Extraction Chromatography
Solids YES No YES YES

Liquids YES YES No YES
Let's analyze the reaction used in previous chapters and look at how effective/
ineffective extraction, distillation, recrystallization, and column chromatography
would be for our example SN2 reaction:
~ Brl)
OMe
rOH
H 0
+
1 2 3
For this reaction, we saw in the Extraction chapter how 3 could be separated from
excess 1 and how the base could be quenched using acid/base extraction. In the
Application chapter, we saw how these three compounds could be separated on a
TLC plate and how important this technique is for monitoring the progress of the
reaction. Once 3 is isolated after extraction, it will need to be purified. Since 3 is a
solid, distillation is immediately ruled out as an option. This leaves you with two
choices: recrystallization or column chromatography. These two scenarios will be
discussed in subsequent chapters.
162
- -- - - - - -- - - - - - -
'
I '
Distillation H Chemi stry 213W
nat COULD distillation be used for in this reaction? Compound 2 is a colorless NOTES H
liquid, and distillation could be used to purify this starting material before it is
:.:..sed in the SN2 reaction. This purification of the starting material could lead to
c.n SN2 reaction with fewer by-products and a higher yield.
:::>istillation is the process of vaporizing a liquid, condensing the vapor, and collect-
mg the condensate in another container. Despite the apparent limitation of distil-
lation, it still has important uses in the organic chemistry lab setting. Distillation
can be used to purify two liquid mixtures with different boiling points. A classic
example of distillation is an alcohol "still" known to almost all cultures in the world.
Fermentation of grains or fruits, such as grapes, leads to alcohol formation and
eventually either beer or wine. The amount of alcohol produced by fermentation
is limited to -123, because the higher alcohol content kills the alcohol-producing
enzymes. To obtain stronger liquors with higher alcohol content, distillation is
necessary. In distillation, the liquid mixture is heated and the lower boiling frac-
tion, in this case ethyl alcohol, will evaporate; it is then condensed and collected
in a receptacle. Distillation can produce liquors of up to 953 ethanol.
Distillation can also be used to purify/ remove water from solvents for use as a "dry
solvent" in water-sensitive organic reactions. Perhaps one of the most useful ap-
plications of distillation is in an actual synthesis. Liquid products can be removed
from an equilibrium reaction using distillation to push the reaction to the right,
taking advantage of Le Chatelier's principle.
Two distillation setups are available to the chemist; simple distillation and frac-
tional distillation. Some situations may require special distillation conditions
such as a simple vacuum distillation or a simple steam distillation. All of these are
discussed in depth in the background material that follows.
Distillation Theory
What Is a Boiling Point?
During distillation, two or more liquid compounds are separated based on the dif-
ferences between their boiling points. A liquid contains closely packed but mobile
atoms or molecules of varying energy. When a molecule of the liquid approaches
the surface of the liquid, it will pass from the liquid phase into the gas phase if
it possesses sufficient energy. At any temperature, a liquid exerts pressure on
the environment because molecules leave the surface of the liquid and become a
vapor. This is called vapor pressure. The conversion of a liquid molecule to a gas
molecule is an equilibrium:
Molecule liquid = Molecule gas
163
Heating the liquid causes more molecules to enter the gaseous state and the
:I NOTES
equilibrium is shifted to the right. As a result, vapor pressure increases. The exact
number of molecules in the gaseous state depends not only on the temperature
but also on the pressure, the volume of the system, and the strength of the inter-
molecular forces exerted in the liquid phase.
The boiling point of a pure liquid is the temperature at which the vapor pressure
of the liquid exactly equals the pressure exerted on the liquid surface by the
atmosphere. It is important to note that an observed boiling point is dependent
on the atmospheric pressure. For example, in New York City (elevation 0 ft, P =
1 atm), the observed boiling point of water is 100°C. However, in Denver, CO
(elevation 5,280 ft, P = 0.83 atm) the observed boiling point of water is 95°C. In
our laboratory, the atmospheric pressure is slightly lower than the standard (about
a half degree difference in boiling point). Since most of the thermometers are only
calibrated to ±5°C, you do not have to correct for atmospheric pressure but you may
want to correct your thermometer's error which you discovered during orientation.
A pure organic compound that is thermally stable (i.e., it does not degrade upon
heating) has a reported boiling point at an indicated pressure. Boiling points de-
pend on molecular structure: stronger intermolecular forces within a liquid mean
a higher observed boiling point. Organic liquids with hydrogen bonding capabili-
ties and dipole-dipole interactions usually have higher boiling points than organic
liquids without these intermolecular forces. For example, propane (CH3 CH 2CH 3)
has a boiling point of -42°C (at 1 atm) but ethanol (CH3 CH 2 0H) has a boiling
point of 78°C (at 1 atm). In addition, increased molecular weight also gives higher
boiling points because a larger molecular surface area gives greater van der Waals
interactions. For example, compare propane, mentioned previously, with the larger
hydrocarbon, hexane, (CH 3 CH 2CH 2CH2 CH2CH 3) which has a boiling point of 69°C.
If a soluble but nonvolatile substance is dissolved in a liquid, the vapor pressure

of the liquid is lowered. This is because the number of liquid molecules that are
able to pass into the gaseous phase is reduced. The lowering of vapor pressure
leads to a boiling point elevation. Think about a common practice when cooking
pasta: putting salt in the water not only adds flavor to the pasta, it also slightly
elevates the boiling point of the water.
Boiling Point of a Mixture

What happens to the boiling point of a liquid if it is comprised of two or more dif-
ferent compounds? If the mixture is an ideal solution, then the boiling point of the
mixture depends on the vapor pressure of its components which are derived from
Raoult's Law. Let's consider the boiling point characteristics of a solution containing
both pentane and hexane. The two compounds are miscible and the interactions
between them are limited to van der Waals forces. Therefore, the boiling point of
the mixture is between the boiling points of the two individual compounds.
164
/ - - - - - - - -
Distillation II Chem istry 213W
:£only hexane was present in a liquid, then the vapor pressure of the liquid would NOTES II
be exclusively due to only hexane (P hexane>· However, when hexane is only a fraction
0
of a liquid mixture, then the partial pressure (Phexane) exerted by hexane is only
a fraction of the vapor pressure exerted by pure hexane. This partial pressure can
be calculated from the mole fraction (Xhexane) in the solution. The mole fraction
is the ratio of moles of hexane to the total number of moles of both hexane AND
pentane in the mixture:
Phexane -- (P0 hexane)(XhexaneJ'
molesheiane
X hexane = ( mo1eshexane + mo1espentane)
The pentane in the mixture ALSO exerts its own partial pressure (Ppentane):
Ppentane -- (P 0
pentane)(Xpentane )
molespentane
Xpentane =(mo1eshexane + mol espentane)
The total vapor pressure of the solution is calculated using Dalton's law of partial
pressures:
p total = p pentane + p hexane
Therefore, the boiling point of a hexane/pentane liquid mixture is the temperature

at which the total pressure of the mixture equals the total pressure exerted on the
liquid by the surroundings.
165
II NOTES
- - + - - - - --- - - - - - - -- -
::.::
co
Cl>
C\J
a; 300
-;::-
g
Q)
5
(/)
(/)
~ 200---+-----1------+--__,_...,__+-~....------i
0
~
Mole fraction of hexane
Figure 8.1. A vapor pressure/mole fraction diagram for hexane and pentane.
If a solution of hexane and pentane contains 503 hexane/503 pentane, the graph
showing the vapor pressure/ mole fraction relationship above (Figure 8.1) indicates
that the vapor above the liquid would be richer in pentane than in hexane. The
vapor would be approximately 753 pentane and 253 hexane. This makes sense
as the boiling point of pentane (36°C) is lower than the boiling point of hexane
(69°C) at atmospheric pressure.
Separation of a Liquid Mixture

Distillation can be used to take advantage of the difference in boiling points and
effectively purify one compound from the other. How does one go about actually
separating a liquid mixture in the laboratory? You will need to choose one of several
different glassware setups. The type of distillation apparatus utilized depends on
the liquid mixture to be separated.
Scenario 1
Consider a liquid mixture containing two compounds, A and B. A and B have boil-
ing points that differ by LESS than 75°C. For this scenario, let's revisit the liquid
166
Distillation H Chem istry 213W
:::llxture of hexane and pentane since their boiling points differ by only 33°C. How NOTES H
can the pentane be removed from the hexane? In the temperature/composition
&gram below (Figure 8.2), consider a 603 hexane/403 pentane mixture. In the
6agram, the lower curve represents the composition of the liquid and the upper
curve represents the composition of the vapor as determined by drawing a hori-
zontal line from the liquid point to the vapor point. A 60% hexane/403 pentane
liquid mixture has a boiling point of S0°C (Al, liquid). The vapor composition can
be determined by drawing a horizontal line from the liquid curve to the vapor
curve; at S0°C, the vapor is comprised of 32% hexane/68% pentane (A2, vapor).
If this vapor was condensed and collected (Bl, liquid), the liquid obtained would
ALSO be comprised of 32% hexane/68% pentane. This is an ineffective separation
of the two components. However, this cycle can be repeated. For example, the 323
hexane/68% pentane liquid mixture now has a boiling point of 42°C (Bl, liquid).
-:::he composition of the vapor at this temperature is 12% hexane/88% pentane (B2,
vapor). Condensation of this vapor to a liquid (Cl, liquid) results in a slightly more
pure pentane/hexane mixture. Repeating this cycle a few more times allows one
to obtain essentially pure pentane. Each condensation/vaporization cycle is called
a theoretical plate. This theory is put into practice via the use of a fractional
distillation apparatus.
0
~ 50--+- -
~
:l
~ 45 --+- - - T -- -t--+- 7 ' - - -t - - -- -t-- ---t
~ 82, vapor
~ 40-+_ ...,....,_ _____
F
0 0.2 0.4 0.6 0.8
Mole fraction of hexane
Figure 8.2. A temperature and composition diagram for a hexane and pentane
mixture at 1 atm.
167
H NOTES
Scenario 2
Again, consider a liquid mixture containing two compounds, A and B. If the boiling
point of A is lower than the boiling point of BAND the difference between their
boiling points is 75°C or greater, then PA will be much greater than P8 . As long as XA
andX8 are both significant, the amount of Bin the vapor phase above the solution
will be very small. Under these circumstances, if the vapor is condensed, almost
pure A would be obtained. This situation is ideal when using a simple distillation
apparatus. This is illustrated best by another temperature/composition diagram
below (Figure 8.3). A liquid mixture containing 40% pentane and 60% octane boils
at 61°C (Al, liquid). The composition of the vapor at this temperature is comprised
of 89% pentane and only 113 octane (A2., vapor). One additional vaporization/
condensation cycle would give a vapor (B2, vapor) and liquid composition of 98%
pentane and 2% octane. Thus only two theoretical plates are needed to effectively
separate the pentane and octane mixture. Using a simple distillation apparatus
would be reasonably successful at this separation.
140
130
120
110
~ 100
0
~
~ 90
::>
~
Q) 80
a.
E
~ 70
40--tf---'--::;;_..::;._~---,r-~~-1-~~~+-~~-1
8 2, vapor
30 --t~~~-,---~~---,,...-~~-+-~~~~~~---1
0 0.2 0.4 0.6 0.8

Mole fraction of octane
Figure 8.3. A temperature and composition diagram for an octane and pentane
mixture at 1 atm.
In general, organic chemists use simple distillation when the boiling point differ-
ences in a liquid mixture are greater than 75°C, a liquid mixture is essentially pure
(10% or less impurity), or a liquid mixture contains only a trace amount of an inor-
ganic impurity. Fractional distillation is a better choice when separating mixtures
with close boiling points, although it tends to take longer and use more energy.
168
l' • "I
.lj
Distillation H Chemistry 213W
Distillation Apparatus NOTES : :
Simple Distillation
In a simple distillation, a liquid mixture is heated until it boils. The liquid is va-
porized and subsequently condensed to collect the purified condensate. A simple
distillation apparatus can be seen in Figure 8.4.
Figure 8.4. Simple distillation setup. NOTE: Water flows IN to the bottom of the condenser
and OUT the top!
The liquid mixture to be purified is placed in the round-bottom flask that is in

contact with a heat source (typically a heating mantle or oil bath). When heated,
the vapors rise through the distillation head and come into contact with the ther-
mometer. The temperature of the vapor can be recorded over the duration of the
distillation. In the distillation head, about two vaporization-condensation cycles
(theoretical plates) are able to take place. The condenser is attached to the side of
the distillation head and has cold water running through it. When the vapors reach
this point, condensation happens and the purified liquid is able to flow down the
condenser into a receiving flask at the end.
Several important rules must be followed when setting up and running a simple
distillation:
1. The round-bottom flask should be no more than half-full of the liquid mixture
to be distilled. For example, if 100 mL of a liquid mixture are to be distilled, a
250 mL round-bottom flask should be used.
2. Make sure that a magnetic stir-bar is placed in the round-bottom flask. This
way, the mixture can be stirred constantly during the distillation process to
prevent superheating and "bumping" of the liquid.
169
Chemistry 213W :: Chapter8
3. The round-bottom flask must be securely clamped over the heat source. If
== NOTES
a heating mantle is used, make sure that round-bottom is nestled securely
inside. If there are exposed coils inside the heating mantle, a small amount of
sand should be used to cover them before securing the round-bottom: Other
heat sources that can be used include a sand bath, an oil bath, or a hot water
bath. DO NOT IMMEDIATELY TURN ON THE HEAT SOURCE! It should only
be turned on AFTER the entire apparatus is assembled and the condenser is
cooled.
4. The distillation head must be inserted into the round-bottom fl.ask. Before this
is done, make sure that the glass joints are LIGHTLY greased with silicon. Too
much grease will contaminate the liquid mixture but little to no grease often
results in the glass joints becoming stuck together. When assembling the rest
of the apparatus, make sure that ALL glass joints that are put together are
lightly greased. The round-bottom fl.ask and the distillation head MUST be in
a completely VERTICAL position.
5. Assemble the thermometer adapter. There are TWO pieces that comprise the
thermometer adapter: the Teflon rubber sleeve and the glass joint. Gently
slide the Teflon rubber sleeve over the smooth glass joint of the adapter. The
ground-glass joint is then placed in the top of the distillation head. A ther-
mometer can now be pushed through the Teflon so it is suspended within the
distillation head. The bulb of the thermometer needs to be fully BELOW
the opening of the side-arm in the distillation head. This is because it
needs to be completely bathed in the vapors during the distillation to
record an accurate temperature.
Knowing the temperature of the vapors (that are becoming the distillate) gives
valuable information about identity and purity of the distillate at that time. If
the thermometer bulb is placed too high, it will not be completely surrounded
by vapors and will read a lower temperature than the actual temperature of the
vapors. If the thermometer bulb is too low it will also read a lower temperature
because it is measuring the temperature of vapors just above the liquid; no
separation has taken place via the theoretical plates in the distillation head.
6. Attach thin-walled rubber tubing to the condenser. Clamp the condenser to a

ring stand or support and affix the condenser to the distillation head. A rub-
ber band is often used to hold the condenser and distillation head together.
Make sure that the angle of the connection is correct; remember that the
round-bottom and distillation head must maintain a vertical position.
7. Cool water should continuously fl.ow through the condenser during the distilla-
tion. The water should enter the lower end of the condenser and fl.ow upwards
towards the distillation head. Affix the bottom hose to the water source and
170
make sure that the top hose is placed into a sink or drain. Tum the water on NOTES :I
slowly; the water must flow at an even rate but not TOO fast (otherwise the
hoses will pop off because of the water pressure!).
B. Affix the curved collection joint to the end of the condenser. Again, a rubber
band is typically used to secure the two glass pieces together.
9. A receiving flask should be positioned under the collection joint. Often, the
flask is cooled with ice to minimize vaporization of the collected distillate.
Once the apparatus is completely assembled, the stirring mechanism of the stir/
hotplate is turned on and then the heating mantle or other heat source. As the
liquid is heated and reaches a boil, a ring of condensate will begin to move up the
round-bottom and the distillation head. The temperature reading on the ther-
mometer will not rise until the vapor reaches the thermometer bulb (remember:
the thermometer is measuring the VAPOR temperature, not the boiling liquid
temperature). Once the vapor hits the thermometer, a sharp increase in tempera-
ture will be seen. Condensate will soon fl.ow down the condenser to be collected
in the receiving flask.
If two compounds are being purified in the distillation, make sure that a second
receiving flask is prepared. The flasks can be switched out when the temperature
reading indicates that the second component begins distilling.
:-emperature should be recorded as a function of volume; begin recording when

::he first drop of distillate is obtained. If the distillation is proceeding very slowly,
the temperature of the heat source can be increased or the distillation head can
be insulated with glass wool and aluminum foil.
A dose eye should be kept on the round-bottom distillation fl.ask. The round-
oottom should never be heated to the point where it runs dry (all of the liquid
:::nixture is gone). This potentially dangerous situation could lead to overheating
and shattering of the round-bottom.
Mr. Benzene says: In any distillation, the flask

should never be more than two-thirds full at the
start. Great care should be taken not to distill
,I
1 ,, to dryness! There always exists the possibility
,.c C, that certain liquids, especially ethers, contain
some explosive peroxides formed by exposure to
air. Peroxides are higher boiling liquids and can
D concentrate in the distilling flask as you distill.
If you distill all the liquid from the flask, the
D temperature will rise, and this could cause the
peroxides to explode violently.
171
When the distillation has ended, remove the round-bottom from the heat source
H NOTES
and make sure that the distillate collected is sealed up for workup or characteriza-
tion.
Fractional Distillation
Fractional distillation is utilized when two liquids with similar boiling points need
to be separated. In a fractional distillation apparatus, MANY vaporization/con-
densation cycles can occur before the distillate is collected because of the presence
of a fractionating column. The presence of the fractionating column is the only
difference from the simple distillation apparatus. It is placed between the round-
bottom flask and the distillation head. Figure 8.5 shows a fractional distillation
setup. Note that the thermometer bulb is in the same position-fully below the
opening of the side-arm in the distillation head.
Figure 8.5. Fractional d istillation setup.
The fractionating column is filled with a material that increases the number of
theoretical plates in the system. Many types of fractionating columns exist. In
this course, the wider "West Condenser" is used. It can be filled with a packing
material that rests on the three glass spikes near the bottom of the condenser.
Steel chips with bumpy surfaces are used; the increased surface area provides nu-
merous sites for vapors to condense and then re-vaporize. As the vapor travels up
the fractionating column, it cools and condenses on the chips. It is re-vaporized
when it comes into contact with hotter vapors rising up the column. The vapor
that reaches the distillation head first should be relatively pure (the compound
with the lower boiling point in the mixture) as seen in Figure 8.6.
172
Distillation 11 Chemistry 213W
NOTES I:
Lower boiling e
point compound
Higher boiling e
point compound
Figure 8.6. The separation of two compounds with different boiling points in a fractionating
column during fractional distillation.
The fractionating column MUST be insulated with glass wool to maintain the
~emperature within the system, which facilitates the maintenance of equilibrium
conditions up the length of the column.
·.'hen assembling the fractional distillation apparatus, the same rules and consider-
ations that were outlined in the previous section also apply: lightly grease all joints,
:he heat source should be turned on LAST, use a properly sized round-bottom flask
\\ith a magnetic stir-bar, the thermometer in the distillation head must be placed
correctly, water flows in the condenser from the bottom to the top, and a receiving
:1.ask must be in place. Again, temperature is monitored/recorded as a function of
"":'"O}ume and the receiving flask should be switched out at the proper time (when a
steep increase in temperature is seen) to separate the two liquids being collected.
Comparison of Simple and Fractional Distillation Curves

?lotting the data of a simple and a fractional distillation with the volume of distil-
late on the x-axis and the temperature on the y-axis give distillation curves (Figure
8.7, that depict the difference between the two setups. In terms of efficiency, you
173
can see from the plateaued ends that fractional distillation gives a larger volume
I: NOTES
of very pure compounds, and along with that give the boiling points closest to the
actual values. Again, recall that while fraction distillation gives better separation,
it often takes much more time than simple distillation and more energy.
Distillate volume in mL or drops ~
Figure 8.7. Simple vs. fractional distillation data.
Vacuum Distillation
For compounds that have very high boiling points (above 200°C) or that decompose
easily when heated, a modified (almost always simple) distillation setup is used.
Vacuum distillation is a reduced pressure distillation that substantially lowers
the boiling point of the compound(s) distilling. The setup is the same except that
a vacuum is applied to the sealed system to reduce the pressure inside. Vacuum
distillation is also useful in circumstances when distilling certain compounds
known to react with itself or oxygen in the air when heated.
Derivations from Raoult's Law
Azeotropes
Liquid solutions that approximate the behavior of ideal solutions can be separated
via the distillation apparatuses previously described because the compounds in
the solution only slightly interact with one another. However, many solutions that
deviate from ideal behavior cannot be completely separated via simple OR fractional
distillation because of additional intermolecular forces that occur within the liquid,
such as hydrogen bonding. Liquid mixtures that fit this description have a vapor
phase that is the SAME composition as the liquid phase and results in a constant
boiling point. Such liquids are called aze otropic mixtures. Examples of solvent
mixtures that result in azeotropes can be seen in Table 8.2 .
174
Distillation 11 Chemistry 213W
Table 8.2. Examples of azeotropes formed by common solvents.

NOTES II
Percent of
Compound Compound Azeotrope
Compound T Compound T T Compound
1 8 m mg 2 8 01 mg 8 OI mg .
1 2 2
Point (°C) Point (°C) Point (°C) Az ;n
eo rope
I water 100 ethanol 78.3 78.6 95.6%
I water 100 benzene 80 69.2 913
I water 100 toluene 110.7 84.1 863

ethyl
water 100 77 70.3 91%
acetate
methanol 65 acetone 56 55.5 88%
acetoni trile 81 ethanol 78.3 72.5 56%
One of the best known examples of an azeotropic system is an ethanol/water

mixture (Figure 8.8). The azeotrope is comprised of 95.63 ethanol and 4 .43 wa-
t er which boils at 78.2°C. A liquid that has this composition can never be purified
because the liquid and vapor curves in the diagram intersect (the liquid phase and
the vapor phase have the same composition). The azeotropic composition will
always distill first; even if fractional distillation was used, the distillate collected
will always contain 95.63 ethanol (190 proof). Absolute (200 proof) ethanol must
be obtained by alternative methods.
100
~ ~~-~--boiling point i
of-azeotrope
~~ ~ij
1 0
~
2:
:J
Ol
90
fr]
Qi - - i ..;
!
~ 80 : !
~ 78.5
78.2
u·_~ d,:~~L~:i!~~
95%
50% ethanol 100%
ethanol
Mole fraction of ethanol
Figure 8.8. Temperature composition diagram for an azeotropic disti llation.
Steam Distillation
Other mixtures that do NOT follow Raoult's law are heterogeneous immiscible
liquid mixtures. Each liquid component in the immiscible mixture has a vapor
pressure that is dependant ONLY on the temperature and NOT the mole fraction
of the component. Additionally, the vapor pressure of each component is inde-
pendent of the other component. 175
Chemistry 213W :: C hapter 8
H NOTES The phenomenon has practical applications for isolating compounds in what is
called steam distillation. In steam distillation, an immiscible organic compound
is co-distilled with water; the mixture will boil at a lower temperature than the
boiling points of the separate components. It can be thought of as a special kind
of azeotropic distillation. Stearn distillation is used in the flavor and fragrance in-
dustry as a way to separate volatile organic flavor oils and/or essences from plant
materials. For example, limonene can be separated from citrus peels and eugenol
can be separated from cloves via steam distillation.
To illustrate the deviation from Raoult's law, consider the steam distillation of
limonene (boiling point 176°C) with water (hp 100°C). In steam distillation, the
total vapor pressure is the sum of the pure vapor pressures of the two components
at a given temperature and is independent of both the mole fraction of each com-
ponent AND each other:
p total = polimonene + Powater = 760 Torr
The vapor pressures of both substances will increase with temperature, but the
vapor pressure of water will always be higher than the vapor pressure of lirnonene
because water is more volatile. The mixture will boil at the temperature in which
the total pressure of the system is equal to the pressure exerted on the liquid by the
atmosphere. As a result, limonene will distill despite its lower vapor pressure and
0 0
higher boiling point. At 97°C, P wat er is 695 Torr and P limonene is 65 Torr. Since the
sum of the pressures is equal to 760 Torr, the mixture will boil and co-distillation
occurs. The steam distillation of most volatile organic compounds that are im-
miscible with water occurs between 80°C and 1oo·c.
The setup for a steam distillation is basically the same as for a simple distillation,
except that a source of water and/ or steam is needed. Often a separatory funnel
containing water is simply substituted for the thermometer in a simple distillation
apparatus. Since it takes a lot of water vapor to sweep out the higher boiling organic
oils, it is often necessary to add water to the distilling fl.ask at frequent intervals
throughout the distillation until the organic compounds have been removed from
the mixture (Figure 8.9).
The distillate of steam distillation is a cloudy mixture of water and the immiscible
organic compounds. An organic solvent is then used to extract and isolate the oil
from the water. You may get to perform a steam distillation during the synthetics
portion of this course!
176
11 I
I
I 1111 I
Distillation II Chemistry 213W
NOTES H
Water condenser
C Hayden· McNcil. U...C
figure 8.9. A simple distillation setup. No thermometer is needed since the temperature will
be - 100°C throughout the distillation. Make sure you CLAMP the round bottom to a ring
stand as well as the condenser!
Sublimation
Sublimation is the conversion of a solid to the vapor state without passing through
the liquid state (not necessarily a type of distillation but the process is similar).
~.fost solid organic compounds cannot be distilled but COULD be a candidate for
sublimation. Before most solids can become a vapor they will melt, and at even
!:i.igher temperatures they will decompose before vaporizing. Some substances,
::towever, have an appreciable vapor pressure below their melting point and can be
sublimed. Examples include dry ice (solid carbon dioxide), camphor, iodine, and
naphthalene (found in mothballs). Sublimation is used as a purification method
for an organic solid when it can vaporize without melting, it is thermally stable
and does not decompose when heated, if the vapor can be condensed back to the
solid (deposition), and the impurities do NOT sublime.
Special apparatuses exist to accomplish purification via sublimation, but for the
purposes of this course, a very simple sublimation apparatus can be used: a large
LeSt tube (found on the common shelf) containing the compound to be sublimed
?S sealed with Parafilm. The end of the test tube is buried in a heated sand bath.
:he compound in the test tube sublimes because of the heat, turns into a vapor,
and travels up the test tube. The portion of the tube that is NOT buried in the sand
is much cooler and the vapor returns to a solid state (deposition). The impurities
177
usually remain behind in the bottom of the test tube. The purified crystals can t hen
: : NOTES
be scraped off of the sides of the test tube. You may get to perform sublimation
during the synthetics portion of this course!
Distillation Distilled Down

Simple distillation is used when the boiling points of the components in a liquid
mixture differ by MORE than 75°C, the liquid mixture is essentially pure (less than
103 impurities), or the impurities are nonvolatile. In some cases, simple distilla-
tion must be used because of time limitations, like in the case of the synthesis of
methylcyclohexenes.
Fractional distillation is used when the boiling points of the two components in
a liquid mixture differ by LESS than 75°C.
Vacuum distillation is used when the boiling point of a liquid is over 200°C or an
organic compound is thermally unstable.
Steam distillation is used when higher boiling organic compounds need to be

extracted from plant or spice materials .
Common Issues
1. What if the thermometer reading seems too low?
If the reading is between 25 and 30°C: the vapors have not yet reached the
distillation head. Be more patient!
If the reading is lower than the reported boiling point of the liquid being dis-
tilled: the thermometer may be improperly placed in the distillation head.
If the readings just seem "off": did you calibrate your thermometer to check
for accuracy during orientation?
2. If I'm separating two compounds, when do I change the receiving fl.ask?

In simple distillation, it's best to collect (in a separate flask) the liquid that
distills at S"C or less from the expected boiling point of the compound.
In fractional distillation, the receiving flask is changed soon after a sudden
increase in temperature. The large spike in temperature indicates that the
lower-boiling component is no longer present in the vapors at the distillation
head.
3. The temperature suddenly dropped during my distillation!

A sudden drop of temperature usually means that the thermometer is no longer
bathed in vapors. If there is still liquid in the distillation flask, increase the
temperature of the heat source. If there is very little liquid in the distillation
flask, the distillation is done!
178
Distillation II Chemistry 213W
Reagents used in this technique: NOTES II

2-methylcyclohexanol, 4-methylcyclohexanol, methylcyclohexene isomers,
85% phosphoric acid, 0.5 M NaHC03 solution, saturated NaCl solution, an-
hydrous sodium sulfate

In your drawer-all of the simple distillation pieces seen in Figure 8.9, separa-
tory funnel and stopper
Specialty items from the common shelf-stir/hot plate, heating mantle, large
stir-bar, glass wool, silicon grease, clamp holders, clamps, rubber bands
Correcting Your Boiling Points

First, your thermometer SHOULD have been checked for inaccuracies
during your orientation activities. If not, please do so before you begin!
Make sure that you correct ALL ofyour recorded temperatures to account
for the inaccuracies.
Second, the boiling point in all cases will be corrected to 760 Torr. If
the atmospheric pressure recorded in the lab is less than 760 Torr, then
the observed boiling point is depressed so you will need to add a correc-
tion factor. If the atmospheric pressure in the lab is greater than 760 Torr
then you will need to subtract a correction factor from your recorded
boiling point. The correction factor is 0.5°C for every 10 Torr difference
in atmospheric pressure from 760 Torr. For example, if your thermom-
eter is accurate (see above) and reads 108°C for the boiling point of tolu-
ene when the barometer reading is 720 Torr, the corrected boiling point
of toluene would be about ll0°C (at 760 Torr); see calculations below. A
barometer (with instructions for use) is available at the south end of Lab 215.
Calculation of the corrected boiling point of toluene:

Boiling point of toluene is observed to be 108°C at 720 Torr.
760 Torr - 720 Torr= 40 Torr; add 0.5°C for every 10 Torr below 760 Torr
Set up a simple equation to get the corrected boiling point of toluene at 760 Torr:
osc (4) + 108°C = 11o·c
Mr. Benzene says: The pressure in the labs will

USUALLY be below 760 Torr, somewhere between
720 and 750 Torr. The difference between the
observed boiling point and the corrected boiling
point for pressure will not be that different. It is
MORE important to correct for your thermometer
inaccuracy than it is to correct for pressure.
179
II NOTES
Procedures 1 and 2: Dehydration and Purification of
Methylcydohexanols
Substitution and elimination reactions are widely studied in sophomore or-
ganic chemistry classes. Specifically, acid-catalyzed dehydration of alcohols oc-
curs via an El (elimination, unimolecular) mechanism. Unlike E2 (elimination,
bimolecular) reactions, El mechanisms may involve rearrangements to form
a more stable carbocation. As a result, multiple products are often observed
when an El mechanism is involved.
Distillation is not only useful to separate two generic liquids used as solvents,
it is also useful in organic syntheses. In this experiment, a dehydration reaction
will be carried out by heating an isomer of methylcydohexanol in the pres-
ence of phosphoric acid; this El elimination reaction is an equilibrium process
(Figure 8.10). According to Le Chatelier's principle, removing a product from a
chemical system at equilibrium shifts the equilibrium to favor the formation
of products. This dehydration reaction will be done in a distillation apparatus
so that the alkene products will be removed from the reaction mixture by
continual distillation thus shifting the equilibrium to the RIGHT.
Mr. Benzene says: le Chatelier's principle!

Dehydration reactions! Zaitsev's rule!
Isn't Organic Lab exciting?!
or
+
Heat
2-rnethylcyclohexanol 4-rnethylcyclohexanol rnethylcyclohexenes
The products of this elimination reaction CAN

include the following isomers:
c5
Figure 8.10. Synthesis of methylcyclohexenes, Day 1.
180
,,
! .I
Distillation ;; Chemistry 213W
You will be assigned a starting material of either 2-methylcydohexanol or NOTES II

4-methylcydohexanol. Several alkene products are possible in each case due
to the El mechanism, some in greater proportions than others. Keep in mind
that the distribution of alkene products will depend on the starting material
you are assigned. The major products resulting from the different starting
materials will be dependent upon kinetic control (4-methylcydohexanol)
or thermodynamic control/Zaitsev's rule (2-methylcyclohexanol). If you are
unclear about the rules governing dehydration mechanisms, please refer to
your organic chemistry textbook!
The synthesis and purification will be accomplished over two lab periods, and
two separate distillations will be required. The first distillation in Procedure 1
is the REACTION: as the alcohol dehydrates in the round-bottom you will be
distilling over the alkene products. You want this reaction/distillation to go
slowly; if you heat the reaction too hot too quickly, you'll be distilling over a
large proportion of alcohol starting material in addition to the products. The
second distillation in Procedure 2 is the PURIFICATION by distillation. If any
alcohol did distill over with your products, you can separate the two via simple
distillation. Your alkene product mixture will be characterized by IR and NMR.
The identity and distribution of alkene products will be assigned by GC analysis.
Procedure 1 : Synthesis of Methylcyclohexenes

ODD-numbered desks, use 2-methylcyclohexanol. EVEN-numbered desks,
use 4-methylcydohexanol.
Mr. Benzene says: This reaction involves

concentrated (85%) phosphoric acid, which is
corrosive, and 2- or 4-methylcyclohexanol, which
are irritants. Use gloves when handling, and change
gloves frequently. Avoid any contact with eyes or
skin.
Running the Reaction

Assemble a simple distillation apparatus on top of a stir-plate (see Figure 8.4,
s ee pieces needed on the next page in Figure 8.11) with a 10 mL graduated
cylinder as the receiver.
181
II NOTES
Figure 8.11. Pieces needed for simple distillation from the BLUE KIT. A. Heating mantle
+ iron ring. B. 100 ml Round-bottom flask. C. 3-way distillation head. D. Thermometer
adapter. E. Teflon seal to hold thermometer. F. Thermometer. G. Skinny condenser.
H. Collection adapter. I. Collection flask. J. Thin-walled tubing. Water flows IN to the
condenser at the bottom and flows OUT at the top. K. Rubber bands, used to hold the
distillation head and collection adapter to the condenser (see Figure 8.4). L. Stopcock
grease, use to lightly grease all of the glass joints.
Pour 20 mL of your assigned methylcyclohexanol and 5.5 mL of 85% phos-

phoric acid into a 100 mL round-bottomed flask. Add a 1/2-inch magnetic stir
bar, and swirl to mix. Keep the graduated cylinder in ice at all times during the
reaction as you collect, only removing it intermittently to check the volume.
Heat the 100 mL flask with the mixture in a heating mantle without sand
(except to cover exposed coils), with Varistat set at 50.
You may use a small amount of insulation (glass wool) to help keep the distil-
lation head warm during the reaction. The glass wool is located on the com-
mon shelf. Keep in mind that you MUST wear gloves when handling. Wrap
the glass wool from the round-bottom's neck up to the thermometer. You
can hold the insulation in place with some aluminum foil (also located on the
common shelf).
182
: ;[
Distillation :: Chemistry 213W
NOTE: Once you turn your Varistat to 50, it will be at least 20 to 40 minutes NOTES :I
before you see the 1st drop of distillate collected in the graduated cylinder.
Remember, the reaction has to get hot enough to undergo a dehydration and
then maintain a temperature high enough to distill over the products! Once
the distillation begins, the ideal rate of collection is about one drop per second
or less. If the distillation is going too quickly, turn your Varistat level down!
Do not allow the temperature to exceed 120°C. The water that co-distills with
the alkenes reduces the alkene boiling point, so the temperature reading may
be lower than the expected boiling point of the product. It is normal for the
liquid in the reaction flask to turn yellow as the reaction progresses. If your
reaction isn't progressing at a reasonable rate, then you may turn your Varistat
to level 60 or 70.
Mr. Benzene says: Be patient! Let the science of

distillation do its thing!
As distillate is collected you will be recording data (time, volume, temperature).

