Fundamentals of Organic Chemistry

Instructor: Girma Birhanu

AAU, Chem

2025

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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.

O
Heat
NH4+NCO- H2N-C-NH2
Ammonium cyanate Urea
(inorganic salt) (organic)

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

z
y z z z
y y
y
x
x x x

s- orbital Py
Px Pz

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.
 
1s2 2s2
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
x y z
a)   
1s2 2s2 2p2

b) 
1s2

2s2
 
2p2
ü
    
Nitrogen(Z=7): 1s , 2s , 2p
2 2 3
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1s2 2s2 2p3
 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.

H + H H  H H H
sigma bond ()
1s 1s H2 molecule end-to-end overlap of two atomic orbitals

 In order to overlap during covalent bond formation, the two overlapping orbitals must
be half-filled.
H
H C H C: 1s2, 2s2, 2p2 :    

H 1s2 2s2 2p2

 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
1s 2s 2p
Ground state C:    

Exited state C:     

hybridization C

   
3
sp orbitals
 By mixing ("hybridizing") the 2s, 2p x, 2py, and 2pz orbitals, four new orbitals obtained (sp 3).
 Each sp3 hybrid orbital has 25% s character and 75% p character.

H sp3- s :overlap
H

H
H H 109.5o
C C
C
H
H H H
H H 13
H
 H H
Ethane H C C H
sp3- s overlap
H H H

C C C C

sp3carbon sp3carbon sp3-sp3  overlap

sp2Hybridization
H H
CH2=CH2 C C
H
H
p
2s 90°
1s 2p
Ground state C:    
C
2
sp
Exited state C:      sp2

sp2
hybridization
The three sp2orbitals lie in a plane at angle of 120.
    The remaining p orbital perpendicular to the sp2 plane.
sp2 pz

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

One of the 2p orbitals is left unhybridized.
 -bond
-bond

C C C C

sp2 orbitals

sp2 carbon sp2 carbon Carbon-carbon double bond

Sigma bond () resulted due to end- to-end overlap of orbitals

Pi bond () resulted due to side-to-side overlap of p orbitals
H 120° H

C C

H H

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sp Hybridization 1s 2s 2p py pz

H-CC-H Ground state C:    

C
Exited state C:     
sp sp

hybridization

   
 bond
180° sp py pz

H C C H

 bond  bond

sp
O
sp3
CH3 CH2 CH2 C C CH3
C CH3
CH3 CH2
sp3 sp3 sp
3 sp3 sp3
sp2 sp
sp3

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.
H H F F

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.
to write a H
Combine C and four H Lewis structure H C H
for methane H

to write a F
Combine C and four F Lewis structure F C F
for tetrafluoride F

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

Hydrogen cyanide H C N or H C N

Multiple bonds are very common in organic chemistry

Ex. Write the most stable Lewis structure for

a) Ozone, O3

b) Tetrafluoroethylene, C2F4
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c) Acrylonitrile, C3H3N.
 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.
O
e.g HNO3: H O N
O

The positive and negative charges on each atom in a compound or an ion are
called formal charges.
-
Formal charge = no. of valance e Number of bonds Number of unshared electrons
O

e.g thionyl chloride, SOCl2:

Cl S Cl

O
Valence e- Formal charge
Cl S Cl
Sulfur 6 6-3-2= +1
Oxygen 6 6-1-6= -1
The formal charge in thionyl chloride 21
Chlorine 7 7-1-6= 0
Example: Calculate the formal charge on each of the atoms in HNO 3

O
Formal charge of N= +1
H O N
Formal charge of double bonded O = 0 O

Formal charge of single bonded O = -1

Formal charge of single bonded O (bonded to H) = 0

Ex. Calculate the formal charge on atoms in

a) POCl3 b) H2SO4

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 RESONANCE
Resonance structures are sets of Lewis structures that describe the delocalization of
electrons in a molecule or a polyatomic ion.
For O3, two equivalent Lewis structures may be written
O O
O O O
O
I II

 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

O O O
O is equivalent to 1 O O 1
O O O 
2 2
Curved arrow notation Dashed arrow notation
Electron delocalization in ozone
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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

O O

H3C N H3C N
O O

Rules for resonance

1. Individual resonance forms are imaginary, not real.

2. Resonance forms differ only in the placement of their  or non bonding e-
H H

H C H H C H
C C C C

C C C C
H C H H C H

H H

3. The resonance hybrid is more stable than any individual resonance forms. 24
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.
H H
H
H C
H
H C H C C
H
H
H H H
C C
H
C H
H C C C C H H
H
C
H H H H
H H
C5H12
C7H12

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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
H groups attached to a particular atom.
H C H
CH3
H H H
H C C C C H CH3CH2CHCH3 or CH3CH2CH(CH3)2
H H H H
Structural formula Condensed structural formula

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.
H H H H
H H
CH3CH2CH2CH3 becomes simplified to
H H H
H Bond line formula 26
 2H
2H O

3H
1H zero H

3H
1H

2H
molecular formula, C10H14O

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

H
(wedge): a bond projecting from the plane.
C (dash): a bonds projecting in to the plane.
H
H
H (line ): a bond that lies on the plane.

Is useful to show the stereochemistry of a molecule.

OH
CH3
C
CH2CH3
H
CH3
CH3

EX. Find the molecular formula of H

N

N 27
 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
CH3 C OH -5  As more chlorine groups which exert
1.75 x 10
O
-5
electron withdrawing inductive effect exist,
ClCH2 C OH 1.86 x 10
O the acidity strength increases (bigger Ka
Cl2HC -5
C OH 5530 x 10 acidity
O
Value)
Cl3C C OH -5
23,200 x 10

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

CH3CH2CH2COH 4.82
O

ClCH2CH2CH2COH 4.52  The last compound is strong acid than the

O

CH3CHCH2COH 4.05 rest of the compounds because chlorine is

Cl acidity
O closest to the reaction center.
CH3CH2CHCOH 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).

O
E.g acidity of acetic acid and ethanol. CH3 C OH CH3CH2OH
Acetic acid 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.
H H H H
C C Br2
H C C H
H H
ethene Br Br

Br2

HO
HO Br
Br
cholestrol

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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 CH3 CH3
Halide CH3CH2Cl
C X
O O
(X=F,Cl,Br, I) Carboxylic acid CH3 C OH
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
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Many compounds contain more than one functional group.
O
ketone O Acid OH
alcohol
CH3SCH2CH2CHC-OH
alkene
NH2
sulfide arene
amine

O OH
C
O O
CH3 HO NH C O CH3
O

Asprin Paracitamol

Ex. Identify the functional groups in each of the following

O O NH2
H
O N S CH3
OH
H O N CH3
HO O O
HO HO
OH
Prostagladin E1 amoxicillin

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Many compounds contain more than one functional group.
O
ketone O Acid OH
alcohol
CH3SCH2CH2CHC-OH
alkene
NH2
sulfide arene
amine

O OH
C
O O
CH3 HO NH C O CH3
O

Asprin Paracitamol

Ex. Identify the functional groups in each of the following

amine

O O NH2
H
O N S CH3
OH
H CH3
O N
HO O
HO O
OH HO
amide
Prostagladin E1
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