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ASC0303

ORGANIC CHEMISTRY

Chapter 1

Introduction to Organic Chemistry


(Part 1)
PUSAT ASASI SAINS

COURSE TITLE: ORGANIC CHEMISTRY


COURSE CODE: ASC 0303
CREDIT:
2+1
LECTURE:
2 HOURS/WEEK
LAB:
3 HOURS/2 WEEKS
TUTORIAL:
2 HOURS/2 WEEKS
ASSESSMENT
TEST 1: WEEK 5 15%
TEST 2: WEEK 10
20%
LAB REPORT:
15%
ASSIGNMENT:
10%
FINAL:
40%
REFERENCE BOOK:
John McMurry, Fundamentals of Organic Chemistry, 7th. Ed.,
Brooks/Cole

PUSAT ASASI SAINS

COURSE TITLE:
ORGANIC CHEMISTRY
COURSE
CODE:ASC 0303
CREDIT:
2 + 1 (120 hrs)
DURATION:
14 weeks
Activities
Lecture
Revision
Prelab report
Laboratory
Group discussion
Tutorial presentation
Test 1 preparation

Hours
2 hrs x 14
2 hrs x 14
1 hr x 7
3 hrs x 7
2 hrs x 7
2 hrs x 7

28
28
7
21
14
14
2.5

Test 1

1.5

Test 2 preparation

2.5

Test 2
TOTAL

1.5

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120

Wk

Topics

1. Introduction Part 1

1. Introduction Part 2

Wk Tutorial
1

2. Alkanes and Cycloalkanes

1,2

3. Alkenes and Cycloalkenes

4. Arenes

5. Haloalkanes

6. Alcohols and Phenols Part 1

6. Alcohols and Phenols Part 2

7. Aldehydes and Ketones

10

8. Carboxylic Acid and Derivatives Part 1

11

8. Carboxylic Acid and Derivatives Part 2

12

9. Amines

13

10. Amino acids

14

11. Carbohydrates and Polymers

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1st test
7

4,5

6,7
2nd Test

11

13

9,10,11

Learning Outcomes
a. Identify types of bonds for carbon atoms
b. Define functional group and homologous series
c. Identify functional groups of the following homologous series:
i.

Alkanes, alkenes, alkynes and arenes

ii. Haloalkanes
iii. Alcohols and phenols
iv. Aldehydes and ketones
v. Carboxylic acids and their derivatives (acyl chlorides, amides, anhydrides, nitrile and esters)
vi. Amines

d. Explain general characteristics of homologous series


e. Identify the structural formula of organic compounds
f. Draw structural formula in the form of expanded, condensed and skeletal
structures based on molecular formula

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Learning Outcomes
g. Define isomerism, constitutional and stereoisomerism
h. Explain three types of constitutional isomerisim
i.
ii.
iii.
i.

Describe cis-trans, E and Z isomerism due to restricted rotation in:


i.
ii.

j.

Chain isomers
Positional isomers
Functional group isomers
Double bonds
Cyclic compounds (single bond)

Define chiral centre and enantiomers

k. Identify chiral centre of a given structural formula


l.

Draw a pair of enantiomers using 3-dimensional formula

m. Explain optical activity of a compound


n. Deduce the possible isomers for an organic compound of known molecular
formula

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Organic Chemistry
sub-discipline within chemistry involving the scientific
study of:
structure,
properties,
composition,
reactions, and
preparation (by synthesis or by other means)
of carbon-based compounds, and their derivatives.

Sometimes few other elements are involved such as


oxygen, nitrogen, sulphur, phosphorus and the
halogens.
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Hydrocarbons
contain only two elements, which are C and H.
Hydrocarbons that contain a delocalized ring of -bonds such as
benzene ring are called aromatic hydrocarbons.
Those without delocalized systems (contain only -bonds) are
called aliphatic hydrocarbons.
Saturated contains only single bonds
Unsaturated contain at least one double or triple bond
Hydrocarbons
Aliphatic
hydrocarbo
ns

