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Study Material
Engineering Chemistry (BBS00010)

Table of Contents

MODULE-V:

STEREOCHEMISTRY

● Representations of 3-dimensional structures, structural isomers.

● Stereoisomers, configurations, symmetry and chirality.
● Enantiomers, diastereoisomers, optical activity.
● Absolute configurations and conformational analysis.
● Basic idea on isomerism in transition metal compounds.

ORGANIC REACTIONS

● Introduction to reactions involving substitution

● Elimination, Addition.
● Oxidation, Reduction.
● Cyclization and Ring Openings.
● Synthesis of commonly use drags molecule.

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Stereochemistry
Symmetry Elements
● A point of reference about which symmetry operations can take place.
● A symmetry element can be identities, mirror planes, axes of rotation (both proper and improper), and
centers of inversion.
Symmetry operations
● It is an action that leaves an object looking the same after it has been carried out.
● Example: If we take a molecule of water and rotate it by 180° about an axis passing through the central
O atom (between the two H atoms) it will look the same as before, thus, rotation of a molecule about
its axis is symmetry operation.

Different Symmetry elements

i. Axis of symmetry: It is an axis obtained when a molecule is rotated by 2π/n radian (or 360°/n)
around an axis and arrangement similar to the original is obtained.

Water

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Benzene

⮚ The operation when repeated n times gives the exact original molecule.
⮚ Proper axis of rotation, (Cn):
Where, n = 1, i.e., 360° rotation (present in every molecule).
n = 2, i.e., 180° rotation
n = 3, i.e., 120° rotation
n = 4, i.e., 90° rotation
n = 5, i.e., 72° rotation
n = 6, i.e., 60° rotation …..
n = ∞, i.e., any rotation

⮚ Principal axis of rotation, (Cn): Highest order of axis of rotation present.

ii. Plane of symmetry: It is an imaginary plane that bisects a molecule into halves that are mirror
images of each other.

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iii. Centre of symmetry: It is a point, within an object or figure, through which any straight line also
passes through two points on the edge of the figure at the same distance from the centre but on
opposite sides.

iv. Alternating axis of symmetry: It is an axis aroused if there is a rotation of the molecule about
the axis by 2π/n radian (or 360°/n) followed by reflection through a plane perpendicular to this
axis produces an indistinguishable with the original.

BASIC INTRODUCTION TO STEREOCHEMISTRY

It is the sub-discipline of chemistry that deals with the study of the relative spatial arrangement of
atoms that form the structure of molecules, their representation and manipulation.

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The study of stereochemistry focuses on the relationships between isomers, which by definition
have the same molecular formula but differ in sequence of bonded atoms (constitution) and structural
formula (the three-dimensional orientations of their atoms in space). For this reason, it is also known
as 3D chemistry—the prefix “stereo-” means “three-dimensionality”.

Isomers and isomerism

● Compounds having same molecular formulae but different relative arrangement of atoms in 3-D
space, i.e., different chemical structures. They may have different chemical and physical properties.
The phenomena is known as Isomerism.
● Greek ‘Isos’ means equal and ‘mers’ means parts. The term ‘isomerism’ was coined by the Swedish
chemist Jacob Berzelius in the year 1830.

⮚ Types of Isomers:

i. Constitutional/Structural isomers:
a. Chain/Skeletal/Nuclear isomers.
b. Position isomers.
c. Functional group isomers.
d. Metamers.
e. Tautomers.
f. Ring-chain isomers.

ii. Stereoisomers:
a. Configurational isomers:
● Geometric isomers – ‘Cis-’ and ‘Trans-’.
● Optical isomers – Enantiomers and Diastereomers.
b. Conformational isomers:
● Rotational isomers – Staggered, Gauche and Eclipsed.
● Amine inversion.

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STRUCTURAL/CONSTITUTIONAL ISOMERS

Two (or more) molecules are known as structural isomers when they have difference in structures
due to different sequence of the atoms and the functional groups in the molecules.

They have different IUPAC names, chemical properties and physical properties such as melting
point, boiling point, etc.

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Note: Resonance structures are not structural isomers.

i. Chain/skeletal isomers: Molecules having different branching of carbon skeleton, e.g., C5H12
have three skeletal isomers, viz.,

ii. Position isomers: Molecules having different positions of functional groups or constituent
atoms, e.g., C3H7Cl have two different position isomers, viz.,

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iii. Functional group isomers: Molecules having different functional groups attached to them, e.g.,
C3H6O have two different functional group isomers, viz.,

iv. Metamers: Molecules having different alkyl chain on each side of the functional group, e.g.,
C4H10O have two different metamers, viz., Diethyl ether (Ethoxy ethane) and Methyl propyl
ether (Methoxy propane). Also, Pentan-2-one and Pentan-3-one are two metamers of molecular
compound C5H10O.

v. Tautomers: A tautomer of a compound refers to the isomer of the compound which only differs
in the position of protons and electrons, which exist together in equilibrium and are easily
interchangable. It occurs via an intramolecular proton transfer. An important example of this
phenomenon is Keto-enol tautomerism, e.g.,

vi. Ring-chain isomers: In ring-chain isomerism, one of the isomers has an open-chain structure
whereas the other has a ring structure. They generally contain a different number of pi bonds,
e.g., C3H6 has two ring-chain isomers, viz., propene and cyclopropane.

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STEREOISOMERS
Two (or more) molecules are known as stereoisomers when they have similar structure, i.e., similar
sequence of constituent atoms and functional groups but different relative orientation in 3-D space, e.g.,
It is of two types, viz., Configurational and conformational stereoisomers.

i. Configurational stereoisomers: Two molecules are known as configurational stereoisomers if they

are interconvertible to each other by bond breaking and formation.
It is further sub-divided into two groups, viz.,

a. Geometric isomers: Two configurational isomers are known as geometric isomers when
they differ by restricted rotation about a double bond.

The two configurations are ‘cis-’ and ‘trans-’. When the two functional groups are
present on the same side of the double bond then it is the ‘cis-configuration’ and when the
two functional groups are present on the opposite side of the double bond then it is the
‘trans-configuration’.

b. Optical isomers: Two configurational isomers are known as optical isomers when they have
different spatial arrangements of constituent atoms.

