ORGANIC CHEMISTRY (CY2002D)

Dr. Janardhan Banothu

Assistant Professor
Department of Chemistry
Ammonium cyanate
Room No.: 210(C)
Contact No: 0495-228-5324 (Office)
+91-8111938615 (Mobile)
Email: janardhan@nitc.ac.in
Friedrich Wöhler
(German chemist)
 ORGANIC CHEMISTRY (CY2002D): Syllabus

Module 1: (11 hours)

• Concept of chirality and molecular dissymmetry, Recognition of symmetry elements and
chiral centers, Projection formulae and their interconversions, Prochirality, homotopic,
enantiotopic and diasteriotopic groups and faces, Racemic modifications, R and S
nomenclature, geometrical isomerism, E and Z nomenclature, Conformational analysis:
cyclohexanes

Module 2: (11 hours)

• Definition of reaction mechanism, thermodynamic and kinetics data, substituent effects,
Linear free energy relationships, Hammett equation and related modifications, Basic
mechanistic concepts like kinetic vs thermodynamic control, Hammond postulate, Curtin-
Hammett principle, isotope effects, Nucleophilic substitution, stability and reactivity of
carbocations, Bucleophilicity and basicity, Leaving group effect, steric effects in
substitution reactions, Classical and non-classical carbocations
Module 3: (17 hours)
• Functionalization of alkenes: hydroboration, dihydroxylation, epoxidation and oxidative
cleavage, Oxidation: oxidation of hydrocarbons, alcohols and ketones, Reduction:
catalytic hydrogenation, reduction by dissolving metals and reduction by hydride transfer
reagents, Methods of polymerization: Radical chain polymerization, Step polymerization:
polycondensation, polyaddition, ring opening-lactams, lactones, electrochemical
polymerization, group transfer polymerization, Ion chain polymerization: cationic and
anionic and emulsion polymerization, Molecular weight determination of polymers,
Polymer reactions: hydrolysis, acidolysis, aminolysis, hydrogenation and cyclization,
Cross linking: sulphur and peroxides. Stereochemistry of polymers
References:
1. T.W.G. Solomon and C.B. Fryhle. Organic Chemistry, New York: Wiley, 2013.
2. R.T Morrison and R.N. Boyd. Organic Chemistry. New Jersey : Prentice Hall, 1992.
3. E.L. Eliel and S.H. Wilen. Stereochemistry of Organic Compounds. New York: Wiley, 1994.
4. P. Sykes. A Guidebook to Mechanism in Organic Chemistry. New York: Pearson Education,
2003.
5. R.O.C. Norman and J.M. Coxon. Principles of Organic Synthesis. UK : CRC Press, 1993.
6. W. Carruthers and I. Coldham, Modern Methods of Organic Synthesis. UK : Cambridge
University Press, 2000.
7. J. March. Advanced Organic Chemistry : Reactions, Mechanisms and Structure. New York:
Wiley, 2006.
8. F.A. Carey and R.J. Sundberg. Advanced Organic Chemistry : Part A: Structure and
Mechanisms. New York : Springer, 2008.
9. F.A. Carey and R.J. Sundberg. Advanced Organic Chemistry. Part B: Reactions and
Synthesis. New York : Springer, 2008.
10. O. Geroge. Principles of Polymerization. India : Wiley, 2008.
11. V.R. Gowariker, N.V. Viswanathan and J. Sreedhar. Polymer Science. India : New Age
International, 2015.
12. K.J. Saunders. Organic Polymer Chemistry : An Introduction to the Organic Chemistry of
Adhesives, Fibres, Paints, Plastics and Rubbers. London : Chapmann and Hall, 2012.
 ORGANIC CHEMISTRY (CY2002D): Course Outcomes

CO1: Student should be able to apply the principles of organic stereochemistry

CO2: Student should be able to deliver the fundamental concepts of reaction mechanism

CO3: Student should be able to deliver the principles and applications of organic synthesis

CO4: Student should be able to deliver the methods of polymerization and polymer reactions
 Evaluation Pattern
Total Marks: 100

Mid Sem Exam Assignment Test End Sem Exam

(30 M) (20 M) (50 M)
Exam date: Exam date: Exam date:
21/02/23 to 28/02/23 Intimated Later 27/04/23 to 11/05/23

