Atomic and Molecular structure

Dr.Omkaramurthy B M
MSc.PhD

Molecular orbital (MO: Atoms join to form molecules. When two atoms move closer
together to form a molecule, atomic orbitals overlap and combine to become molecular
orbitals.
Molecular orbitals are regions around molecules where electrons are most likely to be found.
The number of newly formed molecular orbitals is equal to the number of combined atomic
orbitals. The molecular orbital surrounds the two nuclei of the atoms, and electrons can move
around both nuclei. Similar to atomic orbitals, molecular orbitals maximally contain 2
electrons, which have opposite spins. Molecular orbitals are of two types, bonding molecular
orbitals and antibonding molecular orbitals. Bonding molecular orbitals contain electrons in
the ground state and antibonding molecular orbitals contain no electrons in the ground state.
Electrons may occupy in the antibonding orbitals if the molecule is in the excited state.

Differences between Atomic and Molecular Orbital

Atomic orbital Molecular orbital

Atomic orbital is the region having the Molecular orbital is the region having the
highest probability of finding an electron in an highest probability of finding an electron of
atom a molecule
Atomic orbitals are inherent property of an atom. Molecular orbitals are formed by combination of
atomic orbitals that have nearly the same
Formed by the electron cloud around the
energy
atom
The shape is determined by the type of The shape is determined by the shapes of
atomic orbital(s,p,d or f) atomic orbitals that make the molecule.
Theyhave complex shapes.
Schrodinger equation is used Linear combination of atomic
orbitals(LCAO) is used
Monocentric as it is found around a single Polycentric as it is found around
reaction different nuclei

Molecular Orbital Theory

Valence Bond Theory fails to answer certain questions like Why He 2 molecule does not exist
and why O2 is paramagnetic Therefore in 1932 F. Hood and RS. Mulliken came up with
theory known as Molecular Orbital Theory to explain questions like above. According to
Molecular Orbital Theory individual atoms combine to form molecular orbitals, as the
electrons of an atom are present in various atomic orbitals and are associated with several
nuclei.
Molecular orbital (MO) theory is a method for determining molecular structure in which
electrons are not assigned to individual bonds between atoms, but are treated as moving
under the influence of the nuclei in the whole molecule.

Postulates of MOT :
 Two atoms come together, interact and forms a bond. All the atomic orbitals on either
nuclei mix together to form a new orbital called molecular orbital.
 The molecular orbitals are formed by mixing of the atomic orbitals of same energy
level and symmetry.
 After formation of molecular orbital, the atomic orbitals lose their identity.
 Each and every electron in the molecular orbital belongs to all the nuclei of the
molecules.
 Atoms have atomic orbitals with one nuclei and Molecules have molecular orbitals
with n nuclei. Thus, atoms are monocentric while molecules are polycentric.
 The number of molecular orbitals formed is equal to the atomic orbitals mixing.
 Molecular orbitals can be bonding, anti-bonding, and non-bonding orbitals.
 Bonding molecular orbitals are lower in energy than the corresponding anti-bonding
orbitals.
 Each molecular orbital is described by a wave function Ψ, which in turn is associated
with a set of quantum number.
 Electrons fill up these orbitals in the same way as atomic orbitals in accordance to the
3 principles (Aufbau, Hunds and Pauli Principle).
 The Aufbau principle states that orbitals are filled with the lowest energy first.
 The Pauli exclusion principle states that the maximum number of electrons occupying
an orbital is two, with opposite spins.
 Hund’s rule states that when there are several MOs with equal energy, the electrons
occupy the MOs one at a time before two occupy the same MO.
Electrons may be considered either of particle or of wave nature. Therefore, an electron in an
atom may be described as occupying an atomic orbital, or by a wave function Ψ, which are
solution to the Schrodinger wave equation. Wave function is a mathematical function
related to probability of finding the particle in a particular region of space.
Electrons in a molecule are said to occupy molecular orbitals. The wave function of a
molecular orbital may be obtained by one of two methods:
1. Linear Combination of Atomic Orbitals (LCAO).
2. United Atom Method.
Linear Combination of Atomic Orbitals (LCAO)
As per this method the formation of orbitals is because of Linear Combination (addition or
subtraction) of atomic orbitals which combine to form molecule. Consider two atoms A and
B which have atomic orbitals described by the wave functions ΨA and ΨB .If electron cloud
of these two atoms overlap, then the wave function for the molecule can be obtained by
a linear combination of the atomic orbitals ΨA and ΨB i.e. by subtraction or addition of wave
functions of atomic orbitals
ΨMO= ΨA + ΨB
The above equation forms two molecular orbitals

Bonding Molecular Orbitals

When addition of wave function takes place, the type of molecular orbitals formed are called
Bonding Molecular orbitals and is represented by
ΨMO = ΨA + ΨB.
They have lower energy than atomic orbitals involved. It is similar to constructive
interference occurring in phase because of which electron probability density increases
resulting in formation of bonding orbital. Molecular orbital formed by addition of
overlapping of two s orbitals shown in Figure 1. It is represented by s.

