Unit one: Bonding, Structure and Reactivity

1.1 Historical Development of Organic Chemistry

What is organic chemistry?
During the end of 18th century, scientists began to classify chemistry into two categories: organic chemistry
and inorganic chemistry. The classification was based on the source of the compounds

Organic chemistry: was concerned with matter obtained from natural or living source
Inorganic chemistry: dealt with substances derived from nonliving matterminerals and the like
Vitalism held that living systems possessed a vital force which was absent in nonliving systems.
Compounds derived from natural sources (organic) were thought to be fundamentally different
from inorganic compounds; it was believed that inorganic compounds could be synthesized in the
laboratory, but organic compounds could notat least not from inorganic materials
For the synthesis of organic compounds there must be a vital force, which is provided only by living
system. Because chemists could not create life in the laboratory, they assumed that they could not
create compounds with a vital force.
Friedrich Wohler (18001882) changed the thinking that vital force is required to produce organic
compounds in a laboratory.

1.2 Energy Level and Atomic Orbital

In its brief description, an atom contains a small, dense nucleus made up of chargeless neutrons
and positively charged protons. The nucleus accounts for most of the mass of an atom. The
nucleus is surrounded by negatively charged electrons taking much larger extranuclear space.
Nucleus

Extranuclear space
containing electrons

Table 1: Distribution of Electrons in Shells

Number of Electrons Relative Energies

Shell Shell can hold
4 32 Higher
3 18
2 8
1 2

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 Shells are subdivided into subshells represented by the letters s, p, d, and f, and within these
subshells electrons are grouped in orbital. An orbital is a region in the space where there is
high probability of finding electrons

Shell Orbitals contained in the respective shells

3 3s, 3px, 3py, and 3pz, plus five 3d orbitals
2 2s, 2px, 2py, and 2pz
1 1s

What are Pauli Exclusion Principle and Hunds Rule?

1.3 Bonding in Carbon Compounds

Ionic or Electrovalent Bonds

Ionic bond formation involves lose and gain of electrons. It is formed when one atom loses
electron(s) and the other atom gains electron.

Li + F Li + F

The two oppositely charged species, the lithium ion and fluoride ion, attract each other, and
hence ionically bonded to one another.

2 Covalent bonds

Covalent bond is formed when atoms achieve the nearest inert gas electronic configuration by
sharing electrons. The shared electrons are attracted by both nuclei, and this attraction makes the
atoms to be bonded to one another.

H
H H
H C H H C H H C H
H H
H
Methane

It can clearly be seen that in methane each atom has attained the desired filled orbital by virtue of
electron sharing.
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Hopefully you are not! In a covalent single bond between unlike atoms, the electron pair forming
the bond is never shared absolutely equally between the two atoms; it tends to be attracted a
little more towards the more electronegative atom of the two. Thus in hydrogen chloride, below,
the electron density tends to be greater nearer chlorine than carbon, as the former is the more
electronegative; this is generally represented as in (A) or (B): The symbols + and - indicate
partial positive and partial negative charge, respectively.

H Cl or H Cl
A B
The hydrogen chloride molecule, therefore, is called a dipole. Associated with this dipole is a
dipole moment , defined as the charge e (either the positive or the negative charge, since they
must be equal) multiplied by the distance between the centers of charge?
=exd
2.1 Valence Band Theory
According to VBT, a covalent bond is formed when two atoms approach each other closely
so that a singly occupied orbital on one atom overlaps with a singly occupied orbital on the
other atom. The two electrons, one from each atom, occupy the overlapping orbital and they are
paired. The two electrons are attracted by nuclei of both atoms, hence bonding the atoms
together.

H + H H H

H2 Molecule

The question still arises! How close are the nuclei in hydrogen molecule? It is obvious that
the nuclei repel each other if they are too close, as they both are positively charged. On the other
hand, if they are far apart they cannot have efficient overlapping of orbitals. This implies that,
there is an optimum distance between nuclei that leads to maximum stability. The distance
between nuclei at the minimum energy is the bond length. It has been found that hydrogen
molecule attains maximum stability if the bond distance is about 74pm.

2.1.1 Orbital Hybridizations

The idea of hybridization was offered by Linus Pauling which has solved the troublesome
puzzle in the early days of valence bond theory concerned the bonding in methane (CH 4).
According to this idea, the four valence orbitals of carbon (2s, 2px, 2py, and 2pz) mix together

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(hybridize) to give four half-filled orbitals of equal energy. These new orbitals are called sp3
hybrid orbitals since they are composed of one s and three p orbitals (Figure 1.3). All the sp 3
orbitals are of equal energy; each has one-fourth s character and three-fourth p character.
Energy

2p3
2p2
sp3

2s1 sp3 hybrid

2s2 state of carbon
Ground state electronic Excited state electronic
configuration of carbon configuration of carbon

Schematic representation of formation of sp3 hybrid state of carbon

The four sp3 orbitals are directed toward the vertices of a regular tetrahedron, with carbon at the
center of tetrahedron

