What is Organic Chemistry? Why Study It?

 In old days it was considered that Organic compounds can only be

obtained from plants or animal sources and cannot be prepared in
the laboratory.
 It was thought that a Vital force was required for their
production . Hence, the theory was regarded as " Vital Force
Theory".
 Because chemists could not create life in the laboratory, they
assumed they could not create compounds with a vital force.
 For the first time in 1828 when Friedrich Wöhler produced
urea compound known to be excreted by mammals by heating
ammonium cyanate, an inorganic mineral.
 What is organic chemistry

 Organic chemistry is the area of chemistry that involves the study of carbon and
its compounds.
 The compounds of carbon are the central substances of which all living things on
this planet are made.

For example:
 DNA-contain all the genetic information for a given species.
Why
 Enzymes: catalyze the reactions that is carbon
occur a unique
in our bodies
element?
 Proteins: blood, muscle, and skin and many more are contain carbon.
• Carbon is now known to form a seemingly unlimited
number of compounds.
• What makes carbon so special? Why are there so
many carbon-containing compounds? The answer lies
in carbon’s position in the periodic table. Carbon is in
the center of the second row of elements. The atoms
to the left of carbon have a tendency to give up
electrons, whereas the atoms to the right have a
tendency to accept electrons (Section 1.3).
• Because carbon is in the middle, it neither readily
gives up nor readily accepts electrons. Instead, it
shares electrons. Carbon can share electrons with
several different kinds of atoms, and it can also share
electrons with other carbon atoms. Consequently,
carbon is able to form millions of stable compounds
with a wide range of chemical properties simply by
sharing electron
 Why is carbon a unique element?
• its ability to form bonds with itself by covalent bond(Tetravalent)

• Carbon, alone of all elements, is able to form an immense diversity of

compounds, form the simple to the staggeringly complex-from.
• methane, with one carbon atom, to DNA, which can have tens of billions
• The unique ability of carbon atoms to bond together, forming long chains and
rings.

• Carbon has the property of forming single, double and triple bonds with itself and
with other atoms.
• Besides this, Carbon bonds to other elements like H, O, N and S.
• All of these possibilities generate an immense range of molecular structures and
shapes.
 Significance: We live in an Age of Organic Chemistry

 Chemistry has got enormous application in day to day life.

 Paints, plastics, pesticides, household items, drugs, petrochemicals,

proteins, nucleic acids, and sugars etc.

 which form the basis of all earthly life processes are applications of

organic chemistry.

 The uses of organic compounds impact our lives daily in medicine,

agriculture, and general life.

• We study organic chemistry

• because just about all of the molecules that make life

possible proteins (that makes up your hair, skin and muscles),

• enzymes, vitamins, lipids, carbohydrates, and nucleic acids

contain carbon (DNA that controls your genetic heritages).

• Organic chemistry is essential in biological and medical fields.
• All living organisms are composed of abundances of organic
substances.
• Evolution of life has been developed from one single organic
compound called nucleotide.
• Nucleotides polymerize, or join together to form the building blocks
of all life, DNA (Deoxyribonucleic acid).
• Proteins, carbohydrates and lipids are organic compounds that
contribute to the structure of the human body.

• Organic compounds are responsible for governing ion transport

channels in the cell
• carrying information from one cell to another and mediating cell to
cell communication.
• All chemical reactions, whether they take place in the

laboratory or in living organisms, follow the same “rules.”

• Reactions in living organisms often look more complex than

laboratory reactions because of the size of the biomolecules

and the involvement of biological catalysts called enzymes,

but the principles governing all reactions are the same.

• To understand both organic and biological chemistry, it’s

necessary to have the knowledge of organic chemistry

 The Structure of an Atom

• An atom consists of a tiny dense nucleus surrounded by electrons that

are spread throughout a relatively large volume of space around the
nucleus.
• The nucleus contains positively charged protons and neutral neutrons,
so it is positively charged.
• The electrons are negatively charged.
• A neutral atom has an equal number of protons and electrons.
 atomic number of an atom equals the number of protons in its
nucleus.
 The atomic number is also the number of electrons that surround the
nucleus of a neutral atom.