Anti-Bonding Molecular Orbitals

When molecular orbital is formed by subtraction of wave function, the type of molecular
orbitals formed are called Antibonding Molecular Orbitals and is represented by
ΨMO = ΨA - ΨB.
They have higher energy than atomic orbitals. It is similar to destructive
interference occurring out of phase resulting in formation of antibonding orbitals. Molecular
Orbital formed by subtraction of overlapping of two s orbitals are shown in figure no. 2. It is
represented by σ* (*) is used to represent antibonding molecular orbital) called Sigma
Antibonding.
 Fig. 1 Formation of Bonding and Anti-Bonding Orbital
Therefore, Combination of two atomic orbitals results in formation of two molecular orbitals,
bonding molecular orbital (BMO) whereas other is anti-bonding molecular orbital (ABMO).
BMO has lower energy and hence greater stability than ABMO. First BMO are filled then
ABMO starts filling because BMO has lower energy than that of ABMO.
Formation of molecular orbitals occurs by the combination of atomic orbitals of proportional
symmetry and comparable energy. Therefore, a molecular orbital is polycentric and atomic
orbital is monocentric. Number of molecular orbitals formed is equal to the number of atomic
orbitals.

Relative Energies of Molecular Orbitals

Bonding Molecular Orbitals (BMO) - Energy of Bonding Molecular Orbitals is less than
that of Anti Bonding Molecular Orbitals because the attraction of both the nuclei for both the
electron (of the combining atom) is increased.
Anti-Bonding Molecular Orbitals (ABMO) - Energy of Anti Bonding Molecular Orbitals is
higher than Bonding Molecular Orbitals because the electrons move away from the nuclei
and are in repulsive state.
The Energies of Bonding Molecular Orbitals and Anti-Bonding Molecular Orbitals are shown
in Fig 2 :

Fig: 2
Molecular orbitals of diatomic molecules:
Molecular Orbitals for diatomic Molecules formed from a Linear Combination of Atomic
Orbitals is shown below:

Filling Electrons in MO Diagrams

The next step in constructing an MO diagram is filling the newly formed molecular orbitals
with electrons. Three general rules apply:
 The Aufbau principle states that orbitals are filled starting with the lowest energy
 The Pauli exclusion principle states that the maximum number of electrons. occupying
an orbital is two, with opposite spins.
 Hund’s rule states that when there are several MOs with equal energy, and the
electrons occupy the MOs one at a time before two occupy the same MO.

The filled MO that is highest in energy is called the Highest Occupied Molecular Orbital, or
HOMO; the empty MO just above it is the Lowest Unoccupied Molecular Orbital, or LUMO.
The electrons in the bonding MOs are called bonding electrons, and any electrons in the
antibonding orbital are called antibonding electrons. The reduction these electrons’ energy is
the driving force for chemical bond formation.
 Energy Level Diagram
The factors upon which relative energies of molecular orbitals depend are:
(i) Energies of the Atomic orbitals combining to form Molecular Orbitals.
(ii) The extent of overlapping between the atomic orbitals. The greater the overlap, the more the
bonding orbital is lowered and the anti-bonding orbital is raised in energy relative to AOs
1s Atomic Orbitals (AOs) of two atoms form two Molecular Orbitals (MOs) designated as σ 1s and
σ *1s.The 2s and 2p orbitals (eight AOs of two atoms) form four bonding MOs and four anti-bonding
MOs as:
Bonding MOs: σ 2s, σ 2pz, π 2px, π 2py
Anti – Bonding MO: σ *2s, σ *2pz, π *2px, π *2py
The order of increasing energy of molecular orbitals obtained by combination of 1s, 2s and
2p orbitals of two atoms is →
σ1s, σ *1s, σ 2s, σ *2s, σ 2pz, π 2px = π 2py, π *2px= π *2py, σ *2pz
(Energy Increases from left to right)

Bond order:
It may be defined as the half of difference between the number of electrons present in thebonding
orbitals and the antibonding orbitals that is,
Bond order (B.O.) = (No. of electrons in BMO - No. of electrons in ABMO)/ 2
Those with positive bonding order are considered stable molecule while those with negativebond order or
zero bond order are unstable molecule.

