ORGANIC CHEMISTRY
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Transcript of ORGANIC CHEMISTRY
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ORGANIC CHEMISTRY
Chapter 1: Introduction
Congratulations, you are taking Organic chemistry. It is likely that you are a science major, in a class of
students with a wide range of interests and career choices. Why is organic chemistry important? The
answer lies in the fact that every aspect of life, mammalian and non-mammalian as well as plant and microscopic
life, involves organic chemistry. In addition, many of the products we use every day (pharmaceuticals; plastics;
clothing; etc.) involve organic molecules. Organic chemistry holds a central place in chemical studies because
its fundamental principles and its applications touch virtually all other disciplines. Several years ago, a T-shirt
at an American Chemical Society meeting (in Dallas) sported the logo "Chemistry: The Science of Everything."
Organic chemistry is certainly an important player in that science.
Most Organic chemistry textbooks have a brief section to describe how Organic chemistry developed as a
science. I was a graduate student when I first read an Organic chemistry book that presented some historical
facts as part of the normal presentatin of facts. This was Louis Fieser's (USA; 1899-1979???) Advanced
Organic Chemistry book.1 This treatment gave perspective to my studies and helped me to better understand
many of the concepts. I believe that putting a subject into its proper context makes it easier to understand, so I
am introducing an abbreviated history of Organic chemistry as the beginning to this book. I will include
material from Fieser's book and also from an outstanding book on the history of Chemistry by Leicester.2 It is
important to remember the great Organic chemists of the past, not only to see how their work is used today but
to understand that it influences how we do chemistry.
1.1. A Brief History of Organic Chemistry
Humans have been using practical applications of chemsitry for thousands of years. The discovery and use
of folk medicines, the development of metallurigal techniques, and the use of natural dyes are simple examples.
For most of human history, humans were able to use chemcials without actually understanding the science
behind them. Organic chemistry became a defined science (the chemistry of carbon compounds) in the 19th
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century, but organic compounds have been known and used for millennia. Plants have been "milked," cut,
boiled, and eaten for thousands of years as folk medicine remedies, particularly in Africa, China, India, and
South America. Modern science has determined that many of these
NH
HO
H
N
H3CO
H
1
OH
CH3
CH3
CH3
CH3 CH3
2
plants contain organic chemicals with effective medical uses, and indeed many of our modern medicines are
simply purified components of these plants or derivatives of them made by chemists. In one example, the bark
of Cinchona trees was
OH
O
O
H
OH
HO
HO
HO
OH
RO
O
3
O
CH34a R = H 4b R =
chewed for years to treat symptoms of malaria, for example, and it was later discovered that this bark contains
quinine (1), which is a modern medicine Ancient Egyptians ate roasted ox liver in the belief that it improved night
vision. Later it was discovered that ox liver is rich in Vitamin A (2), a chemical important for maintaining healthy
eyesight. An ancient antipyretic treatment (this means that it lowers a fever) involved chewing willow bark and it
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was later discovered that this bark contained the glycoside salicin (3), a derivative of salicylic acid (4a).
Eventually, we learned how to make new organic molecules rather than simply isolating and using those that were
found nature. In the mid-19th Century a new compound was synthesized (chemically prepared from other
chemicals) called acetylsalicylic acid (4b), better known as aspirin, and it was found to be well tolerated by
patients as an effective analgesic (this means that it reduces some types of pain). These few examples are meant
to represent the thousands of folk medicine remedies that have led to important medical discoveries. All of these
involve organic compounds.
The symbols used (1-4) to represent the chemicals require some explanation. Each "line" is a chemical
bond. Therefore, C—C is a carbon-carbon bond and — is used as a shorthand notation to represent that bond.
Each "intersection of bonds" such as [ ] is a carbon atom. Various groups can be attached to these carbon
atoms (OH, NH2, CH3, etc.). The symbol C—N is a carbon-nitrogen bond, C—O is a carbon oxygen bond,
and O—H is an oxygen-hydrogen bond. These chemical structures will be explained in greater detail in
chapter 2.
