Basic Terms In Physical Chemistry

Thermodynamic system
The concept (thermodynamic) system as used in this book refers to that part of the world
whose thermodynamic properties are the subject of our interest, while the term surroundings
is used for the remaining part of the universe.
Note: Both a certain part of the real space and a certain part of the imaginary (abstract)
space forming a simplified model system, e.g. an ideal gas, may be chosen as a system.
Systems are classified as isolated, closed and open, based on their inter-relations with their
surroundings.

Isolated system
A chemical system exchanging neither matter nor energy with its surroundings is an isolated
system.

Closed system
A chemical system exchanging energy but not matter with its surroundings is a closed system.

Open system
A chemical system exchanging both energy and matter with its surroundings is an open system.
Example
Differences between individual types of chemical systems may be demonstrated using the example
of making coffee. The pot on the heater represents a (practically) closed system until the water
is brought to the boil. At the boiling point, when steam is leaking from the pot, it becomes an
open system. The ready-made coffee kept in a thermos bottle represents a simple model of an
isolated system.

Phase, homogeneous and heterogeneous systems
The term phase is used for that portion of the investigated system volume in which its properties
are constant or continuously changing in space. If a system behaves in this way throughout
all its volume, we call it a homogeneous system. If a system contains more phases, we call
it a heterogeneous system.
Example
Let us imagine a bottle of whisky. How many phases does this system consist of?

Solution
If we are, from the thermodynamic point of view, interested solely in the liquid content of the
bottle, the system is homogeneous. It contains one liquid phase (a mixture of water, ethanol and
some additives). If, on the other hand, we are interested in the entire content of the bottle but
not the bottle itself, the system is heterogeneous. In this case it consists of two phases, liquid and
gaseous, with the latter containing air and whisky vapour. If, however, we focus our attention
on both the bottle content and the bottle itself, we have a heterogeneous system again, but this
time it also contains other phases in addition to the gaseous and liquid ones, i.e. the glass of the
bottle, its cap, label, etc.

The volume of a system as an extensive quantity. The volume V is the sum of the volumes
of the individual parts (i.e. sub-systems) I, II and III, i.e. V = VI + VII + VIII.

Energy
There are two basic forms of energy exchange between a system and its surroundings, heat
and work. A positive value is assigned to such energy exchange during which the system gains
energy (work or heat) from its surroundings, i.e. energy is added to the system. A negative
value indicates that the system passes energy (work or heat) to its surroundings, i.e. energy is
subtracted from the system.

Heat
When the energy of a system changes as a result of a temperature difference between the system
and its surroundings (e.g. transfer of kinetic energy of disordered movement of molecules), we
speak about exchanged heat.

Work
Other forms of energy exchange, which are usually driven by some forces acting between the
system and its surroundings, are called work. Based on the type of interaction between the
system and its surroundings, we distinguish volume work [see 3.1.2], electrical work, surface
work, etc.

Thermodynamic quantities
Observation of any system allows us to determine a number of its properties. The properties
in which we are interested from the thermodynamic point of view are called thermodynamic
quantities, or, briefly, quantities. Typical thermodynamic quantities are temperature,
pressure, volume, enthalpy and entropy. Neither heat nor work rank among thermodynamic
quantities.
Note: Terms such as thermodynamic function, thermodynamic variable, state quantity
(i.e. a quantity determining the state of a system, see 1.4), state function, or state variable
are used as synonyms of the term thermodynamic quantity.

Intensive and extensive thermodynamic quantities
Let us consider a homogeneous system without any external force fields present. We distinguish
between extensive and intensive thermodynamic quantities of a system. Intensive quantities
are those whose values do not change when the system is divided into smaller sub-systems.
Extensive quantities are those whose values are proportional to the amount of substance of
the system at a fixed temperature and pressure (see Figure 1.1). Temperature, pressure, and
composition expressed by mole fractions are typical intensive quantities. Volume, mass and the
number of particles are typical extensive quantities.
Note: Some quantities, e.g. the system surface, are neither extensive nor intensive.
Every extensive quantity may be converted into an intensive one if we relate it to a certain
constant mass of the system. We then obtain specific or molar quantities (see 3.2.5). For every
extensive quantity X and the respective molar and specific quantities Xm and x we may
write
X = nXm , (1.1)
X = mx , (1.2)

where n is the amount of substance and m is the mass of the system.

We will use the subscript m to denote molar quantities and small letters to denote
specific quantities.

The state of a system and its changes
Any system may be in any moment characterized using a certain number of quantities. These
quantities define the state of a given system. The degree of generality at which we observe
a given system has to be taken into account at the same time. In terms of a microscopic
scale, the state of a system is defined by the position and velocity of all its particles. In terms
of thermodynamics, however, it is enough to know only a few quantities, e.g. temperature,
pressure and composition.

The state of thermodynamic equilibrium
The state of thermodynamic equilibrium (equilibrium state, equilibrium) is a state in which no
macroscopic changes occur in the system and all quantities have constant values in time.
Note: In the state of thermodynamic equilibrium, changes take place at the microscopic
level. For instance, when the liquid and vapour phases are in equilibrium, some molecules
continuously move from the liquid to the vapour phase and others from the vapour to the
liquid phase. However, the temperature and pressure of the system do not change.
The state of thermodynamic equilibrium embraces the following partial equilibria:
• mechanical (pressure) equilibrium—the pressure in all parts of the system is the same 1,
• thermal (temperature) equilibrium—the temperature in all parts of the system is equalized,
• concentration equilibrium—the concentration of the system components is the same in
all parts of each phase of the system, but the composition of individual phases is usually
different,
• chemical equilibrium—no changes in composition occur as a result of chemical reactions,
• phase equilibrium—if a system is heterogeneous (see 1.1.4), the components of its phases
are in equilibrium.

Note: If a system in the state of thermodynamic equilibrium occurs in an external force
field, e.g. the gravitational field, the pressure is not the same in all parts of the system
but it changes continuously. The concentration of the system components also changes
continuously in each phase, with a discontinual change occurring at the phase boundary.

