ORGANIC CHEMISTRY

UNIT-ONE

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 1. BONDING, STRUCTURE AND REACTIVITY
Introduction
What is organic chemistry?
 It is a branch of chemistry which deals on carbon compounds.
 Some exceptions: for example carbonates, carbon dioxide, etc…
are not studied by organic chemistry.
Why do you study organic chemistry?
 Organic chemicals are all around us.
 Food
Carbohydrates
Proteins
Lipids….
 Clothing
 Natural materials
Silk, Cotton
 Synthetic materials
Nylon, Terylene
 Medicine
 Aspirin, Penicillin…..
 Pesticides
 DDT
 Others 2
 PVC, Urea, Paints, TNT….
 1.1 Historical background of organic chemistry
 Prior to 1828, all organic compounds had been obtained from
organisms or their remains.
 The scientific philosophy back then was that the synthesis of
organic compounds could only be produced within living matter
while inorganic compounds were synthesized from non-living
matter.
 A theory known as “Vitalism” state that a “vital force” from living
organisms was necessary to make an organic compound.
 In 1828, a German chemist Friederich Wholer synthesize urea ,
H2NCONH2
, an organic substance using inorganic compound ammonium
cyanate, NH4OCN.

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The uniqueness of carbon
Why can carbon form different bonds?
 There are more carbon compounds than there are compounds of all
other elements combined.
 The property of carbon that makes it unique is its ability to form bonds
with itself and therefore allows a large number of organic chemicals
with many diverse properties.
 The great number of carbon compounds is possible because of the
ability of carbon to form strong covalent bonds to each other while also
holding the atoms of other nonmetals strongly.
Carbon atoms have the special property to bond with each other to form
chains, ring, spheres and tubes.
 Carbon forms four covalent bonds
 Carbon bonds covalently to: H, O, N, P, S and other nonmetals (except
noble gases)
 Carbon atoms join to form chains and rings
 Carbon can form multiple bonds to itself, oxygen and nitrogen.
 Many carbon compounds exist in the form of isomer.

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1.2 Energy levels and atomic orbitals
Atomic Orbitals
 Heisenberg Uncertainty Principle states that it is impossible to define
what time and where an electron is and where is it going next. This
makes it impossible to know exactly where an electron is traveling in an
atom.

 Since it is impossible to know where an electron is at a certain time, a

series of calculations are used to approximate the volume and time in
which the electron can be located. These regions are called Atomic
Orbitals. These are also known as the quantum states of the electrons.

 Only two electrons can occupy one orbital and they must have different
spin states, ½ spin and – ½ spin (easily visualized as opposite spin
states).
 Orbitals are grouped into subshells.
 This field of study is called quantum mechanics.

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 Cont…
How are electrons distributed in an atom?
 An orbital is a region of space where the probability of finding an
electron is large ( the space where an electron spends 90% to 95% of
its time).

What do orbitals look like?

 There are four different kinds of orbitals, denoted s, p, d, and f , each
with a different shape

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 Cont’d
 An s orbital is spherical, with the nucleus at its center;

 A p orbital is dumbbell-shaped;

 And four of the five d orbitals are cloverleaf shaped, the fifth d
orbital is shaped like an elongated dumbbell with a doughnut around
its middle.

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 Cont’d
 Each electron in an atom is described by four different quantum numbers.
 The first three (n, l, ml) specify the particular orbital of interest, and the
fourth (ms) specifies how many electrons can occupy that orbital.
i. Principal Quantum Number (n):  n = 1, 2, 3, …, ∞
 Specifies the energy of an electron and the size of the orbital.
 All orbitals that have the same value of n are said to be in the
same shell (level).
 For a hydrogen atom with n=1, the electron is in its ground state; if the
electron is in the n=2 orbital, it is in an excited state.
 The total number of orbitals for a given n value is n2.
ii. Angular Momentum (Secondary, Azimunthal) Quantum Number
(l):  l =0,..., n-1
 Specifies the shape of an orbital with a particular principal quantum
number.
 The secondary quantum number divides the shells into smaller groups of
orbitals called subshells (sublevels).