Results Declaration
24/05/2023
REX/Make-Up Exam
31/05/2023 onwards

Grading: Relative Grading

Marks range will be decided only after the end examination
6
 Module-1, Lecture-1
Stereochemistry
 Concept of chirality and molecular dissymmetry
 Recognition of symmetry elements and chiral centers
 Projection formulae and their interconversions
 Prochiral relationship, homotopic, enantiotopic and diasteriotopic groups and faces
 Racemic modifications, R and S nomenclature
 Geometrical isomerism, E and Z nomenclature
 Conformational analysis : cyclohexane derivatives, stability and reactivity
 Conformational analysis of disubstituted cyclohexanes

Book References:
1. T.W.G. Solomon and C.B. Fryhle. Organic Chemistry. New York: Wiley, 2013.
2. R.T Morrison and R.N.Boyd. Organic Chemistry. New Jersey : Prentice Hall, 1992.
3. Eliel, Wilen and Mander, Stereochemistry of Organic Compounds, 2004
4. Subrata Sengupta, Basic Streochemistry of Organic Molecules, 2014
 Types of Isomers
Isomerism: Phenomenon of the existence of isomers

(or) Structural isomers

 Constitutional Isomers: Molecules with the same molecular
Structural isomers (or) formula have bonded together in different orders.

(or) chain isomers

(or) Regioisomers
Examples:

Molecular formula: C5H12

Q1. Are these constitutional isomers of pentane?

Ans. Yes
Q2. What type of constitutional isomers are these molecules?
Ans. Chain isomers or Skeletal isomers

Q3. Are these constitutional isomers of pentanol?

Ans. Yes
Q4. What type of constitutional isomers are these molecules?
Ans. Position isomers
Q5. Are these constitutional isomers?
Ans. Yes
Q6. What type of constitutional isomers are these molecules?
Ans. Position isomers
Q7. Are these constitutional isomers?
Ans. Yes
Q8. What type of constitutional isomers are these molecules?
Ans. Functional isomers

Q9. Identify the type of isomer?

Configurational isomers:
Stereoisomers that cannot be
converted into one another by
rotating the molecule around a
single bond.
Stereoisomers: Molecules that have the same
molecular formula and sequence of bonded
atoms (constitution), but differ in the three-dimensional
orientations of their atoms in space.
Conformational isomers:
Stereoisomers that are differ from
one another by rotation of a single
bond.
Geomatrical isomers:
Stereoisomers having the same
molecular formula and same
structure but differ in the relative
arrangement of atoms.
Optical isomers: Stereoisomers
having same molecular formula
and different spatial arrangements
of the atoms.
Module-1, Lecture-2
Stereochemistry
Enantiomers: Enantiomers also known as optical isomers. These are non-superimposable mirror images to each
other.
Examples:

Diastereomers: Diastereomers are stereoisomers not related through a reflection operation. They are not mirror
images of each other.
Examples:
Q10. Write down the two stereoisomers of 1,3-dimethylcyclobutane?

Ans. H3C CH3 H CH3

H H H
H3C

cis-1,3-dimethylcyclobutane trans-1,3-dimethylcyclobutane

Note: Geometric isomers are diastereomers, i.e. they are stereoisomers that are not enantiomers. But
have different physical properties.
Types of isomers
Stereoisomers
 Same molecular formula
 Same bonding connectivity
 Different spatial arrangements of atoms and groups

Stereochemistry
Definition: The branch of chemistry which deals with three dimensional structure of molecule
and their effect on physical and chemical properties. It is a study of chiral molecules.

Why stereochemistry is important:

 Relationships between different molecules that are made up from the same atoms can
be studied.
 Can be studied the effect on the physical or biological properties
 Stereoisomers are critically important in biochemistry and medicine because nearly
every biological molecule - amino acids, sugars, fats, enzymes, etc - has one or more
stereoisomer.
For Example:

CH3 CH3
O O

R S
H H
H3C CH2 H2C CH3
Caraway seeds Spearmint
(Meridian fennel and
Persian cumin)
 Chirality