Each of the four sp3 hybrid orbitals is occupied by one of the four outer shell electrons. Methane
is formed by overlapping of the half-filled 1s orbital of a hydrogen atom with each of the half-
filled sp3 hybrid orbitals of a carbon atom. This gives methane a tetrahedral geometry with bond
angle of 109.5, which agrees with the experimental value.
H

H C
H

Orbital representation of methane

This can be extended to explain the bonding pattern of ethane. In ethane, one of the sp3 hybrid
orbitals of one carbon overlaps with one of the sp3 hybrid orbitals of the other carbon to form a
(sigma) bond. Each the remaining sp3 hybrid orbitals of both carbons overlaps with the half-
filled 1s orbital of a hydrogen atom
H
H

C H
H C

H
H

Orbital representation of ethane

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The sp3 hybridization is not the only possible hybridization for carbon. Other kinds of
hybridizations like sp2 and sp are also possible.
The carbon carbon double bond (sp2 hybridization)
This hybrid orbital is composed of one s orbital and two p orbitals, hence sp2 hybrid orbital.

2p 2p 2p
Energy

sp2

2s
(a) Ground state electronic
configuration of carbon
2s
(c) sp2 hybrid
state of carbon
(b) Excited state electronic
configuration of carbon

Schematic representation of formation of sp2 hybrid state of carbon

This kind of hybridization, sp2 hybridization, can be explained using ethylene (ethene) as an
example.
H
H

C
C

H
H

Unhybrdized 2p orbitals of the carbon

atoms. They overlap with one another
in sideways to form a pi) bond

Orbital representation of ethylene

As it can be seen from figure 1.8, each of the ethylene carbon atoms has on 2p orbital left
unhybridized. The remaining two 2p orbitals of both carbon atoms are hybridized (mixed) with
the 2s orbital to give three orbitals. One of the sp2 hybrid orbitals of one carbon overlaps with
one of the hybrid orbitals of the other carbon to form a (sigma) bond and each of the remaining
two sp2 hybrid orbitals undergo overlapping with four different 1s orbitals of the hydrogen
atoms. The 2p orbital of each carbon atom, which is left unhybridized, undergo lateral
(sideways) overlapping with each other to give rise to what is known as a (pi) bond.
This explains the fact that in ethylene there is a carbon-carbon double bond, one bond and one
pi bond. The three sp2 orbitals are of equal energy; each has one-third s character and two-thirds

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 p character. Their axes are coplanar, and each of the sp2 orbitals has a shape much like that of a
sp3 orbital.
The carbon carbon triple bond (sp hybridization)
Brain storming: Can you think of sp hybridization? How sp hybridization is formed?.

2p 2p 2p
Energy

sp

2s
2s (c) sp hybrid
state of carbon
(a) Ground state electronic (b) Excited state electronic
configuration of carbon configuration of carbon
Schematic representation of formation of sp2 hybrid state of carbon

Overlapping of sp orbital of one carbon atom with sp orbital of another carbon atom leads to
formation of an bond between the two carbon atoms which are supplemented by two bonds
formed by overlap of the remaining half-filled p orbitals.
180 180

H C C H
106 120 106
pm pm pm

The molecule generated by the above process is linear; that is the two hydrogen nuclei and the
two carbon nuclei lie on a straight line. The sp hybridized system you have just gone through is
called carbon-carbon triple bond (two bonds and one bond), and compounds containing triple
bonds are called alkynes.

Dear student, so far we have been dealing with hydrocarbons (alkanes, alkenes, and alkynes) that
have open chain structure. However, there are other classes of hydrocarbon that are called
cycloalkanes, where cyclopropane is the simplest example. This hydrocarbon, cyclopropane
needs special attention as it has some unusual properties.

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 H2C
CH2
H2C or

Cyclopropane
As it can be seen from the structure of cyclopropane, each of the carbon atoms has a sp3
hybridization, which demands a bond angle of 109.5, and on the other hand, the geometry of the
structure demands 60. This phenomenon, obviously leads the structure to deviate from the
normal bond angle of a sp3 which introduces a sort of strain called Baeyer strain into the
molecule. Normally maximum orbital overlapping would be achieved if the orbitals have a
collinear arrangement rather than at an angle to each other.

sp3 orbitals overlapping

sp3 orbitals overlapping
in head-on manner
at an angle

Overlapping of sp3 hybrid orbitals (head on and at an angle)

In the case of cyclopropane, however, the orbitals are forced to have an overlapping pattern at
angle rather than head-on overlapping. Due to this, in cyclopropane, the resulting carbon-carbon
bonds are not a normal bonds. These bonds are actually banana shaped and are sometimes
referred to as banana bonds. This strain is a destabilizing factor and leads to enhanced reactivity
so that the compound gets relief from the strain. The enhanced reactivity is thus can be attributed
to the diminished orbital overlapping. As the overlapped orbitals are bulged out of the
internuclear axes, the electrons are more accessible to electron-seeking reagents.