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 Cont’d
 Usually, a letter code is used to identify l to avoid confusion with n:

 The subshell with n=2 and l=1 is the 2p subshell; if n=3 and l=0, it is the

3s subshell, and so on.
 The value of l also has a slight effect on the energy of the subshell; the
energy of the subshell increases with l (s < p < d < f). 

iii. Magnetic Quantum Number (ml):  ml = -l, ..., 0, ..., +l

 Specifies the orientation in space of an orbital of a given energy (n) and
shape (l).
 This number divides the subshell into individual orbitals which hold the
electrons;
 There are 2l+1 orbitals in each subshell. Thus the s subshell has only
one orbital, the p subshell has three orbitals, & so on.
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 Cont’d
iv. Spin Quantum Number (ms):  ms = +½ or -½
 Specifies the orientation of the spin axis of an electron.
 An electron can spin in only one of two directions (sometimes
called up and down).

How electrons fill the orbitals

 Each atom has an infinite number of possible electronic
configurations. We are here only concerned with the ground-state
electronic configuration, which has the lowest energy. The ground-
state electronic configuration of an atom can be determined by the
following three principles.
i. Pauli Exclusion Principle
 It states that no more than two electrons can occupy each orbital, and
if two electrons are present, their spins must be paired

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ii. Aufbau principle ( Building up principle)

 It states that the orbitals fill in order of increasing energy, from

lowest to highest.
 Because a 1s orbital is closer to the nucleus it is lower in energy
than a 2s orbital, which is lower in energy than a 3s orbital

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iii. Hund’s rule

 It explains that when degenerate orbitals (orbitals that have same

energy) are present but not enough electrons are available to fill all
the shell completely, then a single electron will occupy an empty
orbital first before it will pair up with another electron.

 This is understandable, as it takes energy to pair up electrons.

 Therefore, the six electrons in the carbon atom are filled as

follows: the first four electrons will go to the 1s and
2s orbitals, a fifth electron goes to the 2p , the sixth
x

electron to the 2p orbital and the 2p orbital will remain

y z

empty

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 1.3. Bonding in carbon compounds
 Carbon has the property of forming single, double and triple bonds with
itself and with other atoms.
 The types of bonds used by the carbon atom are known as sigma (σ-)
and pi (π-) bonds.
 Different combinations of these bonds lead to carbon single bonds,
double bonds and triple bonds.

Chemical bond
 Chemical bonds are forces that hold the atoms of a molecule together.
 The driving force for their formation is the greater stability of the
resulting molecules than the isolated atoms.
 Chemical reaction involves the breaking and formation of chemical
bonds.
 Thus, in order to understand the principles that govern chemical
processes, it is better to understand the nature of chemical bonds.

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 Types of chemical bonds
Ionic / Electrovalent / bonds
 Result of the electrostatic attraction between opposite charges.
 Opposite charges are the results of the complete transfer of electrons
from one atom to another.
 Because of the electrostatic attraction between positive and negative
charges,
 ionic compounds tend to be crystalline, non-volatile, have high melting
point, soluble in high polar solvents, etc
Covalent Bonds
 Instead of giving up or acquiring electrons, an atom can achieve a filled
outer shell by sharing electrons.
 A bond formed as a result of sharing electrons is called a covalent bond.
 A covalent bond is the net result of attractive and repulsive electrostatic
forces. i.e The nucleus–electron attractions are greater than the
nucleus–nucleus and electron–electron repulsions, resulting in a net
attractive force that holds the atoms together to form a molecule.

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 Types of covalent bonds (Electronegativity)
 A given bond is either purely ionic, with electrons completely transferred,
or purely covalent, with electrons shared equally.
Non-polar covalent bonds or pure covalent bonds
 are formed between two atoms of the same element, or two
atoms with a very low difference in electronegativity
 Bonding electrons in a covalent bond are may shared unequally between
two atoms but are not completely transferred. Such bonds are said to be
polar covalent bonds.
 The lowercase Greek letter delta (δ) is used to symbolize the resultant
partial charges on the atoms
 Partial positive (δ+) for the atom that has a smaller share of the bonding
electrons or partial negative (δ-) for the atom that has a larger share.
 As examples of different points along the bonding spectrum, let’s
compare
three substances, NaCl, HCl, and Cl2

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 Types of covalent bonds (Overlap of atomic orbitals)
 A covalent bond between two atoms results from the overlap of an
atomic orbital of one atom with an atomic orbital of another atom.
 When two orbitals overlap they share the same region in space and a
new orbital, called a molecular orbital (MO), is formed.
Sigma (σ-) bonds
 Sigma (σ -) bonds are strong bonds formed by head-to-head overlap of
two atomic orbitals.

