Focus 9: The Structure of

Molecules
 Topic 9A: Valence bond theory
Born-Oppenheimer Approximation:
The nuclei are heavier than electrons and
are treated as stationary and electrons are
mobile. A MOLECULAR POTENTIAL ENERGY CURVE
 Diatomic Molecules
• In valence bond theory: e.g.: valence bond
wavefunction for H2 molecule: for electron
1 and electron 2 distributed between HA
and HB
𝜓𝐻−𝐻 1,2 = 𝜓𝐻𝐴 1 𝜓𝐻𝐵 2 + 𝜓𝐻𝐴 2 𝜓𝐻𝐵 1
 Valence Bond (VB) Wavefunction
• 𝜓𝐻−𝐻 1,2 =
𝜓𝐻𝐴 1 𝜓𝐻𝐵 2 + 𝜓𝐻𝐴 2 𝜓𝐻𝐵 1
Valence bond wavefunction 𝜓𝐻−𝐻 1,2 is
substituted in Schrödinger equation to
calculate energy of the molecule.
As two atoms approach, electron density
is accumulated in between nuclei.
Potential energy increases close to nuclei.
VB wavefunction and Pauli’s Principle
 Pauli Principle states that ground state VB wave
function is:
𝜓 2,1 = −𝜓(1,2) -----(A)
For this to satisfy the correct linear combination of
electron (since electrons are fermions) spin with equal
probability is proportional to:
𝛼 1 𝛽 2 − 𝛽(1)𝛼(2)
Sign change in VB Wavefunction as shown in (A) is
obtained by multiplying symmetric part of electron
exchange in VB with anti-symmetric spin part.
(Elements of Physical Chemistry, P. W. Atkins and J.
D. Paula, 6th edition, Derivation 14.1, p.347)
 Electron density between Hydrogen
atoms
• The Electron density in H2 according to
valence bond model. 𝒁𝑨 𝒁𝑩 𝒆𝟐
𝑽 𝑹 =
𝒏𝒖𝒄−𝒏𝒖𝒄
𝟒𝝅𝜺𝒐 𝑹
 Valence Bond Description: N2
molecule
• Valence electron configuration of N atom:
• 2𝑠 2 2𝑝𝑥1 2𝑝𝑦1 2𝑝𝑧1 : σ bond formation along z
axis and π-bonds along x and y.
Writing VB wavefunction: Example for
N2 molecule
• σ − Bond: Along Z −
axis: NA and NB refers to nitrogen atoms
𝜓2𝑝𝑧 (𝑁𝐴 −𝑁𝐵 ),𝜎 1,2
= 𝜓2𝑝𝑧 1 𝜓2𝑝𝑧 2 + 𝜓2𝑝𝑧 2 𝜓2𝑝𝑧 1
𝑁𝐴 𝑁𝐵 𝑁𝐴 𝑁𝐵
• π − Bond: Lateral overlap (𝑖𝑛𝑣𝑜𝑙𝑣𝑖𝑛𝑔 𝑝𝑥 ):
𝜓2𝑝𝑥 (𝑁𝐴 −𝑁𝐵 ),𝜋 1,2
= 𝜓2𝑝𝑥 1 𝜓2𝑝𝑥 2 + 𝜓2𝑝𝑥 2 𝜓2𝑝𝑥 1
𝑁𝐴 𝑁𝐵 𝑁𝐴 𝑁𝐵
 Note: Pauli’s exclusion principle is satisfied when
electrons (1 and 2)are paired to form chemical bond (σ
or π bonds). Repeat for 𝑝𝑦 .
 Valence Bond Description: H2O
molecule
• Valence electron configuration of O atom:
• 2𝑠 2 2𝑝𝑥2 2𝑝𝑦1 2𝑝𝑧1 : The unpaired electrons in
2p orbitals (pz and py) pairs with an
electron in a H 1s orbital.
Experimental bond angle is 104o

Predicted bond angle is 90o

 VSEPR Model
• Valence Bond Theory (VBT):
 Inaccurate prediction of bond angle:
e.g., H2O, NH3

