Organic Chemistry: Some Basic Principles and Techniques

In this chapter: tetravalence and hybridisation of carbon, structural formulas, classification of organic compounds, functional groups and homologous series, IUPAC nomenclature, structural isomerism and stereoisomerism, homolytic and heterolytic fission, carbocations, carbanions and free radicals, nucleophiles and electrophiles, inductive, resonance, electromeric and hyperconjugation effects, types of organic reactions, purification methods, chromatography, and qualitative and quantitative analysis.

Carbon and structural formulas

Carbon is tetravalent and forms strong bonds with itself and other elements. Its hybridisation decides the shape around it: sp³ (tetrahedral, as in CH₄), sp² (trigonal planar, as in C₂H₄) and sp (linear, as in C₂H₂). The s-character increases from 25% (sp³) to 33% (sp²) to 50% (sp); the more s-character, the more electronegative the carbon and the shorter its bonds.

Organic structures are written as complete structural formulas (every bond shown), condensed formulas (CH₃CH₂OH) or bond-line formulas, where each line end and each angle is a carbon and hydrogens on carbon are not drawn. In three-dimensional drawings, a solid wedge is a bond towards the viewer and a dashed wedge is a bond away from the viewer.

Classification

• Acyclic (open chain) or aliphatic: ethane, isobutane, acetaldehyde.
• Alicyclic (closed chain): rings of carbon (cyclohexane, cyclohexene); rings containing another atom such as O, N or S are heterocyclic (tetrahydrofuran).
• Aromatic: benzenoid (benzene, aniline, naphthalene), non-benzenoid (tropolone) and heterocyclic aromatic (furan, thiophene, pyridine).

A functional group is the atom or group that decides the characteristic chemical properties (−OH, −CHO, −COOH). A homologous series is a family with the same functional group, in which successive members differ by a −CH₂− unit.

IUPAC nomenclature

1. Pick the longest carbon chain containing the principal functional group and any multiple bonds.
2. Number it so the principal functional group gets the lowest locant; then multiple bonds; then substituents (lowest set of locants).
3. Write substituents as prefixes in alphabetical order (di, tri, tetra are ignored for alphabetising), then the root, the unsaturation (-ane, -ene, -yne) and the suffix for the principal group.

When several functional groups are present, the principal group is chosen by this order of preference: −COOH > −SO₃H > −COOR > −COCl > −CONH₂ > −CN > −CHO > >C=O > −OH > −NH₂ > >C=C< > −C≡C−. Halogens, −NO₂, −OR, alkyl and phenyl groups are always written as prefixes.

For disubstituted benzenes, the positions 1,2-, 1,3- and 1,4- are also called ortho (o), meta (m) and para (p).

Isomerism

• Chain isomerism: different carbon skeletons, such as pentane and 2-methylbutane (both C₅H₁₂).
• Position isomerism: the same group at different positions, such as propan-1-ol and propan-2-ol.
• Functional group isomerism: different functional groups, such as ethanol and methoxymethane (C₂H₆O), or propanal and propanone (C₃H₆O).
• Metamerism: different alkyl groups on either side of the functional group, such as ethoxyethane and 1-methoxypropane (C₄H₁₀O).
• Stereoisomerism: same constitution but different arrangement of atoms in space. It includes geometrical (cis-trans) and optical isomerism.

Organic reaction mechanism

A covalent bond can break in two ways. In heterolytic cleavage one atom takes both electrons, giving ions: a carbocation (positive carbon with six valence electrons, sp², trigonal planar, with an empty p orbital) or a carbanion (negative carbon with a lone pair, usually sp³ and pyramidal). In homolytic cleavage each atom takes one electron, giving neutral free radicals, usually with heat or light. Both carbocations and free radicals are more stable when more alkyl groups are attached: 3° > 2° > 1° > methyl.

Curved arrows show movement of electrons, from the source (a bond or lone pair) to the sink. A full arrowhead moves a pair of electrons; a half (fish-hook) arrowhead moves a single electron.

• Nucleophiles (nucleus-seeking) donate an electron pair: OH⁻, CN⁻, RO⁻, and neutral molecules with lone pairs such as H₂O, NH₃ and R₃N.
• Electrophiles (electron-seeking) accept an electron pair: carbocations, NO₂⁺, and neutral species like the carbonyl carbon of >C=O and CH₃−Cl (at the carbon).

Electron displacement effects

Inductive effect

When a σ bond joins atoms of different electronegativity, the electron density shifts towards the more electronegative atom, and this shift is passed along the chain with decreasing strength. It is a permanent effect.

