CHEM1643 Organic Chemistry 2024

1
CHEM1643
Organic Chemistry
NQF level 6
12 credits
Chemistry Department
Compiled by
Dr SL Bonnet & Prof A
Wilhelm
2024
CONTENTS
2
UNIT 1 – INTRODUCTION TO ORGANIC CHEMISTRY
1.1 Introduction 1-1

1.2 Identification of organic compounds 1-2
1.3 The chemical bond 1-3
1.3.1 Bond formation 1-3
1.3.2 Electron configuration of the carbon atom 1-4
1.3.3 sp3-Hybridization of carbon atoms 1-5
1.4 Polar covalent bonds 1-8
1.5 Reactions and reaction mechanisms 1-8
1.5.1 Bond cleavage 1-9
1.5.2 Bond formation 1-10
FEEDBACK 1-14
ADDITIONAL PROBLEMS 1-15
UNIT 2 – ALKANES AND CYCLOALKANES

2.2 Basic information 2-1
2.3 Nomenclature 2-2
2.3.1 Nomenclature of alkanes 2-2
2.3.2 Nomenclature of cycloalkanes 2-7
2.4 Alternatives ways of drawing structures 2-9
2.5 Classification of carbon atoms 2-11
2.6 Structural isomerism 2-11
2.7 Chemical behavior of alkanes and cycloalkanes 2-13
2.7.1 Oxidation 2-13
2.7.2 Halogenation 2-14
FEEDBACK 2-16
UNIT 3 – ALKYL HALIDES

3
3.2 Classification of monohalogen compounds 3-2

3.4 Chemical properties 3-5
3.4.1 Characteristics of the functional group 3-5
3.4.2 Nucleophilic substitution reactions 3-7
3.4.3 Ionic elimination reactions (E-reactions) 3-8
FEEDBACK 3-10
UNIT 4 – STEREOCHEMISTRY
4.2 Chiral compounds and enantiomers 4-2
4.2.1 Optical activity 4-4
4.2.2 Racemic mixture 4-5
4.3 Absolute configuration – The R,S convention 4-5
FEEDBACK 4-9
UNIT 5 – ALKENES AND CYCLOALKENES

5.2 sp2-hybridization of carbon atoms 5-2
5.3 Geometrical isomerism 5-4
(a) Cis/trans system 5-5
(b) E/Z system 5-6
5.4 Nomenclature of alkenes and cycloalkenes 5-8
5.5.1 Nature of the double bond 5-10
5.5.2 Hydrogenation (reduction of a double bond) 5-11
5.5.3 Addition of halogens (halogenation) 5-12
5.5.4 Addition of hydrogen halides (halogen acids) 5-13
4
5.5.5 Addition of water (hydration) 5-16
FEEDBACK 5-17
UNIT 6 – ALKYNES
6.2 sp-hybridization of carbon atoms 6-2
6.3 Nomenclature of alkynes 6-4
6.4.1 Acidity of alkynes and reactions 6-7
6.4.2 Addition reactions of alkynes 6-8
(a) Hydrogenation 6-8
(b) Hydration 6-9
FEEDBACK 6-10
UNIT 7 – ALCOHOLS
7.1 Alcohols
7.1.1 Introduction 7-1
7.1.2 Classification 7-2
(a) Monohydric alcohols 7-2
(b) Dihydric alcohols 7-3
(c) Trihydric alcohols 7-3
7.1.3 Nomenclature 7-4
7.1.4 Chemical properties 7-6
(a) Nature of the functional group 7-6
(b) Amphoteric character of alcohols 7-7
(i) Alcohols as weak bases 7-7
(ii) Alcohols as weak acids 7-7
(c) Effect of protonation on the nature of the functional group 7-8
7.1.5 Substitution of the hydroxyl group with a halogen 7-10
5
(a) SN1-mechanism for tertiary alcohols 7-11

(b) SN2-mechanism for primary alcohols 7-13
7.1.6 Elimination of the hydroxyl group with concentrated sulphuric acid 7-14
7.1.7 Oxidation 7-17
(a) Introduction 7-17
(b) Primary alcohols 7-17
(c) Secondary alcohols 7-18
(d) Tertiary alcohols 7-18
FEEDBACK 7-20
UNIT 8 – AMINES
8.2 Classification 8-1
8.4 Reactions of amines 8-3
8.4.1 Amines as bases 8-3
8.4.2 Reactions with amines with acids 8-4
8.4.3 Amines as nucleophiles 8-5
8.4.4 Quaternary ammonium salts 8-6
FEEDBACK 8-7
UNIT 9 – CARBONYL COMPOUNDS (ALDEHYDES AND
KETONES)
9.2 Nomenclature of aldehydes and ketones 9-2
(a) Aldehydes 9-2
(b) Ketones 9-4
9.3.1 The nature of the carbonyl group 9-5
9.3.2 Addition of derivatives of ammonia 9-7
6
(a) Hydrazine (H2N-NH2 where Z ≡ NH2) 9-8
(b) Primary amines (NH2 – R where Z ≡ R ≡ alkyl group) 9-9

9.3.3 Addition reactions with oxygen compounds 9-10
9.3.4 Reduction of aldehydes and ketones 9-11
9.3.5 Oxidation of aldehydes and ketones 9-12
FEEDBACK 9-15
UNIT 10 – CARBOXYLIC ACIDS AND THE FUNCTIONAL

DERIVATIVES
A: CARBOXYLIC ACIDS
10.1 General information 10-1

10.1.1 Carboxylic acids 10-1
10.1.2 Carboxylic acid derivatives 10-2
10.3 Classification of carboxylic acids 10-4
10.4 Structure 10-5
10.5.1 Breaking of the OH-bond with bases 10-5
B: FUNCTIONAL DERIVATIVES
10.6 General 10-7

10.7 Esters 10-8
10.7.2 Synthesis of esters 10-9
10.7.3 Reactions of esters 10-9
10.8 Amides 10-12
10.8.2 Reactions 10-13
10.8.3 Preparations of amides 10-13
7
FEEDBACK 10-14
UNIT 11 – ORGANIC CHEMISTRY IN BIOLOGY

11.1 Functional groups 11-1
11.1.1 Summary of functional groups 11-1
11.1.2 Other biologically important functional groups 11-2
a) Phosphates 11-2
b) Sulphur containing derivatives 11-2
11.2 Important classes of biological molecules 11-4
11.2.1 Lipids 11-4
a) Fatty acids 11-5
b) Fats and oils 11-5
c) Waxes 11-5
d) Isoprenoids 11-6
11.2.2 Biopolymers 11-7
a) Carbohydrates 11-7
b) Amino acids and proteins 11-8
c) Nucleic acids (DNA and RNA) 11-12
FEEDBACK 11-16
************************
1-1
UNIT 1: INTRODUCTION TO ORGANIC
CHEMISTRY
LEARNING OUTCOMES:
By the end of this unit you must:
• know the difference between a structural and molecular formula.
• understand the chemical bond.
• understand hybridization and polar covalent bonds.
• know the different ways to break and form bonds.
• know the definition of an electrophile and a nucleophile.
1.1 INTRODUCTION
Organic Chemistry is described as the chemistry of compounds containing the element

carbon (C). Most organic compounds not only contain carbon, but also hydrogen (H) and
oxygen (O) and to a lesser extent other elements, e.g., sulphur (S), nitrogen (N),
phosphorous (P) and others that play important roles in biological chemistry. Well over
95% of all known chemical compounds are organic in nature.
Currently more than 8 million organic molecules, which grow at a rate of ca 6% per
annum, are known. This huge number of compounds is attributed to the unique property
of carbon atoms to attach themselves to one another to form chains or rings of all sizes.
Organic chemistry is a field of immense importance as it is the chemistry of dyes, drugs,
paints, plastics, rubber tyres; it is the chemistry of the food we eat and the clothing we
wear. The pharmaceutical industry relies mainly on organic compounds.
1-2
The use of certain organic chemicals dates well back into history. An extract
from willow bark, a precursor to modern aspirin, was used by country folk as a
pain reliever in early England.
O
OH
CH3
O
O Aspirin
1.2 IDENTIFICATION OF ORGANIC COMPOUNDS
One task of organic chemists is to determine the chemical structure of newly discovered
compounds. To identify an organic compound, it is necessary to determine:
(a) which elements are present in the compound and in what proportions are they
present.
From qualitative analysis a molecular formula is deduced, e.g. C3H8O.
(b) what is the arrangement of the elements present.
(that is the structural formula for the compound)
H H H H H H
E.g. C3H8O could be H C C C OH or H C C O C H
H H H H H H
(c) Other analytical methods are then utilised to determine which structure is the
correct one.
Activity 1: What is a molecular formula?
See feedback at end of unit→

1-3
1.3 THE CHEMICAL BOND
The chemical bond is the attracting force that keeps atoms together in a molecule. The
chemical bond is based on the view that an atom is comprised of a nucleus and electrons
in atomic orbitals.
1.3.1 BOND FORMATION
The covalent bond results from the sharing of electrons. When two atomic orbitals
(A.O,s) (e.g. the 1s of H) overlap under certain conditions, a new orbital, namely the
molecular orbital (M.O.) is formed, which encircles both the atomic nuclei and is cylindrical
in symmetry (shape) regarding the line that attach the two orbitals.
atomic orbitals overlapping molecular orbital

(e.g. 1s of H) (M.O. of e.g. H2)
For two atomic orbitals to overlap, it is necessary that:

(a) the energy level of the atomic orbitals must be the same
(b) the total number of electrons in the two atomic orbitals must be equal to two, i.e.
each atomic orbital is occupied by one electron or one atomic orbital has two
electrons while the other atomic orbital is vacant.
The two electrons in the A.O,s now occupy the new M.O. and they have opposite spins.
This electron pair is now shared by both nuclei. Each electron is thus attracted by two
positive nuclei. The energy of the M.O. is lower than the sum of the energies of the two
A.O,s. therefore bond formation is an energy releasing process. This attracting force
keeping the nuclei together, is called a COVALENT σ (sigma)-BOND.
1-4
Activity 2: Can we form a covalent bond between two atomic orbitals when each of
them contains two electrons and give a reason?
1.3.2 ELECTRON CONFIGURATION OF THE CARBON ATOM
According to the quantum mechanics theory (See INORGANIC CHEMISTRY, UNIT 2) the
electron structure of the carbon atom in the ground state can be illustrated as follows:
1s2, 2s2, 2px1, 2py1, 2pz0
↑ 2px ↑ 2py 2pz

Energy ↑↓ 2s
↑↓ 1s
It is clear from this that there are only two unpaired electrons (valence electrons)
available to form bonds (and a carbon atom ALWAYS forms four bonds). Addition of a
small quantity of energy transfers one of the 2s-electrons to the empty 2pz-orbital to give
the excited state with four unpaired electrons, which are now available to form four
chemical bonds.
1s2, 2s1, 2px1, 2py1, 2pz1
Activity 3: Illustrate the electron structure of the carbon atom in the excited state.

1-5
1.3.3 sp3-HYBRIDIZATION OF CARBON ATOMS
If the 1s-orbital of hydrogen atoms overlaps with the four atomic orbitals of carbon (2s1,
2px1, 2py1 2pz1), the nature of the resulting molecule (CH4) is not identical to the true nature
of CH4. The fact that the four C-H bonds of CH4 are identical is explicable only in terms of
hybridization (mixing or fusion) of atomic orbitals.
The 2s-orbital and the three 2p-orbitals combine to form 4 identical sp3-hybrid orbitals,
each containing one electron.
2s 2px 2py 2pz orbitals

identical sp3
Only 2 bonds possible 4 bonds possible
These 4 hybrid orbitals are directed towards the corners of a tetrahedron with an
interorbital angle of 109,5o. Each sp3-hybrid orbital has 25% s- and 75% p-character.
sp3-hybrid H
H 109.50
H
overlap of
H H H
atomic
orbitals H
H formation of molecular
tetrahedron orbitals (the molecule)
1-6
Methane is represented as follows (each line represents a covalent bond):

behind
H
In the plane of the paper
H
C
in front H bond angle 109.50
H C-H bond lenght 0.11 nm
This structure is representative of the three-dimensional nature of the molecule, but (if the
three-dimensionality is not required) it can also be represented in the following ways:
H
H C H and CH4
H
The sp3-hybrid orbital of one carbon atom may overlap with the sp3-hybrid orbital of
another carbon atom to form a covalent σ-bond between the two carbons.
1-7
These structures are normally represented as:
Alternatively:
H H
H C C H or CH3 CH3 or CH3CH3
H H
1-8
1.4 POLAR COVALENT BONDS
Two atoms joined by a covalent bond share the electron pair in the M.O. When the atoms
are alike, as in the case of the H-H bond in H2, the electron pair in the bond is shared
equally by the two atoms. In many cases, however, the two nuclei are not identical [they
differ in electronegativity (electronegativity of an atom is the attraction the atom has for
the electrons in a molecule)] like C and Cl in CH3Cl. They do not share the electron pair
equally and the electron cloud is denser around the more electronegative atom (Cl). One
end of the bond is thus relatively negative and the other end is relatively positive. Such a
bond is said to be a POLAR COVALENT BOND.
H
H +
− −
δ δ δ + δ
H C Cl H C Cl
H
H
−
δ+ and δ are partial charges
IMPORTANT: Polar covalent bonds are weaker than C−C and C−H bonds and can
break easier as less energy is required.
Activity 4: Is the bond between the two C atoms in CH3CH3 polar and give your
reason.
1.5 REACTIONS AND REACTION MECHANISMS
It is important to know not only WHAT happens in a chemical reaction but also HOW it
happens. A reaction mechanism is a step-by-step description of what is happening on
molecular level when a reagent is changed into a product by a chemical reaction. A
1-9
mechanism provides information about which bonds are broken, and which bonds are
formed during the reaction.
A curved arrow ( ) shows the movement of electrons when bonds are broken or
formed. The curved arrow always starts at the initial position of electrons and end at their
final position.
Straight arrows ( ) point from reactants to products in chemical reaction

equations.
1.5.1 BOND CLEAVAGE

There are two ways in which covalent bonds are broken:
(a) Homolytic cleavage is the transfer of one electron in the bond to both A and B to
give two neutral fragments called free radicals, which possess an odd
(unpaired) electron. The free radicals are the reactive intermediates in a
mechanism.
A B or A B A + B (free radicals)
Cl Cl 2 Cl
The half-arrow ( ) indicates the flow of one electron.
(b) Heterolytic cleavage is the transfer of the electron pair to the more
electronegative atom to give positive and negative ions.
1-10
Assume B is the more electronegative atom:
A B or A B A + B
H H
H C Cl H C + Cl
H H
The full arrow ( ) indicates the flow of two electrons.
Activity 5: What is the difference between homolytic and heterolytic cleavage?
1.5.2 BOND FORMATION

Bonds can now form in the same way:
(a) Homolytic bond formation (where each atom donates one electron)
(i) A + B A B
(ii) Cl + Cl Cl Cl
(b) Heterolytic bond formation (where one atom donates both electrons)
(i) A B A B
Cl CH3 Cl CH3
(a negative ion can react with a positive ion)

1-11
(ii) A B A B
H
H2O CH3 O CH3
H
(a neutral specie e.g., H2O with a non-bonded electron pair can react with a
positive ion)
IMPORTANT:
* The curved arrow always starts in an area of HIGH ELECTRON DENSITY (that is an
atom with a negative charge or a non-bonded electron pair) and is always moving
towards an area of LOW ELECTRON DENSITY (that is an atom with a positive
charge or an atom which contains a partial positive charge due to a polar covalent
bond.)
* A POSITIVELY charged carbon is called a CARBOCATION.
A NEGATIVELY charged carbon is called a CARBANION.

* Radicals and carbocations are electron-loving (due to a shortage of electrons they
are seeking for electrons) and are called ELECTROPHILES.
* Carbanions and other species which are electron-rich (due to a negative charge or a
non-bonded electron pair which can donate electron density) are called
NUCLEOPHILES. (N have a filled 2s-orbital and O have a filled 2s- and 2p-orbital
which are not used in bonding with other atoms, therefore it is a non-bonded
electron pair.
Examples of electrophiles/electrophilic compounds
(a) CH3 (b) CH3 CH2 (c) CH3 CH2 I
Examples of nucleophiles/nucleophilic compounds
(a) HO (b) I (c) H 2O
(d) NH3 (e) NaCN

1-12
Activity 6: Draw an electron structure for O (oxygen). How many non-bonded

electron pairs are there in O (oxygen) in H2O?
Activity 7: Why is H2O a nucleophile and give a reason for you answer?
Activity 8: Identify the following atoms/groups as electrophiles or nucleophiles.
(a) Cl (b) NH3
(c) CH3CH2 (d) CH3CHCH3
Activity 9: Use arrows to indicate the homolytic cleavage in BrBr and show the
products.

1-13
Activity 10: Use arrows to indicate the heterolytic cleavage in CH3Br and show
the products.

1-14
FEEDBACK FOR UNIT 1

1. A molecular formula describes which elements are present in a compound and in
what proportions are they present.
2. No, the total number of electrons in a molecular orbital is two. For bond formation
there must be one electron in each of the atomic orbitals, or one atomic
orbital must be vacant while the other atomic orbital contains two electrons.
3. 1s2, 2s1, 2px1, 2py1, 2pz1
↑ 2px ↑ 2py ↑ 2pz
Energy ↑ 2s
↑↓ 1s
4. No, the two identical carbon atoms have the same electronegativity. For a polar
covalent bond, you need a difference in electronegativity.
5. In homolytic cleavage one electron goes to each of the atoms. In heterolytic
cleavage both the electrons go to one atom.
6. 1s2, 2s2, 2px2, 2py1, 2pz1
↑↓ 2px ↑ 2py ↑ 2pz
Energy ↑↓ 2s
↑↓ 1s
Two non-bonded electron pairs

7. There is a non-bonded electron pair on the oxygen to make the oxygen electron
rich and able to donate electron density.
8. (a) Nucleophile, (b) Nucleophile, (c) Electrophile, (d) Electrophile

9.
Br Br 2 Br
10.
H H
H C Br H C + Br
H H
1-15
ADDITIONAL PROBLEMS
1. Draw the electron structure of the carbon atom in the excited state.
2. Use arrows to show the homolytic cleavage of Br2 and show the products.
3. Identify the following ions/compounds as nucleophiles or electrophiles?
(a) CN
(b) CH3 I
(c) Br
(d) CH3
CH3 C
CH3
2-1
UNIT 2: ALKANES AND CYCLOALKANES
LEARNING OUTCOMES:
By the end of this unit, you should be able to:

• write down a complete IUPAC name for the alkanes as well as the
trivial names.
• understand the alternative ways of drawing structures.
• be able to classify carbon atoms in a structure.
• answer questions en understand the principle of the octane number
of fuels.
2.1 INTRODUCTION
The alkanes and cycloalkanes belong to a family of organic compounds, which only
contain carbon and hydrogen atoms (hydrocarbons) in their molecular structures. The
main sources of hydrocarbons are fossil fuels, e.g., crude oil and coal. Acyclic
compounds contain no ring systems, while the cyclic compounds always contain at
least one ring system. In this unit we shall look at the system used to name the alkanes,
look at different ways to draw a structure, structural isomerism, and the reactions of
alkanes.
2.2 BASIC INFORMATION

Members in the same family have the same general molecular formula:
(a) ALKANES: CnH2n+2 (n = 1,2,3 ...)