Plants provided ancient humans with many organic chemicals or mixtures of chemicals that were useful for
purposes other than medicine. Ethyl alcohol (5) has been produced by fermentation of grains and fruits, and
H C
H
H
C
H
H
O
H
5
consumed for thousands of years in various forms. In ancient Bengal (part of
India), in Java, and in Guatemala, plants provided a deep blue substance used to
color clothing. In recent times, the main constituent was found to be indigo (6).
The ancient Phoenicians used an extract from a snail (Murex brandaris) found off
the coast of Tyre (now called Lebanon) to color cloth. It was beautiful and very expensive and the dye was
called Tyrian purple. It was so prized that Roman Emperors used it to color their clothing, and for many years
no one else was permitted to wear this color (hence the term "born to the purple"). The actual structure of the
organic chemical Tyrian purple is 7. Notice that the only difference between indigo and Tyrian purple is the
presence of two bromine atoms in the latter. Structural differences that on the surface appear to be minor can
lead to significant changes in the physical properties of organic compounds, such as color.
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N
N
O
OH
H
N
N
O
OH
H
Br
Br
6 7
Organic chemicals have also been used in an unethical manner. The plant Belladona (Deadly Nightshade)
has been used for centuries as a poison. It was made famous by wealthy people in Medieval Europe who used
an extract of this plant to "do away" with rivals and enemies. The principle "poison" in this plant was found to
be atropine (8), which is also found in the stems of tomato plants (not the tomato itself).
These few examples show that organic chemicals have been important to humans for a very long time. For
most of this time, however, humans did not know the actual chemical structures of these compounds, or even
that they were dealing with discreet molecules. What they did know, however, was that a multitude of materials
could be obtained from natural sources, primarily from living organisms. In the following paragraphs, a few of
the chemists who advanced Organic chemistry as a science are introduced. This is certainly not an exhaustive
list but it "hits the high points."
N
H
O
O
OH
CH3••
8
As pointed out above, natural materials have been used for
many years. It was not until the 18th Century that people began
to look for specific chemicals in these natural materials. One of
the first to look for chemicals was Carl Wilhelm Scheele
(Sweden; 1742-1786), who isolated acidic components from
grapes and lemons by forming precipitates with calcium or lead
salts, and then adding mineral acids to obtain the actual
compounds. The compound from grapes is now known to be
tartaric acid (9) and that from lemon is now known to be citric
acid (10). Scheele also isolated uric acid (11) from urine.
5
HOOCCOOH
COOH
HO COOH
HOOC
OH
OH
9 10
N
N N
N
H
O
HH
O
H
O
11
O
HO
HO
N
CH3
H
HH
12
HO
CH3
CH3
H
H H
H3C
13
This practice of isolating specific compounds (now known to be organic compounds) from natural sources
was continued for many years (it continues today). Such compounds are called "natural products." Friedrich
W. Sertürner (Germany; 1783-1841), for example, isolated a compound from opium extracts in 1805. This is
now known to be morphine, 12. In 1815, Michel E. Chevreul (France; 1786-1889) was able to isolate a
crystalline material now known to be cholesterol (13) from animal tissues. In 1820, Pierre J. Pelletier (France;
1788-1842) and Joseph Caventou (France; 1795-1877) isolated a material they called an alkaloid (an alkali-like
base) now known to be strychnine (14). Alkaloids are a large group of diverse compounds that contain
nitrogen and are primarily found in plants. Although difficult to define because of their structrual diversity,
alkaloids are commonly assumed to be basic nitrogenous compounds of plant origin that are physiologically
active.
Clearly, an early step in Organic chemistry was to isolate pure compounds from natural sources and
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N
O
N
O
H
H
HH
H
14
then attempt to identify them. Initially, the compounds were
purified (usually by crystallization) and characterized as to their
physical properties (melting point, boiling point, solubility in
water, etc.). It was not until much later (late 19th century and
early 20th century) that the structures of most of these
compounds were known absolutely. Justus Liebig (Germany;
1803-1873) perfected the science of organic analysis based on
the early work of Antoine Lavoisier. Late in the 18th Century,
Lavoisier (France; 1743-1794) made a monumental contribution to the science of chemistry that was critically
important to understanding organic chemistry. He first discovered that air was composed mainly of oxygen
(O2) and nitrogen (N2). He then burned natural materials in air and discovered that carbon in the material was
converted to carbon dioxide (CO2) and the hydrogen in these compounds was converted to water (HOH). By
trapping and weighing the carbon dioxide and the water, he was able to calculate the percentage of carbon and
hydrogen in molecules. Since we now know that organic molecules are composed mainly of carbon and
hydrogen, this elemental analysis procedure was, and is an invaluable tool for determining the structure of
organic molecules (see chapter 2, section ??).