Magnetic Behavior: If all the molecular orbitals in species are spin paired, the substance is
diamagnetic. But if one or more molecular orbitals are singly occupied it is paramagnetic.

BONDING IN SOME HOMONUCLEAR DIATOMIC MOLECULES

1. Hydrogen molecule (H2 ): It is formed by the combination of two hydrogen atoms. Each hydrogen
atom has one electron in 1s orbital. Therefore, in all there are two electrons in hydrogen molecule
which are present in σ1s molecular orbital.

Electronic configuration of H2 : (σ1s)2

The bond order of H2 molecule can be calculated as given below:
Bond order of H2 is Bond order (b.o.) = ½ ( Nb –Na )
= ½(2 – 0) = 1
This means that the two hydrogen atoms are bonded together by a single covalent bond.
There is no unpaired electron is present in hydrogen molecule, therefore, it is diamagnetic.

2. Helium molecule (He2 ): The electronic configuration of helium atom is 1s2 . Each helium atom contains
2 electrons, therefore, in He2 molecule there would be 4 electrons.

These electrons will be accommodated in σ1s and σ*1s molecular orbitals leading to electronic
configuration:
He2 : (σ1s)2 (σ*1s)2
Bond order of He2 = ½(2 – 2) = 0
He2 molecule is therefore unstable and does not exist.

3. Lithium molecule (Li2 ):

The electronic configuration of lithium is 1s 2, 2s1 . There are six electrons in Li .
The electronic configuration of Li2 molecule, therefore, is Li 2 : (σ1s) 2 (σ*1s)2 (σ2s)2

The above configuration is also written as

KK(σ2s)2 where KK represents the closed K shell structure (σ1s) 2 (σ*1s)2.
From the electronic configuration of Li2 molecule it is clear that there are four electrons present in bonding
molecular orbitals and two electrons present in antibonding molecular orbitals.
Bond order = ½ (4 – 2) = 1.
It means that Li2 molecule is stable and since it has no unpaired electrons it should be diamagnetic. Indeed
diamagnetic Li2 molecules are known to exist in the vapour phase.

4. Molecular orbital energy level diagram of Nitrogen molecule (N2)

The electronic configuration of nitrogen atom is 1s2 2s2 2p 1 2 1 2p

x
1
yand N
z molecule
2 has 14electrons.
The Molecular orbital diagram is shown in Fig. 3

The molecular orbital electronic configuration of the molecule is:

Bond order of N2 = ½ (10-4) =3

Molecular orbital energy level diagram of N2

Thus, nitrogen molecule has three bonds, one σ and two π-bonds. This is in accordance with very high
bond dissociation energy (945 kJ mol-1) and small bond length (110 pm) of the molecule. The molecule
has no unpaired electrons and therefore it is diamagnetic.
 5. Molecular orbital energy level diagram of Oxygen molecule (O2)
Oxygen atom has electronic configuration of is 1s2 2s1 2p 2 2 1 2p 1 Therefore,
x y zoxygen molecule has 16

electrons. In the formation of molecular orbitals, the electrons in the inner shells are expressed as KK
denoting (σ1s) 2(σ*1s) 2. The remaining 12 electrons are filled in molecular orbitals as shown in figure
4 For O2

σ1s, σ *1s, σ 2s, σ *2s, σ 2pz, [π2px = π2py], [π*2px= π*2py], σ *2pz

The electronic configuration of the molecule is

O2 : KK (σ2s)2 < (σ*2s)2 < (σ2pz)2 < (Л 2px)2=(Л2py)2 < (Л*2px)1= (Л*2py)1

Bond Order O2 = ½ (10-6) =2

Molecular orbital energy level diagram of O2

Thus, oxygen molecule has two bonds one σ and one π Further, in accordance with Hund’s rule, the
last two electrons in π*2px and π*2py orbitals will remain unpaired. Therefore, the molecule has
paramagnetic character due to the presence of two unpaired electrons. These facts are in accordance
with experimental observations. The bond dissociation energy in O2 molecule is 498 kJ mol-1and
bond length is 121 pm.
6. O2+
Covalent Bond
Langmuir (1919) refined the Lewis postulations by abandoning the idea of the stationary cubical
arrangement of the octet, and by introducing the term covalent bond.
The bond formed by mutual sharing of two electrons between two atoms having comparable
electronegativity, each atom contributing one electron is called covalent bond.
Eg: The formation of the chlorine molecule, (Cl2).
The Cl atom with electronic configuration, [Ne]3s3p5, is one electron short of the argon configuration.
The formation of the Cl2 molecule sharing of a pair of electrons between the two chlorine atoms, each
chlorine atom contributing one electron to the shared pair. In the process both chlorine atoms attain the
outer shell octet of the nearest noble gas (i.e., argon).
The dots represent electrons. Such structures are referred to as Lewis dot structures

Double bonds in CO2 molecule:

Triple bond in Ethyne molecule.