1.3 Molecular Orbital Theory

Molecular orbital theory (MOT) is another approach (model) applied to describe covalent bond
formation. According to MOT when atoms combine to form molecules the corresponding atomic
orbitals combine to give new set of orbitals called molecular orbitals (MOs). This combination
of atomic orbitals is described as the so called linear combination of atomic orbitals-molecular
orbital (LCAO-MO) method. This means MOT is based on the notion that, as electrons in atoms

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occupy atomic orbitals, electrons in molecules occupy molecular orbitals. In fact they are called
molecular orbitals because they belong to the entire molecule rather than to an individual atom.
Like atomic orbitals molecular orbitals have a specific size, shape, and energy. Exactly like
atomic orbitals, molecular orbitals are mathematical functions called wave functions.

H H Antibonding MO (unfilled)
Energy

H 1s orbital H 1s orbital

H H Bonding MO (filled)

Molecular orbital of H2

The additive combination is lower in energy than the two hydrogen 1s atomic orbitals and is
called a Bonding MO. The electrons that occupy this orbital spend most of their time in the
region between the two nuclei thereby bonding the atoms together. The subtractive combination
is higher in energy than the two hydrogen 1s atomic orbitals and is called an antibonding MO.
Any electron occupying this orbital cannot be in the central region between the two nuclei and
cannot contribute to bonding.

Just as bonding and antibonding molecular orbitals result from the combination of two s
atomic orbitals in H2, so bonding and antibonding molecular orbitals result from the
combination of two p atomic orbitals in ethylene.

Antibonding MO

Combine

Two p orbitals Bonding MO

Molecular orbital of description of the C=C bond in ethylene

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By the way, molecular orbital theory is particularly useful for describing bonds in compounds
that have more than one double bond. This will be dealt with in more detail in subsequent
courses of organic chemistry.

1.4 Factors influencing electron availability and reactivity

1.4.1 Inductive effect
The electron-donating or electron-withdrawing effect of a group that is transmitted through
bonds is called an inductive effect. Such an electron-donating or electron-withdrawing
phenomenon arises from difference in electronegativity. We have already stated that when two
atoms of different electronegativity are covalently bonded to one another, the bond electrons are
strongly attracted by the more electronegative atom than the less electronegative atom. As a
result the more electronegative atom bears partial negative charge (-) and the less
electronegative atom bears partial positive charge (+). Such polarized system in a covalent bond
gives rise to an inductive effect. To understand inductive effect in more depth let us see the
following two olefins (alkenes) as an example.

F H

F C CH CH2 H C CH CH2 CH3 CH2 CH2 Cl
F H
A B C

The fluorinated olefin (A) is much less reactive toward electron seeking reagents than the non-
fluorinated olefin (B). The three fluorine atoms inductively withdraw electron from the carbon to
which they are bonded, making the carbon atom to bear significant amount of partial positive
charge. This situation forces the electron density of the system to shift toward the carbon that
bears partial positive charge, thereby reducing the electron density of the system.

Inductive effect, however, does not affect electron density of the reactive center at a distance.
That is the effect shrinks rapidly with distance. Thus, in n-propyl chloride (C), the carbon
directly bonded to chlorine bears sizeable amount of partial positive charge, whereas the charge
on the next carbon (methylene carbon) is very small. The charge on the methyl carbon is
virtually non-existent.

1.4.2 Resonance effect

Resonance may be defined as bonding or sharing of electrons between more than two atoms
(nuclei). Typical covalent and ionic bonding involves sharing (covalent) or transferring (ionic)
electron pairs between two atoms as shown in the examples of ethane and sodium chloride
below. In these examples the bonding electrons are localized:

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Resonance differs from the two examples above in that it involves the sharing of electrons
between more than two atoms via delocalization. The classical example of resonance is
provided by the pi-bonding system of benzene. Benzene is a six membered ring composed of
six sp2 hybridized carbon atoms in a plane and sharing 6 pi electrons. It can be represented by
the "Kekule" structure shown below which suggests and "alternating" single bond-double bond
bonding pattern. This representation does not really adequately reflect the true electronic
character of benzene since, in reality, all six pi electrons are shared equally by the six carbons.

Thus the "inscribed" circle representation may be more accurate (although it doesn't directly
indicate the number of pi electrons:

The Kekule structure of benzene does represent the electronic and structural requirements for
resonance. For resonance phenomena to exist a "conjugated" electronic system must be present
and the atoms involved in this system must be coplanar or capable of adopting a coplanar
conformation. The type of resonance effect exerted by an atom or functional group electron
donating (+R) or withdrawing (-R) is determined by the electronic nature of the group. Each of
these characteristics/requirements of resonance are defined in more detail below:

"Conjugation": An electronic configuration in which there is an alternating single bonddouble

(pi) bond pattern, or an atom with non-bonded electron pairs (or lacking an electron pair)

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bound to a double bond system. The alternating single bond-double (pi) bond pattern can be
illustrated by butadiene. In this example the resonance structure shows that the electrons can be
"shared" or delocalized (follow the arrows) creating a cationic and anionic center:

Another example of the single bond-double bond resonance pattern is in , -unsaturated

carbonyl compounds. Here the difference in electronegativity between atoms in the pattern
allows for a dipole and reactivity such as conjugate addition:

Examples of resonance resulting from atom with non-bonded electron pairs bound to a
double bond system are shown below. Notice in each case below that that the "resonance
phenomenon" involves an electron rich atom donating a pair of electrons to an electron
deficient multiple bond system, and that in actually, the charges shown are distributed or
delocalized over all of the atoms of conjugation. This resonance phenomenon is what
makes carboxylic acids, and to a lesser extent phenols and protons alpha- to a carbonyl,
acidic! The charged formed upon ionization can be stabilized through resonance
delocalization!

