PHA: 105 Organic Pharmacy 1 Chapter 1: Introduction

PHA: 105
Organic Pharmacy 1
Chapter 1: Introduction
27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 1

History of Organic Chemistry
Papyrus
 The history of organic chemistry can be traced back to ancient times when people
extracted chemicals from plants and animals to treat members of their tribes.
 They didn’t label their work as "organic chemistry", they simply kept records of
the disease healing properties of medicinal plants.

Willow
 The Ebers papyrus (1550 BC), an ancient

Egyptian medical text, refers to willow as an
anti-inflammatory or pain reliever for non-
specific aches and pains.

Berzelius
1779 –1848;
History of Organic Chemistry Swedish chemist
 Organic chemistry was first defined as a branch of modern

science in the early 1800's by Jon Jacob Berzelius.
 He classified chemical compounds into two main groups:

o Organic if they originated in living or once-living matter
o Inorganic if they came from "mineral“ or non-living matter
 Berzelius believed in Vitalism – the idea that organic compounds could only
originate from living organisms through the action of some vital force.

Vitalism
 Up to 19th century, it was argued that the essential
difference between organic and inorganic was the 'vital
force', that was present only in organic material.
 Vitalism states that organic compounds are only produced by living organism.
 Scientists for a long time thought that organic compounds could never be
synthesized from inorganic material.
 However, Friedrich Wohler (1828; student of Berzelius) abolished the concept of
vitalism in the science of chemistry by accidently synthesizing urea (organic
compound) from inorganic components.

Frederich Wohler
1800–1882; German chemist
 Wohler mixed silver cyanate (AgOCN) and ammonium chloride

(NH4Cl) to produce solid silver chloride (AgCl) and aqueous
ammonium cyanate (NH4OCN).

 Wohler tried to purify the aqueous ammonium cyanate by evaporating the water.
To his surprise, the solid left over after the evaporation of the water was UREA!

 Wohler's discovery was a turning point in the history of chemistry for two
reasons.
i. It abolished the idea of Vitalism because an organic compound

was produced from an inorganic one.
ii. It discovered the concept of isomerism - the possibility of two
or more different structures (ammonium cyanate crystals and
urea crystals) based on the same chemical formula (N2H4CO).

August Kekule
1829 –1896
German chemist
 Kekule was the principal founder of the theory of chemical structure

 Theory of chemical structure describes the order of the arrangement of atoms and
bonds in a molecule—as well as the interaction of atoms and the relationship
between a compound's structure and its physical and chemical properties.
 Kekule gave the idea of atomic valence, especially the tetravalence of carbon and
the ability of carbon atoms to link to each other to the determination of the
bonding order of all of the atoms in a molecule.

 Kekulé's most famous work was on the structure of benzene.
 The carbons are arranged in a hexagon, and he suggested alternating double
and single bonds between them.
 Each carbon atom has a hydrogen attached to it.

Scott Couper
1831 – 1892
Scottish chemist
 Couper independently proposed an early theory of chemical structure and

bonding.
 He developed the concepts of tetravalent carbon atoms linking together
and the bonding order of the atoms in a molecule can be determined from
chemical evidence.
 Couper published the theory of chemical structure in June 1858 (Kekule
published it in May 1858).

27/07/2020 12
Nobel Prize in Chemistry 2019
 The Nobel Prize in Chemistry 2019 rewards the

development of the lithium-ion battery.
 This lightweight, rechargeable and powerful battery is now used in everything from
mobile phones to laptops and electric vehicles.
 It can also store significant amounts of energy from solar and wind power, making
possible a fossil fuel-free society.

Organic compound

Organic compound
 In the modern organic chemistry, the commonly accepted definition of organic

compound essentially to any carbon containing compound.
 Due to carbon's ability to catenate (form chains with other carbon atoms),
millions of organic compounds are known.
 Organic compounds are of central importance because all known life is based
on organic chemicals.

