Pharmaceutical Organic Chemistry

Study Notes

Domain 1: Fundamental Knowledge
- Understanding the basics of pharmaceutical organic chemistry.
- Using pharmaceutical chemical terminology, abbreviations, and symbols related to organic chemistry and stereochemistry correctly.
- Applying the rules of fundamental organic chemistry to handle, identify, prepare, and analyze synthetic starting materials and final products.
- Understanding and applying 3D techniques relevant to the pharmaceutical industry.
Domain 2: Professional and Ethical Practice
- Identifying, preparing, and purifying pharmaceutical organic materials from various sources.
- Identifying simple organic compounds using laboratory equipment.
- Writing practical chemical reports for identified samples.
Domain 4: Personal Practice
- Developing teamwork skills and mastering management techniques.

Atoms, Electrons, and Orbitals
- Each element has a unique atomic number (Z), which represents the number of protons in the nucleus.
- A neutral atom has an equal number of protons and electrons.
- Electrons revolve around the nucleus in orbitals, which represent the probable locations of electrons.
- There are four basic types of orbitals: s, p, d, and f.
The Octet Rule
- Atoms tend to have eight electrons in their valence shell, resembling the configuration of noble gases.
- This rule applies to elements like carbon, nitrogen, oxygen, halogens, and generally to the s-block and p-block of the periodic table.
- Atoms achieve this configuration by losing, gaining, or sharing electrons.

Ionic Bond
- Formed by the electrostatic attraction between oppositely charged ions (cations and anions).
- Atoms involved have significantly different electronegativity.
- Forms ionic compounds.
- Example: Sodium chloride (NaCl).
Covalent Bond
- Formed by atoms sharing electrons.
- Usually occurs between nonmetals with similar electronegativity.
- Forms molecules.
- Achieved by overlapping orbitals between atoms.
- Types of Covalent Bonds:
  - Sigma (σ) Bonds: The strongest covalent bonds formed by head-on overlap of orbitals. A single bond is typically a σ bond.
  - Pi (π) Bonds: Weaker bonds formed by sideways overlap of p (or d) orbitals. A double bond has one σ and one π bond, and a triple bond has one σ and two π bonds.
Valence and Non-bonding Electrons
- Valence represents the number of atoms typically bonded to a given atom.
- A non-bonding electron is not involved in chemical bonding. This can be a lone pair localized on a single atom, such as the nitrogen atom in ammonia (NH3) where two electrons are non-bonding.

Valence Bond Theory (VBT) and Orbital Hybridization
- VBT proposes that the overlap of incompletely filled atomic orbitals leads to the formation of a chemical bond.
- Hybridization is the concept of mixing atomic orbitals to form hybrid atomic orbitals that are more suited for bonding.
- Hybrid orbitals are more stable than atomic orbitals.
Mode of Orbital Overlap
- The overlap of atomic orbitals can be either head-on or sideways, leading to the formation of sigma (σ) or pi (π) bonds, respectively.
Molecular Orbital (MO) Theory
- This theory describes the bonding in molecules in terms of the combination of atomic orbitals to form molecular orbitals.
- Molecular orbitals can be bonding (lower energy) or antibonding (higher energy).
- The number of molecular orbitals is equal to the number of atomic orbitals combined.

This theory predicts the geometry of molecules based on the repulsion between electron pairs in the valence shell of the central atom.
- Electron pairs arrange themselves to minimize repulsion.
- The arrangement of electron pairs determines the shape of the molecule.
- There are five basic geometries: linear, trigonal planar, tetrahedral, trigonal bipyramidal, and octahedral.