Resonance can also occur in structural patterns where an atom deficient in an electron pair
is bound to a double bonded system. Consider the case of the reaction of the "allyl
chloride" compound below. This compound can ionize by loss of Cl- (a good leaving
group) because the charge of the resulting carbocation is stabilized by resonance
delocalization of the pi (double bond) electrons. The same is true for benzyl alcohols as
shown below. Benzyl alcohols can ionize because the resulting carbocation charge can be
delocalized throughout the benzene ring via resonance:

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 In every case above, resonance was possible because of an electronic configuration in
which there is an alternating single bond-double (pi) bond pattern, or an atom with non-
bonded electron pairs (or lacking an electron pair) bound to a double bond system. It is
important to realize that resonance is not possible when such an electronic configuration is
NOT possible. Consider the examples below. In the first example (1) resonance is not
possible because the two double bonds are separated by MORE THAN on single bond. In
the second example the negatively charged atom is separated from the double bond by
more than one single bond and in example (3) the charge is separated from the C=C by
more than a single double bond.

1.4.3 Steric Effect

Steric effect is space-filling effect. It is caused by groups occupying a certain volume of space.
A steric effect that decreases reactivity is called steric hindrance. Steric hindrance results when
groups are in the way at the reaction site; which refers to bulky groups at the site of the reaction
that make it difficult for the reactants to approach each other. Hence it decreases reactivity. It can
be illustrated using the rate of a substitution reaction.

R R
Cl
R C Br R C Cl
acetone
R R

Relative rate of substitution reaction (SN2)

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 R Relative rate of the reaction

CH3 30

CH3CH2 1

(CH3)2CH 0.03

(CH3)3CCH2 0.00005

(CH3)3C Too slow to measure

Substitution reaction has two well-known pathways (mechanisms): SN1and SN2. At this point,
we are considering the SN2 pathway. The detail of these mechanisms will be discussed in chapter
four, so you dont have to worry to have the detail understanding of the issue at this point.
The values in the table clearly indicate that the rate of the reaction significantly decreases as the
size of the R groups increases. This is so because as the size of the R groups increases, the space
filling also increases, which blocks the way for the approach of the chloride

2. Functional classification of organic compound

Functional group: an atom or group of atoms within a molecule that shows a characteristic set
of predictable physical and chemical behaviors.
Functional groups are important in organic chemistry because:
They are sites predictable chemical behavior. A particular functional group, in whatever
compound it is found, undergo the same types of chemical reactions.
Determine in large measure the physical properties of a molecule.
Serve as the units by which we classify organic compounds into families.
Serve as a basis for naming organic compounds.
Hydrocarbons: a large family of organic compounds and they contain only carbon and
hydrogen.
Hydrocarbons are divided into two groups:
Saturated hydrocarbon: a hydrocarbon that contains only carbon-carbon single bonds (alkanes,
also called Aliphatic hydrocarbons). Saturated in this context means that each carbon in then
hydrocarbon has the maximum number of hydrogen atoms bonded to it.
Unsaturated hydrocarbon: a hydrocarbon that contains one or more carbon-carbon double
bonds, triple bonds, or benzene rings.

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2.1 Alkane
Alkanes are saturated hydrocarbons
They contain chains of carbon atoms linked by single bonds only
have the general formula CnH2n+2, where, n = 1, 2, 3 . . . CH4 and C2H6 or C2H6 and C3H8,
they differ by one carbon and two hydrogen atoms or CH2 group called the methylene
group. homologous series.
As the number of carbons in an alkane increases beyond three, the number of possible
structures increases
Compounds such as butane and isobutane that have the same molecular formula but differ
in the order in which the atoms are connected are called constitutional isomerstheir
molecules have different constitutions

A primary carbon is a carbon that is bonded to only one other carbon A secondary carbon is a
carbon that is bonded to two other carbons A tertiary carbon is a carbon that is bonded to three
other carbons

Like the carbons, the hydrogens in a molecule are also referred to as primary, secondary, and
tertiary. Primary hydrogens are attached to primary carbons, secondary hydrogens to
secondary carbons, and tertiary hydrogens to tertiary carbon

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 Nomenclature of Alkanes

Physical Properties of Alkanes

Physical properties of alkanes: 1. they are nonpolar compounds (the electronegativity
difference between carbon and hydrogen is 2.5-2.1 = 0.4). 2. The only interactions between their
molecules are the very week London dispersion forces. 3. They are insoluble in water (because
water is polar) and they are soluble in nonpolar organic compounds. 4. They have the lower
density than water (their densities is between 0.7 and 0.8 g/mL). 5. They have the low boiling
points and the low melting points. 6. They can be gases (with 1 to 4 carbon atoms), liquids (with
5 to 17 carbon atoms), or solids (with 18 or more carbon atoms).

