Chapter 15 organic chemistry

Chapter 15 - Organic Chemistry
Dr. Hashim Ali
Post-Doc Uppsala University, Sweden.
PhD Computational Biology, KTH, Stockholm, Sweden.
Federal Board of Intermediate and Secondary
Education (FBISE)

• Define organic chemistry and organic compounds
• Explain why there is such a diversity and magnitude of organic
compounds.
• Classify organic compounds on structural basis.
• Explain the use of coal and petroleum as a source of various
hydrocarbons.
• Explain the use of plants as a source of organic compounds.
• Explain that organic compounds are also synthesized in the lab.
• Define functional groups and homologous series.
• Given a sample of an organic compound with an unknown chemical
formula, determine its elemental composition.
After completing this lesson, you will be able to

Chapter Overview - Sections
• Introduction to organic chemistry
• Importance of organic chemistry
• Sources of organic compounds
• Characteristics of organic compounds
• Uses of organic compounds
• Fullerenes, Bucky balls and their
importance in Chemistry
• Ways of representing organic molecules
• Homologous series
• Functional group
• Detect presence of different elements in
organic compounds

15.0 – Introduction to organic chemistry
Dr. Hashim Ali
Education (FBISE)
Chemistry F.Sc
II

• Two main classes of compounds.
o Inorganic - mineral origin.
o Organic - vegetable or animal origin.
• Examples of inorganic compounds
are table salt, marble and carbon
dioxide etc.
• Examples of organic compounds are
acetic acid (from vinegar), alcohol
(from grapes/wine) and tartaric acid
(from grapes) etc.
15.0.1 - Introduction - Organic compounds

• Organic  Greek. Meaning “relating to or derived from
living matter”.
• Organic compounds were known and classified to humans
since ancient Egypt (2000 B.C.).
• Until beginning of 19th century chemists were unable to
produce organic compounds in labs.
• Theory of vitalism - commonly believed that organic
compounds could only be synthesized in living things and
required a specific force (called vital force or soul).
• Classic definition of ‘Organic chemistry’  chemistry of
living material or substances derived from living things.
• Concerned with living plants or animals, or substances
derived from them (e.g., coal from plants and oil from
microscopic sea organisms).
• Organic compounds were known to show unique
characteristics as compared to inorganic compounds, e.g.,
characterization into families with similar chemical
properties despite different molecular weights (like various
carbohydrates, lipids, proteins and nucleic acids).
15.0.2 - Introduction - History of Organic chemistry

• In 1826, Friedrich Wöhler, a German
chemist synthesized Urea (an organic
compound) from Cyanic acid and
Ammonia (both inorganic compounds).
• Wöhler’s experiments divided chemists
into two groups - vitalists and non-
vitalists.
• Many other organic compounds were
synthesized from inorganic compounds
in subsequent years.
• By 1931, scientists had almost
unanimously abandoned vitalism as an
acknowledged belief.
15.0.2.1 - Introduction - History of Organic chemistry- Refuting
vitalism theory

• Carbon and Hydrogen are essential
elements in all organic compounds.
• Organic chemistry  chemistry of
compounds of Carbon except carbon
monoxide (CO), carbon dioxide (CO2),
carbon disulphide (CS2) carbonates
(CO3
-2), hydrocarbonate (HCO3
-1),
cyanides (CN-1), thiocynates (SCN-1),
which have different chemical
properties to organic compounds.
• Modern definition  Organic
chemistry is the branch of chemistry
that deals with the study of
compounds of carbon and hydrogen
(Hydrocarbons), and their derivatives.
15.0.3 - Introduction - Organic Chemistry in modern times
Important organic
compounds
Carbohydrates Lipids
Nucleic
acids
Proteins
Monosaccharide
Fats
and oils
Nucleotide
Amino
acids
include
that consist of
which contains
Carbon
Hydrogen
Oxygen
Carbon
Hydrogen
Oxygen
Carbon
Hydrogen
Oxygen
Nitrogen
Phosphorus
Carbon
Hydrogen
Oxygen
Sulfur

15.0.3 - Introduction - Organic Chemistry in modern times
Important families that display characteristic organic
compound behavior and obtained from living things
which contain
Carbon
Hydrogen
Carbon
Hydrogen
Oxygen
Carbon
Hydrogen
Oxygen
Nitrogen
Carbon
Hydrogen
Nitrogen
Carbon
Hydrogen
Sulfur
Carbon
Hydrogen
Halogen
Alcohols, aldehydes,
ketones, ethers, esters,
carboxylic acids and phenols
include
Hydrocarbons
Amides and
nitro
compounds
Amines Thiols Halides

15.0 - Introduction to organic chemistry

15.1 – Importance of organic chemistry
Dr. Hashim Ali
Education (FBISE)
Chemistry F.Sc
II

• A field of immense importance to technology.
• Fundamental to biology medicine.
• Living organisms are made up of organic compounds;
o The molecules of “molecular biology” are organic molecules.
o Biology, on molecular level is organic chemistry!
• Tens of thousands of organic compounds exist.
• Behavior of different organic compounds belonging to the same family can
be characterized.
• Organic compounds have a vast number of uses - from food to clothes to
shelter.
15.1.1 – Importance - Why study organic chemistry?

• Carbon is special among all elements.
• Carbon atoms can form extremely
long chains - attaching themselves to
other C atoms to an extent not
possible for atoms of any other
element.
• The number of compounds that
contain carbon due to its atomic
structure and small compact size is
many times greater than the number
of compounds that do not contain
carbon.
15.1.2 – Importance - Diversity and magnitude of Carbon
compounds

Bonding nature of Carbon
Tetravalent
Multiple bonds
Strong C-C bonds
• C-C bonds are much stronger
than bonds between atoms of
other elements.
Bond Bond energy/kJmol-1
C-C 350
Si-Si 222
N-N 160
O-O 150
• Carbon forms four bonds.
• Due to strong C-C bond, it can bond
with itself to form stable straight or
branched chains, or ring structures.
• Carbon can also form single, double
or triple bonds with itself.
• Carbon compounds can have a
varying degree of unsaturation.
15.1.3 – Importance -
Carbon is special!

