Organic Chemistry

CHM113M Course (Lect. 1)

Sem I (2024-25)

Instructor: Dr. V. S. Mothika

Department of Chemistry
IIT Kanpur
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CHM113 Course Contents

1A: Introduction to organic chemistry and molecules

1B: Structure and bonding

2A: Conformational analysis of alkanes and cycloalkanes

2B: Stereochemistry

3A: Substitution and elimination reactions

3B: Introduction to biomolecules

Books:
• Organic chemistry by J. Clayden, N. Greeves, S. Warren
• Fundamentals of Organic Chemistry by T W G Solomons
• Stereochemistry by E. L. Eliel

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What is organic chemistry?
• Definition: Organic chemistry is the study of chemistry (structure, properties,
reactions, and preparation) of carbon-containing compounds.

Human Body
Element %
O 61
C 23
H 10
N 2.6

Nucleic acids Carbohydrates 3

What is organic chemistry?
• Definition: Organic chemistry is the study of chemistry (structure,
properties, reactions, and preparation) of carbon-containing
compounds.

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Nobel Prize in Chemistry 2024

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What is organic chemistry?
Wöhler was honored on a stamp issued by West Germany in 1982

Ammonium Cyanate Urea

(Inorganic) (Organic)

Urea the first synthetic organic compound from

Friedrich Wöhler inorganic compounds (1828)
German Chemist

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Organic compounds: Medicine to materials

Medicine Electronics
Glowing molecules
Aspirin (1897) Food

PC60BM
Fluorescein

Vancomycin (1953)
(antibiotic) Caffeine P3HT
(Coffee beans)

Rhodamine 6G
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Diverse topologies of organic compounds
• why molecules have the shapes they do. What is it about the properties of their
constituent atoms which dictates those shapes?

Fullerene
Spherical structure DNA
Helical structure

Graphite Diamond
Layered structure Tetrahedral structure

Pentacene
Electron microscopy image
Flat 2D structure8
Structure and bonding of organic molecules

sp3

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sp2 hybridization

sp2

10
sp hybridization

sp

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C-C rotations in alkanes
• Both carbons are sp3 hybridized with bond angles close to 109.5°
• Relative continuous rotation about C-C bond occurs in ethane resulting in several
conformations of varied energies

60°

Conformation 1 Conformation 2

In Alkene
No free C-C
rotation
possible

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Isomerism in organic compounds
• Isomerism is a phenomenon in which chemical compounds have same chemical formula
but differing special arrangement of atoms, chemical structures and properties

Isomerism

Structural Stereo

Chain
Configurational Conformational

Positional
Geometrical Optical
Functional

Metamerism Enantiomers Diastereomers

R S
Tautomerism

Ring-chain E Z

Nonsuperimposable Nonsuperimposable
mirror images Non-mirror images 13
Ethane and its structural representation
• Sawhorse projection, allows better visualization of the three-dimensional geometry between adjacent
carbon atoms. Newman projection is a convenient way to judge the stability of the different
conformations of a molecule.

Wedge (3D) Sawhorse Projection (3D) Newman Projection (2D)

2 H1
2
2 1
1
1 H2

Staggered conformation

H2
H1

Eclipsed conformation
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Dihedral angle in conformers
• Dihedral angle is the angle between two intersecting planes made up of at least three
atoms e.g. C1-C1-C2 (plane 1) and C2-C3-C4 (plane 2). Steric effect.

Dihedral angle,
Staggered conformation ɸ = 60°

1 2
1

Wedge Sawhorse Newman 3D model

Rotation about
Eclipsed conformation ɸ = 0° C-C bond

1 2

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Torsional angle and strain in conformers
• Torsional Strain is the repulsive interaction between bonding orbitals (high in the eclipsed
conformation). Electronic effect.
• Torsional angle is the angle of tilting of adjacent C-R bonds (R=H here) due to torsional
strain.

