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FACULTY OF PHARMACEUTICAL SCIENCES

DEPARTMENT OF PHARMACEUTICAL AND MEDICINAL CHEMISTRY
UNIVERSITY OF ABUJA

PCH 202: INORGANIC PHARMACEUTICAL CHEMISTRY

Second semester, 2023/2024 session

Lecturers:
Dr A.M. Alhassan
Pharm Jamilu Maiwada
Dr. Dauda Garba
Course outline:
1. Structure of atoms and Molecules
2. Physico-chemical properties, preparation and uses of the elements of the periodic table and
their compounds of pharmaceutical importance
3. Coordination compounds

Structure of Atom

• What is an atom?
• An atom is defined as the smallest unit that retains the properties of an element.
• The familiar model of an atom is that of a small nucleus composed of protons and
neutrons surrounded by rapidly moving electrons.
• Protons and neutrons have about the same mass (1.00728 and 1.00867 amu respectively)
and each is about 1800 times as heavy as an electron.
• A neutron is electrically neutral, but a proton has a positive charge which is exactly the
opposite of the negative charge of an electron. In a neutral atom, the number of electrons
around the nucleus equals the number of protons in the nucleus.
• The number of protons in the nucleus (the “atomic number”, Z) characterizes a chemical
element. Atoms of a given element all have the same number of protons, yet may have
different masses. The atomic mass number of an atom, A, is given by A = Z + N, where N
is the number of neutrons in the nucleus.

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E = element symbol
A E
Z
A = number of protons + number of neutrons = mass number
Z = number of protons = number of electrons = atomic number
Shorthand writing of element symbol

• Atoms of the same element can have different numbers of neutrons; the different possible versions of
each element are called isotopes. The numbers of protons and electrons are the same for each isotope,
as they define the element and its chemical behavior
• The atomic weight of an element is the weighted average of the atomic masses of the various naturally
occurring isotopes of the element. For example, the most common isotope of hydrogen called protium
has no neutrons at all. There are two other hydrogen isotopes: deuterium, with one neutron, and tritium,
with two neutrons
• Strong nuclear forces bind together the protons and neurons. The binding energy per nuclear particle
(nucleon) amounts to about 1.4 x 10–12 Joules. The greatest nuclear binding energy is found in nuclei of
medium atomic number (such as Fe) where N is approximately equal to Z.
• For nuclei of larger atomic numbers, such as uranium, N is about equal to 1.5 Z, and the binding energy
per nucleon is less. As a consequence of this decreased nuclear stability, some isotopes of uranium, for
example) are unstable. That is, if the uranium isotope, 92U235 (Z = 92, A = 235), is bombarded with
neutrons, the following reaction can take place:
• 235 + n → 39Y94 + 53I140 + 2n
92U

• Generally, heavy nuclei with an unfavorable ratio in the number of protons and neutrons can
spontaneously decay by the emission of α particles (helium ions) or β particles (electrons). These nuclei
are referred to as radioactive. The rate at which the decay of such unstable nuclei takes place varies
greatly and is indicated by the element’s half-life.

ATOMIC MODELS
• To produce the correct representation of atomic structure several atomic theories and
models were developed. Key ones among them were Dalton’s atomic theory, Thompson’s
atomic model, Rutherford’s model, and Bohr’s model.
• Dalton's Atomic Model (1803): Proposed by John Dalton, this model suggested that atoms
are indivisible and indestructible spheres with different sizes and masses for different
elements. Dalton's model also introduced the concept of chemical reactions occurring
through the rearrangement of atoms.
• Thomson's Plum Pudding Model (1897): J.J. Thomson
proposed that atoms consist of a positively charged sphere
with negatively charged electrons embedded within it, much
like raisins in a plum pudding. This model was developed
based on Thomson's experiments with cathode rays
Thomson's Plum Pudding Model

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• Rutherford's Nuclear Model (1911): Ernest Rutherford's model suggested that an atom has a
small, dense, positively charged nucleus at its center, surrounded by orbiting negatively
charged electrons. This model was proposed based on the results of Rutherford's famous gold
foil experiment.