System’s transition to the state of equilibrium
If a system is not in the state of equilibrium, its properties change in time in such a way that
it tends toward equilibrium. Thermodynamics postulates that every system under invariable
external conditions is bound to attain the state of thermodynamic equilibrium. The time needed
for a system to attain equilibrium varies considerably, ranging from fractions of a second needed
for pressure equalization up to hundreds of years needed for glass transition to the crystalline
state. A measure of the velocity of a system’s transition to equilibrium is called the relaxation
time.
Example
If we immerse several crystals of copper(II) sulphate pentahydrate (CuSO4·5H2O) into a closed
vessel containing water, the system thus created will be in a non-equilibrium state at the beginning.
There will be neither a phase equilibrium between the crystals and the liquid phase
nor a concentration equilibrium. After some time the crystals will dissolve (phase equilibrium).
If we do not mix the system, the dissolved copper(II) sulphate pentahydrate will slowly diffuse
through the solution from the bottom up to the surface, and after many weeks (relaxation time),
concentration in all parts of the system will become equal as well (thermodynamic equilibrium).

Thermodynamic process
If the properties of a system change in time, i.e. if at least one thermodynamic quantity changes,
we say that a certain thermodynamic process takes place in the system. The term process
relates to a very broad range of most varied processes, from simple physical changes such as,
e.g., heating, various chemical reactions, up to complex multistage processes. Individual kinds
of processes may be classified according to several criteria.

Reversible and irreversible processes
The course of any process depends on the conditions under which the given system changes.
If we arrange the conditions in such a way that the system is nearly at equilibrium in every
moment, and that, consequently, the direction of the process may be reversed by even a very
slight change of the initial conditions, the process is called reversible or equilibrium. A
reversible process is thus a sequence of (nearly) equilibrium states of a system.
However, processes in the real world are mostly such that the system is out of equilibrium
at least at the beginning. These processes are called irreversible or non-equilibrium (the
direction of the process cannot be reversed by any slight change of external conditions, and
the process is a sequence of non-equilibrium states). An equilibrium process is thus actually a
limiting case of a non-equilibrium process going on at an infinitesimal velocity.
Example
Infinitely slow heating or infinitely slow compression of a system may serve as an example of
equilibrium processes which cannot be carried out in practice. In contrast, water boiling at a
temperature of 100 C and pressure of 101 325 Pa is an example of an equilibrium process which
may take place in practice. If we lower the temperature slightly, the direction of the process will
be reversed and boiling will be replaced by water vapour condensation.

Processes at a constant quantity
In most investigated processes, one or more thermodynamic quantities are maintained constant
during the whole process. These processes are mostly termed using the prefix iso- (is-), and
denoted using the symbol [X], with X indicating the given constant quantity. The following
processes are encountered most often:

Name of the process               Constant quantity            Symbol
Isothermal                                temperature                        [T]
Isobaric                                    pressure                              [p]
Isochoric                                 volume                                [V ]
Adiabatic                                  heat                                    [ad]
Isentropic                                entropy                               [S]
Isenthalpic                               enthalpy                             [H]
Polytropic                                heat capacity                     [C]

Example
In the initial state, a system of a constant volume has a temperature of 300K and a pressure
of 150 kPa. A certain process takes place in the system, and in the final state the system’s
temperature is 320K and its pressure is 150 kPa. Does the process take place under a constant
thermodynamic quantity?
Solution
The initial and the final temperatures of the system are different. Consequently, the process
cannot be isothermal. Both the initial pressure and the final pressure are identical. In this case
it may be, but not necessarily is, an isobaric process. The specification does not allow us to find
out whether pressure changes in any way in the course of the process. However, the process is
definitely an isochoric one because the system has a constant (i.e. unchanging) volume.

Cyclic process
A cyclic process is such at which the final state of the system is identical with its initial state.
In a cyclic process, changes of thermodynamic quantities are zero.
Note: Heat and work are not thermodynamic quantities and therefore they are not zero
during a cyclic process.

Example
Let our system be a cube of ice with a mass of 1 g, and the initial state be a temperature of
−10 C and a pressure of 100 kPa. The sequence of processes taking place in the system was as
follows: the cube was heated to 0 C at which it melted. The liquid water was electrolyzed at this
temperature. The resulting mixture of hydrogen and oxygen was expanded to 200 Pa and ignited.
The water vapour resulting from the reaction had a temperature of 500 C at the end of the
reaction. It was then cooled to −10 C and compressed to 100 kPa. In the course of compression
desublimation (snowing) occurred, and the system returned to its initial thermodynamic state. A
cyclic process took place.

Drawing Organic Structures

Molecules are actual, three-dimensional entities. Their structure is a major factor that determines their physical properties and the way one molecule interacts with another molecule. Because molecules are normally too small to see, chemists have devised ways to visually represent molecules. One way is by using a two-dimensional structural formula like that of the hydrocarbon heptane.

A two-dimensional structural formula of a hydrocarbon shows all of the atoms with all of their bonds in the plane of the page.

Hydrocarbons provide the backbone of all organic compounds. Each carbon atom in a hydrocarbon forms a total of four bonds. These bonds are combinations of single bonds with hydrogen atoms and single or multiple bonds with other carbon atoms.

For molecules that contain a large number of atoms or complex structures, drawing every bond and every atom is time and space consuming. A common notation developed to abbreviate the drawing without sacrificing the clarity of the structure is the condensed structural formula shown below for heptane:

CH3-CH2-CH2-CH2-CH2-CH2-CH3  (Heptane)

Hydrocarbons are compounds composed only of carbon and hydrogen atoms.

A condensed structural formula includes all of the atoms but uses line bonds to emphasize the main structural characteristics of the molecule.

Taking out the lines representing the carbon—carbon bonds condenses this formula still more:

CH3CH2CH2CH2CH2CH2CH3  (Heptane)

Heptane has five repeating —CH2— groups, called methylene groups. Because many organic molecules have such repetitive groups, an even more condensed notation shows these repeating units. Using this notation, the formula for heptane is as follows:
CH3(CH2)5CH3  Heptane

The bond-line structural formula is the notation that most organic chemists prefer to use. Bond-line formulas are easy to draw and quickly convey the essential structure of a molecule. Both the ends and the angles of the structure represent the carbon atoms. C—H bonds are not shown, but you should assume that the appropriate number of hydrogen atoms is present to complete the four bonds required by carbon to have its octet of electrons. The bond-line formula for heptane looks like this:

Bond-line formulas represent the carbon atoms as the intersection of lines and as line ends. You assume all the hydrogens needed to complete carbon’s valences.

