Atomic and Molecular Structure

Topics

• Fundamentals of atom, subatomic particles, atomic number

• mass number, atomic models, orbit and orbitals,
• Schrodinger equation. quantum mechanical model of atom.
Particle in a box - solutions and their applications.
• Significance of ψ and ψ2 orbital concept,
• quantum numbers, electronic configuration, periodic
properties.
• Formation of cation and anion by electronic concept of
oxidation and reduction, theories on bonding- Octet,
Sidgwick and Powell, VSEPR and VBT-MOT, Hybridization,
Shape of molecules.
Fundamentals of atom
Atomic Models: Atomic models were proposed to explain the distributions of these charged
particles in an atom.

Thomson Model of Atom J. J. Thomson, in 1898, proposed that an atom possesses a

spherical shape (radius approximately 10–10 m) in which the positive charge is uniformly
distributed. The electrons are embedded into it in such a manner as to give the most stable
electrostatic arrangement (Fig. 2.4). Many different names are given to this model, for
example, plum pudding, raisin pudding or watermelon.

An important feature of this model is that the mass of the atom is assumed to be uniformly
distributed over the atom. Although this model was able to explain the overall neutrality of
the atom, but was not consistent with the results of later experiments.
Rutherford’s Nuclear Model of Atom : Rutherford and his students (Hans Geiger and
Ernest Marsden) bombarded very thin gold foil with α–particles. The outcomes of
Rutherford’s famous α–α-particle scattering experiment are

(i) The positive charge and most of the mass of the atom was densely concentrated in
an extremely small region. This very small portion of the atom was called the nucleus
by Rutherford.

(ii) The nucleus is surrounded by electrons that move around the nucleus with a very
high speed in circular paths called orbits. Thus, Rutherford’s model of atom resembles
the solar system in which the nucleus plays the role of sun and the electrons that of
revolving planets.

(iii) Electrons and the nucleus are held together by electrostatic forces of attraction
 Limitation of Rutherford’s Nuclear Model of Atom

i. It does not account for the electron’s mass. Rutherford’s model cannot explain
why the electron does not fall into the nucleus due to the force of the nucleus’s
gravitational pull.

ii. Rutherford model does not account for the electron’s orbital motion.

iii. The Rutherford model does not account for the interaction between the electrons
and the nucleus.

iv. The Rutherford model does not account for the electron’s energy levels.
 The Bohr model

In 1915, Bohr postulated a number of general assumptions:

a) Atoms have ‘stationary states’ of definite total energy. In these stationary states,
the electrons do not radiate.
b) Emission or absorption of electromagnetic radiation occurs only in transitions
from one stationary state to another. The frequency of the electromagnetic
radiation is proportional to the energy difference of the two states, and the
constant of proportionality is Planck’s constant.
c) Classical physics describes the dynamical equilibrium of the atom in a stationary
state but does not describe transitions between stationary states.
d) The mean value of the kinetic energy of the electron–nucleus system is quantized.

For a circular orbit, Bohr pointed out that the quantization of kinetic energy was
equivalent to the angular momentum of the system being an integer multiple of ℏ.

The integer n is called the principal quantum number.

Atomic Number and Mass Number The presence of a positive charge in the
nucleus is due to the protons in the nucleus. As established earlier, the charge on
the proton is equal but opposite to that of the electron. The number of protons
present in the nucleus is equal to atomic number (Z ).
For example, the number of protons in the hydrogen nucleus is 1, and in the
sodium atoms, it is 11. Therefore, their atomic numbers are 1 and 11, respectively.
To keep electrical neutrality, the number of electrons in an atom is equal to the
number of protons (atomic number, Z ). For example, the number of electrons in
the hydrogen atom and sodium atom are 1 and 11, respectively.

Atomic number (Z) = number of protons in the nucleus of an atom = number of

electrons in a neutral atom

While the positive charge of the nucleus is due to protons, the mass of the nucleus, due to
protons and neutrons

Mass number (A) = number of protons (Z) + number of neutrons (n)

Quantum numbers are parameters that describe the distribution of electrons in the
atom and, therefore, their fundamental nature. There are four quantum numbers.

1. Principal quantum number (n) - Represents the main energy level, or shell,
occupied by an electron. It is always a positive integer, that is n = 1, 2, 3 ...

2. Secondary quantum number (l ) - Represents the energy sublevel, or type of

orbital, occupied by the electron. The value of l depends on the value of n such that l
= 0, 1, ... n-1. This number is sometimes also called azimuthal, or subsidiary.

3. Magnetic quantum number (ml ) - Represents the number of possible

orientations in 3-D space for each type of orbital. Since the type of orbital is
determined by l, the value of ml ranges between -l and +l such that ml = -l, ...0, ...+l.

