Chapter 1

Introduction
Introduction
Organic chemistry
 The study of compounds of carbon (i.e Organic cpds).
-Concerned with properties, structure, synthesis and reaction of carbon compounds

 The term was originally coined by Jons Jacob Berzelius (1807)

-To refer to the study of substances connected directly with animals and plants

 Before year 1828 a “vital force" was believed to direct synthesis of

Chemicals found in nature

 In 1828 F. Wöhler synthesized urea in the laboratory by heating

ammonium cyanate
-This discovery disproved the idea of vitalism

AgOCN(aq) + NH4Cl(aq) AgCl(s) + NH4OCN(aq)

(H2N) 2CO
Introduction cont…
Why do you study Organic chemistry ?
 Because organic compounds are so dominant and diverse (>50
million) that
 Constitute the essence of life (Plant, animal and microbial matter)
-Lipids, carbohydrates, proteins, DNA , natural products

 Impact our everyday lives greatly

-Food staffs (Carbohydrates, Lipids, Proteins, Vitamins etc.)
- Polymeric products (plastics, fibers , rubber, composites , etc.)
- Natural fiber(cotton, silk etc.)
-Solvents and thinners
-Pharmaceuticals
-Diagnostic agents
-Cosmetics
-Agrochemicals ( pesticides, fertilizers etc)
-Cleansing agents (soaps , detergents, toothpastes etc)
- Sweeteners ( natural, artificial)
- Fuels ( Kerosene, naphtha etc)
- Dyes and colorants
- Surface coatings (films )-Adhesives, Varnish , Lacquers
- Lubricants, etc...
Introduction cont…
Why then Organic compounds are so dominant/ in the Universe?

 Carbon is known to form infinite variety of organic compounds

 Due to its ability to form

-Stable covalent bonds (at most four) with other carbon atoms-

(catenation)

-form chains or rings

-Single or multiple bonds with many other atoms

- such as H, O, N, P, S, Mg, Zn etc

Structure of the atom
 Complete understanding of organic chemistry require the concept of atoms and
chemical bonding

 All matter is composed of atoms.

 Theory about atoms

 Was began early in 1900’s (after Dalton) and
 Appeared with ending solution around 1926 (after Heisenberg and Schrödinger)

 According to modern theory of atoms

 Atoms are tiny entities of an element consisting of:-
-Nucleus:- A small, dense, positive charge in the center of an atom that contains protons & neutrons.
-Electrons :-Diffuse region of negative charge(electrons) surround the nucleus.

 Electrons exist in quantized energy levels that surround nucleus of the atom.
 Energy of these levels increases as they get farther from the nucleus
 Within these shells other energy levels, called subshells or orbitals exist
 Structure of the atom cont…
Atomic orbitals
 Region in space where electrons reside

 Are contained in different shells at different distances away from the

nucleus.

 Are represented by letters s, p (three), d (five) & f (seven) and have different
size and shapes

 Each orbital is
- Represented by a unique quantum numbers. Principal (n) & azimutal (l)

- Capable to hold at most two electrons

- Differ in their size, shape, orientation and energy

Structure of the atom cont…
 Shapes of atomic orbitals
 s-orbitals p-orbitals

 d- Orbitals

 f-orbitals

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 Structure of the atom cont…
Electronic configuration
 Refers to specific arrangement of electrons in an atom
 Usually done based on three governing rules
 Aufbau principle :- orbitals are filled according to increasing energy
 Pauli exclusion principle :-electrons will occupy orbitals so that they have parallel spins
 Hunds rule:- orbitals are filled singly before they are paired
Examples
Element At. No Electronic configuration
H 1 1s1
C 6 1s2 2s2 2p2 =[He] 2s2 2p2
N 7 1s2 2s2 2p3 =[He] 2s2 2p3
O 8 1s2 2s2 2p4 =[He] 2s2 2p4
P 15 1s2 2s2 2p63s2 3p3 =[Ne]3s2 3p3
S 16 1s2 2s2 2p63s2 3p4 =[Ne]3s2 3p4
Cl 17 1s2 2s2 2p63s2 3p5=[Ne]3s2 3p5
The Chemical bond cont…
The force that holds two atoms together

Usually occurs between valence electrons of

neibouring atoms to be bonded
 Until atoms have 8 electrons in their valence shells

The two most common bond types are :-

 Ionic bond

 Covalent bond
 The Chemical bond cont…
 Ionic (electrostatic) bond

 A bond formed by complete transfer of electrons between two atoms

 Is an electrostatic attractive force that hold ions with opposite charges together

 Is less common among organic cpds.