15.1 - Importance of organic chemistry

15.2 – Sources of organic compounds
Dr. Hashim Ali
Education (FBISE)
Chemistry F.Sc
II

• Fossil remains
o Coal
o Petroleum
o Natural Gas
• Plants and animal products
• Partial and total synthesis
o Fermentation/Biotechnology
15.2 – Sources of organic compounds

• A fossil is the remains of (a) living
thing(s) that died millions of years ago.
• Subsequently, it was covered by layers
of sedimentary sand over time and got
buried in the Earth’s crust.
• Under high pressure and temperature,
the fossil is converted to coal, oil and
natural gas - all called fossil remains or
fossil fuels.
• Fossil fuels are the one of the main
sources of organic compounds.
15.2.1 – Sources of organic compounds - Fossil remains

15.2.1 – Sources of organic compounds - Fossil remains

• Coal is a fossil fuel and is the altered remains of
prehistoric vegetation that originally
accumulated in swamps and peat bogs.
• One of the major source of organic compounds.
• Yields coke, coal tar, ammoniacal liquor and
coal gas on “destructive distillation (pyrolysis)”.
• Fractional distillation of coal gas yields methane
(CH4) and Benzole.
• Fractional distillation of coal-tar yields more
than 200 organic compounds.
• These coal-tar products form the starting
materials for the manufacture of useful aromatic
(meaning cyclic organic compounds)
compounds, including perfumes, drugs, dyes,
paints, and others.
Fractional
Distillation
Benzole methane
Cyanides Sulphur
compounds
Fractional
Distillation
Benzole Toluene
Xylene
Naphthalene
Phenols Other aromatic
compounds
Coal tar
Coal
Destructive
Distillation
Ammoniacal
liquor
CokeCoal gas
15.2.1.1 – Sources of organic
compounds - Fossils - Coal

• What are the products of fractional distillation of coal tar? (15.2.1.1)
• What we obtain by fractional distillation of coal gas? (15.2.1.1)
• How many types of distillation are used in the laboratory? (Many, more
than 10, types of distillation exist but mainly Fractional and Destructive
distillation are used extensively.)
15.2.1.1.1 - Sources of organic compounds - Fossil remains - Coal -
Quick quiz

• Petroleum or crude oil is a black thick sticky liquid.
• It is a complex mixture of many hydrocarbons, whose
composition varies according to its place of
occurrence, time since fossilized and
temperature/pressure constraints.
• The hydrocarbons can be separated using fractional
distillation.
15.2.1.2 – Sources of organic compounds - Fossil remains -
Petroleum

• It is a complex mixture of many hydrocarbons, most of which are used in everyday
life activities.
15.2.1.2 – Sources of organic compounds - Fossil remains -
Petroleum

• Mixture of low boiling and light-
weight hydrocarbons.
• Contains methane (about 85%),
ethane, propane and butane.
• Formed by the decomposition of
organic matter.
• Usually found over petroleum
wells, where lighter hydrocarbons
vaporize and are collected over oil.
• In Pakistan, there are vast reserves
of gas in Baluchistan (Sui), Sindh
and Punjab (Mianwali).
butane
Natural Gas
Fractional
Distillation
methane ethane propane
15.2.1.3 – Sources of organic
compounds - Fossil remains
- Natural gas

• Many organic compounds are obtained directly
from plant and animal sources by suitable
methods of isolation.
• Typical examples of natural products are
carbohydrates (cellulose, starches, sugars),
proteins (silk, wool, casein, food proteins), fats
and oils (cottonseed and soybeans oils), lard,
butter, animal oils and fats, alkaloids (quinine,
morphine, strychnine), hormones, vitamins,
perfumes, flavors and so on.
• Many of these compounds are still extracted
from natural resources because they would be
far too expensive to produce artificially.
15.2.2 – Sources of organic compounds - Plant and animal
products

• Organic compounds obtained from plants
and animals.
o Most sugars.
o Some alkaloids: A naturally occurring organic
molecule that contains nitrogen.
o Some terpenoids: A large class of natural
products consisting of isoprene (C5) units.
o Certain nutrients such as vitamins, antigens,
carbohydrates, enzymes, hormones, lipids and
fatty acids, fats and oils, neurotransmitters,
nucleic acids, protein peptides and amino
acids, and lectins (sugar-binding proteins).
products

• Quinine:
o An alkaloid.
o An antimalarial and antipyretic (reduce fever) medicine.
o Obtained from Cinchona ledgeriana (quinine tree).
• Nicotine:
o An alkaloid.
o An insecticide.
o Obtained from Nicotina tabacum (tobacco) but also present in
eggplants, potatoes and tomatoes.
o Highly addictive!
• Menthol:
o Local anaesthetic and counterirritant substance.
o A rubefacient substance - a substance for topical application that
produces redness of the skin e.g. by causing dilation of the capillaries
and an increase in blood circulation. Commonly known as ointment.
o Obtained from Mentha avensis.
• Henna:
o A natural occurring dye to color hairs and hands.
o Used in weddings and Eids in Pakistan.
15.2.2 – Sources of organic compounds -
Plant and animal products

• Camphor: ( ‫)کافور‬
o A rubefacient.
o Obtained from Cinnamomum camphora (camphor tree).
• Rutin and hesperidin:
o Used for treatment of capillary fragility.
o Obtained from citrus species.
• Curcumin: (‫)ہلدی‬
o A choleretic - substances that increase the volume of
secretion of bile from the liver as well as the amount of
solids secreted.
o Obtained from Curcuma longa (turmeric).
• Cocaine:
o A local anesthetic.
o Obtained from erythroxylum coca (coca plant).
• Caffeine:
o A Central Nervous System (CNS) stimulant.
o Obtained from Camellia sinensis (tea, coffee and cocoa).
• Bromelain:
o An anti-inflammatory drug.
o Obtained from ananas cosmosus (pineapple).
products

