PHARM 151/155

Basic Pharmaceutical Chemistry

AYENSU ISAAC (PhD)

Dept. Pharm. Chem.
FPPS
College of Health Sciences
KNUST (2015/16)

Recommended Literature
 Organic Chemistry Demystified – Daniel Bloch DOI: 10.1036/0071459200
 Graham T & Solomons, Oganic Chemistry 1988
 Finar vol.1&2 , Organic Chemistry (latest Edition)
 Morrison & Boyed, Texbook of Organic Chemistry (latest edition)
 Wingrove A S & Caret R L, Organic Chemistry (1981)
 Beckett & Stenlake Practical Pharmaceutical Chemistry Vol. 1 &2 (latest edition.)

Course objectives
 This module provides the chemical basis for understanding
 Molecular structures,
 Physical and chemical properties of compounds and chemical processes that help
drugs bind to receptor sites.

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  The module, in addition, provides the essential knowledge for subsequent modules in
pharmaceutical chemistry and related disciplines in pharmacy

Exit Learning Outcomes

 Explain the key concepts in chemical structure and bonding
 Be able to describe/explain the different kinds of bonding existing in molecules and
 How bonding influences molecular shapes.

Relevance of Pharmaceutical Chemistry to Pharmacy Practice

• Pharmaceutical/Medicinal chemistry embraces chemistry, (synthetic organic
chemistry), pharmacology and various other biological specialties.
• It involves design, chemical synthesis and development for market of pharmaceutical
agents, or bio-active molecules (medicines).
• Organic compounds
• Small organic molecules (e.g. Paracetamol)
• Biologics (Insulin and other proteins of natural or recombinant origin), etc.)
• Inorganic and organometallic compounds are also useful as medicines (e.g., lithium
and platinum-based agents such as lithium carbonate and cis-platin
Area of Pharmaceutical Chemistry

• Drug discovery- Identification through synthesis of new chemical agents.

• "Discovery Hits", Assay of compounds for an aspired biological activity.

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 • Initial hits can come from resigning existing drugs toward new pathologic
processes.
• Observations of biologic effects of novel or existing products of natural origin
e.g. bacteria, fungi, plants, etc.
• Development of new therapeutic entities
• Process optimisation of the synthetic route for pilot and eventual upscale for
industrial production.
• Identification of the most appropriate dosage form and formulation for
delivery.
• Preparation of suitable dosage forms for therapeutic purposes.
• The Critical requirement at this stage is the application of Good
Manufacturing/Laboratory Practice (GMP/GLP)
• Material sourcing,
• Handling, and
• Chemistry.
Pharmaceutical Chemistry further involves;
• Structure-Activity –Relationship (SAR): Studies the synthetic and computational
features of existing medicinal agents in development in relation to their biological
activities and characteristics
• Quality assurance and quality control Pharmaceutical chemistry is focused on
quality aspects of medicines and aims to assure fitness for purpose of medicinal
products.
• An interdisciplinary Science which combines at the interface with biochemistry,
pharmacology, veterinary and human medicine.
• Along with statistics, pharmaceutical business practice and project management
assures the safety and efficacy of pharmaceutical formulations for use as suitable
agents for disease treatment.

THE ATOMIC STRUCTURE

 The behaviour of an atom seems to depend just on its number of protons, neutrons and
electrons
 An electron carries an atomic unit of negative electric charge
 A proton carries an atomic unit of positive charge
 The number of protons in the nucleus of an atom is called the atomic number, Z
 The mass of an atom is determined by the total number of protons and neutrons in its
nucleus This total is called the mass number, A

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  Therefore neutron number is ………?

Composition of an Atom

Figure 1: Composition of an atom.

The Bohr Model
 In 1913 Bohr proposed his quantized shell model of the atom to explain how electrons
can have stable orbits around the nucleus.
 The motion of the electrons in the Rutherford model was unstable because, according
to classical mechanics and electromagnetic theory, any charged particle moving on a
curved path emits electromagnetic radiation;
 Thus, the electrons would lose energy and spiral into the nucleus.
 To remedy the stability problem, Bohr modified the Rutherford model by requiring
that the electrons move in orbits of fixed size and energy.
 The energy of an electron depends on the size of the orbit and is lower for smaller
orbits.
 Radiation can occur only when the electron jumps from one orbit to another. The
atom will be completely stable in the state with the smallest orbit, since there is no

orbit of lower energy into which the electron can jump.

