Chapter 8: Organic Chemistry – Some Basic Principles And Techniques

Carbon Compounds and Their Importance

• Catenation Carbon forms covalent bonds with other carbon atoms, creating chains and other structures.
• Other elements Carbon also bonds covalently with hydrogen, oxygen, nitrogen, sulphur, phosphorus and halogens.
• Applications Organic compounds occur in DNA, proteins, clothing, fuels, polymers, dyes and medicines.

Development of Modern Organic Chemistry

• Vital-force theory Berzelius proposed that a special force was needed to form organic compounds; Wöhler’s synthesis challenged this idea.
• Modern development The electronic theory of covalent bonding helped establish the modern approach to organic chemistry.

How Hybridisation Affects Bonds

• Bond length and strength More \(s\) character brings the hybrid orbital closer to the nucleus, producing shorter and stronger bonds.
• Trend Bond length increases in the order \(sp < sp^2 < sp^3\); bond strength follows the reverse order.
• Electronegativity Carbon’s electronegativity increases with \(s\) character: \(sp > sp^2 > sp^3\).

Pi-Bond Properties

• Planarity In \(\ce{H2C=CH2}\), all atoms lie in one plane; the parallel \(p\) orbitals are perpendicular to this plane.
• Restricted rotation Rotating one \(\ce{CH2}\) fragment disrupts \(p\)-orbital overlap, so rotation about a \(\ce{C=C}\) bond is restricted.
• Electron cloud The \(\pi\)-bond electron cloud lies above and below the plane of the bonding atoms.
• Reactivity \(\pi\) electrons are readily available to attacking reagents, making \(\pi\) bonds reactive centres in molecules with multiple bonds.

Ways to represent organic compounds

• Types: Organic structures may be shown as Lewis (dot) structures, dash structures, condensed structural formulas or bond-line formulas.
• Lewis structure: Shows covalent bonds as shared electron pairs; a dash structure simplifies each shared pair to a line.
• Bond marks: One dash represents a single bond, two a double bond and three a triple bond.
• Lone pairs: Lone pairs on heteroatoms such as oxygen, nitrogen, sulphur and halogens may be shown or omitted.

• Examples: Complete structures show the individual bonds in ethane, ethene, ethyne, methanol and ethanol.

Condensed formula examples

• Simple molecules: Ethane is \(ce{CH3CH3}\), ethene is \(ce{H2C=CH2}\), ethyne is \(ce{HC#CH}\) and methanol is \(ce{CH3OH}\).
• Repeated units: \(ce{CH3CH2CH2CH2CH2CH2CH2CH3}\) can be shortened to \(ce{CH3(CH2)6CH3}\).
• Nitrile example: \(ce{N#C-CH(OH)-C#N}\) can be condensed to \(ce{HOCH(CN)2}\).

Reading bond-line formulas

• Carbon atoms: Each line junction and line end represents a carbon atom.
• Hydrogens: Each carbon has the number of implied hydrogens needed to complete its valency of four.
• Heteroatoms: Atoms such as oxygen, nitrogen and chlorine are written explicitly.
• Terminals: A line terminal usually represents a methyl group, \(ce{-CH3}\), unless another group is shown there.
• Shape: Carbon chains are drawn in a zigzag pattern; cyclic compounds are shown as skeletal polygons.

Converting between representations

• Expansion: \(ce{CH3CH2COCH2CH3}\) becomes \(ce{CH3-CH2-C(=O)-CH2-CH3}\) when bonds and the carbonyl group are shown explicitly.
• Condensation: \(ce{HOCH2CH2CH(CH3)CH(CH3)2}\) can be written as \(ce{HO(CH2)2CH(CH3)CH(CH3)2}\).
• Reading a skeleton: Add the implied carbon atoms at every endpoint and junction, then add enough hydrogens to give each carbon four bonds.

• Solid wedge: The bond projects out of the paper towards the observer; its broad end points towards the observer.
• Dashed wedge: The bond projects behind the plane of the paper, away from the observer.
• Normal line: The bond lies in the plane of the paper.

• Materials: Physical models may be made from wood, plastic or metal.
• Framework model: Shows only the bonds connecting atoms, emphasising the bonding pattern rather than atom sizes.
• Ball-and-stick model: Shows atoms as balls and bonds as sticks; springs may replace sticks to represent double bonds such as \(ce{C=C}\) in ethene.
• Space-filling model: Shows relative atom sizes based on van der Waals radii; bonds are not displayed, so the model conveys the volume occupied by the molecule.
• Computer modelling: Computer graphics can also be used to model molecules.