In 1807, a Swedish chemist named Jöns J. von Berzelius (Sweden; 1779-1848) described the substances
obtained from living organisms as organic compounds, and he proposed that they were composed of only a
few selected elements, including carbon and hydrogen. Up to this point, all organic compounds had been
isolated as products of "life processes" from living organisms (hence the term organic). Early in the 19th
Century, Berzelius and Charles F Gerhardt (France; 1816-1856) described what was known as the vital force
theory that subscribed to the notion that "all organic compounds can arise with the operation of vital force
inherent to living cells." The vital force theory was widely believed at the time, but in 1828 Friedrich Wöhler
(Germany; 1800-1882)
N
H
H H
H
O C NH2N
O
NH2
HEAT
15 16
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synthesized (prepared from other chemicals) the organic molecule urea (16, a component of urine and also a
major component of bird droppings which have been used for centuries as fertilizer from chemicals that had not
been obtained from living sources. When he heated ammonium cyanate (15), the product was urea (16). This
work, along with that of others, was contrary to the vital force theory because it showed that an organic
compound could be produced from a "non-living" system. However, it was not until Marcellin Berthelot
(France; 1827-1907) showed that all classes of organic compounds could be synthesized that the vital force
theory finally disappeared.
N
N
N
N
NH
H3C
H2NH2N
N
H
CH3
+
17 18
Synthesis of organic molecules began in the mid-19th Century and many compounds were prepared.
Hermann Kolbe (Germany; 1818-1884) prepared ethane (CH3CH3) by electrolysis of potassium acetate and
Sir Edward Frankland (England; 1825-1899) prepared butane (CH3CH2CH2CH3) from iodoethane
(CH3CH2I) and zinc (Zn). Charles A. Wurtz (France; 1817-1884) discovered amines in 1849 and August W.
von Hofmann (Germany/England; 1818-1892) prepared many amines as well as their ammonium salts.
Amines contain nitrogen in addition to carbon and hydrogen. At about the same time, Alexander W.
Williamson (England; 1824-1904) showed how ethers (ethers contain the C-O-C linkage) could be prepared
from the potassium salt of an alcohol (contains a C-O-H unit) and an alkyl iodide (contains a C-X bond, where
X is a halogen). The first secondary alcohol (a molecule with an OH attached to a carbon atom attached to two
other carbon atoms) was prepared by Charles Friedel (France; 1832-1899) in 1862 and the first tertiary alcohol
(a molecule with an OH attached to a carbon atom attached to three other carbon atoms) was prepared by
Alexander M. Butlerov (Russia; 1828-1886) in 1864. The nomenclature for this compound and all others will
be described in chapter 3.
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At about this same time (1863), William H. Perkin (England; 1838-1907) prepared the first commercially
useful synthetic dye (made by humans), mauve. He reacted pseudomauvein (17) and mauveine (18) and
obtained a dye with a purple color that had not been previously isolated from nature. In 1869, the synthesis of a
natural dye was reported by Carle Graebe (Germany; 1841-1927) and Carl Liebermann (Germany; 1882-
1914). They prepared the natural dye alizarin (20) from anthracene (19, obtained from petroleum distillates) by
the sequence shown. Adolf von Baeyer (Germany; 1835-1917) was the first to synthesize the dye indigoO
O
O
O
O
O
Br
Br
OH
OH
19
20
HNO3 Br2
KOH
(6). Aspirin (4) was first prepared in the mid-19th century and commercialized later in that century. The
synthesis of the various dyes and of aspirin were enormously important to the economies of both England and
Germany in the late 19th and early 20th centuries. Clearly, a major step in organic chemistry involved the
chemical synthesis of the compounds that could be isolated from nature, and then expanding this to prepare
compounds that were not known in nature. Once accomplished, these products were commercialized and this
led to the development of chemical industries.