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 “Electrons occupy discrete orbits
of constant energy. These orbits
are described using the ordinary
mechanics, while the passing of
the system between different
stationary states cannot be
treated on this basis”
“In making a
transition
between
stationary
states, a
single
photon will
be
radiated…”
Figure 2: Electrons in orbit
Key Themes to Atomic Modelling

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 Stability
of the atom

Dynamics Chemical/spectral
of its parts properties
Figure 3: Atomic Modelling themes
Quantum Theory (Proposed by Max Plank, 1900)
 E1- E2=hν where h is Planks constant, v is frequency
 But v =c/λ ,c is the velocity of light, λ is wavelength
 Thus, E1- E2= hc/λ
Quantum of Energy released/ Absorbed has definite frequency
Hence, definite Wavelength
 De Broglie(1924); Investigation led to Dual wave-particle nature of Light
Electromagnetic Radiation
 Electromagnetic Radiation = Light:

 radiation energy that propagates through space in wave form

 The speed of light is constant in a given medium

 The speed of light through space is c = 2.998 x 108 m/s

 c = ln (where l = wavelength, n = frequency)

 Light with longer wavelength has lower frequency, and one with higher
frequency has shorter wavelength.

 According to Quantum Theory: Radiation Energy depends only on frequency:

En = hn

 where the Planck constant and h = 6.626 x 10-34 J.s

Quantum Mechanical Model
 Also called wave mechanics – treating all motions of particles as wave-like;

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  Louis de Broglie originated the idea that, like light, all particulate motions have wave
characteristics;
 a new mathematical formula that incorporates both particulate and wave
characteristics was needed.
 Heisenberg uncertainty principle implies that we cannot know the position and energy
of an electron in atom at the same time with some degree of certainty.
 If we determine precisely the energy of electrons in atoms, we can only
approximate their where about
 Erwin Shrödinger derived a mathematical model for hydrogen that assumed electron
to behave a standing wave.
Schrödinger’s Wave Function, ψ (x,y,z)

(h2/8p2me)[(d2/dx2) + (d2/dy2) + (d2/dz2)] – (Zq1q2/r)y

= Ey
 The equation is a bit complicated and Schrödinger wasn’t even sure if it works
 We’ll try to understand the meaning of this equation
 The wave function ψ (x,y,z) has no physical meaning, but [ψ (x,y,z)]2 implies
probability
 The square of the wave function yields a probability about finding an electron having
a particular energy at a given location in the atom – just probability, not a definite
location.
 The sum of the squares of these wave functions yields a probability space called
orbital.
Atomic Orbital
 It is a probability space inside the atom where the chances of finding an
electron with particular energy value is greater than 90%
 Each orbital is described by a set of three quantum numbers: n, l, and ml ;
 The number of orbitals in a subshell is equal to (2l + 1) and the number of
orbitals in a shell is equal to n2;
 As a consequence of the Pauli exclusion principle, each orbital can
accommodate a maximum of two electrons, which must have opposite spins
Quantum Numbers
 A set of numbers that describe an orbital or an electron
 The principal quantum number (n) has the integral values: 1, 2, 3,…, ∞. It is related
to the size and energy of the orbital

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  The angular momentum quantum number (l) has the integral values: 0, 1, 2,…,(n – 1).
It is related to the shape of atomic orbitals. Each value of l is designated a letter
symbol, which is summarized below:
 Values of l: 0 1 2 3
 Letter symbols: s p d f
 The magnetic quantum number (ml) is related to the orientation of the orbital in the
Cartesian coordinates x, y, and z.
 ml has values from – l to +l (including 0)
Other Meanings of the Quantum Numbers
 The principal quantum number (n) also describes the primary electronic shell or main
energy level
 The angular momentum quantum number (l) also implies the sub-shell or energy sub-
level
 The number of sub-shell in a given energy shell is equal to n:
1. Shell n = 1 has one subshell - the 1s-subshell;
2. shell n = 2 has two subshells - the 2s- and 2p-subshells;
3. shell n = 3, has three subshells - the 3s-, 3p-, and 3d-subshells, and so on,…
 The number of orbitals in a given subshell is determined by the possible values that ml
can have, which is equal to (2l + 1):
1. subshell l = 0 has one orbital; l = 1 has three orbitals; l = 2 has five orbitals; l =
3 has seven orbitals, and so on…
Quantum Numbers and Orbital Designations
 The combination of quantum numbers: n, l, and ml, describes a particular orbital in the
atom.
1. n = 1, l = 0, and ml = 0, è orbital 1s;
2. n = 2, l = 0, and ml = 0, è orbital 2s;
3. n = 3, l = 0, and ml = 0, è orbital 3s;
4. n = 2, l = 1, and ml = 0, è orbital 2p;
5. n = 3, l = 1, and ml = 0, è orbital 3p;
6. n = 3, l = 2, and ml = 0, è orbital 3d;
 All orbitals with l = 0 have spherical shape, but the size becomes larger as the value
of n increases;
 Each orbital-p has two lobes, like a dumb-bell, with a nodal plane
1s- Spherically symmetrical with lowest energy
2s- Spherical about nucleus but next higher energy
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Figure 4: Is and 2s Orbitals
3*2p- Dumbbell shape and perpendicular to each other.
Three dimensional character designated x, y, z axis ie. 2px,2py,2pz

