1

1.1. INTRODUCTION TO ORGANIC

CHEMISTRY

Everybody might know “C” as the symbol of carbon.

However, it is not only a symbol but also a special key for

about 20.000.000 known compounds.

Organic chemistry is chemistry of carbon atom, a huge

branch of the chemistry tree and it can be said that we live in

an Organic Chemistry Age in the 21th

century.

The substances studied in organic chemistry are called organic

compounds and they are vital for all living things on this

planet.

Petroleum, natural gas and coal are the main sources of

organic compounds.

All living systems obtain their energy from organic

compounds like carbohydrates (sugars) and fats, using amino

acids and proteins (organic) to grow. They transmit genetic

information from one generation to the next through organic

compounds called nucleic acids. The clothes we wear are of

natural fibers like cotton, while wool or silk or synthetic

materials like polyester are organic compounds. Most of the

drugs and pharmaceuticals are also organic compounds. In

agriculture too, organic chemistry is well represented.

Fertilizers like urea, pesticides and plant growth regulators are

all organic chemicals. Among various energy sources, fossil

fuels like coal, lignite, petroleum and natural gas are of

organic origin. Commonly used polymers natural and

synthetic like wood, rubber, paper and plastics are again

organic compounds. Thus, organic compounds play an

important part in our daily lives.

Carbon’s ability to form diverse structures and an endless

number of molecules make it an important building block in

the living cells and tissues.

It is interesting to know how every chemical in our body is

produced, moved, modified and used by a sequence of amino

acids that are related to DNA. The more we understand about

how the chemistry of our body works the better our chance of

keeping everything working, as it should.

Figure 1.1. All organic compounds contain carbon and most are formed by living things, although they are also formed by geological and artificial processes.

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1.2. A BRIEF HISTORY OF ORGANIC

CHEMISTRY

For over hundreds of years chemists have classified

compounds as coming either from minerals (non-living origin)

or from plants and animals (living origin).

In 1807, Jacob Berzelius (1779-1848) divided all the

chemicals into two groups based on their reaction on heating.

He classified the substances, which burnt or charred on

heating as organic chemicals, which were mostly in living

things. The substances, which melted or vaporized on heating

but then returned to their original state, were classified under

inorganic chemicals.

He proposed a theory that: organic compounds are only found

in living animals and plants because live forces or vital force

is present in them. It was popularly known as “vital force

theory” which summarizes that organic chemistry is the

chemistry of life.

In 1828, Friedrich Wohler (1800-1882) reacted ammonia

with cyanic acid, and obtained the well known organic

compound, urea, instead of the expected ammonium cyanate:

NH3 + HNCO → NH2CONH2

Cyanic acid Urea

This famous experiment proved to be the end of the theory

called “vitalism”.

In 1853, the English chemist Edward Frankland used the

term “valency” (latin word valentia – force).

In 1857, two German scientists Kekule and Adolf Korbe

explained the tetravalency of carbon.

Between 1858-1861, August Kekule, Archibald Scott Couper

and Alexander Mikhaylovich Butlerov independently

established one of the fundamental theories in organic

chemistry: “The Structural Theory of Organic

Compounds”.

In 1874, structural formulae were proposed by Van’t Hoff to

represent organic compounds – methane, carbon in the center

and hydrogen at the corners.

Alexander

Mikhaylovich Butlerov

September 15, 1828 – August 17, 1886

Alexander Butlerov was born in Chistopol into a landowning family, was a Russian chemist, one of the principal creators of the theory of chemical structure (1857–1861), the first to incorporate double bonds into structural formulas, the discoverer of hexamine (1859), the discoverer of formaldehyde (1859) and the discoverer of the formose reaction (1861).

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1.3. DIFFERENCES BETWEEN ORGANIC

AND INORGANIC COMPOUNDS

Carbon has the highest bonding capacity of all elements.