H C
H
H
H H H
H
H
C ••
••
••••
21 22
By the middle of the 19th Century, chemists were
beginning to understand that organic molecules were discreet
entities and they were able to prepare them. Determining the
structures of these compounds (how the atoms are connected
together), however, posed many problems. The idea of valence was introduced by C.W. Wichelhaus (1842-
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1927) in 1868. Butlerov (see above) introduced the term "chemical structure" in 1861. There was no accepted
method to determine how atoms in a molecule were arranged in a molecular structure. In 1859, August Kekulé
(German; 1829-1896) "pushed" the idea of discrete valence bonds. It was actually Jacobus H. van't Hoff
(Netherlands; 1852-1911) and Joseph A. Le Bel (France; 1847-1930) who deduced that when carbon appeared
in organic compounds, it was connected to four other atoms and the shape of teh atoms around carbon was
tetrahedral. This means that carbon is joined to other elements by four chemicals bonds, as in 21 (methane),
where each line connecting the atoms represents a chemical bond (see chapter 2, section ?? for a full
explanation of these "lines"). In 1859, however, it was not really known how these four other atoms were
attached. The concept of a bond was vague and largely undefined. It was not until 1916 that Gilbert N. Lewis
(USA; 1875-1946) introduced the concept of a bond formed by sharing electrons. He called a bond composed
of shared electrons pairs a covalent bond. Erich Hückel (Germany; 1896-xxxx) developed theories of bonding
and orbitals and also speculated on the nature of the C=C unit, although it was Alexander Crum Brown
(England; 1838-1922) who first wrote a "double bond" for ethylene in 1864. It was Emil Erlenmeyer
(Germany; 1825-1909) who wrote acetylene with a triple bond (a C≡C unit) in 1862.
Understanding covalent bonds allows us to understand how organic molecules are put together. Returning
to methane, the four bonds to carbon could now be represented as 22, where each ":" represents two shared
electrons. A structure such as 22 is commonly known as a Lewis electron dot structure. In 1923, Lewis came
up with the idea that a molecule that accepts an electron pair should be called an acid and a molecule that
donates an electron pair should be called a base. These are called Lewis acids and Lewis bases to this day.
Clearly, understanding where electrons are in an organic molecule and how they are transferred is important in
understanding both the structure of molecules and also their chemical reactions. In 1925 two physicists, W.
Karl Heisenberg (Germany; 1901-1976) and Erwin Schrödinger (Austria; 1887-1961) described the orbital
concept of molecular structure. In other words, they introduced the idea of orbitals in chemistry and bonding
(see chapter 2). Today we combine these ideas by saying that orbitals contain electrons, and orbital interactions
control chemical reactions and explain chemical bonding. Clearly this area of organic chemistry involved
identifying the chemical structure of organic molecules and relating that structure to organizations of atoms held
together by shared electrons.
The spatial relationships of atoms and groups within these compounds are indicated by the solid and dashed
lines (indicating "up" or "down" respectively in the two-dimensional structure). This three-dimensional
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orientation is called the stereochemistry of that atom or group. It was not until the middle and late 20th century
that the stereochemistry of these compounds could be accurately determined. This was a very important
development because the concept of sterochemistry is almost as old as organic chemistry itself.. In 1848, Louis
Pasteur (France; 1822-1895) found that tartaric acid existed in two forms that differed only in their ability to
rotate plane polarized light in different directions (they are examples of stereoisomers). Because of this
difference, the two forms of tartaric acid are considered to be different compounds. Van't Hoff found that
alkenes existed as a different type of stereoisomer. Pasteur, Van't Hoff and Le Bel are widely considered to be
the founders of stereochemistry. Emil Fischer (Germany; 1852-1919) studied carbohydrates in the late 19th
and early 20th centuries and made many major contributions not only to understanding their chemistry, but also
their structures and stereochemistry. Many scientists have helped develop this concept into the powerful tool it
is today, including John Cornforth (Austria/England; 1917-), Vladimir Prelog (Yugoslavia/Switzerland; 1906-),
and Donald J. Cram (USA; 1919-).
