Organic Chemistry: Some Basic Principles and Techniques

1. Tetravalence of Carbon & Shapes of Organic Molecules

Organic compounds are compounds of carbon, which forms covalent bonds with other carbon atoms (catenation) as well as with hydrogen, oxygen, nitrogen, sulphur, phosphorus and halogens. Wohler's 1828 synthesis of urea from ammonium cyanate (an inorganic salt) disproved the "vital force" theory and showed organic compounds could be synthesised from inorganic sources.

Carbon's tetravalence and the shapes of organic molecules are explained by the hybridisation of s and p orbitals:

• sp³ hybridisation (e.g. methane, CH₄): tetrahedral geometry, bond angle 109.5°.
• sp² hybridisation (e.g. ethene, C₂H₄): trigonal planar geometry, bond angle 120°; the unhybridised p orbitals on adjacent sp² carbons overlap sideways to form a π bond, whose electron cloud lies above and below the plane of the molecule. Rotation about a C=C bond is restricted because it would break this π overlap.
• sp hybridisation (e.g. ethyne, C₂H₂): linear geometry, bond angle 180°; two mutually perpendicular π bonds form the triple bond.

Hybridisation and electronegativity: the greater the s-character of a hybrid orbital, the greater its electronegativity. Thus: sp (50% s-character) > sp² > sp³ in electronegativity — this affects bond length, bond enthalpy, and acid strength of the attached groups.

2. Structural Representations: Complete, Condensed & Bond-Line

• Complete (Lewis/dash) structural formula: every bond is shown explicitly as a dash; lone pairs on heteroatoms may or may not be shown.
• Condensed structural formula: dashes are omitted and identical groups on an atom are grouped with a subscript, e.g. CH₃CH₂CH₂CH₃ for butane.
• Bond-line formula: the most abbreviated representation — carbon and hydrogen atoms are not shown at all; only lines (drawn zig-zag for chains) represent C–C bonds. Each line terminus or junction represents a carbon atom with enough hydrogens to satisfy its valence of four; heteroatoms (O, N, Cl, etc.) are written explicitly.
• Cyclic compounds are represented as regular polygons in bond-line notation (a triangle for cyclopropane, a pentagon for cyclopentane, a hexagon for cyclohexane).
• 3-D representation: a solid wedge (▬◄) shows a bond projecting towards the observer (out of the plane of the paper); a dashed wedge shows a bond projecting away from the observer; a plain line shows a bond lying in the plane of the paper.

3. Classification of Organic Compounds

Organic compounds are broadly divided into:

• Acyclic (open chain) compounds, also called aliphatic compounds — straight or branched chains (e.g. ethane, isobutane).
• Cyclic (closed chain/ring) compounds, further divided into:
  • Alicyclic compounds — carbon atoms joined in a ring, non-aromatic (e.g. cyclopropane, cyclohexane); may contain a heteroatom in the ring (heterocyclic, e.g. tetrahydrofuran).
  • Aromatic compounds — benzenoid (benzene and its derivatives, e.g. aniline, naphthalene) and non-benzenoid (e.g. tropone); heterocyclic aromatic compounds contain a heteroatom in an aromatic ring (e.g. furan, thiophene, pyridine).

A functional group is an atom or group of atoms that determines the characteristic chemical properties of a compound (e.g. –OH, –CHO, –COOH). A homologous series is a family of compounds with the same functional group, represented by a common general formula, where successive members differ by a –CH₂ unit (homologues).

4. IUPAC Nomenclature

The IUPAC name of a compound is derived by identifying the parent hydrocarbon chain and attaching the appropriate functional group prefix/suffix. A saturated hydrocarbon (only C–C single bonds) is called an alkane.