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The optical isomers which can rotate the plane polarized light (PPL) are known as
‘optically active’ compounds; and which cannot are known as ‘optically inactive’
compounds. The optically active compounds which can rotate the PPL in right (or
clockwise) direction are known as ‘Dextro-rotatory’ or ‘D’ and are denoted by ‘+’ sign,
whereas, the optically active compounds which can rotate the PPL in left (or anti-clockwise)
direction are known as ‘Levo-rotatory’ or ‘L’ and are denoted by ‘–’ sign.

The optical activity is shown by tetrahedral complexes containing a ‘chiral carbon’.

The optical isomers are of two types:

● Enantiomers: Two optically active molecules are called enantiomers if they are non-
superimposable mirror images to each other.

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● Diastereomers: Two optically active molecules are called diastereomers if they are
non-superimposable non-mirror images to each other.

⮚ NOTES:
● Monochromatic light: The light which has a single discrete wavelength but vibrates in infinite
no of planes.
● Plane polarized light: The light having a single wavelength and the electronic vector vibrates in
a particular single plane perpendicular to the direction of propogation of light.

● Angle of rotation: The angle at which the analyte is rotated to obtain maximum intensity of the
emergent radiation.

⮚ BIOTS LAW: At a particular temperature and wavelength, for a particular set of sample and analyte,
the optical angle of rotation is proportional to

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i. Concentration of the optically active molecules.

ii. Length of the polarimeter tube.

Where, [α] is the Specific rotation (in degrees), ‘α’is the observed rotation (in degrees),
‘l’ is the length of polarimeter (in decimetre) and ‘c’ is the concentration of sample (in g/100
ml).

Thus, finally, specific rotation of any sample at a particular tmeperature and wavelength is
given by

The specific rotation is the rotation in degrees causing by a solution containing 1gm of an
optically active substance dissolved in per ml of a solution taken in a polarimeter tube of 1 decimetre
length at a specific temperature and wavelength.

⮚ Factors on which optical angle of rotation depend:

i. Concentration of optically active substance.
ii. Length of the polarimeter tube.
iii. Temperature of the medium
iv. Wavelength of light used.
v. Nature of sample and solvent.

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ii. Conformational stereoisomers: Two molecules are known as conformational stereoisomers if they
are interconvertible to each other by rotation about a C–C single bond. Different conformers of a
molecule are separated by distinct energy barriers.
There are two conformations, viz., Eclipsed and Staggered.
Example: Conformations of Ethane (C3H6)

Staggered form is highly stable due to favorable stabilizing interaction between C–H σ
bonding orbital and C–H σ* antibonding orbitals, whereas the Eclipsed form is unstable due to
unfavorable destabilizing interaction between the bonding and antibonding C–H orbitals.

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The angle between the substituted functional groups are known as ‘dihedral angle’.

When the dihedral angle is 0° or 360°, then it is ‘eclipsed/syn’ conformation.

When the dihedral angle is 60° or 300°, then it is ‘gauche’ conformation.
When the dihedral angle is 120° or 240°, then it is ‘partially eclipsed’ conformation.
When the dihedral angle is 180°, then it is ‘staggered/anti’ conformation.

Thus, the stability order of the above conformations is

Staggered/Anti > Gauche > Partially eclipsed > Eclipsed/Syn

The energy profile diagram of different conformations is given below.

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A. PROJECTION FORMULA OF STEREOISOMER & INTERCONVERSION OF ONE FORM

TO ANOTHER

The purpose is to represent a 3-dimensional structure of molecule in 2-dimension and vice-versa.

Different types of projections are

i. Fischer projection (2-D projection)
ii. Sawhorse projection (3-D projection)
iii. Newman projection (2-D projection)
iv. Flying wedge projection (3-D projection)

1. FISCHER PROJECTION:
● Vertical bonds projected below the plane of the paper and directed away from viewer.
● Horizontal bonds projected above the plane of the paper and pointed towards the viewer.

COOH
Away from
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H3 C OH

Towards the ≡

viewer

⮚ Rules for writing the formulae:

● As this projection is 2-dimensional it cannot be turned over.
● But this projection may be rotated by 180° about the molecular plane (or both the axes) to keep
the molecule identical.

Rotation by 180°
clockwise

● Also this can be achieved by rotating a group of any 3 substituents in a clockwise or anti clockwise
direction at an angle of 90° keeping the 4th substituent fixed.
COOH COOH H
H OH CH3 H CH3 OH
CH3 OH COOH

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(R)-lactic acid (R)-lactic acid (R)-lactic acid

● Rotation by 90° about the molecular plane will give rise to enantiomers.

● Interchanging of any two ligand will change the absolute configuration.

2. SAW HORSE PROJECTION:

● This is a 3 dimensional projection which is applicable for molecules with at least two carbon atoms.
● A diagonal line is drawn on the plane of the paper where the terminal points represent the two main
carbon atoms.

● Other bonds are represented by small lines above or below the plane.
● Free rotation about C–C bond is possible, so, 3 groups attached to one C may be rotated clockwise
or anticlockwise.

⮚ Conversion of Fischer to Sawhorse projection formulae:

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(I) is Fischer projection; (Ia) is Sawhorse eclipsed and (Ib) is Sawhorse staggered projection.

While converting the Fischer into Sawhorse, first we have to draw the eclipsed conformation
and then convert it into the staggered one. Direct conversion of Fischer into staggered results into
formation a diastereomers.

Examples:

3. NEWMANN PROJECTION:
● The molecules bearing the C atoms are viewed along the bond joining the C atoms. The above C
atoms are drawn by two superimposed circles. Only one circle is drawn.
● The C atom away from the viewer is the rear carbon atom represented by the circumference of the
circle.
● The C atom facing the viewer is the front carbon atom represented by the centre of the circle.
● Bonds joined to the front carbon atom are intersecting through the centre and bonds joined to the
rear C atom are shown on the circumference.