Main structural classes

• Acyclic (open-chain) compounds: Aliphatic compounds with straight or branched carbon chains.
• Cyclic (closed-chain) compounds: Compounds whose atoms form one or more rings; these include alicyclic and aromatic compounds.
• Ring atoms: A ring may contain only carbon atoms (homocyclic) or carbon plus heteroatoms (heterocyclic).

Key features

• Members: Each member is called a homologue.
• Representation: Members can be represented by a general molecular formula.
• Difference: Molecular formula changes by \(\ce{CH2}\) between successive members.
• Examples of series: Alkanes, alkenes, alkynes, haloalkanes, alkanols, alkanals, alkanones, alkanoic acids and amines.

How an IUPAC Name Is Built

• Identify the parent hydrocarbon and the functional group or groups attached to it.
• Modify the parent name with prefixes and suffixes to show substituents and functional groups.

Straight-Chain Alkanes and Homologues

• Naming: Names end in “-ane” and use a prefix indicating the carbon count; for \(\ce{CH4}\) through \(\ce{C4H10}\), these prefixes come from the traditional names methane, ethane, propane and butane.
• Homologues: Successive alkanes differ by one \(\ce{CH2}\) group.

Branched Alkyl-Group Naming

• Common names: Propyl groups may be \(n\)-propyl or isopropyl; branched butyl groups include sec-butyl, isobutyl and tert-butyl.
• Neopentyl: The group \(\ce{-CH2C(CH3)3}\) is called neopentyl.
• Attachment point: In a branched substituent, number from the carbon attached to the parent chain; this is carbon 1.
• Parentheses: Enclose the name of a branched alkyl substituent in parentheses within the compound name.
• Alphabetical order: Count iso- and neo- as part of the substituent name; do not count sec- and tert-.
• Use of common prefixes: Iso- and related common prefixes may be used when the alkyl group is not further substituted.

Locants and Alphabetical Order

• Lowest locants: Choose the numbering with the lowest set of substituent positions, such as 2,5,6 rather than 3,4,7.
• Alphabetical tie-break: If substituents have equivalent positions, give the lower number to the substituent that comes first alphabetically.
• Example: The correct name is 3-ethyl-6-methyloctane, not 6-ethyl-3-methyloctane.
• Punctuation: Separate locants with commas and locants from words with hyphens; do not insert spaces within the name.

Substituted Cycloalkanes

• Side chains: Apply the same substituent and alphabetical-order rules used for branched-chain alkanes.
• Numbering: Number the ring to give substituents the lowest possible locants; use alphabetical order to resolve equivalent choices.

Naming a Compound

• Similar reactions: Compounds with the same functional group often undergo similar reactions; for example, alcohols react with sodium to liberate hydrogen.
• Identify: Find the functional group; it determines the appropriate suffix and, in polyfunctional compounds, helps select the principal group.
• Select and number: Choose the longest carbon chain containing the principal group and number it to give that group the lowest possible locant.
• Name: Use the principal group’s suffix and add the locants and prefixes needed for other substituents.

Choosing and Naming the Principal Group

• Principal group: In a polyfunctional compound, the highest-priority functional group determines the suffix.
• Subordinate groups: Name the other functional groups as substituents using their appropriate prefixes.
• Always prefixes: Alkyl, phenyl, halogen, nitro and alkoxy groups are named as prefixes.

Priority and Numbering Examples

• Alcohol and ketone: Ketone has higher priority, so the alcohol is named with the prefix hydroxy-.
• Example: \(\ce{HOCH2(CH2)3CH2COCH3}\) is 7-hydroxyheptan-2-one, not 2-oxoheptan-7-ol.
• Bromo-substituted alkene: In \(\ce{BrCH2CH=CH2}\), number from the end nearest the double bond; the name is 3-bromoprop-1-ene.

Worked Naming Examples

• Alcohol: An eight-carbon chain with the hydroxyl group on carbon 3 is octan-3-ol.
• Aldehyde: An eight-carbon chain ending in \(\ce{-CHO}\) is octanal; the aldehyde carbon is carbon 1.
• Ketone: A seven-carbon chain with the carbonyl group on carbon 4 is heptan-4-one.
• Carboxylic acid: A six-carbon chain containing \(\ce{-COOH}\) is hexanoic acid.