Therefore, more than 5 million organic compounds have

already been synthesized or isolated from natural sources. But

there are about 400,000 inorganic compounds reported until

now. The composition, the molecular structure and properties of

organic compounds are highly different from those of inorganic

compounds.

Organic compounds Inorganic compounds

1. Organic compounds are

formed from only a few

elements, mainly C, H, O, N,

S, P and halogens

1. Inorganic compounds

are formed from more than

100 different elements

2. There are covalent bonds

between the atoms of organic

molecules and these

molecules are large,

containing long chains and

rings

2. Ionic bonds are used in

inorganic molecules to

form simple and small

molecules

3. Organic compounds are in

the state of gases and volatile

liquids and their solids have

low melting points

3. Most of inorganic

compounds are non-

volatile solids and they

have very high melting and

boiling points

4. Many organic compounds

have their characteristic color

and odor

4. Most of inorganic

compounds, except a few

metallic salts, are colorless

and odorless

5. They are insoluble in water,

but soluble in organic solvents

5. They are generally

soluble in water, but

insoluble in organic

solvents

6. Organic reactions are slow

and complicated

6. Inorganic reactions are

fast, but simple

Table 1.1. Differences between organic and inorganic compounds

DEFINITIONS

Volatile means to be turned into a vapor easily. The volatility of a covalent liquid depends on the strength of the intermolecular forces, as these must be overcome in order for the particles to change from liquid state to gaseous state.

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1.4. STRUCTURAL THEORY OF

ORGANIC COMPOUNDS The way in which component atoms of an organic substance

are bod between them and influence each other, defines the

chemical structure. This fundamental idea has been developed

within "Theory of organic compounds' structure" of

A.M.Butlerov (1861). Being enriched with new remarkable

theoretical gains such as stereochemical theory, electronic

theory in organic chemistry and others, the theory of structure

of the organic compounds allowed scientific systematization

of the wide experimental material of organic chemistry,

correct explanation of the already known phenomenons and

getting to discover new ones. On the foundation offered by

this theory, through the tireless work of thousands of

scientists, the modern organic chemistry has been created and

developed.

Structural theory of organic compounds

1. Atoms in compounds connect one to another according

to “valency concept”. Carbon is tetra covalent in compounds;

it means it forms four bonds. The order of connection of

atoms in a molecule and the character of bonds is called as

chemical structure. Valency of elements is shown by dash.

Representation of molecules structure is known as structural

formula.

2. Properties of compounds determined not only by their

composition but also with chemical structure (the order of

connecting atoms in molecule). By using the structural

formulas, the existence of isomers is explained.

Isomers are compounds, which have the same molecular

formula, but different structural formulas. Chemical and

physical properties of isomers are different. For instance, to

use a very simple case, ethyl alcohol and dimethyl either,

although possessing widely different properties, have the

same empirical formula: C2H6O (Fig. 1.2.)

3. The structure of molecule can be determined by using

the properties of compound and vice versa by using the

structure of molecule the properties of compound can be

predicted.

4. Atoms and group of atoms influence each other.

Ethyl alcohol, C2H6O

Dimethyl ether, C2H6O Figure 1.2. Ethyl alcohol and dimethyl ether

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1.5. ORGANIC STRUCTURE

Carbon atoms possesses some remarkable properties:

They can form strong, stable covalent bonds to other

carbon atoms and many different types of atom.

They can build up chains of carbon atoms to form a

carbon 'skeleton'.

They can form multiple bonds, both with other carbon

atoms or chains, and with other elements.

These three factors allow carbon to produce, literally, millions

of different compounds, many of which are found in living

systems. The definition of organic compound is now taken to

mean a compound of carbon that is not a simple mineral

compound. Again, this is pretty vague, but means that

carbonates, hydrogen carbonates and oxides are excluded

from the definition.

Carbon is often bonded to hydrogen and oxygen in its

compounds. Those compounds that contain carbon and

hydrogen only are called hydrocarbons.