Resonance (mesomeric) effect

When a molecule cannot be described by one Lewis structure, the real molecule is a resonance hybrid of contributing structures that differ only in the position of electrons, not atoms. Benzene is a hybrid of two Kekulé structures, so all six C−C bonds are identical (139 pm). The hybrid is more stable than any contributing structure; the difference is the resonance energy. Among contributing structures, those with more covalent bonds, a complete octet on every atom, less charge separation and negative charge on the more electronegative atom contribute more.

• +R effect (electron-releasing into a conjugated system): halogens, −OH, −OR, −OCOR, −NH₂, −NHR, −NR₂, −NHCOR.
• −R effect (electron-withdrawing): −COOH, −CHO, >C=O, −CN, −NO₂.

Electromeric effect

A temporary effect in compounds with a multiple bond, seen only while an attacking reagent is present: the π electrons shift completely to one of the two atoms. In the +E effect they move towards the atom to which the reagent attaches; in the −E effect they move away from it. It disappears when the reagent is removed.

Hyperconjugation

The σ electrons of a C−H bond on a carbon next to a carbocation (or next to a double bond) can delocalise into the empty p orbital (or the π system). It is also called no-bond resonance. The more such α-hydrogens, the greater the stabilisation, which explains why (CH₃)₃C⁺ (nine α-hydrogens) is more stable than CH₃CH₂⁺ (three), and why alkenes with more alkyl groups on the double bond are more stable.

Organic reactions are broadly substitution, addition, elimination and rearrangement reactions.

Purification of organic compounds

Chromatography

The mixture is applied to a stationary phase and a mobile phase (liquid or gas) moves over it, carrying the components at different rates. In adsorption chromatography (column chromatography and thin layer chromatography, TLC) the stationary phase is an adsorbent such as silica gel or alumina, and components separate by how strongly they are adsorbed. In partition chromatography (paper chromatography) the stationary phase is water held in the paper, and components separate by partition between this water and the mobile phase. Colourless spots are seen under UV light, in iodine vapour or by spraying a reagent (ninhydrin for amino acids).

Qualitative analysis

Carbon and hydrogen are detected by heating the compound with copper(II) oxide: carbon gives CO₂, which turns lime water milky, and hydrogen gives water, which turns anhydrous copper sulphate blue. For N, S, halogens and P, the compound is first fused with sodium metal (Lassaigne's test), converting these elements into NaCN, Na₂S and NaX, which are extracted by boiling with water (sodium fusion extract).

Quantitative analysis

• Nitrogen, Dumas method: N is converted to N₂ gas, and % N = (28 × V × 100)/(22400 × m), where V is the volume of N₂ in mL at STP and m is the mass of compound in g.
• Nitrogen, Kjeldahl method: the compound is heated with conc. H₂SO₄ to give (NH₄)₂SO₄; NaOH releases NH₃, which is absorbed in a known excess of standard acid and the leftover acid is titrated. It does not work for nitro and azo compounds or nitrogen in a ring (pyridine).
• Halogens, Carius method: heating with fuming HNO₃ and AgNO₃ gives AgX; % X = (atomic mass of X × mass of AgX × 100)/(molar mass of AgX × m).
• Sulphur: oxidised to H₂SO₄ and weighed as BaSO₄: % S = (32 × mass of BaSO₄ × 100)/(233 × m).
• Oxygen is usually found by difference: 100 minus the sum of the other percentages.

Worked example: 0.30 g of an organic compound containing C, H and O gave 0.44 g of CO₂ and 0.18 g of H₂O on complete combustion. Find the percentage composition.
Solution: % C = (12 × 0.44 × 100)/(44 × 0.30) = 528/13.2 = 40.0%. % H = (2 × 0.18 × 100)/(18 × 0.30) = 36/5.4 = 6.67%. % O = 100 − 40.0 − 6.67 = 53.3%. (This gives the empirical formula CH₂O, using the method from Chapter 1.)

Common mistakes: (1) Numbering the chain from the end nearer a substituent instead of the principal functional group. (2) Confusing inductive (permanent, through σ bonds) with electromeric (temporary, needs a reagent) effect. (3) Calling NH₃ or H₂O an electrophile; with lone pairs they act as nucleophiles. (4) Forgetting to boil the fusion extract with HNO₃ before the AgNO₃ test for halogens. (5) Measuring R_f from the bottom edge of the plate instead of the baseline.

JEE and NEET focus

• IUPAC names of compounds with one or two functional groups, using the priority order.
• Types of structural isomerism and counting isomers for simple formulas.
• Stability order of carbocations and free radicals, and the reasons (+I and hyperconjugation).
• Classifying groups by inductive and resonance effects, and identifying nucleophiles and electrophiles.
• Choosing the right purification method, and R_f calculations.
• Lassaigne's test colours and percentage calculations (C, H, N by Dumas and Kjeldahl, halogens, S).

Practice questions