Not all hydrocarbons are straight chains; many are rings. Chemists use the same structural formulas for them. Because the illustration of the two-dimensional structural formula of methylcyclopentane is so cluttered, it does not clearly show the ring.

Methylcyclopentane

The condensed structural formula is clearer.

Methylcyclopentane

The bond-line structural formula is even clearer. Thus, chemists use it most frequently.

Often, chemists combine the bond-line and condensed notations to clarify a structure or emphasize specific features. This formula also represents methylcyclopentane.

Developing Study Methods for Success

The key to your success in organic chemistry is in what you learn. Build your foundation to gain this knowledge by carefully studying the book and actively participating in the lectures. The more you apply your developing knowledge to understanding the design of the various organic syntheses and reaction mechanisms, the more you will grow in creativity as a student of organic chemistry.
Studying organic chemistry is like combining the elements of a foreign language class with the elements of a logic, or math, class. As with a foreign language, you must learn the vocabulary (names of compounds, chemical structures, reagents, and reactions), as well as the grammar (electron movements). As with a math class, you must understand the logic (reaction mechanisms). You combine these elements by practicing the grammar and vocabulary; then following the logic as you apply your knowledge to new situations (working the exercises in your book). Finally, you demonstrate your mastery of both the grammar and the logic (by doing well on the examinations your instructor writes).
To succeed in this class, you must develop a consistent knowledge base of concepts, theories, and techniques. In other words, what you learn in the early chapters is essential for your understanding of the material in later chapters. Failure to retain the things that you have studied will make learning organic chemistry seem overwhelming. When you study, make it your central objective to thoroughly understand the concepts, theories, and techniques being covered, then retain them. Could you repeat that, please? When you study, make it your central objective to thoroughly understand the concepts, theories, and techniques being covered, then retain them. These concepts, theories, and techniques are your knowledge base and the foundation for all of your continued efforts in learning organic chemistry.
Developing and maintaining your knowledge base of organic chemistry requires some learning strategies that are different from those used for many other classes. Primarily, learning organic chemistry requires consistent time, effort, and, most of all, thought. Organic chemistry has a reputation for being a difficult subject to master because it covers a lot of information and some students struggle over some of the concepts. Regular study diminishes this difficulty level. Some people can stuff in lists of facts in an all night cram, but few people can learn facts and the accompanying logic, then integrate those facts and the logic with previously learned facts and logic in a last minute effort. The most important move you can make on the road to success in organic chemistry is to establish a regular program of study.
Ideally, a schedule of regular study involves five steps.
Step 1 When your instructor assigns a new chapter, quickly read through it before your instructor lectures on it. Your goal is not to get everything from the chapter in this first reading but to get an overview of the main ideas.
Step 2 Immediately after the lecture, reread the material and work the in-text exercises. If you have difficulty with an exercise, then review your lecture notes and reread the material in that section. Be sure that you understand that section and can work the exercises before continuing.
Step 3 As you read and work the in-text exercises, begin memorizing the important facts from the chapter. Remember that memorizing facts is an essential part, but only a part, of success in organic chemistry.

Step 4 After you finish reading the chapter and working the in-text exercises; develop your logic skill by working the end of the chapter exercises.
Step 5 Prepare for the examination by working more of the end of chapter exercises. Your problem solving skills will show if you grasp what you have studied. Ask questions. Find someone who needs help and teach them what you have learned.
Problem solving in the real world of scientists seldom proceeds in the organized fashion that most textbook authors, classroom instructors, and scientists would have you think. Problem solving requires a lot of struggling, puzzling, trial-and-error, false starts, and dead ends. Chemists do not wait for divine inspiration to solve a problem. Instead, they write down what they know, then analyze and manipulate that information. When the next step becomes apparent, they take that step, then stop again to analyze and manipulate the new information. In this way chemists work toward a solution to the problem. As with them, so with you—the more problems you solve, the easier it will become to solve them.
There are two general strategies for problem solving. The most common form of problem solving is rote problem solving. With rote problem solving, you need to know only the proper formula to reach the correct answer. As long as you remember the formula and make no mistakes plugging in the facts and solving the formula, you will solve the problem correctly. This form of problem solving requires little understanding of the formula. Less common, but far more useful, is conceptual problem solving. Here you need to analyze and rearrange the statement of the problem to identify the underlying concepts involved. Once you identify the underlying concepts, you apply those concepts to the data and solve the problem.
Successful chemists use conceptual problem solving. To succeed as an organic chemistry student, you must also learn how to solve problems conceptually. Skill with conceptual problem solving requires much practice. When working the exercises in this book or those on your quizzes and examinations, seldom can you rely on “divine inspiration” for the solution. You must systematically dissect the exercise and apply the underlying principles of the particular concepts involved to find the solution. Even with this systematic work, many students find that, at first, they come up with the wrong answer to a problem. Don't let wrong answers discourage you; right answers will come more and more readily as you gain a larger foundation of principles and logic to work with.

Learning to Think Like a Chemist

To learn to think like an organic chemist, you must first know how an organic chemist thinks. The following three points are an overview of their thought processes.  (1) Organic chemists learn the facts. (2) They use these facts to construct concepts by organizing the facts into a coherent picture. (3) As organic chemists learn new facts, they update their picture of concepts.
From the scientific viewpoint, facts are important because facts are the basis of science. A fact is an observation based on experimentation. Scientists, and that includes organic chemists, form

their hypotheses based on the facts that they know about a certain topic. They make a speculation based on the hypothesis and do some experiments based on that speculation. These experiments lead to new facts, which lead to an updated hypothesis and further speculation and more experiments. Thus, the whole process in all sciences is designed to produce a coherent but expanding understanding of the universe.
Facts alone are not important to organic chemists. What is important is the way those facts fit together to form a coherent picture. Most organic chemists can produce an amazing variety of facts within the context of a particular concept. However, if asked to provide a list of the facts of organic chemistry, an organic chemist would probably be unable to produce a very impressive list. On the other hand, many beginning organic chemistry students can produce an amazing variety of facts on demand, but have little idea how they fit into a clear picture. A part of thinking like an organic chemist is to learn as many facts as you can about organic chemistry and, at the same time, to continually organize those facts in a way that allows you to synthesize new ideas. This method of learning can help you better understand and use the facts.
The important part of learning organic chemistry is the concepts you construct from the set of facts that you learn. Chemistry is, above all, a science. As a science, the only way to learn anything meaningful about organic chemistry is to work with the concepts. These concepts are not inviolable. They are subject to constant reconstruction and reinterpretation as you learn new facts. The authors of this book and your lecturer can only present the facts and provide you with the vehicle from which you can build your own understanding.