Bonding in carbon compounds

Carbon has four electrons in its highest energy level (outer

shell). It must share four more electrons to attain a full outer

shell. There are four ways that carbon atoms can do this.

By forming four covalent bonds to four other atoms.

By bonding covalently to two other atoms using one

shared pair of electrons and a third atom using two

shared pairs of electrons (a double bond).

By bonding covalently to two other atoms by means of

two shared pairs of electrons (two double bonds - this

is unusual).

By bonding covalently to two other atoms, one using a

single bond and to the other by means of a triple bond

(three shared pairs)

Carbon single bonds are the type of sigma bond, caused by

direct orbital overlap along a linear axis. (Figure 1.3.)

KEY POINT

The ability of carbon to form strong bonds to four other atoms, including carbon atoms, results in a huge range of organic compounds.

DEFINITION

Hydrocarbons are compounds containing only carbon and hydrogen.

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Figure 1.3. Formation of sigma bond.

Carbon double bonds consist of one sigma bond and one 'pi'

bond, caused by lateral (sideways) overlap of two parallel

orbitals. Notice that the overlap happens above and below the

sigma bond. These two overlaps constitute only one pi bond.

(Figure 1.4.)

Figure 1.4. Formation of π-bond

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Triple bonds formed by carbon atoms comprise one 'sigma'

and two 'pi' bonds. The 'pi' bonds are at right angles to one

another. In a triple bond with two 'pi' bonds there are four

regions of overlap corresponding to the two pi bonds and one

region of overlap along the axis joining the two atoms

corresponding to the sigma bond.

Shapes of organic molecules

The shape of a molecule depends on the geometry of the

bonding electrons that join all of the atoms together. Carbon

atoms may adopt one of three geometries depending on the

number of atoms to which they are bonded. (Figures 1.5., 1.6.,

1.7.)

Functional groups

The average bond strength of a carbon - carbon single bond is

346 kJ/mole and a C=C double bond has a bond strength of

602 kJ/mole.

To break carbon-carbon bonds requires large amounts of

energy, meaning that the carbon skeleton is particularly stable.

Organic compounds react in many different ways, but the

carbon skeleton is rarely broken. For this reason, the atoms

that are attached to the carbon skeleton are very important as

they often confer reactivity to the molecule. Such atom or

groups are called 'functional groups' - they give the molecule

functionality. Common functional groups are given in table

1.2.

Atom or grouping Name

-Cl Chlorine atom

-F, -Cl, -Br, -I Halide group

-OH Alcohol group

-CHO Aldehyde group (Carbonyl group)

-COOH Carboxyl group

-NH2 Amine group

-CONH2 Amide group

-CN Nitrile group

Table 1.2. Common functional groups

Figure 1.5. The geometry of a four-bonded carbon is tetrahedral with bond angles of 109.5º.

Figure 1.6. The geometry of carbon bonded to three other atoms is trigonal planar (bond angle 120º)

Figure 1.7. The geometry of carbon bonded to two other atoms is linear (bond angle 180º)

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1.6. FORMULA REPRESENTATION

Representation of chemical formula in organic chemistry

must leave the structure unambiguous. There are several

accepted ways to do this.

Empirical formula

The empirical formula is the simplest ratio of the atoms

within a molecule of the compound. It emerges from

calculations of formula using a consideration of the

percentage composition by mass of each element.

Traditionally, the method of determining the nature of a

substance was based on a direct analysis of the elements

within the compound, taking advantage of the fact that most

organic compounds are flammable. When burnt, all of the

carbon turns to carbon dioxide and all of the hydrogen turns

to water. Thus, if the mass of carbon dioxide produced from

a known mass of an unknown compound is found, the actual

mass of carbon and hence the percentage carbon in the

original compound can be calculated.

Worked problem 1.1.: 5g of an unknown organic

compound produced 11.0g of carbon dioxide on complete

combustion in excess air. Calculate the percentage carbon

in the compound.