Figure 5: The p orbital.

Electronic Structure & Configuration
Developing the Ground State Electron Configurations for Multi-electrons Atoms
 Three Rules Govern the Distribution of Electrons in an Atom;
 Afbau principle
 Hund’s Rule
 Pauli’s Exclusion Principle
 Atomic Structure consists of Main shells & sub-shells. Main shells used to be referred
to as K,L,M,N shells
 Now letter designation is discontinued. It is replaced by Numbers ie. K=1, L=2, M=3
& N=4 etc
 Advantage; Up to N=4, the Number of sub-shells in a main shell may be predicted.
Examples
 When K=1,One Sub-shell is obtained,(1s)
 “ L=2, Two Sub-shells are obtained, (2s & 2p)
 “ M=3, Three Sub-shells are obtained (3s,3p & 3d)
 “ N=4, Four Sub-shells are obtained (4s,4p,4d & 4f)

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  Order of filling shells is based on Energy levels ie. Orbitals of lower energy are filled
first with Electrons- Aufbau
 Sub-shells are filled as follows; 1s,2s,2p,3s,3p,4s.3d,4p,5s,4d,5p,6s,4f etc, etc.
The Aufbau method
Suggests that electrons be assigned to orbitals starting with the lowest energy;
Pauli Exclusion Principle
 An orbital can hold 0, 1, or 2 electrons only, and if there are two electrons in the
orbital, they must have opposite (paired) spins.
 A maximum of two electrons are assigned to each orbital; The total number of
electrons in a shell or sub-shell depends on the number of orbitals in it;
 For a given shell n, there are n2 number of orbitals, and the maximum number of
electrons in that shell is 2n2.
Hund’s rule
If a sub-shell contains degenerate orbitals (orbitals having the same energy), such as 2p,
3p, 3d, etc., each orbital must be assigned an electron with the same spin before the
second electron is added to it.

Figure 6: Electron Configurations for Multi-electrons Atoms

Electron Configuration of Multi-Electron Atoms

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  He (Z = 2): 1s2

 Li (Z = 3): 1s2 2s1  Na (Z = 11): 1s2 2s2 2p6 3s1 = [Ne] 3s1
 Be (Z = 4): 1s2 2s2  Mg (Z = 12): [Ne] 3s2

