Stereochemistry and Isomers

Definition of Isomers

• Isomers are molecules with the same molecular formula (same number and types of atoms) but different structures or different connections between atoms.

• They can be divided into:

  1. Structural (Constitutional) Isomers

  2. Spatial (Stereoisomers) — includes Geometric (cis/trans) and Optical (D/L) isomers.

1. Structural Isomers

Definition:

• Compounds that differ in the attachment or connectivity of atoms, even though they share the same molecular formula.

Key Points:

• Functional groups can occupy different positions in the molecule.

• The type of functional group may change.

• Chain length or branching pattern may vary.

• The overall molecular formula remains constant, but the name and structure differ.

Example concepts:

• Butanol vs. isobutanol (same formula C₄H₁₀O but different structures)

• Position isomerism (e.g., 1-propanol vs. 2-propanol)

2. Spatial (Stereoisomers)

Definition:

• Molecules that have the same connectivity (same atoms attached in the same order) but different spatial (3D) arrangements of atoms.

A. Geometric Isomers (Cis/Trans)

How they differ:

• Occur due to restricted rotation around a double bond (C=C) or within a ring structure.

• Cis = substituents are on the same side of the double bond.

• Trans = substituents are on opposite sides of the double bond.

Example:

• Cis-2-butene vs. Trans-2-butene

B. Optical Isomers (D and L Forms)

How they differ:

• Have the same connectivity and molecular formula but differ in the direction they rotate plane-polarized light.

  • D-form (dextrorotatory): rotates light to the right.

  • L-form (levorotatory): rotates light to the left.

3. Chirality and Enantiomers

Chiral Center:

• A carbon atom bonded to four different atoms or groups.

• This carbon is known as a chiral center (stereocenter).

Enantiomers:

• Non-superimposable mirror images of each other (like left and right hands).

• They are a type of optical isomer.

• Identical physical properties (melting point, boiling point, etc.) except:

  • The direction in which they rotate plane-polarized light.

  • Their interactions with other chiral molecules, especially in biological systems.

Biological Significance:

• Biological receptors are usually chiral.

• They often interact only with one enantiomer (the correct “handedness”).

• This is why D and L forms can have different biological effects (e.g., one can be therapeutic, the other toxic).

Summary Table