 Chiral meaning handedness (derived from the Greek word cheir, meaning hand)
 Chirality is the property of handedness.
 Chiral objects are not superimposable on its mirror image, like our hand
 When an sp3 hybridized tetrahedral carbon is attached to four different groups, it is called
chiral molecule and the carbon is called as chiral carbon/asymmetric carbon/chiral
center/stereo center.
 Molecules such as 1 and 2 are specifically termed as enantiomers (Greek ‘enantio’
meaning opposite) which are non-superimposable mirror images to each other
 Achiral
 An achiral molecule is superimposable with its mirror image and do not have
handedness
 Prochirality
• Prochiral: Prochiral molecules are those that can be converted from achiral to chiral in a
single step.
• Proprochiral: An achiral species which can be converted to a chiral in two steps.
Enantiomers:
 Enantiomers have exactly the same chemical properties (except for their reaction
with chiral non-racemic reagents) and physical properties (melting point, boiling
point and solubility) except direction of rotation of the plane of polarized light.
They are described as optically active.
 Many drugs are chiral and often must react with a chiral receptor or chiral enzyme to be
effective. One enantiomer of a drug may effectively treat a disease whereas its mirror
image may be ineffective or toxic.
 Optical Activity
o Optical Activity: The ability of a substance to rotate the plane polarized light (when the
light passed through the substance) is called optical activity and the substance is called
optically active.
o The substance which cannot rotate the plane of a polarized light is called Optical Inactive.
o Optical activity was first observed in 1815 by a French physicist Biot.
o The simplest class of optically active molecules has one carbon bonded to four different
substituents.
o Measurements of optical activity are carried out with a polarimeter.

 Plan polarized light waves are the

light waves in which the vibrations
occur in a single plane.
 Dextrorotatory (d / +): Enantiomers that rotate the plane polarized light to the right, i.e.
clockwise.
 Laevorotatory (l / −): Enantiomers that rotate the plane polarized light to the left, i.e.
anticlockwise.
 Dextro- and Laevorotatory are defined with the observer looking into the propagating
beam.
 Note: It is not possible from inspection of a particular enantiomer to say in which direction
the plane polarized light is rotated.

 Optical Rotation: It is the angle through which the plane of polarization is rotated when
polarized light passes through an optically active substance.
Optical Rotation depends upon several factors:
 Concentration of the optically active substance —
o Higher the concentration higher is the magnitude of optical rotation
 Length of the polarimeter tube —
o Higher the length of the polarimeter tube higher is the magnitude of optical rotation
Optical Rotation is caused by individual molecules of the optically active compounds

 The amount of rotation depends upon how many numbers of molecules of optically active
substance encounts by the plane-polarized light while passing through the polarimeter tube

 Evidently higher the concentration of the optically active substance and higher the length of
the polarimeter tube higher will be the number of molecules that will encounter the plane-
polarized light

o Therefore, in order to characterize the extent of rotation, an index called specific rotation
[a] is used;
o Specific rotation [a]: Specific rotation of an optically active substance can be defined
as the optical rotation per unit concentration (gm/mL) of sample per unit length (dm)
of the polarimeter tube.
o 1 dm = 0.1 m = 10 cm
 Units of specific rotation: deg·mL·g−1·dm−1
Specific Rotation of 2-methyl-1-butanol : -5.90° mL·g−1·dm−1
20
a = - 5.90o
D

Here '20' is the temperature and ‘D’ is the wave length of the radiation used in
the measurement (D line of sodium, 5893 Å).
Module-1, Lecture-3
Stereochemistry
Which substances are Optically Active?
• Only those substances whose molecular configuration is not
superimposable on its mirror image are optically active

Case of cis-2-butene:
Case of trans-1,3-dimethylcyclobutane:

Case of propionic acid:

Case of lactic acid:

Case of trans-1,2-dimethylcyclopropane:
Enantiomers can be defined as the two stereoisomers having
COOH COOH
o Same bonding-connectivity.
C C
o Different molecular configurations. H H3C H
CH3
HO OH
(A) (B)
o The molecular configurations are mirror image of each other.

Enantiomers have identical physical and chemical properties except the sign of
rotation.
Q. If the specific rotation of pure (R)2-bromobutane is 48
deg·mL·g−1·dm−1 what will be the specific rotation for pure
(S)2-bromobutane ?
 Human body’s are structurally chiral, with the heart lying to the left
of center and liver to the right.
 Helical sea shells are chiral and most are spiral and right-handed
screw.
 Even DNA is chiral molecule and double helical form of DNA turns
in a right-handed way.
 Similarly protein building bolck e.g. amino acids are chiral (except
glycine) and all of these are classified as being left handed. The
molecule of natural sugars are almost all classified as being right-
handed. In fact most of the molecules associated with life are
chiral and often found only in one mirror image form.
 Chirality has tremendous importance in our daily lives. Most of the pharmaceuticals
are chiral and usually only one mirror image form of a drug provides the desire effect.
Other mirror image form is often found inactive or less active even sometime toxic
(e.g. thalidomide).