Solution:

m (CO2) = 11.0g, M (CO2) = 44.0 g/mole

First, we can find mole number of CO2

𝑛 (𝐶𝑂2) = 𝑚

𝑀 =

11 𝑔

44𝑔

𝑚𝑜𝑙

= 0.25 𝑚𝑜𝑙𝑒

n (CO2) = n (C) = 0.25 mole

m (C) = n (C)× A(C) = 0.25 mole × 12 g/mole = 3.0 g

𝑤% (𝐶) = 𝑚 (𝐶)

𝑚 (𝑐𝑜𝑚𝑝) × 100% =

3.0

5.0 × 100% = 60%

Answer: w% (C) = 60%

DEFINITIONS

The empirical

formula shows the

simplest whole

number ratio for

the atoms of each

element in a

compound.

The molecular

formula shows the

actual number of

atoms of each

element in one

molecule of the

compound.

The structural

formula shows how

the different atoms

are joined together,

and the positions of

functional groups.

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Worked problem 1.2: 5g of an unknown organic compound

produced 3.3g of water on complete combustion in excess air.

Calculate the percentage carbon in the compound.

Solution:

m (H2O) = 3.3 g, M (H2O) = 18.0 g/mole

First, we can find mole number of H2O

𝑛 (𝐻2𝑂) = 𝑚

𝑀 =

3.3 𝑔

18𝑔

𝑚𝑜𝑙

= 0.183 𝑚𝑜𝑙𝑒

n (H) = 2 × n (H2O) = 2 × 0.18 = 0.366 mole

m (H) = n (H)× A(H) = 0.366 mole × 1 g/mole = 0.366 g

m (C) = m(organic compound) – m (H),

m (C) = 5-0.366 = 4.634 g

𝑤% (𝐶) = 𝑚 (𝐶)

𝑚 (𝑐𝑜𝑚𝑝) × 100% =

4.634

5.0 × 100%

= 92.68%

Answer: w% (C) = 92.68%

Molecular formula

The molecular formula shows the actual number of atoms of

each type in the molecule. For example, the molecular

formula of ethanol is C2H6O.

There are two fundamental problems with using the molecular

formulae to represent molecules:

They give no indication as to the actual arrangement of

the atoms within the molecule.

There may be many different molecules with the same

molecular formula.

The mass

spectrometer is an

instrument, which

turns atoms and

molecules into ions

and measures their

mass.

When an organic

compound passes

through a mass

spectrometer, its

molecules get

broken into

positively charged

particles. These

fragments provide

useful information.

Each fragment

gives a

corresponding line

in the mass

spectrum. From the

position of the line,

we can find the

relative mass of the

fragment, and use

this to work out its

formula.

By piecing together

the fragments, we

can deduce the

structure of the

parent molecule.

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However, in analysis the molecular formula is a good start

when working out the identity of a compound. A high

definition Mass Spectrometer can determine the relative

formula mass of a compound to such a high degree of

accuracy that the molecular formula can be obtained directly.

It is then up to other techniques to identify the actual

arrangement of the atoms within the molecule.

Structural formula

The structural formula shows the actual arrangement of the

atoms in a molecule by drawing the bonds as lines between

letters representing the atoms. A single bond is shown as one

line only and a double bond is shown as a double line.

Structural formula of ethanol is:

Condensed formula

The condensed formula is a shorthand method of representing

the structural formula which relies on some knowledge of

chemical structures. The structure is written starting at one

end of the chain with each carbon shown along with any

attachments. There are no single bonds shown between carbon

atoms, as it is assumed that the reader understands that the

atoms must be joined together in the chain, using at least one

bond.

Where groups are attached to the carbons in the chain they can

be show by using brackets immediately after the carbon to

which they are attached.

CH3CH(OH)CH2CH3

In this case there is an -OH group attached to carbon number

2 in the chain.

