Organic Chemistry Fundamentals

Organic chemistry is the chemistry of carbon compounds. Although it is a small section of the PMDC MDCAT 2026 syllabus, it underpins every chapter that follows — hydrocarbons, alkyl halides, alcohols, aldehydes, carboxylic acids and macromolecules. Master the basics here (hybridisation, IUPAC, reaction types, reactive intermediates) and the rest of organic chemistry becomes pattern recognition rather than memorisation.

Definition and Classification of Organic Compounds

Organic chemistry is the branch of chemistry dealing with compounds of carbon, except for a few exceptions traditionally classed as inorganic (oxides of carbon, carbonates, bicarbonates, cyanides, carbides). Carbon's unique properties — tetravalency, small size, and the ability to catenate (bond to itself in long chains and rings) — allow it to form millions of compounds.

Hybridisation in carbon

The ground state of carbon is 1s² 2s² 2p², but in compounds carbon is always tetravalent. To explain this, one 2s electron is promoted to a 2p orbital and the resulting orbitals mix (hybridise).

• sp³ hybridisation — one s + three p orbitals mix to give four sp³ orbitals at 109.5° (tetrahedral). Forms four σ (sigma) bonds. Example: methane CH₄, ethane C₂H₆, all alkanes.
• sp² hybridisation — one s + two p mix; three sp² orbitals at 120° (trigonal planar) and one un-hybridised p. Forms three σ bonds and one π (pi) bond. Example: ethene C₂H₄, benzene.
• sp hybridisation — one s + one p mix; two sp orbitals at 180° (linear) and two un-hybridised p. Forms two σ bonds and two π bonds. Example: ethyne C₂H₂, HCN.

Sigma (σ) and pi (π) bonds in carbon

• σ bond — formed by head-on (axial) overlap of orbitals; symmetric about the bond axis; strong; allows free rotation. Every single bond is a σ bond.
• π bond — formed by sideways (lateral) overlap of un-hybridised p orbitals; weaker than σ; restricts rotation; gives rise to cis-trans isomerism.
• A double bond = 1σ + 1π. A triple bond = 1σ + 2π.

IUPAC numbering rules (basic)

1. Find the longest continuous carbon chain containing the principal functional group — this is the parent chain.
2. Number the chain so the principal functional group (or, if absent, the first substituent) gets the lowest possible locant.
3. List substituents alphabetically (ignoring di-, tri-, tetra- prefixes).
4. For double/triple bonds, assign the lower locant to the multiple bond (suffix –ene, –yne).
5. If two numbering schemes give the same lowest locant for the suffix, choose the one giving the lowest locant to the substituent at the first point of difference (the "lowest set of locants" rule).

Homologous series

A homologous series is a family of organic compounds with the same general formula, the same functional group, and consecutive members differing by a –CH₂– unit (relative molar mass differs by 14). Members show a gradual change in physical properties (melting point, boiling point, density) and similar chemical properties.

• Alkanes: C_nH_2n+2 (methane, ethane, propane …)
• Alkenes: C_nH_2n
• Alkynes: C_nH_2n−2
• Alcohols: C_nH_2n+1OH
• Carboxylic acids: C_nH_2n+1COOH

Classification of organic compounds

• By skeleton: open-chain (acyclic / aliphatic) vs cyclic. Cyclic compounds split further into alicyclic (cyclohexane), aromatic (benzene), and heterocyclic (pyridine, furan).
• By functional group: alkanes, alkenes, alkynes, alkyl halides, alcohols, ethers, aldehydes, ketones, carboxylic acids, esters, amines, amides, nitriles.
• By saturation: saturated (only single bonds — alkanes) vs unsaturated (one or more double/triple bonds — alkenes, alkynes, aromatics).

Types of organic reactions

Addition

Two molecules combine to give one product, with the breaking of a π bond. Typical of alkenes and alkynes. Example: CH₂=CH₂ + Br₂ → CH₂Br–CH₂Br.

Elimination

The reverse of addition — one molecule splits into two, generating a π bond. Example: dehydration of ethanol over hot Al₂O₃ → CH₂=CH₂ + H₂O.

Substitution

An atom or group is replaced by another. Typical of alkanes and aromatics. Example: CH₄ + Cl₂ (hν) → CH₃Cl + HCl. Subtypes: SN1, SN2, SE (electrophilic substitution in benzene).

Rearrangement

Atoms within a molecule reorganise to give a structural isomer of the starting material. Example: 1-butene ⇌ 2-butene under acid catalysis; carbocation rearrangements (1,2-H or 1,2-CH₃ shifts).

Reactive intermediates — electrophiles, nucleophiles, free radicals

Electrophile (E⁺)

"Electron-loving" species; electron-deficient; accepts an electron pair to form a new bond. Examples: H⁺, NO₂⁺, SO₃, Br⁺, AlCl₃, carbocations (R₃C⁺).

Nucleophile (Nu:⁻)

"Nucleus-loving" species; electron-rich; donates a lone pair to form a new bond. Examples: OH⁻, CN⁻, NH₃, H₂O, Cl⁻, R⁻ (carbanions).

Free radical (R·)

Species with an unpaired electron; formed by homolytic bond fission (each atom keeps one electron). Highly reactive. Generated by UV light or peroxides. Drive chain mechanisms in halogenation of alkanes and combustion.

Bond breaking patterns:

• Homolytic fission — each atom keeps one electron, giving free radicals. Favoured by non-polar solvents and UV/heat.
• Heterolytic fission — one atom keeps both electrons, giving an ion pair (carbocation + carbanion or similar). Favoured by polar solvents.

Worked MCQs

Five MCQs that capture the high-yield testing patterns for this chapter. Read the explanation even when you get the answer right — it's where the deeper concept lives.

Quick Recap

• Carbon is tetravalent and catenates — the basis of organic chemistry.
• sp³ = tetrahedral 109.5°; sp² = trigonal planar 120°; sp = linear 180°.
• Single = 1σ; double = 1σ + 1π; triple = 1σ + 2π. σ = head-on overlap; π = sideways.
• Homologous series: same general formula and functional group, differ by –CH₂– (mass ↑ 14).
• Reaction types: addition, elimination, substitution, rearrangement.
• Electrophiles accept electron pairs (H⁺, NO₂⁺); nucleophiles donate lone pairs (OH⁻, CN⁻); free radicals have unpaired electrons (homolytic fission).