Chemistry I: Foundations (Atomic Structure, Bonding, Calculations, Gases, and Energetics)
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The NIE Chemistry syllabus has fourteen units: Atomic Structure; Structure and Bonding; Chemical Calculations; Gaseous State; Energetics; Chemistry of s, p, and d Block Elements; Basic Concepts of Organic Chemistry; Hydrocarbons and Halohydrocarbons; Oxygen-containing Organic Compounds; Nitrogen-containing Organic Compounds; Chemical Kinetics; Equilibrium; Electrochemistry; and Industrial Chemistry and Environmental Pollution (NIE, n.d.-d). Chemistry is essential for medicine, since drugs, metabolism, and physiology are chemical in nature. This chapter and the next three summarize the syllabus with a biological emphasis; a fuller treatment of the same syllabus appears in the companion volume Advanced Level Physical Science.
Atomic Structure
- Protons (+1), neutrons (0), electrons (−1); atomic number Z, mass number A; isotopes (including medically used radioisotopes).
- Quantum numbers n, l, mₗ, mₛ; orbitals s, p, d; the Aufbau principle, Pauli exclusion principle, and Hund's rule. Exceptions: Cr [Ar] 3d⁵4s¹ and Cu [Ar] 3d¹⁰4s¹.
- Periodic trends: atomic radius decreases across a period and increases down a group; first ionization energy generally increases across a period (dips at group 13 and 16); electronegativity increases across a period and decreases down a group.
- Hydrogen spectrum: 1/λ = R_H(1/n₁² − 1/n₂²).
Bonding and Structure
| Topic | Key ideas |
|---|---|
| Ionic and covalent bonds | Electron transfer and sharing; Lewis structures, formal charge, resonance |
| VSEPR shapes | 2 pairs linear (180°); 3 trigonal planar (120°); 4 tetrahedral (109.5°); 5 trigonal bipyramidal; 6 octahedral (90°); lone pairs reduce angles (NH₃ about 107°, H₂O about 104.5°) |
| Hybridization | sp, sp², sp³; σ and π bonds |
| Polarity | Electronegativity differences; dipoles |
| Intermolecular forces | London dispersion, dipole-dipole, hydrogen bonding (N, O, F). Hydrogen bonding is central in biology: it holds DNA base pairs, shapes protein structure, and gives water its properties |
| Metallic and giant structures | Metals; diamond, graphite, silica |
Chemical Calculations
- Mole: n = m/M = N/N_A; molar volume 22.4 dm³ at STP.
- Concentration c = n/V (mol dm⁻³); dilution c₁V₁ = c₂V₂; percentage and ppm (important in clinical solutions and drug doses).
- Empirical and molecular formulae; limiting reagent; percentage yield; titration calculations.
- Example: 25.0 cm³ of NaOH is neutralized by 20.0 cm³ of 0.100 mol dm⁻³ HCl; moles HCl = 2.00 × 10⁻³ mol; [NaOH] = 2.00 × 10⁻³ ÷ 0.0250 = 0.0800 mol dm⁻³.
The Gaseous State
pV = nRT (R = 8.314 J mol⁻¹ K⁻¹); Dalton's law of partial pressures (important in respiratory physiology: the partial pressure of O₂ in air is about 21 kPa, about 21 percent of 101 kPa); Graham's law (rate of effusion ∝ 1/√M); kinetic theory and the Maxwell-Boltzmann distribution; real gases and the van der Waals equation.
Energetics
- Enthalpy change ΔH (negative for exothermic reactions); Hess's law; ΔH°ᵣₓₙ = ΣΔH°f(products) − ΣΔH°f(reactants); bond enthalpies; Born-Haber cycles; calorimetry q = mcΔT.
- Entropy and Gibbs free energy: ΔG = ΔH − TΔS; spontaneous if ΔG < 0; ΔG° = −RT ln K.
- Biological link: the hydrolysis of ATP has a negative ΔG and drives many reactions; coupled reactions make unfavourable processes possible.
Common Mistakes
- Not balancing equations before calculating.
- Mixing volume units (cm³ and dm³).
- Forgetting to convert temperatures to kelvin.
CHAPTER 16