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Front carbon Rear Carbon

⮚ Conversion of Newman to Sawhorse projection formulae:

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4. FLYING WEDGE PROJECTION:

● This kind of representation is usually done for a molecule containing a ‘chiral carbon.’
● A solid line (─) represents the bond on the plane while a solid wedge and a dashed wedge
represents the bond above and below the plane, respectively.

⮚ Conversion of Flying Wedge to Fisher projection:

⮚ Rules for writing the formulae:
● Vertical bonds in flying wedge projection are considered to be on the plane of the paper and
the horizontal bonds are considered to be above/below the plane of the paper.

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● Upper vertical bond is drawn straight and lower vertical bond is bend on the left side.
● Groups on the left side in the horizontal bond is written above the plane of the paper.
● Groups on the right side in the horizontal bond is written below the plane of the paper.

CH3

OH H

COOH

Tricks: If the lower vertical group is bent towards left then the left side group is drawn above the
plane and if it is bent towards right then the right side group is drawn above the plane.

B. NOMENCLATURE OF ABSOLUTE AND RELATIVE CONFIGURATIONS

1. Absolute Configuration: The absolute configuration at a chiral center in a molecule is a time-

independent and unambiguous symbolic description of the spatial arrangement of ligands (groups)
bonded to the chiral center, e.g., R/S Convention (or CIP Convention).

2. Relative Configuration: The relative configuration is the experimentally determined relationship

between two enantiomers even though we may not know the absolute configuration, e.g., D/L
convention, E/Z convention.

⮚ R/S Convention:

This is an unambiguous method of nomenclature for molecules baring either one chiral carbon
atom (Flying Wedge projection) or more than one chiral carbon atom (Fischer projection). This
is also known as CIP (Cahn-Ingold-Prelog) convention.

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In this nomenclature, the stereocenters are labeled as ‘R’ and ‘S’.

In the first figure, the arrow points in a counter-clock wise direction, i..e., left when leaving the 12
o’ clock position, then the configuration at stereocenter is considered as S (Latin ‘Sinister’ means
‘Left’). Again, in the second figure, the arrow points in a clock wise direction, i..e., right when leaving
the 12 o’ clock position, then the configuration at stereocenter is considered as R (Latin ‘Rectus’ means
‘Right’).

● Rules to write the convention (CIP rules):

i. First, examine the constituent atoms according to their increasing atomic numbers. The
constituent atom with highest atomic number is the highest priority group and the one with
lowest atomic number is the lowest priority group.

Hydrogen is the lowest possible priority substituent, because it has the lowest atomic
number.

ii. If there are two substituents with equal rank, proceed along the two substituent chains until
there is a point of difference.

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iii. If a chain is connected to the same kind of atom twice or three times, check to see if the
atom it is connected to has a greater atomic number.

Remember that being double or triple bonded to an atom means that the atom is connected
to the same atom twice. In such a case, follow the same method as above.

Caution!! Keep in mind that priority is determined by the first point of difference along
the two similar substituent chains. After the first point of difference, the rest of the chain is
irrelevant.

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After all the substituent groups are assigned according to the CIP Priority rules,

i. For Fischer projection:

Draw an arcing arrow connecting the priority groups 1 🡪 2 🡪 3 and determine if the direction
from 1 to 3 is clockwise or counter-clockwise.

a. If the lowest priority ligand is on a vertical bond, meaning that it is pointing away
from the viewer, then

b. If the lowest priority ligand is on a horizontal bond, meaning that it is pointing

towards the viewer, then

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ii. For Flying Wedge projection:

Draw an arcing arrow connecting the priority groups 1 🡪 2 🡪 3 and determine if the direction
from 1 to 3 is clockwise or counter-clockwise.

a. If the lowest priority ligand is placed below the plane, then clockwise direction indicates
the R-configuration and counter-clockwise direction indicates the S-configuration.

b. If the lowest priority ligand is placed above the plane, then clockwise direction indicates
the S-configuration and counter-clockwise direction indicates the R-configuration.

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⮚ D/L Convention:

● This is an oldest method of assigning the nomnclature to chiral carbohydrate and amino acid
molecules by relating them to the molecule Glyceraldehyde. It is a chiral molecule and have two
isomers. The two isomers are labeled as ‘D’ and ‘L’.
● The D/L system is named after the Latin ‘Dexter’ means right and ‘Laevus’ means left.

● Glyceraldehyde has four different constituent groups on the chiral carbon, viz., –H, –CHO, –
CH2OH and –OH. The D-configuration has the –OH group on the right side and the –H on the
left side of the chiral carbon which is opposite for the L-configuration.

● The Flying Wedge projections of D- and L-glyceraldehyde is given below:

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● This is a relative configuration because the nomenclature includes (+) and (-) notations to indicate
whether the compound's stereochemistry is related to that of the dextro- or levo- enantiomer of
glyceraldehyde.
This does not tell anything about the nature of optical activity, i.e., whether dextrorotatary
or levorotatary.

● Limitation of this nomenclature: The D and L descriptors are derived from only one stereogenic
center and are used to name the entire molecule.

Thus, D- and L-glyceraldehyde, both having one stereogenic center, can be assigned R- and
S- configuration, respectively, but any other molecule with more number of stereogenic centres
cannot be named.

● More examples:

⮚ E/Z Convention:

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● This convention is appicable for 2D-compounds where each carbon across a double bond is attached
to a hydrogen and/or a non-hydrogen susbtituent.
● The E/Z system analyzes the two substituents attached to each carbon across the double bond and
assigns each either as a high or low priority. If the higher priority group on both carbons across the
double bond has the same side, the alkene is said to be a Z-isomer (from German Zusammen =
together). If the higher priority groups are on opposite sides, the alkene is said to be an E-isomer
(from German Entgegen = opposite).

This is very common to say that Z-isomer resembles the cis-configuration and E-isomer resembles
the trans-configuration.

● But what to do if the substituent groups across the double bond are different? Here E/Z will always
work, even when cis/trans fails. For example,

Here also the CIP priority rule is applied to assign the subdtituents on each carbon across the double
bond, i.e., the ‘first point of difference.’

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So, for the first two examples, because, the higher priority
groups on each carbon across the double bond, viz., I and Cl, are on same side in first example, thus
Z-isomer, and on oppsite side in second example, thus E-isomer.