3.0 kcal/mol

Torsional strain Low

torsional strain

Eclipsed conformation Staggered conformation

Dihedral Dihedral
angle (ɸ) of 0° angle (ɸ) of 60°

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Ethane conformations and their energy
• Eclipsed conformation is 3.0 kcal/mol (12.6 kJ/mol) higher in energy than Staggered conformer
• This energy barrier is too low, and the molecule constantly cross the barrier and shifts between
conformers
• Infinite number of conformations are possible in between eclipsed (most stable) and staggered
(most unstable)

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Torsional angle and strain in conformers
• Torsional Strain is low in staggered conformation.
• Electronic stabilization of anti by σC–H to σ*C–H is best in Staggered conformer.
• It is hyperconjugation induced stabilization of Staggered conformer

Changes in energy of conformer

with torsional angle

Visualization of orbital overlap

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Torsional strain in n-Butane
• Torsional strain in higher in Butane than ethane due to bulkier size of Methyl than
‘Hydrogens’ of ethane.
• Butane posses both steric plus torsional strain energy in eclipsed conformation and this
makes the rotation little difficult compared to ethane.
Torsional + Steric strain

180°
5 kcal/mol

ɸ = 0° ɸ = 180°
Eclipsed Staggered

Eclipsed conformation
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Conformations of n-Butane
• Anti Clockwise rotation of front ‘Carbon’ along central C-C single bond over 360°,
conformation I and VII are same

60° 60° 60° 60° 60° 60°

I II III IV V VI VII

0° 60° 120° 180° 240° 300° 360°

Eclipsed Eclipsed
Syn-periplanar Syn-periplanar

Most Unstable Eclipsed Eclipsed

Staggered Staggered
Gauche Staggered Gauche
Anti periplanar
Most stable 20
Energy of n-Butane conformer
• All these conformers exists in solution and are in dynamic motion. The population of most
stable conformer will be higher. So, the population order is Anti-periplanar > Gauche >
Anticlinal > Syn-periplanar

5.0 kcal/mol 5.0 kcal/mol

3.6 kcal/mol 3.6 kcal/mol

0.9 kcal/mol 0.9 kcal/mol

0 kcal/mol

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Strain energy quantification
• In a long chain alkane zigzag arrangement keeps all carbons staggered and anti and is
stable conformer

Zig
zag

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Stabilizing Gauche interactions
• The Gauche effect is an electronic effect describing higher stability of ‘Gauche conformer’
over ‘anti conformer’.
• It is a special case where the electronic stabilization in Gauche dominates steric effects
• In gauche form, hyperconjugation between C–H σ orbital and C–F σ* orbital stabilizes the
conformer (σC–H to σ*C–F is strong)
• In anti conformer, interaction occurs between C–F σ orbital and C–F σ* orbital occurs which
is very weak due to high electronegativity of F. (σC–F to σ*C–F is weak)

ɸ = 60°
Most stable

X=F X=Cl, Br, I

Gauche favored Anti favored
(electronic effect > steric)
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Note: pls refer to conformations of 1,2-dichlorethane for conformer energies
Stabilizing Gauche interactions
• In gauche form, σC–H → σ*C–Cl is good
• However, anti conformer gets better stabilization due to good σC–Cl to σ*C–Cl and lone
pair on ‘Cl’ interaction with σ*C–Cl (nCl → σ*C–Cl)
• There are two electronic stabilizations in anti compared to one stabilization in Gauche

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Stabilizing Gauche interactions
• So, in 1,2-difluorethane, Gauche form is most stable and fully eclipsed form is least stable
• In 1,2-dihaloalkane (X = Cl, Br, I), anti form is most stable and fully eclipsed form is least
stable

> > >

ɸ = 60° ɸ = 0°
Gauche Fully eclipsed
Most stable least stable

> > >

ɸ = 180° ɸ = 0°
Anti periplanar Fully eclipsed
Most stable least stable

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Stabilizing Gauche interactions
• H-bonding can also stabilize Gauche over Anti conformer.