 For example, the atomic number of carbon is 6, which means that a

neutral carbon atom has six protons and six electrons.

 The mass number of an atom is the sum of its protons and neutrons
 6+6 = 12
 The Distribution of Electrons in an Atom

• the electron configuration of an atom is the representation of

the arrangement of electrons distributed among the orbital
shells and subshells.
What do orbitals look like?
 There are four different kinds of orbitals, denoted s, p, d, and f , each with
a different shape
• Each shell contains subshells known as atomic orbitals. Each
atomic orbital has a characteristic shape and energy and
occupies a characteristic volume of space, which is predicted by
the Schrödinger equation. An important point to remember is that the
closer the atomic orbital is to the nucleus, the lower is its energy. The
first shell consists of only an s atomic orbital; the second shell
consists of s and p atomic orbitals; the third shell consists of s, p,
and d atomic orbitals; and the fourth and higher shells consist of
s, p, d, and atomic orbitals (Table 1.1). Each shell contains one s
atomic orbital. The second and higher shells—in addition to their
s orbital—each contain three degenerate p atomic orbitals.
Degenerate orbitals are orbitals that have the same energy. The
third and higher shells—in
 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.
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).
 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.
 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
 ii. Aufbau principle ( Building up principl

 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 o
rbital, which is lower in energy than a 3s orbital
 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 2px, the sixth electron to the 2py orbital

and the 2pz orbital will remain empty

 COVALENT BONDS
• Instead of giving up or acquiring electrons, an atom can
achieve a filled outer shell by sharing electrons.
• For example, two fluorine atoms can each attain a filled
shell of eight electrons by sharing their unpaired valence
electrons.
• A bond formed as a result of sharing electrons is called
a covalent bond.
There are two types of covalent bonding

1. Non-polar bonding with an equal sharing of

electrons.
2. Polar bonding with an unequal sharing of
electrons.
The number of shared electrons depends on the
number of electrons needed to complete the
octet.
• In the and covalent bonds,F-F and H-H the atoms
that share the bonding electrons are identical.
• Therefore, they share the electrons equally; that is,
each electron spends as much time in the vicinity of
one atom as in the other.
• An even(nonpolar) distribution of charge results.
Such a bond is called a nonpolar covalent bond.
• In contrast, the bonding electrons in HCl,H2O, and NH3 are
more attracted to one atom than another because the atoms
that share the electrons in these molecules are different and
have different electronegativities.
• Electronegativity is the tendency of an atom to pull bonding
electrons toward itself.

The bonding electrons in HCl,H2O, and NH3 molecules are

more attracted to the atom with the greater electronegativity.
This results in UNEQUAL (a polar) distribution of charge.
• A polar covalent bond is a covalent bond between atoms of
different electronegativities.
Anonpolar covalent bond involves equal
sharing.
Polar covalent bonds involves un equal sharing
• Electronegativity difference
• If the Electronegativity difference is below 0.5,
the nature of the bond is non-polar bond

• If the Electronegativity difference is 0.5-1.7 the

nature of the bond is polar bond
 Nonpolar Covalent Bonds
A nonpolar covalent bond

• occurs between nonmetals.

• is an equal or almost equal sharing of electrons.
• has almost no electronegativity difference (0.0 to 0.4).
Examples:
Electronegativity
Atoms Difference Type of Bond
N-N 3.0 - 3.0 = 0.0 Nonpolar covalent
Cl-Br 3.0 - 2.8 = 0.2 Nonpolar covalent

28
 Polar Covalent Bonds

A polar covalent bond

• is an unequal sharing of electrons.

• has a moderate electronegativity difference (0.5 to 1.7).