Make a chart in your notebook like the following:
Observed Temp Corrected Temp

Time (minutes) Volume (ml) (oC)
(°C)
1
2
3
The amount of distillate that you will collect will most likely exceed 10 mL. If
your graduated cylinder gets full and the reaction is still progressing, quickly
pour your collected distillate into a small Erlenmeyer flask and seal it with a
cork.
Remember: You WANT the distillation to go slowly so that you form the alkenes
in the pot, then distill the product over. If you heat your reaction too fast and
all of your liquid distills over in a short period of time, starting material will
be collected with your product.
Stop distilling when only a few milliliters of liquid remain in the flask. It will
turn dark yellow and start to foam. DO NOT DISTILL TO DRYNESS!
183
II NOTES
'c
,.
.....
, 80 I
~
c ...
D
Mr. Benzene says: This product sure does stink!
Keep your hood sash low and rinse all your
glassware with acetone befor it leaves the hood!
The Workup
There should be two layers in the receiving flask; the alkene layer is ALWAYS
the TOP LAYER. Transfer the liquids to your separatory funnel and drain
off the bottom aqueous layer. Wash the upper alkene layer twice with 5 mL
of 0.5 M sodium bicarbonate. Each time, drain the lower aqueous layer with
each wash and always keep the upper organic layer in your separatory funnel.
CAUTION: Gas will evolve so make sure you let the neutralization take place
before you put the stopper in your separatory funnel. Vent adequately when
you shake the mixtures!
Next, wash the organic layer twice with 5 mL of saturated sodium chloride
solution each time. Drain the lower aqueous layers off each time. Finally, drain
your upper organic layer into a small beaker, and dry the organic layer with an
adequate amount of anhydrous sodium sulfate for at least 10 minutes.
Decant the organic layer into a dry 50 mL round-bottom flask. Stopper and
Parafilm the round-bottom containing the crude alkene mixture so that it can
be purified by distillation the next lab period. You must seal your RB flask!
Otherwise, all of your products will evaporate before the next lab period.
Procedure 2: Purification of Methylcyclohexenes

Add your stir bar to the 50 mL round-bottom containing your alkene mixture
and redistill using a simple distillation apparatus and a heating mantle plugged
into your Varistat (put at level 50 again once the entire apparatus is set up).
Make sure apparatus is fully dry, and the receiving flask (the 10 mL graduated
cylinder) must be in ice.
Collect your product when the temperature reading remains fairly constant.
It's okay if you collect over a 5-degree temperature range; you may not get a
constant reading due to the different concentrations of the different isomers
in your products. Record the data in the same format as Procedure 1 in your
notebook. The liquid obtained between 95°C and 112°C (range collected will de-
< pend on your isomer) should consist exclusively of methylcyclohexene isomers.
184
I ll
11
T
'' '
I I .I
Disti llation II Chemistry 213W
'c
,,.
.......
tJG I
~
c,
D
Mr. Benzene says: Remember, don't distill to
dryness! Keep a close eye on your distillation
round-bottom flask!
NOTES II
After you are done collecting your alkene mixture, determine mass and calculate
the percent yield of your alkene products. Instead of weighing the liquid you
could also use the total volume you collected and the density of the alkenes
(0.80 g/mL) to calculate the mass in grams.
Characterization of the Alkenes

All students will discuss IR, NMR, GC, and GC-MS in their reports. However,
it is time consuming to collect all this data individually. Your TA will assign
you to run either NMR and IR or GC. GC-MS data will be provided to you by
the course instructor. Exchange data with another student for your isomer.
Spectral Data
Some students will analyze the distribution of alkene products via gas chro-
matography; alkene peaks should appear on the GC in order of the alkene
boiling points.
To prep your GC sample, put ONE DROP of your alkene mixture in a shorty
vial and fill the vial to the top with dichloromethane. For the GC, set the initial
temperature to 40°C, hold for 5 minutes (initial time), heat up the oven at a
rate of 10°C per minute to a final temperature of 150°C.
Make sure that your GC data is good: if it's too concentrated the peaks of
interest (ignore the dichloromethane peak before 2 mins) will have plateaus.
If it's too dilute, you won't be able to see the peaks of interest and their areas
may not print out at the end of the GC run.
The only information you can obtain from the GC is the number of isomers(#
of peaks) and their relative concentrations (area of the peaks). The identity of
the alkene isomers can be verified by GC-MS data that will be provided
to you by comparing the order of your peaks AFTER the dichlorometh-
ane to the order of the peaks on the GC-MS. To interpret your GC and
the GC-MS data, please read the GC Tutorial on ANGEL and/or look at the GC
chapter found in this lab guide. Make sure that the GC and GC-MS data are
properly annotated for your report and that you calculate the 3 composition
for both sets of data.
185
II NOTES Some students will characterize the alkenes by IR and NMR. For the IR, you
can use liquids directly on the diamond plate. For the NMR, put a few drops
in your NMR tube and dissolve in deuterated chloroform. The NMR data will
NOT integrate properly because your sample is a mixture of isomers. Instead
of relying on integration values, focus instead on the chemical shifts of the
peaks and whether or not you synthesized an alkene. The IR will confirm the
functional groups present in your mixture and whether or not you have alco-
hol starting material as a contamination. Make sure your data are properly
annotated.
'c
,,. ......
~
~G I
c ...
D
Mr. Benzene says: Authorized collaboration makes
for some great science! Please exchange your data
with someone in your section for your assigned
alcohol so that you have GC, IR, and NMR data to
analyze for your report. Make sure you properly
cite the data you receive from another student. You
D also MUST include the GC-MS data for your isomer
that is provided to you.
Summary of Data that You Need

% yield of alkene mixture
NMR, IR, and GC/GC-MS data for your alkene mixture
% composition of the alkene mixture using the areas on the GC and GC-MS data
186
_
1
j~- _ _ Ill .
NOTES •.•.
I. Experiment Info
II. Purpose

Include subsections in this section for each procedure; use subheadings.
Remember, this section should be written in bullet form. It should be written
as you complete the steps of each procedure, making sure to include pertinent
data and observations (as the steps are performed).
IV. Calculations
3 yield of your alkene mixture.
3 composition of your alkene mixture via GC data and GC-MS data.
V. Experimental
Write an experimental for the synthesis of your cyclohexenes. Follow the
example provided in Chapter 3.
VI. Discussions and Conclusions

A short introduction discussing the utility of distillation in organic syn-
thesis/ importance of this reaction to illustrate the use of distillation.
An analysis of your dehydration reaction. Explain why the reaction was
done as a distillation and then a second distillation had to be performed.
Was distillation effective for the synthesis and purification? Remember
to think about not only purity based on spectral data but also 3 yield.
A discussion about the data obtained from the synthesis:
A qualitative discussion of NMR and IR data. Remember, integration
values in your NMR are useless since you obtained a mixture of iso-
mers. Instead, discuss chemical shifts and what is indicative of product
formation. Does your NMR correlate with your IR data? Discuss what
peaks in your IR indicate the formation of product or the presence of
starting material.
187
A quantitative discussion of the GC and GC-MS data. Here, you should

include what isomers you formed and the 3 composition based on
the area of both the GC and GC-MS. Include a discussion of ther-
modynamic vs. kinetic control to support your findings. Remember
to discuss Zaitsev's rule and if it's relevant to your assigned starting
material.
A short conclusion: summary, improvements, etc.
VII. Spectral Data

NMR and IR data, fully annotated and labeled as figures.
GC and GC-MS data, fully annotated and labeled as figures.
VIII. References
Submitting your Notebook Pages Report for Chapter 8

l. Rip out the white, original Notebook Pages.
2. Download and attach the Distillation grade sheet to the front of your
assignments.
188
,~, - - '
, ,,
I '
I 'I
1d
CHAPTER 9
Recrystallization
Prelab Assignment
Your PrelabAssignment (worksheet on ANGEL) must be completed before coming
Assignment at the beginning of the class period. You will also be assessed a 103
1. Synthesis of acetanilide
2. Choosing a suitable recrystallization solvent
3. Macroscale recrystallization of acetanilide
4. Melting points of acetanilide (pure and impure) and IR, NMR (pure)
Quiz for Chapter 9

for the experiment.
Activity Breakdown
Day 1: Procedures 1 and 2
Day 2: Procedure 3
189
II NOTES Introduction
Recrystallization is the second of the three purification techniques. It is commonly
used to purify solids contaminated with relatively small amounts of impurities.
In general, during recrystallization the desired solid (called the solute) as well as
the impurities are placed in a suitable hot solvent and upon cooling, the desired
compound precipitates in its pure crystalline form while leaving the impurities in
the recrystallization solvent.
Let's take a look at our model SN2 reaction and assess the usefulness of recrystal-
lization as a purification technique.
(;' BrQ)
OMe
H
TOH 0
+
1 2 3
Remember that in the last chapter, we concluded that distillation was NOT a use-
ful purification technique for the solid product of this reaction. However, because
3 is a solid, recrystallization is an ideal technique to utilize. The process followed
to purify 3 would be:
Choosing a suitable solvent

Dissolving the compound in a minimum amount of solvent
Removing insoluble impurities
Crystallization
Collecting and washing the collected solids
Drying the crystals
Why does recrystallization work so well and how are the impurities separated out
from the desired compound to be purified? The concepts that are vital to the expla-
nation of why recrystallization purifies compounds are as follows:
Solubility. See next page.

Saturation Level. Let's say that 95% of the molecules in a sample are the desired
compound and 5% are impurities, which you're trying to separate out. During
recrystallization, the concentration of the desired solute is significantly higher
than the concentration of the impurity in solution . Therefore, when the solu-
tion cools, the desired solute will be forced out of the solution back to a solid
while the impurities will remain soluble.
190
11111
Recrystallization 11 Chemistry 213W
Exclusion. Every solid, pure organic compound has a defined crystalline struc- NOTES : :
ture. As the solution begins to cool very slowly, the desired solute's crystal lat-
tice starts to take shape. Only molecules of its own kind can fit into this crystal
lattice. Impure molecules cannot fit properly into the newly forming lattice
and will therefore not be incorporated into the lattice. Thus, the recrystallized
solute will not contain any impurities. The impurities stay in solution and are
,.,
filtered away from the pure solid.
'C ....
C,
, t'JG I Mr. Benzene says: Thermodynamics to the rescue!
~ 0
Nucleation. Crystallization is initiated at a point of nucleation-a seed crys-

tal, a speck of dust, or a scratch on the wall of the test tube if the solution is
supersaturated with the solute.
The success of a recrystallization is based on the amount of pure solid crystals

that can be obtained using this technique (called 3 recovery). Ideally one would
like to obtain 100% of the original weight of material. This is rarely possible, but
recovery of 80 to 903 of the original weight can be obtained if: 1) a suitable solvent
is chosen and 2) the recrystallizing technique is carried out correctly.
Six Steps of Recrystallization

1. Choosing a Suitable Recrystallization Solvent
Selecting an appropriate recrystallization solvent is the first and normally the most
difficult step in the purification process. A successful recrystallization depends on
the solubility differences between the substance and the impurity. Recrystallizing
a known substance makes choosing a solvent of similar polarity simple. Reference
textbooks such as the Handbook of Chemistry and Physics, or an online chemical
database such as SciFinder Scholar can be used to find information on the solubil-
ity of organic compounds.
If the material you will be recrystallizing is unknown, then the process of choos-
ing a solvent is not as straightforward and is achieved mainly by trial and error;
dissolve the unknown compound in a variety of solvents, heat, and observe the
results. However, you can narrow down a list of suitable solvents based on the
polarity of the compound to be purified.
191
I: NOTES
Solubility: Same vs. Similar Polarities
Italian salad dressing is a classic example of an everyday solubility problem. It is
clear from observing the interaction between vegetable oil and water that they
are not compatible and do not mix well. This phenomenon can be understood
by the simple principle "like-dissolves-like." Water (a small polar molecule) and
vegetable oil (a long saturated non-polar alkane chain) possess dramatically differ-
ent polarities and thus do not mix well. However, methanol (CH 3 0H) or ethanol
(CH3 CH 2 0H), which are small organic molecules containing a functional group
that can H-bond, are readily soluble in water. We would find that the vegetable
oil, which contains molecules with large hydrocarbon chains, is readily soluble in
hydrocarbon solvents such as hexanes.
Solubility depends on the polarities and interactions between the solute molecules
(the solid to be purified) and the solvent molecules. For recrystallization, a solvent
is selected based on a polarity SIMILAR to the polarity of the compound you are
attempting to purify. Remember that in order to evaluate the polarity of your
compound you need to consider the functional groups present: extent of hydrogen
bonding, number of electronegative atoms, polarizability of bonds/atoms, and the
net dipole moment of the molecule. Refresh your memory on the evaluation of
molecule polarity by re-reading the TLC introduction material.
.•.
'c
,. VG\
~
c,....
0
Mr. Benzene says: We like our recrystallization
solvent to be not too polar, not too non-polar, but
juuuuuuust right.
During recrystallization, we do not want to choose a solvent of the SAME polar-

ity as our molecule of interest, otherwise the compound will remain dissolved in
that solvent even at low temperatures. We want to choose a solvent of a SIMILAR
polarity so that the solute will be only partially soluble in that solvent. Table 9 .1
lists some common organic solvents in order of polarity. This table can be used
to select solvents with polarity SIMILAR to the polarity of your solute. It is quite
unlikely that a solvent with polarity that is very different from your solute will
work at all, since you need to have solubility in the solvent at high temperatures
for it to be a possible recrystallizing solvent.
192
" --,111ill
I I
Recrystallization H Chemistry 213W
Table 9.1. List of common solvents by decreasing polarity. NOTES II

Most Polar
Water (HzO)
Acetic Acid (CH3COOH)
Methanol (CH3 0H)
Ethanol (CH3CHzOH)
Acetone (CH3COCH3)
Dichloromethane (CH2 Clz)
Chloroform (CH3 Cl)
Ether (CH3 CHzOCH2 CH3)
Benzene (C6HJ
Toluene (C 6H5 CH3)
Hexane (CH3 (CHz) 4CH3)
Hexanes (C 6H14 isomers)
Least Polar
For example, phthalic acid is an aromatic compound with two carboxylic acid sub-
stituents. Solubility data in various solvents can be seen in Table 9.2.
Table 9.2. Solubility data for phthalic acid.

Solvent Solubility (M, moles/L) at 25°C
DMSO 3.6M
Chloroform O.SlM
Methanol 0.43M
Water 0.02M
Phthalic acid is VERY soluble in DMSO and partially soluble in chloroform and
methanol at room temperature; therefore, its polarity considering the two polar
c.arboxlyic acid groups and the non-polar benzene ring is almost the SAME as those
3 solvents. However, it is not that soluble in water at low temperatures, making
water a good candidate to test as it has SIMILAR polarity to water.
Solubility: Temperature
The second factor affecting solubility is temperature. The temperature of the sol-
vent directly relates to the amount of material that can be dissolved. One example
is making rock candy from sugar. In order to obtain the saturated sugar solution
needed to make rock candy, the water is brought to a vigorous boil. More sugar
v.ri.ll dissolve in the water when the temperature is increased. This is a very impor-
tant factor in recrystallization because these differences in solubility at different
temperatures will be used to our advantage.
193
II NOTES
The best solvent for the recrystallization of a solute should be sparingly soluble
at room temperature and completely soluble at higher temperatures. Figure 9.1
shows the solubility of a typical organic compound in three different solvents as a
function of temperature. At any given temperature, the compound has a very low
solubility in solvent B. Solvent C is exactly the opposite, its solubility is too great
at all the temperatures. However, solvent A seems to be a good choice because it
has a low solubility at moderate temperatures, and the solubility of the compound
changes significantly as the temperature increases. This difference in solubility with
small changes in temperature is an ideal solvent for recrystallization.
B
~
Temperature (°C)
Figure 9.1. Solubility differences of a solid in three solvents, A, B, and C versus temperature.
In an ideal system, the compound should be completely soluble in the hot solvent
and quite insoluble in the cold solvent, and the impurities should be soluble at all
temperatures. (The impurities present can also be INSOLUBLE at all temperatures
and filtered off in step 3.)
This ideal situation is often not obtainable. Although a single-solvent system is

always the best for recrystallization, a two-solvent system may be necessary to
achieve the ideal system. When choosing a two-solvent system, the two solvents
must be miscible or capable of being mixed in all proportions. Table 9.3 summarizes
the miscibility of some common solvents. Notice that with only one exception,
organic solvents are miscible with each other, but many are not miscible with water.
'c
..
.......
t)G i
~
c ....
D
Mr. Benzene says: Miscible means capable of being
mixed.
194
'I
. i1ll
----
Table 9.3. Miscibility of common solvents (M = miscible, I = immisci ble).

NOTES II
cii
c
-E
~
.s::.
cii
E
...
Miscibility
"C
"i:i
~
-<
a>
-=
c - ...
a>
c
..
Q
...
...
Q
Q
0 a>
c
0
c cii
c
-- - -
a> Q ~
•!::! Q c ~ .s::. cii a>
a> cii
N
c ..2 .s::. ~ a> l< ::I
.!::! .s::. .s::.
~
{J {J a> .s::. a> cii
;§
< u Q 1.1..1 1.1..1 ::c ~
Acetic Acid M M M M M M M M M M
Acetone M M M M M M M M M M
Benzene M M M M M M M M M
Chloroform M M M M M M M M M
Dichloromethane M M M M M M M M M
Ethanol M M M M M M M M M M
Ether M M M M M M M M M
Hexane M M M M M M M M
Methanol M M M M M M M M M
Toluene M M M M M M M M M
Water M M M M
Some typical two-solvent systems include ethanol-water, methanol-water, acetone-

hexane, ethanol-toluene, and acetic acid-water. (Notice that each of these combi-
nations are miscible.) When using two solvents, it is best to find one solvent that
will completely dissolve the compound to be recrystallized at high temperatures
and the second that dissolves it poorly at high temperatures. To test a two-solvent
system, dissolve the compound in a minimum amount of the good solvent (dis-
solves the compound well at the boiling point), then add the bad solvent (dissolves
the compound poorly) dropwise until the solution becomes slightly cloudy. Reheat
the solution until clear and then cool slowly. Upon cooling, the compound should
crystallize. If you are having problems crystallizing the compound, reheat and add
more of the more insoluble solvent. The compound should eventually precipitate,
although this can lead to the production of an oily noncrystalline mass.
Choosing a Solvent: Practical Concerns

There are several practical concerns when choosing a recrystallization solvent:
A solvent with a very high boiling point could lead to issues; if too much sol-
vent is used during the recrystallization process, it would be very difficult to
reduce the volume to obtain a more concentrated solution.
A solvent with a very low boiling point could also be problematic; often the
solvent can evaporate during the heating process before dissolving the solute.
195
For obvious reasons, the solvent should not react with the solute.
H NOTES
The solvent should have a boiling point lower than the melting point of the
compound. If the boiling point of the solvent is higher than the melting poin:
of the solid it will tend to "melt" instead of dissolve. "Oiling out" is the t~
used to describe when a solid turns to an oil instead of dissolving. Oils are hard
to handle and don't recrystallize. Rather the oil will transition back to a sob.:
upon cooling without any impurities being removed. By choosing a differer::
recrystallization solvent, oiling out can normally be avoided.
Mr. Benzene says: If it oils...cool it then re-boil!
The impurities present must be SOLUBLE in the chosen solvent at all tem-
peratures or INSOLUBLE at all temperatures.
In addition, a nontoxic, inexpensive, volatile, and nonflammable solvent is the
best choice. However, since most solvents do not fit all these requirements.
you will have to find the best compromise for your specific recrystallization.
2. Dissolving the Compound in the Chosen Solvent

Once a suitable single solvent or solvent pair has been found, the impure material
is dissolved in the solvent with heat. The most common mistake when dissolving
the compound is adding too much solvent. For an efficient purification, adding the
minimum amount of hot solvent is essential. The minimum amount is completely
dependent on the quantity of material and the solubility of that material in the
solvent used. If the compound's identity is known, the solubility data can be used.
to calculate the approximate amount of solvent needed.
This data is convenient for a known compound, but if your substance is unknown
or has been synthesized for the first time, this data would not be available. ~
this case, the amount of solvent needed to dissolve the compound is determinee
experimentally. Begin with just enough solvent to cover the material and heat
Once the solute- solvent mixture comes to a boil, continue to add hot solvent
(Adding hot recrystallization solvent will avoid cooling the solution, which can
lead to precipitation or poor quality crystals.) If a good recrystallization solvent
was selected, the solid will completely dissolve at the solvent's boiling point. The
substance is completely dissolved when the solution is translucent. If the complex
is white, then it will be a colorless translucent solution. However, if the compound
is yellow, then the solution will be a translucent yellow solution. Recognizing when
the solid just dissolves completely is very important. DO NOT add too much so:-
vent. This will cause problems when attempting to collect the solid. The goal when
196
Recrystallization ;; Chemistry 213W
heating this mixture is to create a saturated solution in hot solvent. (Just like our NOTES II
rock candy example.) By creating a completely saturated solution, the less soluble
compound will crystallize upon cooling. If an appropriate solvent was selected,
-~ur compound will crystallize with ease. Too much solvent will hold more solid
on cooling and it may not crystallize. However, if too much solvent is added, there
is a simple solution: heat the solution to the boiling point and evaporate some of
the solvent to reduce the volume of the solution. It is very easy to add too much
solvent while learning to recrystallize organic compounds.
One practical consideration when dissolving the compound in a heated solvent is

avoiding a phenomenon called superheating or bumping. Superheating is when
the temperature of the solvent reaches a temperature greater than that of the boiling
point of the solvent. When this occurs, the solvent will very rapidly and sometimes
violently bump or splash. Bumping is the sudden explosive boiling of the liquid near
the bottom of the flask. Bumping can be avoided by using a Teflon boiling chip (small
white chips found on the common shelf) or a wooden boiling stick (also found on
the common shelf). These two methods allow the solution to heat evenly and boil
smoothly.
Mr. Benzene says: Use boiling chips or a boiling

stick to avoid bumping because bumping is bad,
okay?
3. Removing Insoluble Impurities

Once a hot saturated solution is obtained, there may still be some remaining par-
ticles, including dirt, sand, or insoluble impurities. If these particles are dense and
settle to the bottom, the liquid can often be poured off or decanted from the solid.
If you are working on a larger scale, an alternative to decanting is to use the hot
filtration apparatus shown in Figure 9.2. It is essential to have the entire flask and
funnel heated. This can be accomplished by heating a small amount of recrystalliza-
tion solvent in the bottom of the Erlenmeyer flask. This allows the vapor to rise,
warming the flask, funnel, and filter paper. If the entire apparatus is not warm,
the product will crystallize along the inside of the filter paper.
'c
..
.......
VG I
~
c,
0
Mr. Benzene says: Heating the entire hot filtration
apparatus is essential to the process. Otherwise
crystals will form when they come into contact
with cold glassware.
0
197
H NOTES
CHayden·l'olcNeil. LLC
Figure 9.2. Hot fil tration setup.
4. Crystallization
Once you have obtained a translucent saturated solution in h ot solvent free of
insoluble or colored impurities, it is time to crystallize your solid product. Crystal-
lization can sometimes occur within seconds or take days . It should be mentioned
that crystallization is different from precipitation:
Precipitation is defined as the formation of a solid product from a reaction that

separates from solution. Precipitation normally occurs very rapidly and results in
very fine crystals.
Crystallization is similar to precipitation in that you separate a solid from the re-
maining solution; however, crystallization normally refers to the slow growth of
crystals. Slow crystal growth yields purer crystalline formations.
Mr. Benzene says: Remember! Slow cooling leads to

the best crystals.
198
' ; ' .1111
Recrystallization II Chemistry 213W
There are three ways to initiate crystallization: cooling, scratching, and seeding. NOTES H
Slow cooling is the easiest method to yield crystals and works well in most cases.
Simply allow the hot saturated solution to cool slowly without agitating or disturb-
ing the solution in any way. Allow the hot solution to cool to room temperature by
placing the fl.ask on a book or paper towel (to allow a slow release of heat), then
move it to the cooler benchtop and finally put it in a beaker of ice. The slower the
solution cools, the more likely it will form perfect crystals, which can exclude the
impurities from disturbing the crystalline lattice of the compound, and result in
a pure compound. Alternatively, you may cool the solution slowly to room tem-
perature and then place the solution in the refrigerator until the next lab period.
1
• ote: All solutions placed in the refrigerator must be in capped, labeled contain-
ers!) This slow cooling process normally yields beautiful crystals.
Sometimes it is difficult to obtain crystals even after the solution is cooled in an ice
::iath. In this situation, crystallization can be induced by scratching the inside of the
beaker or fl.ask with a glass stirring rod. This will produce microscopic fragments
of glass that may act as surfaces on which crystal growth can begin.
If slow cooling and scratching does not produce crystals, crystallization may be
induced by seeding. Seeding is accomplished by taking a small crystal from the
original solid and dropping it into the solution. This will provide a nucleation site
for similar crystals to grow. However, by adding some of the original material,
you are inevitably increasing the amount of impurity in the resulting solid. This
can be avoided by seeding with a crystal from a pure bottle of substance-if the
substance is known. Seeding is normally used only as a last resort .
'c
..
.......
t>G I
~
c,
D
Mr. Benzene says: One crystallization method that
is not encouraged is evaporation.
_-aturally, if you are having trouble crystallizing a solid, evaporating the solvent
completely will recover the material. This method defeats the purification process;
a:ot only have you recovered the pure material, but also the impurities. When com-
?:.ete evaporation occurs, the recrystallization procedure must be carried out again.
199
H NOTES 5. Collecting and Washing the Crystals
Mr. Benzene says: The filtration method used

depends largely on the amount of crystals collected.
Use your Hirsch funnel (found in your Red Kit) for
small-scale applications. Use your Buchner funnel
(found in your drawer) for large-scale applications.
The filtration method used to separate the crystals from the remaining solution
and to "collect" the solid depends largely on the amount of crystals and solution.
Gravity filtration through filter paper can be used for recrystallizations involving
1gto100 g or more. More commonly, organic chemists use a fast and effective
filtration method called vacuum filtration for recrystallizations involving at least
0.1 g up to 100 g or more. But for small quantities of 10-100 mg in a few mL of
solution, pipette filtration is quick and effective.
The first method, gravity filtration is used when there is at least a half a gram of large,
well-defined crystals. A glass funnel fitted with fluted filter paper is used to collect
the crystals. With very large amounts of solid, this process can consume a lot of time.
A quicker and more efficient method is vacuum filtration. Vacuum filtration is

probably the most common filtration type used by chemists. The funnel used for
this method is called a Hirsch funnel (Figure 9.3), if small, or a Buchner funnel
(Figure 9.4), if large. These funnels have a fl.at plate inside which can either be
made from ceramic materials that contain lots of small holes or from a porous
polyethylene disk.
To use these funnels, a round piece of filter paper of a matching diameter is placed
over the perforated or porous plate. The Hirsch or Buchner funnel is put into a
vacuum filter fl.ask with a rubber adapter in between to assure a vacuum tight
seal. The filter fl.ask has a connecting tube or "side arm," which is connected to
the house vacuum using the THICK-WALLED tubing. Wet the filter paper with
a small amount of solvent or recrystallization solution to prohibit loss of product
under the filter paper. Once the vacuum is turned on, the wet filter paper is sucked
down on the plate so that it seals uniformly. The crystals and solution are swirled
or agitated and quickly poured onto the filter funnel. The vacuum quickly draws
the liquid (aka, the filtrate or mother liquor) through the filter paper disk, leav-
ing the crystals behind. Any crystals remaining behind in the beaker are scraped
out with a spatula and/ or washed out with some of the recrystallizing solution
from the filter fl.ask or with small amount of cold recrystallizing solvent. This step
requires great care. Using too much solvent that is not cold enough can dissolve a.
lot of solid product, thus decreasing your recovery and yield significantly.
200
I . --- -
c::>- Flatpaper
filter
N OTES H
Rubber adapter
Thick-walled
tubing
Hirsch Funnel
Figure 9.3. Vacuum filtration apparatus using a Hirsch funnel for small scale.
C)-- Flat filter
Porcelein
Black rubber
Buchner
adapter
funnel
Thick-walled
tubing
to vacuum
125 ml
filter flask
Buchner Funnel
Figure 9.4. Buchner funnel filtration for large scale.
201
For very small quantities of materials, pipette filtration is the preferred method.
II NOTES
Figure 9.5 shows the pipette filtration method for collecting solid products.
(·~~l:;J - Flat-tipped
~'.:.t:tf pipette
~
_.,;(
Figure 9.5. Pipette filtration of solid product.
When you have solid material leftover in a reaction tube or small test tube, there
will be less product loss if you remove the solvent and leave the solid behind. This
can be easily achieved by pipette filtration. Select a pipette with a perfectly fiat tip
(when looked at from the side), and without chips on the tip. Push out all the air by
squeezing the pipette bulb. Slowly lower the pipette into the solution and ease your
way to the very bottom of the reaction tube. Once the pipette tip is squarely and
firmly pressed against the bottom of the tube, slowly release the pipette bulb while
keeping the pipette tip pressed against the bottom of the tube. The solvent will be
slowly drawn up into the pipette and the product should remain behind. Initially you
may see a small amount of product move up the pipette. Don't panic! This is a normal
loss for this technique. This technique is a little trickier than vacuum filtration and
normally requires some practice (practice with some inert materials from the com-
mon shelf, such as sodium sulfate and hexane). The separation is easier if you have
big, chunky crystals; very fine crystals will be difficult to separate using this method_
After the crystals have been successfully separated from the solvent, washing the
crystals with cold recrystallization solvent will put the finishing touches on your
purification. This will wash away any last t races of soluble impurity that have been
left on the surface of the crystals. It is essential to use cold solvent; hot or room
temperature solvent will dissolve too many of your crystals. If you used gravity
filtration or vacuum filtration to collect the crystals, drop the cold liquid directly
onto the crystals with a pipette. If you performed a pipette filtration, add the cold
202
Recrystallization :: Chemistry 213W
solvent directly to the tube while immersing it in ice, stir the solvent and then NOTES : :
remove the solvent using pipette filtration as you did before. Remember, careful
pipette filtration will increase your percent recovery of the product.
6. Drying the Crystals

The easiest way to dry the collected crystals is to be patient and allow the residual
solvent to evaporate over the course of a few days. Leave the crystals in a container
open to the air in your desk. Over a period of a few days, depending on the boil-
ing point of the solvent, they will dry. If there is not sufficient time to allow this
slow drying process or if you are using t est tubes, reaction tubes or solvents with
higher boiling points, such as toluene or water, there are several other methods
including vacuum drying or using a stream of nitrogen. In addition, a simple way
to remove a major proportion of a solvent is to press the solid between pieces of
filter paper or paper towel.
Recrystallization: A Case Study

Let's re-visit the SN2 example reaction and apply the background knowledge just
discussed to the purification of 3 by recrystallization. If the reaction didn't go
as planned, there MAY be leftover 1 and 2 after the workup that will need to be
removed. Getting rid of 2 is easy: since it's a liquid, it won't co-crystallize with 3
during the recrystallization process; it will remain dissolved in the solvent and can
be filtered away. Getting rid of 1 is a little trickier. The polarity of 1 is very similar
to the polarity of 3. It will most likely co-crystallize during the recrystallization
process if it's present in a large amount. If both 1 and 3 are still present after an
attempted recrystallization, column chromatography is probably the best choice
for purification.
~
OMe
Br~
'.::::::
KzC03
+
DMF
OH l o-
H 0
1 2 3
!.....et's assume that the workup was effective at removing excess 1 from the reaction
::ilirture, and that 2 is present in relatively small amounts (as detected by TLC).
How will the purification process work?
.?irst you need to choose a suitable solvent. Remember, a solvent of SIMILAR po-
larity but not the SAME polarity is a good place to start. Compound 3 is slightly
polar. it has many electronegative atoms, but it has very few functional groups
203
Chemistry 213W II Chapter9
capable of hydrogen bonding. It also has two aromatic rings, which are relatively
== NOTES
non-polar. Considering the molecule as a whole, it possess a "middle-of-the-road"
polarity. Solvents that make good candidates for testing of SIMILAR solubility
would be: dichloromethane and benzene. Testing revealed that 3 is soluble at
room temperature in dichloromethane; the polarity of 3 and the solvent are too
much the same. Benzene is a suitable solvent because 3 is of SIMILAR polarity.
The solute is insoluble at low temperatures but very soluble at high temperatures
and the impurities are soluble at all temperatures. NOTE: while benzene is actu-
ally the best solvent experimentally, in this course benzene is usually NOT chosen
because of its carcinogenic properties.
Second, once a suitable solvent is chosen, the entirety of 3 is recrystallized. The

glassware chosen and the amount of solvent used during the purification process
are dependent on the scale of the reaction. Ifless than 500 milligrams of material,
a small beaker or even a test tube with less than 10 to 20 mL of solvent seems
suitable. If more the 1 gram of material, a larger beaker and 20 mL or more of sol-
vent is best. The crystals are covered with a small amount of solvent and the test
tube/beaker is gently heated and warm benzene is added until all of the material
is completely dissolved.
Third, if there are no insoluble impurities to address, then crystallization is achieved

by slow cooling the beaker/test tube first on the lab bench THEN in a cold ice-water
bath for 15 to 20 minutes.
Fourth, the crystals are collected via vacuum filtration (remember: Buchner funnel
for large-scale and Hirsch funnel for small scale) .
Fifth, the crystals are allowed to dry before analysis.
In this experiment, you will synthesize acetanilide. Once isolated you will then
determine the best solvent to recrystallize the acetanilide in, and carry out this
purification. Selecting an appropriate recrystallization solvent is a critical part of
the process and requires experimentation. You will evaluate the effectiveness of
your purification through melting point, 1 H NMR, and IR analysis.
204
Recrystallization :: Chemistry 213W
During the FIRST lab period: Complete Procedures 1 and 2. NOTES I:

During the SECOND lab period: Complete Procedure 3.
Mr. Benzene says: Since you will be macroscale

recrystallizing your acetanilide on the second day
of this lab, you must let it dry in your locker before
you can take a melting point and prepare for NMR/
IR analysis.

