Basic Organic Chemistry Laboratory Techniques

Purification, Identification and Reporting

First Edition - Revised

Ron Davis, Jr., Ph.D.

Chapter introductions with Alexander Clarke
2011 - 2016 - Ron Davis, Jr., Ph.D. - All Rights Reserved

A ChemSurvival Enterprises Production

in collaboration with LAD Custom Publishing, Inc.

Basic Organic Chemistry Laboratory Techniques

Purification, Identification and Reporting
With gratitude to Richard and Juliette for allowing an inspired student to pursue his dream of teaching,
and to Mary Jo and Katherine for showing him the way.

The author wishes to thank the Georgetown University Chemistry Department faculty, staff and students
who so graciously gave their valuable time in the form of thoughtful discussion and careful reading of
this manuscript. In particular:
Akil Joseph
Daniel Seidenberg
Andrea Griffiths
Monique Koppel
Mo Itani, Ph.D.
Tim Warren, Ph.D.
Ray Gephart, Ph.D.
Thanks also to George Manning for his insightful commentary

Dr. Davis earned Bachelors degrees in Chemistry and Geology from The Virginia Polytechnic Institute and
State University in 1998. He has held positions as a Research Chemist at Middlebrook Pharmacteutical
Corporation and Quality Chemist at Barr Pharmaceutical. He received his Ph.D. in Chemistry from The
Pennsylvania State University in 2007, where he was the recipient of the Dan Waugh Graduate Teaching
Award and the Dalalian Research Fellowship. He now teaches organic chemistry laboratories at Georgetown University in Washington, D.C. and is a member of the Chemical Education division of the American
Chemical Society.

2011 - 2016 - Ron Davis, Jr., Ph.D.

All rights reserved. No portion of this work protected by the copyright hereon may be reproduced in
any form or by any means without written permission of the author.

If I have seen further it is only by standing on the shoulders of giants. - Sir Isaac Newton

II

Basic Organic Chemistry Laboratory Techniques

Purification, Identification and Reporting

To the Student
Welcome to the organic chemistry laboratory, one of the richest and most sophisticated learning
environments in undergraduate education. As a student of laboratory organic chemistry, you will be
faced with many challenges including learning to properly prepare for, execute, reflect upon and
report on synthetic projects in the lab. The purpose of this text is to provide a resource with which
to prepare yourself before you enter the laboratory. You will not find any detailed procedures for
experimental projects in these pages. Instead, you will find material which should be read and
digested before attempting to perform the procedures selected by your professor. In short, the goal
of this text is to make you aware of the reasons behind each step of the procedures that you will be
following.
Most of the chapters in this text are organized into several distinct sections:
Theory sections are meant to explain how phenomena and laws that you learned about in
General Chemistry can be used to predict and explain the techniques that you will use in your lab
exercises.
Practice sections point out the practical considerations which must always be kept in mind
when attempting to perform the technique of interest.
General Procedures sections offer a step-by-step explanation of how to perform the most basic
operations in the lab. These techniques are typically just a small portion of a synthetic projcet
andmust be performed efficiently and effectively in order to finish on time.
Chapter Questions sections provide questions for reflection in two sub-sections: General and
Scenario-based. Use the general questions to test your understanding of the concepts presented
within the chapter, and use the scenario questions to better understand how these concepts are
applied in actual laboratory situations.
The chapters of this text have been written (to the greatest extent possible) to be modular. They
may be presented in any order that your course requires. The exception to this is the first two chapters. These chapters are dedicated to helping you to become familiar with standards of safe behavior and proper use of the materials issued to you. Read and understand them well, as successful
completion of manipulations in all subsequent chapters will rely on your mastery of the information
they contain.

Most people say that is it is the intellect which makes a great scientist. They are wrong: it is character.
- Albert Einstein

III

Basic Organic Chemistry Laboratory Techniques

Purification, Identification and Reporting

Chapter List
Laboratory Basics
Chapter 1 - Introduction to Working in the Laboratory
Chapter 2 - Basic Laboratory Tools and Techniques

Purification Techniques
Chapter 3 - Recrystallization and Melting Points
Chapter 4 - Distillation and Boiling Points
Chapter 5 - Liquid-Liquid Extraction
Chapter 6 - Chromatographic Separation
Chapter 7 - Advanced Separations

Scientific Reporting
Chapter 8 - Chemical Drawing
Chapter 9 - The Chemical Literature

Product Identification
Chapter 10 - Optical Spectroscopy
Chapter 11 - Mass Spectrometery
Chapter 12 - Nuclear Magnetic Resonance Spectroscopy

IV

Chapter 1 Introduction to Working in the Laboratory

Few introductory science courses are offered simply as a lecture series. In nearly all cases, an
accompanying laboratory course is required. In the coming year your lecture instructor will present to you
many principles and rules governing our understanding of organic chemistry. These assertions are
supported by over two hundred years of research conducted by countless hard working individuals.
Nonetheless, because the laws of chemistry are grounded in empirical observation it stands to reason
that conducting such inquiries ones self should be an integral part of any organic chemistry course. In
short, your laboratory course is a chance to test some of the rules set forth by your lecture professor. It is
an opportunity to develop sound organizational skills, time management strategies, diligent preparation
habits and thoughtful critical analysis skills. In doing so, the students goal should be to better understand
how the body of chemical knowledge is created, expanded and even corrected from time to time.