Classification according to the structure

Systematic naming of organic compounds
 Systematic naming of organic compounds

follows a guideline in organic chemistry as
set by the International Union of Pure and
Applied Chemistry (IUPAC).
 (IUPAC) is the world authority on chemical nomenclature and terminology,

including the naming of new elements in the periodic table; on standardized
methods for measurement; and on atomic weights, and many other critically-
evaluated data.
 IUPAC is about much more than nomenclature and the naming of elements. It also
resolves critical global issues that involve every aspect of chemistry

 General rules of IUPAC for naming of organic compounds
o Select the longest continuous carbon chain to which a functional

group is attached
o Number the chain to give the lowest number to the functional group
o Name the longest chain

 General rules of IUPAC for naming of organic compounds
o Prefix the position of the functional group

o Number other substituents, name and place as prefixes in
alphabetic order.
o Commas are used between numbers
o Dashes are used between letters and numbers.
o There are no spaces in the name.

Practice

Structural theory in Organic chemistry
 The structural theory was proposed by August Kekule, Scott Couper, and
Aleksandr Mikhailovich.
 The structural theory is the framework of ideas about
o how atoms are put together to make molecules
o the order in which atoms are attached to each other
o arrangement of electrons that hold them together.
 The structural theory also deals with the shapes and sizes of the molecules.
 According to structural theory, from the structural formula of a molecule it is
possible to derive physical and spectroscopic data and to predict chemical
reactivity

Structural theory in Organic chemistry
 A molecule is often represented by a picture or

a model sometimes by several pictures or
several models.
 The atomic nuclei are represented by letters or
wooden balls, and the electrons that join them
by lines or dots.
 These crude pictures and models are useful to
understand physical and chemical behaviour of
the compound.

Structural Theory: Shapes of atomic orbitals
 Electron is pictured as a cloud. It is a blurred

photograph of the rapidly moving electron.
 The shape of the cloud is the shape of the orbital.
 Cloud is not uniform, but is densest in those
regions where the probability of finding the
electron is the highest, i.e. the region where the
electron density is the greatest.
 The electrons are never in a single point location.

Structural Theory: Shapes of atomic orbitals
 Electron cloud can make two shapes of orbital in covalent bonding:

o 's' orbital: spherical shape
o 'p' orbital: dumbbell shape

 The overlapping can take place by two ways:
(1) Axial or end to end: the bond is known as sigma (σ) bonding
(2) Lateral or parallel: the bond is known as pi (π) bonding

Hybridization of orbitals in carbon atom

SP3 Hybridization in methane

SP2 Hybridization in Ethene

SP Hybridization in Acetylene (Ethyne)

Polar covalent bonds
 Electrons in covalent bonds are not necessarily shared equally by the two
atoms that they connect. If one atom has a greater tendency to attract
electrons toward itself than the other, electron distribution is said to be
polarized, and the bond is referred to as a polar covalent bond.
 Because electrons have a negative charge, the unequal sharing of electrons
within a bond leads to the formation of an electric dipole: a separation of
positive and negative electric charge.
 The amount of charge separated in such dipoles is denoted as δ+ (delta
plus) and δ− (delta minus).

Polar covalent bonds: water
 Water is a polar molecule because oxygen is more electronegative than

hydrogen, and therefore electrons are pulled closer to oxygen.
Polar covalent bonds: water
 The oxygen atom in water molecule (H2O) attracts the shared electrons more
strongly than the hydrogen atoms.
 As a result, the oxygen atom becomes slightly negative in charge, and the
hydrogen atoms become slightly positive in charge.
 The water molecule is made up of oxygen and hydrogen, with respective
electronegativities of 3.44 and 2.20. The electronegativity difference polarizes
each H–O bond, shifting its electrons towards the oxygen (illustrated by
arrows). These effects make the overall molecule polar.
 The dipoles do not cancel out, resulting in a net dipole.

All polar compounds contain polar bonds. But having polar
bonds does not necessarily result in a polar compound.
 In the molecule of formaldehyde and carbon dioxide, in both molecules,

the oxygen atoms attract electrons more strongly than the carbon or
hydrogen atoms. However, formaldehyde is a polar compound and
carbon dioxide is nonpolar.