STUDY TIP

Do not forget that

carbon always

forms four bonds.

This can help when

drawing a

structure. If you

end up with

carbons with 3 or 5

bonds then you

have done it

wrong!

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Skeletal formula

This is another way to represent the molecular structure. In a

skeletal formula each carbon is represented by an angle, or

termination in a line and the hydrogen atoms are just assumed.

Double bonds are shown as a double line and heteroatoms are

draw as usual. A certain amount of logical reasoning must be

used to understand the structure from a skeletal representation.

This type of representation is very useful when the molecule

is large and the number of atoms becomes too unwieldy for

other representations.

Lewis structure

These are structural formula in which the bonds are not

represented by lines, but rather by the electron pairs that make

up the bonds. Any lone (non-bonding) electron pairs must also

be shown. The electron pairs may be shown as two dots, or

two crosses, or even a line.

The Lewis structure of ethanol C2H6O is represented as

follows:

Notice that the two lone pairs on the oxygen are also shown.

When drawing Lewis structures there are nearly always eight

electrons around each atom (except hydrogen). There are

some exceptions, but not in organic chemistry.

Butane Skeletal formula

Butane Structural formula

Benzene Skeletal formula

Benzene Structural formula Figure 1.8. Skeletal and structural formulas of butane and benzene

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1.7. HYBRIDIZATION

Covalent bonds are formed when atomic orbitals

overlap. There are two types of orbital overlap that an organic

chemist needs to be familiar with. Sigma, s, overlap occurs

when there is one bonding interaction that results from the

overlap of two orbitals. Pi, p, overlap occurs when two

bonding interactions result from the overlap of orbitals.

Figure 1.9. Sigma and pi overlap of orbitals

The organic chemist also needs to realize how these orbital

overlaps relate to the type of bonding that is occurring

between atoms:

single bond s overlap

double bond s and p overlaps

triple bond s and two p overlaps

sp3 Hybridization

Unfortunately, overlap of existing atomic orbitals (s, p, etc.) is

not sufficient to explain some of the bonding and molecular

geometries that are observed. Consider the element carbon

and the methane (CH4) molecule. A carbon atom has the

electron configuration of 1s2 2s

2 2p

2, meaning that it has two

unpaired electrons in its 2p orbitals, as shown in Figure 1.10.

Figure 1.10. Orbital configuration for carbon atom.

The Valence Shell

Electron Pair

Repulsion (VSEPR)

model is based on

the idea that

electron pairs will

repel each other

electrically and will

seek to minimize

this repulsion. To

accomplish this

minimization, the

electron pairs will

be arranged around

a central atom as

far apart as

possible.

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According to the description of valence bond theory so far,

carbon would be expected to form only two bonds,

corresponding to its two unpaired electrons. However,

methane is a common and stable molecule, with four

equivalent C−H bonds. To account for this, one of

the 2s electrons is promoted to the empty 2p orbital

(see Figure 1.11).

Figure 1.11. Promotion of carbon s electron to empty p

orbital.

Now, four bonds are possible. The promotion of the electron

“costs” a small amount of energy, but recall that the process

of bond formation is accompanied by a decrease in

energy. The two extra bonds that can now be formed results

in a lower overall energy and thus greater stability to the

CH4 molecule. Carbon normally forms four bonds in most of

its compounds.

The number of bonds is now correct, but the geometry is

wrong. The three p orbitals (px, py, pz) are oriented at

90o relative to one another. However, as was seen from

VSEPR theory, the observed H−C−H bond angle in the

tetrahedral CH4 molecule is actually 109.5o. Therefore, the

methane molecule cannot be adequately represented by simple

overlap of the 2s and 2p orbitals of carbon with the 1s orbitals

of each hydrogen atom.