Organic Chemists Are People, Too

At the root of all science, including organic chemistry, is people’s unquenchable curiosity about the world and themselves. Everywhere are objects, living organisms, and events that people have had questions about. Scientists investigated these questions and discovered other questions. They investigated these new questions and found still more questions. Research, they learned, not only answers questions but uncovers new ones. Although scientists have learned many answers, they also have found that the answers to some questions must wait for the development of better investigative methods and tools. The job of scientists is to find answers to the multitude of questions about the world and to develop better methods and tools to answer the more and more sophisticated questions that they come up with along the way.
Because much of the world is based on the chemistry of carbon, organic chemists have provided many answers to the questions about the world. Many creative and curious people have been attracted to organic chemistry. The following stories illustrate the hard work and ingenuity of two such chemists.
In 1874, Othmer Zeidler reported the synthesis of DDT in his

doctoral dissertation. Some years later, Paul Hermann Müller discovered the insecticidal properties of DDT and in 1948 received the Nobel Prize in Medicine and Physiology for his discovery. Today DDT has a bad reputation because of its persistence in the environment. Its intended use was to kill disease-bearing insects, but it also caused harm to a number of birds and animals. DDT is no longer used in most areas of the world, but in the 1940s it was a “magic bullet” that killed many disease-bearing insects and saved many hundreds of thousands of lives. During World War II, the military used DDT, but it was not available for civilian use until Frank Mayo happened to read about it.
Frank Mayo is an example of an ambitious person who, with determination and hard work, coupled with a sound chemical foundation, made an impact on society (See Friedman, J. Chem. Educ., 1992, 69, 362). Mayo attended Georgia Tech leaving just one semester from completing the three year degree in chemistry. He turned down a job offer for eighteen dollars per week because he thought he could earn more working on his father's farm.
A few years later he began manufacturing and marketing chlorine based bleaching compounds. In 1944, while looking for other products to manufacture, Mayo happened on an article in the Atlanta Constitution describing DDT and its uses. He became interested. DDT was available only to the military; but even there, it was available only in limited quantities. The article stated that the synthesis for DDT was classified. However, it did give one important clue—a brief mention of the original synthesis by Zeidler in Germany. That was just enough information for a determined chemist!
Mayo knew that usually graduate students published their doctoral dissertations four to six months after graduation. He also knew that Othmer Zeidler received his degree in May or June of 1874, so Mayo expected to find the published report in the renowned journal Berichte der Deutschen Chemischen Gesellschaft (Reports of the German Chemical Society) by October, 1874.
Mayo went to the Georgia Tech library but found they did not begin subscribing to Berichte until 1910. Nearby Emory University began in 1915. He next decided to try the University of Georgia library 75 miles away in Athens. Since his daughter Bebe was a student there, he phoned her and asked her to check the library for him.
She found that indeed the University of Georgia had the 1874 issues of Berichte, but they were in boxes stored in the attic of the library. Only after many delays and much persuasion did Bebe gain permission to look through the issues Berichte in the attic. The librarians were notably reluctant to get them out of storage for a freshman who was studying neither German nor Chemistry. Bebe examined the title pages of the 1874 volume of Berichte beginning with October. “Believe it or not,” says Mayo, “There it was, in the October issue.” Word for word in the unfamiliar German, Bebe copied the paper by hand, then she called her father.
Mayo rushed to Athens, only to arrive after visiting hours in the dormitory. They wouldn't even let a father see his daughter after visiting hours! He drove around the dormitory, parked under his daughter's window and honked the horn. Bebe placed the transcript in an envelope and threw it out the window. Carefully shielding the paper from the falling rain, he read Bebe's copy in the headlight of the car then immediately drove back to Atlanta. He had the synthesis of DDT!
The synthesis required three ingredients: chlorobenzene, sulfuric acid, and chloral. He already had the chlorobenzene and sulfuric acid, but he had no chloral. Ignoring the fact that it was midnight, he drove to the neighborhood druggist and asked for a pound of chloral. The sleepy druggist grumpily informed him that he needed a prescription, and that no physician was likely to give him a prescription for a pound of the stuff. The typical prescription for chloral was measured in minims (about 16 minims per milliliter).
Mayo explained the reason for wanting the chloral, and the druggist finally agreed to sell him a pound.
With the precious chloral in hand, Mayo went home to try to make DDT. He measured the chemicals into a fruit jar packed in ice, using a wooden kitchen spoon to stir the mixture. Twenty minutes later, floating white lumps covered the top of the liquid. He separated the solid from the mixture with a buttermilk strainer and dried the powder. Then he slept.
The next morning, he made up a 5% solution in mineral spirits and sprayed the laundry area of his basement. Fleas from his dogs infested the area. An hour later, he and his wife returned to the basement. “Not a flea jumped to my wife's ankles,” he said. “Nothing happened—no fleas! The fleas, formerly plentiful, were dead. Cockroaches were lying with their feet in the air as if waving good bye to me. I was a happy man.”
Mayo then built a plant to manufacture DDT. Because of the war, he could not buy the equipment he needed. However, being resourceful, he built his plant with scraps and old metal drums that most people would consider junk. Mayo made hundreds of thousands of pounds of DDT powder and DDT solutions in deodorized kerosene and shipped it all over the world. Because of the benefit DDT gave to people, Mayo received much praise. Later, problems showed up that scientists traced to DDT so he stopped making and selling it. Since the banning of DDT, insect born diseases are again on the rise, but because DDT causes damage to helpful animals, it is not an acceptable insecticide. So far no one has discovered a good substitute.
Are you ever heading in one direction with a particular project only to find it turning out differently than you had expected? Do you just junk the project, or do you find yourself trying to figure out what went wrong or how you can use the project some other way? Many of the great discoveries of chemistry were made because the chemist investigated the reasons for an unexpected result. That was the case for Roy J. Plunkett, a young Ph.D. chemist who graduated from Ohio State University in 1936.
Plunkett was working for DuPont attempting to find a non-toxic refrigerant. On April 6, 1938, he and his assistant, Jack Rebok, opened the valve on a cylinder of tetrafluoroethylene to begin an experiment. No tetrafluoroethylene came out. In fact, nothing came out, although the weight of the tank indicated it should be full. He pushed a wire into the valve to determine if it was blocked. The wire went in freely. Plunkett had no understanding of what was wrong, but instead of discarding the “empty” tank and getting another to continue his research, he decided to investigate. Sawing the tank open, he found it filled with a waxy white powder. The molecules of tetrafluoroethylene had reacted together to form a polymer, or plastic, that they called polytetrafluoroethylene.
No one had ever observed the polymerization of tetrafluoroethylene before, but somehow it had occurred inside an otherwise “empty” tank. What caused it? On further investigation, Plunkett found some iron oxide inside the tank and discovered that it had catalyzed the polymerization reaction. Plunkett and other DuPont investigators soon developed ways to make polytetrafluoroethylene.
This new polymer had some remarkable properties. It was inert—it would not react with either strong acids or strong bases. It was heat stable, and no solvent could dissolve it. It was also extremely slippery. In spite of these interesting properties, if it had not been for World War II, probably no one would have done anything with it. Tetrafluoroethylene was too expensive.
General Leslie R. Groves happened to hear about the new material and asked to test it. General Groves was in charge of the Manhattan Project, the group working to develop the atomic bomb. In their research, they used enriched uranium. To make the enriched uranium, they converted uranium to uranium hexafluoride, an extremely corrosive gas. The project needed a gasket material that was resistant to uranium hexafluoride, so DuPont made some gaskets and valves for Groves. The scientists at the Manhattan Project tested them and found them very resistant to uranium hexafluoride. DuPont manufactured Plunkett's polymer for the Manhattan Project under the name TeflonTM.
Unlike DDT, Teflon's usefulness has stretched well beyond its wartime beginnings. Who hasn't used Teflon coated cookware? Of greater significance than the cookware is the fact that Teflon is a substance that the body does not reject. Thus, millions of people have benefited by receiving such things as artificial hips and knee joints or aortas and pacemakers made of Teflon. Another use of Teflon is in the space program. Space suits, wire and cable insulation, spaceship nose cones, and fuel tanks all use Teflon.