 Examples -NaCl, CaCl2, K2O , CH3COONa, in Soaps, some drugs

 Process involve several step –taking formation of LiF(s) as example

i) Li (s)  Li (g) (Gaseous atom formation)
ii) Li (g)  Li + (g) + e- (Ion formation, Ionization energy)
iii) F(g) + e-  F - (g) (Ion formation, Electron affinity)
iv) Li + (g) + F - (g)  LiF (s) (Formation of ionic bond, Lattice energy)

 Properties of ionic compounds: They are

 Mostly solids at ordinary T & P
 Good conductors of electricity in solution or when fused
 High temperature melting and boiling substances 10
The Chemical bond cont…
Formation of an ionic bond. e.g NaCl

-
+ Cl
Na
electron transfer and the
formation of ions

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 The Chemical bond cont…
Covalent Bond
 A bond formed by sharing electron pairs b/n neighboring atoms

 Usually involve non-metallic elements of comparable electronegativity

 Binding is due to attraction b/n shared e- pairs and nuclei of bonded atoms
- Thus it is a balance of attractive and repulsive forces
 Is common among organic cpds.

Examples: O2, CO2, C2H6, H2O, SiC, C6H6, CH4

 Properties of covalent cpds:-

 Stable non-ionizing molecules

 Mostly liquids or gases at room temperature

 Generally insoluble or less soluble in water and other polar solvents

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 Poor conductors of electricity in the fused or dissolved state
The Chemical bond cont…
Covalent Bond
Formation of a covalent bond. e.g Cl2

Cl Cl

sharing of a pair of electrons

and the formation of molecules

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 The Chemical bond cont…
 Polar and Non-polar Covalent bonds
 Non-polar covalent bonds:
 Electron pairs are shared equally
 Occurs b/n two atoms with similar electronegativity
Example: H2, O2, F2 etc

Polar covalent bonds:

 Electron pairs are shared unequally
 Occurs b/n two atoms with different electronegativity
Example: HF, H2O, NH3

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 The Chemical bond cont…
 Polarity of bonds
 Bond polarities can range from non-polar covalent, through polar covalent, to
totally ionic.

 The polarity of an individual bond is measured as its bond dipole moment (),
defined as
where δ - amount of charge at either end of the dipole and
d - distance between the charges.
The Chemical bond cont…
 Molecular Dipole
 The vector sum of the individual bond dipole moments.
 Depend on the magnitude and direction of the bond dipoles

.. ..
:O=C=O:

 = 0.0 D
Carbondioxide 0.0 D 1.87 D
The Chemical bond cont…
 Formal charge
 Local charge associated with particular atom in a molecule

Can be calculated by the following formula:

FC= No of valence - unshared valence + half shared

electrons electrons valence electrons

+1

Examples
0
The Chemical bond cont…
 Hybridization
 Refers to mixing of atomic orbitals to make them suit bonding situation

 This gives rise to formation of new set of orbitals – called hybrid orbitals

 Six types are possible

sp hybrid orbitals:-obtained from mixing of one s and one p orbitals

sp2 hybrid orbitals:-obtained from mixing of one s and two p orbitals
sp3 hybrid orbitals:-obtained from mixing of one s and three p orbitals
sp3d hybrid orbitals:-obtained from mixing of one s, three p and one d orbitals
sp3d 2 hybrid orbitals:-obtained from mixing of one s, three p and two d orbitals

 Covalent bond has definite direction in space which is responsible for

molecular shape
Thus hybridization and molecular geometry are closely correlated
The Chemical bond cont…
The sp Hybrid Orbitals
Two sp hybrid orbitals are formed from one S and one P atomic orbitals
S P SP
+ + + - = + -

+ – + - = - +

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The Chemical bond cont…
The sp2 Hybrid Orbitals
Three sp2 hybrid orbitals are formed from one S and two P atomic orbitals

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The Chemical bond cont…
The sp3 Hybrid Orbitals
The Chemical bond cont…
 Sigma and pi Bonds

Sigma (s ) bond :- by overlap of atomic (hybrid) orbitals) of two atoms

Pi (p) bond :-formed by overlap b/n unhybridized p orbitals of two bonded atoms
The Chemical bond cont…
 Sigma and pi Bonds
The Chemical bond cont…
 Hybridization in methane

 Hybridization in Ethene
Structure of organic molecules
Ways to represent structure of organic cpds

