University of Sydney

Chemistry 1B (CHEM1102)

Organic Chemistry Lecture Notes

Topic 1 Introduction & isomers 2

Topic 2 Alkenes, alkynes, arenes 20

Topic 3 Structure determination 27

Topic 4 Alcohols and amines 33

Topic 5 Stereochemistry 37

Topic 6 Alkyl halides, carbonyls 42

Topic 7 Carboxylic acids & derivatives 53

Summary of Reactions 61

Inorganic & General Chemistry Lecture Notes

Topic 8 Acids and Bases 65

Topic 9 Phases diagrams & solubility 76

Topic 10 Coordination Chemistry 84

Topic 11 Kinetics 91

Unless otherwise stated, all images in this file have been reproduced from:

Blackman, Bottle, Schmid, Mocerino and Wille,

Chemistry, 2007 (John Wiley)
ISBN: 9 78047081 0866

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 Topic 1 – Introduction to Organic chemistry,
representation of structures, functional groups,
nomenclature, isomers

Introduction
Definition of Organic Chemistry

 Organic chemistry deals with compounds in which carbon is the principal element
 Organic substances arise in all sorts of places - plants, animals, food, medicines,
industry, research laboratories
 Every living organism is made of organic chemicals
 14 million organic substances - number increases by 10,000 per week!!

The Unique Nature of Carbon – Bonding in Organic Carbon

 Catenation - Carbon atoms can bond together to form

 Stable extended chains of atoms
 Rings
 Multiple bonds

 Carbon has atomic number = 6

 Electronic configuration: 1s2 2s2 2p2
 Valence of 4 – four bonds to completely fill outer electron shell of carbon

 Carbon forms bonds to

 Itself – single, double, triple
 Metals – Na, K, Fe, Cu, Mg …
 Heteroatoms – N, P, O, S, X

 C-C and C-H bonds are strong

C-C 348 kJ mol-1
C-H 412
Si-Si 176
N-N 163
O-O 146
I-I 152

 C-C and C-H bonds are non-polar

 A combination of the strength and non-polar nature make C-C and C-H bonds
unreactive

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 There are four experimentally observed bonding arrangements for carbon:

Type of bonds Hybridisation Geometry Examples

4 single bonds sp3 Tetrahedral CH4, CH3CH3

2 single, 1 double bond sp2 Trigonal planar CH2=CH2, CH2=O

1 single, 1 triple bond sp Linear H-CC-H

2 double bonds CH2=C=O

Hybridisation

Hybridisation is a convenient way of describing the sigma-bonding orbitals and lone pair
orbitals (if present) of an atom.
In alkanes, hybridisation gives four identical sp3 orbitals, which form a tetrahedral shape
to minimise repulsion between the orbitals.

Energy

Hybridisation

Carbon - Carbon - Carbon -

ground state bonding state four sp 3 orbitals
In alkenes, each pi-bond results from the combination of a p-orbital on adjacent carbon
atoms and consequently the orbitals available for sigma bonding result from an s-orbital
and the remaining p-orbitals.

Question: Work out the hybridization of carbon in the following molecules. Note: A
quick way of determining the hybridisation of an atom is to count the  bonds and lone
pairs around that atom and assign one hybrid orbital to each.
2 electron pairs  sp, 3 electron pairs  sp2, 4 electron pairs  sp3

C O H C C H O C O

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Representation of Organic Molecules

Organic compounds may be represented in several ways as illustrated in the examples

below.

H H

H C C O H

H H

CH3CH2OH

C2H6O
H H
H
C H
H H C O

O
H

Concept
 Catenation – chains and rings of carbon atoms
 Bonding – single, double, triple bonds possible
 Geometry – depends on hybridisation of carbon atom
 Valence – 4 for carbon (3 – N, 2 – O, 1 – H, Cl, Br, I)
 Reactivity – often associated with heteroatoms (atoms other than C or H)

In the stick representation:

 C is basis of structure
 Carbon atoms are not usually shown but assumed to be at the intersection of 2 or
more bonds and at the end of each line
 1, 2 or 3 lines to represent single, double and triple bonds
 Indicate bond angles (~ 1200 or 1800)
 Omit all C-H bonds, hydrogen count assumed
 Specify all heteroatoms (O, N, F, Cl, B, I, S etc) and H – heteroatom bond
 When drawing neutral organic molecules:
 C always has a valence of 4
 N always has a valence of 3
 O always has a valence of 2
 X (halogen) always has a valence of 1

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 Condensed Structural Structural Formula Stick representation
Formula