Repeated Functional Groups and Multiple Bonds

• Repeated groups: Use di-, tri- and similar prefixes, with locants for each group.
• Multiple suffix groups: Write the full parent alkane name before the class suffix; for example, \(\ce{HOCH2CH2OH}\) is ethane-1,2-diol.
• Multiple double or triple bonds: Drop the final e of the parent alkane before the unsaturation ending; \(\ce{CH2=CH-CH=CH2}\) is buta-1,3-diene.

One or Two Substituents

• One substituent: Place its name as a prefix before “benzene”; many substituted benzenes also have common names.
• Two substituents: Number the ring to give the substituents the lowest possible locants; for example, use 1,3-dibromobenzene, not 1,5-dibromobenzene.

Three or More Substituents

• Locants: Do not use ortho-, meta- or para-; identify each substituent position using the lowest-locant rule.
• Base compound: If a common benzene derivative is used as the base, assign its substituent position 1.
• Numbering direction: Choose the direction that gives the next substituent the lowest number.
• Name order: List substituent prefixes in alphabetical order.

Position Isomer Examples

• Propan-1-ol: The \(\ce{-OH}\) group is on carbon 1; it is a primary alcohol.
• Propan-2-ol: The \(\ce{-OH}\) group is on carbon 2; it is a secondary alcohol.
• Key difference: Both have formula \(\ce{C3H8O}\); the position of the hydroxyl group changes.

Functional Group Isomer Examples

• Propanone: Its carbonyl group is within the carbon chain, so it is a ketone.
• Propanal: Its terminal \(\ce{-CHO}\) group identifies it as an aldehyde.
• Key difference: Both have formula \(\ce{C3H6O}\), but their functional groups differ.

Types of Stereoisomerism

• Main types: Geometrical isomerism and optical isomerism.

Substrate and Reagent

• Organic reactions: Ions are generally not the reacting starting materials; molecules usually participate as such.
• Substrate: The reactant whose carbon supplies carbon to a new bond; the other reactant is called the reagent.
• If both reactants supply carbon: The choice of substrate is arbitrary and depends on which molecule is being considered.
• Why mechanisms matter: They help explain organic reactivity and plan synthesis.

Carbocation Structure and Stability

• Classification: Primary, secondary and tertiary carbocations have one, two or three carbon groups attached to the positively charged carbon.
• Shape: The charged carbon is \(sp^2\) hybridised and trigonal planar, with a vacant \(p\) orbital perpendicular to the plane.
• Stability: Alkyl groups stabilise carbocations through inductive and hyperconjugation effects; stability increases from methyl to tertiary.

Carbanion Structure

• Geometry: Carbon is generally \(sp^3\) hybridised; the lone pair gives a trigonal-pyramidal, distorted tetrahedral structure.
• Reactivity: Carbanions are unstable and reactive intermediates.

Radical Stability

• Classification: Alkyl radicals are primary, secondary or tertiary according to the number of carbon groups attached to the radical carbon.
• Stability: Radical stability increases from methyl/primary through secondary to tertiary.

Identifying Substrate and Reagent

• Substrate: In general, the molecule whose carbon is involved in forming a new bond.
• Reagent: The other reactant that attacks or interacts with the substrate.
• Carbon–carbon bond formation: If both reactants supply carbon to the new bond, assigning substrate and reagent is arbitrary and depends on the molecule being considered.

Reactive Centres and Examples

• Electrophilic centre: An electron-deficient part of a substrate that accepts an electron pair from a nucleophile.
• Nucleophilic centre: An electron-rich part of a substrate that supplies an electron pair to an electrophile.
• Attack: Nucleophiles attack electrophilic centres; electrophiles attack nucleophilic centres.
• Nucleophiles: \(\ce{HS-}\), \(\ce{C2H5O-}\), \(\ce{(CH3)3N}\), \(\ce{Cl-}\) and \(\ce{H2N-}\) have available electron pairs to donate.
• Electrophiles: \(\ce{BF3}\), \(\ce{CH3CO+}\) and \(\ce{NO2+}\) can accept an electron pair; the listed electron-deficient centres have incomplete valence shells.
• Partial positive carbon: In \(\ce{CH3CH2OH}\), \(\ce{CH3CN}\) and \(\ce{CH3I}\), the electrophilic centre is the carbon made partially positive by bond polarity: the carbon attached to oxygen, the carbon adjacent to the cyano group, and the carbon attached to iodine, respectively.

