Chem 120- Biochemistry

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 Chemical Reactivity (CHEM 120)
Aim:
 To introduce students to different organic molecules, organic functional groups, simple organic reactions and
introductory reaction mechanisms.

Learning Objectives:
 The objective of this course is to equip students with the necessary skills to solve basic theoretical and practical
chemistry problems. These skills form a fundamental component of many higher level chemistry and non-chemistry
programmes

Learning Outcomes: On completion of this module students are expected to:

 Systematically draw and name simple structures of organic compounds.
 Recognize organic functional groups, predict their reactivity, and describe and explain simple reaction mechanisms.
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Introduction to Organic Chemistry

S Sithebe
School of Chemistry and Physics
Chemistry building
Room 7

Lecture Notes 1
 PowerPoint to accompany

Chapters 21
& 23

Alkanes, Alkenes
and Alkynes
 Organic Chemistry
 Is the scientific study of the structure, properties (chemical
and physical), reaction mechanism (behaviour) and
applications of organic compounds.

 Organic compounds: Compounds which consist of carbon

(C) usually bonded to other atoms such as N, O, S, H and
Halogens (Group 17).

 Aim: Gives us a background of the behaviour (reactivity),

preparation and identification of organic compounds.

Medicinal Food Pharmaceutical

Chemistry Biochemistry Science Chemistry
Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
The benefits of Organic World
O

OH

Asprin

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Hydrocarbons
Hydrocarbons

Saturated Unsaturated

Alkanes Alkenes Alkynes Arenes

H H
H
H C C H H H
C C H C C H H C H
H H C C
H H
C C
H C H
 Hydrocarbons: compounds made of C and H. H

 Alkanes are saturated: each carbon atom has greatest

number of hydrogen possible
Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Hydrocarbons
Hydrocarbons

Saturated Unsaturated

Alkanes Alkenes Alkynes Arenes

H H
H
H C C H H H
C C H C C H H C H
H H C C
H H
C C
H C H
 Hydrocarbons: compounds made of C and H. H

 Alkanes are saturated: each carbon atom has greatest

number of hydrogen possible
Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Properties of Alkanes

Table 21.1
Names ends in –ane, general formula
CnH2n+2

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Properties of Alkanes
 Held together by weak intermolecular forces Van der
Waals force or London dispersion force.
 Strength of London forces increases with an increase in molecular
weight.

 The longer the chain, the stronger the London forces.

 Decane has a higher boiling point temperature than pentane

because decane has larger molecular formula which mean the
London forces holding decane molecules are stronger, therefore more
energy (temperature) is needed break those forces in order for
decane to boil (evaporate).

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Hydrocarbons
Hydrocarbons

Saturated Unsaturated

Alkanes Alkenes Alkynes Arenes

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

CnH2n+2 CnH2n CnH2n-2 H

Alkenes, Alkynes and arenes are unsaturated

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
Structure and Bonding of Hydrocarbons
Hybridise/
mix
          
2s 2p 2s 2p sp3
New hydride
orbitals

Hybridisation:
sp3 sp2 sp

Shape :
Tetrahedral Trigonal Planar Linear

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
Structure and Bonding of Hydrocarbons

3 sigma & 2 sigma &

4 sigma
1 pi-bond 2 pi-bonds
bonds

Hybridise
/mix
          

2s 2p 2s 2p sp2 2p

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
Drawing Organic molecules
Structural Condensed
Line structure
formula: structural
formula:

H2CCH2

HCCH

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
Drawing Organic molecules
CH3CH2CH2CH3

CH3CH2C(F)HCH2CH2CH3
F

CH3CH(CH3)CH2CH2CH(CH3)CH3

OR
(CH3)2CHCH2CH2CH(CH3)2

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Exercise A
Draw the line structures of the following compounds

 H2CCHCHCHCH3

 H3CCH2CH(OH)CH2CH(NH2)CH2CH3

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Past Examination
 Indicate the hybridizations of the numbered carbon atoms

C1……..

C2……..

C3……..

C4…….

C5…….

C6……..

C7….………….C8… .…………..C9……………C10…………...

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Newman Projection
 A three dimensional arrangement of atoms is called
conformation.
 Two or more molecules with the same molecular formula but
different three-dimensional structures are said to be
conformational isomers.

 Conformational isomers or conformers are formed as the result

of rotation about a C-C single bond.