• Synthesis is the process of making a compound
in lab.
• Partial synthesis refers to the process of using
simpler organic compounds to form complex
organic compounds.
• Total synthesis is the process of using inorganic
compounds to produce organic compounds.
• Simpler organic compounds have been
converted to thousands of more useful materials
by synthesis.
• In many cases, synthetic compounds have
replaced naturally occurring organic compounds
due to their superior properties, e.g., dyes,
rubbers, fibers, plastics, drugs and vitamins.
• In other cases, the synthetic compound do not
occur or are rare in nature, e.g., ether, glycol,
mercurochrome, aspirin and the sulpha drugs.
• In short, synthetic chemistry touches almost
every phase of life.
15.2.3 – Sources of organic compounds - Synthesis

• Fermentation is a metabolic process that
consumes sugar in the absence of oxygen.
• Fermentation is the production of chemicals
(i.e., organic acids, gases or alcohol) by the
action of micro-organisms.
• Alcohols, acetone, glycerol, antibiotics, acids,
and the like are derived by the action of
microorganisms upon organic matter.
• It occurs in yeast and bacteria, and also in
oxygen-starved muscle cells, as in the case of
lactic acid fermentation.
• The science of fermentation is known as
zymology.
15.2.3.1 – Sources of organic compounds - Synthesis -
Fermentation/Biotechnology

• All three products have found human uses.
o The production of alcohol is made use of when fruit juices are converted to
wine, when grains are made into beer, and when foods rich in starch, such as
potatoes, are fermented and then distilled to make spirits such as gin and
vodka.
o The production of carbon dioxide is used to leaven bread, e.g., for our ‘rotis’ .
o The production of organic acids is exploited to preserve and flavor vegetables
and dairy products.
• Food fermentation serves five main purposes:
o to enrich the diet through development of a diversity of flavors, aromas, and
textures in food substrates;
o to preserve substantial amounts of food through lactic acid, alcohol, acetic
acid, and alkaline fermentations;
o to enrich food substrates with protein, essential amino acids, and vitamins;
o to eliminate antinutrients; and
o to reduce cooking time and the associated use of fuel
15.2.3.1 – Sources of organic compounds - Synthesis -
Fermentation/Biotechnology

• Define modern definition of organic chemistry (15.0.3).
• Enlist different sources of organic compounds (15.2).
• Write important products from petroleum (15.2.1.2 - The fractional
distillation image).
• What are alkaloids (15.2.2)?
• Define fermentation (15.2.3.1).
• What is coal? (15.2.1.1.)
15.2.4 – Sources of organic compounds - Quick quiz

15.2 - Sources of organic compounds

15.3 – Pyrolysis (Destructive distillation) of coal
Dr. Hashim Ali
Education (FBISE)
Chemistry F.Sc
II

• When coal is heated in the absence of air
(temperatures ranging from 500-1000 0C)
- a process called destructive distillation or
pyrolysis, it is converted into
o Coke
o Coal gas
o Coal tar.
• Coal tar contains a large number of organic
compounds, separated by fractional
distillation - heating the mixture gradually,
where different gases have different boiling
points and vaporize separately!
• The total coal reserves of Pakistan are
estimated by the Geological survey of
Pakistan to be 184 billion tons.
15.3 – Pyrolysis (Destructive distillation) of coal

15.3 - Pyrolysis (Destructive distillation) of coal

15.4 – Characteristics of organic compounds
Dr. Hashim Ali
Education (FBISE)
Chemistry F.Sc
II

• Organic compounds differ from inorganic
compounds in several aspects!
• Carbon is an essential constituent of all organic
compounds.
• Less soluble in water but generally soluble in
organic solvents such as alcohol, ether,
benzene, etc.!
• Generally combustible in nature with high
percentage of Carbon.
• Low melting and boiling points, and are
volatile in nature.

• With low melting and boiling points,
organic compounds decompose at
high temperature into simpler
substances.
• Due to the absence of ionic bonds,
organic compounds are poor
conductor of electricity both in fused
state and in solution form.
• Most organic compounds are obtained
from plants and animal sources.
• Can have extremely high molecular
weights, often well over 1000.
• Most organic compounds can serve as
a source of food for bacteria.

• Due to presence of covalent bonds
instead of ionic bonds, the rate of
reaction for organic compounds are
very slow and require specific
conditions.
• In organic compounds, several
different compounds may exist for
the same chemical formula - a
phenomena called isomerism, e.g.,
o C3H6O3 or
o C5H11Cl.
Isomers of Lactic acid
1-chloropentane 2-chloropentane

15.4 - Characteristics of organic compounds

15.5 – Uses of organic compounds
Dr. Hashim Ali
Education (FBISE)
Chemistry F.Sc
II

• No field of science is so closely related with
our daily activities as is organic chemistry.
• The tremendous importance of organic
compounds in modern everyday life is
illustrated in the following list:
1. Food items. (e.g., proteins, fats,
carbohydrates, oils).
2. Clothing items. (e.g., natural fibers like
cotton, silk and wool. Synthetic fibers like
nylon, rayon and dacron).
3. Shelter: (e.g., wood, paints and
varnishes).
4. Power and transportation: (e.g., natural
gas, petroleum products and coal).

5. Medicines and drugs. (e.g., Penicillin and
streptomycin).
6. Insecticides. (e.g., DDT).
7. Hormones and steroids.
8. Vitamins and enzymes.
9. Antiseptics and anesthetics.
10. Pigments and dyes.
11. Paper and inks.
12. Perfumes, flavors and cosmetics.
13. Plastics, rubbers and resins.
14. Propellants, explosives and refrigerants.

