Organic Chemistry: Some Basic Principles and Techniques

Organic chemistry is the study of hydrocarbons and their derivatives. Carbon is unique because it can catenate — form long chains, branched chains and rings by bonding to other carbon atoms — and because it forms strong, largely covalent bonds with H, O, N, S, halogens and phosphorus. This gives millions of compounds from just a handful of elements.

Wöhler's 1828 synthesis of urea (NH₂CONH₂) from ammonium cyanate, an inorganic salt, disproved the old 'vital force theory' which held that organic compounds could only be made inside living organisms. This single experiment opened the door to synthetic organic chemistry as we know it today.

Carbon has 4 valence electrons (2s²2p²) and forms 4 covalent bonds. To explain this, carbon undergoes hybridisation, mixing its 2s and 2p orbitals into new orbitals of equal energy before bonding.

sp³ hybridisation (e.g. methane, CH₄): one s + three p orbitals mix to give 4 identical sp³ orbitals arranged tetrahedrally, bond angle 109°28′. All four C–H bonds are sigma (σ) bonds.

sp² hybridisation (e.g. ethene, CH₂=CH₂): one s + two p orbitals mix to give 3 sp² orbitals in a trigonal planar arrangement, bond angle 120°. The unhybridised p orbital on each carbon overlaps sideways to form a π bond, so the C=C double bond is one σ + one π bond.

sp hybridisation (e.g. ethyne, CH≡CH): one s + one p orbital mix to give 2 sp orbitals arranged linearly, bond angle 180°. Two unhybridised p orbitals on each carbon form two π bonds, so C≡C is one σ + two π bonds.

Bond length order: C–C (154 pm) > C=C (134 pm) > C≡C (120 pm), because greater s-character pulls the bonding electrons closer to the nucleus and more bonds between the same two atoms shorten the bond further.

Organic molecules are shown in several shorthand forms. Complete structural formula shows every atom and every bond. Condensed formula groups atoms attached to a carbon together, e.g. CH₃CH₂OH for ethanol. Bond-line (skeletal) formula is the fastest to draw: carbon and hydrogen atoms are not written; each line-end or vertex represents a carbon, and the number of hydrogens on it is whatever completes its valence of 4. Only atoms other than C and H, and multiple bonds, are shown explicitly.

3-D representations use wedge-and-dash notation: a bold wedge shows a bond coming out of the plane of the paper towards the viewer, and a dashed/hashed wedge shows a bond going behind the plane. Plain lines lie in the plane of the paper. This is essential for showing the tetrahedral geometry at an sp³ carbon.

Organic compounds are classified by their carbon skeleton and by functional groups.

Acyclic (open chain) compounds: straight or branched chains, e.g. CH₃CH₂CH₃ (propane).

Cyclic (closed chain) compounds, divided into: (i) Alicyclic — ring compounds that behave like open-chain compounds, e.g. cyclohexane; (ii) Aromatic — benzene and its derivatives (benzenoid), or heterocyclic aromatic rings such as furan and pyridine (non-benzenoid).

Homocyclic rings contain only carbon atoms in the ring; heterocyclic rings contain at least one atom other than carbon (N, O, S) in the ring, e.g. pyridine, furan, thiophene.

A functional group is an atom or group of atoms within a molecule that gives it its characteristic chemical properties — e.g. –OH (alcohol), –CHO (aldehyde), –COOH (carboxylic acid), –NH₂ (amine). A homologous series is a family of compounds with the same functional group and general formula, where successive members differ by a –CH₂– unit and show a regular gradation in physical properties (e.g. alkanes: C_nH_2n+2).

IUPAC (International Union of Pure and Applied Chemistry) names are built from three parts: word root (number of carbons in the parent chain: meth-1, eth-2, prop-3, but-4, pent-5, hex-6, hept-7, oct-8, non-9, dec-10), primary suffix (-ane, -ene, -yne for saturation), and secondary suffix for the principal functional group (-ol for alcohol, -al for aldehyde, -one for ketone, -oic acid for carboxylic acid, -amine for amine, etc.).

Steps for naming a substituted compound: (1) Identify the longest continuous carbon chain containing the principal characteristic group — this is the parent chain. (2) Number the chain from the end that gives the lowest locant to the principal characteristic group first, then to unsaturation, then to substituents (in that priority order). (3) Name and locate every substituent as a prefix, arranged alphabetically, with a locant number before each. (4) Use di, tri, tetra for repeated identical substituents (these multiplying prefixes are ignored while alphabetising). (5) Assemble as: locants-substituent prefixes (alphabetical) + word root + primary suffix + secondary suffix.

Priority order of functional groups for choosing the principal characteristic group (highest to lowest): carboxylic acid > sulphonic acid > ester > amide > nitrile > aldehyde > ketone > alcohol > amine > ether. A group lower in this list, if present alongside the principal group, is named as a prefix (e.g. hydroxy-, oxo-, amino-).