(For n = 1, you get the formula C1H2x1 + 2 = CH4; for n = 3, you get the
formula C3H3x2 + 2 = C3H8)
(b) CYCLOALKANES: CnH2n (n = 3,4,5 ...)
(Cycloalkanes are saturated hydrocarbons in which the carbon atoms form a
ring)
2-2
A series of compounds in which each member differs from the next member by a constant
number of atoms, is called a homologous series.
e.g. CH4, CH3CH3 or (C2H6), CH3CH2CH3 or (C3H8) ⇒ differ by a (CH2) group
The C-atoms of alkanes and cycloalkanes (except for the highly strained cyclopropane and
cyclobutane) are sp3-hybridized with a bond angle of ca. 109.5o between C-atoms. (
Unit 1, par. 1.4).
2.3 NOMENCLATURE
2.3.1 NOMENCLATURE OF ALKANES
IUPAC rules will be applied to name alkanes and cycloalkanes systematically. IUPAC
stands for the International Union of Pure and Applied Chemistry who control, revise and
expand the rules for naming compounds.
(a) Basic names
According to the IUPAC rules each alkane is given a name by

(i) using a Greek prefix for the number of carbon atoms followed by
(ii) the -ane ending indicating it to be an alkane.
2-3
No of carbons Structure Name

1 CH4 Methane
2 CH3-CH3 Ethane
3 CH3-CH2-CH3 Propane
4 CH3-CH2-CH2-CH3 Butane
5 CH3-CH2-CH2-CH2-CH3 Pentane
6 CH3-CH2-CH2-CH2-CH2-CH3 Hexane
7 CH3-CH2-CH2-CH2-CH2-CH2-CH3 Heptane
8 CH3-CH2-(CH2)4-CH2-CH3 Octane
9 CH3-CH2-(CH2)5-CH2-CH3 Nonane
10 CH3-CH2-(CH2)6-CH2-CH3 Decane
(b) Alkyl groups
When a hydrogen atom is removed from an alkane molecule, the remaining group is called
an alkyl group and named by dropping the -ane ending from the name of the
corresponding alkane and replace it by -yl. Alkyl groups are extensively used in the
nomenclature of complex alkanes, cycloalkanes, and other compounds.
Basic names Alkyl groups
Structure Name Structure Name
CH4 Methane CH3- Methyl
CH3-CH3 Ethane CH3CH2- Ethyl
CH3-CH2-CH3 Propane CH3CH2CH2- Propyl
CH3-CH2-CH2-CH3 Butane CH3CH2CH2CH2- Butyl
CH3 t-butyl or ters-butyl#
H 3C C
CH3
# t or ters (tertiary) means that there are three carbon atoms bonded to the central carbon atom of the alkyl
Group
2-4
Activity 1: Name the following groups or compounds: (a) CH3CH3, (b) CH3-,
(c) CH3CH2CH2CH2CH2CH2CH3 (Hint: Count the number of carbon
atoms).
See feedback at end of unit →
(c) IUPAC rules for naming complex alkanes
(i) Select the longest continuous (not necessarily straight or horizontal) carbon
chain as the parent structure. The base name of the branched-chain alkane is
corresponding to the number of carbon atoms in the longest chain. Hydrogens
can be replaced by alkyl groups, which are called substituents.
Alkyl group (substituent)
CH3
CH3CH2CHCH2CH3
longest carbon chain (parent structure)
There are five carbons in the longest carbon chain, so the base name is pentane.
Alkyl group (substituent)

CH3CH2CH2CHCH3
CH2
CH3 longest carbon chain (parent structure)
There are six carbons in the longest carbon chain, so the base name is hexane.
(ii) The name of a substituted alkane must tell us the nature of the substituent and
the number of the carbon atom to which it is attached. The carbon atoms in the
longest straight chain are numbered starting from one end, so that we can identify
the carbon atom to which the substituent is linked. You start numbering from
whichever end will give the lower number for the position of the substituent. To
write down the IUPAC name:
2-5
(a) Indicate the position of alkyl groups on the carbon chain by giving the
number of the carbon atom to which it is attached.
(b) Give the name of the alkyl group,
(c) followed by the name of the parent structure.
1 2 3 4 5 6 7 7 6 5 4 3 2 1
CH3CH2CHCH2CH2CH2CH3 not C H3C H2C HCH2CH2CH2CH3
CH3 CH3
3-Methylheptane 5-Methylheptane
Note: The name of the substituent and the base name are written as a single word, with
a hyphen following the number (position of the substituent) e.g. 3-methylheptane.
Activity 2: Number the carbon atoms correctly to indicate the position of the
substituent and give the complete IUPAC name.
(a) CH3 (b) CH3CH2CHCH3 (c) CH3CH2CH2
CH3CHCH2CH2CHCH2CH3 CH2CH3 CHCH3
CH3 CH2CH3
(iii) If there are several different alkyl groups e.g. a methyl and ethyl group attached to
the parent chain, number the longest carbon chain to give the substituents the
lowest possible numbers and name them in alphabetical order.
CH3 C H3
8 7 6 5 4 3 2 1 1 2 3 4 5 6 7 8
CH3C H2C H2C HC H2C H2CHC H3 not C H3CH2CH2C HC H2CH2C HC H3
C H2CH3 C H2C H3
5-Ethyl-2-methyloctane 4-Ethyl-7-methyloctane
2-6
Explanation: If you start numbering the carbon chain from the right hand side the
numbers of the substituents are [2,5]. From the left hand side the numbers of the
substituents are [4,7], so numbering from the right hand side gives you lower numbers and
is the correct option. The ethyl group is then at position 5 and the methyl group is at
position 2. To write down the IUPAC name you must arrange the substituents in
alphabetical order so the ethyl group at position 5 will be written first, followed by the
methyl group at position 2.
Note the use of hyphens.
Activity 3: Give the complete IUPAC names for the following compounds. (Hint:
Identify the longest carbon chain and number the carbons likewise to
give the substituents the lowest possible numbers.)
(a) CH2CH3 (b) CH3
CH3CHCH2CHCH2CH3 CH3CH2CH2CHCH2CHCH3
CH3 CH2CH2CH3
(iv) If the same alkyl group occurs more than once as a side chain, indicate this by the
prefix di- (for two alkyl groups), tri- (for three alkyl groups), tetra- (for four alkyl
groups), etc. to show how many of these alkyl groups there are, and indicate by
various numbers the position of each group. (NB: If there are three methyl
groups you must have three numbers e.g. 3,3,4 followed by tri to indicate it is three
methyl groups)
IMPORTANT: If you are arranging the substituents according to the alphabet you don’t
consider prefixes like di- and tri-. You only consider the names of the
alkyl groups. (See the following example)
2-7
CH3
1 2 3 4 5 6
CH3CCH2CHCH2CH3
CH3 CH2CH3
4-ethyl-2,2-dimethylhexane
Explanation: Numbering from the left-hand side gives you two substituents on carbon 2
and one substituent on carbon 4. [2,2,4] Numbering from the right-hand side gives you
one substituent on carbon 3 and two substituents on carbon 5. [3,5,5] It is therefore
[2,2,4] vs. [3,5,5]; for the lowest possible numbers the correct way is thus numbering from
the left-hand side. 4-Ethyl is written down first (4 to indicate the position of the ethyl group
and the ethyl group is before the methyl group in the alphabet) followed by 2,2-
dimethylhexane. (2,2 indicates there are two methyl groups on carbon 2 and dimethyl
indicates it is two methyl groups attached to the carbon)
Note: The position numbers of the substituents are separated by a comma and are
followed by a hyphen e.g., 2,2-dimethylhexane.
Activity 4: Give the complete IUPAC names for the following compounds.
CH3 CH3 CH2CH3 CH3
(a) (b)
CH3CHCH2CHCHCH3 CH3CH2CHCHCH2CHCH3
CH3 CH3
2.3.2 NOMENCLATURE OF CYCLOALKANES
(a) The cycloalkane are named by adding the prefix cyclo- to the name of the alkane
having the same number of carbon atoms.
2-8
C H2 C H2 C H2
C H2 CH2 C H2 CH2
Cyclopropane Cyclobutane
(b) In the cycloalkane, WHEN THERE ARE TWO ALKYL SUBSTITUENTS,

numbering starts at the alkyl group coming first when the groups are arranged in
an alphabetical order and proceeds around the ring in a clockwise or
counterclockwise manner in such a way as to give the lowest number for the
other alkyl group. If there are THREE OR MORE ALKYL GROUPS, the
numbering is done in order to give the substituents the lowest combination of
numbers regardless the alphabetical order.
(c) Substituents (alkyl groups) are written in alphabetical order with numbers of the
carbon atoms to which they are attached as a prefix to the basic name of the
cycloalkane.
6
CH2
5CH 1
2 CHCH2CH3
substituents
4
CH2 CHCH3
CH2 2
3
1-Ethyl-2-methylcyclohexane
Explanation: Identify the number of carbon atoms in the ring. There are six carbons in
the ring, so the base name is hexane with the prefix cyclo to indicate it is a ring system.
There are two alkyl groups, so you start numbering at the substituent which is first in the
alphabet: in this case ethyl. If you number clockwise the methyl substituent will be at
carbon 2. If you number counterclockwise the methyl substituent will be at carbon 6, so to
give the methyl group the lowest possible number you must number clockwise.
2-9
acyclic alkane
H H H H H2
H C H C CH3
C C C or H 3C or
C
H H H H H2
cyclic alkane
H H
H H
C H2
C
H C C H
or H 2C CH2 or
C C
H H H2C CH2
H H
Activity 5: Give the complete IUPAC name for the following compounds.
a) b) CH3
H 2C CH2
CH
HC CH H 2C CHCH2CH3
CH3 CH3 H2C CHCH3

C
H2
2.4 ALTERNATIVE WAYS OF DRAWING STRUCTURES
For convenience, structures of compounds are often represented by simple geometric

figures. It is understood that hydrogens are omitted and that the 'beginning', 'end' and
each 'bend' of a line represents a carbon atom.
H2
C
H 3C CH3
propane
2-methylbutane 2,3-dimethylbutane 1,2-dimethylcyclobutane

2-10
H H H
H2
H C C C H C
H 3C CH3
H H H
HH HH
H2
H H C
H 2C CH2
H H
H2C CH2
H H
Activity 6: Write down the following structures according to the shorthand method
and give the complete IUPAC name.
CH3
a) H2 b) CH3CHCH2CHCH3
C C CH3 CH3
H3C C H CH3
H2
Activity 7: Write down the following structures in full and give the complete IUPAC
name for each of them.
a) b)

2-11
2.5 CLASSIFICATION OF CARBON ATOMS
(a) Primary (10): Carbon atom bonded to no other carbons or bonded to one
other carbon atom.
(b) Secondary (20): Carbon atom bonded to two other carbons.
(c) Tertiary (30): Carbon atom bonded to three other carbons.
(d) Quaternary (40): Carbon atom bonded to four other carbons.
ο
2 ο
ο
1
4
ο 3
ο
3
ο
1
Activity 8: Classify carbons (a) - (e) as primary, secondary etc.
(a)
(d)
(b)
(c) (e)

2-12
2.6 STRUCTURAL ISOMERISM
Compounds that have the same molecular formula, but differ in molecular structure, are
called STRUCTURAL ISOMERS. (The atoms are attached to one another in different
ways).
In the case of n-butane (not N-butane) there is only an UNBRANCHED carbon chain
(there are only primary and secondary C-atoms present). If a compound has tertiary
and/or quaternary C-atoms, the compound has a BRANCHED carbon chain e.g. 2-
methylpropane or isobutane.
We can also write structural isomers for pentane (C5H12).
Activity 9: Give a structural isomer for 2,2-dimethylbutane.
Activity 10: Give a structural isomer/s for the following compounds:
CH3
(a) CH3CHCH2CH3 (b)
(c) Cl (d) H3CHC CHCH3

2-13
2.7 CHEMICAL BEHAVIOUR OF ALKANES AND
CYCLOALKANES
For chemical reactions to take place, it is necessary to break bonds. The bonds
associated with alkanes and cycloalkanes (excluding cyclopropane and cyclobutane) are
strong bonds. The bond-dissociation energies for C-C and C-H bonds are respectively
404 and 355 kJ mol-1, which are considerably more than e.g., the weaker C-Br bond which
requires ca. 290 kJ mol-1 to break. Due to the high dissociation energies, alkanes, and
cycloalkanes (excluding cyclopropane and cyclobutane) are chemically inert under
normal reaction conditions. (Alkanes and cycloalkanes do not react easily.)
There are only two reactions of interest to you for the alkanes:
(a) Oxidation (combustion)
(b) Reaction with halogens e.g., chlorine or bromine
2.7.1 OXIDATION
Oxidation (combustion) of hydrocarbons is one of the most important organic reactions.
The burning of huge amounts of natural gas, gasoline and fuel oil involves mostly
combustion of hydrocarbons. These reactions lead to the formation of carbon dioxide and
water with the liberation of energy, usually heat.
 3n + 1
CnH2n+2 +   O2 → nCO2 + (n+1)H2O + Energy
 2 
E.g. CH4 + 2O2 → CO2 + 2H2O (∆H = -882 kJ mol-1)
Activity 11: Write down all the possible products for the following reaction.
O2
complete combustion

2-14
2.7.2 HALOGENATION
Alkanes react with halogens when the reaction mixture is heated or irradiated:
IMPORTANT: Without the addition of heat or light to the alkanes, NO reaction

will take place.
The proposed MECHANISM for the reaction must be in accordance with all the
experimental evidence. Remember a reaction mechanism is a step-by-step description
of what is happening on molecular level when a reagent is changed into a product by a
chemical reaction. A mechanism provides information about which bonds are broken, and
which bonds are formed during the reaction (read Unit 1, page 1-8: 1.5 REACTIONS AND
REACTION MECHANISMS.)
The following observations can be made for the chlorination of methane:

(a) An H-atom of CH4 is substituted by a Cl-atom (substitution reaction).
(b) Two bonds are broken, viz. C-H and Cl-Cl.
(c) Two bonds are formed, viz. C-Cl and H-Cl.
It was determined that the halogenation of alkanes proceeds according to a radical

mechanism. Thus, bond cleavage and bond formation will occur homolytically (see Unit
1.5, page 1-9). Remember, in an alkane each carbon in the molecule can be substituted:
Cl
∆
CH3-CH2-CH3 Cl-CH2-CH2-CH3 + CH3-CH-CH3 + HCl
Cl2
only mono-halogenized products
thus, only 1 Cl for each molecule)
2-15
Activity 12: Write down all the possible products for the following reactions.
∆
a) H 3C CH3 mono-halogenated products
Cl2
b) ∆
mono-halogenated products
Cl2
c)
∆
mono-halogenated products
Cl2

2-16
FEEDBACK FOR UNIT 2

1. (a) ethane (2 carbons)
(b) methyl (1 carbon, 1 H is removed)
(c) heptane (7 carbons)
2. a)
2,5-dimethylheptane
b)
3-methylpentane
c)
3-methylhexane
2-17
CH2CH3
1 2 3 4 5 6
3. (a) CH3 CHCH2 CHCH2 CH3
CH3
4-ethyl-2-methylhexane
CH3
7 6 5 4 3 2 1
(b) CH3CH2CH2CHCH2CHCH3
CH2CH2CH3
2-methyl-4-propylheptane
CH3 CH3
6 5 4 3 2 1
4 (a) C H3CHC H2CHCHC H3
CH3
2,3,5-trimethylhexane
CH2CH3 CH3
(b) CH3CH2CHCHCH2CHCH3
7 6 5 3 2 1
CH3
5-ethyl-2,4-dimethylheptane
5.a) 1,2-dimethylcyclobutane
b)
CH3
6 1 CH 2
H 2C CHCH2CH3
H2C CHCH3
5 4C 3
H2
2-ethyl-1,3-dimethylcyclohexane
There are three alkyl groups, so you must number the substituents to have the lowest
possible numbers.
2-18
6.a)
4 2
5 1
3
2-methylpentane
b)
3
1 2 4 5
2,4-dimethylpentane
7.a)
CH3
6 1 CH 2
H 2C CH2
H2C H CH2
5 C 3
4
CH3
1,4-dimethylcyclohexane
b)
7
6 CH3
H 2C
H2 1
CH 4 C H CH3
H3C 5 C 3 C
H2 2
CH3
2,5-dimethylheptane
8. (a) 10
(b) 30
(c) 20
(d) 40
(e) 10
9 or or
2-19
10.
a) b)
Cl
c) Cl d)
Cl
11. CO2 + H2O + Energy
12.
H2
a) Cl C CH3
Cl
b) Cl + Only 2 products
Cl Identical to top structures

when you rotate the
Cl structures
Cl
c) +
Cl
2-20
ADDITIONAL PROBLEMS
1. Write down the complete IUPAC names for the following compounds.
(a)
CH3 CH3
.................................................................................
(b)
(CH3)3CH
.................................................................................
(c) CH2CH3
CH3CHCH2CHCH2CHCH3
.................................................................................
CH2CH3 CH3
(d)
.................................................................................
Br
(a) (b) CH3CHCH2CHC(CH3)3
F CH3
Br
(c) (d) CH3(CH2)3CH3
3. Write down two structural isomers for C5H10.
4. Consider the following reaction:
(A)
(a) What is the hybridization state of the carbon atoms in (A)?

