🥼Organic Chemistry Unit 1 – Structure and Bonding

Key Concepts

• Atoms form bonds by sharing or transferring electrons to achieve a stable electronic configuration
• Covalent bonds involve the sharing of electrons between atoms (hydrogen molecule, H2)
• Ionic bonds involve the transfer of electrons from one atom to another resulting in oppositely charged ions (sodium chloride, NaCl)
  • Cations are positively charged ions formed by losing electrons
  • Anions are negatively charged ions formed by gaining electrons
• Electronegativity measures an atom's ability to attract electrons in a chemical bond
  • Atoms with higher electronegativity tend to pull electrons towards themselves (fluorine, oxygen)
• Lewis structures represent the arrangement of atoms and electrons in a molecule using dots and lines (water molecule, H2O)
• Valence electrons are the electrons in the outermost shell of an atom that participate in bonding
• Octet rule states that atoms tend to gain, lose, or share electrons to achieve a full valence shell of 8 electrons (noble gas configuration)

Types of Chemical Bonds

• Covalent bonds form when atoms share electrons to achieve a stable electronic configuration
  • Single bonds involve the sharing of one pair of electrons (methane, CH4)
  • Double bonds involve the sharing of two pairs of electrons (ethene, C2H4)
  • Triple bonds involve the sharing of three pairs of electrons (ethyne, C2H2)
• Polar covalent bonds occur when electrons are shared unequally due to differences in electronegativity (hydrogen fluoride, HF)
• Nonpolar covalent bonds occur when electrons are shared equally between atoms with similar electronegativity (dinitrogen, N2)
• Ionic bonds form when electrons are completely transferred from one atom to another resulting in oppositely charged ions held together by electrostatic attraction (potassium chloride, KCl)
• Metallic bonds involve a sea of delocalized electrons surrounding positively charged metal ions (copper, Cu)
• Coordinate covalent bonds (dative bonds) form when one atom donates both electrons to form a shared pair (ammonium ion, NH4+)

Molecular Structure and Geometry

• Molecular geometry refers to the three-dimensional arrangement of atoms in a molecule
• VSEPR (Valence Shell Electron Pair Repulsion) theory predicts molecular geometry based on the number of electron pairs around a central atom
  • Electron pairs repel each other and arrange themselves to minimize repulsion
• Electron pair geometries include linear, trigonal planar, tetrahedral, trigonal bipyramidal, and octahedral
• Molecular geometries include linear, bent, trigonal planar, tetrahedral, trigonal pyramidal, seesaw, T-shaped, and octahedral
• Lone pairs of electrons on the central atom affect molecular geometry by occupying more space than bonding pairs (ammonia, NH3)
• Polarity of a molecule depends on the arrangement of polar bonds and molecular geometry (water, H2O)

Hybridization and Orbital Theory

• Atomic orbitals are mathematical functions that describe the probability of finding an electron in a certain region around the nucleus
• s, p, d, and f orbitals have different shapes and energy levels
• Hybridization is the mixing of atomic orbitals to form new hybrid orbitals with specific geometries
  • sp hybridization results in linear geometry (beryllium chloride, BeCl2)
  • sp2 hybridization results in trigonal planar geometry (boron trifluoride, BF3)
  • sp3 hybridization results in tetrahedral geometry (methane, CH4)
• Hybrid orbitals form stronger, more stable bonds compared to unhybridized orbitals
• Sigma (σ) bonds are formed by the overlap of orbitals along the internuclear axis (ethane, C2H6)
• Pi (π) bonds are formed by the sideways overlap of p orbitals (ethene, C2H4)

Intermolecular Forces

• Intermolecular forces are attractive forces between molecules that determine physical properties like boiling point and solubility
• Dipole-dipole forces occur between polar molecules due to the attraction of opposite partial charges (acetone, (CH3)2CO)
• London dispersion forces (induced dipole forces) occur between nonpolar molecules due to temporary fluctuations in electron density (pentane, C5H12)
  • Strength of London dispersion forces increases with molecular size and surface area
• Hydrogen bonding is a strong dipole-dipole interaction involving hydrogen atoms bonded to highly electronegative atoms like oxygen, nitrogen, or fluorine (DNA base pairs)
  • Hydrogen bonding plays a crucial role in the structure and properties of water and biological molecules
• Ion-dipole forces occur between ions and polar molecules (sodium ion and water, Na+ and H2O)
• Van der Waals forces is a general term that encompasses dipole-dipole, London dispersion, and induced dipole forces

Structural Representations

• Lewis structures use dots and lines to represent the arrangement of atoms and electrons in a molecule (ammonia, NH3)
  • Atoms are represented by their chemical symbols
  • Electrons are represented by dots placed around the atoms
  • Covalent bonds are represented by lines connecting the atoms
• Condensed structural formulas show the connectivity of atoms without depicting individual bonds (butane, CH3CH2CH2CH3)
• Skeletal structures (bond-line structures) represent carbon atoms as the ends and intersections of lines, with hydrogen atoms implied (cyclohexane)
  • Heteroatoms (atoms other than carbon and hydrogen) are shown with their chemical symbols
• Fischer projections are used to represent the three-dimensional structure of chiral molecules (glucose)
  • Horizontal lines represent bonds coming out of the plane, and vertical lines represent bonds going behind the plane
• Newman projections depict the conformation of a molecule by looking down the axis of a carbon-carbon bond (ethane, C2H6)
  • Dashed lines represent bonds going behind the plane, and solid wedges represent bonds coming out of the plane

Properties and Reactivity

• Melting point and boiling point depend on the strength of intermolecular forces
  • Stronger intermolecular forces lead to higher melting and boiling points (water vs. methane)
• Solubility depends on the relative strength of solute-solute, solvent-solvent, and solute-solvent interactions ("like dissolves like")
  • Polar molecules dissolve in polar solvents, and nonpolar molecules dissolve in nonpolar solvents (ethanol in water, hexane in benzene)
• Reactivity is influenced by factors like bond strength, steric hindrance, and electronic effects
  • Molecules with weaker bonds tend to be more reactive (alkenes vs. alkanes)
  • Steric hindrance can slow down reactions by blocking access to reactive sites (tertiary vs. primary alcohols)
• Resonance structures are alternative Lewis structures that represent the delocalization of electrons in a molecule (benzene)
  • Resonance stabilizes molecules by spreading out the electron density
• Inductive effects describe the influence of electronegative atoms on the distribution of electron density in a molecule (trichloromethane vs. methane)

Real-World Applications

• Pharmaceuticals: Understanding molecular structure and properties is crucial for drug design and development (aspirin, ibuprofen)
  • Structure-activity relationships (SARs) help optimize drug molecules for desired therapeutic effects and minimize side effects
• Materials science: Tailoring the properties of materials by controlling their molecular structure and interactions (polymers, composites)
  • Kevlar, a high-strength polymer used in bulletproof vests, relies on strong intermolecular hydrogen bonding
• Biochemistry: The structure and function of biological molecules like proteins, nucleic acids, and lipids depend on chemical bonding and interactions (enzymes, DNA)
  • Hydrogen bonding between complementary base pairs stabilizes the double helix structure of DNA
• Environmental chemistry: Understanding the behavior of pollutants and their interactions with the environment (pesticides, greenhouse gases)
  • The persistence of polychlorinated biphenyls (PCBs) in the environment is due to their stable, nonpolar structure
• Renewable energy: Developing new materials for solar cells, batteries, and fuel cells based on molecular properties (organic photovoltaics, lithium-ion batteries)
  • Dye-sensitized solar cells use organic molecules to absorb light and generate electricity