Why Two Molecules With the Same Formula Can Smell Completely Different

Organic reactions can look like a long list to memorise. But almost all of them follow a few rules: where electrons are rich, where they are poor, and how bonds break.

Once you can spot isomers, bond fission, electrophiles and nucleophiles, and the electronic effects that push electrons around, reactions start to make sense.

This part covers isomerism, bond fission and reactive intermediates, electrophiles and nucleophiles, and electronic effects with reaction types.

Structural isomers share a molecular formula but differ in how atoms are connected — in the carbon chain, the position of a group, the functional group itself, or the alkyl groups around a functional group (metamerism); stereoisomers have the same connections but different arrangements in space.

Worked examples.

- Chain: C${}_4$H${}_{10}$ — butane and 2-methylpropane
- Position: C${}_3$H${}_8$O — propan-1-ol and propan-2-ol
- Functional group: C${}_2$H${}_6$O — ethanol and methoxymethane; C${}_3$H${}_6$O — propanal and propanone
- Metamerism: C${}_4$H${}_{10}$O — ethoxyethane and 1-methoxypropane

Counting. C${}_5$H${}_{12}$ has three chain isomers: pentane, 2-methylbutane and 2,2-dimethylpropane.

Stereoisomerism. Geometrical isomers such as cis- and trans-but-2-ene differ in the arrangement of groups around a double bond. Optical isomers are non-superimposable mirror images, found when a carbon carries four different groups, as in butan-2-ol.

An everyday example. Anagrams such as "listen" and "silent" use the same letters to make different words — isomers use the same atoms to make different compounds.

The substance. Isomers can have very different properties — ethanol is a liquid, while its isomer methoxymethane is a gas at room temperature.

In homolytic fission each atom keeps one electron of the shared pair, forming free radicals; in heterolytic fission one atom takes both electrons, forming a carbocation (positive carbon) or a carbanion (negative carbon); radicals and carbocations are stabilised by alkyl groups, while carbanions are destabilised by them.

Worked example 1 — the two kinds of fission.

- Homolytic: Cl${}_2$ $\to$ 2Cl${}^{\bullet }$ in ultraviolet light
- Heterolytic: (CH${}_3$)${}_3$C–Br $\to$ (CH${}_3$)${}_3$C${}^{+}$ + Br${}^{-}$

Worked example 2 — carbocation stability. Count the hydrogens on carbons next to the positive carbon, which stabilise it by hyperconjugation:

- (CH${}_3$)${}_3$C${}^{+}$: $9$
- (CH${}_3$)${}_2$CH${}^{+}$: $6$
- CH${}_3$CH${}_2^{+}$: $3$
- CH${}_3^{+}$: $0$

$$3°>2°>1°>\text{methyl}$$

Free radicals follow the same order. Carbanions follow the reverse: methyl > 1° > 2° > 3°.

Resonance stabilisation. Allyl and benzyl carbocations are especially stable because the positive charge spreads over several carbons.

An everyday example. Splitting a box of sweets equally between two friends is like homolytic fission; one friend taking the whole box is like heterolytic fission.

The substance. **A carbocation is sp${}^2$ and planar**, while a carbanion is usually sp${}^3$ and pyramidal.

Electrophiles are electron-poor species that accept an electron pair, nucleophiles are electron-rich species that donate one, and a curved arrow starts at the moving electron pair and ends where it forms a new bond or lone pair.

- Electrophiles: H${}^{+}$, NO${}_2^{+}$, carbocations, BF${}_3$, AlCl${}_3$
- Nucleophiles: OH${}^{-}$, CN${}^{-}$, Cl${}^{-}$, NH${}_3$, H${}_2$O

Worked example 1 — a substitution step. In OH${}^{-}$ + CH${}_3$Cl $\to$ CH${}_3$OH + Cl${}^{-}$:

- one arrow runs from a lone pair on oxygen to the carbon — the nucleophile attacks
- a second arrow runs from the C–Cl bond to chlorine — chloride leaves with both electrons

Worked example 2 — attack on a double bond. When H${}^{+}$ adds to ethene, the arrow starts at the C=C pi bond and ends at H${}^{+}$, leaving a carbocation.

Worked example 3 — classifying. NH${}_3$ has a lone pair, so it is a nucleophile; BF${}_3$ has an incomplete octet, so it is an electrophile; water can act as either.

Arrow types. A full-headed arrow moves two electrons; a half-headed (fish-hook) arrow moves one, as in radical reactions.

An everyday example. A drained phone looking for a charged power bank is like an electrophile seeking an electron-rich nucleophile.

The substance. Curved arrows show electrons moving, never atoms — an arrow must always begin at a lone pair or a bond.

The inductive effect is a permanent shift of sigma electrons towards more electronegative atoms, the resonance effect is delocalisation of pi or lone-pair electrons through a conjugated system, the electromeric effect is a temporary shift of pi electrons when a reagent approaches, and hyperconjugation is delocalisation of C–H sigma electrons into a neighbouring empty or pi orbital.

Inductive effect. –I groups such as –NO${}_2$, –CN, –COOH and halogens pull electrons; +I groups such as alkyl groups push them. The effect fades along the chain.

Worked example 1 — acid strength. Chlorine's –I effect stabilises the anion of chloroacetic acid, so it is stronger than acetic acid: pK${}_a$ about $2.86$ against $4.76$.

Resonance effect. +R groups (–OH, –NH${}_2$, –OR) release electrons into a ring; –R groups (–NO${}_2$, –CHO, –CN) withdraw them. Phenol is more acidic than ethanol because the phenoxide ion is resonance-stabilised.

Hyperconjugation. It explains the carbocation order above and why more substituted alkenes are more stable.

Reaction types:

- Substitution: CH${}_4$ + Cl${}_2$ $\to$ CH${}_3$Cl + HCl
- Addition: CH${}_2$=CH${}_2$ + Br${}_2$ $\to$ CH${}_2$BrCH${}_2$Br
- Elimination: CH${}_3$CH${}_2$OH $\to$ CH${}_2$=CH${}_2$ + H${}_2$O with concentrated H${}_2$SO${}_4$
- Rearrangement: butane changing to 2-methylpropane with AlCl${}_3$

An everyday example. Ripples from a stone fade as they spread across a pond, just as the inductive effect weakens with each carbon along a chain.

The substance. The inductive effect is permanent, but the electromeric effect exists only while the attacking reagent is present.