Module 1 – Organic Chemistry
Topic 1 – Introduction
Learning Objectives:
• To introduce the essential element of the reaction mechanism
• To introduce nucleophile and electrophile and refer it to the concept of Lewis Acid
and Base
• To revise the concept of inorganic chemistry – the structure of the molecule:
polarity, Lewis Acid and Bases and Electronegativity
Reaction Mechanism or reaction pathway – A step-by-step elementary reaction that leads
to the overall chemical reaction
Bond Breaking
• Homolytically (Homolytic fission) – Each atom get one electron from the bonding to
form two radicals. (This is an equal electron distribution between two atoms)
• Heterolytically (Heterolytic fission) – Atom with higher electro negativity gets two
electrons, which creates two atoms with an unequal electron distribution.
Curly headed arrow
• If the head of an arrow is halved, there is only one electron
that has been transferred from one atom/bonding to
another.
• Double-headed curly arrow: If the head of an arrow is full,
two or all electrons has been transferred from one
atom/bonding to another.
Bond Making
• Homogenic (Sharing) – Each radicals donate one electron to share to each other,
forming an electron cloud. Therefore, forms a bond.
Module 1 – Organic Chemistry
o Radicals – Species that has an extra electron(s) that can be donated. (Extremely
reactive).
• Heterogenic (Donating) – One atom with radical can donate an electron to another
species. This forms a bond.
Categories of organic reaction pathway (mechanism)
1. Acid-base equilibria
2. Nucleophilic substitution (Displacement) at a saturated C atom
3. Elimination reactions
4. Electrophilic additions to multiple carbon-carbon bonds
5. Electrophilic aromatic substitution
6. Nucleophilic additions and substitutions at unsaturated atoms (Carbonyl compounds
and acid derivatives)
7. Reduction reactions
8. Oxidation reactions
9. Free radical substitution, addition and polymerisation (Not studied)
Reaction type 1-6 involves with heterolytic breaking and heterogenic bond making and
opposites attract. So, basically positive charges (Lack of electron) attracts with negative
charges (Full of electron).
• This indicates that 1-6 is a polar reaction, basically an unsymmetrical electron
distribution within its cloud. This depends on the structures and importantly the
difference in a electronegativity.
The concept of lack of electron and full of electron are not a proper scientific word. Therefore,
Scientific word should be introduced here.
Nucleophiles and Electrophiles
• Nucleophiles (‘Nucleus-loving’) – Electron-rich molecules or ions – Possess non-
bonding (Lone pair) of electrons.
Module 1 – Organic Chemistry
o This is Lewis Bases.
• Electrophiles (‘Electron-loving’) – Electron deficient ions or molecules. Usually lack
of a stable octet and can accept a pair of electrons. (This species can follow the octet
rule, but not properly)
o Octet Rule – All molecules are trying to reach the Noble gases electron
configuration.
o This is Lewis Acid.
The electrophilic and nucleophilic sites in an organic molecule.
• The bonding, especially functional groups determines the polarity.
• i.e. The unsymmetrical distribution of electrons in a cloud due to the differences in
electronegativities.
Electronegativity (Refer to CHEM10003) – The attraction of electron towards certain species
in a bond.
• Basically, not all bonding are symmetrical covalent bond or electron travels evenly
between the two molecules.
• Most of the time, electron do not travel evenly. Electrons are likely to be attracted
towards one atom than the other.
• However, if the differences in electronegativity are too high, then it is likely to be ionic
bonding.
• Refer to Pauling Scale of electronegativity – Standard used to determine if the bond
between the two molecules are polar, ionic or symmetrical.
• The electronegativities determines the polarities of bond – Basically where will
electron be.
How do we answer some of the question related to organic reactions?
1. How do reactions happen?
• Reaction mechanism or pathway – The curly arrows shows how nucleophile
combines with electrophiles.
2. Why do reactions happen?
• Kinetics – Rate of reaction, rate-determining step (Slow-step), Maxwell-
Boltzmann Curve Distribution etc.
• Thermodynamics – Exothermic or endothermic, free energy etc.
o The energy diagrams shows the reaction coordinate (time – how the
reaction progressed)
o Two main type of energy diagram: One step and two step reaction
One-step Reaction (Reaction with one concave down type graph)
• The energy of the chemical reaction is equal to the difference in energy between the
starting material and the products (ΔH).
Module 1 – Organic Chemistry
• Transition State – Highest energy state along the reaction coordinate (The maximum
point of the diagram)
• The reaction needs to reach sufficient energy to surpass the transition state of the
reaction. This is referred to as activation energy – Energy needed to initiate the
reaction.