 B (Z = 5): 1s2 2s2 2p1  Al (Z = 13): [Ne] 3s2 3p1

 C (Z = 6): 1s2 2s2 2p2  Si (Z = 14): [Ne] 3s2 3p2

 N (Z = 7): 1s2 2s2 2p3  P (Z = 15): [Ne] 3s2 3p3

 O (Z = 8): 1s2 2s2 2p4  S (Z = 16): [Ne] 3s2 3p4

 F (Z = 9): 1s2 2s2 2p5  Cl (Z = 17): [Ne] 3s2 3p5

 Ne (Z = 10): 1s2 2s2 2p6  Ar (Z = 18): [Ne] 3s2 3p6

Orbital Diagrams for the 2nd Period Elements and Transition Elements

 Atoms Orbital Diagram

 Li: [He] ↑  Sc: [Ar] ↑↓ ↑
 Be: [He] ↑↓  Ti: [Ar] ↑↓ ↑ ↑
 V: [Ar] ↑↓ ↑ ↑ ↑
 B: [He] ↑↓ ↑
 Cr: [Ar] ↑ ↑ ↑ ↑ ↑ ↑
 C: [He] ↑↓ ↑ ↑  Mn: [Ar] ↑↓ ↑ ↑ ↑ ↑ ↑
 N: [He] ↑↓ ↑ ↑ ↑  Fe: [Ar] ↑↓ ↑↓ ↑ ↑ ↑ ↑
 O: [He] ↑↓ ↑↓ ↑ ↑  Co: [Ar] ↑↓ ↑↓ ↑↓ ↑ ↑ ↑
 F: [He] ↑↓ ↑↓ ↑↓ ↑  Ni: [Ar] ↑↓ ↑↓ ↑↓ ↑↓ ↑ ↑
 Ne: [He] ↑↓ ↑↓ ↑↓ ↑↓ Cu: [Ar] ↑ ↑↓ ↑↓ ↑↓ ↑↓
↑↓
 2s -----2p-----  Zn: [Ar] ↑↓ ↑↓ ↑↓ ↑↓ ↑↓
↑↓
 4s ----------3d-----------
Periodic table and law
 Elements are classified into four based on Electronic Configuration
 The Noble Gases
 The Representative Elements
 The Transition Elements
 The Inner Transition Elements
 Original proposal for the Periodic Table based on Atomic weights.
 Currently, It is based on Atomic number, Z
The Law states;

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  Physical & Chemical properties of elements are periodic function of their Atomic
number. This has been narrowed down to outermost or Valence shell electronic
structure.
Careful study of the periodic table shows;
 Definite trends in some properties of elements across a period and down a group.

Figure 7: The Periodic table and classifications

Properties of elements
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Atomic Radius.
The radius of an atom can be estimated by taking half the distance between the nuclei of two
of the same atoms. The atomic radius tends to decrease as one moves across a period from
left to right. Effective nuclear charge (increased number of protons create more positive
charge) increases, thereby attracting the orbiting electrons and lessening the radius. However,
going down the group, the principal energy level (shell) increases hence the atomic radius
increases.

Figure 8: Atomic radius

Ionic radii

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Figure 9: Ionic radii of cations and anions
 Cations (positive charge) of the main group elements are much smaller than their
parent atoms due to loss of electron
 Anions are much larger than the atoms from which they form. Acquires an electron
Ionization energy
Energy needed to remove an electron from a gaseous atom:

 M(g) + Ip ® M+(g) + e-;

 (Ip = ionization potential or ionization energy)

Figure 10: Ionization energy

The first ionization energy is the energy required to remove one electron.The nth ionization
energy is the energy required to remove the atom's nth electron, after the (n−1) electrons
before it has been removed.
 Ionization energy increases across a period as a result of;
 Increased number of protons (higher nuclear charge) attracting the orbiting
electrons more strongly. This increases the energy required to remove one of
the electrons.
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Figure 11: Ionization energy-atomic number relationship
There is a small drop between Mg and Al. Mg has its outer electrons in the s sub shell,
whereas Al is starting to fill the 3p subshell. Al’s electron is slightly easier to remove

Figure 12: First Ionization energy of period three (3) elements

Ionization Energy of Magnesium

Mg(g) ® Mg+(g) + e-; I1 = 736 kJ/mol

Mg+(g) ® Mg2+(g) + e-; I2 = 1445 kJ/mol

Mg2+(g) ® Mg3+(g) + e-; I3 = 7730 kJ/mol

Question;
Explain the large energy difference between the second (I2) and third (I3) ionization energy
for magnesium.
There is a small drop between phosphorous and sulphur. Sulphur’s outer electrons is being
paired up with another electron in the same orbital. When the second electron is added to an
orbital there is a slight repulsion between the two negatively charged electrons which makes
the second electron easier to remove.
Electron Affinity

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Figure 13: Electron Affinity
Energy CHANGE when an electron is added to a gaseous atom
Electron affinities of the halogen atoms
EA (kJ/mol)

 F(g) + e- ® F-(g); -328 kJ/mol

 Cl(g) + e- ® Cl-(g); -349 kJ/mol

 Br(g) + e- ® Br-(g); -325 kJ/mol

 I(g) + e- ® I-(g); -295 kJ/mol

Electron affinities of oxygen:

O(g) + e- ® O-(g); DHo = EA1 = -141 kJ/mol

O-(g) + e- ® O2-(g); DHo = EA2 = 878 kJ/mol

¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾

O(g) + 2e- ® O2-(g); DHo = EA = 737 kJ/mol

 EA2 is positive because energy is needed to overcome repulsion force between two
negatively charged particles (O- and e-).
 Atoms that become more stable with the addition of an electron (and so are
considered to have a higher electron affinity) show a decrease in potential energy; i.e.
the energy gained by the atom appears to be negative.
 For atoms that become less stable upon gaining an electron, potential energy
increases, which implies that the atom gains energy

Electronegativity
 The relative ability of bonded atoms to draw (pull) shared electrons closer to its
center.
 The type of bond formed is largely determined by the difference in electronegativity
between the atoms involved, using the Pauling scale.

Trends in Electronegativity
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  Across period, the electronegativity increases due to the stronger attraction that the
atoms obtain with increased nuclear charge.
 Down the group, electronegativity decreases due to the longer distance between the
nucleus and the valence electron shell,
 There is decreased attraction, resulting in the atom having less attraction for electrons
or protons.

Figure 14: Electronegativity of elements in the Periodic Table.

Summary of periodic trends

Figure 15: Summary of Periodic Trends

Melting and boiling points

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  For Na, Mg, Al- Metallic bonding: strong bonding – gets stronger the more electrons
there are in the outer shell that are released to the sea of electrons.
 A smaller positive centre also makes the bonding stronger. High energy is needed to
break bonds.
 Si is Macromolecular: many strong covalent bonds between atoms
 high energy needed to break covalent bonds– very high mp +bp

Trends in Metallic, Ionic, and Covalent Characters

Figure 16: Trends in Metallic, Ionic, and Covalent Characters

Practice questions
 Which atom is larger, Li or Cs? Why?
 Which atom is larger, Na or Cl? Why?
 Which atom requires more energy to remove an electron, Li or Cs? Why?
 Rank the following element in order of increasing (smallest to largest) atomic radii:
1. C, N, Mg, Al, and Si;
2. Li, Na, K, Rb, and Cs;
3. Si, P, S, Cl, and Ar;
 Rank the following atoms in order of increasing ionization energy.
1. Al, Si, P, S, Cl;
2. Li, Na, K, Rb, Cs;
3. Al, C, Ca, Mg, N;

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  Atom A has valence electrons that are lower in energy than the valence electrons of
Atom B. Which atom has the higher ionization energy? Explain.
 Which of the following processes requires the most energy? Explain your choice.

1. Na(g) ® Na+(g) + e-;

2. Na+(g) ® Na2+(g) + e-;

3. Mg(g) ® Mg+(g) + e-;

4. Mg+(g) ® Mg2+(g) + e-;

 Which of the following reaction releases the most energy?

1. N(g) + e- ® N-(g)

2. F(g) + e- ® F-(g)

3. Cl(g) + e- ® Cl-(g)

4. Br(g) + e- ® Br-(g)

Valence electrons

 The electrons in the outermost shell are called the valence electrons. Elements in the
first row (period) in the periodic table, hydrogen and helium, have only a 1s orbital.
 The maximum number of electrons these two elements can accommodate is 2. A 2-
electron configuration will be called a duet. When hydrogen has 2 valence electrons in
its 1s orbital it will be called duet happy.
 Elements in the second row (period) in the periodic table, from lithium to neon, can
hold a maximum of 10 electrons. The outermost shell, the valence shell, has a
principle quantum number of 2 and can hold a maximum of 8 electrons, 2s2, 2p6.
 When the valence shell orbitals are filled, the atom will be called octet happy.
 Hydrogen in Group IA has 1 valence electron, carbon in Group IVA has 4 valence
electrons, and fluorine in Group VIIA has 7 valence electrons.
 An atom can gain valence electrons from, or loose electrons to, other atoms.
 Valence electrons are important since they are involved in forming chemical bonds.
The Octet Rule
 Neon, argon, and the other elements in column VIIIA in the periodic table are called
the noble gases. They have eight electrons in their valence shell.
 Helium is an exception since its valence shell (1s) can hold only two electrons.
 The octet rule states that elements will gain, lose, or share electrons to achieve eight
electrons in their outermost (valence) shell.
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Valences
 The bonding capacity or the number of bonds to an atom is called its valence.
 The valence of atoms in Groups IA to IVA is the same as the group number. Lithium
(Group IA) has a valence of one and will have a single bond to another atom.
 Carbon (Group IVA) has a valence of four and there will be four bonds to each
carbon atom. Carbon is called tetravalent.
 The valence of elements in Groups VA to VIIA is 3, 2, and 1 (or eight minus the
group number) respectively.
Practice question

 What valence does oxygen have? What is the bonding capacity for oxygen?
 What is the bonding capacity for boron?