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Note: In general, both boiling and melting points of alkanes increase with increasing molecular
weight (the number of carbon atoms).
Note: In general, both boiling and melting points of alkanes decrease with increasing the number
of branches (for alkanes with the same molecular weights). As branching increases, the alkane
molecule becomes more compact and its surface area decreases (London dispersion forces act over a
smaller surface area).

2.2 Alkene
Alkenes are unsaturated hydrocarbons containing a carbon-carbon double bond as their
functional group: C C

They are also known as olefins. They form a homologous series represented by the general
formula CnH2n, where n = 2, 3, 4.

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Isomerism in Alkenes
Alkenes containing two and three carbon atoms have only one possible structure. Alkenes
containing four or more carbon atoms exhibit isomerism. Alkenes show the following three types
of isomerism:
1. Chain isomerism: This is due to the difference in the arrangement of the carbon atoms in the
longest continuous carbon chain.
2. Position isomerism: This is due to the difference in the position of the double bond in the
carbon chain.

Geometrical Isomerism

This results from the difference in the relative spatial arrangement of atoms or groups about the
double bond. This isomerism exists because free rotation about the double bond is not possible

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Physical properties of alkenes and alkynes: their physical properties are similar to those of alkanes
with the same carbon skeletons.

Chemical properties of alkenes and alkynes: these organic compounds are more reactive than
alkanes. The most characteristic reaction of alkenes (alkynes) is addition to the carboncarbon double
bond (triple bond): The double bond is broken and in its place single bonds form to two new atoms or
groups of atoms. We can name four important chemical reactions for them: 1. Addition of hydrogen
(Hydrogenation or Reduction). 2. Addition of hydrogen halides (Hydrohalogenation). 3. Addition
of water (Hydration). 4. Addition of bromine and chlorine (Halogenation).

Hydrogenation or Reduction (addition of hydrogen): atoms of hydrogen add to the carbons in a

double or triple bond to form alkanes. A catalyst as platinum (Pt), nickel (Ni), or palladium (Pd) is
added to speed up the reaction. The transition metal catalysts used in this hydrogenation are able to
absorb large quantities of hydrogen onto their surfaces, probably by forming metal-hydrogen bonds.

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Alkynes
Hydrocarbons that contain a carboncarbon triple bond are called alkynes. Noncyclic alkynes
have the molecular formula CnH2n_2. Acetylene (HCPCH) is the simplest alkyne. We call
compounds that have their triple bond at the end of a carbon chain (RC- CH) monosubstituted, or
terminal, alkynes. Disubstituted alkynes (RC- CR_) are said to have internal triple bonds. You
will see in this chapter that a carbon carbon triple bond is a functional group, reacting with
many of the same reagents that react with the double bonds of alkenes.

The most distinctive aspect of the chemistry of acetylene and terminal alkynes is their acidity. As

a class, compounds of the type RCPCH are the most acidic of all simple hydrocarbons. The

structural reasons for this property, as well as the ways in which it is used to advantage in
chemical synthesis, are important elements of this chapter.
Nomenclature
In naming alkynes the usual IUPAC rules for hydrocarbons are followed, and the suffix -ane is
replaced by -yne. Both acetylene and ethyne are acceptable IUPAC names for HC-CH. The
position of the triple bond along the chain is specified by number in a manner analogous to
alkene nomenclature.

Aromatic compounds
Aromatic compounds unsaturated hydrocarbon that contain one or more benzene in their structure
Benzene: a molecule of benzene consists of a ring of six carbon atoms with onr hydrogen atom
attached to each carbon. It has the molecular formula C6H6. The real molecule of benzene is a
resonance hybrid of the two Lewis structures (a unique feature that makes benzene chemically
stable).

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20
Chemical reaction of benzene

21
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23
 Alcohol
Alcohols and phenols can be thought of as organic derivatives of water in which one of the
water hydrogens is replaced by an organic group: H- O -H versus R-O -H and Ar-O- H. In
practice, the group name alcohol is restricted to compounds that have their - OH group bonded to
a saturated, sp3-hybridized carbon atom, while compounds with their -OH group bonded to a
vinylic, sp2-hybridized carbon are called enols.

IUPAC Nomenclature of Alcohols

Functional class names of alcohols are derived by naming the alkyl group that bears the hydroxyl
substituent (- OH) and then adding alcohol as a separate word.

Hydroxyl groups take precedence over (outrank) alkyl groups and halogen substituents in
determining the direction in which a carbon chain is numbered.

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Problem: Write structural formulas, and give the functional class and substitutive names of all
the isomeric alcohols that have the molecular formula C4H10O

Classes of Alcohols
Alcohols are classified as primary, secondary, or tertiary according to the classification of the
carbon that bears the functional group.

Monohydric alcohols are alcohols containing only one hydroxyl group

Dihydric alcohols are those containing two hydroxyl groups per molecule. They are also named
glycols or diols.

Trihydric alcohols are those containing three hydroxyl groups in their molecular structure.
Polyhydric alcohols are those containing three or more hydroxyl groups in their molecular
structure. Trihydric alcohols are also considered as polyhydric alcohols.