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Alkanes

Cycloalkan
es

Alkenes

Alkynes

Aromatic
hydocarbo
ns

Bonding in Carbon Atoms


Type

Hybridisation

Example

Single

H
H

CC
CH
CX

sp
one -bond
3

methane (CH4)
H

C Cl

chloroethane
(CH3CH2Cl)
Double

H
C

sp
one -bond
and one bond
2

C=C
C=O

ethane (CH2CH2)
H3C

H
C

C
CH3

but-2-ene
(CH3CHCHCH3)
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Bonding in Carbon Atoms


Triple

H C

CC
CN

sp
one -bond and
two -bonds

ethyne (CHCH)

sp2
-bonds and
delocalized electrons

benzene (C6H6)

Aromatics

Alternate
C-C &
C=C

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Bonding in Benzene
Each carbon atom uses the sp2 hybrids to form sigma bonds with
two other carbons and one hydrogen atom
The px and py orbital are hybridized to form sp2 hybridization. pz
electron on each carbon atom overlapping with those on both
sides of it.
electrons are no longer held between just two carbon atoms, but
are spread over the whole ring (delocalised).

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Functional Groups
A functional group is an atom or group of atoms within a molecule
that shows a characteristic set of physical and chemical properties
of the compound. Functional groups are important for three
reason; they are
the units by which we divide organic compounds into classes
the basis for naming organic compounds (parent chain)
the sites of characteristic chemical reactions

OH

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Functional Groups
Multiple carbon-carbon bonds
Alkanes have a C-C
single bond
Alkenes have a C=C
double bond
Alkynes have a CC
triple bond
Arenes or Aromatics
have special bonds that
are represented as
alternating single and
double C-C bonds in a
six-membered ring

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Functional Groups
Carbon singly bonded to an electronegative atom

Alkyl halide: C bonded to halogen (C-X)


Alcohol: C bonded O of a hydroxyl group (C-OH)
Ether: Two Cs bonded to the same O (C-O-C)
Amine: C bonded to N (C-N)

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Functional Groups
Carbon-Oxygen double bond (Carbonyl)

Aldehyde: one hydrogen bonded to C=O ( R-CH=O )


Ketone: two Cs bonded to the C=O
( RRC=O )
Carboxylic acid: OH bonded to the C=O
( R-COOH )
Ester: O-C bonded to the C=O
( R-COOR )
Amide: N-C and/or N-H bonded to the C=O ( R-CONH )
Acyl Halide: X bonded to the C=O
( R-COX )

In all of these functional groups the


Carbonyl C has a partial positive charge
(+) and the Carbonyl O has partial
negative charge (-).

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Functional Groups
Priority as parent chain in nomenclature
Functional
Group
Highest priority

Prefix
(substituent)

Suffix
(parent)

-carboxylic
carboxylic acid carboxyacid
-oic acid
ester
(R)-oxycarbonyl-oate
acyl halide
halocarbonyl-oyl halide
-carboxamide
amide
carbamoyl-amide
nitrile
cyano-nitrile
-al
aldehyde
formyl-carbaldehyde
ketone
oxo-one
alcohol
hydroxyl-ol
amine
amino-amine
alkene
alkenyl
-ene
alkyne
alkynyl
-yne
Everything below from here ends in -ane
alkane
alkyl
-ane

ether
alkoxy
-ane

haloalkane
halo-ane

nitro

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nitro-

-ane

Example

ethanoic acid
methyl ethanoate
ethanoyl chloride
ethanamide
ethanonitrile
ethanal
2-propanone
methanol
methylamine
butene
butyne
butane
methoxy methane
bromoethane
nitromethane

Homologous Series
group of organic chemical compounds, usually listed in order of
increasing size,
have a similar structure (and hence also similar properties) and
structures differ only by the number of CH2 units in the main carbon
chain.

alkanes consist of carbon and hydrogen atoms only, in proportions


according to the general formula:

CnH2n+2
where the letter n represents the number of carbon atoms in each
molecule of the compound

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Homologous Series
Name of Series

General chemical formula

Alkanes

CnH2n+2

Alkenes

CnH2n

Alkynes

CnH2n-2

Haloalkanes
Alcohols (primary)

CnH2n+1X
CnH2n+1O or CnH2nOH

Aldehydes and Ketones

CnH2nO

Carboxylic Acids

CnH2nO2

Acyl Halides

CnH2nOX

Amines

CnH2n+1NH2 or CnH2n+3N

Amides

CnH2n-1ONH2 or CnH2n+1ON

Nitriles

CnH2n-3N

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Homologous Series
Name based on number of carbon in the longest or parent
hydrocarbon chain
Number of Carbon