Curved-Arrow Notation

• Electron-pair movement: A full-headed curved arrow starts at the electron pair and points to where the pair moves.
• Single-electron movement: A half-headed fishhook arrow shows the movement of one electron.
• Common shifts: Electron pairs may move from a \(\pi\) bond to a bond position, from a \(\pi\) bond to an adjacent atom, or from an atom to an adjacent bond.

Inductive Effect: Examples

• More polar bonds: Among the given pairs, C–Br is more polar than C–H; C–O is more polar than C–N; and C–O is more polar than C–S.
• Farthest bond: In \(\ce{CH3CH2CH2Br}\), the inductive effect is least at the carbon-3–hydrogen bond, farthest from bromine.

Hyperconjugation: Stability Example

• Tert-butyl cation: \(\ce{(CH3)3C+}\) has nine adjacent C–H bonds available for hyperconjugation, making it more stable than \(\ce{CH3CH2+}\).
• Methyl cation: \(\ce{CH3+}\) lacks hyperconjugative stabilisation: its vacant p orbital is perpendicular to the plane of its C–H bonds and cannot overlap with them.

Choosing a method and checking purity

• Method choice: Depends on the physical properties of the compound and the impurities present.
• Common methods: Sublimation, crystallisation, distillation, differential extraction and chromatography.
• Melting/boiling points: Pure compounds generally have sharp melting or boiling points.
• Modern checks: Chromatographic and spectroscopic techniques are also used to assess purity.

Principle and use

• Separation: Heating vaporises the sublimable solid; the nonsublimable impurities remain behind.
• Use: Purifies a sublimable compound from solid impurities that do not sublime.

Principle and key points

• Suitable solvent: The compound is sparingly soluble at room temperature but appreciably soluble when hot.
• Crystals form: Concentrate the hot solution to near saturation, then cool it; the purified compound crystallises and is filtered off.
• Mother liquor: The filtrate retains impurities and a small amount of the compound.
• Solvent mixture: Can be used when the compound is highly soluble in one solvent but only slightly soluble in another.
• Colour removal: Activated charcoal adsorbs coloured impurities.
• Repeated crystallisation: Needed when impurities have solubilities similar to that of the compound.

Simple distillation

• Uses: Separates a volatile liquid from nonvolatile impurities, or liquids with sufficiently different boiling points.
• Separation: The lower-boiling component vaporises first; its vapour is cooled in a condenser and collected as liquid.
• Example: Chloroform (b.p. \(334\,\mathrm{K}\)) and aniline (b.p. \(457\,\mathrm{K}\)) can be separated by distillation.
• Apparatus: The mixture is heated in a round-bottom flask; a condenser cools vapour and a receiver collects the distillate.

Fractional distillation

• Use: Separates liquids whose boiling points are close, so simple distillation cannot separate their vapours effectively.
• Fractionating column: Fitted above the flask; it provides surfaces for repeated heat exchange, condensation and vaporisation.
• Vapour enrichment: Higher-boiling vapour condenses lower in the column; rising vapour becomes richer in the more volatile, lower-boiling component.
• Products: The lower-boiling component reaches the top, passes to the condenser and is collected; the flask liquid becomes richer in the higher-boiling component.
• Theoretical plate: Each successive condensation–vaporisation unit in the column is called a theoretical plate; commercial columns may have hundreds.
• Application: Used in the petroleum industry to separate crude oil into fractions.

Distillation under reduced pressure

• Use: Purifies liquids with very high boiling points or liquids that decompose at or below their boiling points.
• Principle: Reducing external pressure lowers the temperature at which a liquid boils.
• Boiling condition: A liquid boils when its vapour pressure equals the external pressure.
• Equipment/example: A water pump or vacuum pump reduces pressure; glycerol can be separated from spent-lye in the soap industry this way.

Steam distillation

• Use: Separates steam-volatile substances that are immiscible with water.
• Principle: The mixture boils when the combined vapour pressures of water and the organic compound equal atmospheric pressure.
• Lower boiling temperature: Since the organic compound contributes to the total vapour pressure, it can vaporise below its normal boiling point.
• Separation: Condense the steam–organic vapour mixture, then separate the organic layer from water using a separating funnel.
• Example: Aniline can be separated from an aniline–water mixture; immiscible water mixtures generally boil close to, but below, \(373\,\mathrm{K}\).