Similarly, in the next two examples, the both are E-isomers.

● Rules to remenber:

i. E 🡪 trans. E for enemies which stays on opposite sides.

or
ii. Z 🡪 cis. Z for Zame Zide which stays on the same side.

● In case of more than one double bond:

If the compound contains more than one double bond, then each one is analyzed and declared to be
E or Z.

Example 1:

The configuration at the left double bond is E; at the right double bond it is Z. Thus this compound
is (1E,4Z)-1,5-dichloro-1,4-hexadiene.

Example 2:

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The configuration at the left double bond is Z; at the right double bond it is E. Thus this compound
is (1Z,3E)-1-chloro-2-ethyl-1,3-butadiene.

Basic idea on isomerism in transition metal compounds

The compounds which have the same chemical composition but have different structural arrangement of
their atoms are called Isomers and the phenomena that gives rise to isomers is called Isomerism. Transition
metal elements have an ability to make coordination bond with ligands. These coordination compounds
exhibit two main types of isomerism viz, structural isomerism and stereo isomerism.

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Structural isomers
The coordination compounds with same formula, but have different connections among their constituent
atoms are called structural isomers or constitutional isomers. Four common types of structural isomers are
discussed below.

Linkage isomers:

This type of isomers arises when an ambidentate ligand is bonded to the central metal atom/ion through
either of its two different donor atoms. In the below mentioned examples, the nitrite ion is bound to the
central metal ion Co3+ through a nitrogen atom in one complex, and through oxygen atom in other complex.

Example: [Co(NH3)5(NO2)]2+

Coordination isomers:

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This type of isomers arises in the coordination compounds having both the cation and anion as complex
ions. The interchange of one or more ligands between the cationic and the anionic coordination entities
result in different isomers.

For example, in the coordination compound, [Co(NH3)6][Cr(CN)6] the ligands ammonia and cyanide were
bound respectively to cobalt and chromium while in its coordination isomer [Cr(NH3)6][Co(CN)6] they are
reversed.

Some more examples for coordination isomers

1. [Cr(NH3)5CN][Co(NH3)(CN)5] and [Co(NH3)5CN][Cr(NH3)(CN)5]

2. [Pt(NH3)4][Pd(Cl)4] and [Pd(NH3)4][Pt(Cl)4]

Ionisation isomers:

This type of isomers arises when an ionizable counter ion (simple ion) itself can act as a ligand. The
exchange of such counter ions with one or more ligands in the coordination entity will result in ionization
isomers. These isomers will give different ions in solution. For example, consider the coordination
compound [Pt(en)2Cl2]Br2. In this compound, both Br-and Cl- have the ability to act as a ligand and the
exchange of these two ions result in a different isomer [Pt(en)2Br2]Cl2. In solution the first compound gives
Br - ions while the later gives Cl-ions and hence these compounds are called ionization isomers.

Some more example for the isomers,

1. [Cr(NH3)4ClBr]NO2 and [Cr(NH3)4Cl NO2]Br

2. [Co(NH3)4Br2]Cl and [Co(NH3)4Cl Br]Br

Solvate isomers (Hydration isomer):

The exchange of free solvent molecules such as water, ammonia, alcohol etc. in the crystal lattice with a
ligand in the coordination entity will give different isomers. These types of isomers are called solvate
isomers. If the solvent molecule is water, then these isomers are called hydrate isomers. For example, the
complex with chemical formula CrCl3.6H2O has three hydrate isomers as shown below.

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Stereoisomers:

Similar to organic compounds, coordination compounds also exhibit stereoisomerism. The stereoisomers
of a coordination compound have the same chemical formula and connectivity between the central metal
atom and the ligands. But they differ in the spatial arrangement of ligands in three-dimensional space. They
can be further classified as geometrical isomers and optical isomers.

Geometrical isomers:

Geometrical isomerism exists in heterolytic complexes due to different possible three-dimensional spatial
arrangements of the ligands around the central metal atom. This type of isomerism exists in square planer
and octahedral complexes.

In square planar complexes of the form [MA2B2]n± and [MA2BC]n± (where A, B and C are mono dentate
ligands and M is the central metal ion/atom), Similar groups (A or B) present either on same side or on the

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opposite side of the central metal atom (M) give rise to two different geometrical isomers, and they are
called, cis and trans isomers respectively.

The square planar complex of the type [M(xy)2]n± where xy is a bidentate ligand with two different
coordinating atoms also shows cis-trans isomerism. Square planar complex of the form [MABCD]n± also
shows geometrical isomerism. In this case, by considering any one of the ligands (A, B, C or D) as a
reference, the rest of the ligands can be arranged in three different ways leading to three geometrical
isomers.

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Importance: Cis-platin, an anti-cancer drug, is an example of a square planar complex with two pairs of ligands
whereas, Trans-platin cannot be used in cancer treatment.

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Octahedral complexes:

Octahedral complexes of the type [MA2B4]n±, [M(xx)2B2]n± shows cis-trans isomerism. Here A and B are
monodentate ligands and xx is bidentate ligand with two same kind of donor atoms. In the octahedral
complex, the position of ligands is indicated by the following numbering scheme.

In the above scheme, the positions (1,2), (1,3), (1,4), (1,5), (2,3), (2,5), (2,6), (3,4), (3,6), (4,5), (4,6), and
(5,6) are identical and if two similar groups are present in any one of these positions, the isomer is referred
as a cis isomer. Similarly, positions (1,6), (2,4), and (3,5) are identical and if similar ligands are present in
these positions it is referred as a trans-isomer.

Octahedral complex of the type [MA3B3]n± also shows geometrical isomerism. If the three similar ligands
(A) are present in the corners of one triangular face of the octahedron and the other three ligands (B) are
present in the opposing triangular face, then the isomer is referred as a facial isomer (fac isomer)- Figure
(a).

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If the three similar ligands are present around the meridian which is an imaginary semicircle from one apex
of the octahedral to the opposite apex as shown in the figure (b), the isomer is called as a meridional isomer
(mer isomer). This is called meridional because each set of ligands can be regarded as lying on a meridian
of an octahedron.