Pi (π-) bonds
 Pi (π-) bonds are weaker bonds formed by parallel or side-to-side
overlap of two p-orbitals.

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• LEWIS DOT STRUCTURES
• 1. Arrange the symbols such that the least electronegative
element is in the center and the other elements are
surrounding the central atom.
• O C O
• 2. Give each of the elements their appropriate number of
valence electrons (dots). Remember the number of
valence electrons for a representative element is the same
as the group number.
• .. ..
•• : O
. . : C : O :. .
• 3. Keep track of the total numbr of valence electrons for
the compound by adding the valence electrons from each
atom. If the compound is an ion then add electrons (dots) for each
negative charge or subtract electrons (dots) for each positive charge.
•
• Draw the Lewis Structure for the following molecules.

• 1. H2O
• Oxygen has 6 valence electrons & Hydrogen has 1 valence electron for a total
of 8 electrons.
• ..
• H:O:H
• ..
• 2. CO
• Oxygen has 6 valence electrons & Carbon has 4 valence electrons for a total of
10 electrons.

• :C:::O:
 Coordinate Covalent Bond
 Only one atom provides electrons and the other provides vacant
orbitals.
A + :B → A: B
Example: H+ + :NH3 → NH4+
BF3 + F- → BF4-
 Once the bonds are formed, covalent and dative bonds are same
and indistinguishable.

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Covalent Bonding Theories
 Theories of bonding: explanations for covalent bond, Lewis dot structures
Valence Bond (VB) Theory
 Covalent bonds are formed by overlap of atomic orbitals, each of which
contains one electron of opposite spin.

 In the valence bond model, the strength of a covalent bond depends on the
amount of orbital overlap:
 The greater the overlap, the stronger the bond.
 When a covalent bond is formed by head-to-head overlap of atomic orbitals
a sigma (  is formed.

 The shape of the molecule is determined by the geometry of the overlapping

orbitals.

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 Cont..
Valence bond theory
 provides one approach to deeper understanding of molecular structure.
 has its theoretical foundation in quantum mechanics calculations that
demonstrated that electrons hold nuclei together, that is, form bonds,
when shared by two nuclei.
In general valence bond theory is
 central idea of hybridization ( mixing up) of atomic orbital
 non equivalents atomic orbital can combine / hybridize to give set of
orbital whose orientation reflects the molecule / ion
The theory
 Explains why bonds in many molecules are equivalents
 Explains how atomic orbital’s on central atom of a molecule interact
with the orbital on other atoms
 Provides a useful and convenient method of predicating the shape
of molecules.
 Hybridizations can occurs only when the atomic orbital involved
have very similar energies. it means that:
 2s can hybridize with 2p
 3s can hybridize with 3p but
 2s cannot hybridize with 3p

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 Cont..

 But overlapping of simple atomic orbitals does not explain all the
features. Thus, we have to take another look, or do something about
atomic orbitals – hybridization.

1.3.2 Orbital Hybridization

 In chemistry, hybridization is the concept of mixing atomic orbitals to
form new hybrid orbitals.
 Hybridized orbitals are very useful in the explanation of the shape of
molecular orbital for molecules.
 How does valence bond theory describe the electronic structure of a
polyatomic molecule, and how does it account for molecular shape?
 The three types of orbital hybridization considered important in
organic chemistry are called sp3, sp 2and sp.

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 If the one s and three p orbitals of the second
shell are combined and then apportioned into
four equal orbitals, each of the four resulting
orbitals will be one part s and three parts p
 This type of mixed orbital is called sp3.
 Each sp3 orbital has 25% s character and 75% p
character.
 The four sp3 orbitals are degenerate they have
the same energy

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 Like a p orbital, an sp3 orbital has two lobes.
 The lobes differ in size, because the s orbital adds to one
lobe of the p orbital and subtracts from the other lobe of the
p orbital.
 The stability of an orbital reflects its composition; it is more
stable than a p orbital, but not as stable as an s orbital.
 The larger lobe of the orbital is used in covalent bond
formation.
 The four sp3 orbital arrange themselves in space in a way
that allows them to get as far away from each other as
possible.
 This occurs because electrons repel each other and getting
as far from each other as possible minimizes the repulsion

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• They point toward the corners of a regular tetrahedron (a
pyramid with four faces, each an equilateral triangle).
 