O O O O O O
NH H NH H NH
N O N O
N O
this carbon centre is asymmetric as it is O O
O attached with four different groups
R-enantiomer S-enantiomer

Sedative Teratogen
(Abnormality following fetal
exposure during pregnancy)
• Our sense of taste and smell also depend on chirality. If one mirror image form of
chiral molecule have certain odor and taste, other mirror image may completely different
in odor and taste.
• The food we eat is largely made of molecules of one mirror-image form.
Origin of chirality in space

 In 1969 a meteorite (piece of rock) has discover

that fell to earth near Murchison, Victoria, in
Australia.
 It is one of the most studied meteorites due to its
mass (>100 kg) and richness in organic compounds.
 Upon careful analysis it revealed that, it contains 7-
9% excess of four L-amino acid.
 Origin of distribution is uncertain but some scientist
speculate that electromagnetic radiation emitted in
a corkscrew fashion form the poles of spinning
neutron star could lead to a bias of one mirror
image over another one, when molecule form in
interstellar space.
The Stereogenic Center

Carbon atom with four different groups

w
o Chiral center
x C y o Asymmetric center
o Stereo center
z

H H CH3

Cl C F CH3 C CH2CH3 CH3CH2CH2 C CH2CH2CH2CH3

Br OH CH2CH3
Bromochlorofluoromethane 2-Butanol
 Symmetry elements in organic molecule

 Simple axis of symmetry (C)

 Plane of symmetry (s/sigma)
 Center of symmetry (i)
 Alternate axis of symmetry (S)
 Simple/Proper/Rotational axis of symmetry (Cn)
 A molecule is said to possess an n-fold/n-order of simple axis of symmetry
when the molecule is rotated through angle 360°/n about that axis (imaginary
axis) then obtained form is indistinguishable from the original one or
superimposable with each other. The axis is designated Cn (Latin word:
Circulate) and the operation is called a Cn operation.

C2
water molecule
O O O
H H H H H H contains a C2 axis

C3
H H H bromoform molecule
contains a C3 axis
C C C
Br Br Br
Br Br Br Br Br Br
 C2 H H
H
H Cl
Cl H
H
Cl H H Cl
Cl
H H
H H
H C2
H H
cis-1,3-dichlorocyclobutane
cis-1,3-dichlorocyclobutane trans- 1,3-dichlorocyclobutane
trans- 1,3-dichlorocyclobutane
contains a C2 axis contains a C2 axis
C2 axis passing vertically through centre of molecule

C2 H C3
H
H Br H
H
Br H C2 H
H
trans-1,2-dibromoethane Cyclopropane
contains a C2 axis contains a C3 axis perpendicular
to three C2 axes: D3h
Axis perpendicular to C=C bond C3 axis passing vertically through centre of molecule
 Principal axis: If a molecule containing different values of n, then Cn axis having
maximum value of n (fold) is called the principle axis.
 When there are several Cn axis with same value of n, then the principle axis is the
one that involves maximum number of atoms of the molecule.
 Trivial axis: Rotation through an angle of 360o about any axis through any
molecule gives back the identical structure. Therefore, C1 axis is called as trivial
axis and it is not included in any category of Cn axis.
 C1 axis does not represent a rotational axis in true sense of the definition because
all molecule in the universe must possess C1 axis.
 C6
Cl Cl

8
Cl Cl C2
Cl Cl C2

Hexachlorobenzene
one C6 axis perpendicular
to six C2 axes

8
C6 is principal axis
 Twistane (C10H16)

It has 4 chiral centres, which normally would

admit 16 diasteromeres. But only 2 of them
actually exist.

 Twistane possess three mutually perpendicular C2 axes as shown above. Therefore, it is a

molecule in the point group D2 and is dissymmetric. It is a chiral molecule and thus can
exist in two enantiomeric forms.
 Dissymmetric molecule: A molecule which does not possess plane of symmetry, centre
of symmetry, and alternating axis of symmetry is called dissymmetric.
Q. Triphenylene

Find the symmetry elements