Example: CH₃–CH(CH₃)–CH₂–CH₂OH is 3-methylbutan-1-ol (chain of 4 carbons, –OH gets lowest locant 1, methyl substituent at C3).

For compounds with a double or triple bond, the suffix locant is placed just before -ene/-yne, e.g. pent-2-ene, but-1-yne.

Isomers are compounds with the same molecular formula but different structures or spatial arrangements.

Structural isomerism (differ in connectivity): (i) Chain isomerism — different carbon skeletons, e.g. n-butane and isobutane (both C₄H₁₀). (ii) Position isomerism — same skeleton and functional group but different position of the group or unsaturation, e.g. propan-1-ol and propan-2-ol. (iii) Functional isomerism — same molecular formula but different functional groups, e.g. ethanol (C₂H₆O, an alcohol) and dimethyl ether (C₂H₆O, an ether). (iv) Metamerism — same functional group but different alkyl groups attached to it, e.g. diethyl ether and methyl propyl ether, both C₄H₁₀O.

Stereoisomerism (same connectivity, different spatial arrangement) is covered in detail in later chapters but is introduced here: geometrical (cis-trans) isomerism about a C=C, and optical isomerism due to a chiral (asymmetric) carbon.

A covalent bond can break two ways. Homolysis: the bond breaks symmetrically, each atom keeping one electron (shown by a single-barbed fish-hook arrow), giving free radicals — species with an unpaired electron, e.g. Cl–Cl → Cl• + Cl•. It needs high energy (heat/light/peroxides) and favours the gas phase or non-polar solvents.

Heterolysis: the bond breaks unsymmetrically, the more electronegative atom taking both electrons (full double-barbed arrow), giving a cation and an anion, e.g. CH₃Br → CH₃⁺ + Br⁻. It is favoured in polar solvents.

Reactive intermediates: carbocations (positive, sp², trigonal planar, 6 electrons; stability 3° > 2° > 1° > methyl, from +I and hyperconjugation), carbanions (negative, sp³, pyramidal; stability reversed — methyl > 1° > 2° > 3°, since alkyl groups destabilise the extra electron density), free radicals (unpaired electron; same order as carbocations), and carbenes (neutral, divalent, 6 electrons, e.g. :CH₂, very reactive).

Nucleophiles are electron-rich attackers (lone pair or π electrons, e.g. OH⁻, CN⁻, NH₃). Electrophiles are electron-deficient attackers (e.g. H⁺, NO₂⁺, carbocations, BF₃). Every organic reaction can be classed by which one drives it.

Inductive effect (I): a permanent σ-electron displacement towards a more electronegative atom, transmitted along the chain and fading after about 3 carbons. Electron-withdrawing groups (–NO₂, –CN, halogens, –COOH) show −I; alkyl groups and –O⁻ show +I. It explains why chloroacetic acid is a stronger acid than acetic acid — Cl pulls electron density from –COOH, stabilising the carboxylate anion.

Resonance (mesomeric) effect: when a molecule has two or more valid Lewis structures differing only in electron position, the real molecule is a more stable hybrid of these canonical structures, shown with curved arrows. In phenol, the O lone pair delocalises into the ring (+M), raising electron density at ortho/para positions; in nitrobenzene, –NO₂ withdraws ring electron density by resonance (−M), lowering it at ortho/para. Resonance energy is the extra stability of the real hybrid over the most stable single canonical structure.

Hyperconjugation: delocalisation of a σ C–H (or C–C) bond adjacent to a cationic carbon, a radical, or a multiple bond into the empty/half-filled orbital or π system — more α-hydrogens means more such structures and greater stability, exactly why 3° carbocations/radicals beat 1° ones.

Electromeric effect (E): a temporary effect of a multiple bond, where the π pair shifts fully to one atom only in the presence of an attacking reagent, vanishing once the reagent is removed — unlike the permanent inductive and resonance effects.

Substitution reactions: one atom/group in a molecule is replaced by another, without change in the degree of saturation, e.g. CH₄ + Cl₂ → CH₃Cl + HCl (free-radical substitution).

Addition reactions: a reagent adds completely across a multiple bond (C=C or C≡C), converting it to a single bond, e.g. CH₂=CH₂ + H₂ → CH₃–CH₃. Typical of alkenes and alkynes.

Elimination reactions: two atoms/groups are removed from adjacent carbons (or the same carbon), generating a multiple bond, e.g. CH₃CH₂Br + KOH(alc.) → CH₂=CH₂ + KBr + H₂O. This is the reverse in spirit of an addition reaction.

Rearrangement reactions: atoms within a molecule migrate to give a structural isomer, usually through carbocation intermediates, e.g. the pinacol–pinacolone rearrangement (studied in Class 12).