Safety in the Laboratory

If you are taking an Organic Chemistry Laboratory course, chances are that you are no stranger to the
teaching lab environment. What sets the organic chemistry laboratory apart from others is the level of
risk associated with its contents. Flammable, toxic, carcinogenic and environmentally dangerous
materials abound in these laboratories. When not respected, these materials can present a significant
health, safety or environmental hazard. When approached properly, however, the lab can be a safe and
fun place to learn and explore the practice of science. For this reason, the first step to becoming an
effective lab chemist is to understand these risks and how to manage them.
Personal Protective Equipment
Short of preventing accidents themselves, Personal Protective Equipment (also referred to as PPE) is one
of the most effective safeguards available to protect those working in the laboratory. PPE is defined as any
specialized equipment or garment designed to protect the wearer from safety hazards in the laboratory.
Although PPE cannot prevent lab accidents, it can significantly reduce the consequences of one.
Eye Protection
Eye protection in the form of safety glasses or chemical splash goggles should be worn by everyone in the
laboratory whenever anyone in the laboratory is working with chemicals or evacuated/pressurized
glassware. Remember that it does not have to be your accident to cost you your vision! The best
protection is afforded by chemical splash goggles, which form a seal around the eyes and prevent any
liquid or solid material from reaching the eyes. As an alternative, safety glasses are sometimes used
provided that they meet three important criteria:
Figure 1.1 - Features of Lab Safety Glasses

1.

They must be impact resistant so that an

impact doesnt create multiple shards of broken
plastic when is reaches the eyes.

2.

They must have an articulated brow to help

prevent splashes from coming over the top of the
glasses.

3.

They must have side splash guards to help

prevent splashes from coming around the side of
the glasses.

1-1

front

impact resistant lenses

articulated brow
top

side

side splash guards

Chapter 1 - Introduction to Working in the Laboratory

Safety in the Laboratory
Personal Protective Equipment (continued)
Gloves
The use of gloves in the organic chemistry laboratory at all times is highly recommended. They are
essential when using strong mineral acids, strong bases or organic solvents. It should be noted
that gloves are made of many different materials, the two most common being latex and nitrile.
Each of these materials offers differing levels of protection from various types of solvents. Consult
a glove compatibility chart if you are uncertain which gloves afford the best protection.
Proper Attire
The best way to protect your skin in the laboratory is simple. Cover it! The tops of your feet are the
only horizontal part of your body below the benchtop. This means that when something spills or
falls, it is most likely to end up on your feet! For this reason, shoes of a non-woven material which
cover the feet should always be worn in the lab. Additionally, clothing which is excessively loose
should not be worn.
Know the Location of Safety Equipment
All modern laboratories are equipped with a number of items which, if properly used in an emergency, can significantly reduce the risk and/or impact of lab accidents. As a student, it is your
responsibility to be familiar with the location and operation of this equipment.
Safety Showers
Showers are used only when a large amount of chemical or solvent has spilled on a worker in the
lab, or when clothing is on fire. Pulling the handle releases a very large flow of water, so these
devices should only be used when a large-scale accident has taken place.
Eyewash Stations
Eyewash stations are used when a chemical or solvent has contacted the eye of a worker in the
lab. Affected eyes should be rinsed with the eyewash for no less than 15 minutes.

1-2

Chapter 1 - Introduction to Working in the Laboratory

Safety in the Laboratory
Personal Protective Equipment (continued)
Eyewash Stations
Eyewash stations are used when a chemical or solvent has contacted the eye of a worker in the
lab. In the event that chemicals or other material reach your eyes, use the lab eyewash station(s)
to fluch them with water. Many organic compounds are only sparingly water soluble, so affected
eyes should be rinsed with the eyewash for no less than 15 minutes.
Fire Extinguishers
In the case of very small fires (for example ether igniting in a beaker) it is best to simply cover the
container with a watchglass or other non-flammable object and allow it to extinguish from lack of
oxygen. Before taking the responsibility of attempting to fight a large chemical fire with an extinguisher, one should be absolutely certain that the fire extinguisher used is designed for the type of
fire being fought. As a student, if you are uncertain then it is best to leave the firefighting to your
instructor.
Chemical Fume Hoods
Fume hoods are provided for work with volatile, flammable or particularly reactive materials.
Fume hoods contain a complete working lab bench, including power outlets as well as water,
vacuum and nitrogen gas lines. Additionally, most modern fume hoods are equipped with a movable sash. The sash may be raised to facilitate setting up a glassware apparatus, but must be
lowered to the operating height when chemicals are present!
Chemical fume hoods have several key safety features that make them an acceptable environment for many chemical reactions. A transparent splash and explosion-resistant sash provides
some protection against chemicals or objects escaping the fume hood while still allowing observation of its contents.
As their name implies, chemical fume hoods also prevent the release of potentially dangerous
chemical vapors into the general laboratory space. Fume hoods must remove about 60-100
linerar feet of air per minute in order to effectively prevent chemical vapors from diffusing back into
the main laboratory space. This flow rate can only be achieved when the sash is lowerd to an
operational height indicated by an arrow on the side of the hood. You may raise the sash beyond
this height when setting up an apparatus, but the sash must be lowered to the operational height
once chemicals have been introduced into the hood.

10-4

Chapter 1 - Introduction to Working in the Laboratory

Disposing of Chemical Waste
Segregating Chemical Waste
Chemical waste must be segregated for several reasons. First, compatibility of all chemicals in a waste
container must be assured for the safety of those in the lab and those responsible for removing the waste
containers. Second, certain types of chemical waste are particularly harmful to the environment and are
disposed of using special (and expensive!) methods. Naturally, segregating such material can save a great
deal of money in the waste removal budget for your lab. Your lab will have its own system for identifying
and segregating chemical waste, so defer to your lab instructors policy when in doubt.
The Sink
Only soap and water should ever be poured down the drains of the laboratory sink. Very weakly acidic or
basic aqueous solutions (pH 6-8) are usually allowed, but nothing else may be disposed of in this way. The
drains from most lab sinks lead to the common drain for the building, and water handling plants are not
expecting to receive chemical waste for treatment! To ensure that chemicals do not reach the sink drain,
it is recommended that all glassware be triple-rinsed into an appropriate waste container before washing
with soap and water in the sink.
The Trash Can
All labs will be equipped with trash cans for non-chemical waste. Frequently they are the receptacle for
paper towels, uncontaminated disposable lab equipment such as parafilm and uncontaminated protective gloves. The contents of these trash cans are disposed of just as any other office waste basket
contents, so it is critical to use them only for completley uncontaminated items.
Liquid Chemical Waste
Solvent and solution waste will be collected in one or more containers placed in a chemical fume hood.
Due to the complex and potentially reactive nature of liquid chemical wastes, your disposal plan may
differ from one experiment to the next. Always be certain that you are disposing of the waste in the
appropriate container.
Solid Chemical Waste
Solid waste is segregated from liquid waste to facilitate disposal. Solid chemicals and significantly
contaminated disposable items such as filter paper and contaminated protective gloves should be placed
in the solid chemical waste and NOT into the general trash cans.
Broken Glass Containers
Special containers for broken glass are provided to ensure the safety of those responsible for its removal.
These containers have a very thick liner inside to protect anyone handling the waste after it has
accumulated. Uncontaminated broken glass, pipettes, capillaries, etc. may be placed in this container. If
your waste glass is significantly contaminated with chemical reagents, seek assistance from your
instructor. Incompatible waste may react within the container and cause a very dangerous situation to
develop.