Ionic or Electrovalent bond
The electrostatic force of attraction which holds two oppositely charged ions formed by the complete
transfer of one or more electrons from electron positive atom to electron negative atom is called Ionic bond.

Example:

Na Na+ + e- [Ne] 3s1 [Ne]

Cl + e– Cl– [Ne] 3s2 3p5 [Ne] 3s2 3p6 or [Ar]

Metallic Bonding:
The force that hold the atoms of pure metal together in a crystal as a result of the attraction between
positive ions and surrounding freely mobile delocalized electrons is known as metallic bond.
BAND THEORY OF SOLIDS
Band theory is extension of Molecular orbital theory of covalent bonds to solids.
Salient features of Band theory:
 Solids are made up of giant molecules in which a large number of spherical atoms are arranged in
a regular close-packed pattern.
 When atoms are brought together in solids, the atomic orbitals of the valency shells interact
forming molecular orbitals.
 During their interaction, their outer shells constitute one single system of electrons, common to
entire array of atoms in a crystal.
 Let us take an example of lithium with electronic configuration

1S2 2S1 2P0

 In Li2 molecule- 2S1 electrons from two Li atoms combine to form one Bonding, σ2S2 and
antibonding orbital, σ*2S0.

 Similarly in Lin molecule, n number of atomic orbital (2S of each lithium atom) combine to form a
cluster of molecular orbital which are closely placed to each other. Each original energy level
becomes a band of very closely spaced levels of small energy differences.

 Depending upon the composition of solids, bands are of two types-

a) Overlapping bands- Higher band overlap with empty lower band.
Eg:- Valence 2S band overlap with empty 2P band in Beryllium.
b) Non-overlapping bands- Higher band do not overlap with lower band.
Eg:- Valence 3S band do not overlap with empty 3P band in Sodium.
The band of energy levels occupied by valence electrons is called Valence Band.
It may be
a) Partially filled with electrons. Eg:- Na, Cu
b) Completely filled with electrons. Eg:- Be, Mg
 The next higher permitted band above the valence band is called Conduction band. The
conduction band may be empty or partially filled with electrons which are also called as free-
electrons.
 The gap between the valence band and conduction band is called Forbidden gap.
The width of the forbidden gap is called Energy gap (Eg).
Depending on the Eg, solids are classified into three types.
a) Conductors
b) Insulators
c) Semi-conductors
d)
Conductors- In these materials, the energy gap is almost negligible.
a) When a potential is applied to the half-filled valence band, the free electrons get excited to the empty
conduction band and they begin to conduct. Eg:- Na, Al etc.
b) In elements like Mg, conduction is mainly due to overlapping of filled valence band with higher empty
band.
c) Electrical conductivity of a metals decreases with rise in temperature because of the increased thermal
vibrations of metal atoms which causes scattering of the electrons. Hence their flow is obstructed.

E
Conductors

Insulators- In these materials, the energy gap is or order 5-10eV.

a) In insulators, the valence band electrons are tightly bound to their parent nuclei and require large
amount of electric fields to remove electrons to conduction band.
b) They possess a complete valence band and completely empty conduction band.
c) Eg:- Diamond, glass, solid NaCl, Plastics, ceramics etc.
d) Electrical conductivity increases with increase in temperature. At room temperature, they act as best
insulating materials. At higher temperatures, some of the valence electrons acquire sufficient energy to
overcome the energy gap and enter the conduction band

E Insuators
 Semiconductors- In these materials, the energy gap is of order of 1 eV.
a) Solids having electrical conductivity in between those of insulators and conductors are called
semiconductors.
b) They have filled valence band, almost empty conduction band. Eg:- Si, Ge.
c) Electrical conductivity increases with increase in temperature. The probability of promotion of
electrons from valence band to conduction band decreases with the energy gap and increases with
temperature