H H

H C
1
C H
2
Br Br

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Newman Projection
• Two conformers we can get through C1-C2
rotation, staggered and eclipsed conformers
Back C2

Front C1

staggered H H eclipsed
H C
1
C H
2
Br Br

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Newman Projection
Rotation about C2-C3
Back carbon,C3
Front carbon,C2

H H H H

H 1
C C C C H
2 3 4
H H H H

Figure 21.15
Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Conformational isomers
• Eclipsed isomers are higher in energy (unstable).
• Due to non-bonding interaction strain which is derived
from steric and torsional effects.

• The magnitude of the stain depends on the size of

neighbouring atoms as well as how close the neighbouring
atoms are.
• The bigger the atoms, the greater the strain (the least
stable the molecule is).
• The closer the atoms, the greater the strain (the least stable
the molecule is).
Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Exercise B
 Draw the Newman Projections of the following molecules
considering the rotation about the indicated C-C bond.

Staggered Eclipsed

………………………….. …………………………..

………………………….. …………………………..

………………………….. …………………………..

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
Organic Nomenclature /naming
 Three parts to a compound name:
Prefix-Parent-Suffix

Prefix : Tells what groups (substituents) are attached to

the chain.
Parent : Tells how many carbons are in the
longest continuous chain.
Suffix : Tells what type of compound it is.
(Alkanes, alkenes, alkynes, alcohol, aldehyde, etc.)

IUPAC: International Union of Pure and Applied

Chemistry
Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 To Name a Compound…
IUPAC: International Union of Pure and Applied
Chemistry

IUPAC systematic naming

1. Find the longest carbon chain in the molecule
8
7
1
2
2 4 6 7 5 3
1 3 5 8
6 4

2. Number the chain from the end nearest the first

substituent encountered.

Substituents : group(s) of atoms not part of the longest

chain

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 To Name a Compound…
1
2
7 5 3
3-Methyloctane
8 4
6
Prefix-Parent-Suffix

Full Name Substituents Substituents

Methane (CH4) CH3 methyl
Ethane (CH3CH3) CH3CH2 ethyl
Propane (CH3CH2CH3) CH3CH2CH2 propyl

Iodine (I2) I iodo

Chlorine (Cl2) Cl chloro
Fluorine (F2) F fluoro
Methoxy (OCH3) OCH3 methoxy

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 To Name a Compound…
3. If two or more substituent are present, list them in
alphabetical order.

4. If two or more identical substituent are present, use

prefixes di-(two), tri-(three), etc.

A B
I
I
I 2 6 8
7 5 3 3
6 4
1 1 7
8 5
Cl 4 2
Cl
Cl

3-Chloro-4-iodooctane

F F F
6 2 2 4 6
3
5 B
4 5 7
7 1
3 1
F
F F

A 3,4-difluoroheptane

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Exercise C
Give the IUPAC names of these compounds
2-Iodo- Heptane
2-methyl-
3-ethyl-
4-chloro-
5-nitro-

……………………..

……………………..

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Cycloalkanes
• Hydrocarbons joined to form a ring
• Similar to alkanes except that two hydrogen atoms are
omitted (CnH2n)
Bigger group takes position 1

1-Ethyl-3-methyl-cyclohexane
………………………………………….

CH3

CH3

Trans-1,2-dimethylcyclopentane

CH3
…………………………………………
CH3

Cis-1,2-dimethylcyclohexane

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Nomenclature of Alkenes
1. Find the longest continuous chain of carbon atoms that contain a
double bond (parent).
2. Double bond takes the lowest position number possible.

Alkene Suffix is -ene

1-hexene or hex-1-ene
Cl Cl

7 5 1 Cl
5
4 2 2 CH2
8 6 3 1
3 3 6 4

4
2

X 1
X 5

3-Chloro-2-propylhex-1-ene
CH3

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Exercise D
Give the IUPAC names of these compounds
3-Ethyl-
7-Chloro-
Nona-1,4-diene

…………………….....

………………………..

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Nomenclature of Alkynes
 Triple bond takes the lowest position number
possible.
1
2 CH3
CH3
H2C
CH2

H3C CH2 C C CH3 H3C CH2 C C CH2 C CH3

C CH2 3
2 1 8 7 6 5 4
7 6 5 4 3
F F

X 8
X
7 CH3
H2C

H3C CH2 C C CH2 C CH3

3 6
1 2 4 5
F
Suffix: 6-fluoro
6-methyl 6-Fluoro-6-methyloct-3-yne
Parent: Oct-
Preffix : yne
Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Exercise E
 Name the following alkenes, clearly specify whether the compound is a
Cis or Trans-isomer 6 5 2 1
H3C CH2 CH2CH3
H3C CH2 CH2CH3
C C
C C 4 3
H H
H H
Cis-hex-3-ene