CH3CH2CO2H H H O O
or
CH3CH2COOH H C C C O H
OH
H H

CH3CHClCH=CH2 H H H H
or H C C C C
CH3CHClCHCH2 H
H Cl Cl
O
H H O
C
H C C H
H C C H
H C H
H H

H O H H O
CH3COCH2CH3
H C C C C H
H H H

H H H
CH3OCH2CH3
H C O C C H O
H H H

Questions: Give the stick representation of the following molecules:

CH3CH2CH=CH2 (CH3)2CHCH2CHO CH2=C(CH3)CH=CH2

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Where it is important to represent the three-dimensional shape of a molecule, the
following convention is adopted:

Bonds in the plane of the paper A B

Bonds coming towards the observer A B

Bonds going away from the observer A B or A B

H
For example, CH 4 C
H
H H

Structure of benzene

Benzene is also about 140 kJ mol-1 more stable than predicted for 1,3,5-cyclohexatriene.

Bond length Bond strength

C-C 154 pm 356 kJ mol-1

C=C 133 pm 636 kJ mol-1

benzene 139 pm 518 kJ mol-1

There are two models of bonding in benzene

1. In the valence bond model each of the

H H
carbon atoms in benzene is sp2
hybridised and forms -bonds to two
neighbouring carbon atoms and a -bond H H
to one hydrogen. Each carbon atom has a
p-orbital which can participate in
-bonding. H H

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If the bonds were normal C=C bonds, the
bonding in benzene could be drawn in
either of two identical ways. The valence
bond theory says that the bonding in
benzene is best described as an average or
"resonance hybrid" of the bonding contributors to the
arrangements which can be drawn. hybrid structure of benzene

2. The bonding in benzene can also be

described in terms of molecular orbital H H
theory. Here the p-orbitals of the six
sp2-hybridised carbon atoms overlap with
each other to form a single continuous H H
-bond. The six electrons in this bond
effectively form a toroidal electron cloud
which lies above and below the plane of the H H
carbon atoms.

Irrespective of which theory is used to describe the bonding, benzene is a perfect hexagon
where all the bond angles are 120o and where all six C-C bonds are identical.

When drawing a benzene molecule, some books draw a circle in the

centre of the hexagon of carbon atoms. This implies 'delocalisation' of
the 6 -electrons around the aromatic ring and indicates the real
symmetry of the benzene molecule.

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Functional Groups
Organic compounds are classified by Functional Groups, which are responsible for
chemical behaviour. Functional groups are involved in naming organic compounds.

 C=C, CC and the polar bonds from carbon to heteroatoms are more reactive than
C-C or C-H bonds and hence where the chemistry takes place. This part of the
molecule is called the Functional Group.
 An organic compound can be viewed as a backbone (skeleton) of carbon-carbon
single bonds with other groups of atoms, functional groups, attached at various
points.

Functional group

 The combination of the ability to form a vast range of unreactive carbon frameworks
to which can be added special reactive sites gives the diversity of organic chemistry.

 Functional groups confer the characteristic chemical and physical properties of the
compounds that contain them.

 Functional groups undergo the same chemical reactions irrespective of the type of
molecule that contains them.

 A molecule containing several functional groups displays reactions that represents the
sum of the reactions of each functional group.
O Acetyl salicylic acid (aspirin)
shows the properties of
OH - a carboxylic acid
O - an ester
O CH3 - an aromatic compound

Note: R is the general abbreviation for the “rest of the molecule”.

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 Class General formula Examples

C&H alkane RCH3 CH4 CH3CH2CH2CH3

CH3 CH3
alkene R2C=CR2 C C
CH3 CH3
alkyne RCCR CH3C CH

CH3
aromatic
compound

C, H, O
-O- alcohol R-OH CH3CH2OH OH

ether R-O-R CH3CH2OCH3 O

C, H, O O O
O CH3 C C
=O aldehyde
R C H H H
O O O
ketone
R C R CH3CCH3
O O
carboxylic CH3COOH
acid R C OH
OH
O O O
ester
R C OR CH3COCH3
O
C, H, N amine R3N (CH3)3N NH2
C, H, O CH3 O
N, O amide O
C N C
R C NR2 H CH3 NH2
C, H, O
O
Cl, O acid CH3COCl C
chloride R C Cl Cl

C, H, X Alkyl R-X CH3CH2Br Cl

halide (X = Cl, Br, I)

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Question: Name the functional groups in the following molecules:

OH Vitamin A

O
OH Acetyl salicylic acid
O
O CH3

HO
Morphine

O
NCH3

HO

(CH3CH2)2N NCH3

O Lysergic acid diethyl amide

NH

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Nomenclature
The name of an organic molecule consists of several parts:

Number(s) Substituent Stem Ending

The stem indicates the number of carbon atoms in the longest chain containing the
functional group. The ending indicates the nature of the functional group present.
Substituents are indicated by prefixes and a number is used to locate any substituent or
functional group unambiguously in a molecule.