 Fails to explain tetravalence of carbon

e.g., CH4
 VSEPR Model qualitative explanation for
bond angle: The repulsive interactions of lone
pair (LP) and bond pair (BP) are in the order:
 LP-LP > LP-BP > BP-BP
 Concept of Hybridization
• Ground state electronic configuration of
carbon: 2𝑠 2 2𝑝𝑥1 2𝑝𝑦1 2𝑝𝑧0
• Experimentally, it has been found that
molecular formula of methane is CH4 and
not CH2.
• Promotion of an electron to vacant p
orbital and formation of 4 orbitals of equal
energy.
 2𝑠1 2𝑝𝑥1 2𝑝𝑦1 2𝑝𝑧1 # sp3 hybridization
 Linear Combination Principle
• A linear combination of two functions f and
g that gives a function h is:
𝑕 = 𝑐1 𝑓 + 𝑐2 𝑔
The squares of the coefficients (𝑐1 and 𝑐2 )
gives the proportion of each function to
overall function h.
Linear combination is a more general term
than ‘sum’.
 Hybridization of Orbitals-sp3
hybridization
• The atomic orbitals interfere constructively
or destructively in different regions to give
rise to hybrid orbitals.

𝒉𝟏 = 𝒔 + 𝒑 𝒙 + 𝒑𝒚 + 𝒑𝒛
𝒉𝟐 = 𝒔 − 𝒑 𝒙 − 𝒑𝒚 + 𝒑𝒛
𝒉𝟑 = 𝒔 − 𝒑 𝒙 + 𝒑𝒚 − 𝒑𝒛
𝒉𝟒 = 𝒔 + 𝒑 𝒙 − 𝒑𝒚 − 𝒑𝒛
Writing VB wavefunction using hybrid
orbitals: Example for CH4
• Label wavefunctions of 4 lobes of sp3 hybrid orbitals at
carbon as:
𝑕1𝐶 , 𝑕2𝐶 , 𝑕3𝐶 , 𝑕4𝐶 and
4 hydrogen 1s orbitals as:
𝜓1𝑠,𝐻𝐴 , 𝜓1𝑠,𝐻𝐵 , 𝜓1𝑠,𝐻𝐶 , 𝜓1𝑠,𝐻𝐷
• 𝜎 bond between 𝜓ℎ1𝐶 and 𝜓1𝑠,𝐻𝐴 results in 𝑕1𝐶 −𝐻 1, 2
𝐴 ,𝜎
= 𝑕1𝐶 (1) 𝜓1𝑠,𝐻𝐴 (2) +𝑕1𝐶 (2) 𝜓1𝑠,𝐻𝐴 (1)
 Repeat for 𝑕2𝐶 , 𝑕3𝐶 , 𝑕4𝐶 to complete the VB description
of σ bond formation in CH4
 Note: Pauli’s exclusion principle is satisfied when electrons (1
and 2) are paired to form chemical bond.
 sp2 hybridization
Note: All hybrids are normalized .
• Hybridization in C2H4: See for example:
Problem 14.34 . (6th Edn.)
𝒔+𝟐𝟏/𝟐 𝒑𝒙
𝒉𝟏 = The coefficients 𝐢n
𝟑 the hybrid refers to the
𝟏
𝟏 𝟏 𝟐 𝟏 𝟏/𝟐 directional property
𝒉𝟐 = 𝒔 − 𝒑𝒙 + 𝒑𝒚 as well as coefficient for
𝟑 𝟔 𝟐 linear combination,
𝟏
𝟏 𝟏/𝟐
square of which refers to
𝟏 𝟏 𝟐
𝒉𝟑 = 𝒔 − 𝒑𝒙 − 𝒑𝒚 proportionate
𝟑 𝟔 𝟐 mixing of orbitals
 sp hybridization
• Hybridization in C2H2:
The hybridization of
𝒉𝟏 = 𝒔 + 𝒑𝒛 N atomic orbitals result
𝒉𝟐 = 𝒔 − 𝒑𝒛 in N hybrid orbitals
Shape and Hybridization
 Shape and Hybridization
• Example Problems:
1. Predict the shape and hybridization in SF6
and PCl5.
2. Write an example each for following
specified shapes of molecules.
The variation of hybridization ratio,λ,
with bond angle