5
1
H3C H
3 H3C H
or 3
C C
H3C H 4 C C
2
C C H CH2CH3
2 1 H CH2CH3
X
4 5
H CH2CH3
Trans-pent-2-ene

5 2 1
H3C CH2 CH2CH3
6 3
H3C CH2 CH2CH3 C C
4
C C H CH3
H CH3
Cis-3-methylhexn-3-ene
Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 E/Z-Isomerism
• E-
L H • 3-iodo-
1 2 6
5
• Hex-3-ene
H3C CH2 CH2 CH3
C C E-3-iodohex-3-ene
3 4
H I H L
Higher Higher Lower Higher

C C C C

Lower Lower Higher Lower

Z-same side E-opposite side

(1) (6) (7) (8) (17) (35)

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Exercise F
 Arrange the following groups in order of increasing priority
according to Cahn-Ingold-Prelog rules?

O O O O O
C H C OH C Cl C NH2 C CH3
a b c d e

 Specify configurations of the following alkenes using the E,Z

system

Cl CH3 H CH3 I CH3

C C C C C C
H3C CH CH3 H3C CH CH3 H3C CH CH3
CH3 CH3 H

a b c
Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Exercise G

4-cychlopropyl-
Octa-2,6-diene

NO2

………………………………

Br

………………………………

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Constitutional Isomers
 Have same molecular
formulae, but atoms are
bonded in a different
order.

 Physical properties vary

C4H10 with the degree of
branching.

Figure 21.17
Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
 Constitutional Isomers
 Molecules with the same molecular formulae but
different atom arrangement.

Hexane 2-methylpentane 3-methylpentane

2,3-dimethylbutane

2,2-dimethylbutane
C6H14

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
Constitutional Isomers for multiple bonds

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
Constitutional Isomers for multiple bonds

Brown, LeMay, Bursten, Murphy, Langford, Sagatys: Chemistry 2e © 2010 Pearson Australia
Chemical Reactivity

Reaction
Mechanism
 Bond cleavage
• Homolytic cleavage: break of bond in which electrons are shared equally
between atoms. E.g. free radicals.
• Equation: Cl Cl 2Cl

 Heterolytic cleavage: break of bond in which electrons are not shared

equally between atoms. E.g. formation of electrophile and nucleophile.
 Equation:
H3C Cl CH3 + Cl
 Reactions of Alkenes
• Unlike alkanes, Alkenes are reactive because of the double bond.

• Reactivity: π-bonds are weaker (more reactive) than σ-bonds.

• π-bonds are electron-rich : Nucleophiles (Nu-), negatively charged species.

• Electron-poor species : Electrophiles (E+), positively charged species.

Nu- E+ Nu E
Arrow notation : movement of two electrons
 Practice 1
• Classify the following molecules as electrophile or nucleophile. Give a
reason.
 Stability of Carbocation
 A species containing a positively charged carbon atom: carbocation
(carbon + cation).

 Major product depends on the stability of carbocation formed.

H H CH3 CH3

H C+ H H3C C+ H H3C C+ H H3C C+ H

H H H CH3

Primary Secondary Tertiary (3⁰)

Methyl cation carbocation (1⁰) carbocation (2⁰)

Increasing Stability
 More stable carbocation produces a major product
 Why is tertiary carbocation (3⁰) stable?

Increasing Stability
H H CH3 CH3

H C+ H H3C C+ H H3C C+ H H3C C+ H 3°

H H H CH3
2°
1°
Six electrons : electron
deficient !!!

• Atoms directly attached to the electron-deficient central carbon are able to donates electron to stabilise it (‘make it happier’).
• The donating ability of atoms directly attached to the central carbon increase with increasing the molar mass as well as
branching.

CH3
H CH3 CH3
CH CH3
H3C C+ H H3C C+ H H3C C+ H
H3C CH2 C + H
H H CH2 CH3
CH3

Increasing stability
 Practice 2

• Which of the following carbocations is least stable?

• When reacted with bromide ion, which carbocation will produce a

major product? Explain.
 Exercise H
• Arrange the following carbocations in order of increasing stability.