(b) What type of carbon is C-1 in (A) e.g. 3º?
3-1
UNIT 3: ALKYL HALIDES
LEARNING OUTCOMES:
By the end of this unit you should be able to:

• classify monohalogen compounds.
• write down a complete IUPAC name for the alkyl halides.
• understand the characteristics of the functional group.
• write down the products in nucleophilic substitution reactions.
• write down all the possible products in ionic elimination reactions using
Saytzeff's rule.
• demonstrate your knowledge of the practical application of alkyl halides.
3.1 INTRODUCTION
Substitution of one or more of the hydrogen atoms in alkanes with a halogen atom
(F, Cl, Br or I) results in the formation of a group of organic compounds known as the alkyl
halides. The bond between the carbon and halogen is a covalent bond so the carbon
atom is sp3-hybridized.
Functional group: C X
General formula for monohalogen compounds:

CnH2n+1X with X = F, Cl, Br or I
Alkyl halides are usually symbolized by R-X where R = an alkyl group and X = a halogen
atom. According to the number of halogen atoms in the compounds, the alkyl halides can
be divided into mono-, di- and polyhalogen compounds.
3-2
3.2 CLASSIFICATION OF MONOHALOGEN COMPOUNDS
Monohalogen compounds are compounds where only one of the hydrogen atoms is
substituted with a halogen. The classification of the monohalogen compounds is based on
the nature of the halogen bearing carbon atom in the molecule. If the halogen atom is
for example bonded to a secondary (2°) carbon, the compound is known as a secondary
alkyl halide, e.g.:
CH2 R
R- CH2
R CH2 CH2 X CH X R CH2 C X
R- CH2
CH2 R
1° alkylhalide 2° alkyl halide 3 -alkyl halide
°
where X = halogen
Activity 1: Classify the following alkyl halides.

a) Cl
b) Br
3.3 NOMENCLATURE
In the case of the alkyl halides, hydrogens in the hydrocarbon are replaced by halogen
substituents. The -ide suffix of the halide is replaced by “o” and these substituents
indicated as fluoro-, chloro-, bromo- and iodo-. Halogens are treated just like alkyl
substituents in the IUPAC system (i.e. subordinate groups indicated as prefixes with no
priority rules; see Table A-1 in Appendix A-1).
Halogens ≡ Alkyl groups

3-3
(a) The base name is determined by the number of carbons present in the longest
continuous carbon chain.
(b) The chain is numbered from the side closest to the first substituent, whether alkyl
or halogen, and the substituents listed in alphabetical order.
Br
3-bromo-2-methylpentane
Br Br
3-bromo-2-methylpentane 5-bromo-2,4-dimethylheptane
Br
3-bromo-2,4,6-trimethylheptane
(c) If (b) is not conclusive and substituents are at equal distances from the end,
numbering starts at the end nearer to the substituent that comes first when placed
in alphabetical order.
CH3CH2CHCHCH2CH3
Cl CH3
3-chloro-4-methylhexane
(d) Halo-cycloalkanes follow the same rules as cycloalkanes.
Br
Br
1-bromo-2-methylcyclobutane 1-bromo-3-ethyl-5-methylcyclohexane
3-4
Cl
1-chloro-3-ethyl-2-methylcyclopentane
I
(a) CH3CH2CHCH2CHCH2CH3 (b) Br
CH2
CH3
Activity 3: Write down the complete IUPAC names for the following compounds.
a) Cl b)
Br
c) d)
Cl
I

3-5
3.4 CHEMICAL PROPERTIES
3.4.1 CHARACTERISTICS OF THE FUNCTIONAL GROUP
In contrast to the chemically stable alkanes, the haloalkanes readily undergo a wide
spectrum of reactions e.g. substitution and elimination reactions. The reactivity of
especially the chloro-, bromo- and iodo-alkanes is ascribed to:
(a) the lower dissociation energy of the carbon-halogen (C-Cl, C-Br and C-I) bonds
compared to the carbon-hydrogen (C-H) bond in alkanes - you need less energy to
break a carbon-halogen bond. For C-Cl you need ≈ 338 kJ mol-1, C-Br ≈ 290 kJ
mol-1 and C-I ≈ 224 kJ mol-1 in contrast with the C-H bond which needs ≈ 404 kJ
mol-1.
(b) the difference in electronegativity between carbon and halogen (halogens are
more electronegative) that results in polarized carbon-halogen bonds.
Explanation: Owing to the higher electronegativity of the halogen, the valence electrons
(electrons in the outer shells) involved in the halogen-carbon bond are attracted more
towards the halogen. This results in the induction of a fractional negative charge (δ-)
on the halogen and a fractional positive charge (δ+) on the α-carbon (the carbon directly
bonded to the halogen) and thus a polarized covalent bond. A polar covalent bond
needs less energy to break than a C-H bond.
(c) the inductive effect.
Explanation: The α-carbon (C-atom directly attached to the halogen atom) tries to
compensate for the induced electron deficiency (the fractional positive charge) by
competing for the valence electrons of the β-carbons (β-carbons are the carbons
directly bonded to the α-carbon). The latter polarization is smaller in magnitude than that
in the carbon-halogen bond but still significant enough to induce electron deficiency (δδ+)
on the β-carbons. This phenomenon where the polarization is propagated further into the
carbon skeleton to the β-carbons can be depicted as follows:
3-6
−
δδ+ δ+ δ
R CH2 CH Cl
α 2
β
The polarization of a bond by an adjacent atom or group is known as the inductive

effect.
IMPORTANT: Owing to the induced fractional charge (δ+), the α-carbon of alkyl
halides becomes an excellent point of attack (electrophilic centre)
for electron donating species (nucleophiles) like
OH CN and NH3
The electron deficiency on the α-carbon can also be released if an H-ion is removed from
the β-carbon resulting in the formation of a double bond between the α- and β-carbons
and the departure of the halogen as a leaving group.
These two reactions (frequently encountered for the haloalkanes) can be summarized as
follows:
H
_
H C C Z + X
_
βC Cα X + Z
_
C C + ZH + X
X_= halogen
Z = nucleophile and/or base
In the top reaction (substitution) the halogen (X) is substituted by a nucleophile (Z) which
can be a neutral specie or an anion ( UNIT 1, p. 1-11). In the elimination reaction, base
abstracts the H on the β-carbon to form a double bond between the α- and β-carbons and
the halogen (X) acts as a good leaving group.
3-7
3.4.2 NUCLEOPHILIC SUBSTITUTION REACTIONS
Nucleophilic substitution reactions for the alkyl halides are basically those reactions where
the halogen atom is replaced (substituted) by an attacking nucleophile.
− δ+ δ-
In general: Nu: + RX → NuR + :X−
e.g.: CH3-Cl + aqKOH → CH3-OH + KCl
CH3-CH2-Br + aqKCN → CH3-CH2-CN + KBr
Activity 4: Write down all the possible products for the following reactions.
a)
CH3CH Br NaCN
CH3
b) Cl
KOH
c) NH3
CH3Cl

3-8
3.4.3 IONIC ELIMINATION REACTIONS (E-reactions)
Elimination reactions are characterized by the simultaneous removal of the halogen

and a hydrogen atom from the β-carbon in alkyl halides. The elimination reaction that
normally results in the formation of an alkene, is initiated by the addition of a hindered
strong base like the sodium or potassium salt of t-butanol (potassium tert-butoxide).
Aqueous NaOH or KOH is not sufficiently strong.
In general:
β α
R C H2 C H2 X + R O K R C H CH2 + R OH + KX
alkyl halide alkene
e.g. C H3 C H3
C H3 C H2 C H2 Br + C H3 C O K C H3 C H C H2 + C H3 C OH + KBr
1-bromopropane C H3 propene C H3
potassium tert -butoxide
The rule of Saytzeff: Saytzeff's rule states that in a situation where a compound
contains more than one β-carbon, thus making it necessary to exercise a choice to
predict the major product in the reaction, the H+ will preferably be removed from the β-
carbon with the fewer hydrogen atoms e.g.
from β′
β′ α β
° ° Major product
2 1 +
(CH3)3C O Na from β
Br
Byproduct
3-9
Activity 5: Write down all the possible products if potassium tert-butoxide reacts
with the following reagents. Indicate the major product where
applicable. (HINT: First identify the α- and all the β-carbons)
a) c) I
Br
b) d) Cl
Cl

3-10
FEEDBACK FOR UNIT 3

1. (a) 2° alkylhalide
(b) 3° alkylhalide
2. (a) 3-ethyl-5-iodoheptane
(b) 1-bromo-2-methylcyclohexane
3. (a) 4-chloro-2,2-dimethylpentane
(b) 3-bromo-2-methylheptane
(c) 3-iodo-4-methylheptane
(d) 1-chloro-1,2-dimethylcyclohexane
4.
(a) H
H 3C C CN
CH3
(b) OH
(c) CH3NH2
5.
(a)
(b)
major product
(c)
major product
(d)
major product
3-11
ADDITIONAL PROBLEMS
1. Give the complete IUPAC name for each of the following compounds.
a) Cl c)
...................................................... ......................................................
b) Br d) Cl
...................................................... ......................................................
2. Give all the products for the following reactions. Indicate the major product where
applicable.
a) OK
Br
b) aq. KOH
CH3CH2CHCH3
CH2Br
NH3
c)
I
3.
Br KCN
(A)
(a) Give a structural isomer for (A).

(b) Give the product for the above reaction.
4-1
UNIT 4: STEREOCHEMISTRY
LEARNING OUTCOMES:
By the end of this unit, you should:

• be able to identify a chiral centre.
• know the definition of an enantiomer and a racemic mixture.
• be able to determine the absolute configuration of a molecule.
4.1 INTRODUCTION
In UNIT 2 (par. 2.6) we looked at STRUCTURAL ISOMERISM where we had different

molecular structures for the same molecular formula - the atoms are attached to one
another in different order. Stereochemistry is that part of chemistry that deals with
structures in THREE DIMENSIONS. Stereoisomers are isomers which have the same
molecular formula, but they differ ONLY in the way the atoms are ORIENTED IN
SPACE.
CH3 CH3
H vs. Br
H3CH2C Br H3CH2C H
(1) (2)
Considering the above structures, you will see that the bromine atom is bonded to carbon
2 in both structures. The only difference is the orientation in space, where the bromine
atom in structure 1 is situated to the front and in structure 2 is situated to the back of the
plane of the paper. (Remember: a wig indicates an atom which is situated to the front
and a dotted line indicates that the atom is situated to the back. Straight lines are in the
plane of the paper.). Structures 1 and 2 is thus stereoisomers of each other. (Note that to
move from structure 1 to structure 2, bonds must be broken and reformed, thus it is not
just rotation).
4-2
4.2 CHIRAL COMPOUNDS AND ENANTIOMERS
At a first approximation, your right hand is identical to your left hand, and they are mirror
images of each other. These mirror images are NOT SUPERIMPOSABLE (you cannot
match them). This property that an object is not superimposable upon its mirror image is
called CHIRALITY.
Careful inspection of 2-bromobutane, reveals the following:

4-3
*
Careful inspection of 2-bromobutane, CH3 CH CH2CH3 reveals the following:
Br
(a) The three-dimensional structure of 2-bromobutane is not superimposable upon

its mirror image, so it is a chiral molecule.
CH3 CH3
C H H C stereocentrum
CH3CH2 CH2CH3
Br Br
enantiomer enantiomer
mirror
(b) These enantiomers can also be drawn by using the Fischer projection formulas.
C H3 CH3 CH3
Br H H Br H Br
C H3 C H2 CH2 C H3 CH2C H3
mirror
The centre of the cross indicates the chiral carbon atom. The two horizontal lines
indicate the two bonds to the front of the plane of the paper (in the direction of the
reader). The two vertical lines indicate the two bonds to the back of the plane of
the paper (away from the reader). This implies that the chiral centre is in the plane
of the paper.
(c) The two mirror images of 2-bromobutane are called ENANTIOMERS.
(d) The two mirror images are also stereoisomers because they differ in the relative
disposition of their atoms in space.
(e) The carbon atom is attached to four different groups or atoms, so it is referred
to as a CHIRAL CENTRE, STEREOCENTRE or ASYMMETRIC CENTRE.
(f) The specific orientation of the atoms/groups attached to a stereocentre is

referred to as the ABSOLUTE CONFIGURATION of the stereocentre.
4-4
Activity 1: Determine whether the following molecules are chiral or not and
indicate the position of the chiral centre where applicable.
a) b) c)
Cl H
Cl
4.2.1 OPTICAL ACTIVITY
Enantiomers have identical physical and chemical properties, but they differ with
respect to their interaction with PLANE-POLARIZED LIGHT.
When a chiral compound is placed in the path of plane-polarized light, the plane of
polarization is affected and ROTATION of the plane of the polarized light is observed (this
rotation is measured in degrees by an instrument called a polarimeter). One enantiomer of
a chiral compound will rotate the plane of polarized light CLOCKWISE (+ sign) and such a
compound is said to be DEXTROROTATORY, whereas the other enantiomer will rotate
4-5
the plane of the light COUNTERCLOCKWISE (− sign) and is said to be

LEVOROTATORY.
4.2.2 RACEMIC MIXTURE
A mixture of equal quantities of enantiomers (e.g. 50% D- and 50% L-configuration or

50% of R-enantiomer and 50% of S-enantiomer) is called a racemic mixture and such a
mixture is optically inactive (rotation equals zero degrees).
4.3 ABSOLUTE CONFIGURATION: THE R,S CONVEN-
TION
45 min
A system of nomenclature was introduced by Cahn, Ingold and Prelog whereby the
PRECISE ARRANGEMENT of the atoms/groups attached to a stereocentre is specified,
i.e. the ABSOLUTE CONFIGURATION of the stereocentre (asymmetric carbon atom) is
assigned.
4-6
The system involves the following:

(a) Identify the FOUR DIFFERENT SUBSTITUENTS attached to the stereocentre.
Assign each substituent with a PRIORITY according to the following rules.
(i) The priority of each substituent is determined by considering the ATOMS

DIRECTLY ATTACHED to the stereocentre.
(ii) A higher atomic number has higher priority than a lower atomic number.
If two or more atoms directly attached to the stereocentre have the
same priority (that is the same atomic number e.g. 2 C atoms), look at
the next atoms and compare their atomic numbers.
(b) When the PRIORITY of each substituent has been assigned, the molecule is
rotated in space so the substituent with the LOWEST priority is directed AWAY
from you. Observe the arrangement of the remaining substituents and if the
sequence from FIRST TO SECOND TO THIRD PRIORITY is CLOCKWISE, the
ABSOLUTE CONFIGURATION of the stereocentre is specified as R. If the
sequence is COUNTERCLOCKWISE, it is specified as S.
CH2CH3
1 2 3 4
C Priorities: Br>CH2CH3>CH3>H
H
Br
H 3C
(S)-2-bromobutane
Explanation: Bromine has the highest atomic number and has therefore the highest
priority. The other atoms directly attached to the chiral centre are two carbons and a
hydrogen. As hydrogen has an atomic number of one, it will always have the lowest
priority. The atomic number of the carbons is the same, so we look at the atoms attached
to the two carbons. The carbon of the CH3-group is attached to three hydrogens [H,H,H]
where the carbon in the ethyl group is attached to two hydrogens and another carbon
[H,H,C]. The ethyl group will therefore have a higher priority than the methyl group. The
substituent of lowest priority, the hydrogen, is already situated to the back (directed away
from you) and the arrangement of the remaining substituents from first to second to third
priority is counterclockwise. Therefore, the absolute configuration is S.
4-7
Activity 2: Give the complete IUPAC name for the following compound.
CH3 Step 1: Identify the four atoms directly attached to the chiral
C H centre.
CH3CH2CH2 CH2CH3
Step 2: Determine the priorities of the four groups.
.................................................................................
Step 3: Determine the absolute configuration.
.................................................................................
Step 4: Write down the complete IUPAC name.
.................................................................................
Step 5: Draw the mirror image of the compound.
Activity 3: Identify the chiral centre and determine the absolute configuration of
the following compounds.
a) b)
CH3 CH2Br
C H C H
HO CH2CH3 Br CH3

4-8
Activity 4: Write down a complete IUPAC name for the following compounds.
a) b)
H H
Activity 5: Write down a complete IUPAC name for each of the following
compounds:
(a) Cl Br
(b) (c) F
H
H

4-9
FEEDBACK FOR UNIT 4
1a) The molecule is chiral since there are four different groups/atoms bonded to the chiral
centre.
*
Cl H
b) No chiral centre; not bonded to four different groups (2 methyl groups).
*
Cl
c) The molecule is chiral since the chiral centre is bonded to four different groups/atoms.
2.
3
CH3
H
1
H3CH2CH2C CH2CH3
2
Step 1: The atoms in bold are directly attached to the chiral centre.
Step 2: CH3CH2CH2 > CH3CH2 > CH3 > H
Step 3: The substituents are arranged in a counterclockwise manner – the absolute
configuration is S.
Step 4: (S)-3-methylhexane
Step 5:
CH3
H CH2CH2CH3
H3CH2C
4-10
3.
3 2
(a) CH3 (b) CH2Br
* 4 *
HO H Br H4
CH2CH3 CH3
1 2 1 3
(S)- (R)-
(S)-butan-2-ol (R)-1,2-dibromopropane
4. a) (R) – 3-methylhexane
b) (S) − 1,2-dimethylcyclohexane
5. a) (R)-2-chloro-3-methylpentane
b) (R)-2-bromo-3-methylpentane
c) (S)-1-fluoro-1,3-dimethylcyclopentane
4-11
ADDITIONAL PROBLEMS
1. Write down the complete IUPAC names (with the absolute configuration) for the
following compounds.
a)
Br
H
b)
H Cl
c)
CH3
C H
H3CH2C
CH(CH3)2
2. Answer question 2(a-e) by writing down true or false next to the appropriate
number.
(a) A racemic mixture is optically active.