Prefix

Meth-

Eth-

Prop-

But-

Pent-

Hex-

Hept-

Oct-

Non-

10

Dec-

11

Undec-

12

Dodec-

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Homologous Series
EXAMPLE 1.1: Homologous series for alkanes
Name

Formula

Methane

CH4

Ethane

CH3CH3

Propane

CH3CH2CH3

Butane

CH3CH2CH2CH3

Pentane

CH3CH2CH2CH2CH3

Hexane

CH3CH2CH2CH2CH2CH3

Heptane

CH3CH2CH2CH2CH2CH2CH3

Octane

CH3CH2CH2CH2CH2CH2CH2CH3

Nonane

CH3CH2CH2CH2CH2CH2CH2CH2CH3

10

Decane

CH3CH2CH2CH2CH2CH2CH2CH2CH2CH3

11

Undecane

CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3

12

Dodecane

CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3

No. of Carbon

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Homologous Series
Organic compounds that are part of the same homologous series
generally have similar chemical properties as each other,
presence of the same functional group in the molecules of all
compounds
there may still be trends through the group
Physical properties of organic compounds that are part of the
same homologous series follow trends through the series.
depends on its size, (it's position within the series)
E.g. boiling points

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Chemical Formulas
The formulas for compounds can be expressed as an empirical
formula and as a molecular(true) formula.
An empirical formula represents the simplest whole number
ratio of the atoms in a compound.
The molecular formula is the true or actual ratio of the atoms in
a compound.
Empirical

Molecular Formula

Formula

(true)

CH

C 2H2

acetylene

CH

C 6H6

benzene

CO2
CH2O
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CO2

Name

carbon dioxide
C5H10O5

ribose

Structural Formula
Expanded Structural Formula
otherwise known as Lewis Structures
used to represent organic compounds and show which atoms are
connected each other.
Basically, a line is drawn between atoms to show a bond, or the
bond can be symbolized with a pair of dots.
Lone pairs of electrons are always shown as pairs of dots.

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Structural Formula
Condensed Structural Formula
written without showing all the individual bonds.
In a condensed structure, each central atom is shown together
with the atoms that are bonded to it.
Expanded

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Condensed

Structural Formula

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Structural Formula
Skeletal Formula
In a skeletal formula, all the hydrogen atoms are removed from
carbon chains, leaving just a carbon skeleton with functional
groups attached to it.
The normal structural formula and the skeletal formula look like
this:

Butane
CH3

butan-2-ol

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CH3-CH2-CH2-

CH3-CH-CH2-CH3

Structural Formula
EXAMPLE 1.2: A hexane molecule can be represented in several
ways. Show the expanded, condensed and skeletal
structure of hexane. (molecular formula: C6H14)
SOLUTION:
Expanded

Skeletal

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Condensed

3D Ball and Stick Model

Structural Formula
EXAMPLE 1.3: Show the empirical formula, expanded, condensed
and skeletal formula for ethanoic acid. The
molecular formula of acetic acid is: C2H4O2
SOLUTION:

Functional group of ethanoic acid is carboxylic acid

Empirical Formula = CH2O


Expanded Structure:

Skeletal Structure:

3D Models
Condensed Structure:

CH3COOH

Structural Formula
EXERCISE 1.1: Represent the succinic acid molecule,
HOOCCH2CH2COOH, through empirical, molecular,
structural, and skeletal formulas
Molecular formula:

C4H6O4

Empirical formula:

C2H3O2

Expanded formulas:

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Skeletal
formula:
O

Isomerism
Isomers are molecules that have the same molecular formula, but
have a different arrangement of the atoms in space. That excludes
any different arrangements which are simply due to the molecule
rotating as a whole.