Physical properties
The hydroxyl group in an alcohol is polar due to the high electronegativity of oxygen. As a
result, there is significant hydrogen bonding in alcohols.

Due to the hydrogen bonding in alcohols, they have higher melting and boiling points than
hydrocarbons of comparable molecular size (mass). Hydrogen bonding is also the cause for even
lower members to be liquids at room temperature. The boiling point of more branched isomer is
lower than that of its isomeric straight-chain alcohol.

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Dihydric and the trihydric alcohols have higher boiling points than monohydric alcohols of
similar molecular size (mass). Ethane-1,2-diol (dihydric alcohol, molecular mass = 62), boils at
197C, while 1-propanol (monohydric, molecular mass = 60) boils at 97.2C.

The first three alcohols, methanol, ethanol and 1-propanol are miscible with water in all
proportions, while the solubility in water decreases with increasing carbon number. The water
solubilities of dihydric and trihydric alcohols are higher than those of monohydric alcohols of
similar molecular mass.
Oxidation of Alcohols
Primary alcohols yield aldehydes or carboxylic acids, secondary alcohols yield ketones, but
tertiary alcohols dont normally react with most oxidizing agents.

Ethers
Ethers (R- O- R) like the alcohols are also organic derivatives of water but have two organic
groups bonded to the same oxygen atom rather than one. The organic groups might be alkyl,
aryl, or vinylic, and the oxygen atom might be in an open chain or a ring. The most well-known
ether is diethyl ether, which has a long history of medicinal use as an anesthetic and industrial
use as a solvent

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Nomenclature of Ethers
Ethers are compounds in which oxygen is bonded to two alkyl substituents. If the alkyl
substituents are identical, the ether is symmetrical ether. If the substituents are different, the
ether is unsymmetrical ether.

The common name of an ether consists of the names of the two alkyl substituents (in alphabetical
order), followed by the word ether. The smallest ethers are almost always named by their
common names.

Cyclic Ethers: Epoxides

Three-membered cyclic ethers are called as epoxides, also called oxiranes. Epoxides are easily made
from alkenes and they undergo a variety of useful synthetic reactions. An alkene can be converted
into an epoxide, a three-membered ring ether, by a peroxyacid

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Physical Properties of ether
Do not have hydrogen bond to one another, as the result they have lower boiling point
than alcohol
The ether oxygen can form hydrogen bond with water, causing low molecular weight
ether to be water soluble, ether with larger organic group are water insoluble
Simple ether are highly flammable solvent
Amine
There are primary amines, secondary amines, and tertiary amines. The classification depends
on how many alkyl groups are bonded to the nitrogen. Primary amines have one alkyl group
bonded to the nitrogen, secondary amines have two, and tertiary amines have three.

Notice that the number of alkyl groups attached to the nitrogen determines whether an amine is
primary, secondary, or tertiary. For an alkyl halide or an alcohol, on the other hand, the number
of alkyl groups attached to the carbon to which the halogen or the OH is bonded determines the
classification

The common name of an amine consists of the names of the alkyl groups bonded to the nitrogen,
in alphabetical order, followed by amine. The entire name is written as one word (unlike the
common names of alcohols, ethers, and alkyl halides, in which alcohol, ether, and halide
are separate words).

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IUPAC name

Physical properties of amine

Primary and secondary amines also form hydrogen bonds, so these amines have higher boiling
points than alkanes with similar molecular weights. Nitrogen is not as electronegative as oxygen,
however, which means that the hydrogen bonds between amine molecules are weaker than the
hydrogen bonds between alcohol molecules. An amine, therefore, has a lower boiling point than
an alcohol with a similar molecular weight

Because primary amines have two bonds, hydrogen bonding is more significant in primary
amines than in secondary amines. Tertiary amines cannot form hydrogen bonds between their
own molecules because they do not have hydrogen attached to the nitrogen. Consequently, if you
compare amines with the same molecular weight and similar structures, you will find that
primary amines have higher boiling points than secondary amines and secondary amines have
higher boiling points than tertiary amines.

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 Aldehydes and Ketones
The major similarity between an aldehyde and a ketone is the carbonyl group. A carbonyl group
is a carbon atom doubly bonded to an oxygen atom.

O O
C ketone R C H aldehyde

Both molecules have a carbonyl group, the difference the number of carbons bonded to the
carbonyl carbon. An aldehyde will have none or one and a ketone will have two carbons.

All aldehydes, except formaldehyde, will have a hydrogen atom on one side of the carbonyl
carbon and at least on carbon on the other side. All ketones have a carbon on each side of the
carbonyl carbon.

Remember that the R symbolizes any carbon side-chain, from one to a million carbons.
Basically, what it comes down to is that in an aldehyde the carbonyl group is on the terminal
(last) carbon and the ketones carbonyl group is not.

These compounds are found at the most fundamental levels of biological existence. Glucose is
the single most important molecule in providing energy at a cellular level. Without glucose you
would die in seconds. Glucose, the most important carbohydrate, not only has a carbonyl group
but is an aldehyde. Another common carbohydrate is fructose, fruit sugar, this compound is a
ketone.