(b) Stereoisomers are isomers which have the same molecular formula, but they
differ in the way the atoms are oriented in space.
(c) An asymmetric centre is a carbon atom which is attached to four different
groups.
(d) In the determination of the absolute configuration, Cl has a higher priority
than Br.
(e) In the determination of the absolute configuration -C(CH3)3 has a higher
priority than -CH(CH3)2.
5-1
UNIT 5: ALKENES AND CYCLOALKENES
LEARNING OUTCOMES:
By the end of this unit you should be able to:

• write down a complete IUPAC name for the alkenes and cycloalkenes
from their structures.
• understand sp2-hybridization of carbon atoms and how double bonds
are formed.
• determine the geometrical isomerism by the two possible notational
systems.
• write down the products in addition reactions and indicate the major
product where applicable.
5.1 INTRODUCTION
The alkenes (or olefins) and cycloalkenes (or cyclo-olefins) are hydrocarbons containing at
least one carbon-carbon double bond per molecule. Alkenes, cycloalkenes and other
hydrocarbons containing one or more double and/or triple bonds (see the next unit) are
known as unsaturated hydrocarbons, as opposed to alkanes and cycloalkanes which
are called saturated hydrocarbons. The double bond represents the functional group
in alkenes which are responsible for the greater reactivity of alkenes (alkanes have no
double bond and are thus much more unreactive).
C C
Functional group:
Alkenes and cycloalkenes represent homologous series with general formulae CnH2n (n =
2,3,4 ...) for alkenes and CnH2n-2 (n = 3,4,5 ...) for cycloalkenes respectively. If n = 3, you
get the formula C3H2x3 = C3H6 for alkenes and C3H2x3-2 = C3H4 for cycloalkenes.
5-2
Activity 1: Write down the structural isomers for C5H10 (unsaturated compounds).
Activity 2: C5H10 is the general formula for another group of molecules as well.
Name the group of molecules. ………………………………………….
The double bond between adjacent carbons is considered as two inequivalent covalent
bonds originating from sp2-hybridization of the two carbons.
5.2 sp2-HYBRIDIZATION OF CARBON ATOMS
If the 2s and two of the existing three 2p orbitals of a carbon atom (e.g. the 2px and 2py
orbitals) are mixed, three identical orbitals known as sp2-hybrid orbitals are formed.
The remaining 2p orbital remains unchanged.
2s 2px 2py 2pz

3 identical sp2 2pz
unhybridized atomic orbitals hybridized orbitals unhybridized
Each of the four orbitals (the three sp2-hybrids and the remaining 2p-orbital) contains one
electron. The three sp2-hybrid orbitals are arranged in a plane, pointing to the corners
of an equilateral triangle, while the 2p orbital intersects this plane at a right angle. This
may be represented graphically as follows:
5-3
unhybridized p -orbital perpendicular

on the plane of the hybridized orbitals
p
sp 2 Hybridized sp 2 -orbital
sp 2
120 o
sp 2 120 o
Bonding between sp2-hybridized carbon atoms occur as follows:
Linear overlap of the sp2-hybrid orbital of one carbon with that of a second carbon atom
provides a σ-bond, while lateral overlap of the unhybridized 2p orbitals (one from each
carbon) produces the second bond, called the π-bond. Together these two bonds
represent the double bond between the two carbon atoms. The remaining two sp2-hybrid
orbitals (two on each of the carbons joined by the double bond) are available for bonding
with other carbon or hydrogen atoms.
The formation of an ethene molecule from two sp2-hybridized carbon and four hydrogen
atoms may be represented graphically as follows:
H
H
C C
H H
Unhybridized p-orbital π -Bond 90 0
H σ -bond H
C C sp2-hybrid orbitals
120 o
H
H
σ-bond
Linear overlap of the sp2-hybridized orbitals and lateral overlap of the two unhybridized 2p
orbitals (one from each carbon) form the double bond.
5-4
1/2 π - Bond
H H
σ σ
C σ - Bond C
σ σ
H H
1/2 π -Bond
(C H2 = C H 2 )
Formation of molecular orbitals and the double bond
It is important to note that overlap of the unhybridized 2p orbitals is only possible with the
two orbitals aligned parallel to each other. Rotation between the two carbon atoms is
thus only possible if this overlap, representing the π-bond, is broken. This requires
considerable energy so rotation around a carbon-carbon double bond is normally
prohibited.
5.3 GEOMETRICAL ISOMERISM
The absence of rotation around the carbon-carbon double bond results in the phenomenon
of geometrical isomerism which is displayed by alkenes with different groups on both
double bond carbons e.g. H and CH3 (see compound A).
Compounds in which the same groups are attached twice to a particular double bond
carbon do NOT display geometrical isomerism (see compound B).
H3C CH3 H3C H

C C C C
H H H H
A B
Geometrical isomers may be defined by two possible notational systems, the CIS/TRANS
system, or the E/Z system.
5-5
(a) CIS/TRANS SYSTEM
If TWO SIMILAR ATOMS/GROUPS occur on the two double bond carbons, the cis-
isomer represents the compound with the similar atoms/groups on the same side of the
double bond, while the trans-isomer represents the compound with the similar
atoms/groups on opposite sides of the double bond e.g.:
H CH3 H 3C CH3
C C C C
H 3C Cl H Cl
trans- cis-
Explanation: There is a methyl group on each double bond carbon. Divide the molecule
in two by drawing an imaginary line (- - -) through the double bond. If the methyl groups
are on opposite sides of the line, it is a trans-isomer. If the methyl groups are on the same
side of the line, it is a cis-isomer.
WITH FOUR DIFFERENT GROUPS:
(a) Identify the longest continuous carbon chain that contains the double bond.
(b) If the groups that form part of the longest carbon chain are on the same side of the
double bond, it is a cis-isomer. If the groups that form part of the longest carbon
chain are on the opposite side of the line, it is a trans-isomer.
H3CH2C H H3CH2C CH2CH2CH3

C C C C
H 3C CH2CH2CH3 H 3C H
trans- cis-
5-6
Activity 3: Determine the geometric isomerism of the following compounds

according to the cis/trans system.
(a) H3C Cl (b) H3C CH2CH2CH3
H3C CH2CH2CH3 H H
H3C CH2CH2CH2CH3 (d) H3CH2C CH2CH2CH3

(c)
H3CH2C H H3C CH2CH3
(b) E/Z SYSTEM

When an alkene is tri- or tetra-substituted (three or four different groups or atoms attached
to the double bond carbons), use of the cis/trans notation may become confusing because
you may have some problems in identifying the longest carbon chain e.g.
Br F H CH3
H CH3 Br CH2CH3
The E/Z notation was devised to eliminate this possible confusion and can be used for all
geometrical isomers.
Consider each double bond carbon and determine which group or atom has the highest
priority. The priorities are determined by the Cahn-Ingold-Prelog convention.
Step 1: Determine the two atoms directly attached to the double bond carbon e.g. Br and
H (see the following example).
Step 2: The atom with the highest atomic number has the highest priority therefore Br
has the highest priority.
Step 3: Repeat the process on the other double bond carbon.
5-7
Step 4: If the substituents of the highest priority are on the same side of the double
bond, the isomer is classified as the Z-isomer. If the substituents of highest
priority are on opposite sides, it is classified as the E-isomer.
1 Br F 1 2 H CH2CH3 1
C C
2 H CH3 2 1 Br CH3 2
(Z)- (E)-
REMEMBER: Only the two groups or atoms bonded to the same C-atom are compared
with each other.
Activity 4: Determine the geometric isomerism of the following compounds

according to the E/Z system.
(a) Cl CH3 (b) Cl H
H H Br CH2CH3
H F
(c) (d)
H
Br H
5.4 NOMENCLATURE OF ALKENES AND CYCLOALKENES

According to the priorities of functional groups as defined by the IUPAC system, double
bonds have preference over alkyl and halogen substituents (see Table A-1 in
Appendix A-1).
> Halogens and Alkyl groups

5-8
IF THE DOUBLE BOND REPRESENTS THE FUNCTIONAL GROUP OF HIGHEST PRIORITY, the following
rules apply when naming an alkene or cycloalkene:
(i) The base name is determined by the number of carbons present in the longest
carbon chain (or the cyclic parent structure) CONTAINING THE DOUBLE
BOND. The ending -ane is however changed to –ene, e.g., if there are six
carbons in the longest carbon chain containing the double bond, hexane changes
to hexene.
(ii) The chain is numbered in such a way that the double bond carbons are
designated the lowest possible numbers. This implies that double bond
carbons in cycloalkenes will be numbered 1 and 2. The position of the double
bond is indicated by the number of the lowest-numbered carbon atom in the
double bond. This is unnecessary for cycloalkenes, since this carbon will always
be number 1, e.g.
3
4 2
5 2 3 4 6 7
1 1 5
6
cyclohexene (E)-hept-3-ene
(iii) If the double bond occurs in the middle of the longest chain, the order of
numbering will be determined by the position of other substituents on the chain.
(iv) Substituents must always have the lowest possible numbers. In cycloalkenes,
this will imply a clockwise or counterclockwise numbering of the ring to give the
lowest possible values to the other substituents on the ring e.g.
1 Br
CH3
2 H3C C CH CH3
1-methylcyclohex-1-ene 2-methylbut-2-ene 4-bromo-3-methylcyclohex-1-ene
(v) Where applicable, geometrical isomers must be indicated (as cis/trans or E/Z)
before the name.
5-9
(vi) Carbon branches and other substituents are indicated as prefixes to the parent
name together with their respective positions, as in the case of alkanes.
H 3C H
H3CH2C CH2CH2CH3
(Z)-5-methylhept-3-ene (E)-3-ethylhex-2-ene
The position of the double bond can be indicated in front of the base name or in the middle
of the base name (e.g. 3-heptene ≡ hept-3-ene).
Hint:
(a) Determine geometrical isomerism where applicable.
(b) Determine the longest chain containing the double bond.
(c) Number the chain in such a way that the double bond has the lowest
possible numbers.
(d) Make sure the substituents have the lowest possible numbers.
(e) Write down the complete IUPAC name.
(a) H3CH2CH2C C C CHCH3 (b)

H H
CH3
(c) Cl Cl H
(d)
H CHCH2CH3
CH3
(e) (f)
Br
5-10
5.5.1 NATURE OF THE DOUBLE BOND
Electrons located in the π-bond of a double bond are not associated with one carbon but
are delocalized over the two double bond carbons ( par. 5.2). These ‘exposed’
electrons are responsible for the NUCLEOPHILIC PROPERTIES of the double bond,
which makes it vulnerable for attack on electrophilic species such as H+. The greater
reactivity of alkenes and cycloalkenes, if compared to alkanes, is thus attributed to the π-
electrons of the double bond.
Characteristic reactions of alkenes include ADDITION REACTIONS (as opposed to
substitution reactions encountered for alkanes,  UNIT 2, par. 2.7.2) which may be
generalized as follows:
C C + A B C C
A B
Explanation: During addition reactions two atoms or groups (e.g. A and B) are added
respectively to the two double bond carbons, exclusively with the aid of the π-electrons
in the double bond. The two new bonds that develop are σ-bonds, which denotes a
change of hybridization of the original double bond carbons from sp2 to sp3.
5-11
5.5.2 HYDROGENATION (REDUCTION OF A DOUBLE BOND)

Hydrogenation implies the addition of H2 to a double bond, in other words the electrons in
the π-bond are used to form two σ-bonds between the hydrogen atoms and the double
bond carbons. This hydrogenation reaction requires a catalyst (usually a transition metal
e.g. Pt, Pd of Ni) to proceed and gives an alkane as product.
In general:
R H H2 H H
C C R C C R1
H R1 catalyst H H
e.g.
H H H2 H H
C C H C C CH3
H CH3 catalyst H H
propene propane
Important: As the reaction involves the addition of hydrogens to the double bond, you
only consider the double bond carbons for the reaction – not any of the other carbons
in the structure. Make sure that you understand why the double bond changes to a single
bond.
Activity 6: Write down the products and/or reagents for the following reactions.
a) H2
Pt
b) H2
CH3CH CHCH3
Pd
c)
?
d) H2
Pd

5-12
5.5.3 ADDITION OF HALOGENS (HALOGENATION)
Alkenes react in the absence of light at room temperature with Cl2 and Br2 to give
addition products. Addition with I2 does not readily occur while addition with F2 usually
leads to collapse of the σ-bonds. Inert solvents such as CHCl3 and CCl4 are normally
employed.
In general:
R H Br H
Br2
C C R C C R1
H R1 H Br
alkene dihaloalkane
e.g.
H H Br H
Br2
C C H C C H
H H H Br
ethene 1,2-dibromoethane
Activity 7: Write down the products for the following reactions.

Br2
(a)
Cl2
(b)
(c) Br2

5-13
5.5.4 ADDITION OF HYDROGEN HALIDES (HALOGEN ACIDS)
Electrophilic addition of hydrogen halides, HX (X = I, Br, Cl, F) to double bonds

occurs in non-aqueous media to yield alkyl halides as products.
In general:
R H H H
HX
C C R C C R1
H R1 H X
alkene haloalkane (alkylhalide)
e.g.
H H H H
HBr
C C H C C H
H H H Br
ethene bromoethane
This reaction occurs according to an ionic reaction mechanism and involves heterocyclic
bond formation and bond cleavage (the negatively charged bromide ion acts as a
nucleophile, which attack on the region of low electron density – the carbocation
(electrophile) − to form the product).
Thus, 1 bond is cleaved, namely the π-bond between the two carbons, and two new bonds
are formed namely a C-X bond and a C-H bond.
Break π-bond Form C-H-bond Form C-Cl-bond

H Cl:
H 2C CH H 2C CH3
+ = electrophile
C
- = nucleophile
Cl:
Addition of HX to unsymmetrical substituted alkenes (different groups are bonded to the

double bond carbons) may proceed by two possible routes to give two possible products.
Considering propene, you shall see that one of the double bond carbons is bonded to two
hydrogens and the other double bond carbon is bonded to a hydrogen and methyl group.
5-14
Form C-H bond Form C-Cl bond

H Cl:
H H2
H 3C C CH2 H 3C C C H 3C C CH2
3 2 1 3 2 1 3 2 1
H H H H Cl
Break π-bond + = electrophile
C
- = nucleophile
Cl:
HCl
CH3CH=CH2
3 2 1
Form C-H bond Form C-Cl bond

H Cl: Cl
H 3C C CH2 H 3C C CH3 H 3C C CH3
3 2 1 3 2 1 3 2 1
H H H
Break π-bond + = electrophile
C
- = nucleophile
Cl:
Explanation: The addition of the hydrogen atom can take place on carbon 1 or 2. In the
first reaction the hydrogen bonds to carbon 2 to form a primary carbocation which
eventually forms 1-bromopropane. In the second reaction the hydrogen bonds to carbon 1
to form a secondary carbocation which eventually forms 2-bromopropane.
The preferred product (major as opposed to the minor product) is determined by

Markovnikov's rule. During ionic addition of unsymmetrical reagents to unsymmetrical
alkenes, the more positive fragment of the electrophile e.g., the hydrogen ion adds
preferentially to the double bond carbon bearing the most hydrogen atoms to yield the
major product. To form the major product in propene the hydrogen bonds to carbon 1
which has two hydrogens in contrast to carbon 2 with one hydrogen, to form 2-
bromopropane as the major product.
Markovnikov's rule is explained as follows: The overall rate at which a reaction

proceeds is determined by the slowest step in the mechanism, therefore in the above
examples, the formation of the carbocation is the slowest step. Carbocations of higher
stability, however, form easier and faster to give higher concentrations, thus leading by
completion of the reaction to the major product. The stability of carbocations is increased
by a positive inductive effect (+I effect) from alkyl groups attached to the positively charged
carbon. Carbocations can be represented in increasing order of stability as follows:
5-15
CH3
CH3 < CH2CH3 < CHCH3 < C CH3
CH3 CH3
increasing stability
A tertiary carbocation is therefore more stable than a secondary carbocation and a

secondary carbocation is more stable than a primary carbocation.
Activity 8: Write down all the possible products for the following reactions and
indicate the major product where applicable.
(a) (b) HCl
HBr
(c) (d) HBr

HBr
(e) HCl

5-16
5.5.5 ADDITION OF WATER (HYDRATION)
Hydration represents the addition of the elements of water to a double bond

according to the rule of Markovnikov with the aid of a catalyst (usually a small amount of
acid) to yield an alcohol as product (instead of the addition of H and Cl you now have the
addition of H and OH on the double bond).
In general:
R H H H
H /H2O
C C R C C R1
H R1 H OH
alkene alcohol
e.g.
H 3C H OH H H H
H /H2O
C C CH3 C C H + CH3 C C H
H H H H H OH
propene 2-propanol 1-propanol
major product minor product
Activity 9: Write down all the possible products for the following reactions and
indicate the major product where applicable:
(a) H 2O
+
H
(b) H 2O
+
H
(c) H 2O
+
H

5-17
FEEDBACK FOR UNIT 5

1.
2. Cycloalkanes
3.
(a) H 3C Cl (b) H3C CH2CH2CH3
H 3C CH2CH2CH3 H H
cis- cis-
H 3C CH2CH2CH2CH3 (d) H3CH2C CH2CH2CH3

(c)
H3CH2C H H 3C CH2CH3
trans- trans-
4.
(a) 1 Cl CH3 1 2 Cl H 2
(b)
1 Br 1
2 H H
2 CH2CH3
(Z)- (Z)-
2H 1 1F
(c) (d) 1
2H
1 Br H 2
2
(E)- (Z)-
5-18
5.
(a) H3CH2CH2C C C CHCH3 (b)

H H
CH3
2-methylhept-3-ene (cis)/(E)-4-ethyl-3-methyloct-3-ene
(c) Cl Cl H
(d)
H CHCH2CH3
CH3
(trans)/(E)-2-chloro-3-methylhex-3-ene
(E)-1-chloro-3-methylpent-1-ene
(e) (f)
Br
3-bromo-6-methylcyclohex-1-ene 3,3-dimethylcyclopent-1-ene
6.
(a)
(b) CH3CH2CH2CH3
(c) H2/Pt, Pd or Ni
(d)
5-19
7.
(a) Br
Br
Cl
(b)
Cl
(c) Br
Br
8.
Br
(a)
Cl
(b)
Br
(c) Br
MP/HP
(d)
Br
Br
MP/HP
(e)
Cl
Cl
MP/HP
5-20
9.
(a)
OH
OH
Major product
(b)
OH
OH
Major product
(c) OH
5-21
ADDITIONAL PROBLEMS
a)
_____________________________________________
b) CH3CHCH2CH CHCH2CH3
CH3
_____________________________________________
c)
_____________________________________________
d) H3CH2C CH3
C
C
H Br
_____________________________________________
e)
_____________________________________________
5-22
2. Write down the products and/or reagents for the following reactions. Indicate the
major product where applicable.
(a) H2
Pd
Br
(b) ?
Br
(c)
HI
(d) H 2O
+
H
Cl
(e) ?
6-1
UNIT 6: ALKYNES
LEARNING OUTCOMES:
• write down complete IUPAC names for the alkynes from their
structures.
• understand sp-hybridization of carbon atoms and how triple bonds are
formed.
• understand why alkynes have acidic properties.
• write down the products in addition reactions.
6.1 INTRODUCTION
The alkynes (or acetylenes) are hydrocarbons containing at least one carbon-carbon
triple bond per molecule, which acts as the functional group or centre of reactivity. Like
alkanes and alkenes, the alkynes also represent a homologous series with general
formula CnH2n-2 (n = 2,3,4 ...)
Functional group: C C
Activity 1: Which other group of molecules are represented by a general formula

of CnH2n-2?

