Clayden J. - ''Organic Chemistry''.pdf

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What is organic chemistry?
1
Organic chemistry and you
You are already a highly skilled organic chemist. As you read these words, your eyes are using an
organic compound (retinal) to convert visible light into nerve impulses. When you picked up this
book, your muscles were doing chemical reactions on sugars to give you the energy you needed. As
you understand, gaps between your brain cells are being bridged by simple organic molecules (neuro-
transmitter amines) so that nerve impulses can be passed around your brain. And you did all that
without consciously thinking about it. You do not yet understand these processes in your mind as
well as you can carry them out in your brain and body. You are not alone there. No organic chemist,
however brilliant, understands the detailed chemical working of the human mind or body very well.
We, the authors, include ourselves in this generalization, but we are going to show you in this
book what enormous strides have been taken in the understanding of organic chemistry since the
science came into being in the early years of the nineteenth century. Organic chemistry began as a
tentative attempt to understand the chemistry of life. It has grown into the confident basis of vast
multinational industries that feed, clothe, and cure millions of people without their even being
aware of the role of chemistry in their lives. Chemists cooperate with physicists and mathemati-
cians to understand how molecules behave and with biologists to understand how molecules
determine life processes. The development of these ideas is already a revelation at the beginning of
the twenty-first century, but is far from complete. We aim not to give you the measurements of the
skeleton of a dead science but to equip you to understand the conflicting demands of an
adolescent one.
Like all sciences, chemistry has a unique place in our pattern of understanding of the universe. It
is the science of molecules. But organic chemistry is something more. It literally creates itself as it
grows. Of course we need to study the molecules of nature both because they are interesting in their
own right and because their functions are important to our lives. Organic chemistry often studies life
by making new molecules that give information not available from the molecules actually present in
living things.
This creation of new molecules has given us new materials such as plastics, new dyes to colour our
clothes, new perfumes to wear, new drugs to cure diseases. Some people think that these activities are
unnatural and their products dangerous or unwholesome. But these new molecules are built by
humans from other molecules found on earth using the skills inherent in our natural brains. Birds
build nests; man makes houses. Which is unnatural? To the organic chemist this is a meaningless dis-
tinction. There are toxic compounds and nutritious ones, stable compounds and reactive ones—but
there is only one type of chemistry: it goes on both inside our brains and bodies and also in our flasks
and reactors, born from the ideas in our minds and the skill in our hands. We are not going to set
ourselves up as moral judges in any way. We believe it is right to try and understand the world about
us as best we can and to use that understanding creatively. This is what we want to share with
you.
H
O
11-cis-retinal
absorbs light when we see
HO
NH 2
N
H
serotonin
human neurotransmitter
We are going to give you
structures of organic compounds
in this chapter—otherwise it
would be rather dull. If you do not
understand the diagrams, do not
worry. Explanation is on its way.
Organic compounds
Organic chemistry started as the chemistry of life, when that was thought to be different from the
chemistry in the laboratory. Then it became the chemistry of carbon compounds, especially those
found in coal. Now it is both. It is the chemistry of the compounds of carbon along with other ele-
ments such as are found in living things and elsewhere.
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2
1 . What is organic chemistry?
You will be able to read towards the
end of the book (Chapters 49–51)
about the extraordinary chemistry that
allows life to exist but this is known
only from a modern cooperation
between chemists and biologists.
The organic compounds available to us today are those present in living things and those formed
over millions of years from dead things. In earlier times, the organic compounds known from nature
were those in the ‘essential oils’ that could be distilled from plants and the alkaloids that could be
extracted from crushed plants with acid. Menthol is a famous example of a flavouring compound
from the essential oil of spearmint and cis -jasmone an example of a perfume distilled from jasmine
flowers.
O
N
OH
HO
menthol
cis-jasmone
MeO
quinine
N
Even in the sixteenth century one alkaloid was famous—quinine was extracted from the bark of
the South American cinchona tree and used to treat fevers, especially malaria. The Jesuits who did
this work (the remedy was known as ‘Jesuit’s bark’) did not of course know what the structure of
quinine was, but now we do.
The main reservoir of chemicals available to the nineteenth century chemists was coal. Distil-
lation of coal to give gas for lighting and heating (mainly hydrogen and carbon monoxide) also
gave a brown tar rich in aromatic compounds such as benzene, pyridine, phenol, aniline, and
thiophene.
OH
NH 2
S
N
pyridine
benzene
phenol
aniline
thiophene
Phenol was used by Lister as an antiseptic in surgery and aniline became the basis for the dyestuffs
industry. It was this that really started the search for new organic compounds made by chemists
rather than by nature. A dyestuff of this kind—still available—is Bismarck Brown, which should tell
you that much of this early work was done in Germany.
H 2 N
NH 2
H 2 N
NH 2
N
N
N
N
Bismarck Brown Y
You can read about polymers and
plastics in Chapter 52 and about fine
chemicals throughout the book.