Organic Chemistry in the Everyday World

Organic chemistry touches every aspect of your life. This includes such areas as the clothes you wear, the food you eat, and the car you drive. Common to each of these items are chemical compounds based on the element carbon. Organic chemistry has both positive and negative attributes, and organic chemistry involves you.
All living creatures, both plant and animal, consist largely of complex carbon-containing molecules. These molecules provide for the day-to-day operation and maintenance of each organism as well as for the continuance of the species. Interestingly, as chemists learned how to synthesize these complex molecules of life and the molecules that interact with them, organic chemistry came back to its roots. A part of the beginnings of organic chemistry was the study of compounds derived from the “organs” of living creatures—thus the name organic chemistry. Now the knowledge gained from that research provides the basis for healing the diseases of many of those organs.
Looking in a totally different direction for the presence of carbon atoms in your life, what can you find that is more commonplace than plastic? You use plastics, or polymers, virtually all day long from the “disposable” packaging of your bath toiletries to the sophisticated polymeric materials in your car and computer. The plastics that make up all these items are based on organic compounds. The polymer industry has impacted modern society more than any other industry.
The above discussion covers some of the positive contributions of organic chemistry. Unfortunately, however, organic chemistry has made some negative contributions to the world too. There is a wide variety of commercial products that do not readily degrade when discarded or that cause other sorts of environmental problems. In spite of their usefulness, plastics are among those products. Because of the negative side of plastic, and other products, chemistry has gained a bad reputation in modern society. Adding to this reputation are the unscrupulous entrepreneurs who inappropriately dump hazardous materials thus contaminating the soil, air, and water.
Few chemists and chemical companies intentionally market products that will cause harm to a customer or to the environment

Those that do usually are considering only how much profit they can make and may even cover up evidence showing harm from their product. In many cases, the problems with a product come to light after the product reaches the market—sometimes long after reaching the market. This may occur because the company simply did not thoroughly test its product. Also, the shortfall in testing is often in the areas where the customer uses the product in ways unrelated to its intended use. Most chemists and chemical industries are good citizens with sound environmental concerns.
So, besides being a consumer, how could you fit into organic chemistry? Are you good at thinking up new ideas or looking at old ideas in new ways? The marketplace always welcomes new products. Do you have a concern for the environment? There is a worldwide need for solutions to the multitude of environmental problems and to find new products to replace those products causing harm to the environment. Related to the environment are the needs for solutions to the many other problems of modern society. Have you always been one to ask, “Why?” and “How does it work?” Chemists have just begun to learn about chemistry. Perhaps you could do research in

chemistry—just because it's there. Or you could use organic chemistry as an important foundation of your profession in medicine—either as a medical researcher or as a physician working with patients. Both biochemistry and many areas of biology depend heavily on a thorough understanding of organic chemistry. Biochemistry is the study of the molecules found in living organisms. Biology is increasingly directed to molecular biology, which is designed to learn more about living organisms by understanding the molecular processes of life.

What is Organic Chemistry?

