Bonding Theories: Explaining Molecular Geometry (Chapter 5 Study Notes)

Chapter 5: Bonding Theories – Explaining Molecular Geometry

5.1 Biological Activity and Molecular Shape

The shape of a molecule plays a crucial role in its biological activity. Bonding theories help explain how atoms bond together to form molecules with specific geometries, which in turn affect their interactions in biological systems.

• Molecular shape determines how molecules interact with biological targets, such as enzymes and inhibitors.

• For example, the HIV-protease enzyme interacts differently with and without an inhibitor, due to changes in molecular geometry.

• Application: Drug design relies on understanding molecular shapes to create effective inhibitors for enzymes.

5.2 VSEPR and Molecular Shape

The Valence-Shell Electron-Pair Repulsion (VSEPR) model is a method for predicting the three-dimensional shape of molecules based on the repulsion between electron groups around a central atom.

• Electron groups include lone pairs, single bonds, double bonds, and triple bonds.

• Electron groups orient themselves as far apart as possible to minimize repulsion.

• Steps to predict molecular shape:

  1. Draw the Lewis structure of the molecule.

  2. Count the number of electron groups around the atom of interest (usually the central atom).

  3. Predict the molecular geometry based on the arrangement of electron groups.

Definition of Electron Group:

• Lone pair electrons

• Single bond

• Double bond

• Triple bond

Example: In water (H2O), the central oxygen atom has two bonding pairs and two lone pairs, resulting in a bent molecular geometry.

Number of Electron Groups	Basic Geometry	Bond Angle (approx.)
2	Linear	180°
3	Trigonal Planar	120°
4	Tetrahedral	109.5°
5	Trigonal Bipyramidal	90°, 120°
6	Octahedral	90°

Additional info: Lone pairs affect molecular geometry by reducing bond angles due to increased repulsion compared to bonding pairs.