Ernest Rutherford's atomic model

Bohr Atomic Model

• The Bohr atomic model was proposed by Neil Bohr in 1913. it was
the first atomic theory in quantitative agreement with some
experimentally determined facts. He postulated that:
1. In an atom, electrons( negatively charged) revolve around the
nucleus( positively charged) in a circular path called an orbit.
2. Each orbit has a fixed energy and these circular orbits are
known as shells
3. The energy level are represented by an integer n=1,2,3.. Known
as quantum number. The range of the quantum number starts
from the nucleus side with n=1 being the lowest energy level.
The orbits n=1,2,3.. are represented as K, L, M N.. Shells
respectively. When an electron is in its lower energy level, it is
said to be in the ground state.
4. The electron in an atom moves from a lower to a higher level by Bohr Model
gaining the required energy (absorbing radiation), while an
electron moves from a higher to a lower energy level by losing
energy (emitting) radiation).
• This is the bases upon which the concept of absorption and
emission spectroscopy was developed.

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• Bohr atomic model has some limitations

• i. It is applicable to hydrogen atom but cannot be applied to multi electron system.
For example, the uranium atom would require 92 electronic orbits and it would have to
assume a size which is incompatible with the experimental facts.
• ii. The Bohr model was modified by introducing additional quantum numbers,
namely; the Azimuthal (orbital or angular momentum) quantum number (l). magnetic
number (m), the spin quantum number (s), while the number of shell n is designated as
principal quantum number.

Four main quantum numbers

symbol Values
Principal quantum number n 1, 2, 3…..
Azimuthal quantum number l 0, 1, ……..(n -1)
Magnetic quantum number m -l….0…..+l
Spin quantum number s ± 1/2

Principal quantum number (n): it describes the energy level of an electron and the most
probable distance of the electron from the nucleus. It designate the principal electron
shell. It has integer values ranging from 1, 2, 3…..

Azimuthal quantum number (l): This gives the number of sub shells and describe shape of the
orbitals in a given shell. A value of Azimuthal quantum number can indicate either an s, p, d, or f
orbitals which vary in shape. This value depends on the value of principal quantum number. For
example, when n =3, Azimuthal number can take the following values; 0, 1,… (n-1) Where l = 0, l
=1, and l = 2 represent s, p and d orbitals respectively. Thus at n =3, you will have 3s, 3p and 3d
orbitals.
Magnetic number (m): This give the total number of orbitals in a sub shell and the orientation
of these orbitals. It is dependent on the value of l. It splits sub shells such as s, p, d, f into
individual orbitals. It has values of –l, ..+l

Spin quantum number (s): This describes the orientation of the electrons spin in orbital. It can be
clockwise or anticlock wise. It has values of -1/2 and +1/2

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Aufbau Principle
• Aufbau principle dictates the manner in which electrons are filled in the atomic orbitals of
an atom in ground state. It states that;
• Electrons are filled into atomic orbitals in the increasing order of orbital energy.
• According to this principle the atomic orbital with the lowest energy levels are occupied
before those of higher energy levels. This implies that electrons enter orbitals of higher
energy only when the orbitals with lower energy are being completely filled.
• The order in which the energy of the orbitals increase can be determined with the help of
the n + l rule, where the sum of the principal and Azimuthal quantum number determine
the energy level of the orbital.
• Lower n + l values corresponds to lower orbital energies. If two orbitals share equal n + l
values, the orbital with the lower n value is said to have lower energy associated with it.
Hence the order in which orbitals are filled with electrons is 1s, 2s, 2p, 3s, 3p, 4s, 3d, 4p,
5s, 4d, 5p, 6s, 4f, 5d, 6p, 7s and so on.

Pauli Exclusion Principle

• It states that, no two electrons will have an identical set of the same
quantum numbers n, l, m and s. The principle follows two rules
known as the Hund’
• 1. Only two electrons can Occupy the same orbital.
• 2. The two electrons in the same orbital must have opposite spin.
• This principle help us to understand electron arrangement in atoms
and molecules, and provides an understanding of the classification of
element in the periodic table.
• It help us predict which atoms are likely to donate or accept
electrons.

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The Periodic Table

Chemical elements are arranged in order of their increasing atomic number into groups (columns) and
periods (rows). Elements in the same group tends to show similar characteristics.The IUPAC has
recommended that the main groups and the transition metals should be numbered from 1 to 18.