NH3C
H3C CH3
OH
CH3
O
23 24
Over the years, the molecules that could be synthesized have become increasingly complex. Apart from
simply synthesizing the molecules, this research also contributes to the development of new chemical reactions,
as well as new chemical reagents (molecules that induce a chemical transformation in another molecule). It is
useful to examine a handful of syntheses of organic molecules to show the structural challenges, and also how
more sophisticated methods and reagents might be necessary. The choice of the compounds prestend here is
largely due to the book3 by Elias J. Corey (USA; 1928-) who described the theory and practice of modern
organic synthesis. In 1904, William H. Perkin Jr. (England; 1860-1929) synthesized α-terpineol (23) and in
1917, Sir Robert Robinson (England; 1885-1975) synthesized tropinone (24). In 1929, Hans Fischer
(Germany; 1881-1945) synthesized protoporphyrin (hemin, 25) and quinine (1) was synthesized in 1944 by
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Robert B. Woodward (USA; 1917-1979) and William von E Doering (USA; 1917-). Hemin contains the unit
found in hemoglobin, the oxygen-carrying component of blood, and quinine is an effective anti-malarial drug.
In 1951, Sir Robert Robinson and Robert B. Woodward synthesized strychnine (14), Gilbert Stork
(Belgium/USA; 1921-) synthesized cedrol (26) in 1955, Woodward synthesized reserpine (27) in 1956, and
Elias J. Corey synthesized helminthsporol (28) in 1963. Strychnine is a poisonous alkaloid that acts as an
analeptic (stimulates respiration—used in acute respiratory failure). Cedrol is an odoriferous component of
cedar wood oil, considered to be rare and valuable in ancient times. Reserpine has been used to treat
hypertension because it lowers high blood pressure and it also acts as a tranquilizer. Helminthsporol is a
natural plant-growth regulator isolated from Helminthospronium sativum. The structural complexity of these
molecules consistently increased
N
N
N
N
CH3
H3C
H3C
COOH
CH3
COOH
Fe
25
CH3
HOCH3
H
H3CCH3
26
12
N
N
H
H3COH
H
H
OCH3
O
O
OCH3
OCH3
OCH3
O
H3CO
27
H3C
H3CH
CH3O
H
H
CH3
OH
28
over the years. This trend continues with syntheses of organic molecules
reported today. Several molecules synthesized in the last few years
include taxol (29) by Robert Holton (USA; 1944-), avermectin B1a (30)
by Samuel Danishefsky (USA; 1936-), and naphthyridinomycin (31) by
David Evans (USA; 1941-). Taxol is a naturally occurring compound
used to treat cancer. Avermectin B1a is a natural product with potent
anthelmintic properties. It exerts its insecticidal activity by interfering with
invertebrate neurotransmission. Naphthyridinomycin is also a natural product that is a broad spectrum
antibiotic. There have been a huge number of syntheses reported in the last fifty years that have contributed
enormously to Organic chemistry. Notice that the stereochemistry of these molecules is included. Preparing
compounds with only that particular arrangement of atoms and groups can be most challenging. There is no
question that another area of organic chemistry has involved developing chemical reactions to the point that
virtually any molecule can be prepared. Understanding chemical reactions, the reagents used in those reactions,
and the developing new reagents and reactions is a critical part of the synthesis of organic molecules (including
those shown here), and this has profound influences in all areas of organic chemistry.
