ATOMIC STRUCTURE AND BONDING

STRUCTURE OF AN ATOM

Each atom consists of a very small nucleus composed of protons and neutrons, which is encircled
by moving electrons. Both electrons and protons are electrically charged, the charge magnitude
being 1.602 x10-19 C, which is negative in sign for electrons and positive for protons; neutrons are
electrically neutral.

Atomic number (Z) is the number of protons in the nucleus for characterizing each chemical
element.

Atomic mass (A) of a specific atom may be expressed as the sum of the masses of protons and
neutrons within the nucleus.

Isotopes are element with the same atomic number but different atomic mass due to varying
number of neutrons.

Electrons orbit the nucleus in shells or energy levels. Bohr suggested that when an electron
receives energy it move from lower to higher level within the shell. Conversely when it gave up
that energy it will fall back again to its former level (quantum theory).

Electrons surrounding the atomic nucleus are at different energy levels. Electrons are therefore
grouped into shells with different energy characteristics. The greatest number of electrons in a
given shell is 2n2 where n is known as the quantum number of the shell.

Pauli’s exclusion principle states that there are definite rules governing the energy levels and
probable position of electrons which are in orbit around an atom. This is against quantum shell
concept which suggests electrons within a shell are equal whereas in practice they are not.

All elements are classified according to electron configuration in a periodic table.

TYPES OF BONDS

All materials are made up of a collection of atoms held together by bonds.

The bonds formed depend on the electronic distribution of the individual atoms.

First Ionization Energy (IE); is the energy required to remove the most weakly bound (usually
outermost) electron from an isolated gaseous atom.

atom  g   IE  positive ion (g) + e-

This can be calculated using the energy of the outermost electron as given by the Bohr model and
Schr o dinger’s equation (in eV):
 13.6Z 2
IE 
n2

Where Z is the effective nuclear charge and n is the principle quantum number.

General trend in the periodic table is for the ionization energy to increase from bottom to top and
from left to right.

Electron Affinity (EA); is the reverse process to the ionization energy; it is the energy change
(often expressed in eV) associated with an isolated gaseous atom accepting one electron:

atom  g  + e-  negative ion (g)

The EA is positive if energy is released upon formation of the negative ion. If energy is required,
EA is negative. The general trend in the periodic table is again toward an increase in EA as we go
from the bottom to top, and left to right.

Atomic and Ionic Radii; in general, positive ions are smaller than neutral atoms, while negative
ions are larger.

Electronegativity (X); it is relationship of the electron affinity and ionization energy between two
atoms to measure the attraction an atom will have on the electrons in the bond formed. There are
several methods of calculating this energy. Based on scale developed by Mulliken
electronegativity is given by:

IE  EA
X
2

Electronegativity is very useful quantity to help categorize bonds, because it provides excess
binding energy between atoms. It also provides bond dissociation energy. The bond dissociation
energy is the energy required to separate two bonded atoms. The greater the electronegativity
difference, the greater the excess binding energy. These quantities give us a method of
characterizing bond types. More importantly, they relate to important physical properties, such as
melting point.

The bonds may be grouped into two main classes:

1. Primary bonds
a) Ionic bonds
b) Covalent bonds
c) Polar covalent
d) Metallic bonds
2. Secondary bonds
 a) Permanent dipole bonds
b) Molecular bonds
c) Vander Waals bonds

1. PRIMARY BONDS

These are due to exchange or sharing of electrons by atoms and are therefore very strong. In the
exchange or sharing of electrons only the outer orbital shell of electrons are utilised.

a) Ionic bonds or heteropolar bond

These are formed by the electrostatic attraction between positive and negative ions. Electrons are
transferred from the more electropositive atom to a more electronegative atom e.g. NaCl. Ions are
formed when atoms gain or lose electrons. Ionic bonds usually result when the electronegativity
difference between two atoms in a diatomic molecule is greater than about 2.0.

b) Covalent bonds or homopolar bond

These are formed by the sharing of valence electrons driven by the need to complete outer orbital
shells of the atom (e.g. H-H). Covalent bonds are typically found in homonuclear diatomics such
as O2 and N2, though the atoms need not be the same to have similar electronegativities.
Electronegativity differences of less than about 0.4 characterize covalent bonds.

Covalent bonds are directional in nature due to the repulsion of electrons in separate bonds giving
rise to fixed angles between bonds. Polymeric materials typify this bond.

Coordination number is the number of covalent bonds that atoms may form with other atoms
e.g. carbon is 4.

c) Polar Covalent;

These are interatomic bonds that are partially ionic and partially covalent formed between two
atoms with an electronegativity difference of between 0.4 and 2.0. An example of a polar covalent
bond can be found in the molecule hydrogen fluoride, HF. The percent ionic character of the bond
can again be related to the electronegativities of the individual atoms:

 
%ionic character=100 1  exp 0.25  X A  X B  
2



Where: XA and XB are electronegativities of the respective elements. The larger the
electronegativity difference, the more ionic character the bond has.
 d) Metallic bonds

Metallic bond is found in an assembly of homonuclear atoms, such as copper or sodium. These
elements are of low electronegativity (usually found in the lower left region of the periodic table).
In metals the outer orbital shell electrons in an atom are shielded from the nucleus by inner orbital
shell electrons. The outer orbital shell electrons are therefore easily lost. These electrons become
“decentralized” and are shared by the core of positive nuclei. The resulting positive ions are held
together by the clouds of electrons resulting in non-directional bonds.