 In formaldehyde, the oxygen atom attracts electrons more strongly than the
carbon atom, resulting in a partial negative charge at oxygen atom and a partial
positive charge at the carbon atom. The dipoles do not cancel out, resulting in a
net dipole and making it a polar compound.
 Carbon dioxide (CO2) has two polar C=O bonds, but the geometry of CO2 is
linear so that the two bond dipole moments cancel and there is no net
molecular dipole moment; the molecule is nonpolar.
Electronegativity
 The electron-pair bonds recognizes that the sharing of electrons by the

nuclei of two different elements is unequal.
 Pauling defined the concept of unequal sharing in terms of
electronegativity, defining the term as “the power of an atom in a molecule
to attract electrons to itself.”
 Electronegativity depends on the number of protons in the nucleus and is
therefore closely associated with position in the periodic table.
 An electronegative element attracts electrons; an electropositive one
donates them.

Carbocation
 A carbocation (previously called carbonium ions) is an ion with a

positively charged carbon atom.
 According to the IUPAC, a carbocation is any cation containing an even
number of electrons in which a significant portion of the positive
charge resides on a carbon atom.

Carbocation
 Carbocations are reactive intermediates in many organic reactions.

 Among the simplest examples of carbocations are the
o methenium CH+3
o methanium CH+5
o vinyl C2H+3 cations

Electrophile
 In organic chemistry, an electrophile is an electron pair acceptor.

 Electrophiles are positively charged or neutral species having vacant orbitals.
 It participates in a chemical reaction by accepting an electron pair in order to
bond to a nucleophile (electron pair donor).

Electrophile
 Because electrophiles accept electrons, they are Lewis acids (Lewis acid is a
chemical species that contains an empty orbital which is capable of accepting
an electron pair).
 Most electrophiles are positively charged, have an atom that carries a partial
positive charge, or have an atom that does not have an octet of electrons.

Nucleophile
 Nucleophile is a chemical species that donates an electron pair to form a

chemical bond in relation to a reaction.
 All molecules or ions with a free pair of electrons or at least one pi bond
can act as nucleophiles.
 Because nucleophiles donate electrons, they are by definition Lewis
bases.

The End

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PHA: 105

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 1

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 2

 The Ebers papyrus (1550 BC), an ancient

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 3

 Organic chemistry was first defined as a branch of modern

 He classified chemical compounds into two main groups:

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 4

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 5

 Wohler mixed silver cyanate (AgOCN) and ammonium chloride

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 6

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 7

i. It abolished the idea of Vitalism because an organic compound

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 8

 Kekule was the principal founder of the theory of chemical structure

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 9

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 10

 Couper independently proposed an early theory of chemical structure and

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 11

 The Nobel Prize in Chemistry 2019 rewards the

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 13

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 14

 In the modern organic chemistry, the commonly accepted definition of organic

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 15

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 16

 Systematic naming of organic compounds

 (IUPAC) is the world authority on chemical nomenclature and terminology,

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 17

 General rules of IUPAC for naming of organic compounds

o Select the longest continuous carbon chain to which a functional

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 18

 General rules of IUPAC for naming of organic compounds

o Prefix the position of the functional group

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 19

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 20

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 21

 A molecule is often represented by a picture or

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 22

 Electron is pictured as a cloud. It is a blurred

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 23

 Electron cloud can make two shapes of orbital in covalent bonding:

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 24

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 25

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 26

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 27

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 28

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 29

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 30

 Water is a polar molecule because oxygen is more electronegative than

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 32

 In the molecule of formaldehyde and carbon dioxide, in both molecules,

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 33

 The electron-pair bonds recognizes that the sharing of electrons by the

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 35

 A carbocation (previously called carbonium ions) is an ion with a

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 37

 Carbocations are reactive intermediates in many organic reactions.

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 38

 In organic chemistry, an electrophile is an electron pair acceptor.

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 39

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 40

 Nucleophile is a chemical species that donates an electron pair to form a

27/07/2020 SZR/IUB/PHA105/CHAPTER 1/INTRODUCTION 41