Acetic anhydride, aniline, acetanilide, distilled water, hexanes, ethanol, di-
chloromethane

In your drawer-SO mL round-bottom flask, 125 mL filter flask, rubber bum-
per, porcelain Buchner funnel, 4 reaction tubes, 100 mL or 250 mL beaker
Speciality items from the common shelf-large stir-bar, stir/hot plate, heating
mantle, sand, filter paper (for Buchner funnel), clamp holders, clamps, thick-
walled tubing, melting point capillary tubes
Procedure 1: Synthesis of Acetanilide

Recrystallization is most often used to purify a crystalline product that has
small amounts of impurities after the reaction has reached completion. Often
times there are more than one solvent choices that can be used to recrystal-
lize a product. The key is to select the best solvent or solvent system. In this
procedure you will be asked to synthesize acetanilide from aniline and acetic
anhydride via a nucleophilic acyl substitution reaction. The product will
p recipitate when formed. After isolation via vacuum filtration you will test a
variety of solvents to find out which one is the most suitable for recrystalliza-
tion of your crude product. Also make sure you save a small portion of your
crude product for melting point analysis . During the second lab period, you
will recrystallize your entire product using the solvent you selected from your
tests the previous day. Make sure you record the weights of all reactants and
products and you obtain a melting point of your purified product. After you
obtain the purified product you will also be asked to characterize it using 1 H
NMR and IR spectroscopy.
205
II NOTES
Mr. Benzene says: TAKE CARE! Aniline is toxic-

please use gloves and handle with caution!
0 0 H 0
H3C JlOJlCH3 + C("'

H20,
2s ·c V"l(cH, • HOJlCH3
~ 0
Acetic anhydride Aniline Acetanilide Acetic acid

C4H503 C6H 7 N C8 H9 NO C2H402
MW: 102.09 MW: 93.13 MW: 135.16 MW:60.05
To measure out small quantities of liquid reagents, use the disposable plastic
syringes located on the common shelf area. For this experiment, use the 3
mL syringe. Make sure that you dispose of the syringe needle in the "sharps"
container! Combine 2.06 g (about 2 mL) aniline, 15 mL of deionized water,
and 3 mL acetic anhydride in a 50 mL round-bottom flask and stir the reac-
tion mixture using your larger stir bar and a stir plate. Heat will be given off
as the reaction progresses. After about 30 minutes, the reaction should be
near completion and the product will have completely precipitated out of
the solution. Normally, all organic reactions should be monitored by TLC to
ensure they go to completion. In this reaction, since the product crashes
out of the reaction as it progresses, this synthesis isn't suitable to
monitor by TLC.
After 30 minutes, isolate the crude acetanilide via vacuum filtration using
your porcelain Buchner funnel and 125 mL filter flask and wash the product
with 1 to 2 mL of ice-cold water. You may need to use additional quantities of
cold water to wash out the round-bottom flask. Let your crude product dry on
your filter paper with the vacuum still on for about 20 minutes before moving
on to Procedure 2.
206
Ii
I
_ ..~Iii
Recrystallization 11 Chemist ry 213W
NOTES : :
Procedure 2: Finding a Suitable Recrystallization
Solvent
Mr. Benzene says: It's the most time efficient to set

up and heat your sand bath while your reaction is
running in Procedure 1 !
Before you do ANYTHING, weigh your acetanilide crude product and

record this weight in your notebook. Also make sure you save a small
amount for melting point analysis.
You will use an electrically heated sand bath to heat solvents. Fill your heating
mantle half full of sand, mount it to a ring stand in your hood, and plug it into
the Varistat. Set the level to 50.
Be sure to use boiling sticks (wooden applicator sticks) to effect smooth boiling
and avoid explosive boiling or bumping of the solvent when heating it. Boiling
sticks also can serve as stirrers.
You will test the solubility of your acetanilide in FOUR different solvents:
water, ethanol, dichloromethane, and hexanes.
Weigh out four portions of your acetanilide into four different labeled reaction
tubes (Tubes 1through4), about 50 mg for each portion.
Reaction tube 1: water

Reaction tube 2: ethanol
Reaction tube 3: dichloromethane
Reaction tube 4: hexanes
Add about 0.5 mL of each solvent to their respective tubes (you can use the
graduations on the sides of the reaction tubes!). Agitate the tubes vigorously for
10-30 seconds by hitting or tapping the bottom with your fingers. If the solid
dissolves, the acetanilide is too soluble in that solvent and the solvent can be
eliminated as suitable for recrystallization. If the solid does not dissolve after
mixing for a short period, place a boiling stick in the tube and heat the reaction
tube gently in your sand bath. The solvent should start to boil within 10-30
seconds. If the boiling becomes too vigorous, pull the tube partially out of the
sand bath. Remember, you want GENTLE heating; you don't want all of the
solvent to evaporate! Continue gently boiling the solvent for about a minute.
207
II NOTES
Wood applicator - -
stick
Cool at this
point - - - - - + \ml'~_,,....,.....~
Temperature
controlled by
depth in sand
CHaydc:n-~1cNeil, U.C
Figure 9.6. Sand bath.
Carefully observe the mass of crystals while you're refluxing the liquid. If the
solid dissolves, place the tube in a small beaker of ice water for one or two
minutes to cool the solution. If you observe solid crystals coming out of solu-
tion you have found a suitable solvent for recrystallization. It could be that
more than one of the suggested solvents works; make sure you observe the
amount of crystals that crash back out of solution, the color of the crystals,
and the quality of the crystals. Make sure you record ALL observations in your
notebook so you can justify which solvent you pick after this process!
If the refluxing of the solvent leads to an observable decrease in the mass of the
solid, but not complete dissolution, try adding more solvent, a few drops at a
time, heating the solution to boiling (refluxing) for 30 to 45 seconds after each
addition to see if all of the solid dissolves. If it does, cool the tube in a small
ice-filled beaker for one or two minutes. If you observe solid crystals coming
out of solution, you may have found a suitable solvent for recrystallization;
however, keep in mind that you don't want to use large volumes of solvent to
recrystallize the bulk of your acetanilide.
If the mass of solid remains unchanged after one or two minutes in t he re-
fluxing solvent, then the unknown is obviously insoluble in both cold and hot
solvent , and the solvent is unsuitable for recrystallization.
208
I. . - l (-
Recrystallization II Chemistry 213W
NOTES II
Mr. Benzene says: Be alert to the difference
between melting and dissolving! Compounds that
melt just above the boiling point of water when
pure may melt just below the boiling point of water
when small amounts of impurities are present (the
maximum solvent temperature in these experiments
is approximately that of the boiling point of the
solvent). Solids that melt but do not dissolve will
form two immiscible liquids in the tube: upon
crystallization, little impurities will stay in the
solvent, so the degree of purification of the solid
will be rather small.
Cleaning Up
Place organic solvents and solutions in the halogenated or nonhalogenated
organics waste container, whichever is appropriate. Dilute the aqueous solu-
tions with water and flush down the drain. Carry your sand bath to the side
shelf and dump the HOT sand back into the sand supply bowl. Do NOT dump
it in the waste bins.
Procedure 3: Purification of Acetanilide

Before you do ANYTHING, weigh the remaining amount of your crude
product and record this weight in your notebook. You will need this
weight to calculate a% recovery of your product after recrystallization.
In a 100 mL beaker, you will recrystallize THE ENTIRE REMAINING AMOUNT

of your crude product in the solvent you chose in Procedure 2.
Use a hot plate on a low heat setting and NOT your sand bath (the sand bath
is too hot and will melt your crystals before they go into solution). Heat -75
mL of your chosen solvent on your hot plate. Add this HOT solvent in incre-
ments to your crude crystals, starting with 20 mL of solvent added. You'll use
between 30 and 75 mL total. Now, place your solution containing your crystals
and solvent on the hot plate alongside of the pure (HOT) solvent. Heat gently
and continue to add the HOT solvent in -5 mL increments until all of your
crystals are dissolved. Make sure you continually stir your solution of acetani-
lide until it's all dissolved so the solid doesn't settle to the bottom and melt!
209
== NOTES
Mr. Benzene says: Make sure that your acetanilide

doesn't melt before it dissolves; heat GENTLY!
If you get a "foam" on the surface of your solution, add 1 to 2 mL of ethanol

as a co-solvent and continue heating.
Once your solution is translucent let your beaker cool to room temperature
and crystallization will begin. Then place your beaker on ice for 10 minutes to
complete the recrystallization. Isolate the crystals by vacuum filtration using
your porcelain Buchner funnel and allow them to dry until your next lab period.
Sometime during the next lab period, weigh your recrystallized product and
record this weight in your notebook. You will need this weight to calculate a
purified 3 yield, and your 3 recovery of your product after recrystallization.
Analysis of Your Product

You will need to obtain the melting points of your purified acetanilide and
the impure acetanilide.
Prep your purified sample for NMR analysis by following the protocol on the
inside back cover of this lab guide. Also put some of your sample in a shorty
vial for IR analysis. Make sure you sign up for an NMR and IR timeslot!
Figure 9.7. NMR of acetanilide.
210
Recrystallization :: Ch em istry 213W

NOTES I:
Melting points of the crude and purified acetanilide
NMR and IR data of the purified acetanilide
% recovery (compare impure weight of acetanilide to purified weight)
% yield using the crude weight of the acetanilide
% yield using the purified weight of the acetanilide
211
II NOTES NOTEBOOK PAGES REPORT
I. Experiment Info
II. Purpose

Include subsections in this section for each procedure; write in bullet form
and use tables to summarize data whenever possible. It should be written as
you complete the steps of each procedure, making sure to include pertinent
data and observations (as the steps are performed).
Remember, what you write in your notebook during your lab period is un-
changeable! It is a written and legal record of what occurred while you were
in lab once you and your TA sign the page.
IV. Calculations
Crude % yield of acetanilide (before recrystallization)
Purified % yield of acetanilide (after recrystallization)
3 recovery of acetanilide (compare weight before recrystallization to
weight after recrystallization)
V. Experimental
Write an experimental for the synthesis of acetanlide. Follow the example
provided for you in Chapter 3.
VI. Discussion and Conclusions

Consider the following when writing this section:
Discuss the reaction chemistry.
Discuss the importance of recrystallization as a purification technique.
Discuss the process of finding a suitable recrystallization solvent for the
acetanilide. How/ why did you pick your solvent? Saying that the solvent
was "good" isn't acceptable; use valid scientific arguments, thinking about
the recrystallization background. Think about the polarity of your chosen
solvent and the polarity of your molecule.
212
Recrystal Iization H Chemistry 213W

NOTES II
Discuss the purification of acetanilide using your chosen solvent. Evaluate

the success based on melting point data, 3 recovery, and purity of your
product (NMR and IR data). Did you make your product? Was it success-
ful? Discuss 3 yield and your NMR and IR data in detail (discuss chemical
shifts, splitting patterns, integration values for NMR and specific frequen-
cies and stretches/bending for IR).
Overall conclusions about this lab technique.
VI I. Spectral Data
Include your NMR and IR data, fully annotated and labeled as figures for you
to refer to in your discussion.
VIII. References
Submitting your Prefab and Notebook Pages for Chapter 9

2. Download and attach the Recrystallization grade sheet to the front of your
assignments.
3. Attach your notebook pages AND spectral data to the grade sheet.
213
H NOTES
214
~~ (\ JD CHAPTER
~~~~~~~~~~~~~~~~~~~~~~~~~~-
10
Co Ium n Chromatography
'c
..
.......
t>C3 I
~
c ....
D
Mr. Benzene says: Again, TLC plates will be used! To
conserve TLC plates, it may be prudent to cut them
in half.
OHayden-McNeil. lLC
Prelab Assignment
Your Prelab Assignment (worksheet on ANGEL) must be completed before coming
1. Synthesis of fiuorenone from fiuorene and monitoring the reaction by TLC

2. Separation of fiuorene from fiuorenone by column chromatography
Quiz for Chapter 10

215
- - - --~~~ - --
II NOTES
for the experiment.
Mr. Benzene says: Column chromatography uses the

same principles as TLC. You are also responsible for
the content of Chapter 6 on this quiz.
Activity Breakdown
Day 1: Procedure 1
Day 2: Procedure 2
Introduction
Despite tending to be the most expensive and time-consuming, column chromatog-
raphy is the purification technique most commonly utilized in organic chemistry.
Remember, recrystallization is inherently limited to only solids with relatively
small amounts of impurities. Distillation is inherently limited to liquids and is only
efficient on a larger scale. Column chromatography can be used to purify almost
any mixture of solids and/or liquids with some difference in polarity on both the
large and small scale.
OMe
+Br~ DMF
2 3
Taking a final look at our SN2 example reaction, we determined that distillation
cannot be used to purify 3, but recrystallization could be utilized since 3 is a solid.
The condition for recrystallization was that 3 must have relatively small amounts
of impurities in order to be effective.
But what if this reaction does not go to completion and there are significant quan-
tities of 1, 2, and 3 present after the work-up? In this scenario, the only option to
216
Column Chromatography II Chemistry 213W
obtain pure 3 is column chromatography. This purification method involves the NOTES H
same principles as TLC but can be applied t o separate larger quantities of mix-
tures. In the TLC experiment (Chapter 6), we separated and analyzed the different
components that make up over-the-counter painkillers. The technique of TLC was
useful in determining the type and number of compounds in the mixture, but it
was not helpful for collecting the separated components. We could only separate
and visualize the spots on.the TLC plate. Column chromatography allows for the
collection and isolation of the separated components.
Going back to our SN2 reaction example, let's re-visit what we learned about these
three compounds. On a TLC plate, the order of appearance from smallest Rf to
largest Rf in a given solvent system would be 3 < 1 < 2 . If these three are separated
on a column, the order of elution would be from the least polar to the most polar,
so 2 would elute from the column first, followed by 1 , then finally 3 if the column
was run correctly. We'll re-visit this as a column chromatography case study later
in this chapter.
How Do You Run a Column?

The type of stationary phase, the size of the column, the polarity of the mobile
phase, as well as the rate of elution can all affect the separation. These conditions
can be manipulated to get the best separation for your mixture. Typically alumina
or silica is used as the stationary phase. The size of the column is dictated by the
scale of the reaction. The polarity of the mobile phase is determined via TLC. Once
these three parameters are chosen, the column can be set up by packing, loading,
then running the column.
Figure 10.1. A packed and loaded column, ready to run.
217
H NOTES Choosing a Column

Columns can be as thin as a pencil or as wide as several feet (for industrial pro-
cesses). They can separate milligram to kilogram quantities of materials. The
length and width of a column are very important when considering the scale of
the separation. Thin columns work best for small amounts of material whereas
wider columns work best for larger amounts of material. Length is important
when considering separation. If there are two spots of similar Rf value that must
be separated, a longer column is desirable as more interaction with the free vs.
adsorbed equilibrium facilitates separation. Shorter columns are useful and quicker
when two compounds have very different Rf values. In this experiment, we will
be separating a mixture of approximately 50 mg, so a small column can be used.
Figure 10.l shows the typical column used during this experiment.
Choosing Solvents
Solvent systems for use as mobile phases in CC can be determined from previous
TLC experiments, the literature, or experimentally. It's best to run TLC on your
reaction mixture as the reaction progresses AND again after the workup to see
what's in the mixture. Comparing to a starting material standard is always key so
that you know which spots belong to your starting material and product.
'c
,.
1.I,.
ti<3 I
~
c,
D
Mr. Benzene says: It's not optimal to run a column
"blind" and guess what spots are there and how
many. Always run a TLC plate of your reaction
mixture BEFORE you run a column!
D
Normally, a separation on a column will begin by using nonpolar or low polarity

solvent, allowing the compounds to adsorb to the stationary phase, then SLOWLY
increasing the polarity of the solvent to desorb the compounds and allow them
to travel with the mobile phase. The polarity of the solvents should be changed
gradually. If the polarites are changed too quickly, the column can crack; this will
lead to poor separation.
Some typical solvent combinations are hexanes-dichloromethane, hexanes-ethyl

acetate, and hexanes-toluene. Often an experimentally determined ratio of these
solvents can sufficiently separate most compounds. Solvents such as methanol
and water are normally not used because they can destroy the integrity of the
stationary phase by partially dissolving the silica gel.
218
.r~---- --.,-
Column Chromatography H Chemistry 213W
Choosing a Stationary Phase NOTES H

Stationary phases for CC can come in a variety of sizes, activities, acidic and basic
variations for both alumina and silica. The types of stationary phase chosen are de-
termined experimentally or often based on results from a previous TLC experiment.
As with TLC, alumina and silica are the two most popular stationary phases in
column chromatography. For these common phases, the partitioning works in an
analogous manner. The more polar sample will be retained on the polar station-
ary phase longer. Thus, the least polar compound will elute from the column first,
followed by each compound in order of increasing polarity.
Although the interactions between the mobile and stationary phase are based on
the same principles for CC and TLC, be careful when predicting the order of elution.
Since the direction of the solvent flow in TLC moves up and in CC the solvent flows
down, it appears that the order is "upside-down." In TLC the more polar molecules
will have lower Rf values, but in CC they will be retained longer on the column and
elute later during the separation. Remember this when considering the polarities
of the stationary phase as well as the polarity of the compounds being separated
when predicting the order of elution.
Packing the Column

There are several acceptable methods when packing a column. These include dry
packing and the slurry method. The slurry method normally achieves the best
packing results, but there are several occasions when the dry-packing method
works just as well.
Dry packing is the method of choice for a microscale column. Begin by filling the
column to the intended height with the stationary phase and then slowly add your
chosen mobile phase solvent. The solvent can then be forced through the stationary
phase using nitrogen or air. This method is typically used with alumina only,
since silica gel expands and does not pack well with this dry method.
The slurry method is often used for macroscale separations. Combine the solid
stationary phase with a small amount of your chosen mobile phase solvent in
a beaker. Thoroughly mix the two until a consistent paste is formed; the paste
should be capable of fl.owing. Pour this homogeneous mixture into the column as
carefully as possible using a spatula to scrape out the solid as you pour the liquid.
The slurry method normally gives the best column packing, but is also a more
difficult technique to master.
Whether the dry or slurry method is chosen, the most important aspect of pack-
ing the column is creating an evenly distributed and packed stationary phase. As
mentioned earlier, cracks, air bubbles, and channeling will lead to a poor separa-
219
; ; NOTES
tion. Why is this the case? After the column is packed, it will be loaded with your
sample. Cracks, air bubbles, and channels can lead to an uneven rate of travel down
the column by the compounds. When this happens, the compounds often co-elute,
defeating the purpose of running a column.
Mr. Benzene says: Never aJlow your column to run

dry. A cracked column is bad, and you'll be sad.
Once the column is packed, open the stopcock and allow the solvent level to drop
to the top of the packing, but do not allow the solvent layer to go below this point.
Allowing this solvent level to go below the stationary phase (known as letting the
column to "run dry"), should always be avoided since it allows air bubbles and
channel formation to occur leading to a poor separation.
Adding the Sample
'c
,.
......
~
i9G \
C,
0
Mr. Benzene says: Only use the minimum amount
of solvent when adding the sample to the column.
Once the packing is complete, the sample can be loaded directly to the top of the
column. Normally, the smallest amount of solvent possible is used to dissolve
the mixture. The solution is then carefully added to the top of the column using
a pipette without disrupting the flat top surface of the column. A thin horizontal
band of sample is best for an optimal separation. If the band of your loaded sample
is too thick, the components of the mixture will overlap for longer as they travel
down the column and poor separation will result. A thinner band means that the
components will resolve quickly as they travel down the column, resulting in a
good separation (Figure 10.2).
After the sample is loaded, a small layer of white sand is added to the top of the
column. This will help to keep the top of the column level when adding eluent
solvent (mobile phase).
220
1111' 11
II .'
111111 .!:[111111
Thin band
NOTES H
Thick band
Figure 10.2. Thin band (top) vs. thick band (bottom). A thin band leaves more room for
separation on the column. A thick band means that there is little room for separation and
co-elution occurs.
221
: : NOTES Running the Column

Once the mixture is added and the protective layer of sand is in place, continu-
ously add the eluent solvent while collecting small fractions from the bottom of
the column. Use a pipette to add the first bit of solvent to the top of the packing,
sample, and sand; this will minimize disturbance of the column and dilute the
sample. Collecting small fractions is important to the success of your column
separation. Fractions that are too small can always be pooled together; however,
if the collected fractions are too large, you may get more than one compound in
any particular fraction. If this occurs, the only way to complete the separation is
to redo the chromatography. Since column chromatography is time consuming,
collecting large fractions is discouraged. Also keep in mind that you cannot allow
your column to run dry, so it is important to have a sufficient amount of mobile
phase ready at any time. You may want to share this prepared mobile phase with
your hood partner to reduce the amount of solvent waste.
Monitoring the Column
'c
...
......
~
VG I
c ...
D
Mr. Benzene says: Unless you have superpowers,
there's no way to tell what is in the test tube
fractions you collect. Use TLC to reveal what's
inside!
D
If the mixture to be separated contains colored compounds, then monitoring the

column is very simple. The colored bands will move down the column along with
the solvent and as they approach the end of the column, collect the colors in in-
dividual containers. However, most organic molecules are colorless. In this case,
the progress of the column must be monitored by TLC. Spot each fraction on a
TLC plate. Four or five fractions can be spotted on a single TLC plate. Develop the
plate and use the observed spot or spots to determine which compound is in each
of the collected fractions. Spotting some of the starting material or product (if
available) on the TLC plate as a standard will help in the identification.
Isolating the Separated Compounds

Once you believe all the materials have been removed from the column, the spots
from TLC analysis should indicate which fractions contain t he compounds you
are interested in isolating. Combine the like or same fractions and evaporate the
solvent to obtain the pure separated compounds.
222
Column Chromatography ;; Chemistry 213W
Flash Chromatography NOTES ::

Column chromatography is often very time consuming. Allowing the solvent to
elute through the column one drop at a time takes patience. One method to speed
up the process is to use Flash Chromatography. This method uses a pressure of
about 10 psi of air or nitrogen to force the mobile phase through the column.
Because the rate of the mobile phase is increased, in general, this method gives
a poorer separation. However, by using a finer grade of alumina or silica, flash
chromatography can be used to increase the speed without lowering the quality
of the separation.
Reverse-Phase Chromatography
HPLC (High Performance Liquid Chromatography) is a variation on the traditional
liquid chromatographic methods. High pressure pumps are used to force solvent
through a tightly packed column connected to a variety of different types of very
sensitive detectors. Modem HPLC is used extensively in biochemistry to separate
cellular components such as proteins, lipids, and nucleic acids. Mixtures of these
types require aqueous mobile phases such as methanol-water or acetonitrile- water
and these liquids do not work well on normal silica or alumina stationary phases.
Instead of these polar phases, very non polar ones, called "reverse-phase" packing
are used. These are manufactured by bonding lots of hydrocarbon molecules to the
surfaces of a silica gel particles so that the silica gel is like a very nonpolar "grease
ball." In this situation, the order of elution will be exactly opposite the behavior
on an alumina or silica column. On a reverse-phase column, the more non-polar
materials will adhere to the stationary phase (or like material) longer, and the
polar compounds will elute first.
Chiral Separations
Many compounds can be separated using typical chromatographic stationary
phases and solvents. These separations depend on the difference in polarity of the
molecules to be separated. However, how would you separate two compounds with
the identical polarity such as enantiomers? This separation technique is of great
importance in the pharmaceutical industry where the FDA controls the amounts of
impurities, including enantiomers, in prescribed drugs. For example, Thalidomide,
a drug administered in the '60s has two enantiomers. This drug was used as a seda-
tive and an anti-depressant, but was found to cause abnormalities in the fetuses
of pregnant women, making it a potent teratogen. Although this drug was pulled
from the market due to the resulting birth defects, there is recent literature that
suggests that only one of the enantiomers caused the defects. If the enantiomers
could be completely separated, Thalidomide might be used as an FDA-approved
drug and be helpful to people today.
223
: : NOTES
Mr. Benzene says: Chiral columns can be used to

separate enantiomers.
Chiral stationary phases can be used to separate enantiomers . By giving the sta-
tionary phase a "handedness," one enantiomer will be specifically retained on the
column. These columns are very expensive and specific to the particular type of
separation, but have led to great achievements in separation science.
There are many other different types of chromatographic methods including gel
electrophoresis, affinity chromatography, and size exclusion chromatography
that have not been discussed here. Hopefully, with the basic chromatographic
background provided, you can apply this knowledge to the many different types
of chromatography used in many different professions today.
Case Study: Using CC to Purify an SN2 Reaction
~
OMe
~
OH
+Br~ K2C03
DMF
H 0
1 2 3
Let's suppose the SN2 reaction above was set up, run, and monitored by TLC. De-
spite your best efforts, the reaction never went to completion. After the workup,
compounds 1, 2, and 3 are still present in a mixture.
224
r1wr----···· - - -
'I I
I
.ll1111:. 1111111
Column Chromatography 11 Chemistry 213W
NOTES H
• •
••
•
A B C
Figure l 0.3 . TLC plate of SN2 reaction after workup using 30% acetone/70% hexanes. Lane
A: compound 2; Lane B: compound l ; Lane C: reaction mixture. Spots visualized by UV light.
As previously discussed, both distillation AND recrystallization are unsuitable in

this situation given the presence of solids and the similarity of polarity of 1 and
3. The only option is to purify the mixture by column chromatography. Since TLC
was already done of the reaction mixture, the best solvent system for resolution
of the spots on the TLC plate should also be the solvent system used in column
chromatography. In this reaction, 70% hexane/ 30% acetone was determined to
be the best by TLC and was used to slurry-pack a column with silica. The reaction
mixture should be loaded with the thinnest band possible, and fractions should
be collected and evaluated by TLC.
Let's talk about two different scenarios when considering the success of separation
via column chromatography.
Scenario 1 : Poor separation

Twenty-five fractions were collected during chromatography and evaluated by
TLC (below):
•••••••
••• • •••• • •••
--+--+--+--+-+-- --+--+--+-+-+--
••••• •••••
--+--+--+-+-+-- --+--+--+-+-+-- --+-+--+-+-+--
Fractions 1-5 Fractions 6-10 Fractions 11-15 Fractions 16-20 Fractions 21-25
225
Pure 2 can be seen in fractions 4-7. Overlap of 1and2 can be seen in 8- 10. Pure
== NOTES
1 can be seen in fractions 11-15. This overlap of the two starting materials is
not concerning since we are only focused on obtaining pure product 3. However,
starting in fraction 16 to fraction 19 it can be seen that 3 co-elutes with 1 and
only six fractions (fractions 20-25) contain pure product. Based on the TLC plates,
this column was ineffective at separation. Many factors could contribute to this:
wrong mobile phase, too thick of a band, bad packing, or flashing of the column.
The only solution in this scenario would be to re-run the column to separate the
fractions where overlap occurred.
Mr. Benzene says: Compounds that co-elute in

a collected column fraction indicate that your
column conditions are not ideal.
Scenario 2: Good separation

Twenty-five fractions were collected during column chromatography and evalu-
ated by TLC (below):
•• •••
•••••
--+--+--1---1--+-- --+--+--1--+--i--- --+-+--+--1--+--
••• •••••
--+-+--+--1--+-- --+--+-+--1--+--
Fractions 1-5 Fractions 6-10 Fractions 11-15 Fractions 16-20 Fractions 21-25
Pure 2 can be seen in fractions 4-8. Since there are no spots in fractions 9 or 10
it is indicative of just pure solvent in the tubes. Pure 1 can be seen in fractions 11
to 15. The desired product 3 can be seen eluting pure starting in fraction 18. Since
you can still see a spot in lane 25, more fractions would be collected and evaluated
to determine if the product is still eluting from the column.
Mr. Benzene says: If done properly, column

chromatography is your most potent purification
weapon as it can separate complicated mixtures of
compounds efficiently.
In this experiment, column chromatography will be used to separate the starting

material from the product in the oxidation of fiuorene to fl.uorenone, and TLC will
be used to determine the effectiveness of this separation.
226
- --- .-·
I
Synthesis of a Fluorene/Fluorenone Mixture and

NOTES II
Separation by Column Chromatography
The 9-position of fluorene is unusually reactive for a hydrocarbon. The protons
on this carbon atom are acidic by virtue of being doubly benzylic, and, conse-
quently, this carbon can be oxidized by several reagents, including dioxygen.
In the past, a very powerful and versatile oxidizing agent Cr(VI), in the form
of chromium trioxide, was used to carry out this oxidation. Although chro-
mium compounds are facile oxidizing agents, they are not practical in today's
environmentally conscious climate due to chromium's toxicity. One alternate
approach is to use oxygen from the atmosphere as the oxidant. The oxidation
is carried out utilizing methyltricapryl ammonium chloride, commonly known
as Stark's catalyst or Aliquat 336, as a phase transfer catalyst.
Stark's Catalyst
~
H H
~
v-u v-u
Fluorene 0 2 • NaOH, 2s·c Fluorenone
MW 166.2 g/mol MW 180.2 g/mol
M.P. 115' C M.P. 83' C
Although the detailed mechanism for the base mediated oxidation of fluorene
to fluorenone is not exclusively reported, a plausible mechanism might be
suggested based on available evidences (Scheme 10.1). Thus, in presence of
base, fluorene (1) is deprotonated to the aromatic fluorenyl anion 2. 1 Anion
2 is reported to have an orange color, 2 which might be easily masked by the
bright yellow color of other intermediates present in solution3 or the by the
color of the product 7. The formation of anion 2 as a precedent to the products
like 7 is well documented.4 Being electron rich, anion 2 might be oxidized by
aerial oxygen to radical 3 and radical anion 4. Transient radical 3 absorbs at 500
nm and is expected to have a red-violet appearance. 5 But due to its transient
existence and due to the presence of other colored species in the solut ion,
this color may be masked. Thus, color cannot be used to justify the presence
or absence of either anion 2 or radical 3. In fact, the color observed during the
progress of this reaction in lab varies between bright yellow and green. It is
1 Bordwell, F. G.; Hughes, D. L. J. Org. Chem.1980, 45, 3314-3320

2 Xie, X.; Hogen-Esch, T. E. Macromolecules 1996, 29, 1746
3 Higasi, K. Bull. Chem. Soc. Jpn. (1953), 26, 248
4 Brady, E. D. Inorg. Chem. 2000, 39, 6028.
5 Kirmse, W.; Loosen, K.; Sluma, H.J. Am. Chem. Soc. 1981, 103, 5935
227
: : NOTES also to be noted that base acts as a catalyst in this reaction by facilitating the
formation of the electron rich intermediate 2, in the absence of which fl.uorene
1 is stable to aerial oxidation and has a long shelf life. Radical 4 might lead to
anion 6 via intermediate 5. Anion 6 may eventually generate product 7.
Scheme 10.1
H
e
~
H
El OH
d-0 2
aerial oxygen
cPo 3
+ 0 :0-0·
o=o· cm5
..--
6
0-0- H
cfo
0
7
+ 0 0H
NOTE: Arrows for tile mecnanism are NOT displayed. Tile arrows are to be drawn 10 as part of your Prelab.
Credit for mechanism: Ritobroto Sengupta
It must also be mentioned that the mechanism provided above is a simpli-

fied representation of the actual events taking place in solution. In fact, the
transition from anion 2 to product 7 may proceed via several other competing
pathways involving numerous other intermediates.6 However, at this stage the
above mechanism is sufficient for this course.
6 Higasi, K. Bull. Chem. Soc. Jpn. (1953), 29, 1746
228
Column Chromatography 11 Chemistry 213W
I

NOTES II
Fluorene, fl.uorenone, toluene, 10 M NaOH solution, Stark's catalyst, 20%
dichloromethane/80% hexanes, 5% HCl solution, saturated NaCl solution,
anhydrous sodium sulfate, hexanes, dichloromethane, alumina

In your drawer-25 mL round-bottom flask, TLC jar, TLC plates, separatory
funnel, Erlenmeyer flasks, beakers, glass column chromatography column,
test tube rack
From the common shelf-large stir-bar, stir/hot plate, clamp holders, clamps,
small iron ring, silica, column sand, cotton, 10 small test tubes, TLC spotting
capillary tubes
Procedure 1: Oxidation of Fluorene to Fluorenone
Mr. Benzene says: NaOH is a strong base and is

very corrosive. Wash hands immediately if contact
occurs.
First, get the TLC apparatus set up. Prepare the mobile phase, 20% dichloro-
methane in hexanes, and place a small amount in the TLC bottle/ chamber. Cap
the chamber until use. Also, label a TLC plate with the origin line and lanes
for fiuorene and the reaction mixture. Spot the fl.uorene lane with a fluorene
solution (3% fluorene in 30/70 dichloromethane/hexanes), which is on the
side shelf. Check the spot under UV to be sure that enough compound has
been spotted. Now, you're ready to monitor the reaction once the time comes.
You'll want to stop and workup the reaction once half of the fl.uorene has been
consumed. The TLC plate should look as follows:
F Rxn
F = Fluorene
Rxn = Reaction mixture
• •
I
• I
Rt values are relative

here, not exact
229
H NOTES The reaction mixture lane should consist of two spots in equal intensity/con-
centration: one spot for fluorene and one spot for fluorenone.
Running the Reaction

To a 25 mL round-bottom flask clamped to a ring stand above a magnetic stir-
rer, add 5 mL of toluene and 100 mg of fluorene while stirring with a 1/2-inch
stir bar. Add 5 mL of 10 M NaOH and stir until all the solid has dissolved. Add
2 to 3 drops Stark's catalyst (Aliquat 336) to the solution. Stir vigorously, but
without splashing the solution out of the flask. The reaction can take any-
where from 10 minutes to 30 minutes. Monitor the rate of your reaction by
TLC. Run the first TLC after the first 10 minutes of the start of the reaction.
To TLC, stop the stirring and dip the TLC spotter into the top organic layer.
Spot the plate as described above. Once you've dipped, return to stirring the
reaction. Also, spot the plate with fluorene solution (3% fluorene in 30/70
dichloromethane/hexanes), which is on the side shelf. Develop the TLC plate
using 20% dichloromethane in hexanes and use the UV lamp to visualize your
spots. Monitor the reaction every 5 to 10 minutes by TLC.
The Workup
When approximately half of your fluorene has been converted to fluorenone,
as evidenced by the fact that the product spot is about the same intensity
as the starting material spot under the UV light, pour the reaction mixture
into a separatory funnel, rinsing the beaker or flask with an additional 5 mL
of toluene, which is then added to the separatory funnel. Drain the aqueous
layer in order to separate the organic layer from the aqueous layer. Wash the
organic layer in the sep. funnel with 5% HCl (3 separate times with 5 mL each
time) and saturated NaCl (3 separate times with S mL each). After each wash,
drain the aqueous layer from the separatory funnel into a waste beaker. Dry the
remaining toluene layer over anhydrous sodium sulfate (add enough until it no
longer clumps together) in a 25 rnL Erlenmeyer flask. Allow the product to dry
for 5 or 10 min. before decanting the toluene from the solid sodium sulfate.
Transfer the toluene to a 100 mL beaker. Wash the solid sodium sulfate with
3 mL of toluene, adding this to the main portion of toluene to complete the
transfer of product. Reduce the volume of solvent to -1 mL by heating gently
over a warm water bath and using a stream of nitrogen. Please use the warm
water bath suggested; do NOT place the beaker directly on a hot plate as your
product will decompose! The crude mixture of fluorene and fiuorenone will be
separated by column chromatography in the next lab period.
Cleaning Up
The aqueous extracts can be poured down the sink with water. Organic waste
should be placed in the appropriate waste container.
230
Column Chromatography :: Chemistry 213W
NOTES H
Procedure 2: Purification of the Reaction Mixture by
Column Chromatography
Column chromatography is a very important technique for purifying organic
compounds. It often takes some patience and good technique to obtain a good
separation. You will be using either alumina OR silica to pack and run your
column, depending on what your TA recommends.
The following is an outline of the steps you will follow to help you with success:
Packing the column
Adding your sample to the column
Running and monitoring the column
Isolating the separate compounds that elute from the column
Cleaning up
Characterization
1. Packing the Column

First you must make sure that the column is properly prepared so that the
alumina or silica doesn't fl.ow right through the stopcock. Using a boiling stick,
lodge a small piece of cotton into the small neck of the column right above the
stopcock. Now pour a small amount of column sand (NOT the sand from the
silver bowl you use in your sand baths!) so that there is approximately 1/4 to
1/ 2 inch of sand lying evenly at the bottom of your column.
The following procedure best describes how to dry pack the column. Slurry
packing is more efficient when using larger columns but can be problematic
on a small scale. If your TA prefers slurry packing, he or she will give a dem-
onstration during the prelab talk.
After consulting with your TA, fill the column with dry silica or alumina NO
MORE THAN HALF of the way full. Much less will give rather poor separation,
and much more will make the separation longer and more difficult to handle.
Make sure the silica/alumina is fl.at and even on top. (Alumina works better
for this experiment with dry packing but some TAs prefer silica.)
You will be using FLASH chromatography to pack and run your column. Get
a skinny hose from the Common Shelf and affix it to your nitrogen line in the
hood. In your drawer, there is a plastic funnel that when inverted, it will fit
perfectly into the end of the skinny hose AND the wide part of the funnel will
form a nice seal at the top of the column.
231
: : NOTES To pack your column, you will be using HEXANES as the solvent. Add hexanes
as the mobile phase through the funnel at the top of the column, with the
stopcock open and a beaker underneath. Add more solvent up to the top of the
column continuously since the solvent will slowly move down the stationary
phase. To expedite this, ft.ash the column with nitrogen until the solvent is
just above the top of the silica/alumina, draining through the stopcock as you
go. Collect the hexanes solvent in a clean beaker: you can re-use this solvent
during the packing process since it's ft.owing through an unloaded column!
With the silica, you may have to aggressively ft.ash-pack the column to thor-
oughly saturate the stationary phase and eliminate air bubbles. Do not allow
the column to run dry. Remove nitrogen tube and add more solvent, and repeat
until all the silica/alumina gel is uniform in appearance (fully saturated with
solvent). The surface of the stationary phase should be FLAT and EVEN. Tap
the column to even it out. Once the stationary phase is saturated with the
hexanes mobile phase, drain the solvent until it just barely covers the surface
of the silica/alumina. Make sure that the stopcock is CLOSED to prevent dry-
ing/cracking your column .
......
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,.
~
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c ...
0
Mr. Benzene says: Pack your column well! Cracks
and channels lead to wacky separation!
2. Adding ALL of Your Sample to the Column

Dissolve ALL of your crude mixture of ftuorene/ fluorenone in 0.4 mL of
dichloromethane and 0.2 mL of toluene. With a pipette, slowly add ALL of
your dissolved sample to the column by gently pipetting the solution onto the
surface of the silica/alumina. Remember, you want the THINNEST band
possible when your sample is added to the column but still load all ofyour
sample! After your sample is added to the top of the column, drain the solvent
until the band moves into the stationary phase and the surface of the silica/
alumina is slightly dry and close the stopcock. Carefully add a small amount
of sand (no more than 0.5 inches) to the top of the column. You are now ready
to begin running your column! Make sure your stopcock is closed!
232
Column Chromatography : : Chemistry 213W
3. Running the Column NOTES I:
,.1.
~c
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~
c..
D
Mr. Benzene says: Remember, fluorene is
significantly less polar than fluorenone. Therefore
it should elute fairly quiddy using a nonpolar
mobile phase while the yellow fluorenone will
remain on the column longer.
D
Using 20% dichloromethane/80% hexanes as your initial mobile phase,

collect FIVE 10 mL fractions in your test tubes (use the test tubes in the rack
on your door, they hold -10 mL each). Be sure to keep track of your fractions
by labeling them as fraction 1, fraction 2, etc. You may fl.ash your column us-
ing nitrogen. Again, MAKE SURE YOU KEEP REFRESHING YOUR MOBILE
PHASE IN THE TOP OF YOUR COLUMN SO THAT IT DOES NOT RUN DRY!
Check your first five fractions by TLC using 20% dichloromethane/80% hex-
anes as the TLC mobile phase. On a TLC plate you can fit SIX lanes, one for the
fl.uorene standard and five for the fractions. After running your TLC plate, use
the UV lamp to visualize the spots. If all of the fluorene has not eluted in the
first five fractions, collect an additional five 10 mL fractions and re-evaluate
by TLC. Combine all of the fluorene fractions in a preweighed beaker or fl.ask
to free up the test tubes. Dispose of the fractions with nothing in them in the
non-halogenated organic waste. While evaluating your fractions, make sure
your column stopcock is CLOSED so that it does not run dry! The fl.uorene
should all elute within the first ten fractions, but every column is different
(which is why we evaluate the fractions by TLC!).
Once all of the ftuorene has eluted using the 20% dichloromethane/80%
hexanes as the mobile phase, you can switch your mobile phase to
something more polar to elute the ftuorenone. Use 100% dichloro-
methane to elute the ftuorenone. Add it to the top of your column and
using the nitrogen to fl.ash it, collect 10 mL fractions until the yellow band
has eluted from the column. Again, check these fractions you've collected by
TLC to evaluate the separation. Combine all of the fluorenone fractions in a
preweighed beaker or fl.ask.
4. Isolating the Separate Compounds that Elute from the Column

After you've combined the fl.uorene fractions in one preweighed beaker or
flask and the fl.uorenone fractions in a second preweighed beaker or flask, you
may evaporate the solvent using a warm water bath and a stream of nitrogen.
Obtain the dry weights for the recovered starting material fl.uorene and the
product fl.uorenone.
233
: : NOTES 5. Cleaning Up
When you are done with the column, pour out the excess solvent into the proper
waste container. Leave the column upside down in a beaker in your locker. The
column will dry out by the next lab period and then the dry silica/alumina
can be easily emptied into the proper silica/alumina waste container, in the
satellite waste accumulation area. DO NOT THROW THE SILICA/ALUMINA
IN THE TRASH!!!!
6. Characterization
Calculations: Make sure you calculate the % recovery for the starting material
fluorene, the overall % yield for the product fluorenone, and the corrected %
yield of fiuorenone based on the amount of recovered starting material.
Spectral characterization: Obtain an IR of BOTH the fiuorene and fiuorenone.

IR of fluorene
IR of fluorenone
Weight and % recovery of fluorene
Weight and 3 yield of fluorenone
Corrected% yield of fluorenone
234
Column Chromatography : : Chemistry 213W
NOTEBOOK PAGES REPORT NOTES •.•.
I. Experiment Info
II. Purpose

Procedure 1: Oxidation of Fluorene to Fluorenone. Remember, this section
should be written in bullet form. It should be written as you complete the steps
of each procedure, making sure to include pertinent data and observations (as
the steps are performed). Tape the TLC plates onto the Notebook Page; cover
the entire plate with tape.
IV. Calculations
Include all required calculations in this section:
Calculation of percent yield of fiuorenone without considering the recov-
ered fiuorene; assume all of the fiuorene reacted (use the theoretical yield
calculated in your prelab assignment).
Calculation of a corrected percent yield of fiuorenone considering the
recovered fiuorene.
EXAMPLE: You recovered 75 mg of fiuorene starting material. This means
only 25 mg out of the 100 mg reacted to form fiuorenone. Recalculate the
theoretical yield knowing that only 25 mg of starting material was con-
verted to product. Your corrected yield is: (amount of fiuorenone isolated/
new theoretical yield) x 1003
Calculation of percent recovery of fiuorene.
One sample Rf calculation.
V. Experimental
Write an experimental for the synthesis of ftuorenone. Follow the example
provided in Chapter 3.
235
VI. Results and Discussion

Consider the following when writing this section:
A short discussion about the reaction chemistry and monitoring the
progress by TLC.
Discuss your CC results. Was the separation successful? How was this
determined?
IR spectrum of ftuorene and ftuorenone: interpretation, annotation, and
discussion of significant signals seen in your spectrum.
Discuss the success of the experiment with respect to amount of ftuorene
and fl.uorenone (3 yield, corrected 3 yield discussion). Be sure to explain
any loss of material.
VII. Spectral Data

IR of both fluorene and fl.uorenone, fully annotated.
VII I. References
Submitting your Notebook Pages Report for Chapter 10

2. Download and attach the Column Chromatography grade sheet to the
front of your assignments. Don't forget to attach your IR data as well!
236
', ,1111
r\ JD CHAPTER 11
~~~~~~~~~~~~~~~~~~~~~~~~~~
Synthetic/Isolation
Experiments
Now that you have mastered some of the basic experimental organic chemistry
techniques, you will carry out synthetic experiments that use these techniques.
Each person in the lab will be doing a different set of experiments. Each student will
do three experiments from the most current list of experiments found on ANGEL.
There are a number of points that need to be emphasized as you start the synthetic
experiments.
1. Your TA has given you your Synthetic Experiments Assignment sheet that
defines which experiments you will be doing. You will analyze all products by
1
H NMR and IR whenever possible. A couple of synthetic experiments pro-
duce products that are not soluble in an organic solvent or are not amenable
to IR analysis. When this situation arises you will be given instructions for
alternative analyses. Some experiments require both 1 H and 13C NMR and
the ANGEL document will instruct you what to do when this is the case. The
ANGEL document will indicate if the product is amenable to GC analysis and
it will also indicate if GC/MS is required.
2. Instead of having you buy a $90 organic lab text containing 76 experiments,
most of which you will never do in this course, we have placed this collection
of experiments on ANGEL as .pdf files. Once you know which three synthetic
experiments you will be doing, you can go to ANGEL, click on "Synthetic
Experiments," and download the appropriate experiment .pdf files and print
them out.
3. You are required to write a Formal Final Report on each one of the three syn-
thetic experiments that you complete in the second half of the semester. See
Chapter 3 for more details on FFR writing and an example report.
4. You will work at your own pace the second half of the semester. This does NOT
mean that you can slack off and just not show up to lab! You are required to
be in lab and working on your experiments as long as you have work
left to do. Sometimes an experiment won't work well and will have to be re-
237
done. Many students end up finishing all of their synthetic experiments and
II NOTES
analyses one to two weeks before the end of the semester.
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,.
.......
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~
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0
Mr. Benzene says: At this point, if you are
COMPLETELY DONE, you don't have to come to
lab UNLESS AN ASSIGNMENT IS DUE. Now that's
motivation to get things done!
0
Prelab Assignments
The Prelab Assigments for the synthetic/isolation experiments are similar to those
of the technique experiments. Your Prelab Assignment (worksheet on ANGEL)
must be completed before coming to lab. You cannot start any experimental
work until your TA collects your Prelab Assignment at the beginning of the class
period it is due. You will also be assessed a 103 points penalty if you do not have
it complete by the due date. There are no exceptions to this rule! Please check
the course schedule for specific due dates. It is advisable to complete all of your
synthetic experiment Prelab Assignments as soon as possible and hand them in
early so that you can multitask (work on more than one experiment at a time).
Quiz for the Synthetics Experiments