Periodic table of elements showing metals (grey), semimetals (light grey) and nonmetals (white)

Electronic Configuration
• Each element in the periodic table is characterized by a set of electrons, and their configuration can be
described with the help of the quantum numbers.
• The electronic configuration is mostly used to describe the orbitals of an atom in its ground state and
shows how these electrons are distributed between the different orbitals. Nevertheless, this model can
also be used to show valence electrons or ions.
• the electron shell describes a set of electrons that occupy the same principal quantum number n. The
respective electron shell n can be filled with 2n2 electrons. This means the first electron shell can be
filled with a maximum of two electrons, as n =1. The second electron shell can accommodate up to
eight electrons with n=2, and so on.
• The subshells are defined by the quantum number l (l =n−1), correspond to the orbital labels s, p, d and
f. The number of electrons that can be placed in each subshell can be determined by the following
equation: 2(2l +1). This allows two electrons to be placed in the s subshell (l=0), six electrons in the p
subshell (l =1) and 10 electrons in the d subshell (l=2).
• For example the electronic configuration of hydrogen is written as 1s1, Helium (He) 1s2, Lithium (Li)
1s22s1, nitrogen (N) 1s12s22p3.

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Electronic Structure of Molecules

SYNOPSIS

• Molecular bonding
• Ionic bonding
• Covalent boding
• Lewis dot structure
• Hybridization and molecular orbitals
• Bond polarity
• Resonances

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Molecular Bonding

• Molecules are formed when two or more atoms are chemically combined together. This process is
known as molecular bonding.
• Bonding simply refers to the chemical combination of atoms to form a molecule
• It can occur between atoms of the same element (e.g. H2, O2) or atoms of different elements e.g.
CH4, NaCl
• Bonding can be broadly classified into 2 types namely;
I. Ionic bonding (electrovalent bonding)
II. Covalent bonding

• Bonding basically involves the interaction between valence electrons

• The driving force behind chemical bonding is the desire of each element to attain a stable electronic
configuration, similar to that of the nearest noble gas.
• For example,

• For example, He 1s2 Ne 1s22s22p6 Ar 1s22s22p63s23p6 Kr s22s22p63s23p64s23d104p6

• The above four noble gases all have completely filled shell. Hence, they very (unreactive).

IONIC BONDING
• Is the simplest type of bonding to understand. It involves electron transfer between atoms. One atom
donates electron while the other atom accept the electron.
• The atom that donates (loss) electron becomes positively charged, while the one that accept (gain)
electron becomes negatively charged.
• The electrostatic attraction between the charges on the atoms results in chemical bond formation.
• The electron transfer is usually from atom with low ionization potential to an atom with high electron
affinity.
• The atomic objective is to mimic the nearest noble gas electronic configuration
 For example, consider sodium chloride ( NaCl)
 Na (1s22s22p63s1) has one electron more than Ne (1s22s22p6 )
 Cl (1s22s22p63s23p5) has one electron less than Ar (1s22s22p63s23p6)

 Cl has high electron affinity and acquire one electron to become Cl- while sodium which has low
ionization potential loses one electron to be come Na+.

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COVALENT BONDING
Covalent bonding involves the sharing of electrons . Two or more atoms share part or all of
their valence electrons to form molecules. For example, two isolated H atoms share electrons to
form hydrogen molecule.

Each electron belongs to

A covalent bond
an isolated H atom

A covalent bond: A covalent bond is the sharing of two electrons

between nuclei.

Bond length and energy

• The formation of covalent bonds involves energy changes.
For example, when two H atoms separated by a large
distance are brought together, their total energy begins to
decrease.
• At one particular internuclear distance, the energy of the
molecule is at a minimum, while at shorter distances the
energy rises dramatically.
• The internuclear distance at which energy is the lowest is
called the bond length of the H-H bond. The energy that is
required to remove the H atoms from that internuclear
distance to infinity (toward the right in the figure) is the bond
strength, or bond energy, of the H-H. Formation of a chemical bond:
• There must be some energy advantage by bonding, Plot of energy as a function of
otherwise it would not occur. Usually, the molecule formed the inter-nuclear distance for two
has lower energy than the isolated atoms which corresponds H atoms. The H atoms are most
to greater stability. stable at the distance at which
• The figure below illustrates how the energy of two H atoms energy is a minimum.
changes as a function of the distance between their nuclei
bonds.