Angular Trigonal pyramidal

The figure shows the
variation between bond
angle (ϕ) and
hybridization ratio spλ. λ:
1 to 3
As more and more p
character is mixed in
hybridization, bond
angle is decreased.
Out-of-plane
 Contour plots of spn hybrid orbitals
• The p character increases from left top to right
bottom. (Contour plots from Hydrogenic 2s and
2p orbitals, red color ‘+’ part and dark blue ‘-’
part).
 Resonance
• Resonance: the superposition of wavefunctions
representing different electron distribution in the same
nuclear framework.

H-Cl: Covalent description:

 𝜓𝐻−𝐶𝑙 1,2 = 𝜓𝐻 1 𝜓𝐶𝑙 2 + 𝜓𝐻 2 𝜓𝐶𝑙 1
 Needs modification as HCl is polar covalent
 𝜓𝐻 + 𝐶𝑙− = 𝜓𝐶𝑙 (1)𝜓𝐶𝑙 (2) # Ionic form of the wavefunction.
 𝜓𝐻𝐶𝑙 = 𝜓𝑐𝑜𝑣𝑎𝑙𝑒𝑛𝑡 + 𝜆𝜓𝑖𝑜𝑛𝑖𝑐 (trial wavefunction)
where 𝜆2 determines the ionicity of the bond. 𝜆2 >>1
bond is predominantly ionic. 𝜆2 << 1 is
predominantly covalent.
 Resonance Hybrids
• 𝜓 = 𝜓𝑘𝑒𝑘1 + 𝜓𝑘𝑒𝑘2
 The two contributing structures have identical
energy and contributes equally to
superposition.
 Resonance: a close
approximation to true
molecular wavefunction
through a computational
1 2
approach.
 Concept of overlap integral (SAB)
• Probability density in the internuclear
region is measured by the overlap integral
(SAB) using differential volume element
𝑑𝜏(= 𝑑𝑥𝑑𝑦𝑑𝑧)
𝑆𝐴𝐵 = 𝜓𝐴 𝜓𝐵 𝑑𝜏 | overlap integral of 𝜓𝐴
and 𝜓𝐵 . S-very small S-large S-?
 Overlap integral for H2 molecule
𝑅
𝑅 𝑅2 −
• 𝑆𝐻𝐻 = 1 + + 𝑒 𝑎𝑜 where ao is the
𝑎𝑜 3𝑎𝑜2
Bohr radius.
 Concept of Orthogonality
• 𝜓𝐴 𝜓𝐵 𝑑𝜏 = 0 | Condition of orthogonality.
• Example Problem:
Prove that the overlap integral S between any two sp3 hybrid lobes is
zero, if each s and p orbitals are normalized to 1 and 𝒔𝒑𝒅𝝉 = 𝟎,
𝒑𝒙 𝒑𝒚 𝒅𝝉 = 𝟎.
Required to prove: 𝑕1 𝑕2 𝑑𝜏 = 0 given 𝒔𝟐 𝒅𝝉 = 𝟏, 𝒑𝒛 𝟐 𝒅𝝉 = 𝟏,
𝒑𝒙 𝟐 𝒅𝝉 = 𝟏, 𝒑𝒚 𝟐 𝒅𝝉 = 𝟏 𝒔𝒑𝒅𝝉 = 𝟎, 𝒑𝒙 𝒑𝒚 𝒅𝝉 = 𝟎 similarly for other
p orbitals.
𝒉𝟏 = 𝒔 + 𝒑𝒙 + 𝒑𝒚 + 𝒑𝒛
𝒉𝟐 = 𝒔 − 𝒑𝒙 − 𝒑𝒚 + 𝒑𝒛
(𝒔 + 𝒑𝒙 + 𝒑𝒚 + 𝒑𝒛 ) (𝒔 − 𝒑𝒙 − 𝒑𝒚 + 𝒑𝒛 ) 𝑑𝜏 = 0