Every one of these reaction types is classified further by the attacking species: nucleophilic substitution/addition, electrophilic substitution/addition, or free-radical substitution/addition, depending on whether the reagent is a nucleophile, electrophile, or radical.

Simple distillation: separates a volatile liquid from non-volatile impurities, or liquids differing in boiling point by more than ~25 K; the liquid is heated, vapour condensed and collected. E.g. water from salt.

Fractional distillation: for miscible liquids with close boiling points, using a fractionating column (packed with glass beads) that gives repeated vaporisation-condensation cycles, enriching the vapour in the more volatile component. E.g. separating petroleum fractions, or benzene from toluene.

Vacuum (reduced-pressure) distillation: for liquids that decompose near their normal boiling point — lower pressure lowers the boiling point so the liquid distils without decomposing. E.g. glycerol.

Steam distillation: for steam-volatile substances immiscible with water and with fair vapour pressure at 373 K. Steam is passed through the mixture; the substance distils below 373 K, since the mixture boils once the sum of the two vapour pressures equals atmospheric pressure. E.g. isolating clove oil (eugenol).

Differential extraction: shaking an aqueous solution with a solvent in which the compound is more soluble; it distributes between the layers by the distribution law. Several small solvent portions extract more efficiently than one large portion — the basis of separating-funnel extraction.

Chromatography separates mixtures by differential movement of components through a stationary phase under a mobile phase. Adsorption chromatography (solid stationary phase, e.g. silica/alumina) covers column chromatography and TLC; in TLC the ratio of distance moved by a component to that moved by the solvent front is the retardation factor, R_f. Partition chromatography (e.g. paper chromatography) separates by continuous partitioning between stationary phase (water in cellulose fibres) and mobile phase.

Crystallisation: the impure solid is dissolved in minimum hot solvent, filtered hot to remove insoluble impurities, and the filtrate cooled slowly so pure crystals separate, leaving soluble impurities in the mother liquor.

Sublimation: a solid that passes directly to vapour on heating is separated from non-sublimable impurities this way, e.g. camphor, naphthalene, NH₄Cl.

C and H are detected by heating with CuO: C gives CO₂ (turns lime water milky), H gives H₂O (turns anhydrous CuSO₄ blue). Other elements are detected via Lassaigne's test: the compound is fused with sodium metal, converting covalently-bound N, S, halogens and P into water-soluble ionic sodium salts (NaCN, Na₂S, NaX, Na₃PO₄); the fused mass is extracted with water to give the sodium fusion extract, then tested for each element.

Nitrogen: extract boiled with FeSO₄, acidified with dilute H₂SO₄, then a drop of FeCl₃ added. Prussian blue confirms N — Na₄[Fe(CN)₆] forms first, then reacts with Fe³⁺ to give ferric ferrocyanide.

Sulphur: extract acidified with acetic acid + lead acetate gives a black PbS precipitate; or freshly prepared sodium nitroprusside gives a violet colour.

Halogens: extract acidified with dilute HNO₃ (destroys interfering CN⁻/S²⁻), then AgNO₃ added: white ppt soluble in NH₄OH → Cl; pale yellow, sparingly soluble → Br; yellow, insoluble → I. If N and S are both present, boil the extract with conc. HNO₃ first to destroy interfering CNS⁻.

Phosphorus: compound oxidised with sodium peroxide, boiled with conc. HNO₃, then treated with ammonium molybdate — a yellow precipitate confirms P.

C and H: a known mass is burnt in excess O₂/CuO; C converts to CO₂ (absorbed and weighed via KOH), H to H₂O (absorbed and weighed via anhydrous CaCl₂), giving both percentages.

Nitrogen — Dumas method: the compound is heated with CuO in a CO₂ atmosphere; N converts to free N₂ (oxides of N reduced over hot Cu gauze). The N₂ collected over KOH (which absorbs the CO₂) is measured at STP.

Nitrogen — Kjeldahl method: heating with conc. H₂SO₄ converts N to (NH₄)₂SO₄; excess NaOH liberates NH₃, absorbed in a known excess of standard acid, which is then back-titrated with standard alkali. Not applicable to ring nitrogen (pyridine) or nitro/azo nitrogen, which do not convert to ammonium sulphate.

Halogens — Carius method: the compound is heated with fuming HNO₃ and AgNO₃ in a sealed hard-glass tube; C and H oxidise to CO₂ and H₂O, and the halogen is precipitated as AgX, filtered, dried and weighed.

Sulphur — Carius method: heating with fuming HNO₃ oxidises S to sulphuric acid, precipitated as BaSO₄ with BaCl₂, filtered, dried and weighed.

Phosphorus — Carius method: oxidation with fuming HNO₃ gives phosphoric acid, precipitated as ammonium phosphomolybdate or as MgNH₄PO₄, ignited to Mg₂P₂O₇ and weighed.

General rule: % element = (atomic mass of element × mass of precipitate × 100) / (molecular mass of precipitate × mass of compound taken).