15. Soaps and detergents.
16. Herbicides. (e.g., teflon).
17. Photographic films and developers.
18. Biological problems in organic chemistry

15.5 - Uses of organic compounds

15.6 – Fullerenes and Bucky balls
Dr. Hashim Ali
Education (FBISE)
Chemistry F.Sc
II

• Allotropy or allotropism (from Greek meaning 'other form') is the
property of some chemical elements to exist in two or more different
forms, in the same physical state, known as allotropes of these elements.
• Until recently, the element carbon was believed to exhibit only two main
allotropic forms, diamond and graphite.
o Research has now confirmed the existence of a third previously unknown form -
buckminsterfullerene (C60) and its relatives, the fullerenes (C24, C28, C32, C70 etc.).
• A fullerene is a molecule of carbon in the form of a
hollow sphere, ellipsoid, tube, and many other shapes.
• Cylindrical fullerenes are also called carbon nanotubes (buckytubes).
• Fullerenes are similar in structure to graphite, which is composed of
stacked graphene sheets of linked hexagonal rings.
• Unless they are cylindrical, they must also contain pentagonal (or
sometimes heptagonal) rings.
• The discovery of fullerenes greatly expanded the number of
known carbon allotropes, which had previously been limited to
graphite, graphene, diamond, and amorphous carbon such
as soot and charcoal.
15.6.1 – Fullerenes - New allotropes of carbon: fullerenes

• Spherical fullerenes, also referred to as
Buckminsterfullerenes or buckyballs, resemble
the balls used in football.
• The first fullerene molecule to be discovered, and
the family’s namesake, buckminsterfullerene
(C60), was manufactured in 1985 by scientists in
William Marsh Rice University, Texas.
• The name was an homage to Buckminster Fuller,
the architecture, whose geodesic domes in
Montreal Canada it resembles.
• Buckyballs and buckytubes have been the subject
of intense research, both for their chemistry and
for their technological applications, especially
in material science, electronics, medical science
and nanotechnology.
15.6.1.1 – Fullerenes - Bucky balls, a
special case of fullerenes

• What are allotropes? (15.6.1)
• Why it was given the name Bucky balls? (15.6.1.1)
• Define the third allotropic form of Carbon? (15.6.1)
15.6.2 – Fullerenes and Bucky balls - Quick Quiz

15.6 - Fullerenes and Bucky balls

15.7.0 – Ways of representing organic molecules
Dr. Hashim Ali
Education (FBISE)
Chemistry F.Sc
II

• This section explains the various ways that organic molecules can be
represented on paper or on screen - including molecular formulae, and
various forms of structural formulae.
• The main ways to represent organic drawings are:
o 3-Dimensional structure
o Molecular formula
o Empirical formula
o Condensed formula
o Displayed formula
o Structural formula
o Skeletal formula

• A 3 dimensional structural formula shows all the bonds in the
molecule as individual lines along with the bond angles, arrangement
of molecules and direction of all atoms in a 3D setting. You need to
remember that each line represents a pair of shared electrons.
• Generally represented as a ball and stick structure but can be
represented by atoms and specific line types to indicate whether a line
is outwards of paper, on the same plane as paper or going into the
paper as well as with bond angles and distance between atoms.
• The representation is most informative among all representations - it
is almost complete for any purpose in this class.
• The only representation that works for geometric isomers (molecules
with same formula and bonds but with different spatial arrangement
of molecules).
• However, very hard to draw on paper and requires a lot of extra
information, which is not required most of the times, e.g. in chemical
reactions and general structural drawings of molecules.
• Also, for anything other than the most simple molecules, drawing a
fully displayed formula is a bit of a bother - especially all the atoms,
bonds and bond angles.
• However, I have tried to stick to 3-D structures when introducing an
organic compound, discussing geometric isomers and not used it
anywhere else.
Butanoic acid
Ethanol
15.7.1 – Ways of representing organic molecules - 3 dimensional
(3D) structural formula

• The molecular formula of an organic compound simply counts
the number of each type of atom present.
• It tells you nothing about the bonding within the compound.
• Molecular formulae are very rarely used in organic chemistry,
because they don't give any useful information about the
bonding in the molecule and are not necessarily unique to a
compound.
• About the only place where you might come across them is in
equations for the combustion of simple hydrocarbons. In those
cases, the bonding in the organic molecule isn't important.
• I have rarely used molecular formula for organic compounds
(and almost always used for inorganic compounds) in chemical
equations but have always specified the molecular formula
with compound name in text.
Butanoic acid
C4H8O2
Ethanol
C2H6O
15.7.2 – Ways of representing organic molecules - Molecular
formula

• The molecular formula of an organic compound simply gives
the proportion of each type of element present.
• It tells you nothing about the number or arrangement of atoms
within the compound. Due to this, an empirical formula is not
the true formula of a compound.
• Empirical formulae are very rarely used in organic chemistry,
because they are not necessarily unique to a compound and
give no information about arrangement of atoms.
• However, the Empirical formula tells us the ratio of elements
in a compound which is helpful in
• Calculating the percentage composition of the elements in
a compound.
• In elemental analysis of an unknown sample.
• In the synthesis of a new compound.
• I have never used empirical formula in reactions/text in these
slides.
Butanoic acid
C2H4O
Ethanol
C2H6O
Glucose
CH2O
Acetic acid
CH2O
Formaldeyde
CH2O
15.7.3 – Ways of representing organic molecules - Empirical
formula

