SCHOOL OF MEDICINE AND

HEALTH SCIENCES
BASIC SCIENCES DEPARTMENT
CHEMISTRY FOR MEDICAL STUDENTS
COURSE CODE: BMCH 120
 TOPIC OBJECTIVES
• Classification & Structural formulas of
organic compounds.
• Functional groups in organic chemistry.
• Basics of structural isomerism.
• General nomenclature of organic
compounds.
• Resonance structures.
• Calculation and application of IHD.
• Reactions in organic chemistry.
What is Organic Chemistry?
 Organic Chemistry is the…
• Study of the nomenclature, structure,
properties, composition, reactions, and
preparation of carbon-
containing compounds.
• Discipline of chemistry involving the study
of compounds having carbon as the
principal compound.
• NB: Organic compounds can also contain
other elements like: oxygen, sulfur,
nitrogen, phosphorus, or the halogens.
What are Organic Compounds?
• Class of chemical compounds in
which one or more atoms of carbon
are covalently linked to other atoms
of elements.
• Carbon is the principal element for
organic compounds; the primary
constituents of all living organisms.
Some Organic Products…
Classes of Organic Compounds
• Hydrocarbons: e.g. Methane &
Ethene.
• Sugars: e.g. Glucose &
Fructose.
• Lipids: e.g. Phospholipids &
Steroids.
• Proteins: e.g. enzymes &
Hemoglobin.
• Nucleic Acids: e.g. DNA & RNA.
 Application of Organic
Chemistry in Medicine…
• To determine drug
constitution, its
size and shape &
use in medicines
to make it effective
to treat a particular
disease.
Organic Chemistry Vs Medicine…
• Organic chemists study the metabolism,
half lives of drugs & how they interact
with the body.
• It helps to optimize the pharmacological
properties of the drug; such as its
bioavailability, potency, and safety.
The Uniqueness of the Carbon Atom
• The carbon element has extraordinary
properties,
• Has special bonding properties which in
turn give organic molecules characteristic
structural complexity, chemical & diversity.
 Catenation in the Carbon atom.
Χ●
●
Χ C
Χ●
●
Χ

Carbon is able to form 4 covalent

bonds (4 valence electrons) with
other carbon or other elements.
 Why a huge number of Organic
Compounds?
• This is due to Catenation; ability of
Carbon to form strong covalent bonds
with other C, H, O, Br, I atoms…
• Carbon forms multiple bonds; single,
double, triple bonds…
 The Structural Complexity of
Organic Molecules
• The following properties of carbon are
responsible for organic molecules’
structural complexity:
• Electron Configuration, Electronegativity,
and covalent bonding.
• Bond properties, catenation, and
molecular shape.
• Molecular stability.
 The Uniqueness of the Carbon
Atom…
• 1. Bonding to heteroatoms; like O, N, S.
• 2. Electron density and reactivity.
• 3. Nature of functional groups; e.g. -OH,
-COOH, -CHO
 What are the Major Sources of
Organic Compounds?
• Plants & Animals; e.g. Sugars, Proteins, Fats
& Oils, alkaloids, Hormones, Vitamins, etc.
• Natural Gas & Petroleum…
• Coal; yields Coke/Carbon & Coal Tar..
• Laboratory Synthesis and Reaction
Mechanisms; e.g. synthesis of Urea,
Paracetamol, Aspirin, Insulin, etc.
• Fermentation; yields alcohols, acids, vitamins
& antibiotics.
 Characteristics of Organic
Compounds
• They are nonpolar compounds – they do
not dissolve in polar solvents like Water
O-

H+ +H

*Remember the rule –

“likes dissolve likes”
 Organic Compounds have Low M.P –
due to weak intermolecular forces.
C-C ● ● ● C-C
STRONG STRONG
weak

 They Low Boiling Point…

They react slower than Inorganic
compounds – due to strong covalent
bonds between atoms.
 They exhibit Isomerism.
 Classes of Organic Compounds
• Open-chain compounds, (acyclic
compounds) &
• Closed chain compounds (cyclic
compounds).
Classification of Organic Compounds
 Aromatic Compounds – a series of
cyclic unsaturated hydrocarbons.
General formula CnH2n-6
Benzene – C6H6 the simplest in the family
H

C
H
C C H

H C C H
C
H
Types Of Bonds in Organic Compounds
Single Bond – single covalent bond in
which they share 1 pair of electrons. (2 e-)

● ●
C C ● C C
●● ●
● ●
Double Bond – carbon atoms may share 2
pairs of electrons to form a double bond.

● ●
●●
C C ●
C ●● C
●
Triple Bond – carbon atoms may share
3 pairs of electrons to form a triple bond.

C C ●●
●C ●● C ●
●●
 Functional Groups for Organic
Compounds
• A functional Group is the reactive part of
an organic compound that
• Determines the class and reactivity of an
organic molecule/compound.
• Common classes and functional groups of
organic compounds include:
• Alcohols, carboxylic acids, aldehydes,
ketones, ethers, esters amines, amides,
etc.
• Alcohols -OH Hydroxyl