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sp2 HYBRIDIZATION H H

 For example bonding in ethene (C2H4). C C

H
H

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28
sp Hybridization
H C C H

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Molecular Orbital (MO)Theory
 Lewis dot and valence bond theories do not always give satisfactory
account for various properties of molecules.
 The Molecular Orbital Theory does a good job of predicting elctronic
spectra and paramagnetism, when VSEPR and the Valence Bond Theories
don't.
 For example, the dot and valence bond theories do not explain the fact that
O2 is paramagnetic and has a double bond.

 When atomic orbitals overlap, they combine to form molecular orbitals.

 In the case of hydrogen, the overlap of two 1s atomic orbitals results in the
formation of a σ (sigma) molecular orbital.

 This molecular orbital is more stable than each of the separate atomic
orbitals and contributes to the shape of the molecule.

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 Cont’d

ANTBONDING
These two new orbitals have
different energies. 

BONDING

The one that is lower in energy is called the bonding orbital,

The one higher in energy is called an antibonding orbital.

 The MO Theory has five basic rules:
 The number of molecular orbitals = the number of atomic orbitals
combined
Of the two MO's, one is a bonding orbital (lower energy) and one is

an anti-bonding orbital (higher energy)
 Electrons enter the lowest orbital available
 The maximum # of electrons in an orbital is 2 (Pauli Exclusion
Principle)
 Electrons spread out before pairing up (Hund's Rule)
Sigma bond
Sigma (σ-) and pi (π-) bondsPi bond
   

1. Formed by head-to-head overlap of AO’s 1.Formed by lateral overlap of p orbital’s( or p and d

orbitals)

1. Has cylindrical charge symmetry about bond axis 2. Has maximum charge density in the cross-sectional

plane of the orbital

1. Has free rotation 3. No free rotation

1. Lower energy 4. Higher energy 33

1. Only one bond exist b/n two atoms 5. One or two bonds can exist b/n two atoms
Sigma (σ-) bonds
 When two 1s-orbitals combine in-phase, this produces a bonding
molecular orbital.

 When two 1s-orbitals combine out-of-phase, this produces an anti-

bonding molecular orbital.

 Electrons in the p-orbitals can combine to give sigma (σ-) bonds.

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pi (π-) bonds

 Pi (π-) bonds are weaker bonds formed by parallel or side-to-side

overlap of two p-orbitals.

 Only σ- or π-bonds are present in organic compounds.

 All single bonds are σ-bonds, while all multiple (double or triple)
bonds are composed of one σ-bond and one or two π-bonds.

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 Molecular orbital electron configurations and bond order
 Molecular orbital electron configurations can be written in the same
manner as atomic electron configurations.
 The molecular orbitals are written in order of increasing energy and the
population of each MO is given as a right-hand superscript.

 The stability will depend on the relative occupation of bonding MO's

versus anti-bonding MO's.
 This can be measured by the bond order (BO).
 Bond order indicates the strength of a bond.
 If a molecule is to be stable, it must have a bond order greater than 0.
Bond order = 1/2 (# of electrons in bonding orbitals - # of electrons in
anti-bonding orbitals)
 If the bond order is 0, the molecule is unstable and won't form.
 If the bond order is 1 a single bond is formed.
 If the bond order is 2 or 3 a double or triple bond will be formed
respectively.

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 Cont..
 Note that the higher the bond order, the higher the bond energy and
the shorter the bond distance for the same atoms.
 At N2 and below, the relative energies of these MO's are:

 Above N2 the relative energies are:

 N.B. π2py and π2pz orbitals have the same energy, that is, are
degenerate, as are the π2py* and π2pz* orbitals.

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 1.4. Factors influencing electron availability and reactivity of
organic compounds
1.4.1. Inductive effect
 The polarization of a σ bond due to electron withdrawing or electron
donating effect of adjacent groups or atoms is called inductive effect. 

Salient features of inductive effect 

 It arises due to electronegativity difference between two atoms forming
a sigma bond. 
 It is transmitted through the sigma bonds. 
 The magnitude of inductive effect decreases while moving away from
the groups causing it. 

 It is a permanent effect. 
 It influences the chemical and physical properties of compounds.