| sp3 hybrid lobes do not overlap each other

 9B: Molecular Orbital Theory:
Homonuclear diatomics
• Molecular Orbitals (MO) are formed when
electrons spread through entire molecule.
• Single electron H2+ ion:
𝜓 = 𝑐𝐴 𝜓𝐴 + 𝑐𝐵 𝜓𝐵
(𝐿𝑖𝑛𝑒𝑎𝑟 𝑐𝑜𝑚𝑏𝑖𝑛𝑎𝑡𝑖𝑜𝑛 𝑜𝑓 𝑎𝑡𝑜𝑚𝑖𝑐 𝑜𝑟𝑏𝑖𝑡𝑎𝑙𝑠
− 𝐿𝐶𝐴𝑂)
Squares of the coefficients cA and cB
relative proportions of A and B contribution
to MO.
 Valence Bond Theory: Summary
• The names of bond types: σ and π bond
formation
• Hybridization: promotion of valence
electrons to empty orbitals so that there is
a lowering of energy
• Resonance: the superposition of individual
structures towards minimizing total energy.
 LCAO for homonuclear diatomics
• Homonuclear diatomic molecule:
𝜓 = 𝜓𝐴 ± 𝜓𝐵 Molecular wavefunction
without normalization constant.
(since 𝒄𝑩 = ±𝒄𝑨 )
 Bonding MO Wavefunction
• Amplitude is enhanced in between nuclei.
So there is an increased probability of
finding bonding electrons in that region.
Bonding region
 Bonding and Antibonding MO
• BONDING MO ANTIBONDING MO
• Example Problem: Distinguish between
MO and Antibonding MO in terms of
electron density in the bonding region.
 Depletion of Electron density in
Antibonding MO
• There is a decreased probability of finding
the bonding electron in between nuclei.
 Assigning Symmetry to Bonding and
Antibonding MO
• Gerade (g: even) for bonding MO and
ungerade for antibonding MO (u: odd) –
Symmetry notation (Not applicable to
heteronuclear diatomics)
 MO: ground-state electronic
configuration
• H2 Molecule: 1𝜎𝑔2
• He2 Molecule: 1𝜎𝑔2 1𝜎𝑢2 (unstable with respect
He atom as bond order = 0).
1
• 𝐵𝑜𝑛𝑑 𝑜𝑟𝑑𝑒𝑟: 𝑏 = (𝑁 − 𝑁 ∗)
2
• Li2 molecule:
 Li atom: 1𝑠 2 2𝑠1 . Considering only valence
electron for ground-state MO
 1𝜎𝑔2
MO: Writing electronic configuration

Step1: LCAO of valence atomic orbitals

N number of atomic orbitals result in N
number of MO’s.
Step 2: Accommodate valence electrons in
MO as per Pauli principle.
Step 3: For degenerate MO levels
electrons are filled in each orbital as per
Hund’s rule.
 MO: Examples of electronic
configuration
• N2 :1𝜎𝑔2 1𝜎𝑢2 1𝜋𝑢4 2𝜎𝑔2 from each N atom of
valence electronic configuration 2𝑠 2 2𝑝3 .
1
𝑏= 8−2 =3
2
• O2: 1𝜎𝑔2 1𝜎𝑢2 2𝜎𝑔2 1𝜋𝑢4 1𝜋𝑔2
from each O atom of
valence electronic configuration 2𝑠 2 2𝑝4
1
𝑏 = 8−4 =2
2
 Example Problem: What are the bond orders
of N2+ and O2 + species?
 MO Diagrams
• MO from 1s orbitals: (MO according to the
symmetry notation is indicated in boxes in the
diagram).

1σu

1σg
 MO Diagrams
• H2 molecule: (MO according to the symmetry
notation is indicated in boxes in the diagram).

1σg2
 MO Diagrams
• He2 molecule (unstable):
• MO according to the symmetry notation is
indicated in boxes in the diagram

1σu2

1σg2
 MO Diagrams
• Two p orbitals overlap along the internuclear z axis to
form σ MO.