As the number of different ligands increases, the number of possible isomers also increases. For the
octahedral complex of the type [MABCDEF]n±, where A, B, C, D, E and F are monodentate ligands, fifteen
different orientation are possible corresponding to 15 geometrical isomers. It is difficult to generate all the
possible isomers.

Optical Isomerism

Coordination compounds which possess chirality exhibit optical isomerism similar to organic compounds.
The pair of two optically active isomers which are mirror images of each other are called enantiomers.
Their solutions rotate the plane of the plane polarized light either clockwise or anticlockwise and the
corresponding isomers are called 'd' (dextro rotatory) and 'l' (levo rotatory) forms respectively.

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The octahedral complexes of type [M(xx)3]n±, [M(xx)2AB]n± and [M(xx)2B2]n± exhibit optical isomerism.

Examples: The optical isomers of [Co(en)3]3+ are shown in previous figure.

The coordination complex [CoCl 2(en)2]+ has three isomers, two optically active cis forms and one optically
inactive trans form. These structures are shown below.

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Organic Reactions
CONTENTS
Introduction to reactions involving substitution, addition, elimination, oxidation, reduction, cyclization and
ring openings. Synthesis of commonly use drugs molecule.

SUBSTITUTION REACTION
Type of reaction in which an atom or a group in a molecule is replaced by another atom or group to form
a new molecule
TYPES
1. Nucleophilic substitution reaction
2. Electrophilic substitution reaction

NUCLEOPHILIC SUBSTITUTION (SN) REACTION:

The attacking reagent is a nucleophile.

Nucleophile:
▪ Electron rich species
▪ Donate the electron pair to electron deficient species
Examples:
1. Charged Nucleophile: Cl-, Br-, I-, CN-
2. Neutral Nucleophile: NH3, H2O
3. Nucleophile with Partial Negative Charge: R-MgX, R-Li

IMPORTANT POINTS:
▪ As electrophiles are electron rich species and they donate electron pair to other species. So, electrophiles
are oxidized and act as reducing agent
▪ The ability of a Lewis base to act as nucleophile and to donate its unshared electron pair to other species
is known as nucleophilicity
Types of SN Reaction:
▪ Nucleophilic Substitution Unimolecular (SN1)
▪ Nucleophilic Substitution Bimolecular (SN2)

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Nucleophilic Substitution Unimolecular (SN1):

1. Kinetics: First order reaction (unimolecular). It is a two-step reaction.
Rate = k [R-X] [R-X] = Alkyl Halide Concentration, k = Rate constant
2. The nucleophile does not appear in the rate expression. So, changing the nucleophile concentration does
not affect the rate of the reaction. The overall rate of a reaction is dependent upon the slowest step, rate
determining step (r.d.s.).

Fig.-1: Reaction Profile Diagram for SN1 Reaction

3. SN1 reaction mechanism follows a two-step reaction, where in the Step-I a carbocation is formed by
elimination of the Leaving Group.
4. In the Step-II, the nucleophile attacks the carbocation.

Fig.-2: Reaction Mechanism for SN1 Reaction

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5. The carbocation is sp2 hybridized and it has a vacant p-orbital. So, the nucleophile can attack from both
side of the p-orbital.
6. Stereochemistry of the reaction: It gives 50% percent product with retention of configuration and 50%
with inversion of configuration. So overall a racemic mixture is formed.
Factors Effecting SN1 Reaction Rate:
1. Stability of carbocations: Formation of the carbocation intermediate is the rate determining step. Thus,
carbocation stability greatly influences the reactivity. More stable carbocations give faster reaction rate.
Order of carbocation stability is,

R3C+, tertiary (3°) > R2CH+ secondary (2°) > RCH2+, primary (1°) > CH3+

Inductive effect and hyperconjugation from the attached alkyl groups increase the carbocation stability.
Allylic and benzylic carbocations are stabilized by resonance.

2.

2. Effect of leaving group: Better leaving group helps in faster formation of the carbocation, thus increases
the reaction rate. Among alkyl halides the reaction rate order is as follows: R-I > R-Br > R-Cl > R-F
3. The role of the nucleophile: Involvement of the nucleophile in the SN1 reaction is after the rate-limiting
step. Thus, the nucleophile does not appear in the rate expression. The nature of the nucleophile plays no
role in the rate of the SN1 reaction.

4. Effect of solvent: Polar solvents are favored over non-polar for the SN1 reaction. Protic solvents are
favored over aprotic for the SN1 reaction. Polar protic solvents are best suited for SN1 reactions.
Relative Reactivity: EtOH < (40% H2O + 60% EtOH) < (80% H2O + 20% EtOH) < H2O

Nucleophilic Substitution Bimolecular (SN2):

1. Kinetics: Second order reaction (bimolecular). It is a single-step reaction.
Rate = k [R-X] [Nu] [R-X] = Alkyl Halide Concentration, k = Rate constant
[Nu] = Nucleophile Concentration

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2. Reaction rates are dependent upon the concentration of the reactants, i.e, both the concentrations of
substrate and nucleophile. So, at a given temperature, if the nucleophile concentration is kept same and
alkyl halide concentration, [R-X], is doubled, then the reaction rate will be doubled and vice-versa.

Fig.-3: Reaction Profile Diagram for SN2 Reaction

3. In SN2 reaction, the nucleophile attacks the substrate from the back side of the leaving group (LG) (180°
away from the LG) which leads to transition state (T.S.) with a partially formed ‘C-Nu’ bond and partially
broken ‘C-LG’ bond. Then that T.S. leads to the product when C-Nu’ bond is formed fully and LG leaves
the substrate.

Fig.-2: Reaction Mechanism for SN2 Reaction

Note: In the given mechanism nucleophile is OH- and leaving group is Cl
4. Stereochemistry of the reaction: The overall configuration of the carbon center in the product gets
inverted compared to that of the reactant, like an umbrella flipped inside out.

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Factors Effecting SN2 Reaction Rate:

1. Substrate: For an SN2 reaction, the nucleophile approaches the electrophilic carbon from the backside
of the leaving group. In the T.S. the carbon center is virtually attached to five atoms/groups. So, SN2
reaction rate decrease as the steric hindrance increases at the carbon center.