• A displayed formula shows all the bonds in the molecule as
individual lines. You need to remember that each line represents a
pair of shared electrons.
• Notice that the way the formula is drawn bears no resemblance to
the actual shape of the molecule.
• Ethanol and butanoic acid aren't flat with 90° bond angles.
• This mismatch between what you draw and what the
molecule actually looks like can lead to problems if you aren't
careful.
• Geometric isomers (molecules with same formula and bonds but
with different spatial arrangement of molecules) for example can
not be differentiated based on displayed formula representation
of a molecule.
• Also, for anything other than the most simple molecules, drawing
a fully displayed formula is a bit of a bother - especially all the
carbon-hydrogen bonds.
• However, I have tried to stick to displayed formulas in most of the
text for all organic compounds with the possible exceptions of
cyclic/aromatic compounds, representing geometric isomers or
very large molecules.
Butanoic acid
Ethanol
15.7.4 – Ways of representing organic molecules - Displayed
formula

• A condensed formula is a system of writing organic structures
in a line of text.
• It shows all atoms, but omits the vertical bonds and most or all
the horizontal single bonds.
• It uses parentheses to show that polyatomic groups within a
formula are attached to the nearest non-hydrogen atom on the
left.
• It uses parentheses to show that polyatomic groups within a
formula are attached to the nearest non-hydrogen atom on the
left.
• An exception to condensed formulas are the Carbon atoms of
Cyclic parts of molecules, e.g., benzene, which are grouped.
• It is the smallest and easiest way to represent a very large
organic molecule, when bond angles and individual bonds are
not important, e.g., in some chemical equations.
• I have tried to not use condensed formula a lot except using it
for very large molecules.
CH3(CH2) 2COOH
Butanoic acid
CH3CH2OH
Ethanol
15.7.5 – Ways of representing organic molecules - Condensed
formula

• A structural formula is a system of writing organic structures
in a line of text with all bonds represented with bars except for
bonds formed with Hydrogen atoms.
• In a sense it is a hybrid between condensed formula and
displayed formula, where all bonds between carbon carbon
atoms, between carbon nitrogen atoms and carbon oxygen
atoms are retained but all carbon hydrogen bonds have been
condensed.
• It is the smallest and easiest way to represent a very large
organic molecule, when individual bonds are not important,
e.g., in chemical equations.
• Despite its usefulness, simplicity and comprehensiveness, I
have tried to not use condensed formula (except in almost all
chemical equations and for representing cyclic and aromatic
compounds), but can recommend it for students once they
become experts in interpreting bonds with Hydrogen atoms.
Butanoic acid
Ethanol
15.7.6 – Ways of representing organic molecules - Structural
formula

15.7.7 – Ways of representing organic molecules - Skeletal
formula
• In a skeletal formula, most hydrogen atoms are omitted and
line ends or vertices represent carbons.
• Functional groups and atoms other than carbon or hydrogen
are still shown.
• Easiest to draw and commonly used.
• Highly recommended for students to understand but to avoid
in exams and in general usage and I have avoided it in the class
altogether.
Butanoic acid
Ethanol

Dr. Hashim Ali
15.8 – Functional groups
Education (FBISE)
Chemistry F.Sc
II

• Organic compound, any of a large class of chemical
compounds in which one or more atoms of carbon are
covalently linked to atoms of other elements, most
commonly hydrogen, oxygen, or nitrogen.
o The few carbon-containing compounds not classified as
organic include carbides, carbonates, and cyanides.
• Organic compounds can be grouped into families (similar
chemical characteristics) based on ‘functional groups’.
• A functional group is an atom or group of atoms that governs
the chemical properties of an organic molecule.
• In chemical reactions, the ‘change’ occurs at one ‘spot’
(functional group) in the original molecule.
• Double and triple bonds are functional groups as are -Cl, -Br,
-OH and -NH2.
• Note: Functional group is the chemically active component of
the molecule. The Hydrocarbon portion is mainly inert
(chemically non-reactive).
CH3CH2CH2CH2
- OH
-
Functional
Group
Hydrocarbon
portion
15.8.0 – Functional groups - Introduction

• We use the symbol R- to represent the
hydrocarbon portion and term it alkyl
group.
• Thus R- can be any groups of hydrogen
and carbon atoms with one free valence to
which the functional group is attached.
CH3CH2CH2CH2
- OH
-
Functional
Group
Hydrocarbon
portion
R- OH
-
15.8.1 – Functional groups - Representing organic compounds

• Each functional group undergoes characteristic
reactions, i.e., we can predict the reactions of a
molecule with a reactant based on its functional
group.
• Functional groups are important in organic
chemistry because they serve
o As basis for nomenclature (naming) of organic
compounds.
o To classify organic compounds into classes/families.
Same functional group  Same family!
o A site of chemical reactivity in a molecule containing
the group.
• A molecule containing more than one functional
group is called polyfunctional (poly means many)
and the properties of each functional group can be
modified by the other group(s).
CH3CH2CH2CH2
- OH
-
Functional
Group
Hydrocarbon
portion
R- OH
-
15.8.2 – Functional groups - Importance of functional groups

• What is organic compound? (15.8.0)
• What is meant by a functional group? (15.8.0)
15.8.3 – Functional groups - Quick Quiz

S
O
C
X
Hydrogen atom
Carbon atom
Oxygen atom
Sulphur atom
Halogens atom
Single bond
R
Double bond
Triple bond
Hydrocarbon chain
(alkyl chain)
N Nitrogen atom
H
15.8.4 – Functional groups - Color scheme for elements

Alkane
Ethane
CH3CH3  C2H6
Alkene
Ethene/Ethylene
CH2CH2  C2H4
C CR R
H H
CR H
H
H
15.8.5.1 – Functional groups - Common functional groups -
Hydrocarbons

Alkyne
C CR R
XR
Ethyne/Acetylene
CH3CH3  C2H6
Bromoethane/Ethylbromide/Monobromoethane
CH3CH2Br  C2H5Br
Halide
15.8.5.2 – Functional groups - Common functional groups - Alkyl
halides

Aldehyde
Ethanol/Ethyl Alcohol
CH3CH2OH  C2H6O
Ethanal/Acetaldehyde
CH3CHO  C2H4O
C OR
H
Hydroxyl/Alcohol
Oxygen containing groups