Quiz 7 will test your knowledge that you've accumulated so far. You will NOT be
expected to read all of the Synthetic Handouts on ANGEL! However, you will be
presented with a reaction and expected to know how to calculate theoretical yield,
percent yield, etc. In addition, you will be asked to analyze the reaction by TLC,
devise a workup strategy, and describe how to purify the final product. NMR and
IR analysis will also be a part of the quiz.
Formal Final Reports

This course is now designated Chem 213W-the "W" stands for "writing-intensive."
The number and length of the assignments have NOT changed with this new
course number but it is important to remember that the goal of the assignments
has remained the same: learning the scientific writing process in a 200-level lab
course is crucial in the development of a science professional. Regardless of your
major and career path, being able to communicate written results in a scientific
and concise manner is very important.
Reminder about Formal Final Reports: you will write three of them during the
second half of the semester. Print out the Synthetic Grade Sheet on ANGEL so
that you include all appropriate sections and items with your report!
238
Synthetic/Isolation Experiments II Chemistry 213W
The first synthetic FFR you write will be graded very critically, but you will be able NOTES II
to earn back HALF of the points you lost on the Intro, Experimental, and Discus-
sion sections. The last two FFRs will be graded as-is, no re-do's!
For specific details about what is required in each section of your FFR, please refer
to Chapter 3.
General Items about Formal Final Reports

1. Formal Final Reports are to be computer-generated: double-spaced, .75" mar-
gins, 12 point Times New Roman font, inserted page numbers.
2. You must use complete sentences in paragraph form. Grammar and spelling
count! Please proofread a few times and use spell check!
3. Style also counts. The tone should be scholarly and concise. The information
should fl.ow with a logical progression of ideas using appropriate transitions
and varying sentence structure. Avoid "fluff" sentences, wordiness, and being
unnecessarily redundant.
4. Use scientific language, precise terms, and organic chemistry vocabulary
whenever possible.
5. Do not use the first person narrative. Write "The reaction was stirred" rather
than "I stirred the reaction."
6. Do not use contractions. For example, use "could not" rather than "couldn't."
7. Use appropriate capitalization. Capitalize first words of sentences, proper
nouns, section headings, equipment named after people (e.g., Buchner funnel
and Hirsch funnel). Chemical names and techniques should not be capitalized
unless they begin a sentence.
8. Offset section headings from the body text with bold type.
9. If you need to draw out chemical structures, do so very neatly by hand or use
a drawing program.
10. Formal final reports will be read by someone who is familiar with the basic
organic chemistry techniques. Therefore, the information should be interesting
to your target audience (fellow chemists) and you should avoid unnecessary
details and "reteaching" the techniques.
Submitting the Formal Final Report

1 . Print out the grade sheet for the Formal Final Report and attach it to the front
of the report.
2. Hand in the report to your TA on the due date.
3. Upload to Turnltln (details Chapter 3).
H NOTES Using Scifinder Scholar

For writing your introduction and finding relevant information, PLEASE register
and use SciFinder Scholar. It's a great FREE chemistry search Web-based program
that you can use on campus. The most useful feature is structure searching. I'll
be covering how to use this service in the synthetics lab lecture, and instructions
will be provided on ANGEL.
Academic Integrity
A reminder about plagiarism: we take this VERY SERIOUSLY. Every semester,
we catch students who plagiarize their introduction section directly from journal
articles, Web sources, or other students. Please refer to the University guidelines
regarding Academic Integrity. All cases of academic integrity violations will be
brought to the attention of the Academic Integrity Committee and the proper
paperwork will be filed. You must write your own lab reports! If we find that your
lab report is identical to another student's that will be treated as plagiarism and
all appropriate University sanctions will be followed. You are required to submit
all of your FFRs on Turnltln. Please see Chapter 3 for specifics on this.
Comments on Synthetic Experiments

1. It is highly likely that you will have to repeat at least one of your experiments.
Remember, yields and purity count! There should be sufficient time to repeat
experiments if necessary, and many students finish the semester early.
2. Some of the chemicals you will be handling are probably much more reactive
than anything you've ever handled before. Some may react violently with water.
Use extreme caution!
3. You will need to analyze your products by TLC, 1H NMR, and IR whenever ap-
plicable. There will be times when TLC will not be beneficial because products
are not UV active or do not stain well, so spots go undetected. If your product
lacks any conjugation and is relatively small in size this may be the case, so
consult with your TA. The only time you will not be able to run a 1 H NMR will
be when your product is not soluble in any solvent. Your handout will indicate
this problem and advise otherwise. Also there will be times when 13 C NMR
will be extremely helpful because the product and reactants have extremely
similar chemical shifts and splitting patterns. When 13C NMR is advised it will
be suggested in your experimental handout.
4. For all solid products, melting points and yields must be determined. For
liquid products, yields must be determined and boiling points only need to
be determined when specifically asked for.
240
Synthetidlsolation Experiments 11 Chemistry 213W
.:>. Handing in products: While you should show all of your synthetic products NOTES ;:
to your TA and have your notebook initialed, you will rarely turn them in. If
you do, use:
Liquids-glass "shorty" vial in plastic ziplock bag
Solids-plastic ziplock bag
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..
,.1.
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~
c_
D
Mr. Benzene says: If you do not have to hand them
in, please save all your products until the end of the
semester. Keep vials labeled.
D
Troubleshooting
You see, but you don't observe.
-Sherlock Holmes to Dr. Watson
1. NO PRODUCT?
a. Did you get starting material back? Use mp or TLC to t ell.
b. Check reagents (wrong or impure)- try a different bottle.
c. Check times and temperatures.
d. Check calculations.
e. Other conditions:
pH-be sure to stir well.
Wrong layer? Do a drop test?
2. Low yield after recrystallization? Either wrong solvent or too much added so
the solution wasn't saturated. Concentrate mother liquor. Or lower solubility
with a second solvent in mixed solvent recrystallization (trickier!).
3. Product ugly?- heated too strongly, boiling away all solvent. ("Burned the
potatoes.") Reflux more gently.
4. Oily, noncrystalline product. Treat as if a solid and recrystallize. You can run
spectra or GC directly on an oil.
5. Still stumped? See TA or course supervisor. Go on to another procedure or
experiment, i.e., use time wisely and keep working.
241
-- -- -------~~~~~-
.....
II NOTES
242
- - - - -- -
llllli:I .
.:--
mo, ) l
'
,
CHAPTER12
_O_p_t_i-ca_l_R_o_t_a_ti_o_n_,-R-e-fr_a_c-ti_v_e _
n . Index, and Elemental Analysis
Optical Rotation (Polarimetry)

Optical activity is the ability of a compound to rotate polarized light and is di-
rectly related to the asymmetry or chirality of molecules. If a tetrahedral carbon is
substituted with four different substituents, it is said to be asymmetric or chiral.
Two possible configurations of this molecule exist that are mirror images of each
other, just like your left and right hands are mirror images of each other. These
two configurations are called enantiomers and are non-superimposable. Molecules
containing these chiral carbons will rotate plane-polarized light; if a chiral molecule
rotates light a certain degree to the right, then its enantiomer will rotate the light
the same degree to the left. These measurements are made using a polarimeter.
Limonene is an example of a chiral molecule: one enantiomer of limonene can be

found in the peels of citrus fruit, while the other one is found in pine cones (Figure
12.1). The R-isomer oflimonene rotates plane-polarized light to the right, and the
$-isomer rotates it to the left, as indicated by the (+) and(-) in the name. The two
enantiomers have the same melting and boiling points, same behavior on TLC,
and so on. So how do we differentiate the two? Besides the difference in sign of
the optical rotations, we can distinguish them by their smell and taste, because
most receptor sites within your body are chiral, too.
Chirality plays a very important role in pharmaceuticals for the same reason: the
chiral receptor sites in your body's physiology. Thalidomide is a chiral molecule
which was used in the 1950s to quell morning sickness in pregnant women. Tragi-
cally, the two enantiomers had completely different effects, with the R-isomer being
an effective sedative while the $-isomer caused severe birth defects estimated to
have affected at least 10,000 babies, mostly in the UK. The two forms of Thalido-
mide interconvert at the pH in the body; so even if enantiomerically pure Thalido-
mide had been administered, it would still have had the same disastrous effect.
Materials from Making the Connections 2: A How-To Guide for Organic Chemistry Lab Techniques written by Anne
B. Padias, copyright © 2011 are reprinted with permission of Dr. Padias 243
: : NOTES mirror
CH3
R(+)-limonene S(-)-limonene
(citrus) (pine cones)
[aJ 28= +123° [a]~= -123°
~":H=o 0
R(+)-thalidomide S(-)-thalidomide
Figure 12.1. Examples of chiral compounds.
Optical activity is measured in a polarimeter. Ordinary white light consists of waves

with a variety of wavelengths that vibrate in all possible planes perpendicular to the
direction of the propagation. Light can be made monochromatic (of one wavelength
of color) by using filters or special light sources. For polarimetry, a sodium lamp
with a filter is used to obtain the sodium D line at 5893 angstroms. Even though
this light is monochromatic, the individual light waves still vibrate in all possible
planes perpendicular to the beam. A polarizing filter allows only the light which
vibrates in one direction to pass through (Figure 12.2). The polarized light is then
passed through a solution of an optically-active compound; this causes the polar-
ized light to be rotated at an angle a. A second polarizing filter has to be rotated
at the same angle a for the light to pass through and be observed.
filter polarizer sample polarizer
polarized observed
Na lamp Na D line light rotation a
Figure 12.2. Basic setup of a polarimeter.
244
1111'
1
- - "'' l1
I. . ,:il\111
Optical Rotation, Refractive Index, and Elemental Analysis II Chemistry 213W
A polarimeter can be as simple as a lamp and two polarizing filters at each end of NOTES H
a container holding the compound to be measured (Figure 12.2), or as sophisti-
cated as instruments that can cost more than $25,000. The former requires a large
sample, while dilute samples can be accurately measured with the latter.
The observed rotation a depends on the path length, the concentration of the
sample and the specific rotation [a], which is an inherent property of a particu-
lar compound. As shown in Figure 12.1, the specific rotation for R-limonene is
[-123n°. The temperature (20°C) and the wavelength (the Na D line) at which
the measurement was made are reported. The specific rotation is calculated from
the observed rotation a using the following equation:
a = [a] x c x 1or [a = ~ r
[a) = specific rotation
a = observed rotation
1 = length of the sample, in dm
c = concentration of the sample, in g/rnL
How Is It Done in the Lab?

A solution of the compound in question is made. Water and ethanol are very com-
mon solvents for polarimetry, but for organic compounds dichloromethane and
chloroform are often used. Because a can change with solvent, both the solvent and
the concentration must be specified. Usually 10-25 mL of a solution is sufficient, but
larger sample cells do exist. A sample cell is typically exactly 1 dm long, and is made
of quartz to avoid any absorption of the light by glass. The sample cell is cylindrical
and has two openings on t op, as shown in Figure 12.3. These cells are very expensive
and should be handled with great care.
quartz sample cell

for polarimetry
Figure 12.3. Quartz sample cell for polarimetry.
245
I: NOTES
The concentration of the solution is usually 5-10%. Prepare the solution using a
volumetric flask, and accurately report the concentration.
The sample cell must be cleaned meticulously before filling it with the solution;
if possible, rinse the cell twice with a small amount of the solution. Ensure that
there are no suspended particles in the solution and no air bubbles in the cell, as
they will refract the light and affect the measurement. Allow enough time for the
temperature of the sample to stabilize.
The polarimeter is calibrated by using pure solvent and adjusting the zero point.
As it is easier to observe the absence oflight, the rotation is measured at the dark
point and the observed rotation a is read on the dial. If you are using an automatic
polarimeter, follow the instrument instructions.
The specific rotation [a] can be calculated from one measurement. If you are
comparing the optical activity of several samples, it is important to measure each
sample exactly at the same concentration in the same solvent.
Enantiomeric Excess or Optical Purity

A sample of one enantiomer isolated by a resolution method or prepared syn-
thetically is not always 100% optically pure. Frequently, it can be contaminated
by residual amounts of the opposite stereoisomer. Chemists generally use the
term enantiomeric excess (ee) rather than optical purity. Enantiomeric excess is
calculated using the following formula:
[a] observed
%ee = [ ] X 100%
a pure
A "pure" sample of R-limonene isolated from oranges has a specific rotation of 111,
while pure limonene has a [a ] of 123. The enantiomeric excess in this case equals
111
%ee = X 100% = 90.24%
123
What does this mean? You have an enantiomeric excess of -90% R-limonene, so 10
out of every 100 molecules result in zero optical rotation. These 10 molecules are
equally R- and S-limonene molecules; therefore, you have 95 R-limonene molecules
for every 5 S-limonene, or 95% optically pure R-limonene.
Refractive Index
The refractive index, n, is defined as the ratio of the velocity oflight in air to the
velocity of light in the medium being measured, and is another unique physical
246
Optical Rotation, Refractive Index, and Elemental Analysis :: Chemistry 213W
property of a chemical. The refractive index is based on the fact that light travels NOTES : :
at a different velocity in condensed phases (e.g., liquids and solids) than in air.
The refractive index can be used to characterize a pure organic compound and to
assess its purity, or even to determine the composition of mixtures.
The refractive index for a given medium depends on two variable factors. First, it
is temperature-dependent. The density of the medium changes with temperature;
hence, the speed of light in the medium also changes. Second, the refractive index
is wavelength-dependent. Beams of light with different wavelengths are refracted
to different extents in the same medium and give different refractive indices for
that medium.
The effect of refractive index is seen in real life when you put a fishnet under the
water in an aquarium; the pole seems to bend at the point where it enters the
water, which is due to the different refractive indices of air and water. The same
effect makes it difficult to pick up a toy at the bottom of a swimming pool; it never
is exactly where you think it is-unless you put your head under water!
optical fiber cladding

(high n) (low n)
Figure 12.4. Examples of the effect of refractive indices.
247
I: NOTES
The principles of refractive indices are applied in the construction of optical fi-
bers. Because photons travel faster than electrons, optical fibers find more and
more applications in modern telecommunication. Optical fibers are also used to
provide light in otherwise inaccessible places. An optical fiber consists of a core
with a high refractive index, surrounded by a cladding that has a lower refractive
index. When light is sent through the fiber, it will reflect off the sides of the high
refractive index core and stay contained within the core. The larger the difference
in refractive index between the core and the cladding, the more efficiently the light
will be transmitted through the fiber, resulting in minimal loss in signal strength.
In plastic optical fibers, the core is often poly(methyl methacrylate); the cladding
can be a silicone-based material, which also protects the core.
How Is It Done in the Lab?

The instrument used to measure a refractive index is a refractometer. The refractive
index is dependent on temperature and wavelength, and the refractometer may
have a built-in thermometer. The most commonly used refractometer is an Abbe
refractometer; a typical instrument is shown in Figure 12.5. As for the light, the
Na D line is used (the same wavelength as in a polarimeter). The refractometer
can be kept at exactly 20°C by pumping water through the sample block if very
exact measurements are necessary; in most cases, the temperature is noted and
the refractive index at 20°C can be calculated (see page 250).
248
Optical Rotation, Refractive Index, and Elemental Analysis II Chemistry 213W
NOTES II
---+--temperature and
refractive index display
adjustment control
prism assembly
Figure 12.5. Refractometer.
The quartz prisms must be clean. If they are not, rinse with a few drops of dichlo-
romethane or another volatile solvent and blot the surface dry with soft tissue
paper. Do not rub; these quartz surfaces must not be scratched.
Place a few drops of the liquid to be measured on the lower prism, being careful
not to scratch the surface, and carefully close the prism assembly. Most instru-
ments have a locking device to ensure that the prisms are in perfect alignment.
Look through the eyepiece and turn the adjustment knobs. You should see a split
optical field-dark on the bottom, light on top. Turn the knobs to achieve a sharp
separation line between dark and light, and this line must be in the middle of the
cross hairs. You can then either read off the refractive index below this display, or
on an external read-out. In Figure 12.6, the reading is n = 1.3684. Carefully clean
the prisms with soft tissue paper, again without rubbing.
249
: : NOTES
1.360 1.370 1.380

,J,1J1,1111!111!1!1!11ol,1i1,j1.11!11.!ol1l.i.1 ,1,1.l.1.1,1,1
Figure 12.6. Reading a refractive index (reading n = 1.3684).
Practical Tips
To calculate an accurate refractive index, you must make a temperature cor-
rection for measurements above 20°C. For organic compounds, the refractive
index decreases by 0.00045 for each degree Celsius over 20°C.
n i 0 = n io+ x+ x(0.00045)
If the measurement above was done at 26°C, the corrected value for n is
ni = 1.3684 + (6 X 0.00045) = 1.3711

0
If your sample is volatile, you must do your measurement very quickly. It may
take several tries to get an accurate reading before the sample evaporates.
Do NOT touch the prisms with anything sharp, such as a Pasteur pipette,
syringe, or spatula. Remember: only use soft tissue to clean the prism and do
not rub.
The concentration of a solution can be determined using refractive index
readings. For example, this method is routinely used in the wine industry to
determine the sucrose content of the wine. A calibration curve is constructed
using standard samples, then the concentration of the unknown solution is
determined using the refractive index.
Elemental Analysis (Molecular Formula)

Elemental analysis is a method to determine the amount, typically a weight percent,
of an element in a compound. Just as there are many different element s, there
are many different experiments for determining elemental composition. The most
common type of elemental analysis is for carbon, hydrogen, and nitrogen (CHN
analysis). This type of analysis is especially useful for organic compounds and is
performed by specialized vendors. The compound to be analyzed is burned, and
250
Optical Rotation, Refractive Index, and Elemental Analysis :: Chemistry 213W
~e amount of generated C02 , H2 0, and nitrogen oxides is measured. With mod- NOTES ::
em instrumentation only mg quantities or less compound are needed to obtain
an accurate elemental analysis.
The elemental analysis of a compound is used to determine the empirical formula of

a compound; this is the formula that contains the smallest set integer ratios for the
elements in the compound corresponding to the elemental composition by mass.
The elemental analysis results for a specific compound read: 62.103 C, 10.423 H,
and 0.02% N, so we know that this compound contains carbon and hydrogen, but no
nitrogen. The remainder is assumed to be oxygen, which cannot be measured using
this method. Dividing the percentages of each element by the atomic weight of that
element leads to the atomic ratio of each element in this molecule. For example:
#C = 62.06/ 12 = 5.17
#H = 10.35/1 = 10.35
#0 = 27.55/16 = 1.72
Dividing these numbers by the smallest number gives the molecular formula (MF)
with the smallest set of integer ratios. The ratio of C/H/ O is 3.04/ 6.017/1, which
roughly corresponds to 3 C/ 6 H/ 1 0. This means that the MF for this compound
could be C3 H 60, or C6 H12 0 2, and so on. Other physical and spectroscopic measure-
ments help decide if the compound is acetone, or oxetane, or dimethyldioxane, or
even po\y\oxytrimetb.y\ene) -\.-C.H2C.Hl.H 20-1n-·
251
Chemistry 213W ; ; Chapter 12
== NOTES
252
Spectroscopy Introduction
The physical constants described in previous chapters give information about dif-
ferent compounds. But unless you have literature data or have made the compound
before, the fact that, for example, the melting point of a compound is 78.3°C won't
tell you anything about the structure of the compound.
Spectroscopic methods, on the other hand, give you real information about a com-
pound's structure. Spectroscopy involves interactions of molecules with energy-
light-at different wavelengths. In its simplest form, spectroscopy entails shining
light on or through a sample and recording the changes in light intensity. Light
is energy, and different wavelengths correspond to different energies. Therefore,
different facets of the molecules can be probed and specific information about the
structure acquired.
The electromagnetic spectrum ranges from the highly energetic "(-rays to radio
waves with very low energy. The units are expressed in either wavelength or in fre-
quency, depending on which "light" the chemist is dealing with; which unit is used
depends on custom. Wavelength A. and frequency v are reciprocal values, connected
by the speed of light, c, and they are both related to energy by Planck's equation.
E = hu = he
A.
withe being the energy of 1 photon (1 quantum)

his Planck's constant (6.62 X 10-34 J·s)
A. being the wavelength, the distance between one wave's maximum and
the next, expressed in m or nm
v being the frequency, the number of wave maxima per unit time, expressed
in s- 1 or hertz (1 Hz = 1 s-1)
c being the speed of light, equal to 3 X 108 m/ s.
Materials from Making the Connections2 : A How-To Guide for Organic Chemistry Lab Techniques written by
Anne B. Pad.fas, copyright © 2011 are reprinted with permission of Dr. Padias 253
••
•• NOTES
Low energy
10 13 10•
AM radio
NMR
10 11 10• Radio waws MRI
FM radio, lV
109 10•
Cellular phones
10 7 10 "' Microwaw
Microwaw ovens,
satellites
10• 10 12 Infrared JR
Heat lamps
10 3 10 " Visible (400-700 nm)
UV-Vis
Ultraviolet Sun lamps
10 10 16
10-1 10 18 X-rays Medical X-rays

High energy
10- 3 1020 -y-rays
Wavelength Frequency Type of Application Spectroscopy

(nm) (Hz) radiation
Figure 13.1 . Electromagnetic spectrum and its applications.
As the frequency of light varies, so does the related energy. In this context the term
"light" is being used in a very broad sense. Some real-life applications of these waves
are included in Figure 13.1. For example, UV light is used in sun lamps, but these
are the same waves used in UV-visible spectrophotometry. NMR spectrometry-as
well as magnetic resonance imaging (MRis) in h ospitals- uses radio frequency,
the same energy range detected by radio antennas.
Ultraviolet Spectroscopy
The Basic Principles

A conjugated system can be described as consecutive 'IT-orbitals found in a series of
alternating double and single bonds. Examples of these types of systems are shown
in Figure 13.2. Conjugated systems can be quite short, as in 1,3-butadiene, or very
long, as in 13-Carotene, which has eleven 'TT-orbitals. Double bonds other than
carbon-carbon double bonds can participate in conjugated systems, as shown by
methyl vinyl ketone, where the carbon-oxygen double bond also participates in the
multiple bonding. Conjugated systems can be very short, as in the allyl cation (only
three consecutive p-orbitals). In order to be able to absorb UV light, a compound
must have a conjugated system.
254
Molecular Spectroscopy and UltravioletNisibl e Spectroscopy (UVNis) 11 Chemistry 213W
~
0
v ~
0
00 +
~
NOTES II
methylvinyl styrene 1,3-butadiene benzoquinone allyl cation

ketone
13-carotene (found in carrots)
Figure 13.2. Examples of conj ugated systems.
Molecular orbital theory (MO theory) accurately describes conjugated systems,

the geometry of the orbitals involved, and their interactions with UV light. MO
theory dictates that for every atomic orbital that participates in a bond, there is a
corresponding number of molecular orbitals. To illustrate this, consider 1,3-buta-
diene, a simple conjugated system consisting of four sp2 carbons. Each carbon has
three hybrid orbitals in a trigonal planar arrangement, as well as an unhybridized
p-orbital perpendicular to the plane of the hybridized orbitals. Since four of these
unhybridized p-orbitals participate in the conjugated system (as shown in Figure
13.3), four corresponding molecular orbitals are formed. Two of these orbitals,
named tjl1 and tjJ 2, are bonding orbitals, which are the lowest in energy. The other
two, tjJ3*and tjJ4*, are called antibondingorbitals (indicated by the asterisk), and are
much higher in energy than the bonding orbitals. When electrons are found in the
bonding orbitals, the bonding interaction between the two atoms at either end
of the bond is strengthened. Likewise, when electrons are found in antibonding
orbitals (a very high energy and unfavorable condition), the bonding interaction
between the two orbitals on either end of the bond is weakened.
;-- lj/4* --1j14'

... ++++f-lj/3 / *(LUMO)
~
+ lj/3 *
\tt '1'2 (HOMO) + '1'2
\++IJl1 ++'1'1
four p-orbitals four molecular orbitals excited-state

(ground state) configuration
C Haydcn-Mc Ncil. lLC
Figure 13.3. Butadiene and correspond ing molecular orbital diagram.
Each of the four p-orbitals participating in the 'TT-system has one electron, so the
t otal number of electrons in the conjugated system in butadiene is four. These
electrons are all found in the lowest energy orbitals, since this is the most stable
255
configuration that promotes a bonding interaction between the carbons. This low
II NOTES
energy configuration of electrons is called the ground-state configuration.
When one irradiates a conjugated system with UV light (commonly expressed

as hv or sometimes simply "light"), the energy from the light is absorbed and an
electron is promoted from the highest occupied molecular orbital iV2 (HOMO) to
the lowest unoccupied molecular orbital iµ3 (LUMO). This electronic transition,
called a 11 --7 11* transition, creates a new high energy configuration called the
excited-state configuration, with a single electron in an antibonding orbital. As the
system loses energy, the excited electron falls back down into iµ2 , and the ground-
state configuration is restored.
Types of Electronic Transitions

Molecules that have a variety of filled bonding (and unfilled antibonding) orbit-
als leads to a variety of possible electronic excitations and therefore absorptions.
For example, electrons in an n level can be excited t o either 11* or to CJ* levels.
Likewise, 11 electrons can be excited to CJ* orbital. (11 to CJ* or p ton are not often
seen, since these are forbidden due to changes in symmetry.) Finally, CJ electrons
can be excited to either CJ* or to 11* orbitals.
The energy for the different types of transitions vary. The larger the energy gap,
the higher the energy of the photon absorbed must be to effect that transition.
Alkanes contain only single bonds, so only CJ to CJ* transitions are possible. These
are very high energy, therefore have very high energy, and usually cannot be
observed using the commercially available spectrometers. (The 100 to 200 nm
range is referred to as "vacuum ultraviolet"; to observe transitions in this range
of wavelength, the sample must be in a vacuum, as atmospheric gases absorb in
this region, also.)
Molecules that contain only single bonds but also have N, 0, S, F, Cl, Br, or I
contain sigma bonding orbitals and nonbonding orbitals, so CJ to CJ* and n to CJ*
transitions are possible.
Molecules that contain carbon-carbon 1T bonds (alkenes or alkynes) can show 1T

to 'lT* transitions.
Finally, molecules with carbonyl groups (aldehydes, ketones, esters, acids, or am-
ides) or carbon- carbon pi bonds (alkenes or alkynes) can also shown to 1T* transi-
tions. Actually, these transitions are the most often studied, partly because they are
easily observed in the ranges available on commercial UV-Vis spectrometers, and
because they are very sensitive to substitution by other fragments in the molecule.
256
M o lecular Spectro scopy and Ultravio leWisible Spectroscopy (UVNis) :: Chemistry 213W
Notice that not all transitions are possible; some are forbidden and never ob- NOTES II
served, such as er -7 11, a -7 n, 11 -7 n , or 11 -7 er*. Some, such as n -7 1T* are
forbidden by selection rules, but are often observed, although usually weak.
For example, 4-methyl-3-penten-2-one, a conjugated enone, absorbs at 235 nm
(7T -7 7T*) and at 320 nm (n -7 'IT*) . Similarly, 3-buten-2-on~ absorbs at 219 nm
( -7 = 3600, 7T -7 Ti*) and at 324 nm ( -7 = 24, n -7 'IT*).
--er·
--n•
E H H H H
I I I I
H - C- C-C - C -H
--n I I I I
H H H H
all o bonds, so only c; to o * o to cr* and n to o*
--1t
transitions are possible transitions are possible
- - er
H H
\ I
C =C
H
I \ CH -CH
2 3
7t to 7t* and o to o *
transitions are possible
c;*
7t*
r n
E ~E
Occupied
orbitals
I
1 7t
(j
Common electronic transitions: the length of

arrow is roughly proportional to the energy
difference of the two levels, thus the longer
arrow means a higher energy of the electronic Orbital diagram of a 7t to n* transition .
transition. In the excited state , there is still one
electron in the bonding orbital , but now
the antibonding orbital is populated.
Figure 13.4. Relative energy levels for molecular orb itals and the kinds of transitions
possible for various fu nctional groups.
257
Chem istry 213W II Chapter 13
II NOTES 0 H
II I
c
c
H c/ "-c-r "-H
3 I
H
3-buten-2-one 4-methyl-3-penten -2-one
The compound 3-buten-2-one, a conjugated enone, absorbs at 219 nm (e = 3600,