2. Leaving Group: (Same as SN1) Better the leaving group, faster will be rate of SN2 reaction because
leaving group is expelled in rate determining step.
R-I > R-Br > R-Cl > R-F
3. Nucleophile: The better the nucleophile, higher will be reaction rate. Best nucleophiles are weaker bases
and better electron pair donor. A list of nucleophiles is given below
I, HS, RS (Good Nucleophiles); NH3, Cl (Moderate); H2O, ROH, RCO2H (Weak)
4. Effect of solvent: Polar solvents are favored over non-polar for the SN2 reaction. Aprotic solvents are
favored over protic for the SN2 reaction. Polar aprotic solvents are best suited for SN2 reactions.

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Examples: Acetone (CH3COCH3), Acetonitrile (CH3CN), Dimethyl sulfoxide (DMSO, CH3SOCH3),

Dimethyl formamide (DMF, Me2N-CHO) etc.

Problem: Predict the products with probable mechanism of following reactions.

ELECTROPHILIC SUBSTITUTION (SE) REACTIONS:

The attacking reagent is an electrophile.
Electrophile:
▪ Electron deficient species.
▪ Attacks the electron rich centers or the site where electron density is maximum.
Examples:
1. Charged Electrophile: Cl+, Br+, I+, NO2+, RCO+ etc
2. Neutral Electrophile: SO3, CH3Cl etc
Alkyl halides don’t have electron rich centers for an electrophilic attack. SE reactions are mainly shown by
aromatic compounds which have π-electron clouds where the electrophile can attack. These types of
reactions are called Aromatic Electrophilic Substitution (ArSE) reactions.
General Reaction:

Benzene Substituted Benzene

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General Reaction Mechanism:

i) Attack of the electrophile on aromatic ring forming carbocation intermediate: In this step, the
electrophile attacks the aromatic ring to form a resonance stabilized carbocations.

(ii) Aromatization: In this step, the leaving group detaches itself from the aromatic ring to give the final
product.

Fig.-4: Reaction Profile Diagram for ArSE2 Reaction

Types of ArSE2 reactions depending upon attacking electrophile:
(1) Friedel Craft Reaction:
(i) Alkylation:
In Friedel–Crafts alkylation, treatment of benzene with an alkyl halide and a Lewis acid (AlCl 3) forms an
alkyl benzene. This reaction is an alkylation because the electrophile is an alkyl group.

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Formation of the electrophile:

For CH3Cl and 1° RCl, the Lewis acid–base complex itself serves as the electrophile.

With 2° and 3° RCl, the Lewis acid–base complex reacts further to give a 2° or 3° carbocation, which serves
as the electrophile.

(ii) Acylation:
In Friedel–Crafts acylation, a benzene ring is treated with an acid chloride (RCOCl) and AlCl3 to form a
ketone. Because the electrophile is an acyl group it is called acylation reaction.

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Formation of the electrophile:

the Lewis acid AlCl3 ionizes the carbon–halogen bond of the acid chloride, thus forming a positively
charged carbon electrophile called an acylium ion, which is resonance stabilized.

(2) Halogenation:
In halogenation, benzene reacts with Cl2 or Br2 in the presence of a Lewis acid catalyst, such as FeCl3 or
FeBr3, to give the aryl halides chlorobenzene or bromobenzene, respectively. Analogous reactions with I2
and F2 are not synthetically useful because I2 is too unreactive and F2 reacts too violently.

Formation of the electrophile:

Lewis acid–base reaction occurs between Br2 with FeBr3, which forms a species with a weakened and
polarized Br–Br bond. This adduct serves as a source of Br+ in the next step.

(3) Nitration:

Formation of the electrophile:

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(4) Sulfonation:

Formation of the electrophile:

ELIMINATION REACTION
An addition reaction is an organic reaction where a molecule is eliminated from the substrate to form the
product.
Depending upon the positions from where the atom/groups are eliminated, elimination reaction maybe of
several types:
(1) α-elimination (1,1-elimination): Atoms/groups are eliminated from the same C-atom. The final result
is the formation of a carbenes.
Example: An α-elimination of HCl from chloroform, CHCl3, in presence of a strong base gives
dichlorocarbene.

(2) β-elimination (1,2-elimination): Atoms/groups are eliminated from the adjacent C-atoms. The final
result is the formation of an alkene from an alkyl halide. This is the most common type of elimination
reaction.

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Depending upon different mechanism, types of β-eliminations are

(1) Elimination Unimolecular (E1)
(2) Elimination Bimolecular (E2)

Elimination Unimolecular (E1):

1. Kinetics: First order reaction (unimolecular). It is a two-step reaction.
Rate = k [R-X] [R-X] = Alkyl Halide Concentration, k = Rate constant
2. The base used in the reaction, does not appear in the rate expression. So, changing the base concentration
does not affect the rate of the reaction. The overall rate of a reaction is dependent upon the slowest step,
rate determining step (r.d.s.).

3. E1 reaction mechanism follows a two-step reaction, where in the Step-I a carbocation is formed by
elimination of the Leaving Group. This is the r.d.s.
4. In the Step-II, the base abstracts a proton (H+) from the carbocation to give an alkene.

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5. For unsymmetrical alkyl halides more substitutes alkenes (Saytzeff’s product) are major product.

6. For geometrical isomers trans-alkene is usually the major product over cis-alkene.

Factors Effecting E1 Reaction Rate:

Same factors and effects as SN1 only in place of a nucleophile a base is used in the reaction.
Elimination Bimolecular (E2):
1. Kinetics: Second order reaction (bimolecular). It is a single-step reaction.
Rate = k [R-X] [B-] [R-X] = Alkyl Halide Concentration, k = Rate constant
[B-] = Base Concentration
2. Reaction rates are dependent upon the concentration of the reactants, i.e, both the concentrations of
substrate and nucleophile. So, at a given temperature, if the nucleophile concentration is kept same and
alkyl halide concentration, [R-X], is doubled, then the reaction rate will be doubled and vice-versa.

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3. Mechanism: It is a single step reaction where simultaneously three separate things happen, (i) the base
abstraction of a proton from the β-carbon atom of alkyl halide, (ii) forming C=C (double bond) and (iii) the
halogen leaving as halide, to an alkene as product.