• Organic acids -COOH Carboxyl

• Aldehydes O -CHO Carbonyl

• Ketones -C-
Carbonyl

• Ethers -O-
O
• Esters -C-O
• Amines -N- O
• Amides -C-NH
 Organic structural formulae
• Organic chemists use a variety of formats
to write structural formulas.
• The following are some of the common
formats;
• Ball and Stick Model
• Electron dot Formula
• Dash Formula
• Condensed formula
• Bond line Formula
Structural Formulas in Organic Chemistry
 Ball and Stick Model
• The ball-and-stick model is a 3D molecular
model where atoms are represented by spheres
(balls) and chemical bonds are represented by
rods (sticks),
• It is a 3D model where atoms are represented
by spheres of different colors and bonds are
represented by sticks between the spheres.
Ball and Stick Model
 Lewis/Electron dot Formula
• A representation of the valence electrons of
an atom that uses dots around the symbol of
the element.
• The number of dots equals the number of
valence electrons in the atom.
Lewis/Electron dot Formula
 Dash structural formulas
• Show bonding electron pairs, and include
elemental symbols for all of the atoms in a
molecule. They show connectivity of the
atoms.
 Condensed Structural Formulas
• Condensed structural formulas are written
without showing all the individual bond like
shown below.
 Bond-Line Formulas/Line-
Angle Formula
• In bond-line formulas bonds are
represented by lines, and carbon atoms
are assumed to be present wherever two
lines meet or a line begins or ends.
• Nitrogen, oxygen, and halogen atoms are
shown, but hydrogen atoms are not
usually drawn unless they are bonded to
an atom that is drawn
 Three-Dimensional Formulas
• Three-dimensional geometry in molecules
can be depicted using bonds represented
by dashed wedges, solid wedges, and
lines
 TASK
1. Name three main groups of straight chain
hydrocarbons. For each group give a Condensed
formula and Dash structural formula for a two-
carbon molecule.
2. Identify three functional groups found in this
molecule of vanillin:
 Isomerism
• Isomers are different compounds with the same
molecular formula.
• The following are some of the types of different
isomers.
• Constitutional isomers (or structural isomers)
are isomers that differ in their bonding
sequence; that is, their atoms are connected
differently.
• Stereoisomers are isomers that differ only in
how their atoms are oriented in space. Their
atoms are bonded in the same order
Classification of Isomers
 Geometric Isomerism
• Geometric Isomerism is defined as two or more
molecules that contain the same type of atoms
and bonds but have different spatial
arrangements of atoms
 Optical Isomerism
• Describes molecules with the same molecular
formula and connectivity but differ in their
spatial arrangement;
• Resulting in non-superimposable mirror images
called enantiomers, which exhibit different
optical activities.
 What are Hydrocarbons?
• These are organic compounds containing
carbon and hydrogen atoms ONLY.
• Examples of hydrocarbon include:
alkanes, alkenes, alkynes, and benzene.
Hydrocarbons are organic compounds
that consist of only Carbon and
Hydrogen atoms.

H H H
H C H H C C H

H H H
How are Hydrocarbons Classified?
 Hydrocarbons Classification
• Aliphatic (Acyclic) Compounds; open
chain carbon compounds, e.g. Alkanes &
Alkenes.

• Alkane

• Alkene
 Hydrocarbons Classification…
• Saturated (C-C, Single bonds) and

• Unsaturated (C꓿C, Double & Triple Bonds)

Compounds.
Hydrocarbons are organic compounds
that consist of only Carbon and
Hydrogen atoms.

H H H
H C H H C C H

H H H
 Alkanes = CnH2n+2
• A saturated hydrocarbon contains 5
carbons. What is the formula?
C5H2(5)+2 = C5H12
• A saturated hydrocarbon contains 20
carbons. What is the formula?
C20H2(20)+2 = C20H42

Saturated = Single
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Alkanes

• CH4 = methane
• C2H6 = ethane
• C3H8 = propane
• C4H10 = butane
• C5H12 = pentane
 Alkenes – CnH2n
series of unsaturated hydrocarbons
having one double bond (C=C)
• Also called ethylene
series (IUPAC name is
ethene)
• General formula CnH2n
Alkenes

• C2H4 = Ethene
• C3H6 = Propene
• C4H8 = Butene
• C5H10 = Pentene
• To find the number of
hydrogens, double the
number of carbons.
 1-Butene
This is 1-butene, because the double
bond is between the 1st and 2nd carbon
from the end.

ISOMERS: Molecules have the same

molecular formula, but have different
structural formulas.
Pentene

This is 1-pentene. The double bond is

on the first carbon from the end.

This is not another isomer of pentene.

This is also 2-pentene, just that the
double bond is closer to the right end.
 Alkynes –
a series of unsaturated
hydrocarbons that contain 1 triple
bond.
• Also called the acetylene series

General formula CnH2n-2

C C
Alkynes

• C2H2 = Ethyne
• C3H4 = Propyne
• C4H6 = Butyne
• C5H8 = Pentyne
Alkyl Groups – have one less
hydrogen than the corresponding
alkane.
• CH3 is methyl – one less H than
methane, CH4
H
H C H

H
Draw methyl
C2H5 is ethyl – one less H than ethane C2H6

Condensed
Formula:
CH2CH3

Ethane
C3H7 is propyl – one less H than propane C3H8

propane
 IUPAC Naming of
Branched
Hydrocarbon Chains
• 2,2,4-trimethylpentane

CH3
C C C C C

CH3 CH3
Name the following compound:

CH3 - CH2 - CH2 – CH – CH – CH - CH3

CH2 CH3 CH3
CH3
 7 6 5 4 3 2 1
CH3 - CH2 - CH2 – CH – CH – CH - CH3
CH2 CH3 CH3
CH3
• The name of this compound is:

2,3-dimethyl – 4-ethyl heptane

 CH3 CH3
CH3 - CH2 – CH – CH2 – CH - CH3
6 5 4 3 2 1

2,4 dimethyl hexane

When naming with a double/triple bond-
start # carbons closest to the bond.

CH3 CH3

C C C C C
1 2 3 4 5

3,4 dimethyl, 2-pentene

• 2,2,4-trimethylpentane

CH3
C C C C C

CH3 CH3
Organic Chemistry Symbolism…
Organic Chemistry Symbolism…
Organic Chemistry Symbolism…
Organic Chemistry Symbolism…