Bond formation
 Atoms form bonds by transferring or sharing electrons with other atoms.
 Atoms of elements in Groups IA and IIA tend to transfer electrons to elements in
Groups VIB and VIIB. The resulting cation from Group IA or IIA forms an ionic
bond with the resulting anion from Group VIA or VIIA.
 Elements in Groups VIA and VIIA tend to share electrons if they react with elements
in Groups VIA to VIIA.
 Sharing electrons result in covalent bonds.
 Carbon, in Group IVA, tends to form bonds with many other elements.
 The atomic 1s orbital of a hydrogen atom contains one electron (1s 1). If the 1s orbitals
of two hydrogen atoms overlap, they can share their electrons and form a two-electron
bond between the atoms.
 The amount of orbital overlap is a measure of bond strength.
 A key point: generally the greater the orbital overlap, the stronger the bond.
 The overlap of two s orbitals is called head-to-head or end-on overlap.
 The area of overlap is cylindrically symmetrical along a line connecting the two
nuclei. This type of overlap, results in a sigma (σ) bond.

Figure 17: Sigma (σ) bond formation.

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Valence Bond Theory
 Valence bond theory describes bond formation from overlapping valence atomic
orbitals (AOs).
 In the hydrogen molecule, electrons in the sigma bond are shared and each atom can
be considered to have two valence electrons, at least part of the time. Each hydrogen
atom is now duet happy.
 Consider an element in the second row of the periodic table that has electrons in p
orbitals.
 The electron configuration for carbon (1s22s22px1py 1pz0) shows one electron in the
2px orbital and one electron in the 2py orbital.

Figure 18: Electronic Configuration of Carbon.

 The p orbitals on an atom are perpendicular (orthogonal) to each other.

Figure 19: Pie (π) bond formation.

 One of the p orbitals, say 2px , on one carbon atom can overlap in a head-to-head
manner with the 2px orbital on another carbon atom, giving a sigma (head-to-head,
cylindrically symmetrical) bond, as shown above
 The 2py orbitals, one on each carbon atom, will have maximum overlap if they are in
the same plane. The 2py orbitals can overlap in a side-to-side manner. The resulting
bond is called a pi π bond.
 The orbital overlap in a bond is not as great as the overlap in a sigma bond, and thus a
bond is usually weaker than a sigma bond.

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Molecular Orbitals
 Just as the valence electrons of atoms occupy atomic orbitals (AO), the shared
electron pairs of covalently bonded atoms may be thought of as occupying molecular
orbitals (MO).
 Overlapping AOs remain localized on each atom. The AO model gives more
information (energy and bond direction) but it lacks information about excited states
of molecules.
 Excited states exist when all electrons are not in the lowest possible energy levels, the
ground state.
 Molecular orbital (MO) theory explains electron excited states and describes AOs
(mixing) to form new orbitals, MOs.
 AOs cease to exist after they mix to form new MOs.
 The combining (mixing) of orbitals conserves the number of orbitals. That is, two
AOs combine to give two MOs.
 MOs have a defined energy, size, and shape. The electrons are now delocalized
throughout the entire MO.

Bonding and Antibonding MO

 The hydrogen molecule provides a simple example of MO formation.
 In the following diagram, two 1s atomic orbitals combine to give a sigma (σ) bonding
(low energy) molecular orbital and a second higher energy MO referred to as an
antibonding orbital.
 The bonding MO is occupied by two electrons of opposite spin, the result being a
covalent bond

Figure 20: Bonding and antibonding MO

 One of the new MOs formed is more stable (of lower energy) than the originating
AOs. This MO is called a bonding orbital. The other MO is less stable than the
originating AOs and it is called an antibonding MO.

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  Antibonding MOs are indicated by an asterisk (*). There are bonding sigma (σ) MOs
and antibonding sigma (σ *) MOs.

 There are also bonding pi (π) and antibonding pi (π∗) MOs.