(a) (b) (c)

+
+

+
+ +
(a) CH3 (b) CH3 (c) CH2 CH3
 Reactions of Alkenes
(a) Halogenation
• Multiple bonds undergo addition reactions H H H H
C C + Br Br Br C C Br
H H H H

• π-bond breaks, when two atoms (e.g., HBr) add Haloalkane

(b) Hydrohalogenation
across the double bond.
H H H H
C C + H Br H C C Br
H H H H
Haloalkane
(c) Hydration

H H H H
C C + H OH H C C OH
H H H H
Alcohols
(d) Hydrogenation

H H H H
C C + H H H C C H
H H H H
Alkane

Figure 23.20
 Hydrogenation of Alkynes
H3C C C CH3
NB! Product depends on
… . catalyst used.

Li 2H2
NH3 H2 Pd/C
(Pd/CaCO3)

H H
H3C H
C C H3C C C CH3

H CH3
H H H H
Trans-isomer
C C Complete
reduction
H3C CH3
Cis-isomer
(Pd/CaCO3) = Lindlar catalyst
 Practice 3
• What is the product when pent-2-yne react with 1 mol of
Hydrogen gas in the presence of Li/NH3 ?

• State whether the following statement is true or false. Motivate.

• When 2-bromo-hept-3-yne is reacted with 1 mol of H2(g) in the
presence of Pd/CaCO3 it produces cis-2-bromohept-3-ene?
Hydro-halogenation (Mechanism)
• In the first step, -bond breaks and new C—H bond and cation
form.
H3C Br- Minor Product
H H H H
1
H3C3 C2 C H H3C3 C2 C1 H
+
H (C2)
H H Br
3
H3C H 1-bromopropane

C C +
H Br
2 1
H H H H
H H

H3C3 C2 C1 H H3C3 C2 C1 H
H (C1) +
H Br H
2-bromopropane
H3C Br-

Major Product
(Formed in large
quantities)
 In the second step, a new bond forms between negative charged
bromide ion and positive charged carbon atom.
 Markovnikov’s Rule
• In the addition of HX (X = Br, Cl) to an alkene, the hydrogen adds to the carbon atom of the double bond
bearing the greater number of hydrogen atoms bonded directly to it (Major product).

H3C Br- Minor Product

H H H H
1

H (C2) H3C3 C2 C H H3C3 C2 C1 H

+
3 H H Br
H3C H
1-bromopropane
C C +
H Br
2 1
H H H H
H H

H3C3 C2 C1 H H3C3 C2 C1 H
H (C1) +
H Br H
2-bromopropane
H3C Br-

Major Product
 Practice 4
• What is the major product when pent-2-yne react with 1 mol of Hydrogen
gas in the presence of Li/NH3 followed by the addition of HBr?

• An alkyne (A) with molecular formular (C5H8) was reacted with 1 mol of
hydrogen gas in the presence of Lindlar’s catalyst. When HCl was added,
1-chloro-pentane was found to be a minor product.

 What is the structure of A?

What is the structure of a major product?
 Exercise I
Provide a full mechanism for the following reactions. Indicate the major
product and explain briefly.

+ HBr

+ HCl
 Energy Profile
• Two step reaction
Transition
state 1
Transition
E state 2
N
E
R
G C C
Y step 2
E
Nu-

C C
step 1
Nu
Intermediate
C C

E+ E
 Addition of H2O (hydration)
• The hydration of alkenes and alkynes requires the addition of a strong acid catalyst
(usually H2SO4)
H

H2O + H2SO4 O + HSO4

H H

• Hydronium ion is an electrophile (E+, electron loving)

• Second step is the formation of carbocation and water
 Addition of H2O (hydration)
• Third step is the formation of oxonium ion
• Water is a nucleophile (Nu-, positive charge loving)

• Loss of H+ from the oxonium ion leads to formation of an alcohol.

 Exercise J
Draw structural formulae of the products of the following hydration reactions.

a. H2SO4
+ H2 O

H2SO4
b. + H 2O

H2SO4
c. + H2O
 Catalytic Hydrogenation
• Reaction requires molecular hydrogen (H2) and a metal catalyst (Ni, Pd, Pt, Ru)
• Always cis-isomer
• Syn-addition (Hydrogen atoms are added on the same side of a double bond).

Cis-isomer
 Hydrogenation

Blackman, Bottle, Schmid, Mocerino, Wille. Chemistry book, page 638

 Halogenation
• One of the easiest and most dramatic reactions is the
addition of Br2 to an alkene.
• Colour change
• Useful test for alkenes

Trans-
isomer

• Always trans-isomer for cycloalkenes

• Anti-addition (bromine atoms are added on opposite side of the double

Figure 23.23
bond)
 Halogenation
Br Br
Br
+
+ Br Br Br Br
+
Br
Brominium ion
Trans-isomer

Key step: formation of brominium ion.