1-4

Chapter 1 - Introduction to Working in the Laboartory

Working with Chemicals
Know Your Reagents
Any company which manufactures a reagent or solvent for laboratory use is required by law to
produce and publish a document known as its S.D.S. (Safety Data Sheet). The SDS of a reagent
contains a wealth of useful information, including:
The chemical name and common synonyms used for it
Hazard information such as toxicity,flammability, etc
Instructions for proper storage
Chemical and physical properties such as formula, appearance, molar mass, meltingpoint
and boiling point
Transportation and disposal considerations
In short, the SDS is an excellent resource for any chemist to begin familiarizing his/herself with a
new chemical before using it in the lab. The MSDS of most compounds can be found in the
laboratory containing the compound or at the manufacturers website.

Know the Rules for Heating Organic Material

Many organic solvents are flammable. Heating

such materials inappropriately poses significant
risk of fire. In order for a fire to start in the lab (or
anywhere else, for that matter) three components
must be brought together:

1. A fuel
2. An oxidizer
3. An ignition source

oxidizer

fuel

FIRE!
ignition

Image Ron Davis, Jr., Ph.D.

Fig 1.2 - A Recipe for a Fire

Preventing Solvent Fires

Combining oxidizers, fuels and ignition sources in

close proximity can cause a disaster

Many organic solvents often can act as fuels, and atmospheric oxygen is usually a sufficiently
strong oxidizer to allow such fuel to burn. The most common source of ignition in the laboratory is
heat or spark from the device being used to boil and stir solvents. Furthermore, most organic
compounds have what is known as an auto-ignition point, which is a temperature at which the
compound will spontaneously ignite in the presence of oxygen. It is crucial to carefully safeguard
organic solvents from simultaneous exposure to oxygen and excessive heat or spark. This is
accomplished by following several general rules when heating solvents.

1-5

Chapter 1 - Introduction to Working in the Laboratory

Know the Rules for Heating Organic Material (cont)

Three General Rules for Avoiding Solvent Fires

Never heat an open container of organic solvent directly on a heat source.
The surfaces of heat sources can reach temperatures well in excess of
those needed to spontaneously ignite certain solvents. Placing these devices under open containers of solvents brings together the three ingredients
needed to start a solvent fire! Instead, use a water or oil bath to moderate the
temperature of heat source in contact with the solvent container.

Always clamp the lowest piece of glassware in place and set the heat source
on a lab jack with sufficient clearance to lower the heat source away from the
appratus.
In the event that overheating takes place, complex synthesis setups can be
cumbersome to lift away from a heat source. Therefore, it is better to set up your
apparatus so that the heat source can be lowered.

Containers of organic solvent may be heated directly on a heat source if the

opening to the apparatus is distant from the heat source.
When the opening of an apparatus to the atmosphere is distant from the
solvent and heat source, oxygen cannot reach the boiling liquid. This reduces the risk of ignition. In this specific case, organic solvents may be heated
directly on a heat source.

Figure 1.3 - Preventing Solvent Fires

oxygen
organic solvent

oxygen
heat source

organic solvent
heat source

apparatus opening

waterbath

hotplate

hotplate

oxygen
organic solvent
heat source

lab jack

thermowell

(A) Never heat open containers directly on a heat source.

(B) Always clamp the lowest piece of glassware and place the
heat source on a lab jack so that it may be lowered to reduce
heating.
(C) Solvents may be heated directly on a heat source if the
apparatus opening is a significant distance from the boiling
solvent.

1-6

stir plate

lab jack

Image Ron Davis, Jr., Ph.D.

Chapter 1 - Introduction to Working in the Laboratory

Know the Rules for Heating Organic Material (continued)
Preventing Flash Boiling or Bumping
An additional hazard associated with heating of organic solvents is the phenomenon commonly
known as bumping. Bumping of a solvent occurs when a local pocket of heat causes a region of
the solution to boil suddenly (and sometimes violently). The large vapor bubbles created in this
process can cause a container of solvent to froth, foam or even spit solvent out of the confines of
the container. This presents an obvious safety hazard in the laboratory, as well as compromizing
synthetic yields. Bumping is avoided by the addition of a deterrent which either decreases vapor
bubble size or promotes even heating of the sample. In general, three types of bumping deterrents
are used in the lab.
Boiling stones or chips which are later removed by filtration or decanting
Boiling sticks which may be removed by simply pulling them out of the container
A magnetic spin bar which continuously stirs the solution and can be removed with
the aid of a magnetic spin bar retrieval stick

Proper Documentation
At the heart of any scientific project is the
paper documentation of the experiment
and its outcome. There are a number of
time-tested documentation rules which
have been followed by scientists for
centuries. As modern technology pushes
documentation into the digital arena, rules
have changed slightly, but the general
principle remains that a complete,
real-time,
indelible
account
of
a
researchers activities and observations
must be made if their work is to be
considered credible.
All actions and observations in the lab are
recorded in a bound laboratory notebook
using permanent ink as the experiment is
being conducted. This ensures that the
record cannot be altered after the fact

Fig 1.4 - Sample Notebook Entry

page 13

Objective:
To evaluate the ability of simple distillation to separate methanol
ethanol from water.
Materials:

ethanol (b.p. 78 oC) water (b.p. 100 oC)

flammable

Procedure:
-transferred 25 mL ethanol-water mixture to a round-bottomed
flask
-affixed distillation head and west condenser to the flask
-attached a thermometer to the distillation head (placed
thermometer bulb next to side arm).
-attached vacuum adapter to end of West condenser
- attached cooling water to West condenser (in bottom, out top)
-raised thermowell into place and heated the ethanol water
mixture
Observations and Data:

atmospheric pressure = 770 torr

- after ~10 mL distillate collected, thermowell setting needed to
be increased and droplets of condensation became larger
volume distillate (mL)
0.5
1.0
1.5
5.0 2.0

1-7

still head temp (oC)

76.5
76.5
77.0
77.5 Image Ron Davis, Jr., Ph.D.