6-2
6.2 sp-HYBRIDIZATION OF CARBON ATOMS
The formation of three bonds between adjacent carbons is attributed to sp-hybridization

of the two carbon atoms and the triple bond consists of one σ- and two π-bonds.
2s 2px 2py 2pz 2py 2pz

2 identical sp
unhybridized
unhybridized atomic orbitals hybridized orbitals
If the 2s and one of the existing three 2p-orbitals of a carbon atom (e.g., the 2px orbital)
are mixed, two identical orbitals, known as sp-hybrid orbitals, are formed. The remaining
two 2p orbitals are unchanged. Each of the four orbitals (the two sp-hybrids and the
remaining 2p-orbitals) contains one electron. The two sp-hybrid orbitals are arranged
along a straight line with the two unhybridized 2p orbitals intersecting this line at
right angles. This may be represented graphically as follows:
unhybridized p-orbitals
sp sp-hybrid orbitals
180o
Bonding between sp-hybridized carbon atoms occurs as follows:

(a) Linear overlap of the sp-hybrid orbital of one carbon with that of a second carbon
atom provides a σ-bond.
(b) Lateral overlap of two unhybridized 2p orbitals (one from each carbon) produces
the first π-bond.
6-3
(c) The remaining two unhybridized 2p orbitals may, however, also overlap laterally
producing another π-bond.
Together these represent the triple bond (one σ- and two π-bonds) between the two
carbon atoms. The remaining two sp-hybrid orbitals (one on each carbon) are available
for bonding with other carbon or hydrogen atoms. The formation of an ethyne molecule
from two sp-hybridized carbon atoms may be represented graphically as follows:
H C C H
+
two π-bonds
σ-bond unhybridized
p-orbitals
H σ C C σ H 1s-orbital
180 o
σ-bond
sp-hybridized
orbital
Due to the geometry of the four segments constituting the two π-bonds, these form a
single cylindrical sheath about the σ-bond joining the two nuclei. The ethyne molecule can
therefore be represented graphically as follows:
σ-bond σ
H C C H
6-4
6.3 NOMENCLATURE OF ALKYNES
According to the priorities of functional groups as defined by the IUPAC system,

multiple bonds have preference over alkyl and halogen substituents (see Table A-1 in
Appendix A-1).
The order of the priority of the functional groups can be indicated as follows:
and > Halogens and Alkyl groups
(i) IF THE TRIPLE BOND REPRESENTS THE FUNCTIONAL GROUP OF HIGHEST PRIORITY, the
triple bond carbons should have the lowest possible numbers.
(ii) The position of the triple bond is indicated by writing down the lower of the two
numbers of the triple bond carbons.
(i) The parent name is once again given to the longest carbon chain containing
the triple bond and the ending -ane is changed to -yne for the alkynes. The
other rules, except for geometrical isomerism which does not apply to the alkynes,
are the same as for the alkenes.
5
4 6 7
1 3
6-methylhept-3-yne
Explanation: If you start numbering at the left-hand side of the structure, the position of
the triple bond is at carbon 3 and the methyl group at position 6. Starting from the right-
hand side, the position of the triple bond is at carbon 4 and the methyl group at position 2,
BUT the triple bond has a higher priority than the alkyl group, so the triple bond must
have the lowest numbers (in that case you must start numbering at the left-hand side) to
give you 6-methyl-3-heptyne. Also note that you only indicate the lower number of the
triple bond e.g., 3 – that automatically indicates that the triple bond is between carbon 3
and carbon 4.
6-5
Activity 2: Identify the longest carbon chain containing the triple bond, number it
correctly and give the IUPAC names for the following structures.
(a) H3CH2CH2CC CH (b)
CH3
(c) H3CC CC CH3 (d)
CH3
(ii) IF THERE ARE DOUBLE AND TRIPLE BONDS IN THE COMPOUND, the position of the double
bond as well as the position of the triple bond must be indicated. Numbering of an
enyne starts from the end closest to the first multiple bond, whether double or
triple. As –ene is before –yne in the alphabet, the position of the double bond is
written down first, followed by –en and then the position of the triple bond followed
by –yne, e.g.
CH3
HC H2 H
C CH C C
C C C CH3
H2 H2 H
(E)-4-methylnon-7-en-1-yne
When the double and triple bonds are at equal distances from the ends of
the chain, the double bond receives a lower number than the triple bond
since ene is before yne in the alphabet, e.g.
HC CCH2CH2CH CH2
hex-1-en-5-yne
6-6
Activity 3: Give the complete IUPAC name for the following compound.
(i) Determine the functional group of highest priority.

……………………………………
(ii) Determine the longest carbon chain containing the group of highest priority.
(iii) Number the carbon chain correctly.
(iv) If there is a double bond, determine the geometrical isomerism.
(v) Write down the complete IUPAC name.
…………………………………………………………………………………………
(a) (b)

6-7
6.4.1 ACIDITY OF ALKYNES AND REACTIONS
In contrast to alkanes and alkenes, 1-alkynes (alkynes with the triple bond at the end of a
carbon chain) which possess a hydrogen atom attached to a triple bond carbon, show
considerable ACIDITY. As you know from inorganic chemistry an acid is a proton donor
and can react with a base. 1-Alkynes react with metals (e.g. Na), strong bases (e.g. KNH2
or NaNH2) and some basic salts leading to metal derivatives of acetylene, termed
acetylides.
The acidity of a hydrogen atom attached to a triple-bonded carbon is attributable to the

relative stability of the resulting carbanion, where the unshared pair of electrons occupies
an sp-orbital. The terminal hydrogen is substituted by a metal e.g. Na or K.
In reaction with metals e.g. Na:
CH3 C CH + Na CH3 C C Na + 1
2 H2
propyne sodium acetylide
Acetylides are excellent nucleophiles and can attack an electrophilic centre – this is
a very important method to lengthen carbon chains. The carbon-metal bonds are
ionic bonds.
H3CC CH + Na (m) H3CC CNa 3 carbons
H 3C Br
+ NaBr
H3CC CCH3
4 carbons
The same applies to potassium (K).

6-8
6.4.2 ADDITION REACTIONS OF ALKYNES
Like alkenes, alkynes undergo addition reactions for the same reason: availability of
the loosely held π electrons. Addition of hydrogen to alkynes are very similar to the
addition of hydrogens to alkenes. The only difference is that in alkenes only 1 mole of the
reagent is consumed, where in alkynes two moles of a reagent are consumed for each
triple bond.
(a) Hydrogenation
Reaction of alkynes with hydrogen in the presence of catalysts like Ni, Pt or Pd leads to
complete reduction from alkynes up to alkanes as products, using both π-bonds.
H2 H2
HC CH H2C CH2 H3C CH3
Ni Ni
ethyne ethene ethane
(acetylene)
a) H2
H3CH2CH2CC CH
Pt
b) H2
Pt

6-9
(b) Hydration (addition of H2O)
In the presence of certain salts of mercury, alkynes undergo acid catalyzed hydration
at 60°C according to the rule of Markovnikov, leading to carbonyl compounds. (Compare
with the hydration of alkenes, UNIT 5, par. 5.5.5) In contrast to the alkenes it is necessary
to add mercury salts and heat the reaction mixture to 60°C before the alkynes undergo
hydration. (Only the major product is shown.)
E.g.:
diluted OH O
H2SO4
H3C C CH H 3C C CH2 H 3C C CH3
Hg++/60 oC
propyne 2-hydroxypropene acetone
an enol (a ketone)
Only one mole of water is added to the alkyne to form 2-hydroxypropene which forms the
ketone due to keto-enol tautomerism.
Activity 6: Write down the products in the following reactions (only the major
products)
(a) dil. H2SO4

? ?
Hg2+/60 0C
(b) HC CCH2CHCH3 dil. H2SO4

? ?
CH3 Hg2+/60 0C

6-10
FEEDBACK FOR UNIT 6

1. Cycloalkenes
2. a) pent-1-yne
b) 3-methyloct-4-yne
c) 4,4-dimethylpent-2-yne
d) 3,4-dimethylhex-1-yne
3. (i) double bond and triple bond

(ii)/(iii) Numbering occurs to give the lowest possible numbers for the double AND
triple bond!
1
6 4 2
7 5 3
(iv) (E)- or trans

(v) (E)- or trans-3,5,6-trimethylhept-4-en-1-yne
4. a) 2-methylhex-1-en-3-yne
b) 7-ethyl-4,6-dimethylnon-2-yne
5.
a)
CH3CH2CH2CH2CH3
b)
6.
a) OH O
OH O
b) H2C CCH2CHCH3 H3C CCH2CHCH3
CH3 CH3
6-11
ADDITIONAL PROBLEMS
1. Write down the complete IUPAC name for the following compounds.
(a)
.....................................................................
(b)
.....................................................................
(c) H
H3CH2C
C C H CH3
H C C C CH
H
CH3
.....................................................................
(d)
H 3C CH3
H3CCC CCHCH3
H 3C
.....................................................................
2. Write down all the possible products for the following reactions.
(a) H2
Pt
(b)
dil. H2SO4
CH3C CH ? ?
Hg2+/60 0C
7-1
UNIT 7: ALCOHOLS
7.1 ALCOHOLS
LEARNING OUTCOMES:
• classify mono- and dihydric alcohols.
• write down a complete IUPAC name for the alcohols.
• understand the nature of the functional group.
• understand the amphoteric character of alcohols and be able to explain
how an alcohol can act as a weak base or a weak acid by using reactions.
• understand the effect of protonation on the nature of the functional group.
• write down the products and mechanisms for the substitution of the
hydroxyl group with hydrogen halides.
• write down all the possible products in intramolecular dehydration
reactions using Saytzeff's rule.
• write down the products for the oxidation of primary, secondary, and
tertiary alcohols.
• explain where alcohols are used in daily life.
7.1.1 INTRODUCTION
As you all know, alcohol is a constituent of beer, wines, and spirits - the compound in
these drinks is ethanol. Alcohols are also used industrially as solvents and fuels. Alcohols
can be viewed as hydroxyl derivatives of the alkanes, alkenes, or alkynes i.e.,
hydrocarbons in which at least one hydrogen has been substituted by a hydroxyl (OH)
group.
Functional group: C OH
7-2
Alcohols are in general represented by the formula ROH where R = an alkyl group.
Examples of the three types of alcohols:
OH
OH OH
alkanol alkenol alkynol
7.1.2 CLASSIFICATION
Alcohols are classified as mono-, di-, tri-, or polyhydric based on the number of hydroxyl
groups present in the molecule.
(a) MONOHYDRIC ALCOHOLS

Alcohols containing a single hydroxyl group in the molecule are known as monohydric
alcohols and can be classified according to the carbon atom to which the OH is
attached:
R CH2
R CH2CH2 OH R CH2CH OH R CH2C OH
R CH2 R CH2
primary alcohol (10) secondary alcohol (20) tertiary alcohol (30)
Examples of monohydric alcohols are:
CH3OH CH3CH2OH CH3CHOH

CH3
methanol ethanol 2-propanol
CH3
CH3CHCH2OH CH3COH
CH3 CH3
2-methyl-1-propanol 2-methyl-2-propanol
7-3
(b) DIHYDRIC ALCOHOLS

Dihydric alcohols contain two OH groups and are divided into two groups.
(i) Geminal or gem diols
In this group the two hydroxyl groups are attached to the same carbon atom.
OH
CH3CCH3
OH
unstable gem-diol
(ii) Vicinal or vic diols

In this group, the two OH groups are attached to adjacent carbons e.g.
H
H 3C C CH2 H 2C CH2
OH OH OH OH
(c) TRIHYDRIC ALCOHOLS

These alcohols contain three hydroxy groups in each molecule, e.g.:
H
H 2C C CH2
OH OH OH
Glycerol
Activity 1: Classify the following alcohols e.g. 10, 20 for monohydric alcohols and
vic/gem for dihydric alcohols.
OH OH
(a) (b)
OH
(c) OH (d) CH3
CH3CCH2CH2CH3 CH3COH
OH CH3
7-4
See feedback at end of the unit→
7.1.3 NOMENCLATURE
According to the priority list for functional groups, the hydroxyl group has a higher
priority than the multiple bonds (see Table A-1 in Appendix A-1).
Hydroxyl group (OH) > and > halogens (X) and alkyl groups (R)
(i) IF THE HYDROXYL GROUP IS THE FUNCTIONAL GROUP OF HIGHEST PRIORITY in the
molecule, the carbon to which the OH-group is attached should be included
into the longest continuous carbon chain and the chain should be numbered to
give this carbon the lowest possible number.
(ii) The -ane, -ene or -yne ending of the basic name for the hydrocarbon is changed
into -anol, -enol or -ynol depending on whether the hydrocarbon is an alkane,
alkene or alkyne.
(iii) As before, the number of the carbon bearing the OH group should be included
into the name.
2 1
CH3 CH2CH3
6 4
CH3CCH2CCH3
Cl OH
5-chloro-3,5-dimethylhexan-3-ol
Explanation: The longest carbon chain containing the OH-group is identified. The
carbon chain is then numbered to give the hydroxyl group the lowest possible number (3).
To write down the full IUPAC name, 5-chloro indicates the position of the chlorine and is
written first as it is first in the alphabet, followed by the 3,5-dimethyl groups. The base
name hexane changes to hexan-3-ol to indicate the position and presence of the hydroxyl
group.
7-5
(iv) In acyclic alcohols where the OH is situated at the center carbon, numbering
starts from the end closest to the multiple bond. In the absence of a multiple bond,
number so that the first substituent has the lowest possible number and if this still
doesn’t give clarity, the substituent first in the alphabet is allocated the lowest
possible number.
1 2 3 4
5
6 7 7 6 5 4 3
8 8 2 1
9 9
OH OH
7,8-dimethylnon-2-yn-5-ol 2,3,8-trimethylnonan-5-ol
(v) For cyclic alcohols, the carbon bearing the hydroxyl group is always numbered
one (which you do not have to write down). The direction of numbering
(clockwise or counterclockwise) is determined by the first double bond, then by the
substituents or finally alphabetical order of the substituents.
5 6
4
1
3 OH
2
6-methylcyclohex-2-enol
Explanation: In the structure above there is a hydroxyl group, double bond, and methyl
group, but as the hydroxyl group has the highest priority it must have the lowest number
(1). The direction of numbering (clockwise or counterclockwise) depends on the presence
of other functional groups. In this case it is a methyl group versus a double bond and as
the double bond takes preference, it must have lower numbers, so you number clockwise.
Enol indicates the presence of the double bond and the hydroxyl group.
7-6
(a) CH3 (b)

OH
Br Br
OH
Br
OH
(c) CH2Br (d)
CH3CH2CHCH2CH2CHCH3
H 3C
OH CH2CH3
H3CH2C
7.1.4 CHEMICAL PROPERTIES
(a) NATURE OF THE FUNCTIONAL GROUP
Owing to the high electronegativity of oxygen both covalent bonds next to oxygen are polar
(the C-O and O-H bonds), while an unshared electron pair (available for bonding) is
located in a 2p orbital of the oxygen. The hydroxyl group can therefore be written as
follows:
δ+ δ− δ+
C O H
The reactions of alcohols can thus be divided into three categories:

(a) heterolytic cleavage of the OH bond
(b) heterolytic cleavage of the COH bond
(c) reactions where alcohols act as nucleophiles
7-7
(b) AMPHOTERIC CHARACTER OF ALCOHOLS
The term amphoteric means that alcohols, like water, can act as a weak acid and as a
weak base.
(i) Alcohols as weak bases (proton acceptors)
The unshared electron pair on the oxygen atom allows an alcohol to react with a
proton (hydrogen ion), thus leading to the alcohol acting as a base (proton acceptor).
This process is generally known as protonation of an alcohol.
Eg.:
H
H3 C OH + H H3 C O
H
methyloxonium ion
protonated alcohol
As the unshared electron pair is used to form a bond with the proton (hydrogen ion) it
leads to the formation of a positive charge on the oxygen.
Alcohols are stronger bases than water.
(ii) Alcohols as weak acids (proton donors)
Although the acid strength of alcohols is substantially lower than that of water, heterolytic
cleavage (dissociation) of the OH bond in alcohols still occurs to a small extent with
the effect that alcohols may act as acids (proton donors) in some cases. This property is
attributable to the electronegative oxygen, which readily accommodates the negative
charge of electrons left behind.
Alcohols (weak acids) will thus react with electropositive metals like Na and K as well as
strong bases like NaOH to form alkoxides. This alkoxides e.g., potassium tert-butoxide
are strong bases – even stronger than NaOH. ( UNIT 3, par. 3.4.3)
7-8
(i) H3C OH + Na(m) H 3C O Na + 1

2 H2
sodium methylate
(sodium methoxide)
strong base
H2 H2
(ii) H 3C C OH + Na + OH H 3C C O Na + H 2O
sodium ethylate
(sodium ethoxide)
strong base
Activity 3: (a) Write down a reaction to show that ethanol can react as a weak
base.
(b) What do you call the property that alcohols can act as weak bases
and acids?
(c) EFFECT OF PROTONATION ON THE NATURE OF THE
FUNCTIONAL GROUP
Owing to the fact that the carbon atom bonded to the OH group in alcohols is fractionally
positively charged [ par. 7.1.4(a)] like the α-carbon in the alkyl halides, one would
expect substitution reactions (as the carbon is an electrophilic center) and elimination
reactions, comparable to those of the alkyl halides ( Unit 3, par. 3.4.1). Thus:
H
Substitution +
C C Z OH
H
δ−
C Cδ+ OH + Z
C C + HZ + OH
Elimination
7-9
The hydroxide ion which is liberated during the reaction is, however, such a poor leaving
group (good nucleophile and base) that the reaction will not occur in this way and
elimination and substitution reactions of alcohols must be executed along a different
pathway.
PROTONATION of the alcohol allows these reactions to take place. The reasons for
this are:
(i) The electrophilicity of the oxygen bearing carbon (the α-carbon) is increased
Protonation of the oxygen creates a formal positive charge on the oxygen atom with
the effect that the attraction on the electrons in the covalent bond between the oxygen
and the α-carbon will increase and thus intensifies the fractional positive charge on
the α-carbon (increase the electrophilic character of the α−carbon).
δ+
C C O H
H
increased electrophilicity
(ii) The leaving group abilities of the hydroxyl function is increased
Protonation turns the weak OH leaving group (strong base) into the much better H2O
leaving group (weak base). Thus, a drastic increase in reactivity towards substitution and
elimination is observed.
δ+ +
C O H C Nu + H2O
H
Nu:
7-10
Activity 4: (i) Why is it necessary to protonate an alcohol before a substitution

reaction can occur?
(ii) Identify the α- and β-carbons in the following structures.
(a) (b)
OH
OH
7.1.5 SUBSTITUTION OF THE HYDROXYL GROUP
WITH A HALOGEN
By treating alcohols with halogen acids like HCl and HBr these compounds can be
transformed into the corresponding alkyl halides.
In general:
∆
R OH + HX R Br + H 2O
alcohol alkyl halide

e.g.:
i) CH3 CH3
∆
H3C C OH + HBr H3C C Br
CH3 CH3
ii)
H2 ∆ H2
H3C C OH + HCl
H3C C Cl
Based on observations made during experimental work, two different mechanistic

pathways are postulated:
(a) Unimolecular nucleophilic substitution (SN1) for tertiary alcohols

(b) Bimolecular nucleophilic substitution (SN2) for primary alcohols
7-11
Protonation of the alcohols is a prerequisite before the substitution reaction will

occur.
(a) SN1 MECHANISM FOR TERTIARY ALCOHOLS
30 Alcohols react according to an SN1 mechanism (two steps) in which the reaction
rate is dependent only on the concentration of the alcohol. The mechanism for
tertiary alcohols is as follows:
Step 1: Protonation of the alcohol by halogen acids
CH3 CH2
H 3C C OH + H H 3C C OH
CH3 CH3
Step 2: Slow, reversible dissociation of the protonated alcohol
CH3 CH3
slow
H 3C C O H H 3C C + H 2O (water - good leaving group)
CH3 H
CH3
ο
3 carbocation - stable
Step 3. Fast nucleophilic attack by the halide ion

CH3
CH3
H 3C C + Br fast
H3C C Br
CH3
CH3
electrophile nucleophile
7-12
Activity 5: Write down all the products for the following reactions.
a) CH3CHCH3 HCl
OH
CH2CH3
b) HBr
HC OH
CH3
Activity 6: Write down the complete mechanism for the following reaction.
OH
HBr

7-13
(b) SN2 MECHANISM FOR PRIMARY ALCOHOLS
For 10 alcohols reaction will proceed along an SN2 mechanism (one step) with the
reaction rate being dependent on the concentration of both the alcohol and the acid.
The mechanism for primary alcohols will be as follows:
Step 1: Protonation
H2 fast H2
H 3C C OH + H H 3C C O H
H
Step 2: SN2 substitution by the halide ion
H
Cl − H
slow δ δ+ fast CH3
δ+ O + H O
H Cl C OH2
H 3C C CH2
2
H2 H CH3
Cl
transition state

a) OH HCl
CH2CH3
b)
CH2 HBr
CH2OH

7-14
Activity 8: Write down the mechanism for the following reaction.