 If an electron in a bonding MO is promoted to a higher energy MO, the new electron
configuration is called an excited state.
 1s Atomic orbitals and excited state for MO for H• and H2 orbitals
 When MOs form, the AOs (used to make the new MOs) no longer exist,

Figure 21: Before and after mixing MO

Sigma molecular orbital
In the case of bonds between second period elements, p-orbitals or hybrid atomic orbitals
having p-orbital character are used to form molecular orbitals.
 For example, the sigma molecular orbital that serves to bond two fluorine atoms
together is generated by the overlap of p-orbitals and two sp3 hybrid orbitals of
carbon may combine to give a similar sigma orbital.
 When these bonding orbitals are occupied by a pair of electrons, a covalent bond, the
sigma bond results.

Figure 22: Sigma Molecular Orbital

The π orbital
 Another type of MO (the π orbital) may be formed from two p-orbitals by a lateral
overlap
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 Since bonds consisting of occupied π-orbitals (pi-bonds) are weaker than sigma
bonds, pi-bonding between two atoms occurs only when a sigma bond has already
been established.
Thus, pi-bonding is generally found only as a component of double and triple covalent
bonds

2p Atomic orbitals and ground state for molecular orbitals for N• and N2

Figure 23: Before and after mixing MO

Hybrid Orbitals
 The valence shell electron configuration of carbon is 2s2, 2px1, 2py1 & 2pz0.
 The tetrahedral structures of methane and carbon tetrachloride demonstrate that
carbon can form four equivalent bonds, leading to the desired octet.

Figure 24: Tetrahedral structure

sp3 hybrid orbitals
 In order to explain the structure of methane (CH4), the 2s and three 2p orbitals are
converted to four equivalent hybrid atomic orbitals, each having 25% s and 75% p
character, and designated sp3.
 A single 2s AO is combined with three 2p AOs on the same carbon atom to form four
new sp3 hybrid orbitals. The total number of orbitals is conserved (stays the same).
 Four AOs (one 2s and three 2p) combined to give four new sp3 hybrid orbitals.
 These hybrid orbitals have a specific orientation, and the four are naturally oriented in
a tetrahedral fashion

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  Thus, the four covalent bonds of methane consist of shared electron pairs with four
hydrogen atoms in a tetrahedral configuration,
Ground state E xcited state sp 3 Hybridized state

Figure 25: sp3 hybrid orbitals

sp2 hybrid orbitals

Since carbon atoms involved in double bonds have only three bonding partners, they require
only three hybrid orbitals to contribute to three sigma bonds.

Figure 26: sp2 hybrid orbitals

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  A mixing of the 2s-orbital with two of the 2p orbitals gives three sp2 hybrid orbitals,
leaving one of the p-orbitals unused.
 Two sp2 hybridized carbon atoms are then joined together by sigma and pi-bonds (a
double bond)

Figure 27: sp2 hybrid orbital formation

sp hybrid orbitals
 Finally, in the case of carbon atoms with only two bonding partners only two hybrid
orbitals are needed for the sigma bonds, and these sp hybrid orbitals are directed 180º
from each other.

Figure 28: sp hydrid orbitals

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Two p-orbitals remain unused on each sp hybridized atom, and these overlap to give two pi
bonds following the formation of a sigma bond (a triple bond), as shown below.

Figure 29: Triple Bond formation

The valence-shell electron-pair repulsion (VSEPR) theory
 The (VSEPR) theory states that valence electrons, in both bonding and nonbonding
electron pairs, want to be as far from each other as possible.
 The four bonding electron pairs in methane can achieve this arrangement by assuming
a tetrahedral structure. All bond angles in a tetrahedral structure are 109.5°, which is
experimentally observed for methane.
Molecular Geometry:
The Valence Shell Electron-Pair Repulsion (VSEPR) Model
Ammonia

Figure 30: Trigonal pyramidal shape of Ammonia

The tetrahedral arrangement of the electron pairs of an ammonia molecule that results when
the nonbonding electron pair is considered to occupy one corner. This arrangement of
electron pairs explains the trigonal pyramidal shape of the NH3 molecule.
Water

Figure 31: An approximately tetrahedral shape of water

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An approximately tetrahedral arrangement of the electron pairs for a molecule of water that
results when the pair of nonbonding electrons are considered to occupy the corners. This
arrangement accounts for the angular shape of the H2O molecule.
Boron Trifluoride

Figure 32: Trigonal planar shape of Boron trifluoride.