Examples:
Electronegativity
Atoms Difference Type of Bond

Cl-C 3.0 - 2.5 = 0.5 Polar covalent

O-S 3.5 - 2.5 = 1.0 Polar covalent

29
 Representation of Structure

• Atoms link together to form molecules because they "like" to

achieve a filled shell configuration.
• They achieve this by giving up or taking electrons (ionic bonds)
or by sharing electrons (covalent bonds).
• In organic compounds, most bonds are covalent and the
compounds are usually written as Lewis Structures.
• The chemical symbols we have been using, in which the
valence electrons are represented as dots, are called Lewis
structures.
1) Lewis Structure: Representation of a molecule
that shows how the valence electrons are
arranged among the atoms in the molecule
• 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:
 2) Kekulé Structures

• In Kekulé structures, the bonding electrons are drawn as lines and

the lone-pair electrons are usually left out entirely.
• Although lone-pair electrons may not be shown,
you should remember that neutral nitrogen, oxygen, and halogen
atoms always have them:
• one pair in the case of nitrogen, two pairs in the case of oxygen, and
three pairs in the case of a halogen.
 Condensed Structures

• structures are simplified by omitting some (or all) of the

covalent bonds and listing atoms bonded to a particular
carbon (or nitrogen or oxygen) next to it with a subscript to
indicate the number of such atoms.
• These kinds of structures are called condensed structures.
 Theories of Chemical bonding
• Two models have been developed to describe
covalent bonding:
1) valence bond theory and
2)molecular orbital theory.
 VBT
• Valence bond method considers the covalent bond as a result of
overlap of atomic orbitals.
• Electrons stay in regions between the two atoms.
• According to valence bond theory, a covalent bond forms when two
atoms approach each other closely and a singly occupied orbital on
one atom overlaps a singly occupied orbital on the other atom.
• The electrons are now paired in the overlapping orbitals and are
attracted to the nuclei of both atoms, thus bonding the atoms together.
• In the H2 molecule, for instance, the H-H bond results
from the overlap of two singly occupied hydrogen 1s orbitals.
 Hybridization of Atomic Orbitals

• Hybrid orbitals: are mixed orbitals they result from combining

orbitals.
• The concept of combining orbitals, called orbital hybridization
• The mixing of atomic orbitals to form special orbitals for bonding.
• sp3 hybrid orbital
• 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 an (stated “s-p-three” not “s-p-
cubed”) orbital
 Hybridization

Ground state of C 1s2 2s2 sp2

s px py pz

Promote electron at n=2 2s12p3

s px py pz

Hybridize at n=2 sp3 sp3 sp3 sp3

sp3 sp3 sp3 sp3

Four sp3 orbitals of equal length, energy and in tetrahedral shape
• The ground-state electronic configuration of an
atom describes the orbitals occupied by the atom’s
electrons when they are all in the available orbitals
with the lowest energy.
• If energy is applied to an atom in the ground state,
one or more electrons can jump into a higher energy
orbital.
• The atom then would be in an excited-state
electronic configuration.
• Each sp3 orbital has 25% s character and 75%
p character.
• The four sp3 orbitals are degenerate they have
the same energy.
• The four sp3 orbitals 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.
• When four orbitals spread themselves into space as far from each
other as possible, they point toward the corners of a regular
tetrahedron (a pyramid with four faces, each an equilateral
triangle).

• The angle formed between any two bonds of methane is 109.5°.

This bond angle is called the tetrahedral bond angle
• The two carbon atoms in ethane (CH3CH3) are
tetrahedral.
• Each carbon uses four orbitals to form four covalent
bonds.
• One sp3 orbital of one carbon overlaps an sp3 orbital
of the other carbon to form the bond.
• Thus, C-C bond is formed by sp3- sp3 overlap
• Each of the bond angles in ethane is nearly the
tetrahedral bond angle of 109.5.
 sp2 hybrid orbital
• To bond to three atoms, each carbon hybridizes
three atomic orbitals.
• Because three orbitals (an s orbital and two of the
p orbitals) are hybridized, three hybrid orbitals are
obtained. These are called sp2 orbitals.
• After hybridization, each carbon atom has three
degenerate sp2 orbitals and one p orbital:
•
Copyright©2000 by Houghton Mifflin
46
Company. All rights reserved.
• The second carbon–carbon bond results from side-
to-side overlap of the two unhybridized p orbitals.
Side-to-side overlap of p orbitals forms a pi bond (π)
Thus, one of the bonds in a double bond is a σ bond
and the other is a π bond.

