PHA111 Molecular Shape and Bonding Notes

Overview of Molecular Shape and Bonding

  • Pharmaceutical Chemistry in MPharm program focuses on molecular shape and bonding.
  • Emphasizes the role of functional groups in drug characteristics:
    • Route of administration, absorption, metabolism, bioavailability, receptor binding, pharmacokinetics.
  • Learning outcomes include understanding bonding types, functional groups, and their effects on drug properties.

Functional Groups and Examples

  • Key functional groups:
    • Alkenes, alcohols, amines, ketones, etc.
  • Example: Atorvastatin - a competitive inhibitor affecting cholesterol levels, illustrating drug efficiency and market value.

Atomic Structure Basics

  • Nucleus: Contains protons (+) and neutrons; bulk of an atom's mass.
  • Electron Cloud: Negatively charged electrons surrounding nucleus; determines atom's charge and bonding characteristics.
  • Atomic and Mass Numbers:
    • Atomic number (Z) = number of protons.
    • Mass number (A) = protons + neutrons; isotopes differ by neutron count.

Chemical Bonding Theory

  • Ionic Bonds: Formed through electron transfer and electrostatic attraction (e.g., NaCl).
  • Covalent Bonds: Formed by electron sharing (e.g., H2, O2).
    • Types: Non-polar (similar electronegativity) and Polar (different electronegativity).
    • Bond strengths vary, with triple bonds being the strongest.

Hybridization

  • Hybridization affects bonding and geometry:
    • sp3: Tetrahedral (e.g., CH4).
    • sp2: Trigonal planar (e.g., C2H4).
    • sp: Linear (e.g., C2H2).
  • The more s character, the shorter and stronger the bond.

Valency and Lone Pairs

  • Valency reflects an atom's ability to bond based on electron deficiency.
  • Formal charge calculation to assess atom's charge status in molecules.

Polarity and Dipole Moments

  • Molecule polarity arises from asymmetric charge distribution, influencing solubility in solvents.
  • Inductive effects through bonds affect molecular stability and reactivity.

Bond Representations

  • Lewis Structures represent electron arrangement.
  • Skeletal Structures: Simplified representations focusing on connectivity without showing carbon and hydrogen explicitly.

Summary

  • Understanding these concepts is critical for designing drugs and understanding their interactions in biological systems.
  • Knowledge of bonding, hybridization, and functional groups can guide the synthesis of effective pharmaceuticals.