Carboxylic acid
Ether linkage
Ethanoic acid/Acetic acid
CH3COOH C2H4O2
Dimethyl ether/methoxymethane
CH3OCH3  C2H6O
OR R
Oxygen containing groups

Ester
Ketone Dimethyl ketone/Acetone/Propanone
CH3COCH3  C3H6O
Ethyl acetate/ethyl ethanoate/acetic ester
CH3COOCH2CH3  C4H8O2
C
O
R R
C
O
OR R
Carbonyl groups

Acid halide
Carboxylic acid anhydride/
Acetate
C
O
O C
O
R R
Acetic anhydride/Ethanoic anhydride/Acetyl acetate
CH3COOCOCH3 C4H6O3
C O
X
R
Acetyl chloride/Ethanoyl chloride
CH3COCl C2H3OCl
Carbonyl groups

Amide
Ethylamine/Ethanamine/Acetamine
CH3CH2O  C2H7N
Ethylamide/Ethanamide/Acetamide
CH3CONH2  C2H5ON
N R
H
H
C O
N
H
R
H
Amine
Nitrogen containing groups

Nitrile
Nitro
C NR
Ethanenitrile/Acetonitrile
CH3CN  C2H3N
Nitroethane
CH3CH2NO2  C2H5NO2
N
O
R
O
-
+
Nitrogen containing groups

Sulfoxide
Sulfide
SR R
Dimethyl sulfide/methylthiomethane
CH3SCH3 C2H6S
S
O
R R
Dimethyl sulfoxide/Methanesulfinylmethane
CH3SOCH3 C2H6SO
Sulphur containing groups
+
-

Thiol
Sulphone
Dimethyl Sulphone/Methylsulfonylmethane
CH3SO2CH3  C2H6SO2
SR H
O
S
O
R R
Ethane thiol/Ethylthiol
CH3CH2SH  C2H6S
Sulphur containing groups

• Compounds that contain a benzene ring as
part of their structure are called Aromatics
or Arenes.
• Arenes are a special class of homocyclic
compounds - molecules that are, or contain,
ring structures that consist only of carbon
atoms within the ring.
15.8.6.1 – Functional groups - Example - Aromatics (Arenes)

Resonance structure
Delocalized
Electron
cloud

• Due to delocalized electron cloud in
arenes, the benzene ring can be
represented by different symbols
and all are equally accepted.

At first glance, they look the same but aren’t
Benzene (C6H6)
Cyclohexane(C6H12)
15.8.6.2 – Functional groups - Example - Cyclics and arenes

Benzene (C6H6)
Toluene
(C6H5CH3)
CH3
15.8.6.2.1 – Functional groups - Example - Cyclics and arenes -
Some common arenes

Benzeldehyde (C6H5COH)
Phenol
(C6H5OH)
OH
C
O
H
Some common arenes

Aspirin
(C9H8O4)
Naphthalene
(C10H8)
H
H
C
C
C
C
C
C
C
C
C
OO
O
O
H
H
H
H
HH
Some common arenes

15.8.6.3 – Functional groups - Example - Heterocylic compounds
• A heterocyclic compound or ring structure is a cyclic compound that has
atoms of at least two different elements as members of its ring(s).
• Heterocyclic chemistry is the branch of organic chemistry dealing with the
synthesis, properties, and applications of these heterocycles.
Pyrrole
(C4H4NH)
Pyridine
(C5H5N)
Thiophene
(C4H4S)

Class of compound Functional group Name of functional
group
Alkanes Nil Nil
Alkenes C = C Alkene
Alkynes C C Alkyne
Arenes C6H6 ring containing
compounds
Benzene, phenol.
Halogenoalkanes R-X where X = halogen E.g., chloroalkane,
bromoalkane
Aryl halides /
Halogenoarenes
C6H5X E.g., chlorobenzene,
bromobenzene
15.8.7 – Functional groups - Summary

group
Hydroxyl compounds RCH2OH Primary alcohol
RR1CHOH Secondary alcohol
RR1R2COH Tertiary alcohol
C6H5OH Phenol
Carbonyl compounds RCHO Aldehyde
RR1CO Ketone

group
Carboxylic acids RCO2H Carboxylic acid
Carboxylic acid
derivatives
RCOCl Acyl chloride
RCO2R1 Ester
RCONH2 Amide
Amines RNH2 Aldehyde
RR1NH Ketone
RR1R2N Tertiary amine
Nitriles RC N Nitrile

Dr. Hashim Ali
15.9 – Homologous series
Education (FBISE)
Chemistry F.Sc
II

• A homologous series is a series of compound, in which adjacent members of the
series differ by one C unit.
• The individual members are called Homolog of the series.
• Homologs are formed by polymerization - (‘poly’ meaning many and ‘mer’
meaning parts).
• For example, the homologous members of ‘alcohols’ can be represented as ROH
or CnH2n+1OH.
n Name R Formula
1 Methanol CH3
- CH3OH
2 Ethanol CH3CH2
- CH3CH2OH
3 Propanol CH3CH2CH2
- CH3CH2CH2OH
4 butanol CH3CH2CH2CH2
- CH3CH2CH2CH2OH

• The organic compounds are arranged into homologous series and functional
group arrangement for the same reason as to arranging elements in the
periodic table, or classify animals and plants with a system of taxonomy;
simplicity and ease of understanding.
• The chemical and physical properties of compounds in a homologous series
are similar, because they all have a fixed set of functional groups;
o Only the number of repeating units change. e.g. straight-chain primary alcohols,
(CH3–CH2–CH2–CH2–OH) have two main molecules (CH3–) and (–OH) with a
sequential number of –CH2– units between them.