Prior to the late 1940's and 1950's, chemists did not really understand how chemical reactions occurred. in
other words, what happened during the bond making and bond breaking process. Understanding these
processes, now called reaction mechanisms, required an enormous amount of work in the period of the late
1940's throughout the 1960's, and it continues today. The pioneers in this area include Frans Sondheimer
(Germany; 1926-), Saul Winstein (Canada/USA; 1912-), Sir Christopher. K. Ingold (England; 1893-), John
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O
H3C O
O
O
CH3OH
O
H
O
H
O
N
O
H OH
O
O
CH3
O
CH3
HO
29
D. Roberts (USA; 1918-), Donald J. Cram (USA; 1919-), Herbert C. Brown (England/USA; 1912-), George
A. Olah (Hungary/USA; 1927-), and many others. They first studied reactions that were ionic in nature and
identified many types of reactive ionic intermediates such as carbocations or carbanions, and another type of
intermediate called carbon radicals. An intermediate is a transient and usually high energy molecule that is
formed initially and then transformed into a final, and more stable product. The nature and structure of these
intermediates were determined, and methods were developed to ascertain the presence of these intermediates and
also how long they were present in the reaction (in other words, how reactive they were). The idea of reaction
kinetics was developed so that it
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CH3
O
OO
O
H
OH
O
O
H3C
H
CH3
OH
CH3
OO
OH
HH3C
H3CO
H3CO
HO
H3C
CH3
30
could be determined how fast products were formed and reactants disappeared. This information gave clues as
to how the reaction proceeded and what, if any, intermediates were involved. Roald Hoffman (Poland/USA;
1937-) and Kenichi Fukui (Japan; 1918-), along with Robert Woodward (USA; 1919-1970), described the
N
N
N
O
O
O
H3CO
H3C CH3
H
H
H
H
OH
OH
31
concept of frontier molecular orbitals and the use of orbital symmetry to explain many reactions that did not
appear to proceed by ionic intermediates. The concept of reaction mechanism allows a fundamental
understanding of how organic reactions work and it is a relative late-comer to the study of Organic chemistry.
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It is perhaps the most important aspect however, because understanding the mechanism of chemical reactions
allows chemists to predict products and reaction conditions without having to memorize everything.
Finally, how does a chemist know the structure of any organic chemical? How are organic
chemicals isolated? In early work, inorganic materials such as metal salts and acids or bases were added to
force precipitation of organic compounds. In other cases, liquids were distilled out of "organic material" or
solids were crystallized out. In the 1950's, the concept of chromatography was developed by A.J.P. Martin
(USA; 1910-) and Richard Synge (England; 1914-) and this allowed chemists to conveniently separate
mixtures of organic compounds into individual components. Light has always been an important player in
chemistry. In the early-mid 20th Century, ultraviolet light was shown to interact with organic molecules at
certain wavelengths. In the 1940's and 1950's, molecules were exposed to infra-red light, and again molecules
absorbed certain wavelengths. Identification of which wavelengths of light were absorbed and correlating this
with structure was a major step in the identification of organic molecules. Even today, ultraviolet spectroscopy
and infrared spectroscopy are major tools for the identification of organic compounds. In the 1950's and
especially in the 1960's, it was discovered that organic molecules interacted with electromagnetic radiation with
wavelengths in the radio signal range, if the molecules were suspended in strong magnetic fields. Initially, it
was discovered that hydrogen atoms interacted in this manner and chemical differences could often be
discerned. If the different hydrogen atoms in an organic molecule could be identified, the chemical structure
could be puzzled together, giving a major boost to the identification of organic compounds. This technique is
now known as nuclear magnetic resonance spectroscopy (NMR) and is one of the most essential tools for an
organic chemist. With the power of modern computers we can now use NMR to determine the number and
type of carbon atoms, nitrogen atoms, fluorine atoms, lithium atoms, and many more in an organic molecule.
To do this, we use stable natural isotopes of these atoms; 13C, 15N, 19F, 6Li, etc. It is noteworthy that the
important modern tool of medicine (MRI or magnetic resonance imaging) is in reality an NMR technique
applied to medicine and it was developed in the 1970's. In the 1950's and especially in the 1960's and 1970's, it
was discovered that bombarding an organic molecule with a high energy electron beam induced fragmentation
of that molecule and identifying these fragments gave important structural formation. This technique is known
as mass spectrometry. Other tools are constantly being developed and each of the techniques mentioned has
"cutting edge" methodology that allows a chemist to probe very complex structures. This is typified by the use
of x-ray technology, known for many years, to identify crystalline molecules. When the x-rays interact with a
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molecule with a distinct crystal structure, the x-ray scattering patterns can often be analyzed to provide clues to
its chemical structure. With modern computer technology, a picture of the structural features of a molecule can
be produced. With modern electron tunneling microscopes, pictures of atoms have been made. This aspect of
organic chemistry is vital and on-going. Using these techniques to give more information, and developing new
techniques is another major area of organic chemistry.