In the twentieth century oil overtook coal as the main source of bulk organic compounds so that
simple hydrocarbons like methane (CH 4 , ‘natural gas’) and propane (CH 3 CH 2 CH 3 , ‘calor gas’)
became available for fuel. At the same time chemists began the search for new molecules from new
sources such as fungi, corals, and bacteria and two organic chemical industries developed in paral-
lel—‘bulk’ and ‘fine’ chemicals. Bulk chemicals like paints and plastics are usually based on simple
molecules produced in multitonne quantities while fine chemicals such as drugs, perfumes, and
flavouring materials are produced in smaller quantities but much more profitably.
At the time of writing there were about 16 million organic compounds known. How many more
are possible? There is no limit (except the number of atoms in the universe). Imagine you’ve just
made the longest hydrocarbon ever made—you just have to add another carbon atom and you’ve
made another. This process can go on with any type of compound ad infinitum .
But these millions of compounds are not just a long list of linear hydrocarbons; they embrace all
kinds of molecules with amazingly varied properties. In this chapter we offer a selection.
CH 3 (CH 2 ) n CH 3
n = an enormous number
length of molecule is n + 2
carbon atoms
CH 3 (CH 2 ) n CH 2 CH 3
n = an enormous number
length of molecule is n + 3
carbon atoms
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Organic compounds
3
What do they look like? They may be crystalline solids, oils,
waxes, plastics, elastics, mobile or volatile liquids, or gases.
Familiar ones include white crystalline sugar, a cheap natural
compound isolated from plants as hard white crystals when pure,
and petrol, a mixture of colourless, volatile, flammable hydrocar-
bons. Isooctane is a typical example and gives its name to the
octane rating of petrol.
The compounds need not lack colour. Indeed we can soon
dream up a rainbow of organic compounds covering the whole
spectrum, not to mention black and brown. In this table we have
avoided dyestuffs and have chosen compounds as varied in struc-
ture as possible.
HO
O
HO
HO
HO
O
OH
CH 3
CH 3
HO
O
CH 3
OH
CH
C
CH 3
C
H 2
CH 3
HO
sucrose – ordinary sugar
isolated from sugar cane
or sugar beet
isooctane (2,3,5-trimethylpentane)
a major constiuent of petrol
volatile inflammable liquid
white crystalline solid
s
Colour
Description
Compound
Structure
red
dark red hexagonal plates
3 ¢ -methoxybenzocycloheptatriene-
2 ¢ -one
O
p
MeO
orange
amber needles
dichloro dicyano quinone (DDQ)
O
Cl
CN
e
Cl
CN
O
c
yellow
toxic yellow explosive gas
diazomethane
CH 2 NN
green
green prisms with a
9-nitroso julolidine
N
t
steel-blue lustre
r
NO
blue
deep blue liquid with a
azulene
peppery smell
u
purple
deep blue gas condensing
nitroso trifluoromethane
F
F
N
C
to a purple solid
O
F
m
Colour is not the only characteristic by which we recognize compounds. All too often it is their
odour that lets us know they are around. There are some quite foul organic compounds too; the
smell of the skunk is a mixture of two thiols—sulfur compounds containing SH groups.
skunk spray contains:
SH
+
SH
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4
1 . What is organic chemistry?
S
But perhaps the worst aroma was that which caused the evacuation of the city of Freiburg in 1889.
Attempts to make thioacetone by the cracking of trithioacetone gave rise to ‘an offensive smell which
spread rapidly over a great area of the town causing fainting, vomiting and a panic evacuationºthe
laboratory work was abandoned’.
It was perhaps foolhardy for workers at an Esso research station to repeat the experiment of crack-
ing trithioacetone south of Oxford in 1967. Let them take up the story. ‘Recentlyºwe found ourselves
with an odour problem beyond our worst expectations. During early experiments, a stopper jumped
from a bottle of residues, and, although replaced at once, resulted in an immediate complaint of nau-
sea and sickness from colleagues working in a building two hundred yards away. Two of our
chemists who had done no more than investigate the cracking of minute amounts of trithioace-
toneºfound themselves the object of hostile stares in a restaurant and suffered the humiliation of
having a waitress spray the area around them with a deodorantº. The odours defied the expected
effects of dilution since workers in the laboratory did not find the odours intolerable . . . and genu-
inely denied responsibility since they were working in closed systems. To convince them otherwise,
they were dispersed with other observers around the laboratory, at distances up to a quarter of a
mile, and one drop of either acetone gem -dithiol or the mother liquors from crude trithioacetone
crystallisations were placed on a watch glass in a fume cupboard. The odour was detected downwind
in seconds.’
There are two candidates for this dreadful smell—propane dithiol (called acetone gem -dithiol
above) or 4-methyl-4-sulfanylpentan-2-one. It is unlikely that anyone else will be brave enough to
resolve the controversy.