4. Stereochemistry: The transition state of an E2 reaction consists of four atoms from the substrate (one
hydrogen atom, two carbon atoms, and the leaving group, X) aligned in a plane. There are two ways for the
C—H and C—X bonds to be coplanar.

E2 elimination occurs most often in the anti-periplanar geometry. This arrangement allows the molecule to
react in the lower energy staggered conformation, and allows the incoming base and leaving group to be
further away from each other.
Factors Effecting E2 Reaction Rate:
Same factors and effects as SN2 only in place of a nucleophile a base is used in the reaction.

Saytzeff’s Rule:
"The alkene formed in greatest amount is the one that corresponds to removal of the hydrogen from
the alpha-carbon having the fewest hydrogen substituents."
The preference for the more substituted alkene is due to the lower energy transition state. E1 and E2 both
prefers Saytzeff’s rule for alkene product.

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major minor
Hofmann Elimination:
According to this rule, “The major product is always least substituted alkene” i.e., major product is
formed by elimination of H-atom from that β-carbon atom which has maximum number of H-atoms.
i.e., β-carbon atom which is least substituted. The product of the reaction is known as Hofmann product.

ADDITION REACTION
An addition reaction is an organic reaction where two or more molecules combine with each other to form
a larger compound (product).

TYPES
1. Nucleophilic addition reaction to carbonyl compounds
2. Electrophilic addition reaction to alkenes

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Nucleophilic addition reaction to carbonyl compounds:

Carbonyl carbons are sp2 hybridized forming a trigonal planar geometry. The carbon-oxygen double bond
is polar: oxygen is more electronegative than carbon, so electron density is higher on the oxygen side of
the bond and lower on the carbon side. The carbon atom is electron-poor, and acts as an electrophile. It
is a great target for attack by an electron-rich nucleophile.

1. Addition of HCN: Reaction of aldehydes and ketones with HCN and KCN produce cyanohydrins. The
cyanide ion is the nucleophile and adds to the electrophilic carbonyl carbon.

General Reaction:

Mechanism:

2. Addition of Sodium Bisulfite (NaHSO3): The bisulfite ion is a weakly nucleophilic anion which will
only react with aldehydes and methyl ketones.

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3. Addition of Grignard Reagent (RMgX):

(i) Addition with Formaldehyde (HCHO):

(ii) Addition with Other Aldehydes (RCHO):

(iii) Addition with Ketones (R2CO):

ELECTROPHILIC ADDITION REACTION:

Alkenes are electron rich compounds which have π-electron clouds where the electrophile can attack.
Depending upon the attacking electrophile we will two types of addition reaction,
1. Electrophilic addition of HBr to an alkene
2. Electrophilic addition of Br2 to an alkene

Electrophilic addition of HBr to an alkene:

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Addition HBr/HI to an alkene leads to breaking of the C=C (double bond) bond to form a C-C (single bond).
Symmetrical alkenes give a single product.

However unsymmetrical alkenes give rise to a more than one product, where one product is major and the
other one is minor. The addition of HBr (protic acid) to an unsymmetrical alkene give happens in
accordance with the Markownikoff’s Rule.

Markownikoff’s Rule: When a protic acid is added to an unsymmetrical alkene, the acidic hydrogen is
added to the C-atom having greater number of H-atoms and the halide/anion is added to the C-atom having
lesser number of H-atoms.

Mechanism: Consider the addition of HBr to 2-methylbut-2-ene,

The observed product is the one resulting from the more stable carbocation intermediate, because tertiary
carbocations are more stable than secondary.
Stability order is as follows:

Anti-Markownikoff’s Rule:
Some reactions do not follow Markownikoff’s rule and Anti Markownikoff’s products are isolated. This is
shown in the addition of HBr to an unsymmetrical alkene in presence of peroxide which induces a radical

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reaction pathway. The reversal of the major product through the use of peroxides is called the peroxide
effect. It is also called Kharasch effect. Radical additions do not proceed with HCl or HI, only HBr

Mechanism:

Electrophilic addition of Br2 to an alkene:

When an alkene is treated with pure liquid bromine (Br2) or a solution of Br2 in an organic solvent like
CHCl3, CCl4 etc., the Br-Br bond is broken one Br-atom is attached to each of the C-atom. The bromine
loses its original red-brown colour to give a colourless liquid. This reaction is used to identify if there is
unsaturation present in a compound or not.

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Mechanism: Typically, a  bond will attack the bromine molecule kicking out bromide ion and generating
a bromonium ion. (3 membered positively charged ring containing bromine). This halonium ring is then
opened by back side attack of a nucleophile (often the halide) to give the final anti product.

OXIDATION REACTION
Epoxidation of Alkenes:
An epoxide (oxirane) is a three membered ring containing an oxygen. (Heterocyclic version of a
cyclopropane). The most common reagent to convert an alkene to an epoxide is a peroxyacid.

Mechanism: The epoxidation takes place in a concerted one step electrophilic process.

Examples: The stereochemistry of the reactant has no time to rearrange in this one step reaction, and so
any stereochemistry of the reactant is maintained in the product. (mCPBA = meta-chloro perbenzoic acid)

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Academic Session: 2024-2025 (Odd Semester/Semester – I)

Ozonolysis Reaction:
Ozone (O3) cleaves C-C double bonds to form an intermediate called ozonide by 1,3 dipolar cycloadditions.
They can be isolated and decomposed by suitable reagents to give aldehyde and ketones as the products.

Mechanism: In the first step ozone reacts with the double bond to give an unstable molozonide (primary
ozonide), which breaks down into two fragments.

In the second step those fragments undergo 1,3 dipolar cycloaddition reaction to give the stable ozonide.
This ozonide further reacts with suitable reagents like dimethyl sulphide (Me2S), Zn/H2O or
triphenylphosphine (PPh3) to give the desired product.