Semiconducors

CLASSIFICATION OF SEMICONDUTORS
SEMICONDUCTORS
 Semiconductors are materials with electrical conductivities that are intermediate between those of
conductor’s and insulators.
 They acts as insulators at very low temperature, but acts as sizable electrical conductors at room
temperature.
 The width of band gap in semiconductors is intermediate to that of insulators and conductors.
 They are used for electronic purposes as they can carry an electric current by electron migration or
hole propagation.
 The resistance of semiconductors decreases with increase in temperature- negative temperature
coefficient of resistance.
 The resistibility is less than an insulator but more than a conductor.
 When a suitable metallic impurity e.g., arsenic, germanium, gallium, etc is added to a semi-
conductor, its current conducting properties change appreciably.
Semiconductors are classified into the following types-
1. Intrinsic semiconductors
2. Extrinsic semiconductors
a) n-type semiconductors
b) p-type semiconductors
3. Organic semiconductors
1. Intrinsic semiconductors
These semiconductors are pure enough that impurities do not appreciably affect its electrical behavior.
Elements like Silicon, germanium, selenium acts as intrinsic semiconductors which have four valence
electrons in their atoms and their band gap is about 1ev.
Conduction Process:-
 When an electron from the valence band is ejected, a covalent bond is broken and a positively
charged hole is left in the valence band.
 The hole travels to an adjacent atom by accepting an electron from the latter one.
 This forms a new covalent bond and breaks an existing covalent bond by filling up the previous
hole and creating a new hole.
 When electric field is applied, electrons in the conduction band move to the anode and positively
charged hole moves to cathode.
 Hence current is produced due to simultaneous movement of conduction band electrons and
valence bond holes in opposite directions.

2. Extrinsic semiconductors-
Intrinsic semiconductors when added with extremely small amount of substitutional impurities (doping)
are called extrinsic semiconductors. On adding a doping agent, the energy gap gets reduced and makes the
electron flow easy from valence band to conduction band. The conductivity increases by 10,000 times.
Based on the doping agent added, extrinsic semiconductors are classified into two types:-
i) n-type semiconductors-
 These semiconductors contain a small quantity of a penta valent element impurity (like
phosphorous, arsenic or antimony).
 The doping atom forms four covalent bonds with the surrounding four atoms of intrinsic
semiconductor (Germanium, Silicon etc) with the help of its four valence electrons.
 The fifth excess electron remains loosely bound to the donor atom itself. It is easily excited from
the valence band to conduction band on applying electric field.
 Thus conduction is due to movement of extra electron in an n-type semiconductor.

ii) p-type semiconductors

 They contain a small quantity of a trivalent element (like boron, aluminium).
 The three valence electrons present in the trivalent impurity forms three covalent bonds with the
surrounding three of the four atoms. So that one bond in one of the four surrounding atom is left
incomplete.
 This gives rise to a positive hole.
 On applying an electric field, a hole travels to an adjacent atom by acquiring an electron and
establishes a new covalent bond, by breaking an existing covalent bond in the adjacent atom.
 Hence conductivity in p-type semiconductors is due to the movement of positive holes.
3. ORGANIC SEMICONDUCTORS
Organic semiconductors are conjugated organic polymer materials having very high
conductivity.These materials have intrinsic semi-conductivity with an energy gap of 1.0- 2.0
eV.
Conjugated Organic Polymers-

Polyacetylene.

Polyphenylene.

They become more conducting on doping with oxidizing or reducing agents.

If the dopant used is a Lewis acid like AlCl3, I2, FeCl3 or oxidizing agent or electron with
drawinggroup etc. then obtained semiconductor is called p- type semiconductor.
If the dopant used is a Lewis base like NH3, H2O or reducing agent or electron donating
group etc.then obtained semiconductor is called n- type semiconductor.
Conducting process-
 Electron is removed from the valence band by oxidation of the conjugated polymer due
to which avacancy (cation radical) equivalent to hole is formed.
 This partially delocalized cation radical, delocalized over a few monomer units, is called
Polaran-Breaking of two conjugated bonds and formation of a dispositive radical leads
to bipolaran.
 Low doping gives a polaran and high doping gives a bipolaran.

-electron
Polyacetylene Polaran

-electron

bipolaran
The polarans and bipolarans are mobile under the influence of electric field.
They can move along the polymer chain as like electrons and holes move in inorganic
semiconductors.
Advantages of organic semiconductors-
 They are used in photovoltaic cells, electrode photo cells, electro-chromic and memory
devices.
 They are also used in communication devices.
