Structure and bonding

Atomic structure and bonding

Learning outcomes

• At the end of this session the student shall be able to:
• Define organic chemistry
• Recognize sigma and pi bonds
• Draw Lewis and Kekule structures
• Describe structure of alkane, alkenes and alkynes based on

valence bond theory and molecular orbital theory

Atomic structure

• What is an atom?
• Atomic number?
• Mass number?
• What is an ion?

Atomic bonding

• Noble gas?
• Octet of electron?
• Valence shell/valence electrons?
• Ionic bonding?
• Covalent bonding?
• What is a bond? – (sharing of 2 electrons)
• What is valency?
• Double bond/triple bond?

Orbitals

• Quantum mechanics: consider electron as
a wave

• The wave equation give wave function
(Ψ) or Orbitals that represent the space
where electron spend most (~ 95%) of its
time

• Some of the orbitals are s, p, d, f, …..
• The shape of orbitals depends on energy
level

• s is spherical
• p have a dumbbell shape – (px, py and pz)
• Different shells have different numbers
and kinds of orbitals (Remember n, l, ml,
and ms)

Electronic configuration

• How do we find the ground state electron

configuration?

• Aufbau principle
• Pauli exclusion principle
• Hund’s rule

• Examples?

Electronic configuration

Chemical bonding

• Why atoms combine?
• Ionic bonding?

• Ionization energy? – electron affinity?

• Covalent bonding form molecules

Indicated by:
• Lewis (electrons dot) structures
• Kekule structure or line-bond structure

Covalent Bonds – valence bond theory

• Atomic orbitals overlap to form

molecular orbitals

• energy is released = bond strength

(H2 = 104 kcal/mol)

• distance for optimal overlap =

bond length (H2 = 0.74 A)

Sigma (σ) bonds

• Head-on overlap of s orbitals give

a bond with circular cross-section

• Such bond is called sigma ()

bond

pi (π) bonds

• The p orbital can achieve

• head-on overlap to form sigma bond
• OR sideway overlap to form a pi (π) bond

Structure of alkanes - sp3 hybridization
• Bonding in alkanes involves sp3hybrid orbitals
• combining an s orbital and three p orbitals give four degenerate sp3hybrid

orbitals

• They are oriented towards the corners of a tetrahedron

Representation of tetrahedral carbon

Structure of methane

• All four bond in methane are

identical

• Bond energy = 104 kcal/mol
• Bond length = 1.10 A (109 pm)
• Bond angle = 109.5o

(tetrahedral angle)

Structure of ethane

• Bonding involves

sp3hybrid orbitals

• C-H bonds = 98

kcal/mol

• C-C bond = 1.54 A

(154 pm) and 88
kcal/mol

• bond angle = 109.5o.

Structure of alkenes – sp2 hybridization

• Combination of s orbital with only 2 of the p orbitals gives three

degenerate sp2hybrids orbitals

• These orbitals lie in a plane at 120oto each other
• One 2p orbital remains unhybridized and lies perpendicular to the

sp2plane

Structure of ethylene

• A double bond in

ethene is constituted of
a sigma bond due to
head-on overlap of sp2
orbitals and a pi bond
due to sideway overlap
of unhybridized p
orbitals

• Four hydrogen atoms

form sigma bonds with
the remaining four sp2
orbitals

Structure of alkynes – sp hybridization

• Combination of only one 2p orbital with the 2s orbital form two

degenerate sp hybrid orbitals

• The two sp orbitals are linear (180o) – the remaining 2p unhybridized

orbitals are perpendicular to the sp orbital

Structure of acetylene

• A triple bond in acetylene is composed of two pi bonds due to sideway

overlap of the unhybridized p orbitals and a head-on overlap of sp hybrid
orbitals.

• Two hydrogen atoms form sigma bonds with the remaining two sp orbitals

Comparison of bond length and strength

Molecule

Bond

Bond strength

(kcal/mol)

Bond length (Å)

Bond length

(pm)

Methane CH4
(sp3) C – H

104 (436 kJ/mol)

1.10

109

Ethane CH3CH3
(sp3) C – C

90 (376)

1.54

154

(sp3) C – H

101 (423)

1.10

109

Ethylene
H2C=CH2

(sp2) C = C

174 (728)

1.33

134

(sp2) C – H

111 (465)

1.076

109

Acetylene HC≡CH

(sp) C≡C

231 (965)

1.20

120

(sp) C– H

133 (556)

1.06

106

Hybridization of N, O, P and S

• In most cases they are sp3hybridized.

• Note P and S can form more than the typical number of covalent bonds

Molecular orbital theory

• Combination of two s-atomic orbitals results in formation of a pair of -

molecular orbitals

• One lower in energy –  bonding MO
• The other is in higher energy – * antibonding MO

Molecular orbital theory

• Combination of two p-atomic orbitals results in the formation of

two π-molecular orbitals

Molecular representation

Molecular representations

• In organic chemistry molecules

are represented using

1.

Lewis (electron dot) structure

2.

Kekule (line bond) structure

• A correct representation shows

all valence electrons:

• In Lewis structures the e-s are

represented by dot while in
Kekule the bonded electrons
are represented by a line
(bond).

Molecular representations

• For a neat and tidy representation, we also

represent structures of organic compounds
using

1.

Condensed structure:
C-H and C-C bonds are not shown

2.

Skeletal structure:
• at each intersection of two lines and at the end of each line

there is carbon

• Hydrogen are mentally supplied to fill the valence of each

carbon

• All atoms other than carbon and hydrogen are indicated

Skeletal structure examples

OH

N

butane
isoprene

Methylcyclohexane

Phenol

Pyridine