The roots of chemistry go back into antiquity with the development of such techniques as metal smelting, textile dyeing, glass making, and butter and cheese preparation. These early chemical techniques were almost all-empirical discoveries. That is, someone either by accident or observation discovered them. They then passed this knowledge down from one generation to the next. For example, because copper is found in its free metallic state, it was first beaten into various implements. Later it was smelted, being perhaps one of the first metals to be separated from its ore.
Empiricism waned with the Greek philosophers who began the first systematic discussions of the nature of matter and its transformations. There were numerous philosophies and schools that grew up around those philosophers. One that is of particular interest to chemists is that of the atomists. Democritus (460-370 B.C.) elaborated much on the idea of atoms. He thought that atoms were solid particles and that atoms existed in a void but could move about and interact with each other; thus, forming the various natural systems of the world. However, Aristotle and Plato rejected the

philosophy of atoms, and it wasn't until the early nineteenth century that Dalton proposed the beginnings of the modern atomic theory.
Socrates, Plato, and Aristotle had the greatest impact on Greek philosophy. Socrates felt that studying the nature of man and his relationships was much more important than studying the science of nature. He did benefit the later development of science by insisting that definitions and classifications be clear, that arguments be logical and ordered, and that there be a rational skepticism. Plato adopted the philosophy that there were four elements: fire, air, water, and earth. Aristotle added to those four elements four associated qualities: hot, cold, wet, and dry. He believed that each element possessed two of these qualities, as illustrated in Figure 0.1.

Figure 0.1. The relationship between the four elements and their associated qualities. This diagram frequently appears in alchemy literature.
According to this philosophy, one element might be changed (transmuted) into another element by changing its qualities. For example, earth was dry and cold, but it could be transmuted into fire by changing its qualities to hot and dry.
These theories remained important for nearly two thousand years. Of greatest significance was the scientific work that took place in Alexandria. Unfortunately, little of it was in the field of chemistry.
It was in Alexandria, toward the end of the first century BC, that western alchemy began growing. Alchemy was a mixture of philosophy, religious, or spiritual, ideas, astrology, and empirical technical skills. Based on the theory that all matter consisted of fire, air, water, and earth with the associated qualities of hot, cold, wet and dry and that by changing the qualities of one form of matter you could change it to another form, the philosophers thought if they systematically changed matter from one form to another in time they could obtain the perfect metal. Not only were they working to form the perfect metal but also to form an elixir of life that would give them spiritual perfection.

Alchemy is the philosophical and primitively empirical study of physical and chemical transformations.

From Alexandria, alchemy quickly spread throughout the Western world. For the next fifteen hundred years, its many practitioners persuaded wealthy patrons to support them in their research with the promise that unlimited wealth was just around the corner—just as soon as they could convert lead or iron into gold or silver.
Don't think that because alchemists promised to convert base materials into precious metals that they were just con-artists promising something for nothing. Many alchemists truly believed that somewhere in nature there existed a procedure that would form precious metals from base materials. As they worked to find this procedure, they learned much about science, although they were not scientists in a modern sense. What alchemy provided to science was the experimental base from which modern chemical theories arose.
Because alchemists promised impossible chemical feats and did not follow modern scientific methods, historians often call this time period the “dark age” of science. However, their logic was quite sound. Their goal to change matter from one form to another was the result of looking at the many dramatic changes they could see in nature. For example, in a fire, wood simply “disappeared” leaving a small amount of ashes. Thus, as the alchemists observed dramatic changes such as this, they reasoned that it should be as easy to make other sorts of changes—such as changing lead into gold. They had no way of knowing that converting lead to gold involved a totally different type of change than that of using fire to turn wood into ashes.
The move toward modern chemistry took a long time. Physics

and medicine had provided an experimental base, but first the philosopher’s attitude toward nature had to change to a more inductive approach. That is, as René Descartes advocated, accept only those things that you can prove. Perhaps the biggest obstacle to modern chemistry was that of chemical identity. There was the need to replace the alchemist’s four elements with the understanding of atoms. Scientists needed to understand that the identity of a substance stayed the same even when that substance became a part of another substance. For example, copper is always copper even when mixed with zinc to form bronze, an alloy of copper. Robert Boyle (1627-1691) did much to do away with the view of the four elements, as well as to begin the study of gases (or air). Many scientists studied gases and isolated a number of pure gaseous compounds, but they all thought that these gases were either very pure air or very impure air. Antoine Lavoisier (1743-1794) finally moved chemistry into its own as a modern science with his recognition that oxygen was not just very pure air, it was a completely separate element.
Early in the nineteenth century, as modern chemistry began developing, chemists mostly ignored organic chemistry, viewing it as either medically or biologically related because nearly all the known

organic compounds were derived from living organisms, both plant and animal. An exception to this was Lavoisier, who was very interested in organic chemistry and considered it to be a part of chemistry. He looked at some organic compounds and found that they all contained carbon.
Because organic compounds were much more complex and unstable than the inorganic compounds being synthesized at the time, chemists had not knowingly prepared any and, in fact, thought that they were impossible to prepare. They believed that these compounds came only from living organisms. That is, the formation of the known organic compounds, such as urea, starches, oils, and sugar, required some “vital force” possessed by living organisms. Thus, organic chemistry became the study of compounds having a vital force, or vitalism. Some chemists felt that, because of the “vital force,” organic compounds did not follow the same rules that other compounds did.

Unaffected by the attitudes concerning organic chemistry, Michel Chevreul set out to study the composition of fats using the process of saponification, or soap making. In 1816, Chevreul separated soap into several pure organic compounds and found that these compounds were very different from the fat that he had started with. He had unwittingly dealt vitalism a major blow.
To do his work, Chevreul first made soap. He repeated the process many times making the soap from several sources of fat and alkali. Then, after he separated the soap from the glycerin, he separated the soap into its various fatty acids. He called these compounds fatty acids because he had isolated them from the soap, which he had prepared from animal fat. Previously people had not understood that a chemical reaction took place during the soap making process. They thought that soap was simply a combination of the fat and alkali. Unfortunately, other chemists took a long time to recognize the significance of Chevreul's work.
Another chemist that brought vitalism to its end was Friedrich Wöhler with his synthesis of urea in 1828—as he said, “without the use of a kidney”. The following reaction is the synthesis of urea using the starting material aqueous ammonium hydroxide and cyanogen.

