Organic Chemistry Introduction

Junior College 1
 Objectives
• Interpret and use the terms nomenclature, molecular
formula, structural formula, skeletal formula,
homologous series and functional groups
• Use both common naming and IUPAC system of
nomenclature
• Perform stoichiometric calculations in organic
chemistry
• Describe and explain the different isomerism in
compounds
• Understand and give examples of the different
reaction mechanisms in organic chemistry
 Organic Chemistry
Late 18th century:
• Compounds from living organisms - Organic
• Compounds from lifeless matter – Inorganic
• Organic compounds thought to have ‘vital
force’
Ammonium cyanate Urea
(from mineral sources) (from urine)
‘Organic’
‘Inorganic’
 Organic Chemistry
• Friedrich Wohler in 1828 successfully
synthesized the organic compound urea from
ammonium cyanate, an inorganic compound.

Ammonium cyanate

Urea

(Heat)

•Discredited concept of ‘vital force’

•Organic molecules = Carbon-,Hydrogen-based molecules
•Organic chemistry = Chemistry of carbon-,hydrogen-based
molecules
 Some organic chemicals

Medicines
DNA
•Active Pharmaceutical Ingredients
•Excipients

Fuels

Materials Essential oils Pigments

 Nomenclature
• IUPAC – International Union of Pure and
Applied Chemistry – an international
organization devoted to the standardization in
chemistry to include naming (nomenclature),
physical constants and properties of matter.
• IUPAC has developed systematic naming of all
organic compounds
 Nomenclature
• Counting the carbon atoms
Molecular No. of C Prefix Name of Alkyl
Formula atoms Alkane group
present
CH4 1 Meth- methane Methyl
C2H6 2 Eth- ethane ethyl
C3H8 3 Prop- propane propyl
C4H10 4 But- butane butyl
C5H12 5 Pent- pentane pentyl
C6H14 6 Hex- hexane hexyl
C7H16 7 Hept- heptane heptyl
C8H18 8 Oct- octane octyl
C9H20 9 Non- nonane nonyl
 System of Nomenclature
• Compounds without branches are called ‘straight
chain’
• Branched compounds are named as alkyl
derivatives of the longest straight chain in the
molecule
• The length of the longest chain provides the
parent name
• The straight chain is numbered to allow
indication of the point of branching
• The branching alkyl groups (or substituents) are
named from the corresponding alkane
 System of Nomenclature
• Identify the parent chain.
• Number so as to give lower numbers for branch points
• Each branch or side chain must be included in the
name.
• Identical substituents grouped together with a prefix
• ‘di…’ for two identical
• ‘tri…’ for three
• ‘tetra…’ for four,etc.
• Substituents named in alphabetical order
 CH3
CH3 CH2 CH CH3 2-Methylbutane
4 3 2 1
[Straight chain numbered so as to give the lower branch number]

CH3 CH3
CH3 C CH2 C CH3
CH3 H

2,2,4-Trimethylpentane

3,6-Dimethyl-6-ethylnonane
Now try this: Name the following organic
compounds

CH3 CH3
CH3 CH2 C CH2 CH2 C CH2 CH3
H CH2 CH2 CH3
 Structure of Organic Compounds
• Electronic configuration of Carbon = C 1s2 2s2 2p2
• Covalent bonds: sharing of electrons between
atoms Carbon: can accept 4 electrons from other
atoms, i.e. Carbon is tetravalent (valency = 4)
• Ethane: a gas (b.p. ~ -100oC)
• Empircal formula (elemental combustion analysis):
CH3 , i.e. an organic chemical
• Measure molecular weight (e.g. by mass
spectrometry): 30.070 g mol-1, i.e (CH3)n n = 2
• Implies molecular formula = C2H6
Molecular formula: gives the identity and number of
different atoms comprising a molecule

Ethane: molecular formula = C2H6

Valency: Carbon 4
Hydrogen 1

Combining this information, can propose

H H
H C C H
H H

i.e. a structural formula for ethane

 •Each line represents a single covalent bond
•i.e. one shared pair of electrons

H H

H C C H

H H
•Structural formulae present information on atom-to-atom connectivity

•However, is an inadequate represention of some aspects of the molecule

•Suggests molecule is planar

•Suggests different types of hydrogen
 Experimental evidence shows:
•Ethane molecules not planar
•All the hydrogens are equivalent
3 Dimensional shape of the molecule has tetrahedral carbons

•Angle formed by any two bonds to any atom = ~ 109.5o

109.5

109.5
109.5 109.5

Need to be able to represent 3D molecular structure in 2D

Bond coming out of plane of screen

Bond going into plane of screen

e.g.

H H
= H C C H
H H
Or

H H
H
= C C
HH H
Representing larger molecules

Full structural formula for, e.g. octane

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

Condensed structural formula

CH3 CH2 CH2 CH2 CH2 CH2 CH2 CH3

Line segment structural formula
 Line segment structural formula for
octane

•Each line represents a covalent bond between atoms

•C-H bonds not shown, assume they are present

•[so as make up valency of Carbon to 4]