Key points

• Layer formation: The organic solvent and water must be immiscible so they form separate layers in a separating funnel.
• Recovery: Remove the organic solvent by evaporation or distillation to obtain the compound.
• Continuous extraction: Useful when the compound is only slightly soluble in the organic solvent; the same solvent is repeatedly used to extract it.

Principle and classification

• Stationary phase: A solid or liquid phase that remains in place.
• Mobile phase: A solvent, solvent mixture or gas that moves over the stationary phase.
• Separation: Components move differently because their interactions with the two phases differ.
• Main types: Adsorption chromatography and partition chromatography.

Column chromatography

• Stationary phase: An adsorbent, commonly silica gel or alumina, packed into a glass column.
• Eluant: A suitable liquid or liquid mixture flows slowly down the column as the mobile phase.
• Separation: Components travel different distances according to how strongly they are adsorbed.
• Position: The most strongly adsorbed components are retained nearer the top; less strongly adsorbed components move farther down.

Thin-layer chromatography (TLC)

• Stationary phase: A thin layer (about \(0.2\,\mathrm{mm}\)) of silica gel or alumina coated on a glass plate, called a TLC plate or chromaplate.
• Starting spot: Apply the mixture as a small spot about \(2\,\mathrm{cm}\) above one end of the plate.
• Development: Place the plate in a closed jar with eluant; the solvent rises and carries components different distances according to their adsorption.
• Retardation factor: The relative movement of a component is measured by its \(R_f\) value.
• Spot detection: Coloured spots are visible; colourless compounds may be detected under ultraviolet light, with iodine vapour, or using a suitable spray reagent.
• Example: Ninhydrin spray is used to detect amino acids.

Paper chromatography

• Principle: Components partition continuously and differently between the stationary and mobile phases.
• Stationary phase: Water trapped in the chromatography paper.
• Mobile phase: A suitable solvent or solvent mixture that rises through the paper by capillary action.
• Separation: Components partition differently between the two phases and appear as spots at different heights on the developed paper, called a chromatogram.
• Spot detection: Coloured spots are visible; colourless compounds can be detected under ultraviolet light or with an appropriate spray reagent.

Elements in organic compounds

• Common elements: Carbon and hydrogen are present; compounds may also contain oxygen, nitrogen, sulphur, halogens or phosphorus.

Oxidation and confirmation

• Method principle: Heat the compound with copper(II) oxide; carbon is oxidised to carbon dioxide and hydrogen to water.
• Carbon dioxide: Turns lime-water milky by forming calcium carbonate.
• Water: Turns anhydrous copper sulphate from white to blue as it forms the hydrated salt.

Important interferences

• Nitrogen and sulphur together: Sodium fusion may form NaSCN; with Fe³⁺ it gives a blood-red complex. Free cyanide is absent, so the usual Prussian blue test does not occur.
• Excess sodium: Further fusion decomposes thiocyanate into cyanide and sulphide, which then give their usual tests.
• Halogen test interference: If nitrogen or sulphur is present, boil the extract with concentrated nitric acid before adding AgNO₃; this decomposes interfering cyanide and sulphide ions.

Combustion analysis

• Principle: Burn a known mass of the compound in excess oxygen with copper(II) oxide; carbon and hydrogen form CO₂ and H₂O.
• Absorption: Weighed anhydrous CaCl₂ absorbs water; a second tube containing concentrated KOH absorbs CO₂.
• Measurement: The mass increases of the tubes give the amounts of H₂O and CO₂, from which hydrogen and carbon percentages are calculated.

Carius halogen estimation

• Process: Heat a known sample with fuming HNO₃ and AgNO₃ in a Carius tube; carbon and hydrogen oxidise, while halogen forms AgX.
• Measurement: Filter, wash, dry and weigh the AgX precipitate.

Sulphur estimation

• Conversion: Heat a known sample in a Carius tube with sodium peroxide or fuming nitric acid; sulphur is oxidised to sulphuric acid.
• Measurement: Precipitate sulphate as BaSO₄ with excess BaCl₂, then filter, wash, dry and weigh it.

Phosphorus estimation

• Conversion: Heat the sample with fuming nitric acid to oxidise phosphorus to phosphoric acid.
• Precipitation options: Form ammonium phosphomolybdate using ammonia and ammonium molybdate, or precipitate MgNH₄PO₄ and ignite it to Mg₂P₂O₇.

Modern elemental analysis

• CHN analyser: Automatically measures carbon, hydrogen and nitrogen from only about \(1\)–\(3\) mg of sample and displays the results quickly.