Not isomers

F
Isomers

F
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Isomerism

Chain
Position
Functional Group

cis- ; transZ- ; E-

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R-; SD-; L-

Meso

eclipsed
staggered

Constitutional Isomers
Compounds that have the same molecular formula and
different connectivity
Chain
Different arrangement of hydrocarbon chain

Position
Different positions of atoms other than C and H on the
hydrocarbon chain

Functional Group
Different position of functional groups on the hydrocarbon
chain

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Constitutional Isomers
EXAMPLE 1.4: Constitutional isomers (chain) of pentane

n-pentane

isopentane or 2methylbutane

neopentane or 2,2dimethylpropane

arrangement of C and H were different, the molecular formula stays


the same
For alkenes, their constitutional isomers can be a cycloalkane

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Constitutional Isomers
EXAMPLE 1.5: Constitutional isomers of butanol (chain and
position)

OH

OH
butan-1-ol

butan-2-ol

OH
OH

2-methylpropan-1-ol

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2-methylpropan-2-ol

Constitutional Isomers
EXAMPLE 1.6: Constitutional isomers (functional group) of between
aldehyde and ketone

O
H

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butanal (C4H8O)

butan-2-one (C4H8O)

(aldehyde)

(ketone)

Constitutional Isomers
EXAMPLE 1.6: Draw the constitutional isomers of butane (C4H8):
SOLUTION
The constitutional isomers of butene are but-1-ene, but-2-ene, 2methylprop-1-ene, cyclobutane and 1-methylcyclopropane

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Constitutional Isomers
EXERCISE 1.2: Draw six possible constitutional isomers of C6H12 :
SOLUTION

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Stereoisomers: Conformational
Involves rotation about the -bonds
All conformational isomers are the exact same molecule
differ only in terms of the angle about one or more sigma bonds.

There is a complete free rotation about the -bonds,


endless possible way that the molecule can twist itself.
The most stable conformation (isomer) is the one that minimizes the mutual
repulsion of bonded electron clouds on adjacent carbons.
Therefore, each molecule will spend most of its time in its most stable
conformation

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Stereoisomers: Conformational
A convenient way of visualizing the conformational isomers of a
molecule is by using the Newman projection

CH3

H3C

CH2
CH2

CH3

CH3
Condensed structure

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Sawhorse projection

Newman projection

Stereoisomers: Conformational
In ethane, (C2H6), the central carbon-carbon bond rotates freely.
the hydrogen atoms on the adjacent carbon atoms can be either
alternating (staggered) or all lined up (eclipsed)
H

H
H

staggered
H

H
H
H

eclipsed

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Stereoisomers: Conformational
On larger molecule, more conformational isomers are possible:
A

Anti
conformation

Eclipsed
conformation

Gauche
conformation

Fully-eclipsed
conformation

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Stereoisomers: Conformational
Anti has the lowest energy conformation while fully eclipsed is the
least stable of all
D

D
B

C
A

60

120

180

Degrees of Rotation

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240

300

360

Stereoisomers: Geometric
Geometric isomers occur where there is a restricted rotation
somewhere in a molecule.
The common example is the double bond.
double bond comprised of two p orbitals that form a -bond surrounding the
single -bond, it cannot be rotated.
other atoms connected to the two double-bonded carbon atoms can move,
they can be in different position in space.
This create stereoisomers of the molecule. Other types of bond that cannot be
rotated is the -bonds that formed a ring (cyclic) structures.

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Stereoisomers: Geometric
Example: but-2-ene molecule.
Two possible isomers
CH3 atoms are locked on opposite sides of the double bond.
trans isomer (from latin meaning "across" - as in transatlantic).
CH3 atoms are locked on the same side of the double bond.
cis isomer (from latin meaning "on this side").

H3C

CH3

trans- but-2-ene

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H3C

H
cis- but-2-ene

CH3

Stereoisomers: Geometric
Branched cycloalkanes also have the cis-trans isomers

CH3
CH3 CH3
cis- 1,2-dimethylcyclopentane

H3C
trans- 1,2-dimethylcyclohexane

To get geometric isomers you must have:

restricted rotation

two different groups on the left-hand end of the bond and two
different groups on the right-hand end. It doesn't matter whether
the left-hand groups are the same as the right-hand ones or not.