H H H H
O = H C C O C C H
H H H H

= = etc. = pentane
 Functional Groups
• Functional groups are groups of atoms which
gives rise to a homologous series.
• Homologous series are series of organic
molecules with same functional group and
show similar chemical properties.
• Checkpoint: What are the different functional
groups?
 Isomerism
• What are isomers?
• 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, or rotating about particular bonds.
 What are structural isomers?
• In structural isomerism, the atoms are arranged in a
completely different order.
Types of structural isomerism
a) Chain isomerism
• These isomers arise because of the possibility of branching in
carbon chains. For example, there are two isomers of butane,
C4H10. In one of them, the carbon atoms lie in a "straight
chain" whereas in the other the chain is branched.
 Structural Isomerism
B) Position isomerism
• In position isomerism, the basic carbon skeleton remains
unchanged, but important groups are moved around on that
skeleton.
• For example, there are two structural isomers with the
molecular formula C3H7Br. In one of them the bromine atom
is on the end of the chain, whereas in the other it's attached
in the middle.
 Structural Isomerism
C) Functional group isomerism
• In this variety of structural isomerism, the isomers contain
different functional groups - that is, they belong to different
families of compounds (different homologous series).
• For example, a molecular formula C3H6O could be either
propanal (an aldehyde) or propanone (a ketone).
 Structural Isomerism
• Another common example is illustrated by the molecular
formula C3H6O2. Amongst the several structural isomers of
this are propanoic acid (a carboxylic acid) and methyl
ethanoate (an ester).
 STEREOISOMERISM - GEOMETRIC
ISOMERISM
What is stereoisomerism?
In stereoisomerism, the atoms making up the
isomers are joined up in the same order, but
still manage to have a different spatial
arrangement. Geometric isomerism is one
form of stereoisomerism.
Geometric (cis / trans) isomerism
How geometric isomers arise
• These isomers occur where you have restricted rotation
somewhere in a molecule. At an introductory level in organic
chemistry, examples usually just involve the carbon-carbon
double bond.
• Think about what happens in molecules where there is
unrestricted rotation about carbon bonds - in other words
where the carbon-carbon bonds are all single. The next
diagram shows two possible configurations of 1,2-
dichloroethane.
 Geometric Isomerism
• These two models represent exactly the same molecule. You
can get from one to the other just by twisting around the
carbon-carbon single bond. These molecules are not isomers.
• But what happens if you have a carbon-carbon double bond -
as in 1,2-dichloroethene?
 Geometric Isomerism
• These two molecules aren't the same. The carbon-carbon
double bond won't rotate and so you would have to take the
models to pieces in order to convert one structure into the
other one. That is a simple test for isomers. If you have to
take a model to pieces to convert it into another one, then
you've got isomers. If you merely have to twist it a bit, then
you haven't!
• Drawing structural formulae for the last pair of models gives
two possible isomers.
 Geometric Isomerism
• In one, the two chlorine
atoms are locked on
opposite sides of the double
bond. This is known as the
trans isomer. (trans : from
latin meaning "across" - as
in transatlantic).
• In the other, the two
chlorine atoms are locked
on the same side of the
double bond. This is know
as the cis isomer. (cis : from
latin meaning "on this side")
 Effect of Geometric Isomerism on
Physical Properties
The table shows the melting point and boiling point of the cis and trans
isomers of 1,2-dichloroethene.

isomer melting point (°C) boiling point (°C)

cis -80 60
trans -50 48

What do you notice? How is this possible?

isomer melting point (°C) boiling point (°C)

cis-but-2-ene -139 4
trans-but-2-ene -106 1
 Optical Isomerism
• Optical isomerism is a form of stereoisomerism.
• Optical isomers are named like this because of
their effect on plane polarised light.
• Simple substances which show optical
isomerism exist as two isomers known as
enantiomers.
 Optical Isomerism
• How optical isomers arise

• One Carbon atom attached to four different groups

• Rotating either isomer will cause non-superimposable
image, i.e. you couldn't slide one molecule exactly over
the other one.
• One of the enantiomers is simply a non-
superimposable mirror image of the other one.
Optical Isomerism
• A molecule which has no plane
of symmetry is described as
chiral. The carbon atom with
the four different groups
attached which causes this
lack of symmetry is described
as a chiral centre or as an
asymmetric carbon atom.
• The molecule on the left
above (with a plane of
symmetry) is described as
achiral.
• Only chiral molecules have
optical isomers.
 Checkpoint
• Five amino acids are given below. Which amino acid
does not form optical isomers? Explain your answer.
a)HOCH2CH2CH(NH2)COOH
b)H2NOCCH(NH2)COOH
c) CH3CH(NH2)COOH
d)H2NCH2COOH
e)HOC6H5CH2CH(NH2)COOH
• Write displayed formulae for all the structural isomers of
C4H10O that are alcohols.
 Designing Molecules
• Identifying structural features that will
achieve desired result
• Identifying the receptor molecules
• Determining the relationship between the
molecule and the receptor site.
• Determining the routes or the different
reaction mechanisms molecules undergo
• Synthesizing
How are drugs created or discovered?
Natural drug products have been used for millenia
Synthetic drugs came into being during the 19th
century
Today, drugs are still coming from this two sources
Chemicals found in nature or synthesized in labs are
randomly screened for their therapeutic ability
 Drugs from Natural Sources

Atropine from Nightshade (Belladonna) Quinine from Cinchona bark

Morphine from Poppies Taxol from Yew Trees

Drugs from Artificial Sources

Salvarsan

Acetaminophen

Ibuprophen
 Features of a Medicine Molecule
• Shape that fits the receptor molecule
• Groups which are capable of forming
intermolecular bonds to complementary
groups on the receptor molecules.
• These intermolecular bonds may involve
hydrogen-bonding, ionic attractions, dipole-
dipole forces or van der Waal’s forces.