Chapter 1 - Introduction to Working in the Laboratory

Proper Documentation (continued)
All entries into the notebook are made as the experiment is being carried out and placed on the lowest
numbered available page using indelible ink. Erroneous entries should be stricken through with a single
line leaving them legible. Scratching out entries, using white-out, black markers or other methods to
redact entries is strictly prohibited. Scientific documentation is filled with mistakes, but to attempt to
conceal these mistakes is to cast suspicion on the integrity of an experimental record.
Your laboratory instructor will almost certainly have additional documentation rules for your
experimental records. These may seem arbitrary, redundant, or excessive, but one should keep in mind
that even the appearance of impropriety in scientific documentation can be harmful regardless of the
actual intent of the author.

Interpreting Scientific Data

The Process of Scientific Inquiry
A proper analysis of scientific data is not complete without considering what the data are able to tell
us with certainty and what they merely suggest or support. It is a common misconception that
scientists engaged in research are out to find a data set which will prove their hypothesis. In fact,
scientific research is quite the opposite. Scientists spend their days in the laboratory trying to prove
themselves wrong! If testing fails to disprove a hypothesis, then the hypothesis is considered a valid
theory. If extensive testing disproves all other reasonable explanations, then (and only then) is the
hypothesis considered proven. This concept is best conveyed using a simple example.
If one were to hold a tennis ball out at arms length and release it, what is the expected result?
Naturally, one would expect that the ball will fall downward in accordance with the law of gravity. If
after many dozens, hundreds or thousands of trials the ball has fallen downward each time, one
might conclude that the law of gravitational attraction has been proven. But has it really been
immutably proven by this series of observations? After any number of trials, could one ever say
with absolute confidence that the next attempt would not be the one in which the ball falls upward
due to some yet-to-be understood force? The answer in our simple example is no! Of course, after
many trials it becomes reasonably certain that the law of gravity applies because we were unable
to disprove it (not because we proved it definitively!).
A more classical scientific example is that of Newtonian mechanics, which stood as physical law for
centuries. In 1687, physicist Isaac Newton published his now famous law of universal gravitation,
asserting that gravity was a force propagating between two bodies in uniform space. Throughout
the 18th and 19th centuries physicists and astronomers observed the world around them operating
in apparent accordance with Newtons original hypothesis that gravitation was a universal property
propagating between massive objects. Several hundred years later, more sophisticated
measurement techniques made it possible to observe miniscule discrepancies in the actual motion
of heavenly bodies (most notably the planet Mercury) and those predicted by Newtons law. Only
then (and with some help from noted theoretical physicist Albert Einstein) was the scientific
communitys 250 year-old, accepted model of gravitation altered to correct for previously unnoticed
inaccuracies.

1-8

Chapter 1 - Introduction to Working in the Laboratory

What do the Data Really Tell Us?

The results of a soundly designed, hypothesis-driven experiment can tell a researcher one of
several things:
The data can disprove a theory - if it is in direct conflict with the original hypothesis
The data can support a theory - if it is consistent with the hypothesis, but other
reasonable explanations for the observations exist.
The data can prove a theory - it there is no other reasonable interpretation of
the observations. Recall that it is never possible to prove a theory with absolute certainty. Scientists must instead make a judgment about when they feel
reasonably certain that a theory is proven.
Figure 1.5 - Interpreting Scientific Data
Are the data reliable and
self-consistent?

YES

Are the data consistent with YES

the tested hypothesis?

NO

Is the hypothesis the only

reasonable interpretation?

Hypothesis is proven

NO

NO
Repeat experiment or
modify hypothesis

YES

Hypothesis is disproven

Hypothesis is supported

Modify hypothesis

Attempt to disprove
alternate explanations

Image Ron Davis, Jr., Ph.D.

It is not uncommon to feel awkward or uncomfortable injecting subjective judgement into critical
scientific analysis . For example, one may ask, What makes a result consistent with the
hypothesis? or What constitutes a reasonable interpretation?. Scientists regularly debate one
another over such subjective elements of data interpretation, and there are not necessarily right or
wrong answers to these questions of judgment.
It is also not unusual for sets to appear self-contradictory, excessively scattered or otherwise
fundamentally flawed. The temptation in such a situation is to consider the data unreliable or
erroneous. Although this can sometimes be the case, no analysis of a problematic data set is
complete without an attempt to modify the hypothesis to fit the empirical observation. Willingness
to abandon or modify a hypothesis in the face of contradictory evidence is an essential trait in an
effective researcher.

1-9

Chapter 1 - Introduction to Working in the Laboratory

Chapter Questions
General Questions
G-1. What three characteristics are necessary for lab safety glasses to effectively protect.
G-2. Why must broken glassware be clean before disposing of it in the special broken glass
waste containers?
G-3. What does MSDS stand for and what kind of information can be oftained using them?
G-4. What are the three ingredients which have to come together to create a fire? Give at least
one example of each that you might encounter in a chemistry lab.
G-5. Explain what a bump deterrent does and give three examples.
G-6. Describe the proper technique for making corrections to erroneous entries in a laboratory
manual. Why is it so important that this technique be used?