To explain the bonding in methane, it is necessary to

introduce the concept of hybridization and hybrid atomic

orbitals. Hybridization is the mixing of the atomic orbitals in

an atom to produce a set of hybrid orbitals. When

hybridization occurs, it must do so as a result of the mixing of

nonequivalent orbitals. In other words, s and p orbitals can

hybridize but p orbitals cannot hybridize with other p orbitals.

Hybrid orbitals are the atomic orbitals obtained when two or

more nonequivalent orbitals form the same atom combine in

preparation for bond formation. In the current case of carbon,

the single 2s orbital hybridizes with the three 2p orbitals to

form a set of four hybrid orbitals, called sp3 hybrids (Figure

1.12).

DEFINITIONS

Hybridization is the

mixing of the

atomic orbitals in

an atom to produce

a set of hybrid

orbitals.

Hybrid orbitals are

the atomic orbitals

obtained when two

or more

nonequivalent

orbitals form the

same atom

combine in

preparation for

bond formation.

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Figure 1.12. Carbon sp3 hybrid orbitals.

The sp3 hybrids are all equivalent to one another. Spatially, the hybrid orbitals point

towards the four corners of a tetrahedron (Figure 1.13.).

Figure 1.13. The process of sp3 hybridization is the mixing of an s orbital with a set of three

p orbitals to form a set of four sp3 hybrid orbitals. Each large lobe of the hybrid orbitals

points to one corner of a tetrahedron. The four lobes of each of the sp3 hybrid orbitals then

overlap with the normal unhybridized 1s orbitals of each hydrogen atoms to form the

tetrahedral methane molecule.

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sp2 Hybridization

Ethene (C2H4) has a double bond between the

carbons. For this molecule, carbon will

sp2

hybridize. In sp2 hybridization, the 2s

orbital mixes with only two of the three

available 2p orbitals, forming a total of 3

sp2 orbitals with one p-orbital remaining. In

ethylene (ethene), the two carbon atoms form

a sigma bond by overlapping two

sp2 orbitals; each carbon atom forms two

covalent bonds with hydrogen by s–

sp2 overlapping all with 120° angles. The pi

bond between the carbon atoms forms by a

2p-2p overlap. The hydrogen-carbon bonds

are all of equal strength and length, which

agrees with experimental data.

The geometry of the sp2 hybrid orbitals is

trigonal planar, with the large lobe of each

orbital pointing toward one corner of an

equilateral triangle. The angle between any

two of the hybrid orbital lobes is 120°.

(Figure 1.13.)

Carbon atoms make use of sp2 hybrid orbitals

not only in ethene, but also in much other type

of compounds. The table 1.3. shows some of

these compounds:

Formaldehyde Ketene Acetic acid Benzene Acetone

Table 1.3. Compounds, in which carbon atoms have sp2-hybridization.

Figure 1.13. sp2 hybridization

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sp hybridization

When sp hybrid orbitals are used for the sigma bond, the two sigma bonds around the

carbon is linear. Two other p orbitals are available for pi bonding, and a typical compound

is the acetylene or ethyne HC≡CH. The three sigma and two pi bonds of this molecule from

is shown in the figure 1.14.

Figure 1.14. sp hybridization in acetylene molecule

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SUPPLEMENTARY QUESTIONS

1. What are the differences between organic and inorganic compounds?

2. Why is organic chemistry considered the chemistry of Carbon compounds?

3. Give five examples of organic and inorganic compounds that you use at home.

4. Which properties of carbon make it unique?

5. Why is organic chemistry so important?

6. An organic compound was found to contain 10% hydrogen and 90% of carbon by

mass. Find its empirical formula.

7. Find the empirical formula of the organic compound of which 3g contains 0,6

grams of hydrogen and 2,4 grams of carbon.

8. An organic compounds whose molar mass is 88 g/mol contains 55% C, 36% O and

9% H by mass. Find its molecular formula.

9. An organic compound contains only 1,5 grams hydrogen and 9 grams of carbon by

mass. Find its molecular formula if its molar mass is 210 g/mol.