CH2CH2CH3
CH2 HBr
OH
The mechanism for the substitution of secondary alcohols depends on the nature of
different substituents as well as the reaction conditions.
SUMMARY:
SN1-mechanisms SN2-mechanisms
30 alcohols 10 alcohols
The rate of the reaction depends on the The rate of the reaction depends on the
concentration of the alcohols concentration of the alcohol and the
nucleophile
7.1.6 ELIMINATION OF THE HYDROXYL GROUP WITH
CONCENTRATED SULPHURIC ACID
Treatment of an alcohol with sulphuric acid at a very high temperature (approximately

170 0C) leads to intramolecular dehydration, i.e., elimination of a molecule of water from
a single molecule of alcohol, to form an alkene as product.
In general:
CH3 (c)
H H2SO4
H 3C C C OH C C + H 2O
CH 170 0C
CH3 3
7-15
CH3 (c) CH3

(i) H2SO4
H 3C C OH H 2C C + H2O
170 0C
CH3
CH3
(c)
H2SO4
(ii) H2
H 2C CH2 + H2O
H 3C C OH
170 0C
Remark: The β-hydrogen is removed to form the double bond. Water acts as a good
leaving group. The products formed are the same as with the elimination of
alkyl halides – it is only the reagents that differ.
When a compound contains more than one β-hydrogen that can be eliminated, the one
that will be removed preferably is indicated by the rule of Saytzeff, which states that the
hydrogen will preferably be removed from the β-carbon with the fewer hydrogen
atoms.
from β
' H 3C C C CH3
β β H H
H H2SO4 (c)
H3CH2C C CH3 major product
1700C
OH H2
H 3C C C CH2
from β' H
byproduct
Activity 9: Write down all the products for the following reactions and indicate
the major product where applicable.
a) (c)
H2SO4
170 0C
OH
b)
(c)
OH H2SO4
170 0C

7-16
Activity 10: Write down the reagents and/or products for the following reactions.
(Consider the reactions you studied in the previous units as well.)
(c)
H2SO4 Br2
a)
major product only ?
OH 1700C
b) Cl (c)
KOH H2SO4
? ?
1700C
c) CH3C C Na
CH3CH2Cl ?
d) OH HBr ?
?
7.1.7 OXIDATION
(a) INTRODUCTION
Primary (10) and secondary (20) alcohols are oxidised to carbonyl compounds by strong
oxidising agents like KMnO4 in acidic as well as basic medium, K2Cr2O7/H2SO4 or
CrO3/H+. This reaction comprises the REMOVAL OF TWO HYDROGEN ATOMS from the
7-17
alcohol and is also known as dehydrogenation. It can in general be represented as

follows:
[O]
C O H C O
H
carbonyl group
(b) PRIMARY ALCOHOLS
10 Alcohols are oxidised to aldehydes, which are susceptible to further oxidation

leading to carboxylic acids as products. If the aldehyde is the desired product, some
precaution should be taken in order to prevent over oxidation to the acid. This can be
done by removing the aldehyde as it is formed, for example by distillation, or by
employing special reagents like CrO3 and pyridine (C5H5N; an organic base).
In general:
O O
H2 [O] [O]
R C OH R C H R C OH
1° alcohol aldehyde carboxylic acid
e.g:
CrO3 O CrO3 O
H2
H 3C C OH + H 3C C H + H 3C C OH
H H
ethanol ethanal ethanoic acid
(c) SECONDARY ALCOHOLS
20 Alcohols are oxidised to ketones and, since further oxidation would require cleavage
of a carbon-carbon bond, which is impossible under the mild reaction conditions that are
prevailing, no further oxidation will occur.
7-18
In general:
O
H [O]
R C OH R C R
R
2° alcohol ketone
e.g.:
OH K2Cr2O7 O
H 3C C CH3 H 3C C CH3
H H2SO4
propan-2-ol propanone
(d) TERTIARY ALCOHOLS

Since the oxidising conditions employed for these reactions are too mild for cleavage of
carbon-carbon bonds which is a prerequisite for 30 alcohols to be oxidised, no reaction
will occur when a 30 alcohol is subjected to it.
KMnO4
(a) CH3CH2CH2CH2OH +
H
(b) CrO3
+
OH H
O
KOH ?
(c) CH3CH2CH2Br ? CH3CH2CH
OH
(d) K2Cr2O7
?
H2SO4
(e) OH CrO3
+
H
CrO3
(f) CH3CH2OH
pyridine
7-19

7-20
FEEDBACK FOR UNIT 7
1. (a) vic-dihydric alcohol

(b) 20-monohydric alcohol
(c) gem – dihydric alcohol
(d) 30-monohydric alcohol
2. a) 2-bromo-6-methylcyclohexanol
b) (E)-7,7-dibromo-6-ethyldec-8-en-3-ol
c) (S)-1-bromo-2-methylbutan-2-ol
d) 5-ethylheptan-2-ol
3. (a)
+ CH3CH2OH2
CH3CH2OH + H
(b) Amphoteric character
4. (i) To enhance the electrophilicity of the α-carbon

To increase the leaving group abilities of the hydroxyl group.
(ii)
a) β
b) β α
α OH β
β
OH
5. (a) CH3CHCH3
Cl
(b) CH2CH3
CH Br
CH3
7-21
6.
OH OH2
+ fast/vinnig
+ H
slow/stadig
+ H 2O
Br
fast/vinnig
+ Br
7.
a) Cl
b) CH2CH3
CH2
CH2Br
9.
a)
major product
b)
major product
7-22
10.
Br
a)
Br
b)
OH +
major product/hoofproduk
c) CH3CH2C CCH3
d) Br CH3
H 3C CO K
CH3
11.
O O
(a)
CH3CH2CH2C H CH3CH2CH2C OH
(b)
(c) CH3CH2CH2OH ; CrO3/pyridine
(d) No product, as it is a tertiary alcohol
(e) O
(f) O
CH3CH
7-23
ADDITIONAL PROBLEMS
1. Write down the complete IUPAC names for the following structures.
a)
OH
Cl
b) Br OH
c) CH2OH
H C
CH3
H2CH2CH2C
Br
2.
OH HCl
(A)
(a) What type of alcohol is (A) e.g., 1°? ………………………………

(b) Write down a complete mechanism to explain the formation of the product in
the above reaction.
3. Write down all the products and/or reagents for the following reactions and
indicate the major product where applicable.
a) OH
K2Cr2O7
CH3CHCH2CH3
H2SO4
b) ?
OH Cl
c) H2SO4 (c)
OH
170 0C
7-24
CrO3
d)
pyridine
OH
CrO3
+
H
e)
CH3CHCH3 KOH ? CH3CHCH3
?
CH2Br C O
OH
f) OH
Na (m)
8-1
UNIT 8: AMINES
LEARNING OUTCOMES:
• classify amines.
• write down complete CA names for simple amines.
• understand the basicity and nucleophilicity of amines.
• write down the products for the reactions of amines with acids.
• write down the products for the alkylation reactions of amines.
8.1. INTRODUCTION
The element nitrogen is the fourth most common atom in living systems. It is essential to
the structure and function of proteins which carry out most of the work in biological
systems. One group of organic molecules that contain nitrogen is the AMINES. Amines
are related to ammonia the same way as alcohols are related to water (one hydrogen atom
is replaced with an alkyl group). Amines are formed when one or more of the hydrogen
atoms of ammonia are replaced with alkyl groups.
H
General structure of amines: R N
H
One or more of the hydrogen atoms can be substituted by an organic group.
8.2 CLASSIFICATION
Amines are derivatives of ammonia and can be classified according to the number of alkyl
groups attached to the nitrogen. In primary (1º) amines, one of the hydrogens is replaced
by an organic group. In a secondary (2º) amine, two hydrogens are replaced and in
tertiary amines (3º) all three hydrogens are replaced by organic groups.
8-2
N N N N
H H R H R H R R''
H H R' R'
Ammonia Primary amine Secondary amine Tertiary amine
R = R' = R'' = the same or different alkyl groups
Activity 1: Classify the following amines.
CH2CH3 H
(a) CH3CH2 N CH3 (b) CH3 N CH3
CH2CH2CH3
(c) CH3CH2CH2 NH2 (d) H N CH3
8.3 NOMENCLATURE
The IUPAC system is not generally in use for the naming of amines. The nomenclature
system which is the most popular for the naming of amines, is known as the Chemical
Abstracts or CA system.
(i) During the naming of primary amines, the base name is identified as the longest
straight chain bonded to the nitrogen atom. The suffix –amine is added to the
base name. The position of the amine group is numbered in the same way as the
position of alkyl groups.
CH3 NH2 CH3CH2CH2 NH2 CH3CH2CH2CH NH2
propaneamine CH3
methaneamine
2-pentaneamine
8-3
(ii) For secondary and tertiary amines, the biggest alkyl group bonded to the N-atom
is used as the base name. A number indicates the position of the amine group.
The other groups on the N-atom are added as a prefix N-alkyl to the base name.
If there are two groups bonded to the N-atom, the prefix N must be shown each
time.
CH3
CH3 NH CH2CH3 CH3 N CH3
N-methylethaneamine N,N-dimethylmethaneamine
(ethylmethylamine) (trimethylamine)
Activity 2: Each of the following amines has a general name as indicated below.
Name each of them according to the CA system.
H
(a) H3C N CH3 (b) CH3CH2CH2CH2NH2
dimetihylamine butylamine
8.4 REACTIONS OF AMINES
8.4.1 AMINES AS BASES
Amines have the capacity to act as Lewis bases due to the non-bonded electron pair on
the nitrogen atom. The non-bonded electron pair on the nitrogen atom is shared with the
proton of the water molecule to form the alkylammonium ion. Hydroxyl ions are formed to
make the solution basic. As the nitrogen atoms in amines are less electronegative as the
oxygen atom in alcohols, the amines are stronger bases as alcohols.
8-4
NH3 + H OH NH4 + OH
H H
R N + H OH R N H + OH
H
H
amine alkylammonium ion
You can compare the stability of carbocations with amines. Tertiary amines are more
stable than secondary amines (and therefore a stronger base) and secondary amines are
more stable than primary amines. In tertiary amines the three alkyl groups (electron
donating groups) stabilize the positive charge in the ammonium ions better than in
secondary amines with two alkyl groups. The order of basicity is as follows:
Basicity/Stability: 30 amine > 20 amine > 10 amine > ammonia
8.4.2 REACTIONS OF AMINES WITH ACIDS
Since amines are bases, they react with acids to form alkyl ammonium salts. These salts
are ionic and more readily soluble in water than amines. This capability to manipulate the
solubility of amines by forming salts, is very important in the development of medicine.
H H
H 3C N + H Cl H3C N H Cl
H H
methyl ammonium chloride
H 2O
a) CH3CH2NHCH3
HBr
b) CH3CH2CH2NH2
c) HCl
NH2
8-5
8.4.3 AMINES AS NUCLEOPHILES
Amines are good nucleophiles due to the non-bonded electron pair on the nitrogen atom.
Amines act as nucleophiles in substitution reactions with alkyl halides. A base like sodium
hydroxide is necessary to remove the proton from the ammonium ion to form the amine.
H
CH3CH2NH2 + H3C Cl CH3CH2N CH3 Cl
NaOH
H
CH3CH2N CH3 + NaCl + H2O
Activity 4: Write down the product for the following reaction.
CH3
1) CH3CH2Br
CH3 NH
2) NaOH

8-6
8.4.4 QUATERNARY AMMONIUM SALTS
Quaternary ammonium salts are ammonium salts where there are four organic groups
bonded to the nitrogen atom.
General: R4N+X¯ (R = any alkyl group ; X¯ = a halide ion, usually Cl¯)
Tertiary amines can be alkylated by haloalkanes to form quaternary ammonium salts (see
par. 8.4.3).
(H3C)3 N + H 3C Br (H3C)4 N Br
Activity 5: Write down the product for the following reaction.
CH3
CH3CH2N + CH3CH2Cl
CH3

8-7
FEEDBACK FOR UNIT 8
1. (a) 30 amine
(b) 20 amine
(c) 10 amine
(d) 20 amine
2. (a) N-methylmethaneamine
(b) Butaneamine
H
3. (a) CH3CH2N H + OH
CH3
(b) CH3C H2CH2NH3 Br
(c) Cl H3N
4.
CH3
CH3 N CH2 CH3
CH3
5
CH3CH2NCH2CH3 Cl
CH3
8-8
ADDITIONAL PROBLEMS
1. Draw the following structures:
(a) N,N-diethyl-1-pentaneamine
(b) 3-octaneamine
2. Give the products for the following reactions.
(a) CH3 NH2 + HI
(b) (CH3CH2)2NH + HCl
3. Name the following compounds.
(a) CH3CH2CH2N(CH3)2
(b) CH3CH2NCH2CH2CH3
CH3
9-1
UNIT 9: CARBONYL COMPOUNDS
(ALDEHYDES AND KETONES)
LEARNING OUTCOMES:
• write down complete IUPAC names for the aldehydes and ketones.
• understand the nature of the carbonyl group.
• write down the products in the addition reactions of ammonia
derivatives to the carbonyl group.
• write down the products in the addition reactions of oxygen compounds
to the carbonyl group and know the difference between hemiacetals
and acetals.
• write down the products in the reduction and oxidation reactions of
aldehydes and ketones as well as the reagents to do the reduction and
oxidation.
9.1 INTRODUCTION
O
The carbonyl group, C , is the functional group of the carbonyl compounds.
Two main groups of compounds can be distinguished, namely those with a terminal
(end) carbonyl group (the aldehydes), and those with the carbonyl group inside the
carbon chain (the ketones).
O
H 3C C H or H 3C CHO (not H3C COH)
an aldehyde This is the alcohol notation
O
H2
H3C C C CH3 or H 3C CH2COCH3
a ketone
9-2
9.2 NOMENCLATURE OF ALDEHYDES AND KETONES
Ketones have a higher priority than hydroxyl groups (OH), but a lower priority than
aldehydes according to the IUPAC-system (see Table A-1, Appendix A-1).
aldehydes > ketones > hydroxyl group > multiple bonds
(a) ALDEHYDES (RCHO)
The following rules should be followed in cases WHERE THE FORMYL GROUP (ALDEHYDE
GROUP) IS THE FUNCTIONAL GROUP OF HIGHEST PRIORITY:
(i) Determine the longest carbon chain containing the carbonyl carbon atom and
name it by replacing the -e of the corresponding alkane (alkene or alkyne) with -al
(e.g. butane to butanal, propene to propenal and hexyne to hexynal).
(ii) When numbering the carbon chain, the carbonyl carbon should be number one
(not necessary to write it down) and other substituents and branching points are
indicated as before.
O OH CH2CH3
CH3CH2CH CH3CHCH2CHCH2CH
O
propanal 3-ethyl-5-hydroxyhexanal
Explanation: There are three functional groups in the molecule: an aldehyde, hydroxyl
and ethyl group. As the aldehyde group has the highest priority, you identify the longest
carbon chain containing the aldehyde group and start numbering at the carbonyl
carbon. The base name changes to hexanal (due to the aldehyde group, which has a
higher priority than the hydroxyl group,) and the hydroxyl group becomes a substituent like
the ethyl group.
9-3
O
This carbon is bonded to O,O and H
CH3
CH2CH 1
7 3 2 1 4H
H3CHC 6 CH2CH2CHO
3 H 3C CH2CH3 2
5C C4
This carbon is bonded to H, H and H
H 3C H
(Z)-5,6-dimethylhept-4-enal (R)-3-methylpentanal
O
(a) CH3 CH3 (b)
CH3CHCH2CHCH2CHCHO H
OH
Br O CHO
(c) (d) H 3C
H CH2CH3
HO
(b) KETONES (RCOR')
The following rules are applicable for the nomenclature of ketones (i.e. WHEN THE KETONE
GROUP IS THE FUNCTIONAL GROUP OF HIGHEST PRIORITY):
(i) The longest carbon chain containing the keto group is selected and named
according to the basic name for the alkane, alkene or alkyne, but by changing the
-e to -one (e.g. butane to butanone, butene to butenone and butyne to butynone).
9-4
(ii) The longest carbon chain containing the carbonyl group is numbered with the
carbonyl carbon atom carrying the lowest possible number. The position of the
carbonyl group is indicated, except in the cases of propanone and butanone, by
writing the number before the -one ending or in front of the basic name.
OH
O
CH3CHCHCCH2CH3
C
H 3C CH2CH2CH3 CH3 O
pentan-2-one 4-hydroxy-5-methylhexan-3-one
(iii) Carbonyl carbon atoms of cyclic ketones always bear number one. It is therefore
not necessary to write the number in the name in this case.
(iv) In the case of acyclic ketones having the carbonyl group in the middle of the
longest carbon chain or with all cyclic ketones, the direction of numbering is
determined by the first multiple bond, then to give the lowest combination of
numbers with regard to substituents or finally alphabetical order of the
substituents.
(v) Substituents and branching of the carbon chain are indicated as before and written
down in alphabetical order.
OH
2 O OH O
3 6
1 5
4 2 4 7
1 3
6 CH3 Cl
5
2-hydroxy-6-methylcyclohexan-1-one 5-chloro-2-hydroxyheptan-4-one
Explanation: In cyclohexanone, the hydroxy group is allocated a lower number than the
methyl group as it takes alphabetic priority, so numbering takes place counterclockwise
starting at the carbonyl. In 5-chloro-2-hydroxyheptan-4-one, the carbonyl is in the middle
of the longest carbon chain. Numbering starts from the left to give the lowest combination
of numbers to the substituents. The chloro-group takes alphabetic preference over the
hydroxyl group and is written down first.
9-5
O
OH O
(a) H3C C CH3 (b)
H 3C CH3
H H CH3
(c) CH2COCH3 (d)