2σu

2σg

• 𝜓 = 𝑐1 𝜓𝐴2𝑠 + 𝑐2 𝜓𝐵2𝑠 + 𝑐3 𝜓𝐴2𝑝𝑧 + 𝑐4 𝜓𝐵2𝑝𝑧

(Mixing in MO’s: Molecular orbital wavefunction formed
by linear combination of 2s and 2p orbitals of A and B).
 MO Diagrams
• π-MO Molecular Orbital formation and
symmetry notation
 MO Diagrams
• O2 Molecule:
 MO Diagrams
• N2 Molecule:
 MO Diagrams
• The variation of energy levels of MO of
period 2 diatomic molecules:
 Trend in calculated MO levels
• The relative order of the energy of σ and π
depends on energy separation between 2s
and 2p orbitals.
• For example: MO energy level sequence is:
Up to and including N2 :
1𝜎𝑔 < 1𝜎𝑢 < 𝟏𝝅𝒖 < 𝟐𝝈𝒈 < 1𝜋𝑔 < 2𝜎𝑢
For O2 , F2 :
1𝜎𝑔 < 1𝜎𝑢 < 𝟐𝝈𝒈 < 𝟏𝝅𝒖 < 1𝜋𝑔 < 2𝜎𝑢
 MO Orbitals: Symmetry criteria for
orbital overlap
Fig.1(a) (in this slide): σ-bond along
internuclear axis z Fig. 2 (in this slide)

• Example Problem: Assign appropriate parity

symbols (g or u) for Fig.2.
 MO Orbitals: Symmetry criteria for
orbital overlap
• Overlap along the internuclear axis and
side-on overlap involving d orbitals
 Electronic configuration of Period 2
homonuclear diatomics
• Summary of steps in writing electronic
configuration:
 Add the appropriate number of electrons to
the orbitals.
 Charged species: either add or remove
electrons from the appropriate MO and
estimate bond order. (no longer ground state)
 The higher the bond order, the larger the
bond dissociation energy.
 Example Problem: Write the electronic
configuration of F2.
 Criteria for building MO of
homonuclear diatomics
• Use all valence orbitals from both atoms.
• Consider only atomic orbitals of similar
energies and of same symmetry along the
internuclear axis for σ bond.
• Build σ and π orbitals from all atomic
orbitals of a given symmetry.
• Fill the electrons in MO as per Hund’s rule
and Pauli’s exclusion principle.
 9C: MO Theory of heteronuclear
diatomics
• Hetero nuclear diatomic molecule: is a diatomic
molecule formed from atoms of different elements.
e.g.: CO, HCl
• Polar bond: The electron distribution is not
symmetrical.
• 𝜓 = 𝑐𝐴 𝜓𝐴 + 𝑐𝐵 𝜓𝐵 general LCAO
• Polar bond: if 𝑐𝐵2 > 𝑐𝐴2 electrons are close to B.
 Example Problem: For a pure ionic bond A+B- ,
what is the criteria in terms of coefficients?
 MO diagrams of heteronuclear
diatomics
• Electronegativity of Atoms and MO diagram: (𝜒)
(Note: Discussion on Electronegativity scales is not included)
For a chemical bond A-B where
 Bonding orbitals: 𝜒𝐵 >𝜒𝐴 , 𝑐𝐵2 > 𝑐𝐴2
 MO diagrams of heteronuclear
diatomics: HF
• MO orbitals of HF
𝜓 = 𝑐𝐻 𝜓𝐻 + 𝑐𝐹 𝜓𝐹 where 𝜓𝐻 is an H 1s
orbital and 𝜓𝐹 is an F 2pz orbital.
 MO diagrams of heteronuclear
diatomics: CO
• Ground-state electronic configuration of CO:
1𝜎 2 2𝜎 2 1𝜋 4 3𝜎 2
(No parity symbol since CO is heteronuclear)
 Lowest energy molecular orbitals are of O
character as that is the more electronegative
element.
 Highest occupied MO (HOMO) is 3𝜎
 Lowest uncoccupied MO (LUMO) is 2𝜋
MO diagrams of heteronuclear
diatomics: CO
Summary of Equations

For a single electron MO:

e.g, H2+