4. Spin quantum number (ms ) - Represents the two possible orientations that an
electron can have in the presence of a magnetic field or in relation to another electron
occupying the same orbital. Only two electrons can occupy the same orbital, and they
must have opposite spins. When this happens, the electrons are said to be paired. The
allowed values for the spin quantum number ms are +1/2 and -1/2.
The quantum numbers provide us with a picture of the electronic arrangement in the
atom relative to the nucleus in terms of probability distributions and potential energy
levels. As the potential energy of a system increases, the system’s stability is more
easily disrupted.
Orbit and orbital

An orbit, as proposed by Bohr, is a circular path around the nucleus in which an electron
moves. A precise description of this path of the electron is impossible according to
Heisenberg’s uncertainty principle.

An atomic orbital, on the other hand, is a quantum mechanical concept and refers to the
one-electron wave function ψ in an atom. It is characterized by three quantum numbers (n,
l and ml ) and its value depends upon the coordinates of the electron.
Shapes of Atomic Orbitals The orbital wave function or ψ for an electron in an atom
has no physical meaning. It is simply a mathematical function of the coordinates of the
electron. However, for different orbitals, the plots of corresponding wave functions as a
function of r (the distance from the nucleus) are different.

It may be noted that for 1s orbital , the probability density is maximum at the nucleus,
and it decreases sharply as we move away from it. On the other hand, for 2s orbital, the
probability density first decreases sharply to zero and again starts increasing. The region
where this probability density function reduces to zero is called nodal surface or simply
nodes. In general, it has been found that ns-orbital has (n – 1) nodes,
Each p orbital consists of two sections called
lobes that are on either side of the plane and
pass through the nucleus. The probability
density function is zero on the plane where the
two lobes touch each other. The size, shape,
and energy of the three orbitals are identical.
The five d-orbitals are designated as dxy , dyz ,
dxz , dx2–y2 and dz2. The shapes of the first
four d-orbitals are similar to each other, where
as that of the fifth one, dz2, is different from
others, but all five 3d orbitals are equivalent in
energy. The d orbitals for which n is greater
than 3 (4d, 5d...) also have shapes similar to 3d
orbital, but differ in energy and size.
The Aufbau principle: This rule makes reference to the process of building an atom
from the ground up. That is to say, the manner in which electrons are placed in the
atom one by one. We start by placing the first electron at the lowest potential energy
level, which is the 1s orbital, and then following with the rest of the electrons always
placing them at the lowest available level of potential energy. In other words,
electrons always go into orbitals with the lowest possible energy.

Hund’s rule says that when electrons go into degenerate orbitals, they occupy them
singly before pairing begins.

Pauli exclusion principle states that only electrons with opposite spins can occupy
the same orbital. In other words, if two electrons must go into the same orbital, they
must be paired.
Arrangement of Orbitals with Increasing Energy on the Basis of (n+l) Rule
Electronic Configuration of Atoms: The distribution of electrons into orbitals of an atom
is called its electronic configuration.

The electrons in the completely filled shells are known as core electrons and the
electrons that are added to the electronic shell with the highest principal quantum
number are called valence electrons.
Stability of Completely Filled and Half Filled Subshells

1. Symmetrical distribution of electrons: It is well known that symmetry leads to

stability. The completely filled or half-filled subshells have a symmetrical distribution
of electrons in them and are, therefore, more stable. Electrons in the same subshell have
equal energy but different spatial distributions. Consequently, their shielding of one
another is relatively small, and the electrons are more strongly attracted by the nucleus.

2. Exchange Energy: The stabilizing effect arises whenever two or more electrons with
the same spin are present in the degenerate orbitals of a subshell. These electrons tend
to exchange their positions and the energy released due to this exchange is called
exchange energy. The number of exchanges that can take place is maximum when the
subshell is either half-filled or completely filled. As a result, the exchange energy is
maximum, and so is the stability.
Atomic Radius

The atomic radius of an element is half of the distance between the centers of two atoms of
that element that are just touching each other. Generally, the atomic radius decreases across
a period from left to right and increases down a given group. The atoms with the largest
atomic radii are located in Group I and at the bottom of groups.

Moving from left to right across a period, electrons are added one at a time to the outer
energy shell. Electrons within a shell cannot shield each other from the attraction to protons.
Since the number of protons is also increasing, the effective nuclear charge increases across
a period. This causes the atomic radius to decrease.