H C O
Cl CH2CH3

9.3.1 THE NATURE OF THE CARBONYL GROUP
Carbonyl groups possess a double bond between a carbon and an oxygen atom.
All carbonyl groups possess a double bond between a carbon and an oxygen atom.
This double bond is very similar to the one between two carbon atoms. It also consists of
a σ-bond between an sp2-hybridized carbon atom and an oxygen atom as well as a π-
bond generated by overlap of the unhybridized carbon p-orbital and an oxygen p-
orbital that contains only one electron.
parallel unhybridized
p-orbitals overlap to
form the π bond
9-6
This double bond is very similar to the one between two carbon atoms. It also consists of
a σ-bond between an sp2-hybridized carbon atom and an oxygen atom as well as a π-bond
generated by overlap of the unhybridized carbon p-orbital and an oxygen p-orbital that
contains only one electron.
The carbonyl carbon atom is sp2-hybridized and the three attached atoms or groups
therefore all lie in a plane with bond angles equaling 1200:
°
R 120
°
120 C O
R °
120
Owing to the higher electronegativity of oxygen when compared to carbon, the π-

bonding orbital is not symmetrical with respect to the two atoms. The mobile π-
bonding electrons will therefore be positioned closer to the oxygen atom with the
consequence that a polarized bond will exist.
δ+ δ-
C O
The carbon atom of the C = O group thus experiences an electron deficiency and will act
as an electrophilic centre susceptible to attack by nucleophilic reagents.
9-7
- H H
δ O O O
H
C Cδ
+ C
Nu
Nu
The effect of protonation on the electrophilic nature of the carbonyl carbon atom
Because of its high electron density, the oxygen of the CO group is easily
protonated, which in turn enhances the electrophilic nature of the carbonyl carbon
atom (it now carries a formal positive charge compared to only a fractional positive charge
before).
−
δ
O O H O H OH
C H δ+ C
C C
Nu
Nu
Consideration of the above arguments explains why nucleophilic addition with or without
protonation comprises the typical reaction of carbonyl containing compounds.
9.3.2 ADDITION OF DERIVATIVES OF AMMONIA
A variety of NH2-containing compounds (derivatives of ammonia) can be added to the

carbonyl group to form C = N-products (carbon-nitrogen double bond). These
condensation reactions are usually catalyzed by acids and can be considered as
nucleophilic substitution of the oxygen atom by a nitrogen atom (The carbon-oxygen
double bond is replaced by the carbon-nitrogen double bond):
In general:
−
δ
O O H
Nucleophilic Elimination + H 2O
C + NH2-Z C C
δ+ addition
HN Z N Z
condensasion reaction
Two types of ammonia derivatives are covered in this unit: Hydrazine (H2N-NH2) and
primary amines (H2N-R where R = CH3) ( Unit 8). Note that each of these derivatives
contains a NH2-group, which acts as the nucleophile, regardless of the rest of the group.
9-8
(a) HYDRAZINE (H2N-NH2 where Z ≡ NH2)
Aldehydes and ketones both react with hydrazine to form hydrazones. These reactions
are most rapidly carried out in weak acidic medium:
O NNH2
+
+ H
In general: R C R(H) H 2N NH2 R C R(H) + H2O
a hydrazone
hydrazine
O NNH2
+
e.g.: H
H3C C CH3 + H2N NH2 H 3C C CH3 + H2O
acetone
acetone hydrazone
(a) O
NH2NH2
+
H
(b)
NH2NH2
O +
H
(b) PRIMARY AMINES (NH2 - R where Z ≡ R ≡ alkyl group)
Aldehydes and ketones condense with 10 amines to form imines (Schiff bases).
9-9
O NCH3
+
+ H
In general: R C R(H) NH2CH3 R C R(H) + H2O
an imine
e.g.: O NCH3
+
H + H 2O
H 3C C H + NH2CH3 H 3C C H
acetaldehyde methylimine
Due to the instability of aldehydes in biological systems, it is converted to imines. The

imines are called the biological equivalent of aldehydes.

O
NH2CH3
(a) CH3CH2CH +
H
NH2CH2CH3
(b) +
H
O

9-10
9.3.3 ADDITION REACTIONS WITH OXYGEN COMPOUNDS
This unit also deals with the addition of alcohols to carbonyl compounds. Aldehydes and
ketones react with alcohols in acidic medium to form an intermediate hemiacetal and
finally an acetal (+ H2O).
For the formation of the hemiacetal one mole of alcohol reacts with an aldehyde or
ketone to convert the carbonyl group into a carbon which is bonded to the alcohol and an
OH-group. Addition of another mole of alcohol substitutes the OH-group to form a carbon
which is bonded to two moles of alcohol – the acetal.
Remark: Owing to the reversibility of the above reaction, the acetal is susceptible to
hydrolysis in acidic medium with generation of the original aldehyde or
ketone. The acetal thus serves as a masked aldehyde or ketone.
Aldehydes and ketones react with alcohols in an acidic medium to form an intermediate
hemi-acetal and finally an acetal.
In general:
O R1OH/H
+ OH + OR1
R1OH/H
C R C R(H) R C R(H)
R R(H) OR1 OR1
ketone/ hemi-acetal
aldehyde acetal
Hemi-acetal A molecule with an –OH and -OR group bonded to the same carbon.
Acetal A molecule with two -OR groups bonded to the same carbon.
Owing to the reversibility of the above reaction, the acetal is hydrolysed in acidic medium
(H2O/H+) to give the original aldehyde or ketone. The acetal thus serves as a masked
aldehyde or ketone.
9-11
O + OH + OCH3
CH3OH/H CH3OH/H
Example: C H3C C H H3C C H
H3C H
OCH3 OCH3
To ensure that the position of the equilibrium lies towards the acetal, an excess of the
alcohol is used. A dehydrating agent (e.g., anhydrous magnesium sulfate) also removes
the water from the reaction mixture and shifts the equilibrium towards the acetal.
H CH3OH CH3OH
(a) +
? + ?
H H
O
CH3CH2OH CH3CH2OH
(b) O +
? + ?
H H
9.3.4 REDUCTION OF ALDEHYDES AND KETONES
Finely powdered Pt (platinum, PtO2) or Pd (palladium, Pd on C) is utilized as catalysts in

the catalytic hydrogenation (reduction) with H2 (hydrogen gas). It is also possible to use
other reducing agents like LiAlH4 (or NaBH4) in reduction reactions. The reduction of
aldehydes yields 10 alcohols, while 20 alcohols are obtained from ketones.
9-12
9.3.5 OXIDATION OF ALDEHYDES AND KETONES
Aldehydes, but not ketones, are easily oxidized to their respective carboxylic acids by
the Tollens reagent (Ag(NH3)2OH), KMnO4 in acidic or basic medium, K2Cr2O7/H2SO4 or
CrO3/H+.
O O
H 3C C H + Ag(NH3)2OH H3C C OH + Ag
ethanol ethanoic acid silver mirror

aldehyde
O
H 3C C CH3 + Ag(NH3)2OH no oxidation
propan-2-one
ketone
Oxidation is the opposite of reduction.

9-13
Oxidation
Reduction
9-14
LiAlH4
(a) O
O ? OH ?
(b)
CrO3 Ag(NH3)2OH
(c) CH3CH2OH ? ?
pyridine
OH ? O NH2CH3
(d) +
?
H
O
(e) H2 HBr
? ?
PtO2
(f) KMnO4 NH2CH3

OH ? +
H

9-15
FEEDBACK FOR UNIT 9
1.
O
(a) CH3 CH3 (b)
CH3CHCH2CHCH2CHCHO H
OH
4-hydroxy-2,6-dimethylheptanal 4-ethylhept-6-ynal
Br O CHO
(c) (d) H 3C
H CH2CH3
HO
3-bromo-4-ethylhexanal (R)-2-hydroxy-2-methylbutanal
2.
O
OH O
(a) H 3C C CH3 (b)
H 3C CH3
H H CH3
(Z) or (cis) pent-3-en-2-one 4-hydroxy-3-methylpentan-2-one
(c) CH2COCH3 (d)

H C O
Cl CH2CH3
(R)-4-chlorohexan-2-one 3-ethylcyclopentan-1-one
3.
NNH2
a)
b)
NNH2
9-16
4.
a) NCH3
CH3CH2CH
b)
NCH2CH3
5.
a) H H
HO OCH3 H3CO OCH3
b)
OH OCH2CH3
OCH2CH3 OCH2CH3
6.
9-17
ADDITIONAL PROBLEMS
1. Write down the complete IUPAC names for the following structures.
a) O
Br
b) COCH3
H
HO CH3
c)
CHO
2.
NH2CH3
+
H
O
(a) Write down the product that you expect when you add NaBH4 to the ketone.
(b) Give the name of the product which is formed in the above reaction.
3. Write down the products and/or reagents for the following reactions.
a) 1 mol 1 mol
O ? ?
+ +
CH3OH/H CH3OH/H
HO H2NN
b) ? ?
?
10-1
UNIT 10: CARBOXYLIC ACIDS AND THE
FUNCTIONAL DERIVATIVES
A: CARBOXYLIC ACIDS
LEARNING OUTCOMES:
By the end of Part A you should be able to:
• write down a complete IUPAC name for simple carboxylic acids and to
write down the names of the trivial names for some of the common
carboxylic acids.
• understand the classification of the carboxylic acids.
• understand the nature of the carboxylic group and the acidity
properties.
• write down the products for the reactions of carboxylic acids and
bases.
10.1 GENERAL INFORMATION

10.1.1 CARBOXYLIC ACIDS
Carboxylic acids contain the carboxyl group which has two functional groups, i.e. the
carbonyl group and hydroxyl group, BOTH connected to the same carbon atom. The
properties of the carboxyl group differ significantly from those of the carbonyl group in
ketones and the hydroxyl group in alcohols.
O
Functional group: -COOH or C
OH
10-2
10.1.2 CARBOXYLIC ACIDS DERIVATIVES
Functional derivatives of carboxylic acids are compounds that can be prepared from
carboxylic acids and may be transformed to the acids by hydrolysis (reaction with
water).
O
R OH
carboxylic acid
O O
R'
R O R NHR'
ester amide
where R and R' = alkyl groups
In this module we are going to look at two derivatives

(1) An ester is formed where the hydroxyl group (OH) is substituted by an alcohol,
(2) an amide is formed where the hydroxyl group (OH) is substituted by ammonia or
an ammonia derivative,
Activity 1: Identify the functional groups in the following structures.

a) CH3COCH2CH2CH3 b) CHO
c) CH3CHCH2OH d) CH3CNHCH3
CH3 O
e) HOOCCH2CH2CH3 f) O
O

10-3
10.2 NOMENCLATURE
The carboxyl functionality, except for carbocations, has the highest priority according
to the IUPAC-system of nomenclature (see Table A-1, Appendix A-1).
carboxylic acids (RCOOH) > aldehydes (RCHO) > ketones (RCOR’) > hydroxyl groups (OH) >
double bonds and triple bonds > halogens (X) and alkyl groups (R)
The following rules should be followed where the CARBOXYLIC ACID IS THE FUNCTIONAL
GROUP OF HIGHEST PRIORITY:
(a) In molecules, which contain a carboxyl group, the carbonyl carbon has to be
included in the longest carbon chain. The carbon atoms in the appropriate chain
are numbered starting at the carbonyl carbon atom.
(b) The suffix -ane in the corresponding alkane is changed to -anoic acid (or -enoic
acid in alkene or -ynoic acid in alkyne chain systems respectively) while the rest
of the functional groups are named in the usual way.
Cl O O
4 3 2 1 OH 6 5 4 3 2 1 OH
3-chlorobutanoic acid (trans)-5-methylhex-3-enoic acid
Note: Always start numbering at the CARBONYL CARBON.
Activity 2: Give the complete IUPAC name for the following compounds.
(a) O (b) O
OH OH
Cl OH
(c) CH2COOH (d) O
H CH2CH2CH3 OH
H3C
10-4
10.3 CLASSIFICATION OF CARBOXYLIC ACIDS
(a) Monobasic acid (contains one carboxylic group)

Example:
O
CH3CH2CH2C OH
butanoic acid
(b) Dibasic acid (has two carboxylic groups)

Example:
O O
HO CCH2C OH
propane dioic acid
(c) Tribasic acid (has three carboxylic groups)

Example:
O OH O
HO CH2C C CH2C OH
COOH citric acid
10.4 STRUCTURE
The carbon atom of the carboxylic group utilizes three sp2-orbitals in the same plane to
bond with two oxygen atoms and a hydrogen or carbon atom. The remaining
unhybridized p-orbital of this carbon atom forms a π-bond with one of the oxygen atoms.
10-5
Overlap of the parallel orientated

non-hybridized p-orbitals
O
R C
O H
The carbonyl carbon atom and the two oxygen atoms are orientated in the same plane.

10.5.1 BREAKING OF THE O-H BOND WITH BASES
With hydroxides
O NaOH O
CH3C O H CH3C O Na + H O
2
sodium ethanoate
(sodium acetate)
From inorganic chemistry you know that a reaction between an acid and base results in
the formation of a salt and water.
10-6
Activity 3: Write down the reagents and products in the following reaction.
OH ? OH KOH ?
H 2O
O
a) H ? OH
O O
b) NaHCO3
COOH
H 2O
c) NaOH
CH3CH2CH2COOH
H 2O

10-7
B: FUNCTIONAL DERIVATIVES
LEARNING OUTCOMES:
By the end of Part B you should be able to:
• write down the complete IUPAC names for the simple carboxylic acid
derivatives.
• write down the reagents and products for the hydrolysis and substitution
of the different carboxylic acid derivatives.
• write down the reagents and/or products during the preparation of the
derivatives.
10.6 GENERAL
Functional derivatives of carboxylic acids are compounds that can be prepared from
carboxylic acids and may be transformed back to the acids by hydrolysis. We are
going to discuss two derivatives namely an ester (where the OH is substituted by an
alcohol) and an amide (where the OH is substituted by an amine).
O O
R C OR' R C NHR'
an ester an amide
R = R′ = alkyl group R = R′ = H or an alkyl group
The acyl group (R-CO) (which originates from the carboxylic acid) is present in the
structures of all functional derivatives.
A functional derivative possesses higher priority than an aldehyde but lower priority
than a carboxylic group on the priority list in the IUPAC nomenclature system. In the
absence of a carboxylic functionality, the carbon of the acyl group is regarded as the
number one carbon atom and has to be contained in the longest carbon chain.
10-8
carboxylic acid (RCOOH) > functional derivative > aldehyde (RCHO) > ketone (RCOR')
10.7 ESTERS
10.7.1 NOMENCLATURE
(i) The first part of the name is derived from the parent name of the alkyl group
connected to the O atom.
(ii) The second part is represented by the name of the carboxylic acid giving origin
to the ester. The suffix -oic acid in the original acid is replaced by –oate e.g.
ethanoic acid changes to ethanoate.
O 2
O
2
1 3 H O
CH2CH3 O 1 H3C C C OCH3
H O 2 1
CH3
methanoate ethyl ethyl ethanoate
ethyl methanoate ethyl ethanoate methyl 2-methylpropanoate
Explanation: The first part of the name comes from the group bonded to the O – in the
first two examples it is an ethyl group. The second part of the name comes from the
carboxylic acid. In the first example there is only one carbon so the original carboxylic acid
was methanoic acid which now changes to methanoate. In the second example the
original carboxylic acid was ethanoic acid which now changes to ethanoate.
Activity 5: Write down the complete IUPAC name for each of the following
compounds.
(a) (b) (c)
O O H
O O O O

10-9
10.7.2 SYNTHESIS OF ESTERS
O H2SO4 O
CH3C OH + CH OH CH3C OCH3 + H 2O
3
Note: This is a reversible reaction. The equilibrium can be shifted to the right by having
either an excess of alcohol in the reaction mixture or by removal of the water that
is formed during the reaction.
10.7.3 REACTIONS OF ESTERS
(a) Acid catalyzed hydrolysis (transformation of the ester back to the carboxylic acid
and alcohol by using acid)
O H2SO4/H2O O
CH3CH2C O CH3 CH3CH2C O H + CH OH
3
The first part of the molecule (CH3CH2CO) originates from the carboxylic acid and the
second part of the molecule (OCH3) originates from the alcohol, so after hydrolysis the
products are propanoic acid and methanol.
(c) Base catalyzed hydrolysis (saponification of the ester to form the salt of the
carboxylic acid and alcohol)
O NaOH O
+
CH3C OCH3 H 2O CH3C OH HOCH3
NaOH
O
CH3C O Na + H O
2
During the base catalyzed hydrolysis, the ester is broken up to give the carboxylic acid and
alcohol (just like the acid catalyzed hydrolysis), but in a basic medium the carboxylic acid
and the base react to form a salt and water [ par. 10.6.1].
10-10
(d) Ammonolysis (substitution of the alcohol group with ammonia or amine):
O O
CH3C OCH3 + NH3 CH3C NH2 + CH3OH
an amide
Ammonolysis is a method to synthesize amides. (See later)
Activity 6: Write down all the products for the following reactions.
O H2SO4
(a) + CH3CH2CH2OH
CH3C OH
O H2SO4
(b)
H 2O
O
O
H 2C O C CH3 H2SO4
(c)
H 2C O C CH3 H 2O
O
(d) O
NH3
CH3CH2C OCH3
(e) O
NaOH
CH3OCCH2CH2CH3
H2O