The clouds of electrons give metals the good electrical and thermo-conductivity and make the
material opaque (electrons absorb light photons). The atoms are not held rigidly in space and layers
of atoms are able to slide over each other therefore exhibiting ductility. Table 1 below illustrates
the different types of bonding and typical examples.

Table 1: Examples of substances with different interatomic bonding [1].

2. SECONDARY BONDS OR WEAK BONDS

a) Permanent Dipole bonds

When different atoms bond covalently, there is different electronegativity resulting in more
electronegative atom drawing the shared electron towards its nucleus. This induces a dipole in the
molecule e.g. HCL, H2O and NH3.

H  CL  H  CL
  dipole    

In essence, an electric dipole exists whenever there is some separation of positive and negative
portions of an atom or molecule. The bonding results from the coulombic attraction between the
positive end of one dipole and the negative region of an adjacent one.The greater the
electronegativity the greater is the dipole formed.

b) Van der Walls

These are fluctuating temporally dipole bonds. Electrons are in constant motion within the orbital
shell and at some instant the centres of the positive charges and the negative charges may not
coincide. This induces a weak dipole enabling the molecules to interact with other molecules.

Temporary dipoles are due to statistical irregularities in electron distribution (dispersion effect)
and are frequent in molecules formed of atoms with similar electro-negativities.

c) Hydrogen Bonding

This is the attraction between hydrogen in a highly polar molecule and the electronegative atom in
another polar molecule. In the water molecule, oxygen draws much of the electron density around
it, creating positively charged centers at the two hydrogen atoms. These positively charged
hydrogen atoms can interact with the negative center around the oxygen in adjacent water
molecules. Hydrogen bonding plays an important role in many biological and environmental
phenomena. It is responsible for causing ice to be less dense than water, an occurrence that allows
fish to survive at the bottom of frozen lakes.

BONDING FORCES AND ENERGIES

There are two types of forces which influence the type and nature of atomic bonding; Attractive
(FA) or Chemical Affinity and repulsive (FR), and the magnitude of each depends on the
separation or interatomic distance (r). The origin of an attractive force FA depends on the particular
type of bonding that exists between the two atoms. This attraction is due to the electrostatic force
between the nucleus and electron clouds of the separate atoms. It should make sense to you that
the attractive energy (EA) is inversely proportional to the separation distance, r; i.e., the further the
atoms are apart, the weaker the attraction:

a
EA   m
r

Where: a, is a constant and m is a constant with a value 1 for ions and 6 for molecules. Repulsive
forces arise from interactions between the negatively charged electron clouds for the two atoms
and are important only at small values of r as the outer electron shells of the two atoms begin to
overlap (primary constituents of this repulsive energy are nucleus–nucleus and electron–electron
repulsions). As with the attractive energy, the repulsive energy is inversely proportional to the
separation distance;

b
ER 
rn

Where: b and n are constants, the value of n known as repulsive exponent depend on the outer core
configuration of the atom.

The net force between the two atoms is just the sum of attractive and repulsive components:

FN  FA  FR

It is more convenient to work with potential energy than with forces. The mathematical
relationship between energy and force is given by:

E   Fdr

for atomic systems;

r
EN   FN dr


r r
EN   FAdr   FR dr
 

 E A  ER

in which EN, EA, and ER are respectively the net, attractive, and repulsive energies for two isolated
and adjacent atoms.
Figure 1 (a) The dependence of repulsive, attractive and net forces on interatomic separation for
two isolated atoms (b) The dependence of repulsive, attractive and net potential energies on
interatomic separation for two isolated atoms [2].
At equilibrium spacing ro the net force is zero and a state of equilibrium exists. In the plot between
EN, EA, and ER. The minimum point in the net energy curve corresponds equilibrium spacing, ro.
Furthermore, the bonding energy, for the two atoms, Eo corresponds to the energy at this
minimum point. It represents the energy that would be required to separate these two atoms to an
infinite separation.

The magnitude of this bonding energy and the shape of the energy–versus–interatomic separation
curve vary from material to material, and they both depend on the type of atomic bonding.
Furthermore, a number of material properties depend on E0, the curve shape, and bonding type.
For example, materials having large bonding energies typically also have high melting
temperatures; at room temperature, solid substances are formed for large bonding energies,
whereas for small energies the gaseous state is favored; liquids prevail when the energies are of
intermediate magnitude. In addition, mechanical stiffness (or modulus of elasticity) of a material
is dependent on the shape of its force–versus–interatomic separation curve. The slope for a
relatively stiff material at the r =r0 position on the curve will be quite steep; slopes are shallower
for more flexible materials. Furthermore, how much a material expands upon heating or contracts
upon cooling (that is, its linear coefficient of thermal expansion) is related to the shape of its E0-
versus-r0 curve. A deep and narrow “trough,” which typically occurs for materials having large
bonding energies, normally correlates with a low coefficient of thermal expansion and relatively
small dimensional alterations for changes in temperature. Therefore: The deeper ‘well’ or ‘trough’
represents stronger interatomic attraction; hence it is more difficult to melt these substances, which
have correspondingly large elastic moduli and low thermal expansion coefficient. Fig 2 below
illustrates the relation of net energy EN and interatomic distance r.

Figure 2: Schematic representation of the relationship between the shape of the potential energy
well and selected physical properties. Materials with a deep well (a) have a high melting point,
high elastic modulus, and low thermal expansion coefficient. Those with a shallow well (b) have
a low melting point, low elastic modulus, and high thermal expansion coefficient.