1-10

Chapter 2 Basic Laboratory Tools and Techniques

Introduction to Chemical Glassware and Lab Equipment
The items in an organic chemistry laboratory glassware kit may seem strange and unnecessarily
complicated to the introductory student. Be aware, however, that each piece of glassware has
been carefully designed to perform a specific function safely and effectively. Many of these special
functions will become apparent as your course progresses. The purpose of this chapter is to
familiarize the introductory student with many of the most commonly-encountered laboratory tools
used by the organic chemist.

Laboratory Tools and Equipment

Hose Barbs

FIgure 2.1 Tubing and Connectors

Vacuum attachments, water faucets, gas outlets and

many pieces of glassware will have a ribbed, conical
port on the side known as a hose barb. This device is
intended for the attachment of a hose suitable for
transmitting liquid, gas or vacuum as needed. To
attach a tube, simply press the end of the tube over
the hose barb with a slight twist. To remove a tube
from a hose barb it is often easier to push the tubing
off from the top of the barb than to pull it by the hose.
Pulling causes the hose to compress around the barb
and hold fast.

hose barb

m
ng

bi

tu

2-1

uu

c
va

Vacuum tubing is made of more rigid rubber material

and has thicker walls than water tubing. The thick
walls prevent this tubing from collapsing under an
applied vacuum. Because they are bulky, heavy and
less flexible, vacuum tubes are not typically used to
transmit water or low pressure gas. The added
weight of the tubes can make an apparatus unstable,
increasing the risk of breakage or spills.

ng

Vacuum Tubing

bi

The thin walls of water tubing make it prone to

collapse under reduced pressure. This makes water
tubing unsuitable for use in vacuum applications,
since a collapsed tube cannot maintain a vacuum..

tu

Water tubing is usually molded of a soft rubber material and has thin walls which make it flexible and easy
to position within the hood. Water tubing is also
suitable for transmission of gasses under low pressure.

r
te
wa

Water Tubing

Image Ron Davis, Jr., Ph.D.

Water tubing has thin, flexible walls to faciliate

placement of the tubes. Vacuum tubing has thicker,
more rigid walls, making it suitable for evacuation, but
adding considerable weight. Both types of tubing may
be connected to glassware via hose barbs.

Chapter 2 - Basic Laboratory Tools and Techniques

Laboratory Tools and Equipment (continued)
Hotplates and Stirplates
Hotplates and stirplates are very similar in appearance. Both
have a broad flat surface covering a magnetic stirring device
which can be used to actuate a magnetic spin bar in a flask
when that flask rests of the hotplate surface. Hotplates not
only contain a magnetic stirrer, but also have a heat source
which is controlled by a dial on the device. Both of these
devices are plugged into a continuous power outlet.
Thermowells

Figure 2.2 - Common Lab Equipment

hotplate or stirplate

thermowell

Thermowells are heating devices with a hemispherical

depression in which a round-bottomed flask can rest.
Irregularly shaped objects are sometimes heated in
thermowells by first placing a small amount of sand in the
depression, allowing the heating surface to take the shape of
the object to be heated. Thermowells are NEVER plugged
directly into a continuous power outlet. Instead, they are
plugged into a device known as a veristat, which regulates the
power reaching the thermowell. Increasing the voltage
applied to the thermowells outlet increases the maximum
temperature that it will attain.
Ringstands and Rails

three-fingered clamp

lab jack
ringstand

Image Ron Davis, Jr., Ph.D.

Figure 2.3 - Proper Use of a Ring Stand

Most modern fume hoods are equipped with a fixed system of

metal rails onto which devices may be clamped for stability.
Although very stable, these rails cannot be repositioned within
the fume hood for special setups.
When rails are not sufficient for the task at hand, ringstands
provide a moveable, vertical post on which to immobilize
glassware using clamps. Whenever possible, items should be
clamped over the foot of the ringstand to maximize stability
(Figure 2.3).
Clamps

Correct

Incorrect

Image Ron Davis, Jr., Ph.D.

In order to prevent tipping over, ringstands

should always be set up with the base
underneath of the items which are supported.

Clamps are available in two- and three-fingered varieties.

Two fingered clamps usually are used to affix glassware by
the female portion of a ground glass joint. Three-fingered clamps are more useful for clamping
oddly shaped glassware. Both are attached to a ringstand by a thumb-screw.
Lab Jacks
Lab jacks are used to raise and lower devices in the laboratory. The most common use of lab jacks
is raising and lowering heat sources from glassware which has been clamped in place on a
ringstand. Whenever using a lab jack, be sure that the jack has adequate clearance to move up
and down below the apparatus being consructed.

2-2

Chapter 2 - Basic Laboratory Tools and Techniques

Laboratory Glasware
Composition of Lab Glass
In the modern age, new materials such as polymers and ceramics have led to a wide variety of
materials available for the manufacture of vessels that one might find useful in the laboratory. Even
so, one of the oldest and most time-tested materials used in chemical and alchemical laboratories
is glass. Consisting primarily of silicon dioxide, glass is a strong, network-covalent material with
remarkable resistance to a range of chemicals and a range of temperatures. However, not all glass
is created equal.
Inexpensive soda-lime glass is a sodium aluminum silicate material used in many glass products
that you may find in your own home. It is relatively inexpensive and easy to mold into usefull shapes
such as drinking glasses or ornamental pieces. This type of glass, however, suffers from serious
shortcomings in lab applications. Most siginificant is its high coefficient of thermal expansion, which
causes objects made of soda lime glass to expand and contract when heated and cooled. This
process can quickly weaken the glass causing it to fail, sometimes catstrophically. Because of this,
soda lime glass is rarely if ever used in the organic chemistry.
Lab glassware is often constructed from specialized glass develped in the late 1800s by Otto
Schott. This special glass is known as borosilicate glass, and is often sold today under the trade
names Duran or Pyrex. The inclusion of a small amount of boron into a silicates structure has the
beneficial effect of decreasing the extent to which it expands and contracts in response to
temperature changes. This means that borosilicate glassware is far less prone to failure under the
conditions used in most chemical reactions.
Ground Glass Joints
Figure 2.4 - Standard taper 19/22 Ground Glass Joints
19 mm
male joint
22mm
female joint
TS 19/22

TS 19/22
standard taper 19 mm wide and 22 mm tall

Image Ron Davis, Jr., Ph.D .