1T ~ 1T*) and at 324 nm (e = 24, n ~ 1T*). Similarly, the compound 4-methyl-
3-penten-2-one absorbs at 235 nm (1T ~ 1T*) and at 320 nm (n ~ 1T*). Note that
the methyl groups move the 1T ~ 1T* absorption to longer wavelength. Note also
how weak the n ~ 1T* absorption is as reflected by a small e.
Appearance of UV-Vis Spectra

Often, a plot of the UV-Vis spectrum of an organic compound shows a broadened
band of absorption, rather than a discrete sharp absorption. If transitions are
quantized, why do they absorb over a broad range of wavelenths? Molecules in
the ground state and in the excited state can exist at various vibrational levels;
although the excitation of a molecule in the ground state v = 1 level to the excited
state v = 1 level is quantized, so is the jump to the v = 2, v = 3, etc. Each jump
represents a slightly different energy. The variety of energies associated with the
simple electronic transition is further smoothed out by the various rotational
energy levels underlying each vibrational level. The tiptop of the absorption band
represents the energy of the electronic transition from the most likely vibrational
level and rotational level of the electronic ground state to the most likely levels of
the electronically excited state. The bottom line: unless you artifically remove some
of the available energy transitions, the spectra appear as broad bands, not peaks.
v=3
v=4 } Different vibrational energy
v= 2 levels all within the lowest
'~ electronic excited state
'~
V=1
V=O
~{
V=4}
v=3 Different vibrational energy
v=2 levels all within the electronic
v= 1 ground state
v=O
Figure 13.5.
258
Molecular Spectroscopy and UltravioletNisible Spectroscopy (UVN is) H Chemistry 213W
Electronic transitions may also involve transitions between different vibrational NOTES H
levels. Each transition shown corresponds to the same electronic transition, but
the molecules in the ground state may be in different vibrational energy levels,
and may be excited to different vibrational energy levels.
Various transitions of slightly Spectrometer cannot resolve

different energies. the individual absorptions;
rather, a band of absorption
centered near the wavelength
of the major transition.
Figure 13.6.
~wering the temperature during the data aquisition can minimize the rotational/
collisional energy levels so that the spectrum shows the vibrational energy levels
only. Spectra obtained in this way will show fine structure- the jagged peaks
representing the electronic transitions between discrete vibrational levels.
Solvent choice can similarly affect the appearance of the spectrum. Nonpolar sol-
vents will not interact with solute molecules effectively, therefore having a similar
effect on the spectral appearance as cooling the sample solution. Polar solvents
interact more strongly, and fine structure will disappear.
The Instrument
A UV-Vis (ultraviolet-visible) spectrophotometer consists of a UV light source,
in which the light beam is guided through a sample to a detector. The detector
measures the intensity of the remaining light at the different wavelengths. The
spectrum is generated by plotting the absorbance versus the wavelength, and
shows the absorptions in the wavelength range from 200 to 800 nm (Figure 13.7).
The sample must be very dilute, normally in the 10- 3 to 10-6 mol/L range. The
solvent used cannot be UV-absorbing; common solvents are ethanol, chloroform
or dichloromethane.
259
:I NOTES
UV-Vis Sample Spectrum

light source cuvette OHaydc:n-McNc:il. UC
Slits:-\ <
(/\-.. Reference
n C Lenses ' • ••
rf.i
cell
v-_________ --~ H-- ____''i;\-__ - Y

~ and mirrors ~ Rotating beam \ -.._
------l\U.. __oomoto'
Light
source
~ i .
Grating
~ :•
;
.
Mirrors
••• •• - • • • • jI
Iii\~
m·. • __ __ W'" L:::J
C !Uyde11-Me-'fol l.LC ' • •• •
•• -·· Sample
cell
Schematic Diagram of a Double-Beam Ultraviolet-Visible Spectrophotometer
n C
Slits~
Lenses \
~ and mirrors ~ Detector
v--- ---~---~- H-- ~ --- ID ---- ~

I C!hyden-McScil I.LC
Light Grating Sample
source cell
Schematic Diagram of a Single-Beam Ultraviolet-Visible Spectrophotometer
Figure 13 .7. Here, a "blank" spectrum must be obtained first (solvent only in the sample
cell) and subtracted from the spectrum of the sample plus solvent.
The sample is placed in a quartz cuvette, since glass absorbs in the UV range. A
cuvette can be made of glass or plastic if the sample only absorbs in the visible
light range. The standard path length of the light through the cuvette is 1 cm.
The classical setup of a UV-Vis spectrophotometer is an instrument on a bench,

which contains the light and the detector. Optical fiber technology has greatly
expanded the range of instrument assemblies, from submergible probes to detec-
tors that fit on a computer card.
260
Molecular Spectroscopy and Ultraviolet/Visib le Spectroscopy (UVNis) :: Chemistry 213W
The Spectrum NOTES ; ;

_:..._typical UV spectrum is acquired by plotting the absorbance of light by a sample
as the wavelength of UV light is changed from 200 to 400 nm. The wavelengths of
'u-V light required to effect the 'ii~ 'ii* transition are absorbed; this corresponds to
the energy difference between the HOMO and the LUMO. For butadiene, the UV
spectrum would appear as shown in Figure 13.8. Here, the maximum absorbance,
c:alled Amax' occurs at 217 nm and the energy gap between the HOMO and LUMO
can be calculated as follows:
_ he _ (6.626 X 10-34 Js) X (3.00 X l08 ms-1) _ J

E - 'I -
/l.
2 .17 X 10-7 m - 9.16 x 1 091
100
200 220 240 260 280 300 320 340 360 380 400
Wavelength (nm)
figure 13.8. UV spectrum of butadiene.
The UV light is absorbed by a chromophore, the part of the molecule that is con-
jugated. The longer the chromophore, the higher the wavelength of maximum
absorbance, Amax· The Amax is also dependent on the substitution on the conjugated
system, but this is a smaller effect. Table 13.l shows some typical Amax values for
conjugated systems. For molecules with long conjugated systems, such as carotene,
the Amax will shift to higher wavelength into the visible light region; these com-
pounds are colored, indicating their absorption of visible light. The Amax indicates
that carotene absorbs at 451 nm, blue light, resulting in the observed orange color.
261
Table 13.1. Typical A.max values for conjugated systems.

II NOTES
Compound Amax (nm) Molar Absorptivity s (llmol cm)
1,3-butadiene 217 21,000

Isoprene (2-methyl-
220
1,3-butadiene)
1,3-cyclohexadiene 256
Acrolein (2-propenal) 219
1,3,5-hexatriene 258 35,000
1,3,5, 7-octatetraene 290
Carotene 451 139,500
Molar Absorptivity
The amount of UV light absorbed by a sample is directly proportional to the number
of molecules in the path of the light. Lambert-Beer's law relates the percentage of
light absorbed by a sample to its concentration and the molar absorptivity (e), also
called the extinction coeffzdent. The molar absorptivity is a physical constant unique
to every conjugated compound. Lambert-Beer's law states that the absorbance (A)
oflight is directionally proportional to the concentration of the sample (c, mol/L),
the path length traveled by the light (l, cm), and the molar absorptivity:
A= elc
Using this relationship with a known sample concentration, the molar absorptivity
of the compound being studied can be calculated. In general, the molar absorptivi-
ties of most conjugated systems is between e = 10,000- 25,000.
Conversely, if the molar absorptivity of a compound is known, then the concentra-

tion of the sample can be determined using UV spectroscopy and Lambert-Beer's
law.
Absorbance, A, is measured by the instrument; the concentration and path length

is determined by the operator of the instrument; and the molar absorptivity e
is a property of the chemical, influenced largely by the size of the portion of the
molecule that absorbs and whether the transition is forbidden or allowed. Forbid-
den transitions have a low probability of occurring, so have smaller absorptivities,
say 100 to 1,000.
262
Molecular Spectroscopy and UltravioletNisible Spectroscopy (UVNis) 11 Chemistry 213W
The actual spectrum is seldom reproduced for the purpose of reporting data; rather, NOTES H
o.
the wavelength(s) of the absorption maxima md are reported, along withe, the
extinction coefficient, a numerical value of the intensity of the absorptions. In
Chem 203 and 213W we usually only report X.max's and not e's.
Instruments can be designed with either single-beam or with double-beam arrange-

ments. When using an instrument that is a single beam, a background spectrum is
obtained using a cuvette filled with pure solvent. The sample (dissolved in the same
solvent used for background) is then placed in the cuvette. When the spectrum for
the sample + solution is obtained, the computer subtracts the background from
the obtained spectrum to give a spectrum of only the sample. Other instruments
pass light simultaneously through a cuvette of solvent and a cuvette of sample +
solvent, and subtract the spectrum of the reference cell. In the Instrument Lab,
the instruments only require a background with the empty cuvette.
A s a method of determining the structure of an unknown compound, UV-Vis is prob-

ably the least useful of all the common spectrophotometric methods. It is, however,
a powerful method for monitoring the concentration of known compounds or
as a detector for other separation methods, such as liquid chromatography. In
determining the structure of an unknown compound, its real value is apparent
when it is used in combination with some other analytical technique, especially
NMR or IR spectroscopy. Knowing the functional group(s) present and certainly
the history of the compound in question (know the reagents used to produce the
sample and what else has been done to the sample up to this point) can help you
interpret the data that is obtained from the UV spectrum.
Sample Problem
A sample of a solute, concentration of 1 x 10-4 M, shows two absorptions, one at
300 nm (A= 0.50) and another at 250 nm (A= 1.25). Calculate the molar absorp-
tivity for each absorption, assuming the cell path length were 1 cm. If you were
monitoring water for the presence of this compound, which wavelength would be
more sensitive for measuring small quantities of the chemical?
Answers: e =A l (bx c) = 0.50 I (1cmx1x10-4 M) = 5000 cm-1 M- 1 for the 300 nm

absorption
Similarly, e = 12500 for the 250 nm absorption. Since the compound of interest
absorbs more strongly at 250 nm, then small concentrations may be more accu-
rately measured than at 300 nm.
Choice of Solvent and Cuvette

The solvent should be free of absorptions in the region where the solute of interest
is to be measured. Common solvents and the maximum wavelengths where they
can be used without interfering with solute absorptions are seen in Table 13.2.
263
- - - -
. ~----1:;1-ll1
Table 13.2. UVNis solvent absorptions.

II NOTES
water 190nm n -hexane 200nm

ethanol (953) 205nm isooctane 195 nm
cyclohexane 195nm methanol 205nm
Anhydrous ethanol cannot be used for obtaining UV-Vis spectra because the residual
water is removed by azeotropic distillation with benzene; measureable traces of
benzene still remain in the ethanol, and the cutoff for benzene is at much longer
wavelengths.
Since glass absorbs in the lower wavelengths of interest, most cuvettes are made of
quartz, which makes them expensive. Quartz is transparent from 200 nm through
the visible portion of the spectrum. Even with a quartz cuvette, absorptions below
200 nm are impossible to detect due to absorption by atmospheric oxygen and
carbon dioxide. Vacuum techniques are necessary for measuring absorptions below
200 nm, hence the region 100 nm to 200 nm is often referred to as "vacuum ultra-
violet." If only visible spectra are of interest, glass is adequate, and is often used
for the test tubes in which sample solutions are analyzed (colorimetric analysis)
using the "Spec 20."
Different solvents can strongly influence the appearance of the spectrum of a

compound. A good example is that of hexane vs. ethanol: ethanol is a hydrogen-
bonding, polar solvent, and thus will interact strongly with the solute molecules;
this has the effect of making the energy differences between the different vibra-
tional states even smaller. Hexane, on the other hand, does not hydrogen bond,
and the spectrum of the compound will show a lot of fine structure, similar to the
appearance of the spectrum if it were obtained in the gaseous state.
Trends in UV-Vis Absorption Spectra

Although the absorption of ultraviolet and visible light effects the excitation of
electrons from ground states to excited states, the energy difference between the
two states is determined by the nuclei that the bonding electrons are holding
together in the first place. Ultimately, the nature of the atoms held together de-
termine the appearance of the UV-Vis absorption spectrum, and the appearance
of the spectrum can be used to deduce the connectivity in an unknown compound.
A group of atoms that give rise to an absorption is called a chromophore; in other

words, these are functional groups or recognizable fragments that give rise to
absorption. Auxochromes are additional substituents that increase the intensity
and possibly the wavelength of the absorption. Different compounds with the
same chromophore will differ in their absorption spectrum due to the different
auxochromes that are present. As we've said before, the absorptivity depends
264
lllllllllllllliii ·1i; 11i'lll!lllllllllllillilllllll
1
Molecular Spectroscopy and UltravioleUYisible Spectroscopy (UVNis) H Chemistry 213W
on the size of the molecular system that gives rise to the absorption. One of the NOTES H
simplest comparisons is between the simplest alkene, ethene, and the simplest
conjugated diene, 1,3-butadiene.
In ethene, each of the two carbon atoms are sp2 hybridized, the pure unhybridized
7T orbitals of each combining to give 'IT and r.* orbitals. Ethene absorbs at 171 nm
vacuum ultraviolet), a very high energy transition, and in the process an electron
is excited from the 'ii to the r.* orbital.
In 1,3-butadiene, there are four carbon atoms again, all are sp2 hybrids. Since there
are 4 atomic orbitals (the pure p orbitals on each carbon) that go into mal<ing linear
combinations to give the molecular orbitals, we get four MOs out. The lowest in
energy is the all-bonding combination; next lowest is the set where there is one
node (change of phase, indicated by the phase of the component p orbitals); both
of these are bonding in nature. The next lowest is actually antibonding in character,
as there are now two nodes; the very highest MO in energy is very antibonding,
as all the component 'IT orbitals are out of phase with each other. Notice though,
that th e energy difference between the highest occupied orbital and the lowest
unfilled orbital is smaller; smaller energy difference means longer wavelength.
Indeed, 1,3-butadiene absorbs at 217 nm.
The importance of conjugation is shown by comparing the wavelength of absorp-

tion for dienes that are not conjugated. 1,4-pentadiene is an example of an isolated
diene, and absorbs (178 nm) more like ethene than like 1,3-butadiene.
If we continue this pattern for longer conjugated systems, the energy difference
keeps getting smaller and smaller, and the wavelength of absorption longer and
:onger. For 1,3,5-hexatriene, the A.max appears at 274 nm. In 1,3,5,7-octatetraene,
there are four conjugated C=C units, and absorption occurs at 290 nm. For really
long conjugated systems like beta-carotene (11 double bond units, conjugated)
the absorption wavelengths are so long that they are in the visible light region.
Remember, when visible light is absorbed, the light reflected is the color of the
chemical or object. So, in the earlier sample problem, carotene absorbs at 452 nm,
·\·ell within the blue-violet region of the visible spectrum.
The bottom line: the longer the conjugated system, the lower the energy required
for exciting the electrons from the highest occupied orbital to the lowest unoccupied
orbital.
if the wavelength of absorption is large enough, then the compound may show
color. Remember that color is due to light reflected, which is the incident light
minus the absorbed light. When a compound absorbs at 400 nm (violet), then the
!ight reflected (appearance) is yellow.
265
Table 13.3. Visible spectrum.

== NOTES
Wavelength of Color of Light

Observed Color
Light Absorbed Absorbed
400nm violet yellow

450nm blue orange
SOOnm blue-green red
530nm yellow-green red-violet
SSOnm yellow violet
600nm orange-red blue-green
700nm red green
The pattern also follows for enones, or carbonyl-containing compounds where

the C=O is conjugated with a C=C group. For comparison, acetone shows an
n ~'TT* transition at Amax 280 nm (£= 15, n ~'TT*) and another absorption at
189 nm (s = 900, 1T ~'TT*). 3-buten-2-one, a simple enone, shows the same n
~'TT* transition at 324 nm (E = 24), as well as another absorption at 219 nm
(s = 3600) for the p to 'TT* transition. Conjugation therefore results in longer
wavelengths (lower energy) of analogous transitions as well as increasing the
extinction coefficient (molar absorptivity) of that transition.
266
''I 111·
l11,1lll11li ,,11· • ' 1
I .,
:1 I 11'
11
' I I
CHAPTER14
Nuclear Magnetic Resonance
Spectroscopy (NMR)
NMR
Nuclear magnetic resonance (NMR) spectroscopy is the most widely used technique
for characterization of structure in organic chemistry, because it reveals specific
placement and connectivity of atoms. While infrared spectroscopy is used t o
determine which functional groups are present in a molecule, NMR spectroscopy
can help determine the exact location of functional groups and hydrogens. NMR
spectroscopy gives valuable information about the carbon skeleton and about the
molecule as a whole.
NMR spectroscopy can be applied for any nucleus that has a nuclear spin; that
is, any nucleus that has an odd mass number and/or odd atomic number. The
most common type of NMR is 1 H (proton) NMR, and the use of 13 C NMR is also
widespread. For 1 H NMR, the chemist is relying on the most abundant isotop e of
hydrogen, while in the case of 13 C NMR the 13C isotope only represents roughly
1 % of the carbon atoms.
In NMR the nucleus is observed. Consider the nucleus as a tiny magnet that is
positively charged. The nucleus spins and, if placed in a strong magnetic field,
the spin aligns with the magnetic field and precesses very much like a child's top
(Figure 14.1). The spin for 1 His + Y:z and, though aligned with the magnetic field,
the nucleus rotates at an angle.
Materials from Making the Connections 2: A How-To Guide for Organic Chemistry Lab Techniques writ ten by
Anne B. Padias, copyright © 2011 are reprinted with permission of Dr. Padias 267
H NOTES
nucleus spins and aligns child's top

with the magnetic field
(precessional motion)
Figure 14.1. Effect of magnetic field on nucleus spin .
If a radio frequency is applied, the nucleus flips to a higher energy state-against

the magnetic field-and the spin is-% (Figure 14.2). The difference in energy is
very small and corresponds to low en ergy radio waves, and the protons are said
to be in "resonance." When an NMR is run, a very sh ort, powerful "ping" of radio
waves is applied, which flips most spins to the higher energy state (Figure 14.3).
The decay of the signal is then observed for a certain time period while the spins
slowly fall back to the lower-level spin aligned with the magnetic field. This pro-
cess is called free induction decay, or FID. The raw signal is an oscillating curve
that is converted to an NMR spectrum using the mathematical function Fourier
Transform.
-%
activation with
radio wave
-% + FID
+%
activation of spin states and FID (free-induction decay)
Figure 14.2. Effect of radio wave on nucleus spin.
268
- -~.-~~
-- --- ~-- - -- - --~--~- - I!~ I

11m111mmn11111 11 11111111111111111111111111111111111 1,,:1111 1:11,, ,,11111 ,,.
1 1
,, ,.. ~
Nuclear Magnetic Resonance Spectroscopy (NMR) II Chemistry 213W
NOTES II
FID
- --+-- "f" t
NMR spectrum
The FID signal is converted using Fourier Transform
to a conventional NMR spectrum .
Figure 14.3. Free induction decay in NMR.
In 1 H-NMR the hydrogen nucleus, a proton, is observed, and the terms hydrogen
and proton are used interchangeably in NMR. This is somewhat different from
the way a proton is considered in a reaction mechanism when a proton specifically
refers to H +, which after all is actually a hydrogen nucleus!
The Instrument
A nuclear magnetic resonance spectrometer consists of a magnet, in which the
sample is placed. The magnet is very powerful(> 1 Tesla), and objects that might
be affected by the magnetic field, such as credit cards, should not be brought into
the NMR room, nor should people with pacemakers enter these rooms.
The high magnetic fields are achieved using a superconducting magnet, a Nb/ Ti
alloy, which is cooled in liquid He (4 K). The liquid He container is surrounded by
a liquid nitrogen container, to help maintain the low temperature. The probe is
equipped with a radio transmitter and a receiver, connected through an ampli-
fier to a computer for data processing (Figure 14.4). The sample in the NMR tube
is "dropped" into the probe and spins very rapidly. NMR tubes are quite narrow,
5 mm diameter, and rather long (-7-20 cm).
269
II NOTES
liquid nitrogen - - - H - -
liquid helium - -- H---11+-
super-conducting magnet- -=====!==~!~~£;'~

i~~~
RF coil
sample - ---H---¥.!-'t-+=-...:..:;+-W.::::===H-
probe ---T.---tiHt-r-c~-m
l~;;;;;;;;:;:tlj
computer amplifier
Figure 14.4. Basic setup of NMR instrument.
The strength of a particular NMR instrument is indicated by its operating fre-

quency, meaning the frequency at which the nuclei resonate. Older 1 H instruments
are 60 MHz, which is the radio frequency used for protons in this specific magnet.
Newer more powerful instruments range from 200 to 600 MHz, and even 800
MHz. The higher frequencies lead to more detailed spectra, and t herefore more
information. Comparing the two 1 H spectra of m-isopropoxytoluene recorded at
60 MHz and 300 MHz, the difference between the two spectra is obvious. The 300
MHz spectrum shows much more detail, but at first sight the peaks are "crunched"
together. A blow-up of the area at 8 4.5 shows the detail of the spectrum; also notice
the much cleaner peaks around 8 7.0, which correspond to the aromatic protons.
270
Nuclear Magnetic Resonance Spectroscopy (NMR) 11 Chemistry 213W
15
10
& 0
CH,
)__CH
3
Group
2
3
4
6
8
nH
1
1
1
1
1
Shift
6.32
7.11
6.68
6.66
4.55
NOTES II
10 3 2.30
11 9 6 1.30
10
1.29(11.9)
::1 ~
15 1.31(11.91
1 . - - - - --
10 2.30(101
0.00 ' ' '

4.60 4.50
4 57(8(
4.53(81
4.51(8[
10
Figure 14.5. NMR spectra of m-lsopropoxytoluene, at 60 MHz (top spectrum)

and at 300 MHz (bottom, with detailed insert).
For 13 C, the resonant frequency is different from the proton at the specific mag-
netic field; the 1 3 C resonant frequency is roughly 14 of the 1 H frequency. Thus, for
a magnet with a field strength of 7 Tesla, the 1 H resonant frequency is 300 MHz,
while the 13 C resonant frequency is roughly 75 MHz. 13C NMR will be discussed
in further detail later in this chapter.
The Sample
NMR spectra are usually run in dilute solutions. An NMR tube is a long, very thin
tube, as shown in Figure 14.6; the tube has a diameter of -5 mm.
271
I: NOTES Plastic cap
5 mm glass tube
Sample: -35 mg
2-3 in deep
Figure 14.6. NMR tube.
The solvent should either not have an NMR signal at all, or at the very least have a
signal that does not interfere with the spectrum being recorded. For proton NMR,
solvents without protons should be used. The most common solvents are deuter-
ated; deuterium's signal in NMR is very far removed from the proton spectra we
are recording. Another reason to use a deuterated solvent is that the deuterium
signal provides a "lock" for the instrument, which helps to calibrate the instrument
during the consecutive scans. Table 14.1 lists common NMR solvents, as well as
those peaks that the small fraction of non-deuterated molecules would display in
the spectrum. Consider the most common solvent, deuterated chloroform CDC13 .
Chloroform is a very good solvent for most organic compounds, and is not too
expensive. Commercial CDC13 is 99.83 deuterated, which means it still contains
0.23 CHC13 . Therefore each NMR spectrum will contain a very small peak due t o
the remaining CHC13 , and this peak can be found at 8 7.3 ppm.
272
Nuclear Magnetic Resonance Spectroscopy (NMR) :: Chemistry 213W
Table 14.1. Common NMR solvents and thei r NMR signals.

NOTES H
Solvent Formula NMR Signal (O, ppm)
Chloroform-cl CDC~ 7.3 (s)
Acetone-d6 (CD3 ) 2 C=O 2.1 (s)
DMSO-d6 (CD 3) 2S=O 3.6 (m)
Benzene-d 6 C6D6 7.4 (s)
Deuterium oxide D2 0 4-5 (hr)
Tetrahydrofuran-d8 C4D8 0 1.9 (m), 3.8 (m)
Dichloromethane-d 2 CD2 Cl2 5.2 (s)
The 1 H Spectrum
As shown in Figure 14.5, a 1 H spectrum is represented on a scale from 0to10. A
standard is necessary, and for 1 H NMR tetramethylsilane (CH3 ) 4 Si (TMS) is used;
the TMS signal is the 0 point. Note that the peak at 8 0.0 does not appear in the
spectra in this book because these are simulated spectra.
The scale of the x-axis in an NMR spectrum is expressed in ppm. Each ppm in Hz
is equal to the frequency of the instrument divided by 106. Therefore, when using
a 60 MHz (60,000,000 Hz) instrument, 1 ppm is equal to 60 Hz, while for a much
more powerful 600 MHz instrument, 1 ppm equals 600 Hz. As will be shown, the
latter will yield much more structural information.
The position of a peak is expressed as the chemical shift 8; 8 is equal to the signal
frequency in Hz divided by the instrument frequency in MHz multiplied by 106.
In practice, 8 will be on a scale from 0 to 10 or higher.
s: signal frequency (Hz)

u(ppm) = applied
. frequency (MHz) X 10 6
A Simple Explanation of 1H NMR Spectra

For a particular type of atom, such as 1 H in proton NMR, the spectrum shows
peaks or signals, and from these the chemist will deduce information about the
structure of the molecule. As explained above, the signal is due to the FID; we are
observing the energy which is released when the spin of the nucleus flips back to
realign itself with the applied magnetic field (Figures 14.2 and 14.3).
Let's start with me thane, CH4 . If we dissolve methane in CDC~ and run an NMR,
we can only observe one kind of proton; i.e., one peak. All hydrogens, or protons, in
methane are equivalent, and therefore will behave exactly in the same fashion.
273
As shown in Figure 14.7, a peak is observed at o0.3. The first principle of NMR is
== NOTES
that equivalent hydrogens result in only one signal.
3.0
2.5
2.0
1.5
1.0
0.5
0.0 ...
11 10 9 8 7 6 5 4 3 2 0
Figure 14.7. NMR of methane CH 4 in CDCl 3 .
The spectrum of ethane CH 3 CH3 (Figure 14.8) looks very similar, again one peak,
but now the chemical shift is o 0.9; the peak shifted. The protons in ethane are
very similar to the protons in methane, but not quite the same. Again we only see
a singlet, a single peak, and this is consistent with the principle that all equivalent
hydrogens only display one peak.
4.5
4.0
3.5
3.0
2.5
2.0
1.5
1.0
0.5
0.0 .. . .
11 10 9 8 7 6 5 4 3 2 0
Figure 14.8. NMR of ethane CH 3 CH 3 in CDCl 3 .
In the NMR of dimethyl ether CH3 0CH 3 (Figure 14.9), notice that there is still
only one peak, consistent with the rule that all equivalent hydrogens give only
one signal. However, the peak has shifted quite a bit, too 3.0. This is because the
hydrogens in dimethyl ether are in a different environment than the hydrocar-
bon hydrogens in methane and ethane. The hydrogens in dimethyl ether are on a
carbon adjacent to the more electronegative oxygen, and the environment of the
hydrogens in the molecule will influence the energy difference between the two
spin states. Electronegative substituents result in a "downfield" shift, meaning a
shift to higher o. This leads us to the second principle in NMR: The chemical shi~
of a peak is dependent on the molecular environment the protons are in.
274
Nuclear Magnet ic Resonance Spectroscopy (NMR) :: Chemistry 213W
t-Butyl methyl ether CH 3 0-C(CH3) 3 has two kinds of protons: the nine t-butyl NOTES : :
protons are rather hydrocarbon-like, while the three methoxy protons are almost
exactly the same as the dimethyl ether protons. As a result, the NMR of methyl
t-butyl ether, shown in Figure 14.9, has two peaks: one large peak at 8 1.2, cor-
responding to th e t-butyl protons, and one smaller peak at 8 3.1 representing the
CH 3 0- protons.
The area underneath the peaks is directly proportional to the number of protons the
peak represents. The computer calculates the area under the peaks by using integra-
tion, which is represented in the spectrum by the horizontal line. The area of the
peaks is measured by the "rise" in this horizontal line and is directly proportional
to the number of hydrogens the peak represents. In Figure 14.9, the int egration
of the peak at 8 3.1is1.91, and the peak at 81.2 is 5.73. The ratio 5.73/ 1.91 is 3,
which means that one peak represents three times as many protons as the other
peak. The third principle of NMR spectra, therefore, is: The surface under the peaks,
the integration, represents the relative number of protons of each type in the molecule.
5.73
_____
,
1.0
0.5
1.91
O .O "'tn=rrn"TT"n=riT=rr=i=i=orr=TIT"n=="TT"=ri"TT"=iTi=r=T=i=i=~:n==~=;==;=;~'TTT'TT=r=;=r;==n
11 10 9 8 7 6 5 4 3 2 0
Figure 14.9. NMR spectrum oft-butyl methyl ether CH 3 -0-C(CH 3 )3 .
Diethyl ether (CH3 CH2)p also has two kinds of protons, but as shown in Figure 14.10
the spectrum is more complex, because the signals are split: the signal at 8 3.4 is split
in four peaks (quadruplet), while the signal at 8 1.2 is split in three peaks (triplet).
Consistent with the principles outlined above, the protons on the a-carbon next
t o oxygen are at higher chemical shift than the protons on the 13-carbon, which are
more hydrocarbon-like, and the integration indicates a ratio of 2 to 3, respectively.
The methyl protons (8 1.2) are subjected to the instrument magnetic field, but
they can also feel the tiny magnetic fields generated by the spinning nuclei of the
methylene CH2 group. Those spins can either be both aligned wit h the magnetic
field, or both against, or one up and one down. The latter is twice as likely, as shown
in Figure 14.11. Therefore, the methyl protons feel three different magnetic fields
and yield three different peaks, with the middle one being double the size of the
other two.
275
H NOTES
When the situation of the methylene protons is analyzed, there are four possibilities
for the spins of the methyl protons (Figure 14.11). This will result in a quadruplet,
with the inside peaks being three times as large as the outside peaks.
1.0
0.5
10 9 B 7 6 5 4 3 2 0
Figure 14.10. NMR spectrum of diethyl ether (CH 3 CH 2 ) 2 0.
CH 3 proton spins CH 2 proton spins
11111~ ~ ~ 1 ~ ~ ~ 11 1~ ~ ~
Ht
1H ~ 1~ ~1
~ 11 1~ ~
CH2 NMR signal CH3 NMR signal
- J ~
-
J
-- J J
Figure 14.11. Visualization of splitting patterns.
The fourth principle of NMR spectra is: The splitting or multiplicity of a signal is
determined by the number of protons on the neighboring carbon plus one, n + 1.
The distance between the peaks is determined by the coupling constant J. Notice
that the coupling constants, expressed in Hz, are the same for related signals. As
the quadruplet and triplet in the spectrum of diethyl ether are related, the coupling
constant is the same in both multiplets, 7.0 Hz. How was this determined? The
peaks in the triplet are respectively at 1.21, 1.14, and 1.08 ppm, the difference is
276
0.07 ppm, and as this is a spectrum recorded on a 100 MHz instrument 1 ppm = NOTES II
100 Hz. Therefore, J = 0.07 ppm• 100 Hz/ ppm = 7.0 Hz. The coupling constant
is influenced by many factors, such as length of bonds and dihedral angles, and
will be discussed below. Therefore, the fifth principle of NMR spectra is: Coupling
constants of"related" multiplets are the same.
To summarize:
Non-equivalent hydrogens result in different signals.
The chemical shift is determined by the chemical environment of the protons.
The integration corresponds to the number of equivalent protons responsible
for a specific signal.
The splitting pattern is determined by the number of protons on the neighbor-
ing carbon n: the multiplicity of a signal is n + 1.
"Related" multiplets have the same coupling constants.
Equivalent Hydrogens and Integration

Protons in the same chemical environment are said to be equivalent and will result
in one signal in the NMR spectrum; it is therefore essential to be able to recognize
equivalency in a chemical formula.
Each set of equivalent protons results in one signal, but this signal can be split.
Therefore, it is also necessary to be able to distinguish how many types of protons
are in the NMR spectrum, as this is important structural information.
The integration of the signal gives information about the number of the protons
this particular signal represents. Again, the NMR spectrometer will integrate the
NMR signals, which gives relative information about the number of protons.
Figure 14.12 shows different molecules and indicates how many different kinds
of protons are in each. Cyclobutane, benzene, and dioxane have only one type of
proton; therefore, the NMR spectrum will consist of only a singlet. The other two
compounds in Figure 14.12 have two kinds of protons, so the NMR spectrum will
consist of two signals. In these particular cases there are two singlets in each of
these spectra, since equivalent protons do not split each other and there are no
hydrogens on neighboring carbons.
:: NOTES H
c
HC,.... ~CH
II I
HC...._ ~CH
c
H
all protons equivalent, so one NMR signal
0
integration ratio: 2/3 integration ratio: 1/3
two types of protons, so two NMR signals
Figure 14.12. Proton equivalence and integration.
Looking at a more complex system, we can analyze the structure used in Figure
14.5:
Types of
Integration Splitting
Protons
CH 3 toluene 3 1
2* CH3 isopropyl 6 2
CH isopropyl 1 7
1
H aromatic 1 1
H 2 aromatic 1 2
H 3 aromatic 1 2X2
H4 aromatic 1 2
There are 7 kinds of protons in this structure. In Figure 14.5, the signals of the methyl
and isopropoxy groups are easily recognized, but the peaks of the aromatic protons
are somewhat muddled. The lesson here is that it isn't always easy to distinguish
the different types of protons in the spectrum.
The integration of the different types of protons in Figure 14.5 reveals that the
ratio of the signals going from left to right is 1:2:1:1:3:6. In this case, two of the
aromatic protons have roughly the same chemical shift and the signals overlap.
Chemical Shift in 1 H Spectra

One of the major advantages of NMR is that the position of the signals-the
chemical shift-gives us clues about the chemical environment of the protons in
278
lilL. - --
question. The different areas of the spectrum correspond to certain functional NOTES H
groups. A representation of the different chemical shifts is shown in Figure 14.13,
and the same data are collected in Table 14.2.
j HC-Ar
I CH-X
----= _I ---H I -
luHf
10 9 8 7 6 5 4 3 2 0
Figure 14.13. Chemical shifts of common functional groups.
Table 14.2. 1H NMR chemical shifts.
Chemical Shift
Functional Group Proton Connectivity
(0, ppm)
R-CH 3 0.9
Alkane R-CH 2- R' 1.3
R3- CH 1.6
H- C-Br 2.5-4.0
Halide H- C-Cl 3.1-4.1
H-C-F 4.2-4.8
CH-OH 3.4-4.0
Alcohol
C- OH 0- 5
Ether CH- 0 - R 3.2-3.6
CH- NH2 2.5-3.1
Amine
C-NH2 0-5
Ketone CH-C=O 2 .0-2.5
CH-(C= O)H 2.2-2.4
Aldehyde
CH-(C= O)H 9-10
CH-COOR 2- 2.5
Ester
C-(C = O)O-CH- R 3.7- 5
CH- COOR 2 .0-2.6
Carboxylic acid
C-COOH 10-12
HC=C 4.0- 6.8
Alkene
HC-C=C 1.7- 2.2
H-Phenyl 6.5-8.5
Aromatic
CH- Phenyl 2.2-3 .0
279
- - - -- -- ~ -- - --- - - -- - - -- -
-ll',
;; NOTES Two more comments on chemical shift:

The effect of multiple substituents is additive. For example, a CH 2 next to one
Cl will be at o - 3.5, but with two adjacent Cl substituents, as in dichlorometh-
ane, the signal has shifted too 5.2. Detailed tables for chemical shift can be
found in the literature.
Exchangeable protons, such as -OH and-NH 2 can be found in very wide regions
depending on the solvent. They tend to be somewhat broader than protons
one.
Splitting
A signal will be split depending on how many protons are on the next carbon, and
if there are n protons, the signal will be split into n + l peaks . Figure 14.14 shows
a few typical splitting patterns. Two adjacent methylene (CH 2) groups lead to two
triplets, and a methyl next to a CH group results in a quadruplet and a doublet.
An ethyl group is easily recognizable due to its quadruplet/ triplet pattern, while
the isopropyl group is identifiable by its large doublet along with a small multiplet
(septet) . A para-substituted benzene ring is clearly identified by two doublets in
the o 7-8 ppm region.
280
Nuclear Magnetic Resonance Spectroscopy (NMR) :: Chemistry 213W
NOTES ::
''I"., ' "''I
8.00 7.50
* H H
Figure 14.14. A few typical splitting patterns.
Protons between different protons will be split by both. Considering the spectrum
of 1.-chloropropane in Figure 14.14:
The signal for the methyl group is at S 1.0 and is a triplet due to the adjacent
methylene.
The methylene next to chlorine is at S 3 .5 and is also a triplet due to the adja-
cent methylene.
281
II NOTES
The central methylene group (8 1.75) is split by both the methyl and the
methylene next to chlorine. The splitting is therefore (3 + 1) X (2 + 1) = 12.
This is a multiplet, and at the resolution in Figure 14.15 all peaks are not dis-
tinguishable.
8
7
6
5
4
3
2
1·
0-'\;=;=r;=;~~~;=;=;==#===;==;=;==~
.•~.~r=~~~~~=:;~=;=~~==;=;=;=;=;=.
4.0 3.5 3.0 2.5 2.0 1.5 1.0 0 .5
Figure 14.15. NMR spectrum of 1-chloropropane CH3- CH 2-CH 2-CI.
In this discussion, it is important to remember that equivalent protons do not

split each other. Therefore, butane CH 3-CH 2- CH 2-CH 3, which has two kinds of
protons, results in two signals. The signal for the methyl group is a triplet, due to
the adjacent methylene group. The methylene protons are all identical and so do
not split each other, so this signal is therefore split into a quadruplet as only the
3 protons of the methyl contribute to the splitting.
As mentioned above, the coupling constant J is the distance between the individual
peaks in the multiplets created by the splitting and is the same for two related
splitting patterns. The magnitude of J can yield information about the environment
of the protons; Table 14.3 lists some typical proton-proton coupling constants. As
the few listed patterns indicate, the geometric relationship of the adjacent protons
has a significant influence on the J value, which can range from -12 Hz to 18 Hz,
or even larger. The coupling constant of vinyl protons will clearly indicate if the
protons are cis or trans on the double bond, or if they are on the same carbon. More
rigid molecules can lead to more complex splitting patterns. All this information
yields more details about the structure of the compounds.
282
'"i' I'["I I'
I
11 II I I I
Table 14.3. Proton-proton coupling constants (Hz).

