Applied Organic chemistry

A2STU

Industrial Chemistry Department (Organic Stream)

Limenew Abate (Assistance professor)

 1. Bonding & structure

In 1807; Jöns Jakob Berzelius gave names to the two kinds of materials:
 Compounds derived from minerals, those lacking that vital force, were
“inorganic.” Because chemists could not create life in the laboratory.
 Compounds derived from living organisms were believed to contain an
unmeasurable vital force, the essence of life. These he called “organic.”

Friedrich Wöhler (1828) produced urea, a compound known to be excreted by

mammals, by heating ammonium cyanate, an inorganic mineral in the laboratory.
Organic compounds are now defined as compounds that contain carbon.
More generally, organic chemistry is defined as the study of carbon
containing compounds.

There are, however, some exceptions.

• The oxides of carbon (CO2),

• carbonates (CO3-),
• cyanides (CN-), and
• metallic carbides (CaC2)
1. What makes carbon so special?
2. Why are there so many carbon-containing compounds?
carbon is in the middle, it neither readily gives up nor readily
accepts electrons.
 1.2. Energy level and atomic orbitals

• The 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.
• The mass number of an atom is the sum of its protons and neutrons.
• Not all carbon atoms have the same mass number, because, even though they
all have the same number of protons, they do not all have the same number of
neutrons. Isotopes: 12
C, 13C and 14C

PROBLEM 1☺
Oxygen has three isotopes with mass numbers of 16, 17, and 18. The atomic
number of oxygen is eight. How many protons and neutrons does each of the
isotopes have?
 Orbitals and Electronic Configurations
 It is important to understand the location of electrons, as it is the arrangement of
the electrons that creates the bonds between the atoms, and chemical reactions are
just that to form new bonds.
 Electrons are involved in the chemical bonding and reactions of an atom.
Electrons are said to occupy orbitals in an atom.

 An orbital is a region of space that can hold two electrons.

 Electrons do not move freely in the space around the nucleus but are confined to
regions of space called shells.
 Each shell can contain up to 2n2 electrons, where n is the number of the shell.

 Each shell contains subshells known as atomic orbitals.

The first shell contains a single orbital known as the 1s orbital.

The second shell contains one 2s and three 2p orbitals. These three 2p
orbitals are designated as 2px, 2py and 2pz.
The third shell contains one 3s orbital, three 3p orbitals and five 3d orbitals.

Thus, the first shell can hold only two electrons, the second shell eight electrons
and the third shell up to 18 electrons, and so on.
As the number of electrons goes up, the shell numbers also increase. Therefore,
electron shells are identified by the principal quantum number, n = 1, 2, 3 and
so on.
The electronic configuration of an atom describes the number of electrons that an
atom possesses, and the orbitals in which these electrons are placed.

The arrangements of electrons in orbitals, subshells and shells are called electronic
configurations.

Electronic configurations can be represented by using noble gas symbols to show

some of the inner electrons, or by using Lewis structures in which the valence
electrons are represented by dots.

Valence is the number of electrons an atom must lose or gain to attain the nearest
noble gas or inert gas electronic configuration. Electrons in the outer shells that are
not filled are called valence electrons.
The ground-state electronic configuration is the lowest energy, and the excited-
state electronic configuration is the highest energy orbital.
If energy is applied to an atom in the ground state, one or more electrons can jump
into a higher energy orbital. Thus, it takes a greater energy to remove an
electron from the first shell of an atom than from any other shells.

For example, the sodium atom has electronic configuration of 2, 8 and 1.

Therefore, to attain the stable configuration, it must lose one electron from its outermost shell
and become the nearest noble gas configuration, i.e. the configuration of neon, which has
the electronic configuration of two and eight. Thus, sodium has a valence of 1.
Electronic configuration of an atom can be determined by the following three
principles.
The Aufbau principle: 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.

The Pauli exclusion principle: No more than two electrons can occupy each orbital, and if
two electrons are present, their spins must be paired. For example, the two electrons of a
helium atom must occupy the 1s orbital in opposite spins.

Hund’s rule: 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.
 Oxygen has the atomic number 8, and the ground-state electronic configuration
for oxygen can be written as 1s2 2s2 2px2 2py1 2pz1.
Similarly, we can write the others as follows:
 Chlorine (atomic number 17): 1s2 2s2 2px2 2py2 2pz2 3s2 3px2 3py2 3pz1

 Nitrogen (atomic number 7): 1s2 2s2 2px1 2py1 2pz1

 Sulphur (atomic number 16): 1s2 2s2 2px2 2py2 2pz2 3s2 3px2 3py1 3pz1
 Covalent bonding
Atoms form bonds in order to obtain a stable electronic configuration, i.e. the electronic
configuration of the nearest noble gas.

All noble gases are inert, because their atoms have a stable electronic configuration in
which they have eight electrons in the outer shell except helium (two electrons). Therefore,
they cannot donate or gain electrons.

One of the driving forces behind the bonding in an atom is to obtain a stable valence
electron configuration. A filled shell is also known as a noble gas configuration. Electrons in
filled shells are called core electrons. The core electrons do not participate in chemical
bonding.

Electrons in shells that are not completely filled are called valence electrons, also known as
outer-shell electrons, and the energy level in which they are found is also known as the
valence shell.

Carbon, for example, with the ground-state electronic configuration 1s2 2s2 2p2, has four
outer-shell electrons. We generally use the Lewis structure to represent the outermost
electrons of an atom.

 A chemical bond is the attractive force that holds two atoms together. Valence
electrons take part in bonding.
Types of bonding: the two major types of bonds are,
Ionic and Covalent bonds

 Ionic bonds result from the transfer of one or more electrons between
atoms. The more electronegative atom gains one or more valence
electrons and hence becomes an anion. The less electronegative atom
loses one or more valence electrons and becomes a cation.