The triangular (trigonal planar) shape of boron trifluoride maximally separates the three
bonding pairs.
Table 1.1 Molecular geometry

CHEMICAL BONDS
 Atoms without the electronic configuration of a noble gas generally react to produce
such a configuration.
 It is largely the difference between the electronegativities of two atoms which
determines what kind of bond is formed between them.
 The interaction involves Valence electrons
TYPES OF BONDING
 The different types of chemical bonding are determined by how the valence electrons
are distributed among the bonded atoms.
 Two extreme types of Bonds are known;
 Ionic/ Electrovalent Bonding

 Covalent Bonding
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  Other intermediate bonding types also exist

Ionic bonds
 Formed by the transfer of one or more electrons from one atom to another to create
ions.
 Ionic substances, because of their strong internal electrostatic forces, are usually very
high melting solids, often having melting points above 1,000 °C.
 In polar solvents, such as water, the ions are solvated, and such solutions usually
conduct an electric current

Figure 33: Ionic bond formation

Essentially complete electron transfer from an element of low IE (metal) to an element of
high electron affinity (EA) (nonmetal)

Na(s) + 1/2 Cl2(g) ® Na+ + Cl- ® NaCl (s)

Covalent Bonds
Atoms achieve noble gas configurations by sharing electrons.

Figure 34: Covalent bond formation

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 When two identical atoms form a bond to each other, such as two hydrogen atoms or
two carbon atoms, they share electrons equally, giving a nonpolar covalent bond
 The bond arises from the mutual attraction of 2 nuclei for the same electrons.
 If the electrons are not shared equally in a bond and ∆EN for the atoms in a bond is
between 2.0 and 0.4, the bond is called a polar covalent bond

 A covalent bond is a balance of attractive and repulsive forces

Figure 35: Bond types and the periodic table

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Multiple Covalent Bonds

 Double Bonds

Figure 36: Double bond

Co-Ordinate (Dative) Bonding

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INTERMOLECULAR FORCES

 Forces between molecules are responsible for the magnitude of the melting and
boiling temperatures and for solubility characteristics of molecules.

 The greater the attraction between molecules of a specific compound, the higher the
melting and boiling points are likely to be.

 There are five categories of interactions

ION-DIPOLE INTERACTIONS

 Ion-dipole interactions describe the interaction between an ion and the partial charge
(δ) of a polar molecule. Cations are attracted to the negative pole of a dipole, and
anions are attracted to the positive pole of a dipole.

 This interaction is particularly important for solutions of ionic compounds in polar

solvents, such as an ionic Na+ ion interacting with a polar water molecule.

Figure 37: Ion-dipole

DIPOLE-DIPOLE INTERACTIONS

 Dipoles result from unequal sharing of electrons in bonds. If molecules are close to
each other, the negative pole of one molecule is attracted to the positive pole of
another molecule as shown.

 These interactions are generally weaker than ion-dipole interactions.

Figure 38: Dipole-dipole

HYDROGEN BONDS

 This is a special type of dipole-dipole interaction.

 It is a strong interaction between a covalently bonded hydrogen atom and a molecule

containing an atom with nonbonding electrons.

 The hydrogen atom undergoing hydrogen bonding must be covalently bonded to an

oxygen, a nitrogen, or a fluorine atom, resulting in a highly polar covalent bond. This
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 puts a large partial positive charge (δ+) on the covalently bonded hydrogen atom and
it seeks an electron pair on another atom.

 Hydrogen bonds are stronger than most dipole-dipole interactions. An example is

shown for water.

Figure 39: Hydrogen Bonding

DIPOLE-INDUCED DIPOLE INTERACTIONS

 If a polar molecule is close to a nonpolar molecule, it can influence the electron cloud
of the nonpolar molecule, making the latter somewhat polar.

 This results in an attraction between dipoles of unlike charges on two different

molecules, as shown below

Figure 40: Dipole-induced dipole

LONDON DISPERSION FORCES

 At any given instant, the electrons surrounding an atom or molecule are not uniformly
distributed; that is, one side of the atom may have a greater electron density than the
other side.

 This results in a momentary dipole within the atom.

 The dipole on one atom may induce a dipole on another atom. The net result is an
attraction between atoms.

 This explains the interaction between helium atoms that are nonpolar, yet they must
have attraction for each other since they form liquids when cooled sufficiently.

 All molecules exhibit dispersion forces.

Figure 41: London dispersion forces

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