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Why are two hydrogen atoms connected by a covalent bond lower in energy than two isolated hydrogen
atoms?
• It is because of the additional electrostatic attraction experienced by electrons when they are shared
between nuclei.
• In each isolated hydrogen atom, the negatively charged electron is attracted to just one positively
charged nucleus. But when the two hydrogen atoms are close together, each of the two electrons is
attracted simultaneously to both Nuclei.
• This additional attraction lowers each electron’s energy, making the species more stable.

When the atoms are too close together, however, the energy rises dramatically due to the repulsion
between their positively charged nuclei.

Electronegativity, Polar Covalent Bonds, and Bond Dipoles

We’ve seen that covalent bonds are characterized by the sharing of electrons between two atomic
nuclei. If the atoms are identical, the electrons are shared equally and the bond is called a nonpolar
covalent bond. Otherwise, one nucleus will attract electrons more strongly than the other. The ability
to attract electrons in a covalent bond is defined as the element’s electronegativity (EN).

There are a variety of different electronegativity scales that assign values to each element, but the one
devised by Linus Pauling ranges from 0 to about 4.

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• Within the same row, electronegativity values tend to increase from left to right across the periodic
table. Within the same column, they tend to increase from bottom to top.

• As a result, the elements with the highest electronegativities (not counting the noble gases) tend to
be in the upper right corner of the periodic table (e.g., N, O, F, Cl, and Br), whereas the elements
with the lowest electronegativities tend to be in the lower left corner (e.g., K, Rb, Cs, Sr, Ba).

 In a covalent bond, electrons are more likely to be found near the nucleus of the more
electronegative atom and less likely near the nucleus of the less electronegative atom. This creates
a separation of partial positive and negative charges along the bond, called a bond dipole.
Examples of dipoles are shown below for HF, CH4 and CO2 are shown below.

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polar
polar
non-polar
The dipoles are represented by the red arrows. Each arrow points from the less electronegative atom (δ+)
to the more electronegative atom (δ-). The length of the arrow indicates the relative magnitude of the bond
dipole.

Note: Bonds with an electronegativity difference between 0.5 and 1.7

are considered polar.
The magnitude of a bond dipole depends on the difference in electronegativity between the atoms
involved in the bond.
A larger difference in electronegativity results in a larger bond dipole.

Lewis Dot Structures and the Octet Rule

Lewis dot structures (or, Lewis structures) represent a convenient way to describe the connectivity
of atoms in a molecule.
They allow us to know which atoms are bonded together, and by what types of bonds (single, double,
or triple).
They also provide information on which valence electrons participate in bonding and which do not.
The above information guides us toward understanding the chemical behavior of molecules.

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Basic conventions of Lewis structures

• Lewis structures take into account only valence electrons. In a complete Lewis structure, such as the
following for isolated C and Cl atoms, all valence electrons are shown:

4 valence electrons 7 valence electrons

• Bonding and nonbonding electrons are clearly shown. Single, double, and triple bonds are indicated by
one, two, or three lines respectively, which represent the sharing of two, four, or six electrons,
respectively. Thus, each line represents a shared pair of bonding electrons

 Atoms in Lewis structures obey the duet rule and the octet
rule. Atoms are especially stable when they have complete
valence shells: two electrons (a duet) for hydrogen and Each H has a share of 2 electrons
helium, and eight electrons (an octet) for atoms in the second
row of the periodic table.
 These duets and octets can be achieved through the C shared eight electrons (octet)
formation of covalent bonds, where valence electrons are Each Oxygen shared 4 electron
shared between atoms. & has 2 lone pair electrons
In each of these molecules, all atoms have completely filled valence shells

 Nonbonding electrons are indicated by dots and are usually paired. These are called lone pairs of
electrons. In some species, nonbonding electrons are unpaired and are represented by single
dots. These species are called free radicals.

