FYUGP B.Sc Chemistry Semester 1: Unit 5 - Stereochemistry of Organic Molecules

This unit explores the three-dimensional arrangement of atoms in organic molecules, focusing on 2D and 3D representations, geometrical isomerism, chirality, and conformational analysis. These notes are designed to help students understand the spatial aspects of organic molecules and their implications in chemical behavior.

1. Representation of Organic Molecules in 2D and 3D

Organic molecules can be represented in 2D and 3D using various projection formulae:

a. Fischer Projection

• Represents 3D molecules in 2D by projecting them onto a plane.
• Horizontal lines represent bonds coming out of the plane (toward the viewer).
• Vertical lines represent bonds going into the plane (away from the viewer).

Fig 1: Fischer Projection of Glyceraldehyde

b. Newman Projection

• Represents the molecule as viewed along a specific bond (usually a C-C bond).
• The front carbon is represented by a dot, and the back carbon is represented by a circle.

Fig 2: Newman Projection of Ethane

c. Sawhorse Projection

• Represents the molecule at an angle, showing the spatial arrangement of atoms.
• More intuitive than Newman projections for visualizing molecular structure.

Fig 3: Sawhorse Projection of Ethane

Interconversions

Fischer, Newman, and Sawhorse projections can be interconverted to visualize molecules from different perspectives.

2. Geometrical Isomerism

Geometrical isomerism arises due to restricted rotation around a bond, typically a double bond or a ring. Types include:

a. Cis-Trans Isomerism

• Cis: Similar groups on the same side of the double bond.
• Trans: Similar groups on opposite sides of the double bond.

b. Syn-Anti Isomerism

• Syn: Groups on the same side of a ring or double bond.
• Anti: Groups on opposite sides of a ring or double bond.

c. E/Z Notation

• Used for more complex molecules where cis-trans notation is ambiguous.
• E (Entgegen): Higher priority groups on opposite sides.
• Z (Zusammen): Higher priority groups on the same side.

Fig 4: E/Z Notation for 2-Butene

3. Concept of Chirality

Chirality refers to the property of a molecule that cannot be superimposed on its mirror image. Key concepts include:

a. Enantiomers

• Non-superimposable mirror images.
• Have identical physical properties but differ in optical activity.

b. Diastereomers

• Non-mirror image stereoisomers.
• Have different physical properties.

Fig 5: Chirality and Enantiomers

4. Configuration and Conformation

Configuration: The fixed spatial arrangement of atoms in a molecule.

Conformation: The temporary spatial arrangement of atoms due to rotation around single bonds.

5. Barriers to Rotation

Rotation around single bonds is not completely free due to steric and electronic effects. For example:

• In ethane, the staggered conformation is more stable than the eclipsed conformation due to torsional strain.

6. Conformational Analysis

Conformational analysis studies the energy changes associated with different conformations of a molecule.

a. Ethane

• Staggered conformation: Most stable (lowest energy).
• Eclipsed conformation: Least stable (highest energy).

b. Butane

• Anti conformation: Most stable.
• Gauche conformation: Less stable due to steric hindrance.

c. Cyclohexane

• Chair conformation: Most stable due to minimized steric and torsional strain.
• Boat conformation: Less stable due to steric hindrance and torsional strain.

Fig 6: Chair and Boat Conformations of Cyclohexane

Practical Applications

• Drug Design: Chirality and stereochemistry are crucial for the activity of pharmaceutical compounds.
• Material Science: Conformational analysis helps design polymers with specific properties.
• Organic Synthesis: Understanding stereochemistry is essential for controlling reaction outcomes.

These notes provide a comprehensive understanding of stereochemistry and its applications. Practice problems and molecular modeling exercises will help reinforce these concepts.