32 33
HO
N
O
O H
HH
O
N
H
HO
OH
HO
N
O
NH2
1.2 The Variety and Beauty of Organic Molecules
Section 1.1 described how organic chemistry came to be a science. Why is it important? You are alive
because of chemical reactions involving organic molecules. Your DNA and the proteins in your body are
organic molecules. Proteins are large structures composed of individual amino acids such as serine (32) and
DNA is made up of individual units called nucleotides such as cytosine, 33. If you are blinking an eye while
reading, or moving your arm to turn the page, that nerve impulse from your brain was induced by one of several
important organic molecules called neurotransmitters. One important neurotransmitter is acetylcholine
CH3
CH3
CH3
CH3 CH3
34 35
H3C
N
O
CH3
CH3
OCH3
OH
17
(34). If you see this page, the light is interacting with a photopigment in your eye called rhodopsin, which
releases retinal (35) upon exposure to the light. Retinal reacts with a lysine fragment (another amino acid) of a
protein as part of the process we call vision. Note the similarity of retinal to Vitamin A (2), which is simply the
reduced form of 35. What you see, at least the color associated with what you see, is usually due to one or
more organic molecules. If the trees and grass in your yard appear green, one of the chemicals responsible is
called chlorophyll a, 36. The ------ in 36 means the N is coordinated to Mg rather than formally bonded to it.
There are many other things about human physiology that involve organic
N
N
N
N
CH3
H3C
H3C CH3
Mg
36
O
O
phytl-OO
OCH3
OOH
37
HO O
CH3 OH CH3OH
CH3 HH
H H H H
38 39
chemistry. A silly one involves the odor that is noticeable if your feet have not been washed recently. They are
exuding a chemical called butyric acid (37), among other things, with obvious social effects. There are more
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fundamental physiological influences of organic chemicals. If you are female, one of the principle sex
hormones for your gender is β-estradiol (38) but if you are male, your principle sex hormone is testosterone
(39). It should be noted that each sex has both of these hormones (and others), but in quite different amounts.
Notice that the chemical structures of estradiol and testosterone are somewhat similar.
Smells are a very important part of life. What are smells anyway? They are the interaction of organic
chemicals with olfactory receptors in your nose. If you walk into a garden and smell a rose, a chemical called
geraniol (40) is interacting with those olfactory receptors. If your dog or cat has ever been sprayed by aOH
H3C
CH3
CH3
40
skunk, many organic chemicals are part of the spray, including the
mercaptan 41. Clearly, this is an unpleasant smelling organic chemical
and your animal was very unhappy. If you are wearing musk cologne,
you are probably wearing 42 (muscone) if it is natural musk (scraped
from the hind-quarters of a male musk deer). If you are wearing a
jasmine perfume, it probably contains jasmone (43), which is part of the
essential oil of jasmine flowers. These are clearly more pleasant smelling organic molecules.
41 42 43
SH
CH3H3C
O
CH3
O
CH3
CH3
44 45
O
19
Many things around you involve subtle uses of organic molecules. If you see a housefly, know that they
use a chemical called a pheromone (in this case muscalure, 44) in order to attract a mate and reproduce. The
American cockroach (hopefully there are none in your dorm) similarly attracts a mate by exuding 45. To
control insect pests, we sometimes use the pheromone of an insect pest to attract it to a trap. Previously, we
have sprayed insecticides such as DDT (46) or PCB(47) directly on plants, often with
46 47
CCl3
Cl
Cl
Cl
Cl Cl
Cl
devastating environmental consequences. Nonetheless, without pest control and plant growth promoters, we
probably could not feed our enormous population. Understanding these chemicals, how they work and when to
use them is obviously important and requires a thorough understanding of organic chemistry. It is also
important to be able to develop new and environmentally safer compounds.
48 49
O
HO
OH
OH OH
OHH
H
H
H2N
O
N
H
O
OCH3
OOH
20
50 51
CH3
H3C CH3
CH3
H3CO
HO
N
H
O
H3C
CH3
Eating is obviously an important part of life, and the taste of the food is important. What are tastes? They
are the interaction of organic chemicals (and other chemicals as well) with receptors on your tongue. Are you
drinking a soda? Does it taste sweet? If it is not a diet soda, it probably contains a sugar called fructose
(48), but if it is a diet drink it probably contains the "sugar substitute" aspartame, 49. Different chemicals in
different foods have their own unique tastes. Do you like the taste of ginger? The active ingredient that
gives ginger its "spicy" taste is an organic molecule called zingiberene (50). Do you like the taste of red
chili peppers? If so, the "hot" taste is due to an organic chemical called capsaicin, 51. In both cases, these
chemicals interact with your taste buds to produce that characteristic taste. Capsaicin is also used in some
cremes used to alleviate symptoms of arthritis and muscular aches.