Rules for naming branched-chain alkanes:

1. Identify the longest continuous carbon chain as the parent chain.
2. Number the parent chain so that branch points get the lowest possible locants.
3. Name alkyl branches (methyl, ethyl, propyl, etc.) as prefixes, listed in alphabetical order (multiplying prefixes di-, tri-, tetra- are ignored for alphabetisation; iso- and neo- ARE counted, but sec- and tert- are NOT).
4. If two substituents are in equivalent positions, the lower locant goes to whichever substituent is cited first alphabetically.

Nomenclature of compounds with functional groups: the longest chain containing the principal functional group is numbered so the functional group gets the lowest locant, and the suffix corresponding to that group is added (dropping the terminal 'e' of the parent alkane name before a vowel-starting suffix, e.g. propanone, not propaneone). Where two or more functional groups are present, the principal functional group (chosen by a fixed seniority/priority order) is expressed as a suffix, and all others are cited only as prefixes:

Decreasing priority order of some functional groups:
–COOH > –SO₃H > –COOR (ester) > –COCl (acid halide) > –CONH₂ (amide) > –CN (nitrile) > –CHO (aldehyde) > >C=O (ketone) > –OH (alcohol) > –NH₂ (amine) > C=C/C≡C (alkene/alkyne, lowest).

Nomenclature of substituted benzenes: the substituent is cited as a prefix to "benzene" (e.g. nitrobenzene, bromobenzene). For disubstituted benzenes, numbering gives the lowest locants overall; trivial ortho- (1,2-), meta- (1,3-) and para- (1,4-) prefixes are used for disubstitution only, not for three or more substituents.

5. Isomerism

Isomers are compounds with the same molecular formula but different properties.

Structural isomerism (different connectivity of atoms):

• Chain isomerism — different carbon skeletons (e.g. pentane, isopentane, neopentane, all C₅H₁₂).
• Position isomerism — same skeleton and functional group, different position of the group (e.g. propan-1-ol and propan-2-ol, both C₃H₈O).
• Functional group isomerism — same molecular formula, different functional groups (e.g. propanal and propanone, both C₃H₆O).
• Metamerism — different alkyl chains on either side of the same functional group (e.g. methoxypropane and ethoxyethane, both C₄H₁₀O).

Stereoisomerism: compounds with the same connectivity but differing in the spatial (3-D) arrangement of atoms — classified as geometrical and optical isomerism (studied in detail in later units).

6. Fundamental Concepts in Reaction Mechanism

In an organic reaction, the substrate (the reactant supplying carbon for the new bond) reacts with a reagent (the attacking species) to form intermediate(s) and finally product(s).

Fission of a covalent bond can occur in two ways:

• Heterolytic cleavage: the bond breaks so that the shared electron pair goes entirely to one fragment. This produces:
  • A carbocation — a carbon bearing a sextet of electrons and a positive charge (e.g. CH₃⁺). Stability order: 3° > 2° > 1° > methyl, because alkyl groups stabilise the positive charge through the inductive and hyperconjugation effects.
  • A carbanion — a carbon bearing a lone pair and a negative charge, generally sp³ hybridised.
  • Reactions proceeding via heterolytic fission are called ionic or polar reactions.
• Homolytic cleavage: each fragment retains one electron of the shared pair (shown by a single-barbed "fish-hook" arrow), producing free radicals (e.g. R•). Radical stability order: 3° > 2° > 1° > methyl. Reactions proceeding via homolytic fission are called free radical or homolytic reactions.

Nucleophiles and electrophiles: a nucleophile (Nu:, "nucleus-seeking") is electron-rich and donates an electron pair to the substrate (e.g. OH⁻, CN⁻, H₂O:, carbanions); an electrophile (E⁺, "electron-seeking") is electron-deficient and accepts an electron pair from the substrate (e.g. carbocations, BF₃, and neutral molecules with a carbonyl group or C–X bond). Curved-arrow notation shows the movement of an electron pair from the nucleophile to the electrophile.