NOTES I:
H...._
,
//c-c..........
/H
free rotation 7
>=<
H
H
0-3
,,:
H...._ /H
c-c
:.' syn or gauche 2-4 H H
s
H...._
;.
c-c
,,,,,
anti 8-12
>=< H
6-12
,-: 'H
s
'/H
/c, H geminal (-8)-(-12)
H>=< 12- 18
4'Hayden+McNe11. LLC
How to Interpret 1 H NMR Spectra

A systematic procedure, as outlined, will help you solve the structure of compounds.
If the molecular formula of the compound is known, then basic information can
be deduced from this, as discussed in the section on Elemental Analysis. The main
question to address is: How many unsaturations (double bonds and/or rings) does
the compound have?
As for the NMR spectra itself:

How many different kinds of protons are present? Each set of equivalent
protons will lead to one signal, which might be split into several peaks.
How many protons are represented by each signal? The integration of the
peaks reveals the relative number of each kind of protons.
Determine the chemical shift of each signal. This will indicate which kind of
protons are in the compound: Are they aromatic? Vinylic? An aldehyde proton?
Alkane-like? And so on.
Determine the multiplicity of each signal, which reveals how many protons
are on the neighboring carbon. Patterns such as a quadruplet and a triplet,
which integrate for 2 and 3 protons respectively, lead to the conclusion that
an ethyl group is present in the compound. Other patterns can be deduced.
Finally, the coupling constant will yield information about the geometric
relationship of protons. For example, two vinylic protons can be either cis or
trans, and the J value will indicate which one it is.
Combine all acquired information and ensure that the data are consistent with
each other.
283
: : NOTES A Few Simple Examples of 1H NMR Spectra
Spectrum 1: A compound with molecular formula C6 H 72 0 has the

following NMR spectrum:
8
7
6.
5
4
3
2
1
0-'\..=;=~~T'i=T~;=;=~~~~~~~~~~~~~~=;==;~~~~~~
3.0 2.5 2.0 1.5 1.0 0.5 0 .0
How can we deduce the structure?

The molecular formula is used to calculate the number of unsaturations:
#C + 1- [(#H + #X)/2] = 6 + 1- (12/2) = 1 unsaturation, so either 1 double
bond, or 1 ring.
There are four groups of peaks; i.e., four different kinds of protons.
The integration has a ratio of (from left to right) 1:2:6:3 .
Two sets of peaks are at 8 -2.5, which indicates that they are next to an elec-
tronegative functional group such as a halide (not in the MF) or a phenyl (not
enough carbons) or a carbonyl (probably the best choice here), and the other
two sets of peaks are in the hydrocarbon region.
The multiplet at 8 2.65 could be a quintuplet or more, which means there are
lots of protons on the neighboring carbons; it integrates for 1 H. This would
place it next to the protons that are responsible for the doublet at 81.25, which
integrates for 6 H; therefore, this could be an isopropyl group, -CH(CH 3) 2 .
The two other sets of peaks are a quadruplet at 8 2.3 (integration 2 H, 3 H
on the next carbon) and a triplet at 8 1.05 (integration 3 H, 2 H on the next
carbon).
All this information combined leads to the correct structure: 2-methyl-3-
pentanone.
284
Spectrum 2: MF C10H 13CIO NOTES 11

#C + 1 - [(#H + #X)/2] = 10 + 1 - (14/ 2) = 4 unsaturations, so either 4
double bonds, or 3 double bonds and 1 ring, and so on.
Six kinds of protons, integration ratio 4:2:2:1:2:2.
Signal at 8 7 ppm, aromatic protons, corresponds to 4 H, so di-substituted
aromatic ring (probably para), 4 unsaturations (3 double bonds and 1 ring),
which is consistent with the MF.
1 singlet at 8 4.6, integration 2 H, probably doubly substituted, since it is so
far downfield. We know there are no more double bonds in the compound
because the aromatic ring accounts for the 4 unsaturations.
Multiplets at 8 3.5, 2.6, and 1. 7, all integrate for 2 H each, which implies
CH 2-CH2-CH2 , with the multiplet at 8 1. 7 being the middle methylene group
(most hydrocarbon-like).
Lonely singlet at 8 3.0 is somewhat broader and probably due to an OH (ex-
changeable proton).
Assembling all this information leads us to a phenyl ring with 2 substituents: a
propylene chain and a methylene, with either Cl or OH at the end of each one.
Note: In this case it is not possible to differentiate the two possible isomers
by 1 H NMR alone.
or
Cl*'
H2C f
H
H
-
H
~
H
CH
\ 2
H2 C- CH
\ 2
OH
13 C NMR
Carbon is another atom which can be used for NMR to elucidate the structure of
organic compounds. For C NMR, we have to look at the signal of 13 C, because it
is the C-isotope with an odd mass, and therefore a nuclear spin. The most abun-
dant isotope of carbon, 12 C, is NMR inactive. One big disadvantage of having to
use the 13 C-isotope is that its natural abundance is only 1.08% of all carbons in
285
nature; basically only 1 of every 100 C-atoms in a sample will be NMR active. As
: : NOTES
a consequence, the NMR signal will be much weaker. Modern Fourier transform
instrumentation allows the chemist to obtain good spectra in spite of this prob-
lem. Another consequence of this low natural abundance is that the chance of one
molecule containing more than one 13 C is negligible.
For 13C NMR spectra, the zero is determined by the TMS signal, just like in 1 H NMR,
but in this case the carbons of the methyl groups are the source of the reference
signal. The chemical shifts range from 0 to 220 ppm, a much larger range than
for 1 H NMR. The hydrocarbon-like carbons are at the lowest chemical shifts, and
carbons substituted with heteroatoms are at higher chemical shifts, followed by
the carbons involved in double and triple bonds and aromatic carbons. So far the
sequence roughly mimics the sequence seen in the 1 H NMR spectra, even though
the chemical shift differences are larger; the large difference is the position of the
carbons of carbonyl and cyano groups, which are at the chemical shifts above 150
ppm. Table 14.4 lists chemical shift ranges for different kinds of carbons in organic
molecules. More precise values for chemical shifts of carbons can be calculated us-
ing tables available in the literature and more advanced spectroscopy textbooks.
Software packages like ChemDraw have the capability of calculating the 13 C NMR
spectra of many compounds.
Table 14.4. Common approximate chemical shifts in 13 C NMR.
Chemical Shift
Functional Group Carbon Connectivity
(0, ppm)
R- CH 3 5-30
Alkane R-CH 2-R' 15-55
Rg-CH 20-60
C- Br 25-65
Halide
C-Cl 35-80
Alcohol, Ether,
C-0 40-80
Ester rest
Amine C- N 30-65
Alkyne -C=C- 65- 90
Alkene C=C 100-140
Phenyl Cc- 120-160
Nitrile -C=N 110-140

.........
Carbonyl ,,....c=o 155-220
286
Because of the low natural abundance of 13 C, there is basically no chance that two NOTES II
NMR-active carbons will be next to each other, i.e., there is no 13 C- 13 C splitting
(homonuclear splitting). Because of the method used to record most 13C spectra,
the splitting with the neighboring proton is not observed (see below). Therefore
only singlets will be observed in a 13 C spectrum. It is also known that equivalent
carbons give the same NMR signal. As a consequence, the number of peaks in a
13
C spectrum corresponds to the number of non-equivalent carbons present in
the sample.
On the other hand, most carbon atoms will have H-substituents, and the protons are
NMR active. These protons will split the carbon signal following then+ 1 rule; this is
heteronuclear splitting between 13 C and 1H, a one-bond coupling. Most 13 C spectra
are run as proton-decoupled spectra, during which all protons are irradiated so that
the 13 C-1H coupling disappears from the spectrum. This results in the nice and simple
13C NMR spectra with a singlet for each non-equivalent carbon.
A Few Examples of 13 C NMR Spectra
Example 1:
Identify the peaks in the 13 C spectrum of p-methoxy-acetophenone.
200 180 160 140 120 100 80 60 40 20 0

PPM
26.6 H3 C 0
" ,f'
129_o
c 197'.o
129_5 I "":: 129.8
114.2 ,,? 114.2
165.0
0
'-CH
3 55.8
There are seven peaks in the spectrum, while there are 9 carbons in the struc-
ture. Therefore two pairs of carbon s have to be equivalent: symmetry indicates
that the carbons ortho and meta to the carbonyl group are equivalent.
Starting at the high chemical shift end of the spectrum, the peak at -200 ppm
is easily identified as the carbonyl carbon.
287
Chemistry 213W 11 Chapter 14
The four peaks between 170 and 110 ppm belong to the aromatic ring: the
II NOTES
peak at 165 ppm is next to the oxygen, the smaller peak at 129 ppm is the peak
next to the carbonyl group. The other two peaks are larger in this simulated
spectrum, and belong to the other carbons in the aromatic ring. As to which
is which, detailed calculations, which are beyond the scope of this discussion,
reveal that the ortho carbons to carbonyl are at -130 ppm, while the ones at
114 ppm are the meta carbons.
The peak at 56 ppm is the methyl carbon in the methoxy group (larger effect
than carbonyl), while the peak at 27 ppm is the carbon next to the carbonyl
group.
Example 2:
Two samples with a molecular formula C4 H8 0 2 have the following 13C spectra:
Spectrum 1
' I
' I
180 160 140 120 100 80 60 40 20 0

PPM
Spectrum 2
I
I
220 '
200 180 160
I
'
140 '
120 '
100 '
80
I
60
I
40
I
20 0
PPM
#C + 1- ((#H + #X)/ 2] = 4 + 1- 4 = 1 unsaturation, so either a double bond or
a ring.
The peaks at 8170 ppm and at 8 205 ppm in these two spectra are clear indica-
tions of the presence of a carbonyl group in both compounds.
There are 4 peaks in each spectrum, therefore there are no equivalent carbons
in these compounds.
288
Spectrum 1 has two peaks below 20 ppm, an indication of hydrocarbon char- NOTES H
acter, while the third carbon is at -60 ppm, so possibly next to an oxygen.
All signals are at higher chemical shifts in Spectrum 2, indicating that all
carbons are next to a functionality.
Using this MF and knowing that there is a carbonyl in both molecules, there
are only two possible isomers, ethyl acetate and 4-oxa-2-pentanone:
0
II
c 0
H3C
/ "-C / "- CH
3
H2
The peaks and compounds can be assigned as follows:
8 (ppm): 15 (CH 3 in ethyl group),

21 (CH3 next to carbonyl),
Spectrum 1: Ethyl acetate
61 (CH2 next to O),
170 (carbonyl)
8 (ppm): 26 (CH3 next to carbonyl),
Spectrum 2: 4-0xa-2- 57 (CH3 next to 0),
pentanone 82 (CH 2 between carbonyl and 0),
170 (carbonyl)
Other NMR Methods

NMR is dearly the most used method for identification of organic compounds,
and over the years many sophisticated methods have been developed to extract
more information out of NMR. A few of these methods are listed here, with a very
rudimentary explanation:
Proton-coupled 13 C NMR: In this case the protons are not irradiated, and
therefore the 13C- 1 H couplings can be observed. As a consequence the signal
of a methyl group will be a quadruplet, with a methylene being a triplet, etc.
Because the coupling constants are very large, routinely more than 100 Hz,
the spectrum can get very complex.
A solution to this problem is DEPT (Distortionless Enhancement by Po-
larization Transfer) which is a technique which differentiates the different
kinds of carbons through manipulation of the pulse sequences. In a DEPT
spectrum, the phase of the signal will be different depending on the number
of hydrogens attached to that particular carbon. Carbons with an odd number
of hydrogens (1or3) will result in a positive peak, while carbons with an even
number of hydrogens (2) give rise to a negative peak and the carbons without
hydrogens show no peak.
NMR can be obtained for atoms other than 1 H and 13C. The most common
other atoms are 19F, 31 P, and 15N.
289
II NOTES
Two-dimensional NMR techniques: In these spectra there are two axes:
each axis will be used by a spectrum and the two dimensional plot will show
correlations between the atoms in the two spectra. In COSY, each axis has
the representation of the same 1 H NMR spectrum. The diagonal of the two-
dimensional spectrum will represent all the signals in the spectra, but the off-
diagonal signals will give information about the interactions between protons
which are coupled to each other. The same effect can be obtained between a 1 H
and 13 C spectrum; in this case it is known as HETCOR, and the off-diagonal
peaks give information about which protons are coupled with which carbons.
In NOESY (Nuclear Overhauser Effect), the off-diagonal peaks will indicate
protons which are spatially close together.
MRI: Magnetic Resonance Imaging is a very important diagnostic tool in
modern medicine. A patient is placed in the large cavity of a large magnet and
NMR spectra (proton) of cross-sections of the body are recorded. MRI picks
up the signal of the hydrogens in the body, mostly from water molecules.
Depending on the environment, these water molecules will result in different
signals, and a three-dimensional image of the examined area can be obtained.
Notice that the term "nuclear" is deleted in this medical application to avoid
any misconceptions that these tests involve radioactive materials.
Analyzing Your Sample by NMR

"One good spectrum is worth 10 (1000, 106 , an infinite number?) of bad spectra!"
You will find Nuclear Magnetic Resonance (NMR) spectroscopy to be extremely

useful for the characterization of your unknown and synthetic products. Proton
1
( H) NMR spectra often enables you to determine the exact number of proton s
in your compound, the number and arrangement of neighboring protons relative

to a given proton, and the chemical environment in which each proton is located.
The previous sections of this chapter had substantial information on the theory
and practice of NMR.
There are three Anasazi 60 MHz NMR spectrometers located in the Instrument
Room. There are step-by-step instructions for each instrument next to the com-
puter keyboard. You will need a TA's assistance when you run your first NMR
experiment but most studen ts are then able to run subsequent experiments using
just the written instructions. Make sure your spectra are phased and integrated
properly before you ask the TA to sign your spectrum. It is important to point out
that careful sample preparation is critical. Most NMR analysis problems are due
to improper sample preparation. Review the sample preparation instructions on
the back cover of this Lab Guide and note that you need approximately 35 mg of
sample for a 1 H NMR analysis.
290
NMR Sample Preparation and Analysis NOTES I:

1. Sample Preparation
a. NMR Tubes-This is a 6" by 1/ 4" thin-walled glass tube with a plastic cap.
They are included in the "bookstore kit" found in your locker and extras
can be found in the stockroom or purchased from the bookstore. To reuse
an NMR tube, rinse it out well with acetone and place it upside down in a
beaker or flask to dry for at least 24 hours. Otherwise, acetone impurity
peaks are likely to show up in your spectrum.
b. Deuterated solvents-It is essential to use a deuterated solvent with TMS.
The TMS (tetramethylsilane) added to the deuterated solvent is used as a
chemical shift reference. The relatively large single peak generated by this
compound is always by convention assigned a value of 0 ppm and arises
from 12 highly shielded equivalent protons. Deutero-chloroform, CDC13 ,
is the solvent of choice and can be used in 95% of all cases. The solvent is
deuterated for two reasons:
Deuterium (2H) eliminates interfering solvent peaks from the spectrum
that would be huge if protium (1H) were present.
The FT-NMR "locks on" to the deuterium nuclear magnetic resonance to
maintain a very stable magnetic field.
Solids
Materials needed: Your sample, a clean dry NMR tube, a clean, dry pipette,
cl-chloroform (in the brown bottles), and a shorty vial.
Preparation: In the lab, weigh out 30- 35 mg of your sample and place in a
clean shorty vial. Add cl-chloroform until the vial is 1/3 full. Cap and shake till
sample dissolves. Look carefully at your sample solution; if it looks cloudy or
has particles visible to the eye, you need to remove those particles. To remove
all insoluble particles, filter the solution through a filter pipette directly into
the NMR tube. Rinse out the vial, tube, or flask and filter pipette by adding an
additional 0.5 mL of CDC13 to it, swirling, and transferring this to the NMR
tube. Transfer the solution to your NMR tube with a pipette. Your NMR tube
should be filled with about 2 inches of solution.
If your sample is not soluble in cl-chloroform, then use either deutero-acetone

or deutero-DMSO instead; these are both available at the stockroom. (Be
aware that if you dissolve your sample in deutero-DMSO, you will not be able
to retrieve your compound from solution; DMSO is a nonvolatile compound.)
If some material remains undissolved, filter it off as described above.
Liquids
Materials needed: Your sample, a clean, dry NMR tube, 2 clean, dry pipettes,
and cl-chloroform (in the brown bottles).
291
Preparation: In the lab, add 2- 3 drops of your sample to your NMR tube.
II NOTES
Fill your NMR tube with cl-chloroform until it is filled with about 2 inches of
solution.
2. Sign up for NMRAnalysis- Take sample NMR tube to Instrument Room and
label with an NMR tube tag. These can be found on the common shelves and on
the table near the entrance to the Instrument Room. Push your NMR sample
tube through a pre-punched hole in the tube tag as directed. Do not use tape
or sticky labels on NMR tubes as this gunks up the spinner. Place the tagged
sample in your TA's basket on the shelves in the Instrument Room until your
analysis time comes.
3. Acquire the NMR Spectrum on the 60 MHz Anasazi NMR-Run the

sample according to the directions located on the computer table next to the
magnet.
Questions Frequently Asked Concerning the Interpretation

of NMR Spectra
1. Why are there extra peaks in my spectrum?

A prime suspect would be that you have a trace of starting material that has
been recovered along with your product. Check the structure(s) of the starting
material(s) and try to reconcile these extra peaks with starting material. Label these
extra peaks as such directly on your spectrum, the same as you do for the peaks
due to product. Hopefully, these peaks are smaller than comparable peaks due to
your product! If they are not, then you've changed the recipe for the synthesis or
the conditions for the synthesis.
This first question is one rationale for asking you to discuss comparisons of
spectral features of starting material and product in your Prelab exercises.
Correct interpretation of the spectrum obtained is a good first step in deduc-
ing what may have gone wrong in a synthetic experiment.
292
uclear Magnetic Resonance Spectroscopy (NMR) :: Chemistry 213W
2. Why are there peaks in the spectrum that cannot be attributed to NOTES : :
starting material or to product?
Any deuterated solvent (D-substituted) has some trace of nondeuterated (H-
substituted or protio) solvent, as well. The most common of these is deutero-
chloroform, CDC13 , which has a trace of CHC13 , which shows up at about 7.26
or 7.27 ppm. Deuterated acetone, deuterated water, deuterodimethylsulfoxide,
or any deuterated solvent all contain a trace of the protio compound and will
show absorptions (usually rather small compared to the peaks due to solute)
in the chemical shift range expected for those types of hydrogens.
Sometimes tetramethysilane, TMS, is added to the solvent as an internal

calibrant. It has an NMR peak at the farthest right-hand side of the spectrum,
which is, of course, TMS, tetramethylsilane, and is assigned the chemical shift
as 0.0 ppm; all other shifts are measured as shifts downfield of TMS.
When TMS is not present, the spectrum is calibrated relative to the signal of
the residual nondeuterated solvent; spectra obtained in deuterochloroform
are referenced to the trace CHC13 peak at 7.24 or 7.25 ppm.
Mr. Benzene says: NMR spectra showing common

impurities can be found on page 294.
293
Preparation: In the lab, add 2-3 drops of your sample to your NMR tube.
== NOTES
Fill your NMR tube with cl-chloroform until it is filled with about 2 inches of
solution.
2. Sign up for NMRAnalysis- Take sample NMR tube to Instrument Room and
label with an NMR tube tag. These can be found on the common shelves and on
the table near the entrance to the Instrument Room. Push your NMR sample
tube through a pre-punched hole in the tube tag as directed. Do not use tape
or sticky labels on NMR tubes as this gunks up the spinner. Place the tagged
sample in your TA's basket on the shelves in the Instrument Room until your
analysis time comes.
3. Acquire the NMR Spectrum on the 60 MHz Anasazi NMR-Run the

sample according to the directions located on the computer table next to the
magnet.
Questions Frequently Asked Concerning the Interpretation

of NMR Spectra
1. Why are there extra peaks in my spectrum?

A prime suspect would be that you have a trace of starting material that has
been recovered along with your product. Check the structure(s) of the starting
material(s) and try to reconcile these extra peaks with starting material. Label these
extra peaks as such directly on your spectrum, the same as you do for the peaks
due to product. Hopefully, these peaks are smaller than comparable peaks due to
your product! If they are not, then you've changed the recipe for the synthesis or
the conditions for the synthesis.
This first question is one rationale for asking you to discuss comparisons of
spectral features of starting material and product in your Prelab exercises.
Correct interpretation of the spectrum obtained is a good first step in deduc-
ing what may have gone wrong in a synthetic experiment.
292
Nuclear Magnetic Resonance Spectroscopy (NMR) H Chemistry 213W
2. Why are there peaks in the spectrum that cannot be attributed to NOTES : :
starting material or to product?
Any deuterated solvent (D-substituted) has some trace of nondeuterated (H-
substituted or protio) solvent, as well. The most common of these is deutero-
chloroform, CDC13 , which has a trace of CHC13 , which shows up at about 7.26
or 7.27 ppm. Deuterated acetone, deuterated water, deuterodimethylsulfoxide,
or any deuterated solvent all contain a trace of the protio compound and will
show absorptions (usually rather small compared to the peaks due to solute)
in the chemical shift range expected for those types of hydrogens.
Sometimes tetramethysilane, TMS, is added to the solvent as an internal

calibrant. It has an NMR peak at the farthest right-hand side of the spectrum,
which is, of course, TMS, tetramethylsilane, and is assigned the chemical shift
as 0.0 ppm; all other shifts are measured as shifts downfield of TMS.
When TMS is not present, the spectrum is calibrated relative to the signal of
the residual nondeuterated solvent; spectra obtained in deuterochloroform
are referenced to the trace CHC13 peak at 7.24 or 7.25 ppm.
Mr. Benzene says: NMR spectra showing common

impurities can be found on page 294.
293
Chemistry 213W ••
•• Chapter 14
Deuterochloroform (CDCl3) CDCl3 with CH2Cl2 contaminant

CH 2Cl2 - - - - +
+-CHCL3
impurity
7.26 ppm
H20 CHCl3
impurity impurity
-1.6 ppm 7.26 ppm
I I H20
impurity
· 11;~~~~~~~~~ l -1.6 ppm
.. ~-
(
I .
8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 0.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 0.0
CDCl3 with Acetone CDCl 3 with Ethanol Contaminant

Contaminant
0
II - HO-CH2CH3--+
CH3CCH3
2.2 ppm
CHCL3
I H20~
impurity
/ impurity -1.4 ppm
H20 7.26 ppm
impurity
/ CHCL3 -1.6 ppm
impurity
I 7.26ppm I
I ...
..
8.0 7.0 6.0 5.0 4.0 3.0 2 .0 1.0 0.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 0 .0
-CHCL3
CDCl 3 with Water Contaminant CDCl 3 with Ether
Contaminant
--------:
c"7l:p,,
impurtty
7.26 ppm
H20
impurity-+ CHCL3 impurity
-1.6 ppm / impurity -1.6 ppm
7.26 ppm
.L
l
.. \ I
8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 0.0 8.0 7.0 6.0 5 :0 4.0 3.0 2 .0 1.0 0.0
d-DMSO with H20 0 0 20

Contaminant II +-HOD impurity
CD3 SCD2H -4.7 ppm
2.45ppm
H20 impurity /'""
-3.2 ppm
~Acetone
u_ I
8.0 7.0 6.0 5.0 4.0 3.0 2.0 1.0 0.0 8.0 7.0 6.0 5.0 4 .0 3.0 2.0 1.0 0.0
Figure 14.16. NMR solvent impurities and contaminants.

Compi led by Malaine Trecoske.
294
Nuclear Magnetic Resonance Spectroscopy (NMR) :I Chemistry 213W
There is often a small extra peak between 1 and 2 ppm, usually a short one; NOTES H
this is due to water. If the peak is weak, it may be due to trace impurities that
are in the NMR solvent. Polar organics that come into contact with aqueous
solutions or are exposed to atmospheric moisture for any length of time will
contain varying amounts of moisture. If the peak is large, and your procedure
involved precipitating a product from an aqueous solvent, then some water
adhered to the solid. You will need to dry the sample more thoroughly before
analysis. Similar problems arise from distilling liquids from aqueous reaction
mixtures.
Nonaqueous solvents that were used in the synthesis or recrystallization may

also show up in the spectrum, especially if the solvent has a relatively high
boiling point. Toluene (bp ll0°C) is a commonly used high-boiling solvent
that frequently shows up in the spectrum.
3. How can I tell if a peak is too large?

Compare it to peaks you know are due to product or compare integrations.
4. Why does the chemical shift for water vary between different samples
in the same solvent or from one solvent to another?
Protons (hydrogens) attached to oxygen or nitrogen atoms often have a vari-
able range for chemical shifts. This is due to the nature of the functional group
and the varying degrees of hydrogen bonding with the NMR solvent as the
concentration of the solute changes. This can readily be observed by taking
a series of spectra of the compound and adding slightly more sample to the
NMR solvent each time.
In addition, under normal experimental conditions, quite often there is no

coupling seen for these hydrogens. The reason for this is that these hydro-
gens are often undergoing rapid exchange with each other, with the NMR
solvent, or with traces of water that may be present. Quite literally, before the
hydrogen is able to couple to other hydrogens in the molecule, it chemically
is transferred to some other species in the solvent. When samples are run
in D2 0, exchange occurs between a molecule containing hydroxyl group(s)
such as acids, alcohols, or amines, the hydrogens of the hydroxyl or amine
quickly becomes deuteriums, which do not sh ow resonance in the proton
spectrum. This exchange comes to equilibration within seconds (essentially
upon dissolving the solute in the NMR solvent) . Proton exchange is catalyzed
by traces of acid, which often will accompany the water that is contaminat-
ing the sample. In addition to rapid exchange, hydrogens associated with
amines are often not observed due to quadrupole broadening (a noncoupling
interaction between nitrogen atoms and hydrogens bonded to them). This
causes a flattening or broadening of the peaks (which can make it easier to
assign the peaks, if they are observed) such that it is hard to see any "peaks"
rising above the plotted baseline.
295
II NOTES
5. Why does a peak fall outside of the predicted range?
Remember to check for starting material or to consider that the peak is due
to something else altogether. Remember also that effects that cause shifts
are additive.
The following discussion shows h ow to rationalize an inexplicable peak at 4.6

ppm for benzyl chloride.
CH 3 groups are expected to absorb at 1.0 ppm if bonded to another sp 3 carbon;

if bonded to an aromatic ring, they feel some of the same deshielding that the
ring hydrogens feel, so they are shifted to about 2.2 to 2.5 ppm.
CH3 groups absorb at 1.0 ppm if bonded to another sp 3 carbon; if bonded to

chlorine, the methyl hydrogens absorb at 3.05 ppm.
In benzyl chloride, the CH 2 feels deshielding due to the ring and deshielding
due to chlorine; therefore, you'd expect the chemical shift to be greater than
3.05 ppm. Indeed, the CH 2 signal appears at 4.6 ppm for benzyl chloride.
Similarly, the CH 2 group of aliphatic ethers absorb at 3.5 to 3.8 ppm; the CH 2
group ofbenzylic ethers absorb at 3.9 to 4.3 ppm, the proximity to the aromatic
ring further deshielding the hydrogens.
6. Is it necessary to integrate the NMR spectrum?

Sometimes when analyzing a product that is a mixture (for example, in the
methylcyclohexene synthesis in Chapter 8) the peaks are so close together or
overlap so much that the integration values aren't useful.
7. Why doesn't my spectrum look exactly like the reference spectrum?

This is probably due to different spectrometer magnetic field strengths (al-
though the chemical shifts should be the same-see earlier discussion on
chemical shifts) which help to resolve multiplets that have very small coupling
constants. So, your 60 MHz spectrum may show only a triplet, whereas the
300 MHz reference spectrum shows a triplet that is split into tiny doublets.
Sample impurities may differ also, especially with respect to water content,
which will greatly affect the chemical shift of compounds with hydroxyl, car-
boxyl, or amine groups.
8. Why does the structure of my product show 4 different kinds of

hydrogens but only 3 (or 2) are observed?
Apparently some of the hydrogens have very similar chemical shifts and there
is some overlap. A simple example is n-pentane (CH 3 CH 2 CH 2CH 2 CH 3). Those
CH 2 groups are very similar in their shifts and may overlap; instead of seeing
three kinds of hydrogen in 6 to 4 to 2 ratios, the methyls are a well-resolved
triplet (area of 6) and the CH2 are a broadened multiplet (area of 6) . Similar
296
problems arise with longer alkane chains as in hexane, heptane, fatty acid
chains, or hydrogens on aromatic rings.
NOTES ==
9. How are FT-NMR spectrometers different from continuous wave
spectrometers?
In older NMR spectrometers, the radio frequency energy is held constant, and
the magnetic field strength is varied. The modern Fourier-transform (FT) NMR
spectrometers, such as the ones in these labs, maintain a constant magnetic
field and work by exciting all magnetically active nuclei at once and measuring
the decay curve as energy is released as the nuclei relax back to the ground state.
Each different type of hydrogen contributes to the interference pattern, called
an FID, similar to the way different notes contribute to a chord. By application
of the Fourier-transform algorithm to the data on a high-speed computer, this
complex signal can be deconvoluted into the absorption frequencies of each
hydrogen that contributed to the original FID signal.
10. What advantages do FT-NMR spectrometers offer over continuous

wave instruments?
Spectra of nuclei that are in low abundance or samples that are very dilute can
be rapidly and repeatedly scanned and all the scans summed until a decent
signal-to-noise ratio is obtained. Summation in this way with continuous wave
spectrometers would take forever; with FT-NMR, each individual scan can be
done in a few seconds, so that hundreds or thousands of scans can be acquired
and summed in just an hour.
The spectra obtained by FT methods have a better signal-to-noise ratio, thus

signals due to trace chemicals that barely peep above the baseline do so much
more clearly. This is also handy if you have extremely small amounts of the
compound you are trying to analyze.
With FT-NMR, a person can easily take a lot of spectra and store the data in
the computer to be processed later. This is important when say a reaction is
monitored by NMR spectroscopy and the operator cannot wait a long time
between data acquisitions.
11. How do I start interpreting a spectrum of a known compound whose

source is known?
In the fortunate event that you are asked to interpret a spectrum of a known
compound or an isolated product from a reaction where the reagents that
were involved were known, then interpreting a spectrum is usually very easy.
Start by drawing the structures for the organic starting materials and prod-
ucts. Try to evaluate the number of different hydrogens that are present in
each structure. Now, using any correlation table for NMR spectra, predict the
ranges you'd expect for each hydrogen present.
297
:I NOTES
Look at your spectrum now, and begin to make some matches in the chemical
shifts expected for each type of hydrogen. Label the absorptions in your spec-
trum, either by drawing a line from the hydrogen(s) that generated the signal
to the signal plotted on the spectrum, or by labeling each type of hydrogen
in the drawn structure with a letter (a, b, c, etc.) and writing the same letter
over the peak(s). Do this first for the product that you think is being analyzed,
and continue with the (hopefully) smaller peaks that may be due to unreacted
starting material, water, solvent, or NMR solvent.
Be sure to identify the source of splitting of each resonance, and reconcile