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 TYPES OF INDUCTIVE EFFECT
 The inductive effect is divided into two types depending on their
strength of electron withdrawing or electron releasing nature with
respect to hydrogen. 
Negative inductive effect (-I):
 The electron withdrawing nature of groups or atoms is called as
negative inductive effect.
 It is indicated by -I.
 The following are examples of groups in the decreasing order of their -I
effect: 
NH3+> NO2> CN > SO3H > CHO > CO > COOH >COCl> CONH2> F >Cl> Br > I >
OH > OR > NH2> C6H5> H   
Positive inductive effect (+I):
 It refers to the electron releasing nature of the groups or atoms and is
denoted by +I.
 Following are examples of groups in the decreasing order of their +I
effect. 
C(CH3)3> CH(CH3)2> CH2CH3> CH3> H

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 Importance of Inductive Effect
 The inductive effect plays an important role in polarizing the C-X bond
 where X is the substituent affecting
 the rate of the reaction, the mechanism of a reaction, stability of a transition
states and as well as the acidic or basic nature of the organic compounds.
 The inductive effect diminishes as length of carbon chain
increases.

Acidic strength of carboxylic acids and phenols:

 The electron withdrawing groups (-I) decrease the negative charge on
the carboxylate ion and thus stabilizing it.
 Hence the acidic strength increases when -I groups are present. 
 However the +I groups decrease the acidic strength.
Example:
i. The acidic strength increases with increase in the number of electron
withdrawing atoms as shown below. 
CH3COOH < CH2FCOOH < CHF2COOH < CF3COOH

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 Cont…
ii. Formic acid is stronger acid than acetic acid since the –CH3 group
destabilizes the carboxylate ion.
iii. the acidic strength of phenols increases when -I groups are present
on the ring.

Basic strength of amines

 The electron donating groups (alkyl groups) increase the basic
strength of amines whereas the electron withdrawing groups (aryl
groups) decrease the basic nature.
CH3NH2> NH3> C6H5NH2 

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Reactivity of carbonyl compounds
 The +I groups increase the electron density at carbonyl carbon.
 Hence their reactivity towards nucleophiles decreases.
 Thus formaldehyde is more reactive than acetaldehyde and acetone
towards nucleophilic addition reactions. 

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 1.4.2 Resonance effect or Mesomeric effect (M)
 Resonance is the process whereby (generally) pi-electrons can be
delocalized by exchanging double bonds and single bonds.
 Resonance can be used to delocalize both lone pairs of electrons and
cationic charges which are adjacent to double bonds.
 Delocalization of positive and negative charges lead to relatively stable
cations and anions, respectively.
Rules for Drawing Resonance Structure
1. The molecule should be planar.
2. It contains an alternating system of single and double bonds(conjugated
system)
3. The relative positions of nuclei should remain unchanged (e.g.
tautomerism).
4. The negative charge must preferably lie on the most electronegative
atom.
5. The charge needs to be preserved in all the resonating structures.
6. The electrons always move away from a negative charge.
7. Arrows should be drawn to indicate the direction of the movement of
electrons.
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 Types of Resonance
The mesomeric effect is negative (-M) when the substituent is an
electron-withdrawing group
The mesomeric effect is positive (+M) when the substituent is an
electron releasing group.

i. +R or +M effect

+
C C OH C C O H

( + M o r + R e ffe c t o f O H g ro u p )

ii. –R or –M effect

+
C C CH O C C CH O

( R e ffe c t o f C H O g ro u p )

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 Types of Resonance
For substituted benzene
+ +
N H2 N H2 N H2

–
e tc .

– +M effect of a methoxy group in ether

+R effect of –NH2 group.

–M effect of a carbonyl group in acroleine

–R effect of –NO2 group.

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 1.4.3. Steric effect
 Steric effects arise from the fact that each atom within a molecule
occupies a certain amount of space.
 If atoms are brought too close together, there is an associated cost
in energy due to overlapping electron clouds repulsion,
 and this may affect the molecule's preferred shape (conformation)
and reactivity.
 On account of the presence of bulkier groups at the reaction center,
they cause mechanical interference and which result the attacking
reagent finds it difficult to reach the reaction site and thus slows
down the reaction.
 This phenomenon is called steric hindrance or steric effect.
 Tertiary alkyl halides having bulky groups form tertiary carbocation
readily when hydrolyzed
 because of the presence of the three bulky groups on the carbon
having halogen.

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