7. Electron Displacement Effects in Covalent Bonds

Electron displacement effects explain how substituents polarise bonds and stabilise/destabilise reactive intermediates:

• Inductive effect (I effect): the permanent polarisation of a σ-bond caused by the electronegativity difference of bonded atoms; the effect is transmitted along the chain but decreases rapidly, becoming negligible after about 3 bonds. Groups can be electron-withdrawing (–I), e.g. –NO₂, –CN, –COOH, halogens, or electron-donating (+I), e.g. alkyl groups.
• Resonance (mesomeric) effect (R/M effect): occurs in conjugated systems (alternating single/multiple bonds), where the true structure is a resonance hybrid of two or more hypothetical canonical (contributing) structures, which individually do not exist. A more stable canonical structure has more covalent bonds, complete octets, less charge separation, and negative charge on the more electronegative atom.
  • +R effect: electron transfer AWAY from the atom/group attached to the conjugated system (e.g. –OH, –NH₂, halogens, –OR — these increase electron density elsewhere in the ring).
  • –R effect: electron transfer TOWARDS the atom/group attached to the conjugated system (e.g. –COOH, –CHO, >C=O, –CN, –NO₂ — these withdraw electron density from the ring).
• Electromeric effect (E effect): a TEMPORARY effect, seen only in the presence of an attacking reagent, in multiple bonds (C=C, C=O etc.), involving complete transfer of a shared π-electron pair to one of the bonded atoms. It disappears the moment the reagent is removed. +E effect: π-electrons transfer to the atom to which the reagent attaches. –E effect: π-electrons transfer to the atom the reagent does NOT attach to.
• Hyperconjugation: a permanent stabilising interaction involving delocalisation of σ-electrons of a C–H bond (of an alkyl group attached to an unsaturated system or to a carbon bearing a positive charge) into an adjacent empty/unsaturated p orbital. More C–H bonds available for hyperconjugation (i.e., more alkyl groups) means greater stabilisation — this is why tertiary carbocations are more stable than primary ones.

8. Types of Organic Reactions

Organic reactions are broadly classified into four categories: substitution, addition, elimination, and rearrangement reactions (studied in detail from Unit 9 onward).

9. Methods of Purification of Organic Compounds

• Sublimation: separates a sublimable solid from a non-sublimable impurity (solid directly converts to vapour on heating).
• Crystallisation: based on the difference in solubility of the compound and impurities in a chosen solvent; the impure solid is dissolved in hot solvent to near-saturation, then cooled so the pure compound crystallises out, leaving impurities in the mother liquor.
• Distillation: separates volatile liquids with sufficiently different boiling points (e.g. chloroform, b.p. 334 K, from aniline, b.p. 457 K).
  • Fractional distillation is used when boiling points are close; a fractionating column provides repeated vaporisation–condensation cycles (theoretical plates), e.g. separating crude oil fractions.
  • Distillation under reduced pressure purifies liquids with very high boiling points or that decompose at/near their boiling point, by lowering the external pressure so the liquid boils at a lower temperature (e.g. glycerol from spent-lye in the soap industry).
  • Steam distillation separates steam-volatile substances immiscible with water; the liquid boils when the sum of its own vapour pressure and that of water equals atmospheric pressure — so it distills below 373 K (e.g. aniline–water mixture).
• Differential extraction: an organic compound in aqueous solution is shaken with an immiscible organic solvent in which it is more soluble, then separated using a separating funnel; continuous extraction repeats this for compounds with low solubility in the organic solvent.
• Chromatography: a technique to separate, purify and test mixtures, based on differential movement of components between a stationary phase and a mobile phase.
  • Adsorption chromatography (column chromatography, thin layer chromatography/TLC) — based on differential adsorption of components on an adsorbent like silica gel or alumina. In TLC, relative movement is expressed as the retardation factor, $R_f = \dfrac{\text{distance moved by the substance from the baseline}}{\text{distance moved by the solvent from the baseline}}$ — always a value between 0 and 1.
  • Partition chromatography (e.g. paper chromatography) — based on continuous differential partitioning of components between stationary and mobile phases (water trapped in chromatography paper is the stationary phase).