Two-step reaction – Two concave down graph
• Intermediate – Stable chemical species that can be isolated.
Overall Reaction: A + B à C + D
Step One: A + B à E + F
Step Two: E + F à C + D
Therefore, E and F are intermediates.
• For a reaction to occur, the reactants must have sufficient energy to reach the highest
transition state (The highest amongst the maximum point) of the reaction.
Learning Objectives:
To introduce the acid-base equilibria and understand the factor that affects the acidity of
an organic compound
Bronsted-Lowry Definition Lewis Acids and Bases
• Acid – Donates proton • Acid – Accepts an electron pair
• Base – Accepts proton • Base – Donates an electron pair
Module 1 – Organic Chemistry
Example: 𝐻𝐶𝑙 + 𝐻' 𝑂 ⇌ 𝐻* 𝑂+ + 𝐶𝑙 ,
• 𝐻𝐶𝑙 – Stronger acid
• 𝐻' 𝑂 – Stronger base
• 𝐻* 𝑂+ - Weaker acid
• 𝐶𝑙 , - Weaker base
[12 3 4 ][67 8 ]
The acidity constant, 𝐾. = [167]
is large. Therefore, the pKa is small. The pKa data can
be used to predict outcome of the acid-base reaction.
Structural Effects (Organic Acids) – When considering the acidity of organic compounds, the
following factors are important:
• Electronegativity
• Hybridisation of orbitals
• Resonance stabilization of Anions
These effects help stabilize the negative charge of the product (Conjugate base)
Structural Effects (Organic Acids): Electronegativity – Higher EN stabilize the negative charge
well.
Structural Effects (Organic Acids): Hybridization of Orbitals
The s-orbitals are lower in energy and nearer the positively charged nucleus that p-orbitals.
Therefore, a negative charge is more stabilized towards the species with higher s-character
than in an orbital with low s-character.
• i.e. Most stable sp, least stable sp3.
Structural Effects (Organic Acids): Resonance Stabilization of Anions – More resonance
structure – More stabilize and likely to be a stronger acid.
Module 1 – Organic Chemistry
Resonance Forms of phenoxide ion
Influence of substituents:
The acidities of functional groups can be further influenced by substituents. These are
influenced by Mesomeric (“+M” or “-M”) and inductive effects into:
• Electron Donating groups (EDG, “+M”): Have lone pair of electron and stabilize +ve
charges.
o Destabilize conjugate base
• Electron Withdrawing groups (EWG, “-M”): Have full or partial +ve charge and stabilize
-ve charges.
o Stabilize conjugate base
Structural Effects (Organic Bases)
Electronegativity: Lower EN – More basic due to higher pKa
Hybridization of Orbitals: sp3 – Strongest Base – Least “s” character
Resonance Effects – Less Resonance structure – Stronger base
Module 1 – Organic Chemistry
Summary: Organic Acids and Bases
Acids Bases
Electronegativity High Low
Hybridisation of Orbitals sp sp3
Resonance Stabilization More resonance form Less resonance form
Learning Outcomes:
• To introduce organic reactions and reaction mechanism, nucleophiles and
electrophiles
• To introduce Nucleophilic Substitution Reactions
Polar Organic Reactions
• Most organic reactions are polar reactions, because the attraction between positive
and negative. Therefore, the electron rich reacts with electron poor.
o Nucleophile and electrophile react with each other.
Nucleophiles and Electrophiles
• The nucleophiles react with electrophiles.
• Acid-base reactions involve making bonds to H
• Electrophile/nucleophile reactions involve bond breaking and formation at C
• Most molecules can react as either a nucleophile or electrophile depending on what
they react with.
*𝐶𝐻* ', does not exist. Otherwise, it is generated by the laboratory.
• The movement of electrons are indicated rom the nucleophile to electrophile using a
curved arrow.
Module 1 – Organic Chemistry
The reaction between alkyl halides and nucleophiles
• The carbon atom in alkyl halides is electrophilic (Need an electron). So, it reacts with
nucleophile. It can react by either substitution or elimination.
Nucleophilic Substitution at a Saturated Carbon Atom
• The nucleophilic substitution reaction is when the nucleophile replace the halogen.
o i.e. the nucleophilic reagent (Nu) attacks the carbon atom and displace a
leaving group (X) and carries away the bonding electrons.
• Example:
• This reaction is widely used in chemical synthesis.
Reaction Mechanism or reaction pathway – A step-by-step elementary reaction that leads
to the overall chemical reaction