• To minimize electron repulsion, the three sp2

orbitals need to get as far from each other as
possible. This means that the bond angles are
all close to 120°.
• Single bond 1 sigma bond
• Double bond 1 sigma bond and 1 pi bond
• Triple bond 1 sigma bond and 2 pi bonds

49
The orbitals used to form the bonds in
ethylene.

50
Copyright©2000 by Houghton Mifflin
51
Company. All rights reserved.
 sp hybrid orbital

• only two orbitals (an s and a p) are hybridized.

• To minimize electron repulsion, the two sp orbitals point in opposite

directions. Consequently, the bond angles are 180°(a).
• Each of the unhybridized p orbitals engages in
side-to side overlap with a parallel p orbital on
the other carbon, with the result that two π
bonds are formed
• The overall result is a triple bond.
• A triple bond consists of one σ bond and two
π bonds.
Summary of Covalent Bonding Seen in Carbon Compounds

54
Hybridization and the Localized Electron Model

# Electron-pairs on
Central Atom Arrangement Hybridization
2 linear sp
3 trigon planar sp2
4 tetrahedral sp3
 Q1: How many s and p bonds are in the acetic acid (vinegar) molecule

CH3COOH?
H

O
s bonds = 6 + 1 = 7
p bonds = 1
H C C O H

Problem 1 - What is the hybridization of all the labeled atoms in the structure below?
What are the bond angles, shapes, number of sigma bonds, number of pi bonds?

56
• Describe the orbitals used in bonding and the
bond angles in the following compounds.
HCOOH .

Which of the following molecules would you

expect to have a dipole moment of zero? To
answer parts g and h, you may need to consult
your answers to Problem 23 a and b. a. c. e. g.
b. d. f.
 Bonding in the Methyl Cation, the Methyl
Radical, and the Methyl Anion

• The positively charged carbon in the methyl cation is bonded

to three atoms, so it hybridizes three orbitals—an s orbital
and two p orbitals. Therefore, it forms its three covalent
bonds using orbitals.
• Its unhybridized p orbital remains empty.
• The positively charged carbon and the three atoms bonded to
it lie in a plane.
• The carbon atom in the methyl radical is also
hybridized.
• The methyl radical differs by one unpaired
electron from the methyl cation.
• That electron is in the p orbital.
• The negatively charged carbon in the methyl anion has
three pairs of bonding electrons and one lone pair.
• The four pairs of electrons are farthest apart when the four
orbitals containing the bonding and lone-pair electrons
point toward the corners of a tetrahedron.
• In other words, a negatively charged carbon is hybridized.
In the methyl anion, three of carbon’s orbitals each overlap
the s orbital of a hydrogen, and the
fourth orbital holds the lone pair.
Bonding in Water
Because oxygen has two unpaired electrons in its ground-
state electronic configuration it does not need to promote an
electron to form the number (two) of covalent bonds.
• The s orbital and the three p orbitals must
hybridize to produce four orbitals.
• Each of the two bonds is formed by the overlap
of an orbital of oxygen with the s orbital of a
hydrogen. A lone pair occupies each of the two
remaining orbitals.
 Bonding in Ammonia
• Like carbon and oxygen, the one s and three p orbitals of the second shell of
nitrogen hybridize to form four degenerate orbitals:

• The bonds in are formed from the overlap of an orbital of nitrogen

with the s orbital of a hydrogen. The single lone pair occupies an orbital. The
bond angle (107.3°) is smaller than the tetrahedral bond angle (109.5°)
because the electron.
• The bond angle in water is a little smaller (104.5°)
than the tetrahedral bond angle (109.5°) in
methane.
• Consequently, there is more electron repulsion
between lone-pair electrons, causing the bonds
to squeeze closer together, thereby decreasing
the bond angle.