10. Qualitative Analysis of Organic Compounds

Carbon and hydrogen are detected by heating the compound with copper(II) oxide: carbon is oxidised to CO₂ (turns lime water milky) and hydrogen to H₂O (turns anhydrous copper sulphate blue).

Other elements (N, S, halogens, P) are detected via Lassaigne's test: the compound is fused with sodium metal, converting covalently bound elements into ionic (sodium) salts — NaCN, Na₂S, NaX — extracted into the "sodium fusion extract."

• Test for nitrogen: sodium fusion extract + freshly prepared FeSO₄, then acidified with conc. H₂SO₄ → Prussian blue colour confirms nitrogen (via sodium hexacyanidoferrate(II) → ferric ferrocyanide).
• Test for sulphur: (a) extract + sodium nitroprusside → violet colour; (b) extract acidified with acetic acid + lead acetate → black precipitate of PbS.
• Test for halogens: extract acidified with dilute HNO₃ + AgNO₃ → white precipitate (Cl, soluble in NH₄OH), pale yellow (Br, sparingly soluble in NH₄OH), or yellow precipitate (I, insoluble in NH₄OH). If N or S is also present, the extract is first boiled with conc. HNO₃ to destroy interfering CN⁻/S²⁻ ions.
• Test for phosphorus: the compound is oxidised with sodium peroxide, the solution boiled with HNO₃ and treated with ammonium molybdate — a yellow precipitate/colouration indicates phosphorus.
• Special case: if both N and S are present together, sodium thiocyanate (NaSCN) forms instead, giving a blood-red colour with FeCl₃ (not the Prussian blue test) — unless sodium is used in excess, which decomposes the thiocyanate back to cyanide and sulphide.

11. Quantitative Analysis

• Carbon and hydrogen: the compound is burnt in excess O₂ over CuO; CO₂ is absorbed in KOH solution and H₂O in anhydrous CaCl₂, and the mass increase of each gives:

$$\%\text{C} = \frac{12 \times m_1 \times 100}{44 \times m}, \quad \%\text{H} = \frac{2 \times m_2 \times 100}{18 \times m}$$

where m = mass of compound, m₁ = mass of CO₂, m₂ = mass of H₂O.

• Nitrogen — Dumas method: the compound is heated with CuO in a CO₂ atmosphere; nitrogen gas evolved is collected over KOH solution (which absorbs CO₂) and its volume converted to STP:

$$\%\text{N} = \frac{28 \times V \times 100}{22400 \times m}$$

• Nitrogen — Kjeldahl's method: the compound is heated with conc. H₂SO₄ to convert nitrogen to ammonium sulphate; excess NaOH liberates NH₃, which is absorbed in a known volume of standard acid, and back-titration gives:

$$\%\text{N} = \frac{1.4 \times M \times 2(V - V_1/2)}{m}$$

Kjeldahl's method fails for nitro/azo compounds and ring nitrogen (e.g. pyridine), since these do not convert to ammonium sulphate.

• Halogens — Carius method: the compound is heated with fuming HNO₃ and AgNO₃ in a sealed tube; the halogen is precipitated as AgX and weighed:

$$\%\text{halogen} = \frac{\text{atomic mass of X} \times m_1 \times 100}{\text{molecular mass of AgX} \times m}$$

• Sulphur — Carius method: sulphur is oxidised to sulphate and precipitated as BaSO₄:

$$\%\text{S} = \frac{32 \times m_1 \times 100}{233 \times m}$$

• Phosphorus: oxidised to phosphate, precipitated as ammonium phosphomolybdate, (NH₄)₃PO₄·12MoO₃ (molar mass 1877 g/mol):

$$\%\text{P} = \frac{31 \times m_1 \times 100}{1877 \times m}$$

• Oxygen: usually calculated by difference — 100 minus the sum of percentages of all other elements (a direct method also exists, based on CO produced from I₂O₅ reduction).