CLAYDEN, J. (2001). Organic Chemistry.pdf

What is organic chemistry?

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.

11-cis-retinal

absorbs light when we see

NH 2

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.

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.

menthol

cis-jasmone

MeO

quinine

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.

NH 2

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

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

Organic compounds

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.

CH 3

H 2

CH 3

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

Colour

Description

Compound

Structure

red

dark red hexagonal plates

3 ¢ -methoxybenzocycloheptatriene-

2 ¢ -one

MeO

orange

amber needles

dichloro dicyano quinone (DDQ)

yellow

toxic yellow explosive gas

diazomethane

CH 2 NN

green

green prisms with a

9-nitroso julolidine

steel-blue lustre

blue

deep blue liquid with a

azulene

peppery smell

purple

deep blue gas condensing

nitroso triﬂuoromethane

to a purple solid

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:

1 . What is organic chemistry?

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

trithioacetone;

Freiburg was evacuated

because of a smell from

the distillation this compound

HS SH

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

the divine smell

of the black truffle

comes from this compound

damascenone - the smell of roses

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

Organic compounds

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

the sex pheromone of the Gypsy moth

Portheria dispar

f th G

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.

flavouring principle of grapefruit

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

cocaine

- an addictive alkaloid

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.

CLA (Conjugated Linoleic Acid)

cis-9-trans-11 conjugated linoleic acid

dietary anticancer agent

disparlure

What about taste? Take the grapefruit. The main ﬂavour comes from another sulfur compound

and human beings can detect 2

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