10-11
10.8 AMIDES
10.8.1 NOMENCLATURE
The suffix -oic acid in the corresponding carboxylic acid is replaced by -amide. In the
case of a substituted amide, the name of the amide is preceded by the N substituent.
O O
3 O
2
NH2 1 NH2 CH3
H 3C 1 N
2 H
ethanamide 2-methylpropanamide ethanamide methyl
N-methylethanamide
Explanation:
(i) In the first example the original carboxylic acid was ethanoic acid. The OH is
substituted by NH3 to give the amide, so the IUPAC name changes to ethanamide.
(ii) In the second example the original carboxylic acid was 2-methylpropanoic acid
which now changes to 2-methylpropanamide.
(iii) In the third example the original carboxylic acid was ethanoic acid. One of the
hydrogens on the nitrogen is however substituted by a methyl group so the name
of the amide should be preceded by the N-substituent. The first part of the name is
thus N-methyl to indicate there is a methyl group bonded to the N, followed by
ethan from ethanoic acid and then amide.
N is a locant and indicates the position of attachment just like carbon numbers.
O O
3 N
4
3
2 1
N
4 2 1
N,N,3-trimethylbutanamide N-ethyl-N,3-dimethylbutanamide
5 3 N
4 2 1
3-ethyl-N,N-dimethylpentanamide
10-12
(a) O (b) O (c) O
NH2 N NH2
H
10.8.2 REACTIONS
Base catalyzed hydrolysis [compare esters –  par. 10.8.3(b)]
O O
NaOH
+ NH3
CH3C NH2 H2O CH3C O Na
The amide is hydrolyzed to the salt of the carboxylic acid and ammonia.
10.8.3 PREPARATION OF AMIDES
(a) From an ester
O O
CH3C OCH3 + NH3 CH3C NH2 + CH3OH

10-13

a)
NH2 NaOH
H 2O
O
b)
O NaOH
CH3CH2CH2C NH2
H 2O

10-14
FEEDBACK FOR UNIT 10

1. (a) ketone
(b) aldehyde
(c) alcohol
(d) amide
(e) carboxylic acid
(f) ester
2. (a) 2-chloro-4-pentynoic acid or 2-chloropent-4-ynoic acid

(b) 4-hydroxy-3,3-dimethylpentanoic acid
(c) (R)-3-methylhexanoic acid
(d) (trans)/(E)-3-pentenoic acid or (trans)/(E)-pent-3-enoic acid
3.
KMnO4 or K2Cr2O7/H+ or CrO3/H+
O K
4. a) KMnO4 or K2Cr2O7/H+ or CrO3/H+
+H
b) COO Na + CO2 2O
c) CH3CH2CH2COO Na + H 2O
5. (a) Ethyl butanoate

(b) Methyl propanoate
(c) Ethyl methanoate
10-15
6.
O
a) CH3COCH2CH2CH3
b) OH + HO
O
c)
CH2OH + 2 CH3COOH
CH2OH
d) CH3CH2CNH2 + CH3OH
O
e) CH3CH2CH2COONa + CH3OH
7. (a) butanamide
(b) N-ethylbutanamide
(c) 4-methylhexanamide
8.
a) O Na
+ NH3
O
b)
O
+ NH3
O Na
10-16
ADDITIONAL PROBLEMS
a) O Cl
HO
____________________________________________________________
b) O
____________________________________________________________
c) O
CH3CH2C NHCH3
____________________________________________________________
11-1
UNIT 11: ORGANIC CHEMISTRY IN BIOLOGY
LEARNING OUTCOMES:
By the end of Unit 11 you should be able to:
• identify all functional groups in organic compounds
• determine the formal charge on all atoms of an organic structure
• identify the different lipids (fats, oils and waxes)
• understand the different biopolymers (lipids, carbohydrates, amino acids
protein, nucleic acids)
• differentiate between RNA and DNA structures.
11.1 FUNCTIONAL GROUPS

11.1.1 SUMMARY OF FUNCTIONAL GROUPS
Up to now, we have looked at the following functional groups:
Functional group Symbol If substituent,

e.g.,
Halides X 3-halo
Alcohols OH 3-hydroxy
Amines NHRR′ 3-amino
Aldehydes and ketones RCO(R′ or H) 2-formyl or 3-oxo
Carboxylic acids COOH Highest priority
Esters COOR Highest priority
Amides CONHR Highest priority
11-2
11.1.2 OTHER BIOLOGICALLY IMPORTANT FUNCTIONAL GROUPS
(a) Phosphates
Phosphate and its derivatives are widespread in biomolecules. Phosphate linked to a

single organic group is called a phosphate ester, phosphate linked to two organic groups is
called a phosphate diester, linkage between two phosphate groups is called a phosphate
anhydride, while the phosphate derivative of a carboxylic acid is called an acyl phosphate.
O O CH3 O CH3 O O O O
O P O O P O O P O O P O P O R
O P O
O O O O O O
CH3
Phosphate Phosphate ester Phosphate diester Phosphate anhydride Acyl phosphate
(b) Sulfur containing derivatives
Sulfides (compare with ethers), thiols (compare with alcohols) and thio-esters (compare
with esters) are important molecules in nature:
O
S R CH3
H 3C CH3 R SH S
Sulfide Thiol Thioester
O
O R CH3
H 3C CH3 R OH O
Ether Alcohol Ester
Thiols are similar to hydroxy groups and react in a similar fashion, because sulphur is
under oxygen in Group 6 of the periodic table and thus contains 6 valence electrons.
Sulphur forms two covalent bonds (just like oxygen). The only difference is that sulfur is
less electronegative than oxygen and thus forms bonds with electropositive atoms that are
less polar. Thioesters are the product of esterification between a carboxylic acid and a
thiol.
11-3
Activity 1: Identify all functional groups in the following structures. State whether
alcohols and amines are primary, secondary, or tertiary:
(a) H
N
S
O
N
O
O
penicillin O
(b) S
OH O
O OH
(c)
O P S
O
Activity 2: Add all formal charges to the following structures:

(a) NH3 O (b) O
O P
O OH
O
O
(c) OH (d) H 3N
H NH2
H O
H O O
(e) F H (f) O O
N
S
11-4
11.2 IMPORTANT CLASSES OF BIOLOGICAL MOLECULES

11.2.1 LIPIDS
Lipids are a large subgroup that contains fats, oils and waxes. The lipids consist of a
carbon chain which ends in a carboxylic acid group (or carboxylate group if the acid is in
ion form). They can be divided into saturated fatty acids (alkane chain), mono-unsaturated
fatty acids (one double bond usually in the cis configuration), and polyunsaturated fatty
acids if it contains two or more double bonds.
11-5
(a) Fatty acids

O
OH
Saturated fatty acid: palmitic acid
OH
Mono-unsaturated fatty acid: oleic acid
OH
Polyunsaturated fatty acid: arachidonic acid
(b) Fats and oils
Fats and oils are forms of triacylglycerol (glycerol backbone with three fatty acids linked
as esters):
R'
OH
HO O O
O
OH R
O O
Glycerol R''
O
Fats and oils
(c) Waxes
Waxes are esters composed of fatty acids that are linked to long alcohol chains:
11-6
Wax: triacontanyl palmitate
(d) Isoprenoids
Isoprenoids is a broad class of lipids found in all forms of life. The smallest building block
is the isoprene unit in the form of isopentenyl diphosphate.
O O
O P O P O
O O
Isoprene
isopentenyl diphosphate
Examples:
OH
O
Limonene Testosterone
Lycopene
11-7
Activity 3: Identify the following lipids as fatty acids, fats and oils, waxes or
isoprenoid: O
(a) (b)
O
(CH2)15CH3
O O
(c) H (d)
3C(H2C)13 O OH
O O (CH2)18CH3 vitamin A
O
11.2.2 BIOPOLYMERS
The most important biopolymers in nature are carbohydrates, proteins and nucleic acids.
You can visualize polymers by comparing it to a string of beads, with each bead having a
hook on each side.
Chain with repeating units
Building blocks
(a) Carbohydrates
Carbohydrates are chains of monosaccharides (or sugar molecules) formed via

condensation of OH groups (ether bonds). The possibilities for carbohydrate structures
are vast and depend on the single sugar entities (monosaccharides), which are used as
building blocks. They can be linear (single long chain) or angular (branched). An example
of a carbohydrate is cellulose. Carbohydrate chains are commonly bonded to proteins or
lipids, especially on the surface of cells.
Monosaccharides are 4 to 6 carbon molecules with multiple OH-groups and one

aldehyde or ketone group. In aqueous solution they exist in an equilibrium between the
chain and cyclized form.
11-8
OH
6
OH OH O 5 ether bond
HO
HO 4 2 4 O
5 3 1 H 1
6
OH OH HO 3 2 OH
Glucose OH
ether bond
OH OH 6 O OH
1
HO 4 2 OH
5 3 OH HO 5
6 2 1
4 3
OH O
Fructose
Disaccharides are two monosaccharides linked together, e.g. sucrose is a combination of

glucose and fructose.
OH
6
HO 5 OH
4 O 3 4 OH
1 2 5
HO 3 2 O O OH
1
OH 6
OH
Glucose Fructose
Sucrose
Polysaccharides are longer chains of monosaccharides, e.g. cellulose is a polymer with

glucose building blocks.
OH OH OH
6 6 6
HO 5 HO 5 HO 5
4 O 4 O 4 O
1 1 1
O 3 2 O 3 2 O 3 2 O
OH OH OH
Glucose + glucose + glucose etc.
Cellulose
means the chain carries on

11-9
Activity 4: Identify the following carbohydrates as mono-, di-, or polysaccharides:
(a) HO OH (b) OH
H O O O OH
HO
H
HO H OH
H O OH O O
OH
H OH OH
O
HO
(c) O
OH
HO OH
HO
O OH
O
O
OH
OH
(b) Amino acids and proteins
An amino acid is comprised of two elements: a backbone or main chain that consists of
an ammonium group, an α-carbon and a carboxylate (carboxylic acid anion); and a
sidechain, bonded to the α-carbon. The side chain can be any of a number of units. There
are 20 different side chains in naturally occurring amino acids and the identity of the side
chain determines the identity of the amino acid.
11-10
HO
H N
CH3
H H
side chain O O O
H 3N H 3N H3N
R O O O
H
Alanine Serine Tryptophan
α O
H 3N
O pH pH pH
backbone
CH3 HO
H
General structure OH
H 2N H
OH H N
O H 2N
O OH
H 2N
O
Proteins are polymers of amino acids - the amino end of one amino acid condenses with
the carboxylic acid end of another amino acid to form an amide bond (see Derivatives of
carboxylic acids, Amides, Unit 10) with loss of H2O. This bond is called a peptide bond. A
protein contains 50 or more amino acid building blocks, while peptides are shorter
polymers. If we go back to the string of beads analogy – the two hooks on every amino
acid (bead) is the amino group on the one end and the carboxylate group on the other end.
amino end carboxylate end
Peptide (49 or less units) or protein (50 or more units)
Which amino acids are linked and in what order is called the sequence of the peptide or
protein and it is written in the direction of the starting amino acid to the end carboxylate,
with either a 3 letter or single letter abbreviation of the different amino acids making up the
polymer. Below is a four amino acid peptide with the sequence “cysteine-histidine-
glutamate-methionine” or CHEM.
11-11
glu
tam
ate
) O O (E)
C
ne(
tei
cys HS
O O
H H
N N
H 3N N O C-terminus
H
O O
N-terminus N
HN S
histidine (H) methionine (M)
peptide bond
In many cases protein polymers fold into specific forms, creating pockets where other
molecules can bind. Enzymes are proteins which biocatalyze reactions and they can
accommodate only certain substrates in these active sites (pockets) and the wanted
reaction occurs there.
Activity 5: Identify the following compounds as amino acids, peptides or proteins:

O
(a) H (b)
N O HO O
H 2N N
H
O HN HS
O O
H H
O HN O N N
H H 2N 56 N OH
HO N H
N O O
H
O O S
(c) (d)
O
O O
H
H 2N N OH
38 N OH
H NH2
O HO
OH
11-12
(c) Nucleic acids (DNA and RNA)
Deoxyribonucleic acid (DNA) and Ribonucleic Acid (RNA) are polymers composed of
monomers called nucleotides. An RNA nucleotide consists of a 5-carbon sugar phosphate
connected to one of four nucleic acid bases: guanine (G), cytosine (C), adenine (A) and
uracil (U), while DNA has the same backbone but one less hydroxy group and thymine
base instead of uracil base.
Purine bases
NH2 O
N N N NH
N N N N NH2
H H
Adenine (A) Guanine (G)
Pyrimidine bases
O O NH2
HN HN N
O N O N O N
H H H
Uracil (U) Thymine (T) Cytosine (C)

(RNA) (DNA)
NB: YOU DO NOT HAVE TO BE ABLE TO DRAW THE STRUCTURES; WE WILL

ONLY USE THE ABBREVIATIONS.
11-13
Cytosine (C)
O 3 O
O 2 N NH2
O P O 4 O P O
5' O 1' N O C
O 5 O
4' 1 6
2'
3'
HO OH HO OH
Cytidine nucleotide Cytidine nucleotide
Guanine (G)
O 7 O
8 N O
O P O 5 O P O
6
5' O 1' N O G
O 9 4 NH O
4' 1
2' N
3 2
3' NH2
HO OH HO OH
Guanosine nucleotide Guanosine nucleotide
The differences between DNA and RNA are as follows:

• The sugar unit of DNA does not have a hydroxy group on C-2′
• DNA bases include A, G, C, T
• RNA bases include A, G, C, U
Thus, in building a polymer the “hooks” on the monomer units are the phosphate group on
one nucleotide and the 3′ hydroxy group of the sugar of another unit.
RNA
Uradine nucleotide Cytidine nucleotide
O O O
O P O O P O O P O
O
O U + O
O C
O
O C
2' OH group present
HO OH HO OH O OH
Phosphate O P O Uracil only in RNA
diester link O
O U
HO OH
11-14
DNA
Deoxythymidine nucleotide Deoxyadenosine nucleotide
O O O
O P O O P O O P O
O
O T + O
O A
O
O A
HO HO no 2' OH group present

no OH no OH O
Phosphate O P O Thymine only in DNA
diester link O
O T
HO
S = sugar molecule
Bold red = Sugar phosphate backbone
T, A, C, G = bases O
O O
P O P O
O S O O S
O O O
P O P O
C G
O S O O S O
O P O A
T
O
Base Base Base Base
P Sugar P Sugar P Sugar P Sugar
DNA can form a double helix when two single-stranded DNA units combine – the bases
of the first strand form hydrogen bonds with the bases from the second strand to form
“base pairs”:
11-15
Activity 6: Differentiate between RNA and DNA and give a reason for your answer:
(a) (b)
(c) adenine (d) adenine

O uracil O
cytosine
O O OH O O
O O
P OH P
O O O O
O O
P P
O O O
O O O

11-16
FEEDBACK FOR UNIT 11

1. (a) amide
sulfide
H
N
S
O
N
O
O
penicillin O
o amine
ketone 3
carboxylate
(b) S
OH O
alcohol
3o thioester
alcohol
(c) 2o
O OH
O P S thiolate
phosphate O
O
2. (a) (b)
NH3 O
O P
OH
O O
O
(c) (d)
OH H 3N
NH2
H
H O
O O
H
(e) F H (f) O O
N
S
3. (a) isoprenoid (b) wax

(c) Fat or oil (triglyceride) (d) isoprenoid
4. (a) monosaccharide
(b) polysaccharide
(c) disaccharide
11-17
5. (a) peptide
(b) protein
(c) peptide
(d) amino acid
6. (a) RNA - uracil is only found in RNA

(b) DNA - thymine is present and it is a double helix
(c) RNA – uracil and 2′-OH group are present
(d) DNA – 2′-OH group is not present
oooOOOooo

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1

Dr SL Bonnet & Prof A

UNIT 1 – INTRODUCTION TO ORGANIC CHEMISTRY

1.1 Introduction 1-1

ADDITIONAL PROBLEMS 1-15

UNIT 2 – ALKANES AND CYCLOALKANES

ADDITIONAL PROBLEMS 2-20

UNIT 3 – ALKYL HALIDES

3.1 Introduction 3-1

3.2 Classification of monohalogen compounds 3-2

ADDITIONAL PROBLEMS 3-11

ADDITIONAL PROBLEMS 4-11

UNIT 5 – ALKENES AND CYCLOALKENES

5.5.5 Addition of water (hydration) 5-16

ADDITIONAL PROBLEMS 5-21

ADDITIONAL PROBLEMS 6-11

(a) SN1-mechanism for tertiary alcohols 7-11

ADDITIONAL PROBLEMS 7-23

ADDITIONAL PROBLEMS 8-8

UNIT 9 – CARBONYL COMPOUNDS (ALDEHYDES AND

(a) Hydrazine (H2N-NH2 where Z ≡ NH2) 9-8

(b) Primary amines (NH2 – R where Z ≡ R ≡ alkyl group) 9-9

ADDITIONAL PROBLEMS 9-17

UNIT 10 – CARBOXYLIC ACIDS AND THE FUNCTIONAL

10.1 General information 10-1

10.6 General 10-7

ADDITIONAL PROBLEMS 10-16

UNIT 11 – ORGANIC CHEMISTRY IN BIOLOGY

UNIT 1: INTRODUCTION TO ORGANIC

Organic Chemistry is described as the chemistry of compounds containing the element

1.2 IDENTIFICATION OF ORGANIC COMPOUNDS

Activity 1: What is a molecular formula?

See feedback at end of unit→

1.3 THE CHEMICAL BOND

1.3.1 BOND FORMATION

atomic orbitals overlapping molecular orbital

For two atomic orbitals to overlap, it is necessary that:

See feedback at end of unit→

1.3.2 ELECTRON CONFIGURATION OF THE CARBON ATOM

↑ 2px ↑ 2py 2pz

See feedback at end of unit→

1.3.3 sp3-HYBRIDIZATION OF CARBON ATOMS

2s 2px 2py 2pz orbitals

Methane is represented as follows (each line represents a covalent bond):

These structures are normally represented as:

1.4 POLAR COVALENT BONDS

See feedback at end of unit→

1.5 REACTIONS AND REACTION MECHANISMS

Straight arrows ( ) point from reactants to products in chemical reaction

1.5.1 BOND CLEAVAGE

The half-arrow ( ) indicates the flow of one electron.

Assume B is the more electronegative atom:

The full arrow ( ) indicates the flow of two electrons.

Activity 5: What is the difference between homolytic and heterolytic cleavage?

See feedback at end of unit→

1.5.2 BOND FORMATION

(a negative ion can react with a positive ion)

A NEGATIVELY charged carbon is called a CARBANION.

Examples of electrophiles/electrophilic compounds

(a) CH3 (b) CH3 CH2 (c) CH3 CH2 I

Examples of nucleophiles/nucleophilic compounds

(a) HO (b) I (c) H 2O

(d) NH3 (e) NaCN

Activity 6: Draw an electron structure for O (oxygen). How many non-bonded