Fundamentals of Organic Chemistry

AAU, Chem

2024

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 1. Introduction
1.1 Historical Background of Organic Chemistry
 In 1780s, scientists distinguished between organic compounds and
inorganic compounds (Swedish chemist Torbern Bergman). Organic
compounds: as compounds derived from living organisms (vegetables and
animals).
 Vitalism theory - organic compounds couldn’t be synthesized in the
laboratory. Because of the vital force requirement.

 In 1828 Friedrich Wöhler synthesized urea from inorganic compound.

After the synthesis of urea in laboratory, theory of Vitalism has been rejected.
No special force is required to synthesis organic compounds.
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What is organic chemistry?
Organic chemistry is the study of carbon containing compounds.

• Why carbon special?

• There are more than 30 million known chemical compounds, of these
more than 99% of them contain carbon.

 Carbon’s electron structure and its position in the periodic table.

 Group IVA element,
 Carbon can share four valance electrons and form four strong
covalent bonds.
 Carbon atom can bond to one another, forming long chains and
rings.

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 Organic chemistry
What: The study of carbon-containing compounds.
Why: Spreading widely in nature.
Chemical foundation of biology.
Improve standard of living (medicines, plastics, pesticides . . .)
How: Examine structure and analyse how it governs reactivity

How do you differentiate organic compounds from inorganic compounds?

 Compounds containing carbon may or may not be organic.
NH4NCO (ammonium cyanate) is not organic. It is an inorganic salt.
• Organic compounds distinguish from inorganic compounds in that they contain a
characteristic functional group (unit 2).

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What atoms (besides carbon) are important?

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 1.2 Atomic structure of carbon, covalent bond and
hybridization

Atomic orbitals - the region in which there is high probability of finding an electron in
space.

Shape of Orbitals --s, p, d, and f.

 s and p orbitals most commonly found in organic compounds

An atomic orbital contain at most two electrons.

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Electron Configuration

i. The Aufbau principle:- Electrons enter orbitals of lowest energy first.

1s22s2 2p6 3s23p64s2………

ii. The Pauli Exclusion Principle: To occupy the same orbital, two electrons must have
opposite spins.

iii. Hund’s rule: When electrons occupy orbitals of equal energy, one electron enters each
orbital unit all the orbitals contain one electron with spins parallel.
Carbon (Z=6): 1s2, 2s2, 2p2
Two configurations possible

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Nitrogen(Z=7): 1s2, 2s2, 2p3 11
 Bonding in Carbon Compounds
Two models to describe covalent bonding: valence-bond theory and molecular orbital
theory.
 valence-bond theory: a half-filled orbital of one atom overlaps with a half-filled
orbital of the other atom to form a covalent bond.

 In order to overlap during covalent bond formation, the two overlapping orbitals must be
half-filled.

 Only two half-filled orbitals exist in carbon for

bond formation according to VB theory.

But in methane there are four bonds (four overlapping) exist. How do we explain this?
This can be explained by the concept of hybridization
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 Hybridization
• mixing two atomic orbitals to give rise to a new type of hybridized orbitals in order
to form covalent bonding. This hybrid orbitals having entirely different energy,
shapes, etc
sp3 Hybridization

 By mixing ("hybridizing") the 2s, 2px, 2py, and 2pz orbitals, four new orbitals obtained (sp3).
 Each sp3 hybrid orbital has 25% s character and 75% p character.

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 H H
Ethane
H C C H
H H

sp2Hybridization

The three sp2orbitals lie in a plane at angle of 120.

The remaining p orbital perpendicular to the sp2 plane.

2s orbital combines with only two of three available 2p orbitals. 14

One of the 2p orbitals is left unhybridized.
Sigma bond () resulted due to end- to-end overlap of orbitals
Pi bond () resulted due to side-to-side overlap of p orbitals

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sp Hybridization
H-CC-H

H C C H

Ex. What is the hybridization of N in ammonia NH3? The bond angle? 16

 1.4 Lewis structure and Resonance
Lewis structure
Structural formulas in which electrons are represented as dots are called Lewis structures.

Covalent bonding in F2 gives each fluorine eight electrons in its valence shell and a stable
electron configuration equivalent to that of the noble gas neon.