NH4OH + (CN)2 = NH2CONH2

Ammonium Hydoxide + Cyanogen = Urea

Wöhler’s goal was not to synthesize urea; he was trying to make ammonium cyanate (NH4OCN), a compound he needed for his research. In fact, he may have become frustrated because he tried to

make ammonium cyanate by several different routes. He tried reacting silver cyanate with ammonium chloride, reasoning that silver chloride is insoluble and would precipitate from solution. He tried reacting lead cyanate with ammonium hydroxide. Finally, he tried aqueous ammonium hydroxide and cyanogen. But, every attempt led to the same white crystalline substance that was not the desired product.
Wöhler made his mark in the annals of chemistry by deciding to identify this unknown substance. Once he identified it as urea, he also recognized the importance of his discovery. As he wrote in 1828 “[The] research gave the unexpected result . . . that is the more noteworthy inasmuch as it furnishes an example of the artificial production of an organic, indeed a so-called animal substance from inorganic materials.”
Chevreul and Wöhler had forever altered the study of organic chemistry. As other chemists looked at the work that Chevreul and Wöhler had done, they saw that chemists could indeed synthesize compounds of carbon without a living organism. They then began making carbon compounds and studying them. Soon many chemists were achieving remarkable successes in the new art of the synthesis of organic compounds. Thus began the study of organic compounds.
Inevitably, someone would take these new developments from the organic chemistry research laboratory and find ways to market them. William Henry Perkin was the first to do so. In 1856, at the age of 18, while on vacation from London’s Royal College of Chemistry,

Perkin was working in his home laboratory. While naively attempting to make quinine, a task not accomplished until 1944, he accidentally synthesized the dye now called Perkin’s mauve. The next year, using money borrowed from his father, he built a factory and marketed the new dye. From there, he worked with coal tar and found that coal tar was a rich source of starting materials for a variety of new dyes.

Another step in the progress of organic chemistry was the drilling of the first oil wells in Pennsylvania in 1859. The oil pumped from those wells provided a new, cheap, and abundant source of carbon compounds. Today the petrochemical industry supplies the raw materials for thousands of different products including a variety of things from explosives and fuels to pharmaceuticals and agricultural chemicals.
In 1895, the Bayer Company of Germany established the pharmaceutical industry. Then in 1899, the company began marketing aspirin, as a result of the work of Felix Hoffmann. Hoffmann learned how to prepare aspirin from natural salicylic acid. For hundreds of years, people had chewed the bark of the willow tree to relieve minor pain. Willow tree bark contains the analgesic salicylic acid. Aspirin is superior to salicylic acid as an analgesic because it produces less irritation to the stomach and effectively treats the pain.

In the early days of chemistry, chemists learned a great deal about the simple compounds not usually found in living systems, but they learned very little about the organic compounds that are found in living systems. They were far too complex for the simple analytical tools available in the nineteenth century and the early twentieth century. Thus, progress was slow in understanding the chemistry of living systems. The subsequent development of powerful analytical tools allowed many insights into biologically important molecules and opened up new areas for scientific study.

Organic Acids and Bases

Organic acids and organic bases are acids and bases that contain a carbon skeleton. Within these categories are a number of classes of neutral proton acids and bases (that is, uncharged acids and bases.) The first part of this section examines the three main types of

neutral organic proton acids to see why they are acids and why they have widely different acid strengths. The second part looks at the two main types of neutral organic bases. The last part looks at positively charged carbon acids and negatively charged carbon bases.

Three main types of neutral organic Brønsted-Lowry acids are carboxylic acids, phenols, and alcohols. Each of these three functional groups has an —OH group. Each is acidic because of the electronegativity difference between the oxygen and the hydrogen involved in the O—H bond. The differences in acid strength of the three functional groups are due to the differences in stability of the conjugate base. The most acidic of the three groups are the carboxylic acids. Carboxylic acids are characterized by the presence of the carboxyl group:

 

Carboxylic acids are among the most acidic of the neutral organic acids, but they are rather weak acids. For example, the pKa of acetic acid, a common carboxylic acid, is 4.8, indicating that only a small portion of the molecules of acetic acid ionize in an aqueous solution. In contrast, mineral acids, such as HCl, with a pKa of –7.0, and HNO3, with a pKa of –5.2, completely ionize in aqueous solutions. Although carboxylic acids are weaker than mineral acids, they are the strongest of the neutral organic acids that you will study.

The reason for the relative strength of the carboxylic acids is the conjugate base is resonance-stabilized, which makes it a weak base.

 

 In the carboxylate ion the negative charge spreads over the two oxygen atoms as a resonance hybrid. This reduces the energy of the anion and makes the carboxylic acid more acidic.
Another way of visualizing the reason for the acid strength of carboxylic acids is to look at the molecular orbital system of the carboxylate ion. The carboxylate ion includes three p orbitals that contain a total of four electrons. The overlap of these three p orbitals results in a three-centered π molecular orbital system.

The carbon is joined to each oxygen atom by the equivalent of ½ of a π bond. Each oxygen atom bears ½ of the negative charge.

 

The second main type of neutral organic acids are the phenols. Phenols are much less acidic than carboxylic acids. An —OH group attached to an aromatic ring is characteristic of phenols:

 

Phenol has a pKa of 10.0 in aqueous media, indicating that in water only a very small portion of it ionizes.

 

Phenols are moderately strong organic acids because their conjugate bases are resonance-stabilized. The aromatic ring is involved in resonance, which stabilizes the negative charge.

 

However, this stabilization is less significant than it is for carboxylic acids for two reasons: the resonance stabilization of the phenolate ion disrupts the aromaticity of the aromatic ring, and the resonance stabilization places a negative charge on the carbon atoms, which, when compared to oxygen, are not very electronegative.
The third type of neutral organic acids are alcohols. An —OH group attached to an alkyl group characterizes an alcohol:

 R---OH

Alcohols are much less acidic than phenols. In fact, most alcohols have an acid strength slightly lower than that of water.

 

 

A typical alcohol has a pKa of 15 to 18 in aqueous media, indicating only a very small amount of ionization. Alcohols have such a low acidity because there is no resonance stabilization of the conjugate base.
This section discusses only two of the many types of neutral organic bases: amines and ethers. The primary characteristic of neutral organic bases is they contain one or more pairs of nonbonding electrons. These pairs of electrons are available to donate to a Lewis acid or to accept a proton when the base is acting as a Brønsted-Lowry base. The more available the pair of electrons, often called a lone pair, the stronger the base. Any molecule with a lone pair of electrons can act as a base.
The most common of the organic bases are the amines. Amines are derivatives of ammonia (NH3) and most are weak bases in aqueous media.