Name:
Assistant Professor, Department of Chemistry
Brainware University, Kolkata 58
B.Tech. CSE/ CSE(AIR) – 2024
Engineering Chemistry (BBS00010)
Academic Session: 2024-2025 (Odd Semester/Semester – I)

Examples:

CONDENSATION REACTION
A condensation reaction is a reaction in which two molecules combine to form a single molecule. A small
molecule, often water, is usually removed during a condensation reaction.
1. Reaction with Ammonia and its derivatives:
The reaction of aldehydes and ketones with ammonia or 1º-amines forms imine derivatives, also known as
Schiff bases (compounds having a C=N function). This reaction is acid-catalyzed and reversible and a water
is eliminated in the reaction.

Name:
Assistant Professor, Department of Chemistry
Brainware University, Kolkata 59
B.Tech. CSE/ CSE(AIR) – 2024
Engineering Chemistry (BBS00010)
Academic Session: 2024-2025 (Odd Semester/Semester – I)

Examples:

Some of the ammonia derivatives of the carbonyl compounds have been given below, together with the
structures and names.

2. Aldol Condensation Reaction

Aldehydes and ketones that have -hydrogens (slightly acidic), undergo condensation reaction in presence
of alkali such as NaOH, KOH etc. Base first abstract the hydrogen from the more acidic one and then it
acting as Nucleophiles, which add to the carbonyl group of aldehydes and ketones, a larger organic
molecule is formed with loss of water.
Step-I: When acetaldehyde is treated with dilute sodium hydroxide solution, a small but significant number
of molecules are converted to the enolate anion.

Name:
Assistant Professor, Department of Chemistry
Brainware University, Kolkata 60
B.Tech. CSE/ CSE(AIR) – 2024
Engineering Chemistry (BBS00010)
Academic Session: 2024-2025 (Odd Semester/Semester – I)

Step-II: The enolate anion, acting as a nucleophile, adds to the C=O bond of a non-ionized acetaldehyde
molecule left in solution to give an adduct that carries a negative charge on the oxygen. The adduct contains
a newly formed carbon-carbon bond.

Step-III: The negatively charged oxygen abstracts a proton from water to give the final product, 3-
hydroxybutanal (β-hydroxy aldehyde), commonly known as aldol.

The term aldol is derived from the combination of functional groups, aldehyde and alcohol, which are
present in the product. The net overall reaction may be written as

Crossed Aldol Condensation Reaction: When two different molecules of an aldehyde or ketone
are subjected to aldol reaction in presence of aqueous alkali, it is called a crossed aldol condensation.
Generally, an aldehyde or ketone is used that does not have any -hydrogens to get only one crossed aldol
product.
Example: If acetaldehyde is added slowly to an excess of benzaldehyde in the presence of dilute sodium
hydroxide, the crossed aldol product will be formed as shown below.

Name:
Assistant Professor, Department of Chemistry
Brainware University, Kolkata 61
B.Tech. CSE/ CSE(AIR) – 2024
Engineering Chemistry (BBS00010)
Academic Session: 2024-2025 (Odd Semester/Semester – I)

If the β-hydroxy aldehydes/ketones are heated in the reaction mixture a further water molecule is eliminated
to give an , β-unsaturated aldehydes/ketones. For the above example cinnamaldehyde is formed.

SOME SPECIAL REACTIONS

1. Cannizzaro Reaction:
Aldehydes which do not have an -hydrogen atom, undergo self-oxidation and reduction
(disproportionation) reaction on heating with concentrated alkali. In this reaction, one molecule of the
aldehyde is reduced to alcohol while another is oxidised to carboxylic acid salt.
Examples:

Mechanism: The hydroxide ion attacks the carbonyl carbon of the aldehyde giving a hydrate anion, which
can be further deprotonated to give a dianion in a strongly alkaline medium. Now a hydride ion, H- is
transferred either from the monoanionic species or di-anionic species onto the carbonyl carbon of another
aldehyde molecule. The strong electron donating effect of O- groups facilitates the hydride transfer and
drives the reaction further. This is the rate determining step of the reaction. The overall order of the reaction
is usually 3 or 4.

Name:
Assistant Professor, Department of Chemistry
Brainware University, Kolkata 62
B.Tech. CSE/ CSE(AIR) – 2024
Engineering Chemistry (BBS00010)
Academic Session: 2024-2025 (Odd Semester/Semester – I)

Crossed Cannizzaro Reaction: When a mixture of formaldehyde and another aldehyde with no -
hydrogens are treated with a strong base, one aldehyde is reduced to alcohol while the other is oxidized to
carboxylic acid. This is known as cross Cannizzaro reaction.

Intramolecular Cannizzaro Reaction: When one molecule has more than one aldehyde and/or
ketone groups, then those two groups may go Cannizzaro reaction if the hydride (H-) transfer is feasible.
That reaction is called an intramolecular Cannizzaro reaction.
Examples:

Name:
Assistant Professor, Department of Chemistry
Brainware University, Kolkata 63
B.Tech. CSE/ CSE(AIR) – 2024
Engineering Chemistry (BBS00010)
Academic Session: 2024-2025 (Odd Semester/Semester – I)

2. Favorskii Rearrangement:
The rearrangement of cyclopropanones, often obtained as intermediates from the base-catalyzed reaction
of α-halo ketones, leading to carboxylic acids or its derivatives.

SYNTHESIS OF SOME COMMON DRUGS

1. ASPIRIN:
Aspirin is a chemical called acetylsalicylic acid. It is widely used worldwide as an anti-inflammatory and
antipyretic drug.

2. PARACETAMOL:
Paracetamol (acetaminophen) is a non-opioid analgesic and antipyretic agent used to treat fever and mild
to moderate pain. It is a widely used over the counter medication.

Name:
Assistant Professor, Department of Chemistry
Brainware University, Kolkata 64
B.Tech. CSE/ CSE(AIR) – 2024
Engineering Chemistry (BBS00010)
Academic Session: 2024-2025 (Odd Semester/Semester – I)

Model Question.
1. How is Paracetamol is synthesised from Phenol?
2. What happen when acetone is treated with Grignard reagent?
3. What happens when formaldehyde and acetaldehyde reacts with ammonia separately?
4. What happens when acetone is treated with Barium hydroxide?

Name:
Assistant Professor, Department of Chemistry
Brainware University, Kolkata 65