Representing a two-electron covalent bond by a dash (-)

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 Rules for drawing Lewis structures

1. Identify the central atom of the molecule (the first atom written, the least electronegative
atom) Place all terminal atoms around the central atom.
2. Count the total number of valance electrons
3. Complete the octate for all atoms in the structure with lone pairs of electrons
4. Lone electrons (not lone pairs) indicate an ability to form more covalent bonds, resulting
in either double or triple bonds. Make double bond or triple bond by rearrange the lone
electrons.
5. Check the structure by counting the number of valance electrons used
Lewis structure should have the same total between all its bonds and lone pairs.

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E. g Carbon Dioxide, CO2

1.) Carbon is the least electronegative atom, hence the central.

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 HCN

Multiple bonds are very common in organic chemistry

Ex. Write the most stable Lewis structure for

a) Ozone, O3

b) Tetrafluoroethylene, C2F4

c) Acrylonitrile, C3H3N. 20
 FORMAL CHARGE

Lewis structures frequently contain atoms that bear a positive or negative charge. If the
molecule as a whole is neutral, the sum of its positive charges must equal the sum of its
negative charges.
e.g HNO3:

The positive and negative charges on each atom in a compound or an ion are
called formal charges.

e.g thionyl chloride, SOCl2:

Valence e- Formal charge

Sulfur 6 6-3-2= +1
Oxygen 6 6-1-6= -1
Chlorine 7 7-1-6= 0 The formal charge in thionyl chloride 21
Example: Calculate the formal charge on each of the atoms in HNO3

Formal charge of N= +1
Formal charge of double bonded O = 0
Formal charge of single bonded O = -1
Formal charge of single bonded O (bonded to H) = 0

Ex. Calculate the formal charge on each atoms in

a) CO
b) POCl3
b) H2SO4

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 • Resonance attempts to correct a fundamental defect in Lewis formulas.
Lewis formulas show electrons as being localized; they either are shared
between two atoms in a covalent bond or are unshared electrons belonging
to a single atom.
Two resonance structure are possible for CH3NO2

How many resonance possible for

a) CO3

 Structure I and II are resonance structure of ozone.

 We use a double-headed arrow (↔) to represent resonance between these
two Lewis structures.
 curved arrows are used to show this electron delocalization
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 Resonance
 Resonance is a blending of structures with the same arrangement of
atoms but different arrangements of electrons. It spreads multiple bond
character over a molecule and results in a lower energy.

This is the Lewis structure we

would draw for ozone, O3.

• But this is at odds with the true, observed

structure of ozone, in which…
• …both O—O bonds are the same
length.
• …both outer oxygens have a charge
of 1/2.

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• One Lewis structure cannot
accurately depict a molecule
such as ozone.
• We use multiple structures,
resonance structures, to
describe the molecule.
• The true structure is the hybrid
of the two resonance

 We use a double-headed arrow (↔) to represent resonance

between these two Lewis structures.

HCO3

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two resonance possible
• The organic compound benzene, C6H6, has two resonance structures.
• It is commonly depicted as a hexagon with a circle inside to signify the
delocalized electrons in the ring.

Two resonance structure are possible for CH3NO2

Ex.
How many resonance structures possible for the following?
a) SO3
b) SO32–
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c) CO32–
1.4 Formula of organic compounds

A) Molecular Formula
This indicates the total number of atoms present a molecule.
Example: C6H6, C2H5OH, C20H42

B) Structural formula
All bonds present in the molecule should be shown.

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C) Condensed structural formula
We leave out some, many, or all of the covalent bonds and use sub-scripts to indicate the
number of identical groups attached to a particular atom.

D) Bond-line formulas or carbon skeletal structure

 a carbon atom is assumed to be at each intersection of two lines (bonds) and at the end
of each line.
 The hydrogen atoms are not shown. Since carbon always has a valance of 4, we
mentally supply the correct number of hydrogen atoms for each carbon.
 Atoms other than carbon and hydrogen should be written.

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 2H
2H O

3H
1H zero H

3H
1H

2H
molecular formula, C10H14O

E) Wedge- line formula (three-dimensional formula)

Is useful to show the stereochemistry of a molecule.