These compounds are more reactive than your typical alkane, the question you may ask is why?
The answer lies in the location of the electrons in the carbonyl group. First, look at the O
hybridization of a carbonyl carbon. A carbon connected to three other molecules must
be doubly bonded to one of those molecules. For a double bond to form p-orbitals must
overlap over a sigma bond. The hybridization loses one p-orbital, leaving the carbon as
sp2, allowing the formation of the other bond with the free p-orbital, forming a pi-bond.

Back to our question, why are the aldehyde and a ketone more reactive than an alkane.
C
When the pi-bond forms the electrons in this molecular orbital are more exposed,
making them more vulnerable to reacting. Try to visualize the electrons sticking out on each
side of the bond, leaving them accessible to other compounds.

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Nomenclatur: IUPAC Names

31
 Physical properties:
The physical properties of aldehydes and ketones are described as follows. Methanal is a gas at
room temperature. Ethanal is a volatile liquid. Other aldehydes and ketones are liquid or solid at
room temperature. The boiling points of aldehydes and ketones are higher than hydrocarbons and
ethers of comparable molecular masses. It is due to weak molecular association in aldehydes and
ketones arising out of the dipole-dipole interactions. Also, their boiling points are lower than
those of alcohols of similar molecular masses due to absence of intermolecular hydrogen
bonding. The following compounds of molecular masses 58 and 60 are ranked in order of
increasing boiling points.

The lower members of aldehydes and ketones such as methanal, ethanal and propanone are
miscible with water in all proportions, because they form hydrogen bond with water.

However, the solubility of aldehydes and ketones decreases rapidly on increasing the length of
alkyl chain. All aldehydes and ketones are fairly soluble in organic solvents like benzene, ether,
methanol, chloroform, etc. The lower aldehydes have sharp pungent odours. As the size of the
molecule increases, the odour becomes less pungent and more fragrant. In fact, many naturally
occurring aldehydes and ketones are used in the blending of perfumes and flavouring agents.

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Carboxylic acid
Carbon compounds containing a carboxyl functional group, COOH are called
carboxylic acids. The carboxyl group, consists of a carbonyl group attached to a hydroxyl
group, hence its name carboxyl.
Carboxylic acids may be aliphatic (RCOOH) or aromatic (ArCOOH) depending on the
group, alkyl or aryl, attached to carboxylic carbon.
Large numbers of carboxylic acids are found in nature. Some higher members of aliphatic
carboxylic acids (C12 C18) known as fatty acids, occur in natural fats as esters of
glycerol.
Carboxylic acids serve as starting material for several other important organic
compounds such as anhydrides, esters, acid chlorides, amides, etc

IUPAC name

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Structure of Carboxyl Group

In carboxylic acids, the bonds to the carboxyl carbon lie in one plane and are separated by about
120. The carboxylic carbon is less electrophilic than carbonyl carbon because of the possible
reason ance structure shown below:

Physical Properties
Aliphatic carboxylic acids upto nine carbon atoms are colourless liquids at room temperature
with unpleasant odours. The higher acids are wax like solids and are practically odourless due to
their low volatility. Carboxylic acids are higher boiling liquids than aldehydes, ketones and even
alcohols of comparable molecular masses. This is due to more extensive association of
carboxylic acid molecules through intermolecular hydrogen bonding. The hydrogen bonds are
not broken completely even in the vapour phase. In fact, most carboxylic acids exist as dimer in
the vapour phase or in the aprotic solvents.

Simple aliphatic carboxylic acids having upto four carbon atoms are miscible in water due to the
formation of hydrogen bonds with water. The solubility decreases with increasing number of
carbon atoms. Higher carboxylic acids are practically insoluble in water due to the increased
hydrophobic interaction of hydrocarbon part. Benzoic acid, the simplest aromatic carboxylic acid
is nearly insoluble in cold water. Carboxylic acids are also soluble in less polar organic solvents
like benzene, ether, alcohol, chloroform, etc.

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Carboxylic acid derivatives
Carboxylic derivatives are described as compounds that can be converted to carboxylic acids
via simple acidic or basic hydrolysis.
The most important acid derivatives are esters, amides and nitriles, although acid halides and
anhydrides are also derivatives (really activated forms of a carboxylic acid).

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 Unit 3: Stereochemistry
What is stereochemistry?
Compounds that have the same molecular formula but are not identical are called isomers.
Isomers fall into two main classes: constitutional isomers and stereoisomers. Constitutional
isomers differ in the way their atoms are connected. For example, ethanol and dimethyl ether are
constitutional isomers because they have the same molecular formula, C2H6O but the atoms in
each compound are connected differently. The oxygen in ethanol is bonded to a carbon and to a
hydrogen, whereas the oxygen in dimethyl ether

Unlike the atoms in constitutional isomers, the atoms in stereoisomers are connected in the same
way. Stereoisomers (also called configurational isomers) differ in the way their atoms are
arranged in space. Stereoisomers are different compounds that do not readily interconvert.
Therefore, they can be separated. There are two kinds of stereoisomers: cistrans isomers and
isomers that contain chirality centers

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 Chirality

Why cant you put your right shoe on your left foot? Why cant you put your right glove on your
left hand? It is because hands, feet, gloves, and shoes have right-handed and left-handed forms.
An object with a right-handed and a left-handed form is said to be chiral. Chiral comes from
the Greek word cheir, which means hand. Notice that chirality is a property of an entire object.
A chiral object has a nonsuperimposable mirror image. In other words, its mirror image is not
the same as itself. A hand is chiral because if you look at your left hand in a mirror, you do not
see your left hand; you see your right hand. In contrast, achair is not chiralit looks the same in
the mirror. Objects that are not chiral are said to be achiral. An achiral object has a
superimposable mirror image. Some other achiral objects would be a table, a fork, and a glass.

