4.2 THREE DIMENSIONAL STRUCTURE
The Three Dimensional Structure of a molecule is the reality of the molecule. Looking at the
organization of atoms in a molecule is essential as it plays a key role in many chemical
reactions and many biological processes. Examples of the importance of 3D structure are:
 Enzyme-Substrate Complexes – The binding site of an enzyme must be complementary
to the 3-D shape of the molecule binding to the enzyme.
 Receptor Proteins on Cell Membrane – Hormones,
neurotransmitters and other proteins must bind properly
with the receptor to induce various signals in the cell
 Communication between Organisms
 Even two molecules with the exact same 3D structure, but
the orientation of atoms if different gives the molecule
carvone, two different properties – one which gives it a
spearmint smell and one with a smell characteristic of the
caraway plant.
Represent Structures in Three Dimensions:
Used in connection with Simplified Lewis
Structures and Structural Formula
Convention
Instructions Below:
For each molecular arrangement below, draw a
three dimensional structure as well.
Valence Shell Electron Pair Repulsion (VSPER) Theory
Examples:
Linear Arrangement, BeF2
Draw Lewis Structure:
What is the best arrangement for electron pairs to prevent repulsion:
Trigonal Planar Arrangement, BCl3
Draw Lewis Structure:
What is the best arrangement for electron pairs to prevent repulsion:
Description
Tetrahedral Arrangement, CH4
Draw Lewis Structure:
What is the best arrangement for electron pairs to prevent repulsion:
Trigonal Pyramidal Arrangement, NH3
Draw Lewis Structure:
What is the best arrangement for electron pairs to prevent repulsion:
Angular Arrangement, H2O
Draw Lewis Structure:
What is the best arrangement for electron pairs to prevent repulsion:
Comparison of Molecules with One Central Atom and 4 Electron Pairs
INSTRUCTIONS FOR APPLYING VSPER THEORY:
VSPER Theory and Geometry for More Complex Molecules:
 For Molecules that contain more than one central atom, you MUST look at the molecular
geometry of each central atom to get the overlal structure of the molecule.
 For Molecules with double and triple bonds (these bonds are shorter and stronger than
single bonds), treat multiple bonds as a single group of electrons, or simply count the
number of bonded atoms
Example 1: Methylamine, CH3NH2
Draw a Lewis Structure
Determine the Geometry
Around Each Central Atom
Draw the 3-D Lewis Structure and
Structural Formula
Example 2: Dimethyl ether, CH3OCH3
Draw a Lewis Structure
Determine the Geometry
Around Each Central Atom
Draw the 3-D Lewis Structure and
Structural Formula
Example 3: Xenon oxytetrafluoride, XeOF4
Draw a Lewis Structure
Determine the Geometry
Around Each Central Atom
Successes and Failures of VSPER Theory
Success
Failure
Draw the 3-D Lewis Structure and
Structural Formula