Organic Chemistry — Some Basic Principles and Techniques

Classification by carbon skeleton. Organic compounds are divided into two broad classes depending on how the carbon atoms are linked together.

• Acyclic (open-chain) compounds, also called aliphatic compounds: carbon atoms form a straight or branched chain with no ring, e.g. CH₃–CH₂–CH₂–CH₃ (n-butane) or CH₃–CH(CH₃)–CH₃ (isobutane, i.e. 2-methylpropane).
• Cyclic (closed-chain / ring) compounds: carbon atoms are joined to form one or more rings. These are further divided into homocyclic (carbocyclic) compounds, in which every ring atom is carbon, and heterocyclic compounds, in which the ring contains at least one atom other than carbon (commonly N, O or S), e.g. pyridine and furan.
• Homocyclic compounds are further split into alicyclic compounds (ring behaves like an open-chain compound, e.g. cyclohexane, cyclopropane) and aromatic compounds (planar, cyclic, conjugated ring systems showing special stability, e.g. benzene and its derivatives).

Classification by functional group. A functional group is an atom or group of atoms in a molecule that determines its characteristic chemical behaviour, e.g. –OH (alcohol), –CHO (aldehyde), >C=O (ketone), –COOH (carboxylic acid), –NH₂ (amine), –X (haloalkane), –O– (ether), and the carbon–carbon multiple bonds C=C and C≡C. Compounds containing the same functional group and differing from the next member by a –CH₂– unit form a homologous series. Members of a homologous series can be represented by the same general formula, have similar chemical properties, and show a gradual (graded) change in physical properties such as boiling point.

Worked example. Consider the first three members of the alcohol series: CH₃OH (methanol), CH₃CH₂OH (ethanol) and CH₃CH₂CH₂OH (propan-1-ol). Each differs from the previous one by exactly one –CH₂– unit (mass 14 u): going from CH₃OH (32 u) to C₂H₅OH (46 u) adds 14 u, and going to C₃H₇OH (60 u) adds another 14 u. All three share the same functional group (–OH), fit the general formula C_nH_2n+1OH, and show a steady rise in boiling point, confirming they belong to one homologous series.

Because organic molecules can be large, chemists use several shorthand ways to represent the same structure.

• Complete structural (Lewis) formula: every atom and every bond (including C–H bonds) is drawn explicitly, showing all shared electron pairs.
• Condensed structural formula: bonds to hydrogen (and sometimes to other atoms) are omitted; atoms are simply grouped next to the carbon they are attached to, e.g. CH₃CH₂OH for ethanol or CH₃CH(CH₃)₂ for isobutane.
• Bond-line (skeletal) formula: the most compact representation. Each line represents a carbon–carbon bond, each line end and each vertex (corner) represents one carbon atom, and hydrogen atoms attached to carbon are not shown at all — they are assumed to complete carbon's valency of four. Atoms other than carbon and hydrogen (O, N, X, etc.) are always written explicitly, along with any hydrogens attached to them.
• Three-dimensional (wedge–dash) representation: used to show the actual spatial arrangement of atoms around a carbon. A plain line lies in the plane of the paper, a bold wedge represents a bond coming out of the plane towards the viewer, and a dashed (hashed) wedge represents a bond going behind the plane away from the viewer.

Worked example. Convert the condensed formula of isobutane, CH₃–CH(CH₃)–CH₃, into its bond-line formula and verify the hydrogen count. The skeleton has 4 carbons: a central carbon joined to three terminal carbons (a 'Y' shape in bond-line notation, with no atom symbols shown for C or H). Applying the valency rule (carbon must form 4 bonds in total): the central carbon already has 3 C–C bonds shown, so it carries 4 − 3 = 1 hydrogen; each terminal carbon has only 1 C–C bond shown, so each carries 4 − 1 = 3 hydrogens. Total H = 1 + 3 + 3 + 3 = 10, which matches the molecular formula C₄H₁₀ exactly.

IUPAC (systematic) names are constructed in a definite sequence: word root + primary suffix + secondary suffix, together with substituent prefixes and locants.