The pKa of methyl ammonium ion is 10.6 meaning that the methyl ammonium ion is a relatively weak acid. Thus, methylamine is a moderately strong base.
Amines are stronger bases than other neutral organic bases because the nonbonding pair of electrons on the nitrogen is more available than nonbonding pairs of electrons on other neutral organic bases. The atoms that are found in these other neutral organic bases are oxygen, sulfur, or the halogens. Nitrogen holds its electrons less tightly than these other atoms, so its compounds are the stronger bases. Figure 5.3 illustrates the structure of an amine.

Figure 5.3. Structure of the amine nitrogen.
Ethers, the second type of neutral organic bases, have the general structure ROR′. Ethers are weak bases in aqueous media. In fact, they are so weak that they do not appreciably protonate, or accept a proton, even in 1 M HCl. The pKa of the conjugate acid of ethyl ether is –3.8. A pKa of this magnitude indicates that water is a better base than is an ether.
In nonaqueous media, ethers are good Lewis bases, forming stable complexes with Lewis acids. The ability to form stable complexes is extremely important in organic reactions. For example, in organic synthesis, chemists widely use the complex of BH3 with the cyclic ether tetrahydrofuran:

The third category of organic acids and bases discussed in this section are the positively charged acids and the negatively charged bases. Positively charged acids are electron-deficient. That is, they are organic acids that contain a carbon without an octet of electrons. The most significant electron-deficient organic acid is the carbocation (formerly called a carbonium ion). Carbocations are very reactive reaction intermediates, so chemists seldom observe them directly. A carbocation is a Lewis acid because, without a full octet of electrons, it is electron-deficient and "needs" electrons. As a result of this need for electrons, it reacts with the first available Lewis base—although it prefers a hard one because it is a hard acid. As Figure 5.4 shows, the positively charged carbon forms three sp2 hybridized bonds in a plane with an empty p orbital perpendicular to that plane. Chapter 12 examines nucleophilic substitution reactions that involve carbocations.

The negatively charged organic base discussed in this section is the carbanion. A carbanion has bonds to three other atoms and one pair of nonbonding electrons. The structure of a carbanion is much like the structure of an amine (See Figure 5.5). Because carbon is not very electronegative, it holds these nonbonding electrons loosely. Thus, a carbanion is a strong base. (Chapters 19 and 20 cover carbanion reactions extensively.)

Now that you have seen the various types of organic acids and bases, Section 5.5 examines the factors that modify the strength of the specific acids and bases.

Polarizability

Polarizability means the ability of an atom to have a distorted distribution of electrons.

Charge density

Charge density is the volume of space occupied by a charge. A large ion has a lower charge density than a small ion does.

Hardness or softness

Hardness or softness is a qualitative measure of the reactivity of acids and bases. Hard or soft is independent of strength or weakness of acids and bases.

Hard and Soft Acids and Bases

The ease with which an acid-base reaction occurs depends on the strength of both the acid and the base. Strong acids and bases are generally more reactive than weak acids and bases. However, the direction of the reaction and the stability of the products often depend on another quality—the hardness or softness of the acid and base. Although chemists have not created a quantitative measure to describe the qualities that makes an acid or base hard or soft, they do describe them qualitatively. As you look at the following list of characteristics that describe hard and soft acids and bases, remember that an acid has an empty orbital and an unfilled valence shell, and a base has in its valence shell a pair of nonbonding electrons that is available for donation.

Soft Acids. For soft acids, the electron-pair acceptor atoms are large, have a low positive charge density, and contain unshared pairs of electrons in their valence shells. The unshared pairs of electrons are in the p or d orbitals. Also, soft acids have a high polarizability and a low electronegativity. In organic chemistry, the soft acids usually include only the halogens, phosphorus, and sulfur compounds.

Hard Acids. For hard acids, the acceptor atoms are small, have a high positive charge density, and contain no unshared pairs of electrons in their valence shells. They have a low polarizability and a high electronegativity. The hydrogen ion is a good example of a hard acid.

Soft Bases. For soft bases, the donor atoms hold their valence electrons loosely. They have high polarizability, low negative charge density, and low electronegativity. Common soft bases are the cyanide (-CN) and iodide (I-) ions.
Hard Bases. For hard bases, the donor atoms are small, have a high negative charge density, and hold their valence electrons tightly. They have a low polarizability and a high electronegativity. The hydroxide ion is a good example of a hard base.
To visualize a polarizable atom, imagine that an atom is a large floppy ball and you are holding it cupped in both hands. The ball tends to be spherical, but, as you shift one hand higher than the other, it easily deforms. If you raise your left hand a little, the portion of the ball in your right hand becomes larger. Then, if you raise your right hand a little, the portion of the ball in your left hand becomes larger. A polarizable atom shifts its electron density from one part of the atom to another: at one instant, one portion of the atom has the higher electron density; then the next instant, another portion has the higher electron density.

For the concepts of hardness or softness of acids and bases to be of value to you, you must be able to differentiate between them. To do this, your most useful tool is the periodic table. A general rule is that hardness goes to softness moving from the top to the bottom on the periodic table because the size of the atoms increases with increasing numbers of electrons. A larger acid or base has a lower charge density and is more polarizable. For example, base softness in Group VII A on the periodic table decreases in this order: I- > Br- > Cl- > F-. Also, the elements on the left side tend to be acids, and elements on the right side tend to be bases. In this way, chemists approximately rank acids and bases in order of hardness or softness. Base softness within a period on the periodic table decreases in order of increasing electronegativity; for example, -CH3 > -NH2 > -OH > F.
Hardness and softness are difficult to quantify. Rather than relying specifically on these types of sequences, chemists divide acids and bases into three groups: (1) hard acids or bases, (2) soft acids or

bases, and (3) borderline acids or bases. Table 5.2 lists a few examples of each category.

H⊕ is a hard acid because it has no electrons and has a high positive charge density. The HO- ion is a soft base because it has a pair of electrons and only one proton, so it holds the electrons rather loosely. Thus, it is quite polarizable and soft.