Rules:
 Find and name the longest carbon chain  stem alkane
 Identify substituents stemane
 Number longest carbon chain to give lowest numbering
number of carbons
for substituents
 Allocate a number to every substituent
 List substituents in alphabetical order
 Identical side chains are indicated by using prefixes: di (2), tri (3), tetra (4) etc

Methane CH4

Ethane CH3CH3

Propane CH3CH2CH3

Butane CH3CH2CH2CH3

Pentane CH3CH2CH2CH2CH3

Hexane CH3CH2CH2CH2CH2CH3

Heptane CH3CH2CH2CH2CH2CH2CH3

Octane CH3CH2CH2CH2CH2CH2CH2CH3

Nonane CH3CH2CH2CH2CH2CH2CH2CH2CH3

Decane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH3

Alkane Alkyl group substituent

propane CH3CH2CH3 propyl CH3CH2CH2-

butane CH3CH2CH2CH3 butyl CH3CH2CH2CH2-

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Give the stick structures of the following molecules:
2,2-dimethylpentane
1,4-butandiol
3-pentanone

Give the name of the following molecules:

Cl

O Cl

Summary
You should now be able to
 Understand the basis of drawing organic structures
 Convert between a condensed molecular formula and a skeletal or line
structure
 Determine the formula of a molecule from its skeletal representation

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Isomerism
The problem of isomers…
 How many different compounds are there with the formula C2H2BrClO?
(Excluding those with charged atoms and O–Cl or O–Br bonds)
 How do we tell them apart?
 How do we name them?
 How are they different?
 Do they have different properties?

There are 16 different possible compounds

O O O
O
H Cl Cl Br Cl H
C C H C C H C C H
ClCH2 C Br Br H Br

O O O
O Cl H Br Cl Br H
C C Br C C H C C H
BrCH2 C Cl H H Cl

H H OH H OH Br OH
C C C C C C C
Br C H
Cl Br Cl Cl Br Cl H
O

H
Br OH Cl OH Cl OH
C
Cl C H C C C C C C
Br H Cl H Br Br H
O

Isomers are
 Compounds that have the same molecular formula but different structures
 Very important in chemistry but especially important in the chemical reactions
that take place in living organisms - the shape is as important as the functinal
groups present!
 Classified according to type

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 Classification of isomers

Isomers
same molecular formula

Constitutional Isomers Stereoisomers

Different nature/sequence of bonds Different arrangement of groups in space

Conformational Configurational
Isomers Isomers
Differ by rotation about a single bond Interconversion requires breaking bonds

Enantiomers Diastereoisomers
Non-superposable mirror images Not mirror images

Constitutional isomers
Isomers differ in the nature and/or sequence of bonding
 Within a homologous sequence of alkanes, the number of constitutional
isomers increases rapidly

No. of Constitutional
n CnH2n+2 iosmers Constitutional formula
1 CH4 1 CH4
2 C2H6 1 CH3CH3
CH3
3 C3H8 1 CH3CH2CH3
4 C4H10 2 CH3CH2CH2CH3 CH3CHCH3
AND
5 C5H12 3
6 C6H14 5
: : :
10 C10H22 75
20 C20H42 366 319

Question: Draw and name the constitutional isomers of C6H14

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  The physical and chemical properties of constitutional isomers may be very
different, particularly when different functional groups are present
 For example the molecule with formula C4H8O may be a ketone, aldehyde,
alkene/ether or alkene/alcohol

O O OH
O

Stereoisomers
Stereoisomers have the same nature and/or sequence of bonding but differ in the
arrangement of groups in space

 There are two groups of stereoisomers

 Conformational isomers or conformers differ by rotation about a single
bond and can not normally be separated from each other at room
temperature
 Configurational isomers may be interconverted only by breaking and
remaking bonds. This process normally requires considerable energy and
does not happen at room temperature

Conformational isomers

Use ethane as an example (CH3CH3)

H H H

H
H HH H
Sawhorse representation
H H
H H
rotate back carbon 60°
H
HH H H

Newman projection
H H H
H H H
H
eclipsed staggered

Conformers differ in energy

 In ‘straight chain’ alkanes rotation about a C-C single bond occurs rapidly
at room temperature

 The difference in energy between conformers arises from steric interaction

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 HH HH HH HH

H H H H
H H H H H H H H
H H H H
Energy

H H H
H H H H H H

H H H H H H
H H H
12 kJ/mol

0° 60° 120° 180° 240° 300° 360°

Dihedral angle

Question: Draw the energy profile of the butane molecules as the C2-C3 bond rotates
through 360°.
 Start by drawing the appropriate Newman projections to help decide the relative
energies of different conformers.
 The back carbon rotates and the front one stays stationary.