• Word root indicates the number of carbons in the longest continuous chain (the parent chain): meth- (1C), eth- (2C), prop- (3C), but- (4C), pent- (5C), hex- (6C), hept- (7C), oct- (8C), non- (9C), dec- (10C).
• Primary suffix shows saturation: -ane (all single bonds), -ene (one or more C=C), -yne (one or more C≡C).
• Secondary suffix names the principal characteristic (functional) group, e.g. -ol (alcohol), -al (aldehyde), -one (ketone), -oic acid (carboxylic acid), -amine (amine). When several functional groups are present, only the senior-most one is expressed as a suffix; the rest are named as substituent prefixes (e.g. oxo- for a ketone, hydroxy- for –OH).
• Substituent (side-chain) prefixes such as methyl-, ethyl-, chloro-, bromo- are cited in alphabetical order; multiplying prefixes (di-, tri-, tetra-) are used for repeated identical substituents but are ignored while alphabetising.
• Numbering (locants) is chosen so that the principal characteristic group gets the lowest possible locant; if there is a choice, the set of locants for substituents as a whole must be as low as possible (lowest locant rule).

Worked example. Name CH₃–CH(CH₃)–CH₂–CH₂–OH. Step 1: the longest chain containing the –OH carbon has 4 carbons, so the word root is 'but-'. Step 2: all bonds are single, and –OH is the principal group, so the suffix is '-an-1-ol' once numbered. Step 3: number from the end nearer –OH so that it gets the lowest locant: C1(CH₂OH)–C2(CH₂)–C3(CH with a methyl branch)–C4(CH₃). Step 4: the methyl substituent is at C3. Final IUPAC name: 3-methylbutan-1-ol. As a second example, CH₃–CH₂–CO–CH₃ is a 4-carbon chain with a ketone group; numbering from the end nearer the C=O gives it locant 2, so the name is butan-2-one.

Compounds with the same molecular formula but different structures/arrangements are called isomers. Isomerism is divided into two broad types.

• Structural isomerism (different connectivity of atoms):
  • Chain isomerism — differ in the arrangement of the carbon skeleton, e.g. n-butane and 2-methylpropane (isobutane), both C₄H₁₀.
  • Position isomerism — same carbon skeleton and same functional group but the group/substituent is at a different position, e.g. propan-1-ol and propan-2-ol, both C₃H₈O.
  • Functional isomerism — same molecular formula but different functional groups, e.g. ethanol (CH₃CH₂OH) and methoxymethane/dimethyl ether (CH₃OCH₃), both C₂H₆O.
  • Metamerism — same functional group but different alkyl groups distributed on either side of that group, e.g. diethyl ether (C₂H₅–O–C₂H₅) and methyl propyl ether (CH₃–O–C₃H₇), both C₄H₁₀O.
  • Ring-chain isomerism — a cyclic compound and an open-chain compound share the same molecular formula, e.g. cyclopropane and propene, both C₃H₆.
• Stereoisomerism (same connectivity, different spatial arrangement):
  • Geometrical (cis–trans) isomerism — arises from restricted rotation about a C=C double bond; e.g. but-2-ene exists as cis (identical groups on the same side) and trans (identical groups on opposite sides) forms.
  • Optical isomerism (basic idea) — arises when a carbon is attached to four different groups (a chiral centre); the molecule and its mirror image are non-superimposable, giving a pair of optical isomers called enantiomers.

Worked example. Classify the relationship in each pair: (i) CH₃CH₂CH₂OH and CH₃CH(OH)CH₃ — same formula C₃H₈O, same –OH group, but the –OH is on C1 in one and C2 in the other → position isomers. (ii) CH₃CH₂CH₂OH and CH₃–O–CH₂CH₃ (methoxyethane) — both C₃H₈O, but one has –OH and the other has –O– → functional isomers. (iii) For but-2-ene, CH₃–CH=CH–CH₃, since rotation about the C=C bond is restricted, the two methyl groups can lie on the same side (cis-but-2-ene) or on opposite sides (trans-but-2-ene) of the double bond, giving a pair of geometrical isomers.

Inductive effect (I effect). When an electronegative atom or group is attached to a carbon chain, it pulls the shared sigma-bond electrons slightly towards itself, and this small polarity is relayed, with rapidly decreasing strength, along the rest of the chain. This is a permanent effect present in the ground state of the molecule.

• Groups that withdraw electron density (relative to H) show a −I effect: examples in decreasing strength include –NO₂, –CN, –COOH, halogens (–F > –Cl > –Br > –I), –OH.
• Groups that release electron density (relative to H) show a +I effect: alkyl groups, with the order tertiary > secondary > primary > methyl in electron-donating ability.
• The inductive effect explains trends in acid/base strength: electron-withdrawing (−I) groups near –COOH stabilise the conjugate base (carboxylate ion) and increase acid strength; electron-releasing (+I) groups do the opposite.