 The structure of organic compounds can be represented in various ways

i) Lewis (dot) structures:- all electrons (bonding and lone pairs) are shown

Cl Cl

ii) Lewis (Kekule) structures:- bonding electrons are represented as

lines while lone pairs are left as they are (or omitted )
 Structure of organic molecules cont…
iv) Condensed structures:-covalent bonds are partially or totally omited.
-leads to abbreviation of bonds (mostly in common groups)
CH3CH2-OH CH2ClCH2CH(OCH3)CH3 H3CNHCH2COOH
Cl-CH2CH2CHCH3 O
H3C-N-CH2C-OH
OCH3 H
v) Line(Zigzag) structures:- omit lone pairs, hydrogens and carbons
- carbon atoms are assumed to be at the end of every bond

vi) 3-D-structures/Perspective drawings:- represent orientation of

bonds in molecules using dotted-lines, dashes, wedge, ball & sticks etc .
Structure of organic molecules cont…
 Resonance structures
 Are different structures (hypothetical) for the same
molecule
 Only differ in the way their electrons are arranged

Examples
:

:
:

:
:O:- O: : O:- O:
:N :N CH3 C CH3 C
O: :O:- O: :O:-
:

:
:
:

Nitrite ion Acetate ion

(equivalent contributing (equivalent contributing
structures) structures)
Functional Groups
A specific arrangement of atoms in an organic compound
They are the chemically functional part of the molecule
- Involved in characteristic chemical reactions

Serve as the best way to classify organic compounds

Intermolecular Forces
Molecules usually interact with one another

 The type and nature these interactions are dependent on

the functional group .

There are three main types of interactions b/n molecules:

 Van der Waals forces
 Dipole-dipole interactions
 Hydrogen bonding

 Intermolecular forces affect physical properties of molecules

such as [Link], [Link], solubility, physical state, viscocity
 Intermolecular Forces cont…
Van der Waals Forces (London dispersive forces)

 Weak interactions caused by momentary changes in electron density

 Are the only attractive forces present in non-polar compounds.

 But evident in all compounds.

Their strength is dependent on molecular size.

i.e The larger the surface area, the stronger will be the VWF.
Intermolecular Forces cont…
Dipole-Dipole Interactions

 Are the attractive forces between the permanent dipoles of

two polar molecules.
 The dipoles in adjacent molecules align so that the partial
positive and partial negative charges are in close proximity.

These attractive forces caused by permanent dipoles are

much stronger than weak van der Waals forces.
Intermolecular Forces cont…
Hydrogen bonding

Are strong forces( ca. 20% of covalent bonds) that typically

occur when hydrogen is found bonded to O,N or F

Hydrogen is electrostatically attracted to a lone pair of

electrons on an O, N, or F atom in another molecule.
A H … B or A H … A

Hydrogen bonds
Organic reaction types and mechanisms
 Reaction types
Organic compounds undergo nine main types of reactions

 Addition reaction :- leads to addition of a group across a multiple bond

Addition
C C A B A C C B

Elimination reaction :- leads to removal of part of a molecule.

Substitution reaction :- leads to replacement of an atom/group by another atom/group.

Rearrangement reaction :- leads to simple re-organization of atoms in a molecule

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Organic reaction types and mechanisms
 Condensation reaction :- involved in linking
two molecules with removal of simple molecules
like alcohols, water, carbon dioxide

 Hydrolysis reaction :- involve splitting

a bond with the aid of water

 Oxidation reaction :- involve addition of highly

EN atoms (O, N, halogens) or removal of
hydrogen in the reaction.

 Reduction reaction :- involve addition of highly

EN atoms (O, N, halogens) or removal of
hydrogen in the reaction.
.
 Pericyclic reaction :- are concerted reactions
( i.e. involve the simultaneous bond breaking/bond
making process) characterized by cyclic transition
states and high degree of stereoselectivity.
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Organic reaction types and mechanisms
 Writing reaction equations
Equations for organic reactions are usually drawn with a single reaction arrow ()
or opposite sided reaction arrow ( ) between the starting material and
product.

 The reagent, the chemical substance with which an organic compound reacts, can be
drawn on the left side of the equation with the other reactants or above the arrow
itself.

 Most organic reactions take place in liquid solvent and together with temprature it is
indicated above or below the arrow but it is often omitted.