Steps for Drawing Lewis Structures

1. Count the total number of valence electrons in the molecule.
• The number of valence electrons contributed by each atom is the same as its group number (H = 1,
C = 4, N = 5, O = 6, F = 7).
• b. Each negative charge increases the number of valence electrons by one; each positive charge
decreases the number of electrons by one.
2. Write the skeleton of the molecule, showing only the atoms and the single bonds required to hold
them together.
• If molecular connectivity is not given to you, the central atom (the one with the greatest number of
bonds) is usually the one with the lowest electronegativity.
3. Subtract two electrons from the total in Step 1 for each single covalent bond
drawn in Step 2.

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4. Distribute the remaining electrons as lone pairs.

• Start with the outer atoms and work inward.
• Try to achieve an octet on each atom other than hydrogen.
5. If there is an atom with less than an octet, increase the atom’s share of electrons by
converting lone pairs from neighboring atoms into bonding pairs, thereby creating double
or triple bonds

Common numbers of covalent bonds and lone pairs for selected

uncharged Atoms
Atom Number Number of Examples
of Lone Pairs
Bonds
H 1 0

C 4 0
C

N 3 1

O 2 2 O

F, Cl, Br, 1 3 Cl Br I
I
Ne 0 4

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Limitations of Lewis structures

Some species are not described well by Lewis structures.

For example in HCO2-, both of the C-O bonds are identical experimentally;
They have the same bond length and bond strength, which are intermediate between those of a single
and a double bond.
However, the Lewis structure of HCO2- shows one C-O single bond and one C=O double bond,
suggesting that the two bonds are different.
Experiments show that both oxygen atoms carry an identical partial negative charge (δ-), whereas
the Lewis structure suggests that one oxygen atom bears a full negative charge and the other is
uncharged.
In other words, the Lewis structure suggests that the C=O double bond and the -1 charge are both
confined to a specific region in space, or localized, whereas; In the real species, they are spread out, or
delocalized.

How, then, do we reconcile the differences between the Lewis structures of

species like HCO2- and their observed characteristics? The answer is through
resonance theory, the key points of which can be summarized by the
following rules:

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Valence Shell Electron Pair Repulsion (VSEPR) Theory:

Three-Dimensional Geometry

The molecular geometry (3 dimensional shapes) of molecules is one of the factor that
determine the intermolecular interactions of organic molecules.
The intermolecular interactions contributes substantially in determining the physical and
chemical properties of organic compounds.
For example, Carbon dioxide (CO2) and methanoic acid (HCO2H), also called formic acid,
are similar in their chemical makeup, but the boiling point of CO2 is -278 °C, whereas that of
HCO2H is 101 °C. In addition, CO2 is only slightly soluble in water, while HCO2H is highly
soluble in water. Why are their physical properties so vastly different.
These compounds behave differently because the experience different intermolecular
interaction which is partly contributed by their 3 dimensional structure

Basic Principles of VSEPR Theory

1. Electrons in a Lewis structure are viewed as groups. ● A lone pair of electrons, a single
bond, a double bond, and a triple bond each constitute one group
of electrons.
2. The negatively charged electron groups strongly repel one another, so they tend to
arrange themselves as far away from each other as possible.
 ● Two electron groups tend to be 180° apart (a linear configuration).
 ● Three groups tend to be 120° apart (a trigonal planar configuration).
 Four groups tend to be 109.5° apart (a tetrahedral configuration.
3. Electron geometry describes the orientation of the electron groups about a particular atom.
These configurations are summarized in the Table below.
4. Molecular geometry describes the arrangement of atoms about a particular atom. Because
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atoms must be attached by bonding pairs of electrons, an atom’s molecular geometry is
governed by its electron geometry.

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Molecular geometries and approximate bond angles

Angle Strain
Geometric constraints can force an atom to deviate
significantly from its ideal bond angle — that is, the bond
angle predicted by VSEPR theory. Most commonly this
happens in ring structures. For example, the carbon
atoms in a molecule of cyclopropane should have an ideal
bond angle of 109.5°, given that each carbon is
surrounded by four groups of electrons (four single
bonds). To form the ring, however, the C –C-C bond
angles must be 60°. The deviation of a bond angle from Cyclopropane
its ideal angle results in an increase in energy, called Ideal bond angle = 109.5°
angle strain. Angle strain weakens bonds and makes a Real bond angle = 60°
species more reactive.

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