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Stereoisomers: Geometric
EXERCISE 1.3: Draw the cis-trans isomers of the following
compounds:
pent-2-ene
1,2-dichlorobutane
SOLUTION

i)

trans-pent-2-ene

cis-pent-2-ene

ii)
Cl
Cl
trans-1,2-dichlorobutane
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Cl

Cl

cis-1,2-dichlorobutane

Stereoisomers: Geometric
The E-Z notation
when there are more than two different atoms connected to the
carbon-carbon double bond, problem arise on deciding which
atoms to look at when determining the geometrical isomerism
H

Cl

Br

Cl

Cl

trans -1,2-dichloroethene

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?-1-bromo-2-chloro-1-fluoroethene

Stereoisomers: Geometric
For the 1-bromo-2-chloro-1-fluoroethene,
priority needs to be determined between (F and Br)
and (Cl and H) atoms.
Br takes priority before F and Cl takes priority before H.
In this case the two priority atoms are on the same side
of the double bond, and therefore given the notation Z(a German word zusammen which means together).
Therefore, the correct IUPAC name for the molecule is
(Z)-1-bromo-2-chloro-1-fluoroethene.

Br 1

Cl 1

F2

H2

If the priority atoms are on the opposite side of the


double bond, then the E- (a German word entgegen which
means opposite) is used instead.
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Stereoisomers: Geometric
The rule for determining priorities are known as Cahn-IngoldPrelog (CIP) rules. The following rules applies when in CIP:
Rule 1
First, examine at the atoms directly attached to the stereocenter
(or the double bond) of the compound.
A substituent with a higher atomic number takes precedence over a
substituent with a lower atomic number. Hydrogen is the lowest possible
priority substituent, because it has the lowest atomic number.

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Stereoisomers: Geometric
Rule 2
If there are two substituents with equal rank, proceed along the
two substituent chains until there is a point of difference.
First, determine which of the chains has the first connection to an atom with
the highest priority (the highest atomic number).That chain has the higher
priority.
If the chains are similar, proceed down the chain, until a point of difference.

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Stereoisomers: Geometric
Rule 3
If a chain is connected to the same kind of atom twice or three
times, check to see if the atom it is connected to has a greater
atomic number than any of the atoms that the competing chain is
connected to.
If none of the atoms connected to the competing chain(s) at the same point has a
greater atomic number: the chain bonded to the same atom multiple times has the
greater priority
If however, one of the atoms connected to the competing chain has a higher atomic
number: that chain has the higher priority.

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Stereoisomers: Geometric
EXAMPLE 1.7: Determine whether the following compound, 2-bromo-3chloro-4-ethylhept-3-ene should use the E- or Z- notation:

Br

CH3

H3C

Cl

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CH3

Stereoisomers: Geometric
Br

CH3

H3C

Cl

CH3

SOLUTION
1.On the left side of the C=C, Cl takes priority over C-H
2.On the right side, the first immediate atoms is similar (C-H), the second atoms are C-C
at the top and C-H at the bottom. So C-C takes priority.
3.Since the priority atoms are on the opposite side of the C=C, the correct notation is E4.The full IUPAC name of the molecule is:
(3E)-2-bromo-3-chloro-4-ethylhept-3-ene
NOTE: 3E means the C=C is between carbon number 3 and 4.

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Stereoisomers: Optical
Optical isomerism is one form of stereoisomerism. Optical isomers
are named like this because of their effect on plane polarised light

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Stereoisomers: Optical
Only chiral molecule has optical isomer. Consider two
compounds A and B:

F
H3C

F
CH3

Br C

Cl

Cl

(A)

(B)

CH3

In A, two similar groups attached to the central carbon atom,


the molecule has a plane of symmetry.
In B, four different groups attached,
there is no symmetry anywhere in the molecule. chiral.
The carbon atom with the four different groups attached chiral center
or asymmetric carbon atom.
Molecule A is achiral.

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Stereoisomers: Optical
EXERCISE 1.4: Determine whether the following structures are
chiral or achiral molecules:
O

Cl

achir
al

chiral

CH3 Br

CH3
H2N
H3C

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OH

achir
al

H
CH3 Cl

chiral

Stereoisomers: Optical
Enantiomer
Simple substances which show optical isomerism exist as two
isomers known as enantiomers.
rotate the plane of polarization in a clockwise and anti-clockwise
direction.
Two enantiomers are non-superimposable mirror images of
one another (chiral)

Your left and right


hands are enantiomer
to each other!

