Atomic Structure & Chemical Bonds

Biology 189: Fundamentals for Life Sciences

• Instructor: Earl Yoon

• Topic: Atomic Structure and Chemical Bonds

Learning Objectives

• Understand the difference between intramolecular and intermolecular bonds.

• Discuss the significance of electronegativity in determining bond types: polar covalent, nonpolar covalent, and ionic.

• Explain covalent bonding and identify if a bond is polar or nonpolar.

• Apply molecular polarity principles to determine molecule polarity.

• Explain ionic bonding and ion formation.

• Understand hydrogen bonds and their occurrence.

• Discuss van der Waals interactions and their occurrence.

Why Atoms Bond

• Atoms bond to achieve full valence shells:

  • Octet Rule: Atoms will gain or lose electrons to fill their valence shell with eight electrons.

• Result in:

  • Molecules: Two or more bonded atoms.

  • Compounds: Two or more different elements bonded together.

Types of Chemical Bonds

Intramolecular Bonds

• Definition: Bonds within a molecule.

• Types:

  • Covalent Bonds

  • Ionic Bonds

Intermolecular Bonds

• Definition: Bonds between different molecules.

• Types:

  • Hydrogen Bonds

  • Van der Waals Interactions

Covalent Bonds

• Definition: Formed by sharing unpaired valence electrons.

• Properties:

  • Strongest type of chemical bond.

Types of Covalent Bonds

• Single Bond: 1 pair of shared electrons.

  • Example: Water (H₂O), Ammonia (NH₃)

• Double Bond: 2 pairs of shared electrons.

  • Example: Carbon dioxide (CO₂)

• Triple Bond: 3 pairs of shared electrons.

  • Example: Molecular nitrogen (N₂)

Electronegativity

• Definition: Measure of how strongly an atom attracts electrons.

• Electronegativity Values (select elements):

  • Oxygen (O): 3.4

  • Chlorine (Cl): 3.2

  • Nitrogen (N): 3.0

  • Carbon (C): 2.5

  • Hydrogen (H): 2.1

  • Sodium (Na): 0.9

• Trend: Electronegativity increases across the periodic table.

Types of Covalent Bonds Based on Electronegativity

Nonpolar Covalent Bonds

• Definition: Electrons are equally shared between bonded atoms.

• Electronegativity Difference: < 0.5

Polar Covalent Bonds

• Definition: Electrons are unequally shared, resulting in partial charges.

• Electronegativity Difference: ≥ 0.5

Molecular Polarity

• Determines molecule behavior based on:

  1. Type of covalent bonds (polar or nonpolar).

  2. Geometry & symmetry of the molecule.

  • Example: Water (H₂O) is polar due to its bent shape; Methane (CH₄) is nonpolar due to symmetry.

Molecular Geometry

• Influences molecular polarity:

  • Bond Angles (degrees) for common geometries:

    • Linear: 180°

    • Trigonal Planar: 120°

    • Tetrahedral: 109.5°

    • Trigonal Bipyramidal: 90°, 120°

    • Octahedral: 90°

Covalent Bonds and Their Importance

• Join atoms to form macromolecules:

  • Types of Macromolecules:

    • Carbohydrates

    • Lipids

    • Proteins

    • Nucleic Acids

Ionic Bonds

• Definition: Electrostatic attraction between oppositely charged ions.

• Ion Formation:

  • Cation: Positively charged ion.

  • Anion: Negatively charged ion.

• Large difference in electronegativity ( > 1.7 ) results in ionic bonds.

Ionic Bonds in Water

• Ionic compounds can dissolve and dissociate in water forming 3-D lattice structures.

Strength of Chemical Bonds

• General Comparison:

  • Ionic bonds are relatively weak in water compared to covalent bonds which are much stronger.

Hydrogen Bonds

• Definition: Weak attractions between molecules involving a hydrogen atom and electronegative atoms (N, O, F).

Van der Waals Interactions

• Definition: Weak attractions between nonpolar molecules due to temporary charge distributions (δ-, δ+).

Importance of Chemical Reactions

• Chemical reactions convert reactants into products and form biological molecules in cells.

Summary of Chemical Bonds

• Ionic Bonds: Charge-based attractions.

• Covalent Bonds: Electron sharing.

• Hydrogen Bonds: Interaction between molecules.

• Van der Waals: Weak attractions due to temporary charges.