When two or more step sequential reactions are carried out without drawing any
intermediate compound, the steps are usually numbered above or below the reaction
arrow. Numbers signifies order of the reaction

The symbols “h” and “” are used for reactions that require light and heat
respectively. 35
Organic reaction types and mechanisms
 Writing reaction equations - Examples

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Organic reaction types and mechanisms
 Reaction mechanisms
 An Organic reaction mechanism is a full description sequence of molecular events, or
reaction steps, that defines the pathway from reactants to products.

 Writing a reaction mechanism generally requires understanding

• Organic reaction type involved

• Number defined steps that lead from reactant to product

• What takes place at each stage of a chemical transformation

– the types of bonds that are broken and formed

– specify the reaction intermediate type formed

– the energetics of the reaction; Energy Diagrams and Transition States

– the kinetics of a reaction : Rate; order and molecularity

 A proposed mechanism must fit to all the facts available and it is always subject to change as
new facts are discovered. 37
Organic reaction types and mechanisms
Reaction steps
 Organic reactions may occur in one or more steps that involve breakage or
formation of bonds
Concerted reaction
 A concerted reaction is a chemical reaction in which all
bond breaking and bond making occurs in a single step
and doesn't involve reactive intermediates or other
unstable high energy intermediates
Stepwise reaction
 A stepwise (multistep) reaction is a chemical reaction
with at least one reaction intermediate and involving at
least two consecutive elementary reactions.

 In multistep reactions
 Individual (Single step) in a mechanism are called elementary steps (reactions) and
they describes the behavior of individual molecules

 The slowest step (high energy state step) determines the overall rate of a reaction and is
called the rate determining step
Organic reaction types and mechanisms
Bond cleavage/formation
 Curved arrows are used to keep track changes occurred in bonding (formation or
breakage and number of electrons mobilized)

 Arrowheads with a “half” head (“fish-hook”) indicate homolytic and

homogenic steps (called ‘radical processes’)
 Leads to formation of free radicals (atoms with singlet electrons)

 Arrowheads with a complete head indicate heterolytic and heterogenic

steps (called ‘polar processes’)
 Leads to formation of charged species (cations and anions)

(carbocation) 39
Organic reaction types and mechanisms
 Reaction Intermediates
 Reaction intermediates are chemical species that are formed during course of
organic reactions as intermediate molecules

 They are short lived created and destroyed during a particular reaction pathway.

 These include Carbocations, carbanions, free radicals, carbenes, nitrenes,

benzyne

Nitrenes
Benzynes

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Organic reaction types and mechanisms
 Reaction initiation
 Organic reactions are commonly initiated by various chemical species including
 Nucleophiles -electron rich species (neutral /negatively charged) that seeks an e- deficient center
 Electrophiles- electron deficient species (neutral /positively charged) that are attached by
electron rich species
 Free radicals- singlet electron species which tend to propagate its radical

 A nucleophile initiated reactions

 An electrophile initiated reactions

 A free radical initiated reactions

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Organic reaction types and mechanisms
 Reaction initiation

 Electrons should always move from a nucleophilic source (Nu:) to an

electrophilic sink (E)
Organic reaction types and mechanisms
 Energetis of a reaction: Energy diagrams
 A plot of energy of rxn vs reaction progress is termed as Energy diagram
 Energy diagrams clearly indicate energy (of reactant(s), transition state(s) ,
intermediate(s) and product(s) ) and steps involved

 Transition states involve simultaneous partial bond breakage and bond formation processes

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Organic reaction types and mechanisms
 Kinetics of a reaction: Rate laws
 For any general reaction occurring at a fixed temperature
aA + bB → cC + dD

A rate equation (rate law) contains concentration terms for only the reactants
involved in the rate-determining step in a multi-step reaction.

Rate = k[A]m[B]n
Where
-A and B are species that have contribution for overall rate of the reaction

-k = rate constant- is specific for a given reaction at a given T

 Fast reactions have large rate constants.

 Slow reactions have small rate constants.

-m & n = reaction orders - are determined by experiment. and are not

in any way related to the coefficients a and b. 44
Organic reaction types and mechanisms
 Kinetics of a reaction: Molecularity and Order

Molecularity refers to the total number of molecular species that take part in the
reaction
 A reaction thus can be unimolecular or bimolecular
 The rate equation for a reaction need to be expressed interms of these species

The order of a reaction in the rate equation refers to magnitude of rate change in
response to concentration changes of the reactants
 And it can be zero order, first order or second order

 Order can be expressed for the overall reaction of in terms of each species
involved in the rate equation.

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