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Stereoisomers: Optical
Optical isomers have basically the same properties (melting
points, boiling points, etc.)
There are drugs, called enantiopure drugs that have different
effects based on whether the drug is a racemic mixture or purely
one enantiomer.
For example, D-ethambutol treats tuberculosis, while Lethambutol causes blindness.
Optical activity is the interaction of these enantiomers with planepolarized light

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Stereoisomers: Optical
R and S Configurations
The absolute configuration for an enantiomer can be notated by
determining whether it rotate clockwise (to the right) or anticlockwise (to the left).
These are noted as R- (in Latin: rectus) and S- (in Latin: sinister)
respectively.
Other notations can also be used (usually for the more complex
molecules in spectroscopy) such as:
(+)-, D- or d- (dextrorotary) for the rotation to the right, and
(-)-, L- or l- (levorotary) for rotation to the left.

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Stereoisomers: Optical
Example: 3D projection of 2-bromobutane

Br

Br

CH2CH3
H3C

(2R)-2-bromobutane

PUSAT ASASI SAINS

H3CH2C
CH3

(2S)-2-bromobutane

Stereoisomers: Optical
Determination of R- and S- notation
1.

Identify the chiral centre, C

2.

Assign the priority (1 to 4) to the four atoms attached to the chiral


centre using the CIP rule

3.

Reposition the molecule so that the lowest priority (4) group is at the
back as if you were looking along the C-(4) bond
1
4

2
3

3
2

(R)

(S)

4. Assess whether the increasing order of priority follow clockwise (to the
right) which means R or anti-clockwise (to the left) which means S.
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Stereoisomers: Optical
EXERCISE 1.5: Determine whether the following Lactic acid is R or
S enantiomer:
OH

COOH
H3C

SOLUTION

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R enantiomer

Stereoisomers: Optical
EXERCISE 1.6: Draw the R and S enantiomer of 3-chlorohexane
using the 3D projection:
Cl
H5 C 2 C

C 3H 7

SOLUTION

Cl

Cl

C
C2 H 5

H 7C3
(3R)-3-chlorohexane
PUSAT ASASI SAINS

H5 C2

H
C3H 7

(3S)-3-chlorohexane

Stereoisomers: Optical
Larger molecules have the possibility of having two or more chiral
centers.
To determine whether two molecules are enantiomer to each other
needs further evaluation rather than just looking at the one chiral
center.
A pair of isomers that have more than one chiral center can be
diastereomers.
Diastereomers are stereoisomers that are not mirror images
of one another and are non-superimposable on one another.
Diastereomerism occurs when two or more stereoisomers of a
compound have different configurations at one or more (but not
all) of the equivalent (related) chiral centers.

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Stereoisomers: Optical
CH3

CH3

CH3

CH3

Br

Br

Br

Br

Cl

Cl

Cl

H H

Cl

CH3
Mirror image
Enantiomers

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CH3

CH3

CH3

Non-mirror image
Diastereomers

Stereoisomers: Optical
If a molecule with two chiral centers produces a mirror image
within the molecule, it is called a meso compound.
Meso compound is optically inactive.
CH3

CH3

CH3
H

Br

Br

Br

CH3
Enantiomers

H
Br
CH3

CH3

Br

Br

Br
Br
CH3

CH3
Meso

NOTE: meso and enantiomers are diastereomers to each other.

PUSAT ASASI SAINS

Stereoisomers: Optical
EXERCISE 1.7 : Draw the possible geometric and optical isomers of
1-bromo-1,3-dichlorobut-2-ene:

H3C

Cl

Br
Cl

PUSAT ASASI SAINS

Stereoisomers: Optical
SOLUTION
H3C

Br
H3C

Cl

Br
Cl

Cl

(2Z)-1-bromo-1,3-dichlorobut-2-ene

(2E)-1-bromo-1,3-dichlorobut-2-ene

Br

Br

C
Cl

ClH 4C3
(1S)-1-bromo-1,3-dichlorobut-2-ene

PUSAT ASASI SAINS

Cl

Cl

H
C3H4Cl

(1R)-1-bromo-1,3-dichlorobut-2-ene

To be continued
PUSAT ASASI SAINS

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