Homologous Series
Organic compounds in the
same homologous series
Example 1: alkane Example 2: alkene
• Contain the same elements
and the same functional
group
C and H with only single
bonds
functional group H
C and H with one double bond
between C,
functional group H
• Possess the same general
formula
CnH2n+2 CnH2n
• Differ from the previous
member in the series by a
−CH2− group
CH3-H, CH3CH2-H,
CH3CH2CH2−H,
CH3CH2CH2CH2−H,
CH2=CH−H, CH2=CHCH2−H,
CH2=CHCH2CH2−H,
CH2=CHCH2CH2CH2−H
• Possess similar chemical
properties, due to the
presence of some
functional group
• Alkanes are completely
saturated and possess
single bonds.
• Alkanes are acyclic.
• Alkenes possess a carbon-
carbon double bond.
• Alkenes undergo electrophilic
addition reactions.
• Show gradual change in
physical properties due to
increased molecular size
and mass, caused by longer
carbon chains
Ethene b.p = -102°C
Propene b.p. = -48°C
1-Butene b.p. = -6.5°C
1-Pentene b.p. = 30°C
• Can be prepared by similar
methods

• What are the general formulas for alkanes, alkenes and alkynes? (15.9)
• What is a Homologous series? (15.9)
• Why do we arrange compounds in homologous series? (15.9)
15.9.1 – Homologous series - Quick Quiz

Dr. Hashim Ali
15.10 – Detecting elements in organic compounds
Education (FBISE)
Chemistry F.Sc
II

• Carbon is an essential constituent of all organic compounds.
• Hydrogen is almost always present in all organic compounds.
• Other elements present in organic compounds are nitrogen, sulphur,
oxygen, halogens, phosphorus and various metals.
• How do we detect presence/absence of a certain element in a given organic
compound?
15.10 – Detection of elements in organic compounds

• Carbon and Hydrogen are detected by
heating the compound with cupric(II)
oxide(CuO).
• On heating, carbon and hydrogen present in
the compound are oxidised to carbon dioxide
(CO2) and water(H2O).
• If carbon dioxide is produced from heating
(indicating presence of carbon), it will turn
‘lime water Ca(OH)2’ milky and produce a
white precipitate (lime water test).
• Similarly, if water is produced from heating
(indicating presence of hydrogen), it will turn
white anhydrous copper sulphate(CuSO4)
blue.
C + 2CuO  CO2 + 2Cu
CO2 + Ca(OH)2  CaCO3 + H2O
Lime water milky white ppt.
H2 + 2CuO  Cu + H2O
CuSO4 + 5H2O  CuSO4.5H2O
Anhydrous (white) Hydrous (blue)
15.10.1 – Detection of elements in organic compounds - Carbon
and hydrogen

• Nitrogen, sulphur, halogens and phosphorus present in an organic
compound are detected by Lassaigne’s test (also called sodium fusion test).
• The first step involved in this test is to prepare Lassaigne’s solution and then
the particular element test is performed on the sodium fusion extract to
verify presence/absence of the element.
15.10.2 – Detection of elements in organic compounds - Nitrogen,
sulphur and halogens

• Cut a small piece of sodium metal with the
help of knife and put in a fusion tube.
• Heat the fusion tube to melt sodium metal.
• Add a small amount of powdered organic
compound into the molten sodium in
fusion tube.
• Heat the fusion tube again till its bottom is
red hot.
• Break this fusion tube in a China dish
containing 20cm3 of distilled water.
• Mix, boil and then filter the solution.
• The filtrate obtained is called Lassaigne’s
solution or sodium extract.
• Divide this filtrate into three portion and
use one portion each to test the presence of
N, S, and (X) halogens respectively.
2Na + S  Na2S
Na + N + C +S  NaSCN
Na + X  X where X = Cl, Br, I
15.10.2.0 – Detection of elements - Nitrogen, sulphur and
halogens - Preparation of Lassaigne’s Solutions/Sodium Extract

• The sodium fusion extract is mixed
with a few drops of Sodium
Hydroxide (NaOH) to make it
alkaline.
• Then it is boiled with Ferrous
sulphate (FeSO4), and then acidified
with a few drops of iron chloride
(FeCl3) and concentrated
hydrochloric acid (HCl) .
• The formation of Prussian blue color
confirms the presence of nitrogen.
• The formation of blood red color
proves the presence of both nitrogen
and sulphur.
Na + C + N  NaCN
6NaCN +FeSO4  Na4[Fe(CN)6] + Na2SO4
3Na4[Fe(CN)6] + 4FeCl3  Fe4[Fe(CN)6]3 + 12 NaCl
Prussian blue
2Na + 2C + N2 +S  2NaSCN
6NaSCN +FeSO4  Na4[Fe(CNS)6] + Na2SO4
3Na4[Fe(CNS)6] + 4FeCl3  Fe4[Fe(CNS)6]3 + 12 NaCl
Blood red ppt.
halogens - Nitrogen

• The second portion of Lassaigne’s
filtrate is acidified with acetic acid
(CH3COOH).
• The solution is then boiled to
expel hydrogen sulphide (H2S),
which turns lead acetate
(CH3COO)2Pb paper black.
• The black precipitate of lead
sulphide (PbS) indicates the
presence of sulphur in the
compound.
Na2S + 2CH3COOH  H2S + 2CH3COONa
H2S + (CH3COO)2Pb  PbS +2CH3COOH
Black ppt.
halogens - Sulphur

• The sodium fusion extract is mixed with
nitric acid (HNO3) and then boiled to expel
cyanide and sulphur ions.
• Silver nitrate (AgNO3) solution is then
added to this solution.
• A white precipitate, soluble in ammonium
hydroxide (NH4OH), shows the presence
of chlorine.
• A pale yellow precipitate, partially soluble
in ammonium hydroxide (NH4OH) shows
the presence of bromine.
• A deep yellow precipitate, insoluble in
ammonium hydroxide (NH4OH) shows the
presence of iodine.
NaX + AgNO3  AgX + NaNO3
Where X = Cl, Br or I
White/pale yellow/deep yellow ppt
halogens - Halogens