H3CCH3

H
H H
H
Energy

0° 60° 120° 180° 240° 300° 360°

Dihedral angle

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Cyclic alkanes
H H H H
Straight chain alkanes
 Rotation around each C-C bond readily occurs C C H
 Conformational isomers result
H C C

H H H H
Cyclic alkanes
 Rotation is restricted within a ring of carbon atoms
 This is because rotation would require the atoms H H
attached to carbon to pass through the centre of the
ring – this has a high energy barrier C
H
C
H

Disubstituted cycloalkanes

A number of isomers are possible Cl

Cl
 Constitutional: Cl

eg 1,1-dichlorocyclopentane, Cl
Cl

1,2-dichlorocyclopentane and Cl

1,3-dichlorocyclopentane
Cl
Cl
 Configurational: eg two forms of 1,2-
dichlorocyclopentane
Cl Cl

Nomenclature: cis and trans

 These structures are diastereoisomers or diastereomers
 They have different physical and chemical properties
 The terms cis and trans are used to distinguish them
Cl
Cl Cl
Cl Cl

Cl
Cl

Cl

cis-1,2-dichlorocyclopentane trans-1,2-dichlorocyclopentane

Question: Identify the type of isomer represented by the

pairs:

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Isomers resulting from structural rigidity
 Rotation around the C-C bond within a cycloalkane ring is restricted compared to
that of a hydrocarbon chain
 Consequently disubstituted cycloalkanes occur as diastereoisomers as well as
constitutional isomers
 A pi-electron overlap requires a fixed geometry around the bonded carbon atoms

Alkene ‘diastereoisomers’

A double bond is constructed of a σ- and π-bond

 Pi-bonds result from p-orbital overlap and are directional
 Electron density concentrated above and below plane
 Rotation around the C-C axis would require breaking the pi-bond (~128 kJ mol-1)
and does not occur at room temperature

CH3 H

H 3C C Different H3C C
C H compounds! C CH3

H H

melting point = -139 ºC melting point = -106 ºC

boiling point = 4 ºC boiling point = 1 ºC

(Z)- 2-butene (E)- 2-butene  - bond  - bond

Both ends of the C=C bond must have two different groups
 If these conditions are met, TWO diastereoisomers result
H H H Cl
A X The same
C C C C
A B C C XY H Cl
compound!
H H
B Y H H H COOH
Different C C
C C
But A and B can be the same as X and Y compounds!
HOOC COOH HOOC H

Nomenclature – Z and E

The rules
 Z/E determined by assigning a priority to each of the pairs of groups on each
carbon of the double bond
 The higher the atomic number of the atom attached, the higher the priority
 If identical atoms are attached to each carbon of C=C, work outwards along the
chain until the first point of difference is reached
 If groups of high priority are on the same side of the double bond the alkene is
denoted (Z)
 If groups of high priority are on the opposite side of the double bond the alkene is
denoted (E)

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 Higher priority groups Higher priority groups
alkene is alkene is
on the same side on opposite sides
Example of double bond
denoted (Z)
of double bond
denoted (E)

H H H CH3 Br CH3
C C C C C C
H3C CH3 H 3C H H Cl

(Z)- 2-butene (E)- 2-butene (E)-1-bromo-2-chloropropene

higher priority groups higher priority groups higher priority groups
on same side on opposite sides on opposite sides

Question: name these molecules

A....................................... B.......................................

What is the isomeric relationship

between the pairs:
A and B…………………..……
C and D………………………..
C....................................... D.......................................

Note: No diastereoisomers of alkynes

 Two pi bonds and two sigma bonds associated with each carbon of the triple bond
 Geometry of both carbon atoms is linear
 There is only one way to attach two substituents in a straight line

H3C C C H

 - bonds
Summary
You should now be able to
 Understand the difference between constitutional isomers and stereoisomers
 Recognise constitutional, conformational and diastereomeric (cis/trans and Z/E)
isomers
 Name isomeric structures correctly

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