Basics of Organic Chemistry

Organic chemistry is the chemistry of molecules, predominantly associated with living

systems, which consist of carbon skeletons with functional groups attached.
Functional Groups
"An atom or group of atoms responsible for the characteristic reactions of a compound"
These gives organic chemistry its structures and systematic nature.
H

C=C

C C

the alkene functional group, a double bond between to C atoms

e.g. ethene
H

Don't confuse this with benzene, represented as:

It is an arene, not an alkene.
or

-I, -Br or -Cl the haloalkane functional group

e.g. chloromethane

H C Cl
H

-OH

H H

the alcohol functional group

e.g. ethanol

H C C O H
H H

Carbonyls, C=O, show up in four different families

of organic molecules:
-CHO those with the aldehyde functional group
e.g. ethanal
|
C=O those with the ketone functional group
e.g. propanone

H C C
H

H O H
H C C C H
H

-COOH those with the carboxylic acid functional group

e.g. ethanoic acid

H C C
H
H

-COO- and those with the ester functional group

e.g.methyl ethanoate

O H

H C C

O C H
H

and finally we have:

-NH2 the amine functional group
e.g. methylamine

H C N
H

Page 1

To allow us to focus on functional groups, we sometimes use R- to represent rest of the

molecule, so an alcohol might be represented as R-OH or an ester as R-COO-R
Homologous series
Families of molecules with the same functional group(s) have similar chemical properties
and trends in their physical properties. We refer to such a family of molecules as a
homologous series: a series of organic compounds having the same functional groups,
each successive member differing by CH2Any homologous series can be represented by a GENERAL FORMULA. e.g. in the case
of the alkanes it is CnH2n+2
where n is the number of carbon atoms in the alkane.
Classifying organic molecules
Various terms are commonly used:
Aromatic:

a compound containing one or more benzene rings e.g. methylbenzene

Aliphatic:

a compound containing carbon and hydrogen bonded in branched or

unbranched chains e.g. cyclopentane, pentane, methylbutane

Alicyclic:

an aliphatic compound arranged in non-aromatic rings, with or without side

chains e.g. cyclopentane, 1,2-dimethycyclohexane

Saturated:

a straight or branched chain molecule containing only carbon-carbon single

bonds

Unsaturated: containing carbon-carbon double or triple bonds, and the bonds found in
benzene rings (aromatic compounds are unsaturated)

Types of Chemical Formula

We can represent organic compounds using a variety of formulae, each of which conveys
different amounts of structural information:
Using hexane:

empirical formula :

the simplest whole number ratio of atoms of each element

present in a compound
C3H7

molecular formula :

the actual number of atoms of each element in a molecule

C6H14

displayed formula :

shows all bonds and all atoms

(2-D representation of 3-D molecules)

H H H H H H
H C C C C C C H
H H H H H H

Page 2

structural formula :

the minimum info necessary necessary to show how the atoms

are arranged in the molecule
CH3 CH2CH2CH2CH2CH3
we can also use brackets in structural formulae
e.g. CH3(CH2)4CH3

To draw a structural formula, first identify the longest chain of carbon atoms. Then for each
carbon in the longest chain, write the C and then what is connected to it. If anything
connected consists of more than one atom, put it in brackets unless it is the last carbon in
the chain. e.g. for methyl propane the structural formula would be CH 3CH(CH3)CH3 and
for propane-1,3-diol the structural formula could be written as CH 2(OH)CH2CH2OH or
HO(CH2)3OH

For aldehydes, wed see a CHO group e.g. ethanal is CH 3CHO

For ketones wed see CO within the chain e.g. propanone is CH 3COCH3
For carboxylic acids wed see a COOH group e.g. ethanoic acid is CH 3COOH
For esters wed see a COO within the chain e.g. methylethanoate is CH 3COOCH3

skeletal formula

shows the carbon skeleton (but not C and -H)

and emphasises functional groups.

If unsure about drawing skeletal formulae, start with the displayed formula. Remove all C
atoms, make the chain a zig-zag so that you can see where one bond ends and the next
starts. Remove all C-H bonds and the H atoms on them, but leave any other groups
containing H atoms such as OH. Look at examples carefully to see how they work.
Naming organic molecules
IUPAC nomenclature is standardised to precisely describe the structure of molecules
Basic rules apply:
1:
stem of the name comes from the longest carbon chain (which may be bent !)
methane
CH4
hexane
C6H14
ethane
C2H6
heptane
C7H16
propane
C3H8
octane
C8H18
butane
C4H10
nonane
C9H20
pentane
C5H12
decane
C10H22
2:

alkyl side chains have -yl suffix

e.g. methylpropane

H
H

methyl-,

propyl-

H H

H H H

H C

H C C

H C C C

H H

H H H

H
C

ethyl-,

We need to introduce a number if it is ambiguous which carbon in the chain the

alkyl group is connected to. We number from whichever end means using the
smallest number in the name:
e.g. 2-methylheptane, 3-methylheptane, 4-methylheptane
H H H H H H H
H C C C C C C C H
H

H H H H H

H H H H H H H
H C C C C C C C H
H H

H H H H

H C H

H C H

H H H H H H H
H C C C C C C C H
H H H

H H H

H C H
H

Page 3

Check your understanding:

i)
Name this molecule

ii)

Why can't we have 5-methylheptane or 1-methylhexane ?

iii)

Whats wrong with calling a molecule 2-ethylpentane ?