these with the structures that you've drawn. For example, if there is a triplet
in the spectrum, you should indicate the identity of the signal and also that the
splitting is due to two equivalent hydrogens on an adjacent carbon. Finally, if
the integration is plotted on the spectrum, reconcile the ratio(s) of the integral
heights with expected integral ratio(s).
298
mo CHAPTER
~~~~~~~~~~~~~~~~~~~~~~~~~~
15
Infrared Spectroscopy (IR)
Infrared Spectroscopy

Infrared spectroscopy (IR) for organic molecules uses the wavelength region from
2.5 X 10-4 cm to 2.5 X 10-3 cm. For IR spectra, the position of the signals is ex-
pressed in wavenumbers. The wavenumber U is the reciprocal of the wavelength
in centimeters, and therefore is expressed in cm- 1.
-
wavenumber = U = A.1
The useful IR region is from 4,000 to 400 cm- 1, expressed in wavenumbers U.
When organic molecules absorb radiant energy in the IR region, specific bonds
within the molecule become excited and vibrate. If the frequency of the incident
radiation matches the specific vibrational frequency of the bond, the bond is ex-
cited to a higher vibrational state and the amplitude of the vibration increases.
Structurally different molecules do not absorb exactly the same energies of infrared
radiation; therefore, they give differing patterns of absorption.
When absorbed, IR waves affect the vibrational modes of molecules. As shown in

Figure 15.1, a tetrahedron can bend in different ways: the bonds can stretch either
symmetrically or asymmetrically, but they can also bend in and out of the plane.
All these movements require different energies and therefore result in different
absorption signals in the IR spectrum.
Materials from Making the Connections2: A How-To Guide for Organic Chemistry Lab Techniques written by
Anne B. Padias, copyright© 2011 are reprinted with pemtission of Dr. Padias 299
II NOTES
symmetric asymmetric in-plane out-of-plane

stretching stretching bending bending
CHaydcn·McNcil. LLC
Figure 15.1. Possible molecular v ibrations.
The Instrument
In classical dispersive spectrophotometers (Figure 15.2), the IR light is separated
into different frequencies using a prism or grating. After passing through the
sample, the light is sent to a detector. The spectrum is scanned one frequency at
a time, and the absorption is measured.
Figure 15.2. Basic IR spectrophotometer.
In Fourier Transform Infrared Spectrophotometer (FTIRs), the whole spectrum

is obtained at once. Fourier Transform is a mathematical algorithm u sed to con-
vert the information obtained by the detector into a conventional spectrum. Fast
computers scan the entire spectrum several times (usually 8or16 scans) in a very
short period and then average the t ot al spectrum, thus increasing the signal-to-
noise ratio significantly.
-'o'-------!
; I '
IR lamp moving mirror
splitter
sample
detector
Figure 15.3. Basic setup of FTI R.
300
Infrared Spectroscopy (IR) :: Chemistry 213W
The key component in an FTIR is the Michelson interferometer, which modulates NOTES ::
each wavelength of IR light at a different frequency. In an interferometer the light
beam strikes a beam splitter, and about half of the light is reflected from the beam
splitter and directed onto the fixed mirror. The remainder of the light is directed
onto the moving mirror. When the beams combine, constructive or destructive
interference occurs, depending on the position of the moving mirror relative to the
fixed mirror. When both mirrors are the same distance from the beam splitter, the
two reflected beams pass through exactly the same path length and consequently
are totally in phase. The resulting signal intensity is at its maximum.
The modulated beam is reflected from the mirrors to the sample, where selective
absorption takes place. From the sample the beam travels on to the detector, which
translates the beam into an electrical signal. The interferogram is a summation of
all the IR light frequencies, but it cannot be interpreted in its original form. It is
converted into an IR spectrum through a Fourier Transform. The FT calculates the
amplitude of each of the component signals, and the amplitude gives the intensity
at the corresponding wavelength of light.
An FTIR instrument includes a laser, so caution should be used when looking

inside the instrument when the cover is off. Because it emits light at a known and
constant frequency, the laser acts as the internal calibrator, controls the moving
mirror's position, and triggers the capture of data.
The Sample
In the past, to run an infrared spectrum, the compound would have to be placed
in the path of the IR beam using a sample holder or cell made from metal halides
(sodium chloride, potassium bromide, silver chloride) or from polyethylene IR
cards. Now IRs require no sample preparation. The sample whether a solid or a
liquid is placed directly onto the diamond and the tip is lowered.
The Spectrum
IR spectra are usually recorded from 4,000 to 400 cm- 1 in transmittance mode;
alternatively, the signals can be displayed in absorbance mode. The portion of the
spectrum between 1,500 and 400 cm- 1 is called the fingerprint region. It acts as
a human fingerprint; the pattern of the peaks is specific to a compound. A posi-
tive identification of a compound is made if the fingerprint region matches the
literature IR spectrum.
301
: : NOTES
Structural information is obtained from IR spectra, because functional groups
have specific absorptions. The C= 0 group, for example, always has a strong peak
in the 1600-1800 cm-1 region so if you see a peak in that area, it means the com-
pound has a carbonyl functionality. Table 15.1 shows approximate values for the
characteristic absorptions for functional groups.
The same information is also represented in a more visual manner in Figure 15.4,
in which the regions of specific signals are indicated.
- - - - - Functional group region - -- -- + I - Fingerprint region-I
I --·-· - .
i:l
..)
l
OH
'-----~-- - ..f.- ..... -
~· -- - - ---+- - - ..
· - +-- t-
4000 3500 3000 2500 2000 1500 1000 500

Frequency (cm-1)
Figure 15.4. Basic IR absorptions of functional groups.
Table 15.1. Approximate IR absorptions of functional groups.
Main Functional Specific Signal Position Intensity of

Group Functional Group (cm-1) Signal
Carbonyl C= 0 Ketone R-CO-R' 1690-1715 Strong
Aldehyde R-CHO 1680-1725 Strong
C-H aldehydes 2850 Weak
Carboxylic acid
1710- 1760 Strong
-COOH
1610-1550 and
Carboxylate - COO- Strong
1400
Ester-COOR 1720-1735 Strong
Anhydride -C0-0- - 1820 and
Strong
CO- -1760
Acid halide R- CO-
1800 Strong
Cl
Amide R-CO-NH 2 1650- 1690 Strong
302
Infrared Spectroscopy (IR) H Chemistry 213W
Main Specific Signal Position Intensity of NOTES II

Functional Group Functional Group (cm- 1) Signal
Weak to
C=C 1645-1670
Alkene C=C medium
Phenyl group 1600,1500
2 sharp peaks
C-H 2850-3100 Strong
Alkanes C-H
- CH3 -1380 Sharp
Aromatic C-H -3030 (several) Weak
-C=C- 2100-2260 Very sharp
Triple Bonds
-C=N 2210-2260 Very sharp
Strong
R-OH 3500-3600
Hydroxy-OH Strong, very
RCO-OH 2500-3300
broad
R-NH 2 3400-3500 Strong to
1640-1560 medium
Amines-NH 2
R-NH-R' 3310-3350
1490-1580 Weak
Nitro C- N0 2 C-N0 2 1560 and 1350 Strong
Ether C-0-C C- 0-C 1050-1275 Strong
C-Cl 600-800 Strong
Halides C-X C-Br 500-600 Strong
C-I 500 Strong
How to Interpret an IR Spectrum

The signals in an IR spectrum are characteristic of specific functional groups. IR is
used to confirm the identity of a compound, as well as to help in the elucidation
of the structure of an unknown. The process of analyzing the spectrum is always
essentially the same. As mentioned above, the spectrum can be divided into two
parts: 4000-1500 cm- 1 will give information about functional groups and 1500-
400 cm- 1 is the fingerprint region. When analyzing the functional group region,
consider this possible practical approach to analyze the signals:
Table 15.2. Carbonyl group present.

H NOTES
Is a carbonyl group present? (strong peak 160~1850 cm-1 region)

If YES and If NO and
Very broad peak for OH (3500- 2000 cm·1) Strong peak for OH at -3500 cm-1 : alcohol
and C=O at -1700 cm-1: carboxylic add ROH
RCOOH
Strong peak for OH at -3500 cm-1 and C=C at
Strong peak(s) fo r NH (3300- 3500 cm·1) 1600 cm- 1: phenol
and C=O at -1650 cm- 1: amides R-CO-N
Strong peak(s) for NH (3300-3500 cm- 1):
C=O at -1735 cm-1 and strong peak at amine
-1200 cm-1 : carboxylic ester
Strong peak -1200 cm-1: ether
Two strong C=O peaks at 1750-1850
C=C at 1600 cm-1 and C-H at 3300 cm- 1:
cm- 1: anhydride
aromatic group
C=O at 1800 cm-1 and C- Cl (600-800
Weak peaks at - 1650 cm-1 : alkene
cm-1): acid chloride R-CO-CI
Sharp peak at - 2200 cm-1 : acetylene or nitrile
C=O at - 1700 cm- 1 and C-H at -2800
cm- 1: aldehyde R-CHO Strong peak below 600 cm- 1: halide
If only C= O at -1700 cm- 1: ketone Strong peaks at 1560 and 1350 cm- 1: nitro
If no other peaks: alkane
To gain information from the fingerprint region, an authentic spectrum of your

sample is recorded and compared with literature data. Many authentic spectra
can be found in the literature, either in journals or in a collection of spectra, such
as The Aldrich Library of FT-IR Spectra, Sadtler Index, or an online database such as
the Spectral Database for Organic Compounds (Japan).
Practical Tips
Don't try to interpret every peak. Concentrate on the important functional
group peaks.
Be aware that water is often present. A peak in the 3200-3600 cm- 1 region
does not necessarily mean that you have an OH; your sample could just have
absorbed a little water.
Air can also cause peaks, most notably C0 2 and ambient water. Carbon dioxide
results in a doublet at 2360 cm-1, while water has a broad peak at 3600 cm-1
and irregular peaks at 1600 cm-1 due to overtones. Repeat the background
spectrum if these peaks start appearing in your spectra.
Accurate wavenumber readings for peaks can be obtained with modern IR
instruments. Make sure that the obtained reading refers to the maximum of
the peak.
When comparing fingerprint regions, pay close attention to the scale of the
spectra. Different instruments have varying scales in different areas of the
spectra.
304
Infrared Spectroscopy (IR) :: Chemistry 213W
Some Representative IR Spectra NOTES : :

3-Pentanone: The spectrum is shown in Figure 15.5. First, check for a carbonyl
p eak in the 1600-1900 cm- 1 region; in this case, there is a peak at 1715, which
could be a ketone, aldehyde, or ester. No C-H aldehyde peak is observed at 2850,
nor are any strong C- 0 peaks observed in the 1250 cm- 1 region, and there are no
OH bands. Therefore, this spectrum is consistent with 3-pentanone. The sharp
peak at 1365 corresponds to a methyl group.
90.0
80.0
70.0
"'g 60.0
~
!c 50.0
F
. 40.o
'if!.
30.0
20.0
10.0
38003600 3400 3200 3000 2800 2600 2400 2200 20001800 1600 1400 1200 1000 800 600
Wavenumbers (cm-1)
Figure 15.5. Infrared spectrum of 3-pentanone.
1-Pentanol: The spectrum shown in Figure 15.6 shows no carbonyl peaks, but the
OH is very prominent at 3331 cm- 1 . Strong C-H peaks are observed at - 2900 cm-1
and the fingerprint region is consistent with the literature spectrum of 1-pentanol.
80.0
70.0
~ 60.0
..
c
...
co
~
..
c
50.0
~
~
,__
~ 40.0
'if!. <D
~
30.0 ~
o;
M
"'
<D
~
20.0 M
10.0
38003600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 1000 800 600
Wavenumbers (cm-1)
Figure 15.6. IR spectrum of 1-pentanol.
305
II NOTES
Resorcinol (1,3-dihydroxybenzene): The spectrum in Figure 15. 7 is clearly an
alcohol (strong peak observed at 3300) and has no carbonyl peak. The sharp peaks
associated with an aromatic system are clearly visible at 1600and1485 cm-1, and
a weak signal at 2918 is noted for the aromatic C-H stretch.
98
96
."
c
94
92
"'
·e=
. 90
..
c: 88
i=
~ 86
84
82
38003600 3400 3200 3000 2800 2600 2400 2200 2000180016001400 1200 1000 800 600
Wavenumbers (cm-1)
Figure 15.7. IR spectrum of resorcinol.
Acetanilide C6 H5 NH-CO-CH 3 : Figure 15.8 shows a clear carbonyl peak at 1657

cm-1 ; only amides have a carbonyl peak at such low wavenumber, a fact which is
confirmed by the presence of an NH peak at 3288. The sharp aromatic C=C peaks
can again be noticed at 1600 and 1496. This sample is not pure, and seems to be
contaminated with a carboxylic acid; the very broad OH peak is clearly visible over-
lapping with the NH peak. This could be due to some decomposition and possibly
the presence of some acetic acid.
95
90
85
80
75
70
.." 65
..
=
c: 60
..
E
c:
55
50
"'
i= 45
~
40
35
30
25
38003600 3400 3200 3000 2800 2600 2400 220020001800 1600 1400 1200 1000 800 600
Wavenumbers (cm-1)
Figure 15.8. IR spectrum of acetanilide possibly contaminated with acetic acid.

The negative peak at -1700 cm-1 is due to incomplete background correction.
306
IR Interpretation Guide
%T " Generic" IA Spectrum
R, ,.. H
H,..c = c .... R 1675
H i
- - Tri-& tetra-
I R, ,.. A
A H,..C=C, H 1658 substituted
- 1670
·-'-
c E F J 0 G
. cm·' A, ,.. H
1000 500
II R,..C=C, H
4000 3500 3000 2500 2000 1500 - 1653
(.)
,______
.,, (.)
R-C ::C- R' 2260-2190 Weak to none A, ,.. H
H,..c=c, H - 1645
~·
~
.s:;
B
~
"'""
R-0- H 360Q-3200 Phenols 3500
1°-+2 peaks
Ill
(.)
E
- R- C:N
2250 aliph.
if symmetrical
Move and vary

.....
VI
~
t;
:c A
z -N- H
I 3500- 3290 1°
3400-3340 2°
2°-...1 peak
med. to weak
z
Ill
(.)
I---
R- c=c- H
2230arom.
2140-2100
H
H' 0 1600, 1580,
1500, 1450
in intensity;
H' = overtones
2000-1650
I 0 Broad & often
;;o 0 II
- C-O -H 3550-2500 "monstrous"
0
II
1785 4-ring
Depends on
e
:t:
H
-N
//0 1550-1490 Aromatic nitro
c 1355-1315 Both strong
~
V> 1750 5-ring
"O
ro 1715 6-ring
size of ring I 'o
0 R-c =c- H 3300
2 0 1735 aliph. R, C/R
No peaks in II 1490-1440 Scissor bend
3 o c/H R- C- O- R 1720 arom.
-0
cQ) H/ ' H
I I 3300-3000 this area means ,__
no aromatic! 0 1730 aliphatic .0
:J
II 1730-1705 1703 conjugated I H,C/ R
-.
....
B R-C-H I I 1470- 1430 & Umbrella bend Ill
...Cc- H 3300-3100 (.) H/ ' H 1380- 1370 ....
0 0 ro
I
II F II
- 1715 cm· 1
oil
(.)
~
- Cl.
~
1685 conjugated CH3 CH3 1390- 1375 & V>
No peaks in
(.) R,.C, R I "C
R, /R (.) 'c/ !-butyl - 1365 ro
this area means 1370-1360
~ R
/ C=C ,
H
3300-3000
no alkene!
0
II -1710 1680 conjugated
/ ' !l
I R- C- O - H 0
u ln"all" IR 0 1690 1°
I
C-0
ethers
11 50- 1060
alkyl ethers
1270-1200 aryl
& vinyl ethers
V>
('l
c \
- C-C- H
I
2960-2850 spectra II ,.R 1680 2°
Aromatic amides esters and esters 1285 acids
0
"C
I \ R-C-N, R
1650 3°
1675 1° 0 J '<
I -=::
(.) 1150 3°
0 2720 is key 0 C-0 11002° Tertiary Z9
D II 2820&2720 II Aromatic 1690 alcohols 1050 1° Secondary
R-C-H peak 1685
C= C _.C, R Primary
••
••
n
:r
ro
3
~·
....
'<
tv
.....
w
0
'-J
~
: : NOTES Using the IR Spectrophotometer

A primary method for the characterization of organic or organometallic compounds
is infrared spectroscopy. IR spectra allow you to identify a number of functional
groups that may be present in your product, particularly those containing a car-
bonyl (C=O) or alcohol (0-H) group. You will obtain IR spectra yourself using the
Thermo FT-IR with a Diamond ATR accessory. There is no sample prep involved-
both solids and liquids can be analyzed on this instrument.
Questions Frequently Asked about IR Interpretation
1. Where do I find a correlation chart for the various functional

groups?
See Figure 15.9 or the flap of your laboratory notebook.
2. I have several peaks in the spectrum that I cannot assign. Why?

Be sure to evaluate the strongest IR absorbances for any starting materials
or solvents that you used, since these are the most likely candidates for any
extra peaks in the spectrum. (This of course, is why you are asked to write a
spectral features comparison in your Prelab.) Perhaps, during the course of
the procedure, you've collected solvent from the distillation instead of the
liquid product you should have collected. Or, a lower-boiling starting material
or solvent distilled first. An unexpected peak in the 3200- 3600 cm-1 region
often means the sample has absorbed a little water.
Be sure that your spectral interpretation includes an evaluation of the purity

of the sample and, if present, the identification of significant contaminants.
This is, after all, the purpose of analyzing the product!
The FT-IR instruments we use in Organic Chemistry are sensitive enough that
they often detect the carbon dioxide in the air surrounding the sample. This
shows up as a distinct peak around 2360 cm-1 , and often distinguished from
"real" peaks because it is split into two peaks.
If the carbon dioxide peak is really strong and product peaks barely rise above
the baseline, you need to use more sample for obtaining the spectrum. The
software automatically makes the strongest peak present fit the spectrum;
a really strong carbon dioxide peak means there was more carbon dioxide
between the source and detector than there was sample!
Use the relative intensities of the peaks for a qualitative evaluation of the
purity of the sample and to evaluate the nature of the contaminant, if pres-
ent. If the strongest absorption expected for the starting material is but a tiny
blip compared to the strong absorbances for product, use that to justify the
308
Infrared Spectroscopy (JR) :: Chemistry 213W
purity of your sample. A large absorbance due to starting material compared NOTES H
to product and a melting point far below expected implies that you need to
redo the experiment.
For any molecule having a total of N atoms, there are [(3 x N) - 6) modes of
vibration possible, [(3 x N) - SJ for linear molecules. A molecule such as ben-
zene, C6 H 6 , has 12 atoms, so (3 x 12) - 6 = 30 modes of vibration. However,
some modes are not IR active or some modes have energies so close to each
other that they overlap and appear as one broadened absorption, so usually
there are fewer strong absorptions than this equation predicts.
On the other hand, there are numerous weak absorptions that result from
various additive, subtractive, and multiples of the energies of the absorptions
that are present in the molecule. These are not easily interpreted, and not use-
ful at all except in the case of the overtone absorptions for various isomers of
aromat ic compounds.
Your primary focus should be to assign any peaks that logically represent some
segment of the molecule you are analyzing. Draw a structure for the molecule,
and find as much evidence that justifies what you've drawn as possible.
For example, if you were analyzing 2-butanol, you'd hope to see evidence for
a. aliphatic C-H stretching
b . CH3 bending
c. CH2 bending
d. C-0 stretching
e. 0-H stretching
An IR interpretation chart is necessary to predict the position that each of

these groups would show absorbance.
If you were analyzing t-butanol, all of the above should be present, of course,
except for CH 2 bending.
Often, the absence of peaks is just as important as the presence of peaks.
3. Does an IR spectrum prove the identity of an organic substance?

Yes and no.
Yes, in that every organic compound has a unique IR absorption pattern, and
if you had access to absolutely every IR spectrum of every known substance,
then one could make a perfect match. Computer libraries of spectra easily do
this quite rapidly.
309
No, in that the expected patterns can be very similar for similar structural
== NOTES
isomers. One might be able to distinguish 2-butanol from 1-butanol based
on IR if spectra for each could be compared. Without reference spectra one
would find it difficult to decide which spectrum had a stronger CH 3 bending
absorption even though you would predict 2-butanol should, since its structural
formula shows two methyl groups compared to 1-butanol which has only one.
If all you had was one IR spectrum, it would be difficult to make the assign-
ment. This is a case where a second type of analysis (NMR, MS, even just a
boiling point, density, or refractive index measurement) would certainly help.
4. Why is the carbonyl absorption frequency the first peak to

consider in deducing the molecular structure? Why does its
position vary?
First, it is often the strongest absorption in the spectrum, if present, and
is often in the middle of the spectrum. Second, the identification of several
functional groups depends on correct identification of the carbonyl absorp-
tion. Variety here is good! The carbonyl group is very sensitive to the type of
functional group it is part of, and the local connectivity within the molecule.
Conjugation or hydrogen bonding with solvent tend to lower the energy of the
carbonyl stretch, whereas substitution by more electronegative substituents
or a decrease in the <CCC bond angle about the carbonyl (as in cyclobutanone
or cyclopentanone) tends to raise the energy.
So, if two possible structures are being considered, one where the carbonyl is
conjugated with an aromatic ring, and one where it is not, the C=O stretch is
predicted to appear at a lower frequency for the conjugated functional group.
5. Where do I start interpreting an IR spectrum?

Start at the high energy (high cm-1) end-this is where the first evidence of
functional groups is most easily recognized. As a rule of thumb, peaks above
1350 cm- 1 are most likely to be interpretable.
Peaks below 1350 cm-1 tend to be group frequencies and less easily assignable.
Think about all of the data you have collected up to this point for the sample:
History of the compound (i.e., compound W was treated with liquid reagents
X and Y to give Z, isolated as a solid; this means that Wis a strong con-
tender as a contaminant, perhaps X or Y)
Formula or molecular weight (if given/known)
Melting or boiling point
Solubility
310
Infrared Spectroscopy (IR) :I Chemistry 213W
Refractive index NOTES H

Other analysis data from instrumentation
Generic Approach to Inspecting an IR Spectrum

Begin by looking for the presence or absence of a carbonyl group that is often
a prominent peak around 1700 cm- 1 or a little over. If it is present, evaluate
other areas for other functional groups, such as the C-H stretch that is unique
in the structure of aldehydes, or if this is not there, you might conclude the
compound is a ketone, amide, acid, or ester.
If there is no carbonyl, look for a strong 0-H stretch, indicative of alcohols

or phenols. If the compound contains 0, but there is no 0-H, it must be an
ether. (Note again, that an alcohol has an 0-H and a C- 0 stretch; ethers have
only C-0.)
Check now for C=C double bonds or aromatic rings at about 1650 for alkenes
and 1650to1450 cm-1 for aromatic rings. Since these typically are rather weak,
you should also check the C-H stretching region for the presence of aromatic/
olefinic C-H stretching (above 3000 cm-1) or aliphatic C-H stretching (below
3000 cm-1). Ideally, for alkenes/ aromatics, you should see both C=C stretching
and C-H stretching, too.
Check for triple bonds, C=N at 2250, sharp or C=C weak at 2150 cm- 1 .
Check for nitro group absorptions, of which there should be two, one at
1600-1500 and another at 1390-1300 cm-1 .
If none of the above are present, it must be a hydrocarbon or halogenated hy-

drocarbon.
Draw structures for the molecule, using all of the positive evidence available.
311
II NOTES
312
mo CHAPTER
~~~~~~~~~~~~~~~~~~~~~~~~~~~-
Mass Spectrometry (MS)

16
Mass Spectrometry

Mass spectrometry analyzes molecules and particles according to mass. There are
many variations of mass spectrometry instruments, but in its simplest setup, a
sample is introduced in the gas phase and these molecules are b ombarded by an
electron beam, transforming them into charged particles. By applying a magnetic
field, these charged particles are deflected according to their mass and focused on
a detector.
When a molecule is ionized by an e-beam, a radical cation is formed; this is the

molecular ion. Due to the inherent instability of charged particles, the molecular
ion will fracture into smaller pieces, which can fracture into more fragment ions.
The molecular ion and all the fragment ions are analyzed according to their mass/
charge ratio, yielding structural information about the analyte (Figure 16.1).
e0 ionization fragmentation
j
M m~ + m~
molecule molecular ion fragment ions

(cation radical)
Figure 16.1. Basic principle of mass spectrometry.
The Instrument
A mass spectrometer has an injection port, an ionizer, an analyzer, and a detector
(Figure 16.2).
Using a syringe, a sample is injected into a vacuum chamber at a temperature high

enough to vaporize the sample; alternatively, a mass spectrometer (mass spec) can
be connected to a gas chromatograph (GC/MS) or to an HPLC (LC/MS). In these
Materials from Making the Connections2: A How-To Guide for Organic Chemistry Lab Techniques written by Anne
B. Pad.fas, copyright© 2011 are reprinted with permission of Dr. Padias 313
combined instruments, the samples are analyzed as they elute from the column.
II NOTES
and mass spectra are recorded for each fraction.
The sample is ionized by a high-energy electron beam (-70 eV). The electron beam
strikes the molecules with enough energy to eject another electron from the mol-
ecule, resulting in a cation-radical. This process is called Electron Ionization or
Electron Impact (EI). The original cation radical is the molecular ion M +.
The charged particles are accelerated and deflected in a magnetic field. The mo-
lecular ion is unstable, so it will fragment into smaller ions called fragment ions.
This fragmentation can occur at different sites in the molecule, leading to a collec-
tion of smaller fragment ions. Sometimes the molecular ion is so unstable that it
cannot be detected. Because the ions have different masses, they will be deflected
at different angles by the magnetic field. This broad ion beam is focused on the
detector, which records the m/ z value (mass/charge ratio). The smaller the ion, the
more they will be deflected. The detector gives a direct readout of the size of the
ions and the intensity of the signal. In most cases the charge is equal to 1 +, z = 1.
More sophisticated mass spectrometers will have different injection methods,

analyzers, and ionizers, depending on the particular properties of the sample.
The result is always a spectrum giving the m/z ratio for the different fragments.
Injection Electron Magnetic

port beam field
I IONIZER I I ANALYZER I IDETECTOR I

Figure 16.2. Basic mass spectrometer.
The Spectrum
A mass spectrum is a plot of the mass/ charge (m/z) ratio versus relative abundance.
As z is often equal to 1, the x-axis gives a direct readout of the mass of the molecular
ion (if it can be detected) and the fragment ions. Calibration of the instrument is
achieved by injecting a known compound and adjusting the instrument so that
the weights are accurate.
314
Mass Spectrometry (MS) H Chemistry 213W
The spectrum of n-octane is shown in Figure 16.3. Octane has a molecular weight NOTES ::
of 114, and the molecular ion M + is seen in the spectrum.
The major fragment ions have m/ z values of 85, 71, 57, 43, and 29 . The peak at
m/z 43 is the largest and is defined as the base peak; the base peak corresponds
to the most abundant fragment ion and is assigned a relative abundance of 100%.
The relative abundance of all other peaks is measured in comparison to the base
peak. A mass of 43 corresponds to a n-propyl cation.
The difference in m/ z between the major peaks is indicated on the spect rum. A
difference of 14 corresponds to the loss of a methylene CH2 , which is consistent
with the linear structure of n-octane. The first major fragment lost has a mass of
29, corresponding to an ethyl group CH 3CH 2 .
43
100 -
~ 80 -
c
ta
"C
.sc 60 -
ta 29 71 85
27 57
~ 40 -
~ -14 -14 -1 4 -14
Qi
a: 20 - 114
·29
l11s
I I I I I I I I
10 20 30 40 50 60 70 80 90 100 110 120
rn/z
Figure 16.3. Mass spectrum of n-octane.
Starting from then-octane molecule, the molecular ion M + splits off an ethyl group,
yielding the fragment with an m/z value of 85: the n-hexyl cation. Consecutive
losses of 14 explain the appearance of the other fragment ions, with the propyl
cation being the ion with the highest abundance (Figure 16.4).
H2 H2
H3C-CH2 - -CH2 - -C- - C - -CH2 - - CH 2 -CH 3
- -- - 29
- - - - --43
+----------57
29 - ---+
Figure 16.4. Splitting pattern of n-octane.
315
Chem istry 213W 11 Chapter 16
: : NOTES Isotope Patterns

Looking more closely at the mass spectrum of n-octane, a small peak at m/ z 115
is noticed. This is an isotope peak and is due to the small percentage of 13C pres-
ent in the sample. If one of the eight carbons inn-octane is the 13 C isotope, the
molecular weight of this molecular ion will be 115. The relative abundance of 13 C
is 1.11% compared to 12C.
The intensity of the M + 1 peak in a compound with only C and H is equal to the
intensity of the M peak X 1.11 % X # of C in the molecule. For n-octane in the
spectrum in Figure 16.3, this would be equal to 15 X 1.11% X 8 = 1.33% relative
abundance, which explains the small peak at 115.
Other elements have much more abundant isotopes than carbon and will display
isotope peaks in the mass spectrum. The relative abundance of the most common
isotopes in organic chemistry are listed in Table 16.1.
Table 16.1. Relative abundance of common isotopes in organic molecules.
Second Relative
Element First Isotope
Isotope Abundance (%)
Carbon 12c 13c 1.11
Nitrogen 14N lSN 0.38
Sulfur 325 345 4.40
Chlorine 3sc1 37Cl 32.5
Bromine 79Br a1Br 98.0
For most molecules, the isotope peaks will b e very small. But for compounds con-
taining chlorine or bromine, the elements with the most abundant isotopes, very
recognizable patterns of peaks will appear in the mass spectrum. For chlorine,
the ratio of the molecular ion peak abundance and the peak at a mass two units
higher, M/ M + 2 is equal to 3/ 1. For bromine the M/ M + 2 ratio is roughly 1/ 1,
as the two isotopes are present in near-equal abundance.
The mass spectrum of 3-chloro-1-propene (Figure 16.5) shows the molecular ion
peak at m/z 76, with the isotope peak at m/ z 78, roughly about 1/ 3 the size. The
base peak is at m/z 41, M - 35 Ooss of chlorine), which corresponds to the allylic
cation CH2=CH- CH 2+ .
316
Mass Spectrome try (MS ) : : Chemistry 213W
100
41 NOTES I:
~Cl
Cl>
(.)
c:
cu
'O
c:
:::i
.c
: 50
> 39
iQj
a:
-35
M+ 2
78
10 20 30 40 50 60 70 80 90
Figure 16.5. Mass spectrum of 3-chloro-1-propene.
Tue mass spectrum of bromobenzene in Figure 16.6 clearly shows the two peaks
with almost equal abundance at m/ z 156 (M) and m/ z 158 (M + 2), as predicted
by the natural abundance of the two isotopes of bromine, 79Br and 81 Br. The base
peak at m/ z 77 corresponds to the phenyl cation.
77
100
Br
©
Cl>
(.)
c: M+
cu
'O
c: 156 M+2
:::i 158
.c
cu 50
Cl>
.:?
m
Qj
51
a: -79
-81
74
38
20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170
Figure 16.6. Mass spectrum of bromobenzene.
317
H NOTES How to Interpret a Mass Spectrum

Mass spectra yield exact information about the mass of the ions that reach the
detector; as organic molecules are constructed of similar building blocks, some frag-
ment ions occur often. Conversely, the differences between peaks in the spectrum
frequently correspond to specific molecules and molecular fragments. Table 16.2
lists some common fragment ions and frequent fragment losses.
Table 16.2. Common fragment ions and common fragment losses in mass spectra.
Ethyl+ 29 H 20 18
Propyl+ 43 OH 17
Butyl+ 57 co 28
Methyl-co+ 43 co 2 44
Ethyl-co + 57 CH 3 15
Propyl-co+ 71 CH3 CH 2 29
Phenyl+ 77 OCH 3 31
Benzyl+ (C6 H 5 CH 2 +) 91 CH 2 =CH 2 28
Benzoyl+ (C6 H 5co +) 105 CH 3 CO 43
Some Representative Mass Spectra

Benzyl alcohol: The mass spectrum is shown in Figure 16.7. The molecular ion is
clearly visible at m/z 108, along with its little isotope peak at 109. A very prominent
peak is M-1, loss of H, very common in alcohols. Loss of OH (-17) gives a peak at
m/ z 91, which is the benzylic cation- a rather stable cation-and very commonly
seen in mass spectra. The base peak is m/ z 79, which is protonated benzene. The
phenyl cation is visible at m/ z 77; the other peaks result from degradation of the
benzene ring.
318
Mass Spectrometry (MS) II Chemistry 213W
100
79 NOTES II
108
Q)
u
c(11
"C
c
::I
.g 50
@o" 77
~
:o;
(11
a;
cc
51
91
-17
20 30 40 50 60 70 80 90 100 110 120
Figure 16.7. Mass spectrum of benzyl a lcohol.
1-Hexanol: (Figure 16.8). In this mass spectrum the molecular ion at m / z 102 is
not visible, indicating that it is not st able. The peak at m/ z 84 corresponds to the
loss of water (-18), very common for alcohols. The resulting hexene cation loses a
methyl group (-15) to yield m/ z 69. The base peak is at m /z 56, corresponding to
C4 H8 +,with the propyl cation at m/ z 43 the next most abundant peak.
56
100
43
Q)
u ~OH
c 41
(11
"C
c
.s 50
(11
27 31
~
iii
&! 39
15
10 20 30 40 50 60 70 80 90 100 110
Figure 16.8. Mass spectrum of 1-hexanol.
319
Acetophenone: (Figure 16.9). The molecular ion M+ is at m/z 120 (C8 H 8 0). Loss
H NOTES
of methyl (-15) yields the benzoyl cation, the base peak at m/z 105. Further loss
of CO (-28) leads to the phenyl cation at m/z 77.
0 105
100
II
QI C6 H5CCH3 77
g 80
ca
"C
c
..5ca 60 51
QI 120
> -28
~ 40 -15
Qi 43
a: 28
20
10 20 30 40 50 60 70 80 90 100 110 120

mlz
Figure 16.9. Mass spectrum of acetophenone.
Other Mass Spec Techniques

Many variations of the basic mass spectrometry technique have been developed
over the years; now, different injection modes are possible as well as different
ion izations and analyzers. The following list is not meant to be comprehensive,
but will give some idea of the scope of the possibilities.
GC/MS: A gas chromatograph (GC) is connected to a mass spectrometer (MS)

inlet. An injected sample will be separated into its components by the GC, and
the mass spec will detect the peaks as they elute off the column. The output of
this experiment is a gas chromatogram with an accompanying mass spectrum
for each peak.
LC/MS: The sample is injected in an HPLC (high performance liquid chro-

matograph). The column will separate the different components of the sample,
which are analyzed by the MS, analogous to the GC/ MS method. In this case
the instrument must be adapted to deal with the eluting solvent of the HPLC.
Different ionization systems:

CI: Chemical Ionization instead of Electron Impact, which is a "softer"
method to ionize the analytes.
ESI: Electro spray Ionization, which is often used for the analysis of proteins
and other non-volatile samples. It is also a "softer" method, and ions are
often carrying multiple charges using this ionization method.
FAB: Ionization by Fast Atom Bombardment, which is also used for the
analysis of peptides.
320
Mass Spectrometry (MS) H Chemistry 213W
MALDI: Matrix Assisted Laser Desorption Ionization, in which a matrix NOTES H

is mixed with the sample to accomplish ionization in a very "soft" way for
sample with high masses.
Different analyzer systems:

Quadrupole Analyzer, which is an alternate method used to separate the
charged fragments using four parallel metal rods.
TOF: The Time of Flight method separates ions of different masses by
using the differences in time to reach the detector.
321
II NOTES
322
mo
!I CHAPTER 1 7
_ G_a_s_C_h-ro_m
_a_t_og-r-ap_h_y_ (_G_C_)_
Gas Chromatography
In gas chromatography, the stationary phase is liquid and the mobile phase is a
gas. The liquid stationary phase is a high boiling organic compound adsorbed on
the solid inert packing in the column. In classical gas chromatography, the columns
are steel. The column is placed in an oven, which offers temperature control.
Gas chromatography is one of the most useful instrumental tools for separat ing
and analyzing organic compounds that can be vaporized without decomposition.
Separation is based on a combination of volatility of the components of a mixture
and the differing polar interactions with the stationary phase. A carrier gas (usu-
ally helium, argon, or nitrogen) flows through the column, but does not interact
significantly with the analyte on a molecular level. The mixture of compounds to
be separated is introduced into the carrier gas stream, where its components are
equilibrated (or partitioned) between the moving gas phase and the stationary
liquid phase.
The major applications of gas chromatography are:

test the purity of a substance and separate the components of a mixture;
determine the relative amount of th e components in a mixture;
identify a compound;
as preparative method to isolate pure compounds from a small amount of a
mixture.
Materials from Making the Connections 2: A How-To Guide for Organic Chemistry Lab Techniques written by
Anne B. Padias, copyright © 2011 are reprinted with permission of Dr. Paclias 323
II NOTES
carrier gas
signal output
Figure 17.1 . Gas chromatography.
Gas Chromatography Setup

A gas chromatograph, or GC, consists of many different components. Figure 17.1
shows the basic setup, which consists of
a gas cylinder containing the carrier gas with a flow controller attached;
an injector port, which is temperature-controlled;
a column in a temperature-controlled oven;
a temperature-controlled detector;
a recorder or other signal output device.
Injector FID dete<:tor

Pon (under cover)
Carner
and
Detector
Gases
Gas
Panel
Oven
(contains
column)
324 Figure 17.2. GC instrumentation in the chemistry instrument room.