Some pieces of lab glassware contain joints

with textured surfaces which are smoky in
appearance. These joints are referred to as
ground glass joints, and are designed to
form a gas-tight seal when assembled using
a small amount of heavy grease applied to
the male joint before connection. The most
common type of ground glass joint is the
standard taper in which the diameter of the
joint decreases 1mm for every 1cm of
length. This is denoted by a ( T
S ) logo on the
glassware (figure 2.4). Sizes range dramatically, but the most common is the 19/22
joint, in which the large end of the taper is
19 mm in diameter and the joint is 22 mm in
length. If a gas-tight seal between two
pieces of glassware is required, it is essential
that the male and female ground glass
joints are of the same size and taper.

Ground glass joints come in many tapers and sizes. In order to achieve
a gas-tight fit, it is essential that the male and female joints are of the
same size and taper. One of the most common of these is the standard
taper 19/22 joint.

2-3

Chapter 2 - Basic Laboratory Tools and Techniques

Laboratory Glasware
Beakers and Flasks
Beakers and flasks are some of the most commonly employed glassware in the lab (Figure 2.5).
They are suitable for transferring liquids and solutions as well as for use as reaction vessels. Generally, they are suitable for heating since they are made of borosilicate glass. Though some
beakers and flasks are printed with graduations indicating approximate volumes, these markings
are not carefully calibrated and should not be used for volume measurements.
Beakers are cylindrical and usually have an articulated lip for easy pouring of liquids. They are
most commonly used for transfer and collection of liquids and solutions. The wide opening makes
them less desirable for long term solution or liquid storage as evaporation may occur rapidly.
Erlenmeyer flasks are conical with a flat bottom. This
design results in a narrow opening which accomplishes two things. First, it discourages evaporation of
liquids which may alter solution concentrations or
introduce error into measurements. Second, it allows
the user to mix the contents easily by swirling without
the risk of spilling the contents over the side. NEVER
evacuate an Erlenmeyer flask.
Filter flasks look like Erlenmeyer flasks, but have two
distinct and important differences. First, they are
made of thicker glass which is designed to withstand
evacuation without imploding. Second, they have a
small hose barb near the top which is designed to be
attached to a vacuum source.

Round bottomed flasks (figure 2.6) are spherical (with

the obvious exception of the ground glass joint at the
top). This shape allows for easy stirring and even
heating of samples in a thermowell. The spherical
shape also makes them resistant to implosion and
suitable for evacuation. Round bottomed flasks
should never be heated using a hot plate since this
causes a single point of the flask to become hot and
may cause failure.
Three necked flasks are used much like roundbottomed flasks and can be evacuated or pressurized
like their single-necked counterparts, but have two
additional joints on the top for providing multiple ports
for more sophisticated apparatus construction.

2-4

Figure 2.5 - Beakers and Flasks

Image Ron Davis, Jr., Ph.D.

Beakers (A), Erlenmeyer flasks (B) and filter flasks (C) are
all essential parts of an organic chemistry laboratory kit.

Figure 2.6 - Round-Bottomed Flasks

Image Ron Davis, Jr., Ph.D.

Round-bottomed flasks are available with a single

joint (A), or multiple joints (B). Both varieties are
suitable for evacuation and should never be heated
directly on a hot plate.

Chapter 2 - Basic Laboratory Tools and Techniques

Laboratory Glasware (continued)
Adapters and Connectors
Organic chemistry reaction and purification apparatuses are often very complex and specialized to
the task at hand. It is, therefore, often necessary to modify the main components of an apparatus
by changing the number and direction of available connections on those components.
Rather than maintain a large inventory of specialized glassware pieces for all possible applications,
it is much simpler and more economical to maintain a small set of adapters that can be used to alter
the connectivity of just a few types of flasks. Just a few of the adapters often found in the organic
chemistry lab are depicted in figure 2.7.
Claissen adapters are an upward-facing U-shaped connector which splits the joint of a flask into
two ports. One port is directly above the connected flask and is typically used as an addition point
for reagents, solvents and other chemicals. The second is off to the side and commonly is attached
to a condenser or an additional adapter to complete a reaction setup.
Three-way adapters (also sometimes referred to as a still heads) also split the joint of a flask in
two directions. One connection points upward and is commonly closed or connected to a
thermometer. Unlike a Claissen adapter, however, the other connection points down and is usually
connected to a condenser to allow collection of a re-condensed liquid in a separate flask.
Vacuum adapters are bent at a slight angle for use in directing flow of liquids into a receiving
container. They contain a hose barb which may be attached to a vacuum source for
reduced-pressure applications or left open to ensure that a heated system is not closed.
In some cases, a glassware apparatus requires that gas flow through the setup. In cases like this,
inlet adapters are used to connect the ground-glass joint of an apparatus to a vacuum or gas line
via a hose barb.

Figure 2.7 - Common Glassware Adapters

Claissen (A), three-way (B), vacuum (C) and inlet (D) adapters are all used in the contruction of
typical synthetic organic glassware apparatus.

2-5

Chapter 2 - Basic Laboratory Tools and Techniques

Laboratory Glasware (continued)
Funnels
Wide-mouth funnels are used to transfer materials which are resistant to flow, such as dry powders
or viscous liquids.
Glass funnels typically have narrower stems and are used for the transfer of liquids. They also are
used to support filter paper when gravity filtration is being performed.
Buchner funnels are cylindrical, ceramic funnels with a flat, perforated surface designed to accommodate a circular disc of filter paper. When attached to an evacuated filter flask, Buchner funnels
may be used to collect samples by rapid filtration.
Separatory funnels consist of a conical container attached to a flow control device known as a
stopcock. When two immiscible liquids are mixed in a separatory funnel, the liquid of greater
density can be collected by draining it through the stem at the base of the funnel.
Addition funnels allow a
solution to be added to a flask
when the system has been
closed to the atmosphere. A
narrow stem connects the
head space of the funnel to the
head space of the attached
flask, allowing pressure to
equilibrate between the two as
the reagent flows through the
stopcock.