52 53
HO
N
H
O
CH3
H2N
O
O
NH
Cl
Most medicines used today are organic chemicals. Clearly, this is of vital importance to the health and well-
being of humans. Do you have a headache after reading all of this stuff? If so, you are probably looking
for a bottle of aspirin (4) or Tylenol (which contains acetaminophen, 52). Have you been to the dentist
recently? If so, you might have had a shot of Novocain (53, the actual name of this chemical is procaine
hydrochloride) so you would not feel the pain (it is a local anesthetic). If you have recently been ill,
21
54 55
N
S
O
CH3
CH3N
HH
OOH
H
O
H2N
OH
N
S
O
CH3
CH3N
HH
OOH
H
O
you might have received a prescription for an antibiotic from your physician. Commonly prescribed antibiotics
could include amoxicillin (54) or penicillin G (55), or even a tetracycline antibiotic such as aureomycin (56).
56
OH O OHOH
O
OH
NH3C
CH3
O
NH2
HO CH3Cl
There are clearly much more serious and devastating diseases that afflict humans. Has a friend or relative
been treated for cancer? The physician might have used vinblastine (57) or taxol (29) to treat the cancer. Do
you smoke? If so, you are breathing nicotine (58) as well as many other organic compounds into your lungs.
Have you heard of the use of AZT for the treatment of AIDS? The structure of AZT is 59.
22
57
N
N
CH3
H3CO
N
N
H
H OH
O
OH
H
O
OCH3
O
CH3
O
OCH3
H
Finally, there are organic molecules that touch vast areas of your life, often in subtle ways. When I say they
touch you, I mean that quite literally. Are you wearing clothes? If so, you might be wearing a synthetic
blend of cloth made from rayon (cellulose acetate, 60). This is a polymer (a large molecule made by bonding
many individual units together). The "n" beside the bracket represents the number of repeating units (this is
common nomenclature for all polymers). You might be wearing something made from Nylon 66,
58 59
N
N
CH3 O
HO
N3
N
N
O
H
O
CH3
H
whose chemical structure is 61. Have you ever heard of Teflon? It finds uses in many machines and devices
that you use every day. It has the structure shown for 62 and natural rubber is polyisoprene (63). You might
be using a piece of paper to describe your thoughts about organic chemistry at this moment. If so, you are
writing on something with cellulose (64) in it. Notice that rayon is simply a derivative of cellulose, the main
23
constituent of wood fiber. When you crumple up the paper and throw it into a "plastic" waste container, that
container might be made of polyethylene, 65.
60 61
OO
O
O
OH3C
OO CH3
OCH3
n
N
H
O N
H
O
O
N
H
n
62 63
F F
F F
H3C
n
n
I have thrown a lot of structures at you. Why? I am trying to convince you that organic chemistry is all
around you and an integral part of your life. Understanding these things can help you make informed choices.
Virtually every aspect of our life is touched by an organic molecule, every day of our lives. This is why you are
sitting there reading this book. I hope that understanding the concepts in its pages will not only help you in
your career, but also help you to understand the beauty that surrounds you. It might also help you understand
the dangers that surround you in the form of organic molecules; pollution, illicit drugs, chemical weapons. I
hope that understanding organic chemistry will help you to understand some of the debate that swirls around
these subjects. Good luck!
64 65
O
HOHO
O
OHC
C
H H
H Hnn
24
ReferencesReferences
1 Fieser, L.F.; Fieser,. M. Advanced Organic Chemistry, Reinhold, New York, 1961; pp. 1-31.
2 Leicester, H.M.; The Historical Background of Chemistry, Wiley, New York, 1956, pp. 172-188.
3 Corey, E.J.; Cheng, X-M. The Logic of Chemical Synthesis, Wiley, New York, 1989.