Fundamentals of Chemistry: Part 3

Study Notes

Learning Goals:
- Understand how Lewis Dot Structures relate to molecular geometry.
- Predict molecular geometry of simple molecules using VSEPR.
- Understand electronegativity and apply it to polar/non-polar bonds.
- Apply bond polarity and molecular geometry to predict dipole moments of simple molecules.

Shape influences chemical and physical properties (e.g., reactivity, melting points).
Molecules and drugs need precise shapes to fit into enzymes or proteins (biochemistry, pharmacology, and medicine).
Predicting shape improves drug design and development.

Enzymes have binding sites that recognize very precise shapes of molecules.
The substrate (e.g., sucrose) binds to the enzyme, forming an enzyme-substrate complex.
Binding places stress on specific bonds in the substrate, causing them to break.
Products are released, and the enzyme is free to bind other substrates.

Lewis Dot Structures (LDS) show bonding within molecules.
LDS do not show the 3-dimensional shape of a molecule.
Molecular geometry (3-D shape) is derived from LDS based on minimizing interactions between electron pairs.
This is called valence shell electron pair repulsion (VSEPR) theory.

Atoms and molecules want the lowest energy state (most stable).
Electron groups (bonding pairs and lone pairs) around a central atom repel each other.
Electrons try to be as far apart as possible to minimize repulsion.
Constraints of bonding and distance determine molecular geometry.
Molecular shape and bond angles can be predicted.

Coordination Number: Number of bonded atoms.
Steric Number (SN): Number of atoms bonded to the central atom + number of lone pairs on the central atom.
Molecular Geometry (MG): 3-dimensional arrangement of atoms in a molecule.
Electron Geometry (EG): 3-D arrangement of bonding and lone electron pairs around a central atom.
Bond Angle: Angle between bonds.

Draw the Lewis Structure.
Count the number of electron groups and categorize them as bonding pairs or lone pairs.
Determine the electron-pair geometry (e.g., linear, trigonal planar, tetrahedral etc.).
Position other atoms around the central atom.
Determine the molecular geometry.

Carbon Dioxide (CO₂):
- 2 electron groups.
- Linear electron geometry.
- Linear molecular geometry.
- Bond angle is 180°.
Methane (CH₄):
- 4 electron groups.
- Tetrahedral electron geometry.
- Tetrahedral molecular geometry.
- Bond angle is 109.5°.
Carbonate Ion (CO₃^2-):
- 3 electron groups.
- Trigonal planar electron geometry.
- Trigonal planar molecular geometry.
- Bond angle is 120°.
Water (H₂O):
- 4 electron groups.
- Tetrahedral electron geometry.
- Bent molecular geometry.
- Bond angle is < 109.5°.
Hydronium Ion (H₃O⁺): - 4 electron groups. - Tetrahedral electron geometry. - Trigonal pyramidal molecular geometry. - Bond angle is < 109.5°.
Phosphate Ion (PO₄^3-): - 4 electron groups. - Tetrahedral electron geometry. - Tetrahedral molecular geometry. - Bond angle is 109.5°.

Electronegativity: Atom's ability to attract electrons in a chemical bond.
Electronegativity values determine bond type (nonpolar covalent, polar covalent, ionic). Different atoms have different electronegativity values.
Unequal sharing of electrons in polar covalent bonds causes partial charges.
Dipole moment is the measure of polarity, indicated by arrows.

Molecular geometry influences molecule polarity.
Identical polar bonds in symmetrical structure cause dipoles to cancel, resulting in nonpolar molecule.
Asymmetrical structures with polar bonds cause dipoles not to cancel, resulting in polar molecule.

More complex molecules, involving d-orbitals, have even more complex geometries.
Molecular geometry is crucial for understanding how molecules interact (e.g., enzyme-substrate interactions, drug design, solubility in water).