Figure 2.8 - funnels

wide mouth

glass

Buchner

separatory

addition

Image Ron Davis, Jr., Ph.D.

Condensers
Liebig (pronounced Lee-Big) condensers (also called reflux
condensers or fractionating columns) are water-jacketed
columns used to promote the condensation of vapor
produced when the contents of an attached flask boil. These
condensers are commonly attached in a vertical orientation
so that re-condensed liquids drain back into the original
boiling flask. Many of these condensers have small prongs at
the bottom of the interior tube to support solid packing if
desired. Hose barbs allow an exterior water jacket to be filled
with running water as a means of cooling the condenser.
West condensers are usually slimmer than reflux condensers
and are designed to be oriented at a downward angle to
promote the condensation and collection of a liquid in a flask
other than the one in which it was boiled. Hose barbs allow an
exterior water jacket to be filled with running water as a
means of cooling the condenser.

2-6

Figure 2.9 - condensers

Liebig

West

Image Ron Davis, Jr., Ph.D.

Chapter 2 - Basic Laboratory Tools and Techniques

Laboratory Glasware (continued)
Volume Measurement
Several calibrated volume measurement devices are available in most laboratories (Figure 2.10).
All of these items will be labeled with two important codes to remind the user how the device has
been calibrated.
TD or TC indicates whether the device was calibrated To Deliver or To Contain the
amound of liquid indicated by the gradations on the side.
Because liquid densities vary significantly with temperature, the temperature at
which the calibration was performed is indicated (usually 20 or 25 C)
Graduated cylinders are used to contain or transfer accurately measured volumes of liquids. Most
have an articulated lip for easy pouring of contents.
Graduated pipettes are sometimes used to transfer accurately measured small quantities of liquids.
More than the required volume is sucked into the pipette using a bulb or plunger, then the level is
drained to a waste container until the pipette contains only the desired dispensing volume.
Volumetric pipettes, unlike graduated pipettes, are calibrated to deliver only a single volume of
liquid. However, they are highly accurate when properly used and are valuable tools in sensitive
analytical applications.
Volumetric syringes are used when exposure of reagents to air is undesirable.
Figure 2.10 - Volumetric Glassware
calibrated to deliver
the indicated amount
at 20 C

A
TD

TD
o

20 C

20 C

Reading is
taken from the
bottom of the
meniscus

1
mL

Volumetric glassware is calibrated to deliver (TD) or to contain (TC)

an indicated amount of liquid at or near room temperature. (A)
Graduated cylinders are generally used for large, course volume
measurements. (B) gradated pipettes can be used to measure and
dispense any volume desired. (C) volumetric pipettes are highly
accurate, but are calibrated to deliver only the volume indicated. (D)
Graduated syringes are useful for dispensing air-sensitive solvents
and solutions.
Image Ron Davis, Jr., Ph.D.

2-7

Chapter 2 - Basic Laboratory Tools and Techniques

Basic Laboratory Techniques
Weighing Samples
Weights are one of the most basic and yet crucial measurements taken in the organic chemistry laboratory. Take the following steps to ensure that your weight data is as accurate and precise as possible
(Figure 2.11).
Go to the balance with the flask or tube into which the sample will be weighed
Place a piece of folded weigh paper on the balance so that it is centered on the pan and the
edges of the paper do not hang off of the pan.
Tare the balance so that it displays 0.00 g with the weigh paper resting on it.
Place the solid organic material on the weigh paper until the desired weight is obtained and
mark this weight in your notebook.
Transfer the weighed solid into the desired container using the fold in the weigh paper as a
means of directing flow of the powder.
Figure 2.11 - Weighing Powders

weigh paper

place in balance and tare

add dry sample

fold
1.01g

0.00g

transfer sample
using the crease
to direct the
powder into the
container
Image Ron Davis, Jr., Ph.D.

Powder samples are weighed onto a creased piece of weigh paper, then transferred to a container

Liquids are more often weighed directly into the desired container because they are more difficult to
quantitatively transfer. This is accomplished by taring the balance with the container on the pan. Only
liquids of low volatility should be weighed, since mass loss due to evaporation can introduce error into
these measurements.
Cooling Samples
Just as reaction setups can be heated using hotplates and thermowells, they may be cooled to various
temperatures using mixtures of materials to produce a slurry of a desired temperature in a container
beneath the flask.

Mixture

Ice/Water
Ice/Salt (3:1)
Acetone/Dry Ice
Liquid Nitrogen

Temperature
(C)
0
-20
-78
-196

2-8

Chapter 2 - Basic Laboratory Tools and Techniques

Basic Laboratory Techniques
Filtration
Many syntheses and purification processes result in the formation of a solid material under a
solution. When this occurs, separation of the liquid and solid may be achieved using one of several
techniques (Figure 2.12).
Gravity Filtration
When the solid is a coarse particulate and the liquid has relatively low surface tension (such as
hexanes or chloroform), gravity filtration is a suitable technique for separation. A circular piece of
filter paper is fluted by folding it in half twice, then reopening it, then placing it into a glass funnel.
When the mixture is poured into the funnel, the liquid will permeate the filter paper under the force
of gravity while the solid remains trapped in the filter paper flute.
Vacuum Filtration
Solvents of high surface tension may not flow well under gravity and very fine particulates can clog
filter paper, restricting flow further. In either of these situations, vacuum filtration is often used. A
flat filter paper disc is placed inside of a Buchner funnel attached to a filter flask. When the filter
flask is attached to a vacuum and evacuated, the solvent is forced through the filter paper by
atmospheric pressure.
Decanting
In cases involving a very coarse or dense solid, separation can be accomplished by careful pouring
of a liquid from its container while leaving the solid undisturbed in the bottom.
Figure 2.12 - Filtration Techniques

fold once

paper disc
to vacuum

fold again

en

op

(A) Gravity filtration using fluted filter paper inside of a glass funnel works well when separating
solvents of low surface tension from coarse solids. (B) Vacuum filtration using a Buchner funnel and
filter flask can separate higher surface tension solvents and smaller particulates which can clog
gravity filtration setups. (C) Decanting from one beaker to another is a rapid way to remove solvent
from coarse, dense solids.