• X-CH2-CH2-OH (X = OH, NH2, F, Cl, Br, OCH3, NHCH3 etc) prefer Gauche
conformer

Staggered Stabilizing
Staggered H-bonding
1,2-Ethanediol Gauche form
Anti form Dihedral angle (ɸ)
More stable
= 60-70°

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Conformations of cycloalkanes
• Besides torsional strain and steric strain, the conformations of cycloalkanes are also affected by
angle strain.
• Angle strain is an increase in energy when bond angles deviate from the optimum tetrahedral
angle of 109.5°.
• To reduce overall strain cycloalkanes adopts out-of-plane conformations

Cyclopropane Cyclobutane Cyclopentane Cyclohexane

Flat Bent Envelope Chair

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Cyclopropane: Structure and conformation
• sp3 hybridized wrt Carbon, have eclipsed flat structure
• Highly strained due to angle strain, and eclipsed C-H bonds torsional strain and posses
bent bonds

sp3 ‘C’ angle

109.5°

49.5° angle
Compression
(Angle strain)
Actual angle
= 60° Bent bonds
Elongated
C-C bonds

3 2
3
2 1
1

Flat and fully eclipsed bonds

Total ring strain energy = angle strain + torsional strain = 27.6 kcal/mol
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Cyclobutane: Structure and conformation
• sp3 hybridized, Butterfly structure
• Adopts bent structure to reduce torsional strain of eclipsed C-H bonds

sp3 ‘C’ angle

109.5°

18.5° angle
compression

90° actual
angle

2 2
4
1
4
3 1 3

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Cyclobutane: Structure and conformation
• Ring flip via a high energy strained planar conformation

1.45
kcal/mol

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Cyclopentane: Structure and conformation
• Planar cyclopentane would have almost no angle strain but have high torsional strain due
to eclipsing C-H bonds. So, it adopts envelope like structure to reduce overall strain

sp3 ‘C’ angle

109.5°
No angle
strain

108° actual angle

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Cyclopentane: Structure and conformation
• Total ring strain energy = angle strain + torsional strain = 10.8 kcal/mol
• Ring flip via a half chair conformation
Energy

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Cyclohexane: Structure and conformation
• Only cyclic ring with least torsional and angle strain in its chair conformation.
• Planar cyclohexane (Unstable): Bond angle exceeds sp3 angles of 109.5° Torsional strain
due to C-C and C-H bonds eclipsing
• Chair conformation of cyclohexane (stable): C-C bond angle are near sp3 angles of 111.5°
torsional strain is minimal due to staggered C-C(H) bonds
Pull ‘C4’
upwards

Pull ‘C1’
downwards
sp3 ‘C’ angle
109.5° Angle
strain

Actual
angle 120°
Perfect chair for a perfect day
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Cyclohexane conformations and energy
• Ring flipping in cyclohexane is very rapid. 105 ring flips per second at room temperature
• Chair conformer is most stable and then Twist boat
• Out of 1000 molecules 2 molecules exist in next stable conformation i.e. twist boat

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Cyclohexane conformations and energy

Planar conformation
Ring strain energy > 20 kcal/mol
• Angle strain (C-C bond angle Boat conformation
120°) Half-chair conformation Ring strain energy 6.5 kcal/mol
• Torsional strain due to eclipsed Ring strain energy 10.8 • Minimal angle strain
C-C bonds kcal/mol • Torsional strain due some eclipsed
• Some angle strain C-C bonds
(120°) • Van der Waals strain from flag- pole
• Torsional strain due hydrogens
to eclipsed C-C
bonds

Twist-Boat conformation Chair conformation

Ring strain energy 5.5 kcal/mol Ring strain energy 0 kcal/mol
• Least flag- pole repulsions due to twisting • No angle strain
• Minimal angle strain • Minimal torsional strain (all C-C bonds
• Minimal torsional strain due some eclipsed C-C staggered) 35
bonds
Axial and equatorial bonds
• In a chair conformation of cyclohexane one can identify two types of carbon–hydrogen
bonds: axial and equatorial.

Unsubstituted
cyclohexane
can exist in these two
forms equally

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Newman projections of cyclohexane

6
2 3 4 2 4

1 5
1 6 5
3

Look through C1-C2 bond & Newman Projection

C5-C4 bond Fully staggered form Stable

3
3 6 2
4

5 6 1
4 5

2 1

Look through C1-C2 bond & Newman Projection

C5-C4 bond Eclipsed form (unstable)
Falg pole ‘H’ repulsions at C3 and C6
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Compounds with chair conformations

= =

Twistane Norbornane
(Twist boat) (Twist boat and boat)

Amantadine
(Antiviral agent)

Diamond lattice
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Thank You

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