Gas Chromatography (GC) : : Chemistry 213W
Selecting a Column NOTES H

The first decision to make is to select a column; both the size and the packing can
be varied. Columns come in two major varieties: packed columns and glass capil-
lary columns. A packed column is made of steel tubing. A typical size is 2-4 mm
inner diameter and the length can vary between 1- 3 m. The packing consists of an
inert solid support, which is coated with a non-volatile liquid. The effectiveness of
the column is determined by this liquid component. The packing of the column is
selected based on the components to be injected. The liquid component can interact
with the compounds being analyzed by dipolar interactions, hydrogen bonding,
Van der Waals forces, or even specific interactions between functional groups. A
decision as to which kind of column to use can be made by consulting catalogs
listing which mixtures can be separated on which columns. Typical columns are:
Carbowax columns: the liquid phase is polyethylene glycol (polar, contains

OH groups) and it is used to separate carboxylic acids and alcohols.
SE-30 columns: the liquid phase is polydimethyl siloxane (non-polar) and
is very useful in the separation of such non-polar analytes as hydrocarbons,
polycyclic aromatics, PCBs, and steroids .
SE-52 columns: the liquid phase is poly(phenylmethyl dimethyl) siloxane
(non-polar) which is commonly used in FAME analyses (fatty acid methyl
esters), and also for halogenated compounds.
Some of these packings are more temperature stable than others, and the maximum
operating temperature must always be taken into account. The typical temperature
range for a column is either up to 250°C or up to 350°C.
Gas chromatography can also be used for preparative purposes; in this case, the
components of the mixture are physically separated and collected at the end of
the column. For preparative gas chromatography, very large columns can be used;
for example, up to 10 min length. These days preparative GC has been largely
displaced by preparative HPLC methods.
The second type of column is the capillary column, which is a very long, thin glass
capillary tube. The inner diameter of a glass capillary column is less than 1 mm
and it can be several meters in length. The liquid stationary phase is now spread
out on the inside of this capillary tube. Quite good separations are achieved with
capillary gas chromatography, but only very small amounts of solution can be
injected. Because these columns provide much better separation than packed
columns, they are the first choice for analytical purposes.
325
··--------- -- - -
-----------------------
---.--------.~- ~~-~~-~-~
- --~ -
; ; NOTES
tumn to
FID
Figure 17.3. Capillary column inside our GC oven, EC-5 (5% phenyl substituted methyl
polysiloxane). It's 30 m long and has an internal diameter of 0.25 mm.
The Carrier Gas

The nature of the carrier gas is determined by the detection method, as well as the
price. The carrier gas must be inert; it doesn't interact with the analyte, it merely
serves to push the molecules through the column. Helium is the first choice because
it is non-polar and readily available.
The flow rate of the carrier gas will determine how fast the sample will move through
the column. The flow rate can be fixed on the GC itself, but the accuracy should
occasionally be checked with a flow meter. A flow meter can be as simple as a glass
tube with some soap solution in a rubber bulb at the bottom. The gas is led into
the tube, and the flow rate can be observed by how fast the soap bubbles migrate
up the column. High flow rates will minimize the amount of time the molecules
spend in the stationary phase, thereby adversely affecting the separation. If the
flow rate is too slow, the analysis will take too long, and the separation won't be
as effective because the molecules could actually migrate backwards.
Injection
A crucial component of a gas chromatograph is the injection port. Using a
microliter syringe, the sample is introduced onto the column either as an un-
diluted liquid or as a solution. The sample is injected through a rubber septum
into a heated chamber called the injection port. The temperature of the injec-
tion port has to be high enough to immediately vaporize the complete injec-
tion volume; this is essential for good separation. All molecules must start the
separation process at exactly the same time; as in column chromatography,
the complete sample is placed as tightly as possible at the beginning of the
column. The injection port is usually between 250 and 300°C to make sure
everything immediately vaporizes.
326
Gas Chromatography (GC) II Chemistry 213W
The sample is injected through a rubber septum, which is necessary to keep all the NOTES II
injected material inside the GC and to maintain the positive pressure inside the
column. The rubber septum is perforated every time a sample is injected. After a
certain number of injections, the rubber septum will start to wear out and holes
may form; the rubber septum should then be replaced.
Injector
Figure 17.4. Injecting a sample on the GC.
The Microliter Syringe (Figure 17.5)

Microliter syringes are used because the injected sample size has to be carefully
controlled. The needle has a very small gauge, which minimizes the damage done
to the septum with each injection. Too much sample overloads the column and
results in very poor separation, while too little sample will adversely affect the
detection at the end of the column. Microliter syringes are expensive and very
delicate and should be treated with great care.
10 µL syringe gas tight syringe

OH:i.ydcn-McNcil, LLC
Figure 17 .5. Syringes.
The very small gauge needle can easily become clogged, and it is therefore essential
that the syringe is rinsed out immediately after every use. A small bottle of acetone
or ether is usually kept near the GC. After injection, a small amount of the solvent is
pulled into the syringe and expelled several times to remove all remaining traces of
the injected compound. This will also prevent cross-contamination of the samples.
327
; ; NOTES
The plunger on a microliter syringe is made of a chemically resistant alloy, but it
can be bent. Once the plunger is bent, it makes the syringe unusable; therefore,
great care must be taken so that the plunger is pushed without bending.
For injection of gases, gas tight syringes can be provided. Simple plastic syringes
can also be used for injection of gases, but for accurate measurements the gas
tight syringes must be used. These syringes are larger in volume because they are
used only to inject gases.
Detection
The different components of the mixture have to be detected as they come off the
column. Because they are in the gas phase, the concentration of the components
is extremely low. The detector must be very sensitive and its temperature very
high to keep the sample from condensing at this point. The detector temperature
is often 300°C.
The simplest detection method for gas chromatography is thermal conductivity

detection (TCD). The eluting gas passes over a wire, and if the gas contains anything
besides the carrier gas, a spike in conductivity will be registered. These peaks are
recorded using a chart recorder or a computer. TCD is simple and inexpensive,
but not very sensitive.
A more sensitive detector is a flame ionization detector (FID). The gas stream
eluting from the column is led through a continuously burning hydrogen flame
placed between two electrodes, while oxygen is also fed into the detector to assure
effective burning. When an organic compound elutes off the column and enters
the flame, most of the molecules will be burned; that is, they will form co2and
H2 0. However, a small portion of the molecules will ionize. These ions will be
trapped by the electrode and a signal sent to the detector. FID is very sensitive,
but it destroys the sample.
328
Gas Chromatography (GC) H Chemistry 213W
NOTES :I
----Flame
FID Detector
Air inlet
Column inlet
Figure 17.6. FID: Flame ionization detector.
Other detection methods for GC exist; the most widely used of these is GC/MS, in
which the detector is a mass spectrometer and immediately generates information
about the structure of the eluted compounds.
Running the GC
Setting the Parameters

The temperature settings of the injector, column oven, and detector have to be
selected. Both the injector and detector have to be at very high temperature, so
they will be heated to at least 250°C.
The oven temperature will directly affect the separation. If set too high, the dif-
ferent components will elute too fast, and no separation will be observed. If set
too low, the peaks start to broaden and the analysis will be too long. The oven
temperature must always be below the maximum temperature reported for the
liquid stationary phase. If the temperature is higher than the specified temperature
maximum, the liquid phase will start to bleed off the column. Trial and error will
determine the optimum temperature, but a good starting point is 10- 20°C below
the boiling point of the mixture.
329
Chemistry 213W 11 Chapter 17
The fl.ow rate of the carrier gas must also be set. For packed columns, a fl.ow rate of
II NOTES
60-70 mL/min is common; the same fl.ow rate can be used for capillary columns.
Lower fl.ow rates are advisable for longer packed columns or for smaller diameter
column s.
The GC Analysis
Injection of the sample must be clean and accurate, so proper injection technique
is essential. The syringe is filled with the sample and held with two hands-one
hand on the syringe body while the other hand holds the plunger in place-and
is then firmly inserted through the septum. If the plunger is not held, the larger
pressure inside the column can push the plunger out. Make sure the syringe is
inserted straight through the septum, otherwise it could miss the column entirely.
The exact time of injection must be recorded. Some GCs will have a button you
can push that sends a signal to the recorder. If not, mark the exact time on the
recorder with either a pencil mark or by turning the base line knob on the recorder
up and down. Another method is to inject a small air bubble with the sample: pull
the syringe back a bit once it is filled. The air will create a small blip in the chro-
matogram and is used as a reference.
As the mixture reaches the column, the different components of the mixture will
begin to equilibrate between the liquid and gas phases. The length of time required
for a sample to move through the column is a function of how much time it spends
in the vapor phase and how much time it spends in the liquid phase. The more
time it spends in the vapor phase, the faster it gets to the end of the column. In
most separations, the components of a sample have rather similar solubilities in
the liquid phase. Therefore, the time the different compounds spend in the vapor
phase is mostly a function of their vapor pressure, and the more volatile component
arrives at the end of the column first.
Several factors affect the separation:

The boiling point of compounds: Compounds with lower boiling points gener-
ally travel through the gas chromatograph faster than compounds with higher
boiling point. This is because low-boiling compounds always have higher vapor
pressures than compounds with a higher boiling point.
The flow rate of the carrier gas: The carrier gas must not move so rapidly that
molecules of the sample in the vapor phase cannot equilibrate with the liquid
phase. If the rate of flow is too slow the bands broaden significantly, leading
to poor resolution and difficulty in the chromatograph analysis .
The choice of liquid phase used in the column: The molecular weights, func-
tional groups, and polarities of the component molecules in the mixture to
be separated will help determine the choice of the packing of the column.
330
Analysis of the Gas Chromatogram NOTES II

The end result of a gas chromatographic run is a gas chromatogram (Figure 17. 7).
The gas chromatogram will look the same, independent of the detection method
and independent of the recording device. Peaks with different intensities on the
x-axis correspond to time. The position of the peak corresponds to the retention
time; i.e., how much time this particular component stayed on the column. The
chromatogram can be recorded on a simple chart recorder, on a computer, or us-
ing an integrator, which gives you immediate feedback about the position and
size of the peaks.
The injection time is indicated on this chart, as well as the peaks as they elute off
the column. The surface of the peaks roughly corresponds to the amount of the
different components. The position of the peaks relative to the injection point in
GC can be used for two main purposes: to assess the purity of a compound and to
identify the components of a mixture.
~ l
3cm ~ ~
c
~
A
2cm
1 cm
~
~
~
0 i
0 2 3 4 5
Time (min)
Retention time Area (h x w/2)

A 2.25 min 2 cm x 0.5 cm = 1.0 cm 2
B 3.45 min 1.1 cm x 0.25 cm = 0.275 cm2
c 4.1 min 2.8 cm x 0.7 cm= 1.96 cm 2
Figure 17.7. Analysis of a gas chromatogram.
Just as Rf values in TLC yield information about the identity of a certain compound,
so too the retention times in GC. If the parameters of a GC are unchanged, two
separate analyses yielding peaks with the same retention time will lead to the
conclusion that these two compounds may indeed be the same. We can prove that
two compounds are different if they have different retention times, but keep in
mind that two different compounds may have the same retention time. As with
many analysis methods, you can only prove a negative with GC.
331
r
\11
1~11
-
ll
The identity of a component of a mixture can be further evaluated by spiking the

II NOTES
injection mixture with a small amount of the known component. In this case, the
corresponding peak in the chromatogram will be larger. Standards are routinely
used in gas chromatography to help in the identification of compounds.
To completely identify this compound, it will have to be isolated and analyzed by

spectroscopic methods such as IR and NMR.
Quantitative Analysis
A gas chromatogram yields valuable information about the composition of a vola-
tile mixture. Comparing several chromatograms will yield information about the
relative amounts of different components in a mixture. To get accurate informa-
tion, a calibration must be performed. To achieve this, known quantities of known
compounds are injected, and these quantities are then compared to the surface of
the corresponding peaks.
Quite a bit of information can be collected from a GC without going through

the trouble of constructing a calibration curve. Let's assume that the detector's
responses to the different components of a mixture are roughly the same. Now
the peak surface can be used as a direct measure of the amounts of the different
components.
Most peaks approximate the shape of an isosceles (symmetrical) triangle. The sur-
face of the triangle is equal to one half of the base multiplied by the height. But in
a chromatogram it is often difficult to measure the base; the width at half-height
is a more dependable measurement, so the surface of the triangle is equal to the
width at half-height times the height (Figure 17.7).
Internal normalization can be used to calculate the percentage composition of a

mixture, meaning that the total surface of all the peaks is assumed to correspond
to 100%. The percentage of component A in the chromatogram shown in Figure
17.7 can be calculated from the area of peak A divided by the total area of peaks
A + B + C, multiplied by 100%.
Total area = area peak A+ area peak B +area peak C = 3 .235 cm 2
% A = (area peak A/total area) X 100% = (1.0/ 3.235) X 100% = 31 %
Integrators and computers used as output devices to generate the chromatogram

will automatically generate the percentage area for each peak, making the above
calculations unnecessary.
332
Gas Chromatography (GC) :: Chemistry 213W
What to Do if You Need to Run a CC NOTES I:

1. Sample Preparation
a. Place one drop of your liquid sample into a shorty vial using a pipette.
b. Fill the shorty vial % full with dichloromethane using a clean pipette.
c. Label your sample and place it in your TA's basket in the Instrument Room
for analysis.
d. Sign up for GC time. If there are n ot names on the sign-up sheets, the in-
strument will not be prepped for the day because helium is too expensive
to waste if the GC will not be used.
2. Selecting a Temperature Program

a. Check your experiment write-up for GC parameters.
b. If the parameters are n ot in your experimental write-up, then check the
GC compendium in the Instrument Room.
3. Running Your Sample

a. You must look over the GC tutorial before you can run the instrument. The
tutorial is located on ANGEL, and it is also loaded on the laptop computer
located next to the GCs.
b. Pay close attention to the injection t echnique, because if you overload the
GC you will need to allow the run to proceed and at the end continue to
keep the oven temperature high to bake out all the excess sample. Then
you will need to run the experiment again.
c. Pay close attention to the appearance of the solvent peak in the chro-
matogram. See the following example. The solvent is not retained by the
stationary phase so it will typically appear by no later than 2 minutes into
the run. It will be the largest signal in the spectrum.
d. Analyze your data and attach it to your report.
3
Analysis of Pine Oil
Column Condiuons:
40 oC to 260 •c at 5 oC J min
Injector 250 oC
8
8 10 12 14 16 18 20 min
The chromatogram of pine oil contains distinct peaks that have baseline separation.
Figure 17.8. Analyzing your data.
333
II NOTES
What Does My CC Data Tell Me?
1. The number of peaks in your chromatogram excluding the solvent are the
number of components in your sample.
2. The quality of your chromatogram will tell you about the separation of com-
ponents and the concentration of the sample you are analyzing. If your peak
has a fiat top (excluding the solvent peak), your sample is too concentrated
so dilute your sample and re-run the GC. Also check to see if there is good
separation of components with minimal peak overlap.
3 . The relative amount of each component is given in the area counts that appear
at the end of the run. Each peak will have a retention time and an associated
area. If you add the areas of all the peaks of interest then you will have the
total area you need to calculate relative percentages of compounds. Once you
have the total area of the peaks of interest then you divide the area of each
compound by this value to obtain your relative percent composition. If you
wanted quantitative information for each component, then you would need
to run standard solutions for each compound to obtain response factors.
4. Remember you are matching peak patterns when you compare your chromato-
gram to that of a standard one found in an article or in the compendium. The
retention times will not be identical because no two people inject with exactly
the same technique. Also, different instruments have differing parameters
(column length, gas flow, etc.) resulting in different retention times. Precision
of this kind can only be achieved with an autosampler. If you want to confirm
the identity of your peaks you would need to complete an additional run using
a standard or run a GC/MS or a NMR spectrum.
What Do I Need to Put in My Lab Report?

You will need to discuss the purity of your sample by% composition. To do this,
please go over this example, referring to the GC on the following page.
334
'il!i!ll!llll'.1
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Gas Chromatography (GC} H Chemistry 213W
• RUH I 518 MRV 1, 1999 12•18•86 NOTES I:

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3 . 352
7 . 719
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1 . 595 2131 PU . 813 . 01881
1 . 660 20867856 SHB 81 8 98 .06986
1 .89Z 5390 PB . 831 . 02533
3 . 352 7696 PU . 031 . 9361 7
7 . 718 385962 PU . 819 1 . 13365
7 . 790 98687 VB . 013 . 12581
!OIRL RRCA•Z . 1279(•07
Figure 17.9. Undefined GC example.
The dat a with which you need to work appears at the bottom of the GC printout.
You need to be concerned with the RT (Retention Time) column and the Area
column, outlined above. Exclude the solvent peaks, as we are not interested in
them (usually anything t hat appears before 2.5 minutes). The GC above has a di-
chloromethane peak at 1.66 minut es, which can be ignored. We are now left wit h
3 major peaks of interest at 3.35, 7.71, and 7.79 minutes.
NOTE: We are ignoring the other peaks at 1.595 and 1.892 because these are at-
tributed to solvent.
335
II NOTES
To find the percent composition that each peak is contributing to your mixture,
first add the area of the peaks together.
Total Area= 7696 + 305062 + 90607 = 403365
Now, divide the area of each peak by the total area to get a percentage. The per-
centages should add up to 100%!
(7696/403365)*100 = 1.9%
(305062/403365)*100 = 75.6%
(90607/ 403365)*100 = 22.5%
Record the above data in a table format in your report:
Retention Time Area % Composition .

3.352 7696 1.9%
7.710 305062 75.6%
7.790 90607 22.5%
It is important to note that these numbers represent the purity of your sample but
the GC does not tell you what the components of your sample are! For this, you
must run GC-MS or deduce what they are from your NMR and IR data.
Submitting for GC-MS Analysis

Based upon peak separation and sample concentration, talk to your TA to decide if
your sample is good enough to submit for GC-MS analysis. If it is too concentrated
or there are too many peaks or the peaks are too close together, RE-RUN the GC
to optimize your conditions!
Fill out the GC form with your name and the column conditions used and staple it
to your chromatogram. Put it in the submission basket in the Instrument Room.
Dr. Rummel or a designated TA will review your chromatogram and run your
sample. Please allow for a maximum of 1 week for GC-MS turnaround time. Most
samples will be run within two days. When completed, your GC with the GC-MS
data attached to it will appear in the "Completed" box.
Analyzing Your GC-MS Analysis

Interpreting Your GC-MS Data
One of the first pages of your GC-MS data will look like the figure on the next page
(Figure 17.10). This is called a Total Ion Chromatogram (TIC). It is very similar
to the data obtained from the GC and is a plot of signal vs. time. The peak order
336
~-.c relative intensity should mirror that of your GC data but be aware that your NOTES H
:etention times may differ slightly as the GC-MS is a different instrument than
the GC with different parameters! There are two main peaks in Figure 17.10 at
12.04 minutes and 12.94 minutes.
c-..-36\CloYe'901sn525
& ll~SteomO<--olCloves
8
RT 0 00 - 23.03
NL:
100 1 .30E8
95 TIC F· MS
90 I 9016ns2s
85
80
75
70
85
~ 60
f 55
~ 50
•:
:
.. 45
40
35
30
25
20
15
G
10
5 II
0
0 2 4 6 6 10 12 14 16 16 20 22
Time (nwn)
Figure 17.10. Total Ion Chromatogram (TIC) for the components of cloves
obtained from the GC-M S.
The GC-MS collects data in addition to signal vs. time; it also records the mass
of the ion fragments hitting th e detector. Each peak seen in the TIC will have a
mass spectrum associated with it. Figure 17.11and17.12 show two panels. The
top panel is a zoomed-in view of the peaks seen in Figure 17.10; the main thing
to note is that the areas of the peaks are given underneath the retention times.
You can use these areas to calculate a 3 composition as you were instructed to
do in the previous section. The bottom panel is a mass spectrum. Figure 17.11
shows the mass spectrum for the peak at 12.04 minutes with an m/z value of 164
while Figure 17.12 shows the mass spectrum for the peak at 12.94 minutes with
an m/z value of 204.
337
•• Chapter 17
••
•• NOTES C·IX-'chem36\Cl<We\901CT7525
Ex 115 Steam o.st.iletion al Clove>
RT 1181 -1-31 3
NI..
llOEI
100 Total Area= 230763712 + 41716018 = 272479730 TICf ,_iS
ICl$
80 ec11ens2s
BO
• 70
~
I '°
< 50
i •o
"' 30
10
,, . 120 12-1 122 12.3 IU 12.7 1U 129

}\
1'0 131
Mass spectrum for peak @ 12.04 min.
..
10318
BO
s 70
I eo
l 50
i 40
14195
;f 30
130.$<
20 7191
10 sun 18503
.. 100 150
tM.02_ 1901&
""'
227 40 2521S 281 07
'""
Figure 17.11. GC-MS data for cloves showing the mass spectrum for the
peak at 12.04 minutes.
C~\cllem36\CloYe\90tfiT1525
Ex. 115 Steam !Mtilotion al Cloves
RT. t'2..0' NL
..
100
BO
M; 23Q7837Tl 1.lOEI
TIC F
ICl$
eo1en52s
MS
230763712
% = 272479750 x 100% = 84·6%
RT 12M
M.•1718011
,\
20
10
12.J 128 129 1)0 "1
Mass spectrum for peak @ 12.94 min .
90
9097
80
Of 71716018 X 1()()01 15 4 0 1
/O = 272479730 /O = . /O
lOUll
10701
14704
lllt.00
""'10
0
.. 100 150
200 I)
253..0S 274..Z:S
...
250
303 71
300
334_44 364 56
350
.,,. 4(W.
400 ...
Figure 17.12. GC-MS data fo r cloves showing the mass spectrum
for the peak at 12.94 minutes.
338
Not only can the GC-MS computer show us the mass spectrum of a peak, it also
has a library in which it can match the mass spectrum to a compound that resides
NOTES ==
in the library. It takes the mass spectrum experimentally obtained and compares
it the mass spectra in the library and comes up with the closest match. This library
data can be seen in Figures 17.13 and 17.14. The library match for the peak at
12.04 minutes shows that the identity of that compound is eugenol. The library
match for the peak at 12.94 minutes shows that the identity of that compound
is caryophyllene.
!:!!!
1
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971
970
97)
970
~
n..:.Jl!ll,. Eugonol
~
..
l ·Al/l-6·n'l•tho m11inlib
Eo0t nol ,.pll> OH
Cu;oal
Fonnula C10H12QZ. MW 1'4,CASI 97·U-0.bt:ryt Jl))S
'~l'IOt.l•lftltl'M)1!1+tl-iloC10>•"J..
--
9S8 9S8 Pht nol l ·m•t munti>
956 9S8 Euoe nd mai'IJb
948 950 Phe nol l ·mtt m&#'llb
0
Phenol l·m•c m•ll'lti>
945 948 [\11)4: ncl "Pll>
941 941 Phtnoll·me1 ITlf fl'b
10 934 934 Phert0L l·met .. p ...
11 9l0 9S8 Phenol 1-mtc ,.pg, list of hits
12 920 9 l0 PMnoll-mea "'• .,a,
ll 915 Uc Phenol l ·n'l•t rna ...lib
Phenol.1-met m•nlb ID of compound
" 9 1l 911
IS
16
11
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1195 ...,.,
907
961
Pbtonoll·mt l .. p...
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18
19
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186
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P~nol.l·mtt .. pll>
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m•nlt>
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)) 876
...
Phenol >-me1 .. pll>
l.l w cuu. ·UIDl'J•n.IJJ
... .
100-
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,.
...
T110') 1)1
~:'...uL.tLl'::.
... J1" n 111 JJ)
.. .
a~--- -
""
.. library MS
t JOU
Mt11, ASUlt
,.,. "'
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... ...
.
"n lb lJI It.I
...
ll
. .................i. l.,J '"-~--~--~ 50 llX> ... ,.. 150 JOO

••
""'
Figure 17.13. Library match for the peak at 12.04 minutes identifies
that compound as eugenol.
339
•• Chapter 17
••
•• NOTES
.. .... ....
... ~ Caiyophy.,,.
.... l1ty<lolS ..2.0Jr

~
mainlt>
Fo9'\Vb C1,K>4 MW XM. C ASI t1'"""""i.hirpt ..ISi
lief(llt(7.1..~4ec· •-eee. 4, 11 . 11....,..~.,.ltl'Jt-.111t.(llll•,4f..9Si ..
""°
976
968
98S
976
969
C•ryophytltnr
C•ryoph)'llerw
Bicycbf7 20)L
......
ma nib
%2 966 Bicyclol7 :Z OJL 1rp5ib
%1 969 bo<-•tyophll1t1 mainlib
958 9S9 HumuitrHvH m.a#\lb
10
,," ...
9SS
949
947
9SS
9$1
OS<
949
81eyc:lo(7 2 OlL replb
(Ji')'Ophy1'trw ......
tH-Cycloprop ma..,_ll>
longilolitn.-(\ m•i"llb
List of hits
" ...,
14
IS
947
941
...
9Sl
946
tR..lL~.11.1
1H·Cydoptop
Bcycbl7.l..0JL
......
maW'ilb
m•"11ib
16 939 946 tH<ydoprop m•nlib
17 939 944 Bic1clol1.l.Ol l r•phb ID of compound
18 937 9S7 t H.Cydoprop r•p!G
19 935 94J t H-Cycbprop m..iinlib
20 •» 91S ky< lolS.J.O)t: maitlltJ
n 934 938 1S.2S.SR·l,4,4 · tn•nlllo
n 9ll 936 1H-C.ydoprop rrpRb
100
.. .." '" Your MS ""

.u ... t Oi
. Comparison
.... .,.
HL
..
..
"
'" Library MS -·-
...0
~
4'1St , CAS-
11~·S,
..
c;:.uroplo)lrl'll'
.....
... .. 100 ,,.
"" ""
-
JIJO
~
"'
Figure 17.14. Library match for the peak at 12.94 minutes identifies
that compound as caryophyllene.
In your Formal Final Reports you will be expected to discuss your GC and GC-MS
data. In your experimental, list the GC and GC-MS data after your IR data. Format
it as such:
GC (phenyl methylpolysiloxane, 40°C to 275°C at l0°C per min) RT 9.75 minutes

and 11.25 minute; GC-MS (phenyl methylpolysiloxane, 40°C to 275°C at l0°C per
min) RT 12.04 minutes, m/ z 164; RT 12.94, m/ z 204.
Make note that in parenthesis is the stationary phase of the column and the tem-
perature program you used. I just made up a temperature program and retention
times, so make sure you use the correct ones relevant to your compound!
In your discussion, make sure you have a table listing ALL retention times of the
observed peaks (exclude the dichloromethane and pretty much all peaks that come
out in the first 2.5 minutes). Refer to this table in your discussion. Also have a
table for the GC-MS data and the rn/ z values and the identity of the components
based on the library hit, an example is on the following page:
340
Table 17.1. GC-MS data for cloves.

NOTES :I
%
Component RT Area mlz
Composition
l Eugenol 12.04min 230763712 164 84.7%

I Caryophyllene 12.94min 41716018 204 15.3%
Please use the above examples as a guide when interpreting your GC-MS results.
If you still have questions, please see your TA or Dr. Rummel.
341
II NOTES
342
I,
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:1 . • I·:·
I
' };:11
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Have your TA check and inirial this lisc, then rake ic co rhe smckroom co obtain missing or broken equipment. Lab lnstrucmr Initials:_ _ __
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B Stopper, Glass, Solid
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2 Bottle 4-oz Wide Mouth w/ Green Cap (for TLC) 1 Graduated Cylinder, 100 mL
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2 Flasks, Erlenmeyer, 25 mL 1 Thermometer Case (check for both ends)
2 Flasks, Erlenmeyer, 50 mL 2 Watch Glasses
2 Flasks, Erlenmeyer, 125 mL 1 Column, glass for chromatography
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Have your TA check and inirial chis lisr, rhen rake ir m rhe srockroom m obrain missing or broken equipment Lab lnsrrucmr lnirials:_ _ __
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A Funnel, Plastic
B Spatula, Stainless Steel
c Hirsch Funnel, Plastic
D 4 Reaction Tubes
E Filter Adapter, Yellow Rubber
F Flask, Filter, 25 mL
G 4 Flasks, Erlenmeyer, 10 mL
H Tubing, Teflon, 1/ 16 in x 2 ft.
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Blue Kimble Glassware Kit
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A Tube Connecting, 3-way

B Stopper, Glass, Solid
c Adapter, Thermometer, Neoprene; Used w/ E
D Adapter, Thermometer, Glass
E Funnel, Separatory, 125 mL
F Tube Connecting, Vacuum
G Condenser, West
H Distilling Column or Condenser
Flask, Round Bottom, 3 Neck, 500 mL
J Flask, Round Bottom, w/ Side Tube, 250 mL
K Flask, Round Bottom, Single Neck, 100 mL
L Flask, Round Bottom, Single Neck, 50 mL

M Flask, Round Bottom, Single Neck, 25 mL
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A Quick Guide to Sample Preparation
Remember to sign up for a timeslot to use certain instruments in the Instrument Room (206 Whitmore)!
NMR tube with a pipette. Your NMR tube should be

Solids: filled with about 2 inches of solution.
Materials needed: Your sample, 1 shorty vial, 1 pipette, Liquids:
dichloromethane, and anhydrous sodium sulfate Materials needed: Your sample, 1 clean, dry NMR
Preparation: In the lab, add -1 mg of sample to your tube, 2 clean, dry pipettes, and d-chloroform with
shorty vial and fill 3/4 full with dichloromethane; add TMS (in the brown bottles)
enough anhydrous sodium sulfate to cover the bot- Preparation: In the lab, add 2-3 drops of your sample
tom of the shorty vial. to your NMR tube. Fill your NMR tube with d-chloro-
Liquids: form until it is filled with about 2 inches of solution.
Materials needed: 1 shorty vial, 2 pipettes, dichloro- Take sample NMR tube to Instrument Room, label with
methane, and your sample NMR tube tags found by entrance, and leave in storage
rack until your analysis time.
Preparation: Add 1-2 drops of your sample to a shorty
vial and fill 3/4 full with dichloromethane. For 400 MHz NMR analysis, please run your sample on
the 60 MHz NMR first. Follow the instructions located
Put labeled sample in Instrument Room in your TA 's
on the back table in the instrument room and on
basket until your analysis time. Follow instructions by
ANGEL.
instrument.
For GC-MS analysis, please run your sample on the GC, Polarimetry
fill out a GC-MS request form found in the Instrument Solids:
Room, attach it to your GC along with your sample, Materials needed: Your sample (weighed), 1 20 ml
and place it in the appropriate bin adjacent to the GC vial, water or methanol, and 1 pipette
instruments.
Preparation: Look up solubility of your compound in
water or methanol. Weigh out the appropriate amount
Solids AND Liquids: to achieve maximum solubility in 3 ml of solvent. If
all the sample does not dissolve, add more solvent in
Materials needed: Your sample and 1 shorty vial
measured amounts until you achieve complete solubil-
Preparation: In the lab, place -10 to 20 mg of your ity. The exact concentration of your sample must be
solid sample OR a small amount of your liquid sample known to find the specific rotation for your sample.
into a shorty vial. Remember, you will be using the Make sure your solution is completely translucent; oth-
Diamond-ATR attachment on the IR, so there is no erwise, you will not obtain usable data.
sample prep. You can use your sample (pure solid or
In the Instrument Room, transfer your solution to the sam-
pure liquid) as is! REMEMBER: No solutions! Only
ple cell according to instructions found by the polarimeter.
pure samples!
Put your labeled vial in your TA's basket in the Instrument RI
Room until your analysis time. Follow instructions by Liquids (only!):
instrument. Materials needed: Your sample and 1 pipette
MS Preparation: None. Follow instructions by the
Materials needed: Your sample, 1 snap top vial (in the refractometer.
Instrument Room), 1 green mass spec form (in the
Instrument Room)
Solids:
Preparation: Place a tiny amount of your sample
(-equal to the amount needed for a melting point) in Materials needed: Your sample, 95% ethanol (or other
the snap top vial , fill out the green mass spec form solvent as given), and 1 clean 20 ml vial
completely, tape the snap top vial to the form, and Preparation: Add 1 mg of your sample to the vial and
place in the "To Be Run" basket.• dissolve the compound in 10 ml of solvent.
Put labeled vial in your TA's basket in the Instrument
Room until your analysis time. Follow instructions by
Solids:
instrument.
Materials needed : Your sample, 1 clean, dry NMR
tube, 1 clean, dry pipette, d-chloroform (in the brown PLEASE RETRIEVE YOUR SAMPLE FROM
bottles) or the appropriate deuterated solvent, and 1 THE INSTRUMENT ROOM WHEN YOUR
shorty vial ANALYSIS IS COMPLETE!
Preparation: In the lab, weigh out 35 to 40 mg of your
sample and place in a shorty vial for 1 H NMR. Add
d-chloroform until the vial is 1/3 full. Cap and shake
until sample dissolves. Transfer the solution to your
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Sheryl A. Rummel, Kristin M. Beiswenger - Chemistry 213 Introductory Organic Chemistry Laboratory 2015-2016. Lab Guide-Hayden McNeil (2016)

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Sheryl A. Rummel, Kristin M. Beiswenger - Chemistry 213 Introductory Organic Chemistry Laboratory 2015-2016. Lab Guide-Hayden McNeil (2016)

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1H 2H

Introductory Organic Chemistry

Sheryl A. Rummel • Kristin M. Beiswenger

Copyright© 2016 by The Pennsylvania State University, Department of Chemistry

All rights reserved.

Printed in the United States of America

Rummel 7501-3 F15

1. Safety Firs t! .................................................................................................... . 1

1.1 Equipment Used in the Organic Laboratory

1.2 General Safety

Hey, everyone! I'm Mr. Benzene!

Safety is REALLY IMPORTANT so make sure you pay

General Safety Rules

Mr. Benzene says: Spilling chemicals on your bare

• Know the locations of emergency eyewashes and safety showers.

eS\ in the Laboratory NOTES : :

Information on Eye Protection

Using the Laboratory Hood

.3 \ \orking with Flammable, Hazardous, Corrosive, and NOTES ;;

Mr. Benzene says: Be aware of the hazards of the

Women of child-bearing age should be careful when handling any substance of

It is impossible to avoid handling every known or suspected toxic substance, so

Inorganic acids (HCl, H3 P0 4 , H 2 S0 4),

Ethyl acetate, diethyl ether, hexanes,

Halogenated Dichloromethane, chloroform,

HM Heavy Metals Compounds containing Pd, Cr, Zn

SI Silica Waste Silica and alumina

Waste Chemicals That Can Be Flushed Down the Drain (D)

Solutions of Inorganic Alkali or Alkaline Earth Salts such as KBr, CaC12,

Waste Chemicals That Must Be Collected

Other Miscellaneous Laboratory Waste

Broken Glassware and Broken Pasteur Pipettes as well as unbroken useC.

Oeaning Chemical Spills

Mr. Benzene says: If you spill something, notify

Modern organic chemistry involves substantial use of spectroscopic and chromato-

The Instrument Room is an extension of the laboratory classroom and as such

Instrumentation time is available by signing up on the appropriate sign-up sheets

To familiarize all students with the Instrument Room, an Instrument Room

..•• OTES 2.1 Instrument Room Policies

2.2 Sample Preparation

Figure 2.1. The NMR tube.

'c c....... Mr. Benzene says: DON'T THROW YOUR NMR

Dispose of your NMR sample into HALOGENATED ORGANIC WASTE; do not

Preparing UVNis Samples for GC-MS Sample Analysis

_..J nstrumentation ,oT£s •

Figure 2.2. One of the 60 MHz NMR instruments.

Infrared Spectroscopy (IR)

Gas Chromatography (GC)

U traviolet/Visible Spectrophotometer (UVNis)

1. Prelab Assignment: To be completed and handed in at the beginning of every

A detailed description of these assignments is given in this chapter.

Mr. Benzene says: Hand your assignments in on

First day late = 10% of the total possible points

Each additional day late =5 % of the total possible

Academic dishonesty is not limited to simply cheating on an exam or assignment.

LIQUIDS: To prevent loss of liquid products by evaporation, you sh ould use

3.1 Prelab Assignments

1. Chemical Data Tables

: : NOTES Details about Prelab Assignments

1. Chemical Data Table

Mr. Benzene says: This table will be easy to fill out

f. Molecular Weight (MW or formula weight, FW) of reactants, products, NOTES ::

s~\J.. -s ro ~cl rt ~'CJ. N-HD oro..n~

• 541 Ml\ at: ~-l't1Cfuo~ • ,.._, l dYDf / sec