• There is no conclusive test for detecting presence of Oxygen although its
presence in organic compounds is often confirmed by indirect methods.
• Method 1: Water droplets formation after heating
o The substance is heated alone in a dry test tube preferably in an atmosphere of
nitrogen.
o Formation of water droplets on the cooler parts of tube confirm presence of oxygen.
o However, a negative result does not necessarily show absence of oxygen.
• Method 2: presence of various oxygen containing groups
o Test for the presence of various oxygen containing groups such as hydroxyl (OH),
carboxyl (COOH), aldehyde (CHO), and nitro (NO2), etc.
o If any of these is detected, presence of Oxygen is confirmed.
• Method 3:Elemental analysis for other atoms and difference in molecular weight
o Determine percentages of carbon, hydrogen and all other elements present in the
compound.
o If the sum of these percentages is less than 100%, the presence of oxygen is confirmed.
15.10.3 – Detection of elements in organic compounds - Oxygen

• The compound is heated strongly with
an oxidizing agent such as concentrated
nitric acid (HNO3) and a mixture of
sodium carbonate (Na2CO3) and
potassium nitrate (KNO3).
• The phosphorus present in the
substance has oxidized to phosphate.
• The residue is extracted with water,
boiled with nitric acid and then mixed
with a hot solution of ammonium
molydebate (NH4)2MoO4.
• A yellow coloration or precipitate
(ammonium phosphomolybdate)
indicates the presence of phosphorus.
Na3PO4 + 3HNO3  H3PO4 + 3NaNO3
H3PO4 + 12(NH4)2MoO4 + 21 HNO3
(NH4)3PO4.12MoO3 + 21NH4NO3 + 12 H2
Yellow ppt.
15.10.4 – Detection of elements in organic compounds -
Phosphorus

• The substance is strongly heated in a crucible, preferably of platinum till all
motion ceases.
• An incombustible residue indicates the presence of a metal in the substance.
• The residue is extracted with dilute acid and the solution is tested for the
presence of metallic ore by the usual scheme employed for inorganic salts.
15.10.5 – Detection of elements in organic compounds - Metals

15.10 – Detection of metals in organic compounds

 Fossil fuels (coal, petroleum and natural gas) are important resources of organic compounds as are living
animals and plants.
 The study of organic chemistry is organized around functional groups where each functional group defines its
own organic family.
 Organic chemistry is concerned with the chemistry of of living material or substances which were once alive.
It is therefore concerned with living plants or animals or substances like coal and oil which are derived from
living plants (col) or from microscopic sea organisms (oil).
 Coal is produced by the decaying of trees buried under the earth crust under the influence of high temperature
and pressure. These trees got converted into coal.
 The word ‘petroleum’ is derived from the Latin words “Petra” meaning rock and “oleum” meaning oil. It is
also called mineral oil.
 Bacterial decay at high pressure with little oxygen changed the organic matter into crude oil and natural gas.
 The refining of petroleum is carried out by the process of fractional distillation. In this process, various
fractions are separated according to the difference in their boiling points.
 The clothes we wear, the dyes that color them, the soap and starch used to launder them, the leather in our
shoes as well as the dye and shoe polish, are product of organic chemical industry.
Key Points

i. The major portion of natural gas
is
i. Ethane
ii. Propane
iii. Butane
iv. Methane
ii. In organic compounds, carbon
atoms form
a) Ionic bond
b) Metallic bond
c) Covalent bond.
d) None of these.
1. Select the right answer from the choices given
iii. Which of the following is an
aromatic compound
a) Propanol
b) Cyclohexane
c) Acetone
d) Benzene
iv. There are a few homologous series
of compounds. The existence of
homologous series is due to
a) Functional group
b) Cracking
c) Isomerism
d) Polymerization

v. Which of the following compounds
is heterocyclic
a) Pyridine
b) Pyrrole
c) Thiophene
d) All of the above
vi. Select the organic compound from
the following, which is alcohol
a) CH3-CH2-OH
b) CH3-O-CH3
c) CH3COOH
d) CH3-CH2-Br
vii. Lassaigne’s solution is prepared in the
detection of elements of organic
compounds. Which metal is used for
the reaction with organic compound?
a) Aluminum
b) Sodium
c) Iron
d) Copper
viii.When AgNO3 is added to the
Lassaigne’s solution, which color is
formed for Iodine?
a) Blue
b) Violet
c) Green
d) Deep yellow.

ix. When water vapors are passed
over white anhydrous copper
sulphate, which color is formed?
a) White
b) Deep blue
c) Yellow
d) Brown
x. The simplest molecule of Bucky
ball contain _____ carbon atoms.
a) 20
b) 8
c) 60
d) 100
xi. If a molecule contains more than
one functional group, it is known
as
a) Derivative
b) Poly-functional
c) Heterocyclic
d) Isomer

2. Give brief answers to the following questions
i. What is a functional group? (15.8.0)
ii. What is the difference between partial and total synthesis of organic
compounds? (15.2.3)
iii. How organic compounds are derived from the fermentation process?
(15.2.3.1)
iv. What is coal? How is coal used as source of organic compounds?
(15.2.1.1)
v. What is name of the new allotropic form of carbon? Give its definition.
(15.6.1)
vi. What is a homologous series? (15.9)
vii.How sulphur can be detected in organic compounds? (15.10.2.2)

3. Give detailed answers to the following questions
i. What are the main sources of organic compounds? (15.2)
ii. Write down the characteristics of organic compounds that differentiate
them from inorganic compounds. (15.4)
iii. How organic compounds are used in our daily life? (15.5)
iv. Write down any ten functional groups of organic compounds? (15.8)
v. Give reasons for the importance of organic chemistry. (15.1)
vi. Give the chemical tests for the detection of elements in organic
compounds. (15.10)

Methods of purification of organic compounds

Quantitative analysis of organic compounds

Chapter 15 organic chemistry

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