 Covalent bonds result from the sharing of electrons between atoms. In this
case, instead of giving up or acquiring electrons, an atom can obtain a
filled valence shell by sharing electrons. For example, two chlorine atoms
can achieve a filled valence shell of 18 electrons by sharing their unpaired
valence electrons.
More Examples
H

C + 4H H C H CH4(methane)

2H + O H O (H2O)
water
H
H

3H + C + O + H H C O H

H
CH3OH (methanol)

3H + N H N H NH3 (Ammonia)
H
Covalent bonds are formed when atomic orbitals overlap. The
overlap of atomic orbitals is called hybridization, and the resulting
atomic orbitals are called hybrid orbitals.

There are two types of orbital overlap, which form sigma (δ) and pi
(Π) bonds. Pi bonds never occur alone without the bonded atoms also
being joined by a δ bond.

Therefore, a
 double bond consists of a δ bond and a Π bond,
 triple bond consists of a δ bond and two Π bonds.
A sigma overlap occurs when there is one bonding interaction that
results from the overlap of two s orbitals or an s orbital overlaps a p
orbital or two p orbitals overlap head to head.

A pi overlap occurs only when two bonding interactions result from

the sideways overlap of two parallel p orbitals.

The s orbital is spherical in shape and p orbitals are in dumb-bell

shapes.
Let us consider the formation of s overlap in the hydrogen molecule
(H2), from two hydrogen atoms.
Each hydrogen atom has one electron, which occupies the 1s orbital.
The overlap of two s orbitals, one from each of two hydrogen atoms,
forms a s bond.
 Orbital Hybridization
Hybridization is the mixing of atomic orbitals of the same atom. Hybridization results in
equivalent new hybrid orbitals.
Sp3 Hybridization
 Results of hybridization of one s and three p atomic orbitals.
 forms four degenerate sp3 hybrid orbitals.
 The four new orbitals are called sp3 orbitals because they are formed from one 2s and
three 2p orbitals (s1p3).
 possess 25% s character and 75% p character.
 are identical in shape with tetrahedral geometry (bond angle 109O).

2p2 2p3 sp3 hybrid orbitals

sp3
energy

2 2s1 sp3 sp3 sp3 sp3

2s sp3 sp3
C C
C hybridized-state sp3
ground- state excited-state

H(1s1)

sp3 H
sp3 109.5o
1 C
H(1s )
sp3 sp 3
H H
H(1s1) H

H(1s1)
Sp2 Hybridization

 Results of hybridization of one s and two p atomic orbitals.

 forms three degenerate sp2 hybrid orbitals.
 The three new orbitals are called sp2 orbitals because they are formed from one 2s and
two 2p orbitals (s1p2).
 The three sp2 orbitals are identical in shape with planar geometry (bond angle 120O).

unhybridized p orbital
2p2 2p3
energy

2 2s1 sp2 sp2 sp2

2s
C C sp2 hybrid orbitals
C hybridized-state
ground- state excited-state

H(1s1) 120o
H H
2 C C
sp2 sp H H
Sp Hybridization

 Hybridization of one s and one p atomic orbitals forms two degenerate sp hybrid orbitals.
 These new orbitals are called sp orbitals.
 The two sp orbitals are identical in shape with linear geometry (bond angle 180O).
Example formation of covalent bond in ethyne.
Molecular Orbital Theory (MOT)
Molecular orbital theory is a method of accounting for covalent bonds that depends
on quantum theory and mathematical principles. We can speak only about energy
levels/spatial probabilities when reckoning with them.
Combination of Atomic Orbitals
Atomic orbitals are capable of combining or overlapping, to produce new electron
distributions called molecular orbitals (MOs) – one MO for every AO.
Bonding molecular orbitals: have a region of high electron density between the
nuclei.
Anti-bonding molecular orbitals: have region of zero electron density (a node)
between the nuclei.
When two atomic orbitals overlap end-to-end, they form two sigma-molecular orbitals
(MOs).

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 Electron Configuration of Diatomic Molecules
A molecular-orbital diagram shows the relative energy and number of electrons in
each MO, as well as the atomic orbitals from which they form.
Example: H2

Note! The number of molecular orbitals formed must equal the number of atomic orbitals22
The order of energy of molecular orbitals has been determined mainly from spectroscopic

data.

a. In simple homonuclear diatomic molecules (total electrons = 14 or less) the order is:

b. For simple homonuclear diatomic molecules (total electrons greater than 14) the
(π2py=π2pz) comes after σ2px
and the order is:
Bond Order
The term bond order is used to indicate whether a covalent bond is single (bond
order = 1), double (bond order = 2) or triple (bond order = 3). For example, in a
molecular orbital treatment of oxygen, a sigma bond results from the filling of (σ 2px)2.

Since (π∗2py)1 is half-filled therefore cancels half the effect of (π2py)2, half a pi bond

results. Similarly another half pi bond arise from π2pzand π∗2pz, giving a total of:
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The bond order can be calculated as the number of electrons occupying bonding
orbitals minus the number of electrons in antibonding orbitals, all divided by two.

Magnetic Properties
A species with unpaired electrons exhibits paramagnetic property. The species is
attracted by an external magnetic field. A species in which all the electrons are paired,
exhibits diamagnetism. Such species are not attracted (and, in fact, are slightly
repelled) by a magnetic field. The antibonding π∗2py and π∗2pz orbitals for O2 are singly
occupied in accordance with Hund's rule. Since there are two unpaired electrons with
parallel spins, this explains why oxygen is paramagnetic. This was the first success of
the MO theory in successfully predicting the paramagnetisim of O 2 , a fact not even
thought of with VB representation of the oxygen molecule (O=O).

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