EX. Find the molecular formula of

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 1.6 Factors influencing electron availability and reactivity of organic
compounds  Inductive effect
 Resonance effect
 Steric effect

Inductive Effect- the shifting of electrons in a -bond in response to the

electronegativity of a nearby atoms.
F, Cl, Br, I, O, N are more electronegative than carbon, and thus exert electron
withdrawing inductive effects.

X = F, Cl, Br, I, O, N

• the carbon where X is attached feels positive. Moreover,

• the electro withdrawing effect of X is also transmitted through the sigma bond
and carbon-2 will also be positive even though it is less positive than carbon-1.
+
+ H
C -
+ F
H
Inductive effects rationalize reactivities of organic compounds
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Examples: Inductive Effect And Relative Strength Of Carboxylic acids

O Ka
C H3 -5
 As more chlorine groups which exert
C OH 1.75 x 10
O electron withdrawing inductive effect exist,
-5
C lCH 2 C OH 1.86 x 10
O
the acidity strength increases (bigger Ka
C l2 HC -5
C OH 5530 x 10 acidity Value)
O
C l3 C C OH -5
23,200 x 10

The electron withdrawing inductive effect of groups reduces as the group exists far
from the reaction center.
P Ka
O

C H 3 C H 2 C H 2 C OH 4.82
O

C lC H 2 C H 2 C H 2 C OH 4.52  The last compound is strong acid than the

O

C H 3 C HC H 2 C OH 4.05
rest of the compounds because chlorine is
acidity
Cl O closest to the reaction center.
C H 3 C H 2 C HC OH 2.86
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Cl
 Resonance Effect
 This involves delocalization (pi) electrons and non-bonded electrons. It also has effects
on the reactivity of compounds.

 Charge produced in a reaction can be stabilize by resonance (distributed in a molecule).

E.g acidity of acetic acid and ethanol.

The conjugate base of acetic acid (acetate ion) is resonance stabilized while the
conjugate base of ethanol (ethoxide) is not.

 acetic acid is stronger acid than ethanol

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 Steric effect
 The word steric is derived from ‘stereos’ meaning space.
 This effect is manifested when two or more groups or atoms come in close proximity to
each other.
 It is the influence of the spatial configuration of reacting substances upon the rate,
stability, and extent of reaction.

E.g substitution reaction

A substitution reaction on a halide by a hydroxide does not work in this

case because of steric hindrance.
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stability between isomeric alkenes affected by steric effect

more stable less stable

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 1.6 Functionality and classes of organic compounds

A functional group is a particular combination of atoms in a molecule that is

particularly responsible for characteristic set of reactions that the molecule exhibit.

 The chemistry of every organic molecule, regardless of size and complexity, is

determined by the functional group it contains.

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 The importance of classification of organic compounds according to their
functionality

 To study the properties and nature of organic compounds systematically.

 The reactions and physical properties of organic compounds are influenced by
the nature of the functional groups present.
 The chemistry of every organic molecule, regardless of size and complexity, is
determined by the functional group it contains.

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 Structure of Some Functional Groups
Functional Group Functional Group
Name Structure Example Name Structure Example
O
Alkene C C H2C CH CH3 Carbonyl C
O
Alkyne C C H C C CH3 O
C C
Aldehyde H CH3 H
Arene O O
Benzene
Ketone C
C
C
C
CH3CH2Cl CH3 CH3
Halide C X
O O
(X=F,Cl,Br, I) Carboxylic acid
C OH CH3 C OH

Alcohol C OH CH3CH2OH O O
Ester C O C CH3 C OCH3
Ether C O C H3C O CH3 O O
Amide C N CH3 C NH2
Amine C NH2
CH3CH2NH2
O O O O
Acid anhydride C O C
Nitrile C N CH3 C N CH3 C O C CH3

O O
Nitro C NO2 CH3CH2NO2 Acid chloride H3C C Cl
C Cl

Thiol C SH CH3CH2SH

Sulfide H3C S CH3

C S C 37
Many compounds contain more than one functional group.

Ex. Identify the functional groups in each of the following

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