Enantiometers and chirality

Enantiomers are structures that are not identical, but are mirror images of each other
Structures are chiral if they cannot be superimposed upon their mirror image
Achiral structures are superimposable on their mirror images

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Planes of symmetry and chirality
Any structure that has no plane of symmetry can exist as two mirror-image forms
(enantiomers)
Any structure with a plane of symmetry cannot exist as two enantiomers
Asymmetric Carbons, Chirality Centers, and Stereocenters

An asymmetric carbon is a carbon atom that is bonded to four different groups. For example,
in 4-octanol is an asymmetric carbon because it is bonded to four different groups (H, OH,
CH3CH2CH3 and CH3CH2CH2CH3).

Notice that the only carbons that can be asymmetric carbons are SP3 hybridized carbons; Sp2
and sp hybridized carbons cannot be asymmetric carbons because they cannot have four groups
attached to them. An asymmetric carbon is also known as a chirality center.

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R/S NOMENCLATURE SYSTEM (CahnIngoldPrelog convention)
The complete set of rules is given in the textbook, but here are some things to keep in mind when
assigning configuration to chirality center

Assign priorities to the atoms directly attached to the chirality center. The highest priority
goes to the atom with the highest atomic number. In case there are isotopes, use the mass
number instead, since they have the same atomic number.

Notice that since the atomic number of hydrogen is 1, it will always be the lowest priority group,
as long as it is present.

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ASSIGNING ABSOLUTE CONFIGURATION
According to the Cahn-Ingold-Prelog convention, when assigning absolute configuration to a
chiral carbon the lowest priority group thats attached to that carbon must be pointing away from
an observer who is looking at the carbon in question. On paper, that usually means that if the
observer is the person looking at the page, then the lowest priority group is pointing away from
the observer, going behind the plane of the paper. In a 3-D formula this is indicated thus:

42
When the formula is given to us in this way, its easy to assign configuration. All we have to do
is assign priorities to the other three substituents and see if they are arranged clockwise or
counterclockwise when the observer follows them in order of decreasing priorities. We dont
have to mentally reposition either ourselves or the molecule in any way. In the example given
above we can see that the central carbon has the (S) configuration.

If the lowest priority group is not presented to us already positioned towards the back of the
chiral carbon, then it is useful to remember the following basic principle:

Examples

Consider the naturally occurring amino acid, alanine and its enatiomer

Fisher Projections
A Fischer projection symbolizes a 3-D wedge-bond structure whose horizontal bonds at each
chiral C are solid wedges projecting out of the plane of the paper, and whose vertical bonds at
each chiral C are dashed wedges projecting back into the plane of the paper (or lying in the plane
of the paper as is the case for the central C-C bond in the structure with two chiral C's).

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Optical Activity
Enantiomers have the same Boiling points ,Melting points and Density.
Almost all their physical properties are identical, but one exception is their effect on
plane polarized light.
Enantiomeric compounds rotate the plane of polarized light in equal but opposite
directions.
Chiral compounds are called optically active compounds.
Optically active compounds which rotate plane polarized light clockwise (dextrorotatory)
are designated (+) or d.
Optically active compounds which rotate plane polarized light counterclockwise
(levorotatory) are designated (-) or l.

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Plane-Polarized Light through an Achiral Compound

Plane-Polarized Light through a Chiral Compound

Dextrorotatory (+): an optically active compound that rotates plane polarized light in a
clockwise direction
Levorotatory (-): an optically active compound that rotates plane polarized light in a
counterclockwise direction

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Unit 4
a. Substitution and Elimination Reactions (SN2, SN1, E2 , & E1)

46
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 b. Addition Reactions

There are two main types of polar addition reactions: electrophilic addition and nucleophilic
addition. Two non-polar addition reactions exist as well called free radical
addition and cycloaddition. Addition reactions are also encountered in polymerizations and
called addition polymerization.

Scheme 3: Different addition reactions mechanism

Markovnikoves Rule

In organic chemistry, Markovnikoves rule or Markownikoff's rule is a rule describing the

outcome of some addition reactions in organic chemistry. It was formulated by the Russian
chemist Vladimir Vasilevich Markovnikov.

The rule may be summarized as "the rich get richer (Jumi Shin)": A carbon rich in substituents
will gain more substituents and the carbon with more hydrogen attached will get the hydrogen in
many organic addition reactions

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c. Rearrangement reaction

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