Nasty smells have their uses. The natural gas piped to our homes contains small amounts of delib-
erately added sulfur compounds such as tert -butyl thiol (CH 3 ) 3 CSH. When we say small, we mean
very small —humans can detect one part in 50 000 000 000 parts of natural gas.
Other compounds have delightful odours. To redeem the honour of sulfur compounds we must
cite the truffle which pigs can smell through a metre of soil and whose taste and smell is so delightful
that truffles cost more than their weight in gold. Damascenones are responsible for the smell of roses.
If you smell one drop you will be disappointed, as it smells rather like turpentine or camphor, but
next morning you and the clothes you were wearing will smell powerfully of roses. Just like the com-
pounds from trithioacetone, this smell develops on dilution.
Humans are not the only creatures with a sense of smell. We can find mates using our eyes alone
(though smell does play a part) but insects cannot do this. They are small in a crowded world and
they find others of their own species and the opposite sex by smell. Most insects produce volatile
compounds that can be picked up by a potential mate in incredibly weak concentrations. Only 1.5
mg of serricornin, the sex pheromone of the cigarette beetle, could be isolated from 65 000 female
beetles—so there isn’t much in each beetle. Nevertheless, the slightest whiff of it causes the males to
gather and attempt frenzied copulation.
The sex pheromone of the Japanese beetle, also given off by the females, has been made by
chemists. As little as 5 µg (micrograms, note!) was more effective than four virgin females in attract-
ing the males.
thioacetone
?
S
S
S
trithioacetone;
Freiburg was evacuated
because of a smell from
the distillation this compound
HS SH
HS
O
propane
dithiol
4-methyl-4-
sulfanylpentan-
2-one
two candidates for
the worst smell in the world
no-one wants to find the winner!
CH 3
S
S
CH 3
the divine smell
of the black truffle
comes from this compound
O
damascenone - the smell of roses
O
O
OH
O
H
serricornin
japonilure
the sex pheromone of the cigarette beetle
Lasioderma serricorne
the sex pheromone of the Japanese beetle
Popilia japonica
10 –12 g is active as a lure for the males in
field tests. The three pheromones we have mentioned are available commercially for the specific
trapping of these destructive insect pests.
´
The pheromone of the gypsy moth, disparlure, was identified from a few µg isolated from the
moths and only 10 µg of synthetic material. As little as 2
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Organic compounds
5
Don’t suppose that the females always do all the work; both
male and female olive flies produce pheromones that attract the
other sex. The remarkable thing is that one mirror image of
the molecule attracts the males while the other attracts the
females!
disparlure
O
the sex pheromone of the Gypsy moth
Portheria dispar
h
f th G
th
O
O
O
O
O
O
olean
sex pheromone of the olive fly
Bacrocera oleae
this mirror image isomer
attracts the males
this mirror image isomer
attracts the females
10 –5 parts per billion of this compound. This is an almost unimag-
inably small amount equal to 10 –4 mg per tonne or a drop, not in a bucket, but in a good-sized lake.
Why evolution should have left us abnormally sensitive to grapefruit, we leave you to imagine.
For a nasty taste, we should mention ‘bittering agents’, put into dangerous household substances
like toilet cleaner to stop children eating them by accident. Notice that this complex organic com-
pound is actually a salt—it has positively charged nitrogen and negatively charged oxygen atoms—
and this makes it soluble in water.
´
HS
flavouring principle of grapefruit
O
H
N
N
O
O
bitrex
denatonium benzoate
benzyldiethyl[(2,6-xylylcarbamoyl)methyl]ammonium benzoate
Other organic compounds have strange effects on humans. Various ‘drugs’ such
as alcohol and cocaine are taken in various ways to make people temporarily happy.
They have their dangers. Too much alcohol leads to a lot of misery and any cocaine
at all may make you a slave for life.
Again, let’s not forget other creatures. Cats seem to be able to go to sleep at any
time and recently a compound was isolated from the cerebrospinal fluid of cats that makes them, or
rats, or humans go off to sleep quickly. It is a surprisingly simple compound.
CH 3 OH
alcohol
(ethanol)
CO 2 Me
CH 3
N
O
O
cocaine
- an addictive alkaloid
O
NH 2
a sleep-inducing fatty acid derivative
cis-9,10-octadecenoamide
This compound and disparlure are both derivatives of fatty
acids, molecules that feature in many of the food problems people
are so interested in now (and rightly so). Fatty acids in the diet are
a popular preoccupation and the good and bad qualities of satu-
rates, monounsaturates, and polyunsaturates are continually in
the news. This too is organic chemistry. One of the latest mole-
cules to be recognized as an anticancer agent in our diet is CLA
(conjugated linoleic acid) in dairy products.
O
1
OH
11
18
9
12
10
CLA (Conjugated Linoleic Acid)
cis-9-trans-11 conjugated linoleic acid
dietary anticancer agent
disparlure
th
What about taste? Take the grapefruit. The main flavour comes from another sulfur compound
and human beings can detect 2
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