Moving down a group in the periodic table, the number of electrons and filled electron
shells increases, but the number of valence electrons remains the same. The outermost
electrons in a group are exposed to the same effective nuclear charge, but electrons are
found farther from the nucleus as the number of filled energy shells increases. Therefore, the
atomic radii increase.
Ionization Energy

The ionization energy, or ionization potential, is the energy required to remove an

electron from a gaseous atom or ion completely. The closer and more tightly bound an
electron is to the nucleus, the more difficult it will be to remove, and the higher its
ionization energy will be. The first ionization energy is the energy required to remove
one electron from the parent atom. The second ionization energy is the energy required
to remove a second valence electron from the univalent ion to form the divalent ion,
and so on.
Ionization energies increase moving from left to right across a period (decreasing
atomic radius). Ionization energy decreases moving down a group (increasing atomic
radius). Group I elements have low ionization energies because the loss of an electron
forms a stable octet.
Electronegativity

Electronegativity is a measure of the attraction of an atom for the electrons in a

chemical bond. The higher the electronegativity of an atom, the greater its
attraction for bonding electrons. In a group, the electronegativity decreases as the
atomic number increases, as a result of the increased distance between the
valence electron and nucleus (greater atomic radius). An example of an
electropositive (i.e., low electronegativity) element is cesium; an example of a
highly electronegative element is fluorine.
Electron Affinity

Electron affinity reflects the ability of an atom to accept an electron. It is the energy
change that occurs when an electron is added to a gaseous atom. Atoms with
stronger effective nuclear charge have greater electron affinity. Some
generalizations can be made about the electron affinities of certain groups in the
periodic table.

In a period, the halogen will have the highest electron affinity, while the noble
gas will have the lowest electron affinity. Electron affinity decreases moving down
a group because a new electron would be further from the nucleus of a large atom.
The Valence Shell Electron Pair Repulsion (VSEPR) theory is a simple and
useful way to predict and rationalize the shapes of molecules. The theory is based
on the idea of minimizing the electrostatic repulsion between electron pairs, as first
proposed by Sidgwick and Powell in 1940.

The molecular geometry is deduced from the electronic geometry by considering

the lone pairs to be present but invisible.

To use the VSEPR mode,

i. Determine the number of lone pairs on the central atom in the molecule, and
add the number of bonded atoms (a.k.a. bonding domains).
ii. This number (the steric number) defines the electronic shape of the molecule
by minimizing repulsion. For example a steric number of three gives a trigonal
planar electronic shape.
iii. The angles between electron domains are determined primarily by the
electronic geometry (e.g., 109.5° for a steric number of 4, which implies that
the electronic shape is a tetrahedron).
iv. These angles are adjusted by the hierarchy of repulsions: (lone pair - lone pair)
> (lone pair - bond) > (bond - bond)
 Valence bond theory

This theory is mainly due to Pauling. It deals with the electronic structure of the central
metal ion in its ground state, the kind of bonding, geometry, and magnetic properties of
the complexes.
Assumptions of valence bond theory :
1. The central metal atom or ion makes available a number of empty s, p, and d atomic
orbitals equal to its coordination number. These vacant orbitals hybridized together
to form hybrid orbitals which are the same in number as the atomic orbitals
hybridized together. These hybrid orbitals are vacant, equivalent in energy, and have
definite geometry.

– Hybridisation constructs new hybrid atomic orbitals from the AO’s

2. The ligands have at least one sigma orbital containing a lone pair of electrons.

3. Vacant hybrid orbitals of the metal atom or ion overlap with the filled (containing
lone pair of electrons) sigma-orbitals of the ligands to form ligand→ metal sigma-bond.
This bond is known as a coordinate bond and is a special type of covalent bond.
 QUANTUM MECHANICAL MODEL OF ATOM

Quantum mechanics is a theoretical science that deals with the study of the motions of
microscopic objects that have both observable wave-like and particle-like properties. It
specifies the laws of motion that these objects obey. When quantum mechanics is
applied to macroscopic objects (for which wave-like properties are insignificant), the
results are the same as those from classical mechanics.
Quantum mechanics was developed independently in 1926 by Werner Heisenberg and
Erwin Schrödinger

For a system (such as an atom or a molecule whose energy does not change with time)
the Schrödinger equation is written as Hψ = Eψ where H is a mathematical operator
called Hamiltonian. Schrödinger gave a recipe of constructing this operator from the
expression for the total energy of the system. The total energy of the system takes into
account the kinetic energies of all the sub-atomic particles (electrons, nuclei), the
attractive potential between the electrons and nuclei, and repulsive potential among the
electrons and nuclei individually. Solution of this equation gives E and ψ
Dual Behaviour of Matter: The French physicist de Broglie, in 1924, proposed that
matter, like radiation, should also exhibit dual behavior, i.e., both particle and
wavelike properties. This means that just as the photon has momentum as well as
wavelength, electrons should also have momentum as well as wavelength, de Broglie,
from this analogy, gave the following relation between wavelength (λ) and momentum
(p) of a material particle.

Heisenberg’s Uncertainty Principle: Werner Heisenberg, a German physicist in

1927, stated the uncertainty principle, which is the consequence of the dual behavior
of matter and radiation. It states that it is impossible to determine simultaneously, the
exact position and exact momentum (or velocity) of an electron.
 Particle in a 1D Box
First, we will consider a free particle moving in 1D so V (x) = 0
The wave function of 1D box after solving is,