2-9

Image Ron Davis, Jr., Ph.D.

Chapter 2 - Basic Laboratory Tools and Techniques

Basic Laboratory Techniques (continued)
Drying Samples
Water is one of the most common contaminants encountered in the organic chemistry laboratory.
It is often necessary to remove all traces of water before a product can be analyzed or a reaction
run. Both solid and liquid organic materials can be dried using the techniques described below.
Drying of Solids
Removal of residual solvent from solids is accomplished in several ways.
Spreading the solid out on a watchglass or weigh paper is a simple technique
for maximizing exposed surface area, which allows volatile solvents to evaporate quickly.
Gentle heating of the solid is effective when the solid is stable and has a high
melting point relative to the boiling point of the solvent being removed.
Placing the solid in an evacuated container (sometimes called drying in
vacuo) is an effective technique for removing solvents of low volatility.
Drying of Liquids
Water is sparingly miscible in many organic liquids such as ether and dichloromethane. This
makes it necessary to chemically dry such solvents for certain applications. The most common
technique for removal of residual water from these solvents is the addition of a small amount of
anhydrous calcium chloride or magnesium sulfate to the liquid (Figure 2.13). When these inorganic
materials come into contact with water, they form a solid salt hydrate which can be filtered out of
the organic liquid. Drying agent is added to the sample and swirled for about thirty seconds. When
newly added agent flows freely (does not clump) when agitated, the solution is then filtered to
Figure 2.13 - Drying an Organic Liquid

A
wet organic
solvent
anhydrous
drying agent

H2O

H2O

H2O

hydrated
drying agent

dry organic
solvent

H2O

H2O
H2O

MgSO4 + 6H2O

H2O

H2O

H2O

hydrated
drying agent

MgSO4 6 H 2O

dry
organic
solvent
Image Ron Davis, Jr., Ph.D.

(A) Anhydrous minerals such as magnesium sulfate sequester water from organic liquids by
forming hydrate crystals. (B) Once all of the water in a sample is absorbed by the magnesium
sulfate, the solid hydrate is separated from the organic liquid by filtration.

2-10

Chapter 2 - Basic Laboratory Tools and Techniques

Basic Laboratory Techniques (continued)
Refluxing
Since chemical reaction rates can change dramatically with temperature, it is often desirable to boil
reaction mixtures as a means of accelerating a synthesis. Doing so in an open container, however,
is problematic since solvent volume can rapidly dwindle as vapor escapes the system. This
problem is rectified by the attachment of a reflux condenser to a boiling flask (Figure 2.14). A reflux
condenser is a water-jacketed tube in which solvent vapor condenses and falls back into the boiling
flask. When a flask is fitted with a reflux condenser, with water flowing in the bottom and out the
top of the jacket, solvents and solutions may be boiled indefinitely without losing volume. In the
case of a reflux apparatus, direct heating of the solvent in a thermowell is acceptable, since the
opening to the setup is at the top of the system, far away from the boiling solvent.

open to atmosphere

cooling water

cooling water out

cooling water

Figure 2.14 - Reflux Apparatus

cooling water in

thermowell

boiling liquid

(A) A reflux condenser is fitted to a round bottomed flask containing the solution to be boiled. (B) As
solvent vapor reaches the water-cooled condenser, it becomes liquid and falls back into the boiling
flask.

2-11

Image Ron Davis, Jr., Ph.D.

po

va

lab jack

lls

stir plate

ensate fa
nd

r ascends

co

Chapter 2 - Basic Laboratory Tools and Techniques

Chapter Questions
General Questions
G-1. Explain why water tubing should never be used to connect an apparatus to a vacuum.
G-2. Explain why the foot of a ringstand should always be oriented toward the apparatus it supports.
G-3. True or false: All standard taper joints are compatible with one another. Explain your response.
G-4. Match the containers below with the statement which best describes its proper use.
More than one may apply to each description.
a) suitable for heating on a hotplate
Common Lab Containers
beaker
Erlenmeyer flask
round-bottomed flask
three-necked round-bottomed flask

b) can be safely evacuated

c) may be heated in a thermowell
d) may be heated in a water bath
G-5.

Explain the meaning behind the following inscriptions found on laboratory glassware. On
which type of lab glass would you expect to find thise inscriptions?
a. Ts 19/22
b. TC/25

G-6. Explain why it is considered safe to heat a flask containing organic solvents directly in a thermowell
when refluxing a solution.
G-7. True or false: Liquids can never be accurately weighed in the lab because evaporation will introduce
too much error into the measurement. Explain your response.
G-8. When adding a drying agent such as magnesium sulfate to an organic liquid, how does one know
when adequate drying agent has been added?
G-9. Which type of funnel is specifically designed for use in vacuum filtration apparatus? What is the
name of such a funnel?

2-12

Chapter 2 - Basic Laboratory Tools and Techniques

Chapter Questions
Scenario Questions
S-1. A researcher needs to filter a sample containing fine crystals of precipitate in water (a solvent
with very high surface tension). Which filtration method would you recommend he use and why?
S-2. A scientist wants to isolate the organic phase from a mixture of dichloromethane and water.
Which funnel should be used for this purpose?
S-3. List at least four problems with the reflux setup shown below.

cooling water in

cooling water out

hot plate

spin bar
fume hood bench
Image Ron Davis, Jr., Ph.D.

S-4. A researcher has obtained a sample of crystals of 1,3-dinitrobenzene (mp 90 C) under

n-butanol (bp 117 C). After filtering the sample, she wants to ensure that the 1,3-dinitrobenzene
crystals are thoroughly dried of the n-butanol solvent. Would you recommend drying the sample
crystals by heating? Why or why not?

2-13