3:

If we have more than one of the same side group we use a di-, tri- etc. prefix and
position numbers in the form 2,3- where needed
e.g. 2,3-dimethylhexane
2,2,4-trimethylpentane
H

H C H

H C H

H C H

H H H H

H C C C C C C H
H H

H H H

H
H C

H
C

C H

H C H

H C H

iv)

Whats wrong with calling a molecule trimethylhexane ?

4:

If different alkyl groups are present they are named in alphabetical order
H
e.g. 3-ethyl-2-methylpentane
H C H
H
H C

C H

H C H
H C H
H

5:

If the carbon skeleton forms a ring rather than a chain we use a cyclo- prefix
e.g. cyclopentane,
cyclohexane
H

H H

H
H

H H
H
C
H C
C H
H

H C
C H
C
H
H
H H

NOTE: when writing structural formulae for rings we need to show that
they are not chains, so the formula becomes semi-displayed e.g. for
cyclohexane we might write:

H2C
H2C

H2
C
C
H2

CH2
CH2

Check your understanding:

v)
How many different alkanes with C6H14 molecular formula can you make ?
Draw their skeletal formulae and name them.
6:

Alkenes use the same stem, followed by an -ene ending. If the position of the C=C
is ambiguous, an position number is used, referring to the carbon in the chain
where the double bond starts

Page 4

e.g.

but-2-ene

CH3CH=CHCH3

propene

H
H
H C
C H
H
C C
H
H
H

H H

C C C H
H

if we have more than one C=C then the name ends with diene or triene etc. and
we need numbers to show where the double bonds are.
e.g. buta-1,3-diene

7:

C C
H
H
C C
H
H

Halogenoalkanes are named the same way as alkyl-substituted alkanes, with

numbers if needed to show which carbon the halogen is bonded to, and di or tri
prefixes if there are more than one of the same halogen atom.
e.g

bromoethane,

1,1,1-trifluoroethane

H H H H

H H
H C C

1-chlorobutane,

Br

H H

H C C C C H
Cl H H H

Check your
understanding:
vi)
Name the isomers of dibromopropane. (It may help to draw them first).
8:

Alcohols are named in a similar way to alkenes, with an ol ending

and number, if needed, to show which carbon has the OH group on.
e.g.

propan-1-ol,

propan-2-ol (note absence of 'e')

H H H

H H H

H C C C H

H C C C H

O H H

H O H

If there is more than one OH group we have a diol or triol etc. and need
numbers to show where these groups go. We also include the "e" from the alkane
name, which we didn't do when only one OH group was present.
e.g.
H H H

ethane-1,1-diol

propane-1,2,3-triol.

O H

H C C C HH C C H

9:

O O O

O H

H H H

Ketones are named in a similar way to alkenes, with an one ending

and a number, if needed, to show which carbon is in the functional group.
e.g.

propanone,

pentan-3-one

Page 5

H H O H H
H C C C C C H
H H

10:

H H

H O H
H C C C H
H

Aldehyde (-al endings) and carboxylic acid (-anoic acid endings) functional groups
can only occur on the end of a carbon chain, so they do not need a number. There
is only one possible butanoic acid, or butanal. The number of carbon atoms for the
stem- name includes the carbon atom in the functional group. Numbering starts
from that C when needed to show the position of other functional groups.
e.g.

H H H

butanoic acid,
O

H C C C C
H H H

H H H

butanal

2-methylbutanal

H C C C C

O H

H H H

ISOMERS
1) STRUCTURAL ISOMERS
Defined as having the same molecular formula but different structural formulae. We are
familiar with the straight chain alkanes, but alkanes can also be branched so there can be
several different structures.
Check your understanding:
vii) Which is the shortest chain-length alkane to have structural isomers?
2) STEREOISOMERS
Defined as having the same structural formulae but with a different arrangement in space
(i.e. it can't just be rotated to make them the same)
e.g. but-2-ene has two
stereoisomers

These are not the same because there is no free rotation around the double bond.
E/Z ISOMERISM
This is a form of stereoisomerism that we see with alkenes. Because the C=C bond cannot
twist round (we say it has restricted rotation), when we have different groups attached to
each carbon atom there are two ways in which they can be attached.
e.g. Z-but-2-ene

E-

but-2-ene

Cahn-Ingold-Prelog (CIP) rules determine which is the Zand which is the Eisomer. We will examine these rules further when we study the alkene homologous series.