Worked example (inductive effect). Arrange CH₃COOH, ClCH₂COOH, Cl₂CHCOOH and Cl₃CCOOH in decreasing order of acid strength. Each chlorine attached near the –COOH group withdraws electron density through the −I effect, which stabilises the carboxylate anion formed after loss of H⁺ and makes the acid stronger. Since Cl₃CCOOH has three −I chlorines (highest withdrawal), followed by two in Cl₂CHCOOH, one in ClCH₂COOH, and none in CH₃COOH: Cl₃CCOOH > Cl₂CHCOOH > ClCH₂COOH > CH₃COOH.

Resonance (mesomeric) effect (R/M effect). When a molecule can be represented by two or more valid Lewis structures (differing only in the position of pi-bond or lone-pair electrons, never in the position of the nuclei), the actual molecule is a resonance hybrid of all these contributing structures and is more stable than any single structure. Groups that donate electrons into the pi system by resonance show a +R (+M) effect (e.g. –OH, –NH₂, –OR, halogens attached to an unsaturated system); groups that withdraw electrons from the pi system show a −R (−M) effect (e.g. –NO₂, –CHO, >C=O, –COOH, –CN).

Worked example (resonance). The carboxylate ion, CH₃COO⁻, can be drawn with the negative charge on either oxygen, giving two equivalent resonance structures. The true structure is a hybrid in which the negative charge and the pi bond are equally delocalised over both C–O bonds (each C–O bond has equal, intermediate bond length/order). This delocalisation stabilises the carboxylate ion far more than an alkoxide ion (RO⁻, which has no such resonance), which is why carboxylic acids are much stronger acids than alcohols.

Electromeric effect (E effect). This is a temporary effect seen only when a multiple bond (C=C, C=O, etc.) is attacked by a reagent: the pi-bond electron pair is completely transferred to one of the two atoms at the demand of the attacking reagent, and the effect disappears the moment the reagent is removed. It is denoted +E when electrons move towards the atom to which the new bond forms and −E when they move away from it. Unlike the permanent inductive and resonance effects, the electromeric effect operates only during a reaction, at the very moment a reagent approaches.

Worked example (electromeric effect). During the addition of HBr to propene, CH₃–CH=CH₂, the approaching H⁺ (electrophile) triggers a complete shift of the pi-electron pair of C=C towards the carbon that will bond to H, generating the more stable secondary carbocation CH₃–⁺CH–CH₃, which is then attacked by Br⁻ to complete Markovnikov addition. This electron shift happens only because HBr is attacking; it is not present before the reagent approaches.

Hyperconjugation (no-bond resonance). A C–H (or C–C) sigma bond on a carbon directly attached to a carbocation, a free radical, or a double bond can align with the empty/half-filled/pi orbital and delocalise its electron density into it, lending extra stability. The more such adjacent (alpha) C–H bonds available, the greater the stabilisation. This explains the observed stability order of carbocations and free radicals.

Worked example (hyperconjugation). Compare the stability of a primary carbocation CH₃–⁺CH₂ (ethyl cation) with a tertiary carbocation (CH₃)₃C⁺. The ethyl cation has 3 alpha C–H bonds available for hyperconjugation (from the adjacent CH₃ group), giving 3 hyperconjugative (no-bond resonance) structures, whereas the tertiary cation has 9 alpha C–H bonds (three CH₃ groups), giving 9 such structures. More hyperconjugative structures mean greater delocalisation of the positive charge and greater stability, so the tertiary carbocation is far more stable: overall order 3° > 2° > 1° > methyl cation.

Fission of a covalent bond. A covalent bond can break in two ways.

• Homolytic fission (homolysis): the bonding electron pair splits equally, one electron going to each atom, producing two neutral species with an unpaired electron called free radicals. It is favoured by non-polar conditions, heat, ultraviolet light, or the presence of peroxides, e.g. Cl–Cl breaking under UV light into two chlorine free radicals, Cl^•.
• Heterolytic fission (heterolysis): the bonding electron pair goes entirely to the more electronegative atom, producing a cation and an anion. It is favoured in polar solvents, e.g. the C–Cl bond of chloromethane, CH₃–Cl, breaking to give a methyl carbocation CH₃⁺ and a chloride ion Cl⁻.

Worked example (fission). Show homolytic and heterolytic fission of the C–Cl bond in CH₃Cl. Homolysis (typically induced by heat/UV, symmetrical bond-breaking shown with single-barbed/'fish-hook' arrows): CH₃–Cl → CH₃^• (methyl free radical) + Cl^• (chlorine free radical). Heterolysis (typically favoured in a polar medium, both electrons move to the more electronegative Cl): CH₃–Cl → CH₃⁺ (methyl carbocation, electron-deficient, sp², planar) + Cl⁻ (chloride ion, complete octet).