Page 6

CIS-TRANS ISOMERISM
This is a special case of E/Z isomerism in which one of the groups on each C in the C=C is
the same. The cis- isomer has these on the same side, and the trans- isomer has them on
opposite sides across the double bond
e.g. cis-1,2-dichloroethene

C C

C C
H

Cl

trans-1,2-dichloroethene

Cl

Cl

Cl

In order to have E/Z or cis-trans isomerism we have to have 2 conditions fulfilled:

we must have a C=C, which has restricted rotation
neither of these C atoms can have two identical atoms/groups bonded to it
Check your understanding:
viii) Draw all the isomers of C4H8 you can think of. Which are cis- and trans- isomers of
each other?
NOTE: when we draw skeletal formulae or displayed formulae we need to show whether
the E/Z or cis/trans isomerism.
Check your understanding:
ix) Draw skeletal formulae of cis-hex-3-ene and trans-hex-3-ene
Bond Breaking
A covalent bond consists of a pair of electrons lying between the nuclei of two atoms. The
negatively charged electrons attract both nuclei, binding them together. We can break this
xx
type of bond in two ways.
Consider a molecule of hydrogen bromide:

H x

BrH

xx

xx
Homolytic fission:
When we break the H-Br bond each element can take one of the electrons from the bond.
Each element now has a single unpaired electron. Atoms or groups of atoms with
unpaired electrons are known as RADICALS. Breaking in this way is known as homolytic
fission.
If a bond is broken homolytically, the energy to do this is
xx
usually provided by ultraviolet light or high temperature
xx
BrH
H
x
xx

Page 7

Unpaired electrons are represented by a single dot. As an example, the homolytic fission
of chloromethane to form a methyl free radical and a chlorine free radical may be
represented as follows:
CH3-Cl

CH3 + Cl

Heterolytic Fission:
Alternately the bond may be broken so that one element takes both the covalent bond
electrons, hence forming ions. This is heterolytic fission. The more electronegative
element is the one which takes both the electrons.

xx

+
H

BrH

xx

xx

The movement of two electrons from the bond to the same atom is shown using a curly
arrow. For example, the heterolytic fission of bromomethane to form a positive methyl ion
and a bromide ion may be represented as:
H3C - Br CH3+ + :Br

Note: Care with curly arrows. Must come from the bond and go to the atom.
Note: Two dots may be used to show an unbonded (lone) electron pair
-

The CH3+ ion is an example of a CARBOCATION (CH3 would be a CARBOANION).

Free radicals, carbocations and carboanions are all highly reactive and will react with
molecules causing covalent bonds to break and new covalent bonds to form.

Page 8

Answers to Check your Understanding questions:

i) Name this molecule

- the longest carbon chain is 5 long, so its a pentane

- there is a methyl group on the 3rd carbon, so it 3-methylpentane
ii) Why can't we have 5-methylheptane ?
- because if we number from the other end of the chain we'd get a smaller number
in the name. Its correctly named 2-methylheptane
or 1-methylhexane ?
- because a methyl group on the first carbon of a chain just means the chain is one
carbon longer than you thought ! It would be heptane.
iii) Whats wrong with calling a molecule 2-ethylpentane ?
- an ethyl group on the second carbon means you haven't found the longest chain.
In fact the ethyl group is part of the main chain and you have a methyl group on the
second carbon, meaning the molecule is actually 2-methylhexane.
iv) Whats wrong with calling a molecule trimethylhexane ?
- you don't know where the three methyl groups go. There are lots of possible
molecules all of which could be called trimethylhexane, such as 2,2,3trimethylhexane, or 2,3,4-trimethylhexane etc.
v) How many different alkanes with C6H14 molecular formula can you make ?
Draw their skeletal formulae and name them.
hexane,

2-methylpentane,

2,2-dimethylbutane,

3-methylpentane,

2,3-

dimethylbutane

vi)

What are the isomers of dibromopropane ?

1,1-dibromopropane
1,2-dibromopropane
1,3-dibromopropane
2,2-dibromopropane

vii)

Which is the shortest chain-length alkane to have structural isomers ?

butane which has the isomer methylpropane

viii) Draw all the isomers of C4H8 you can think of. Which can have cis-trans isomers ?
but-1-ene; no cis- trans- isomers becuase 2 x H on the first C
but-2-ene; yes, has cis- and trans- isomers

Page 9

methylpropene
cyclobutane
ix) Draw skeletal

no, both C have identical groups on them

no, doesn't have a C=C double bond

formulae of:

cis-hex-3-ene

trans-hex-3-ene

Page 10