Organic Chemistry Fundamentals

🟢 Lite — Quick Review (1h–1d)

Rapid summary for last-minute revision before your exam.

Organic chemistry is the chemistry of carbon compounds. Carbon’s unique ability to form four covalent bonds — and to bond with itself to form long chains, rings, and branched structures — makes it the basis of all known life. Understanding electron distribution and movement in organic molecules is essential for predicting their reactivity.

Electron Displacement Effects:

Organic reactions involve the movement of electron pairs. Several effects describe how substituents influence electron density in a molecule:

• Inductive Effect (±I): A permanent effect arising from electronegativity differences. Electron-withdrawing groups (-I) pull electrons through sigma bonds. Common -I groups (strongest first): -NO₂, -CN, -COOH, -F, -Cl, -Br, -I. Electron-donating groups (+I): alkyl groups (-CH₃, -C₂H₅), -O⁻, -COO⁻. The inductive effect weakens with distance (felt only through 2-3 bonds).

• Resonance Effect (±R): A delocalisation effect where pi electrons move to accommodate electron deficiency or stabilise excess electron density. Curved arrows show electron pair movement. Common +R groups: -O⁻, -OR, -NR₂, -NHR, -NH₂, -OH, -NHCOR. Common -R groups: -NO₂, -CN, -COOH, -CHO, -COR, -CONH₂, -SO₃H. Only pi electrons move in resonance — the total number of unpaired electrons remains constant.

• Hyperconjugation: The delocalisation of sigma electrons (specifically C-H or C-C sigma bonds) into an adjacent empty or partially filled p-orbital. This stabilises carbocations, carbenes, and free radicals. More α-hydrogens (hydrogens on carbons adjacent to the reactive centre) means greater hyperconjugative stabilisation. Tertiary carbocations are more stable than secondary than primary precisely because of this effect.

⚡ Exam Tip (MDCAT): Hyperconjugation requires adjacent C-H or C-C sigma bonds — it does NOT involve pi electrons. Resonance involves pi electron delocalisation. These are two different phenomena. In aromatic systems, resonance is the dominant stabilisation mechanism, not hyperconjugation.

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🟡 Standard — Regular Study (2d–2mo)

For students who want genuine understanding and reaction mechanism mastery.

Carbocations, Carbanions, and Free Radicals — Stability and Reactivity:

Carbocations (positively charged carbon, sp² hybridised, planar geometry) are stabilised by:

1. Resonance (allylic and benzylic positions: $Ph-CH_2^+$, $CH_2=CH-CH_2^+$)
2. Hyperconjugation (tertiary > secondary > primary > methyl)
3. Inductive electron donation (+I effect of alkyl groups)

Stability order: 3° > 2° > 1° > methyl (for aliphatic carbocations)

Carbanions (negatively charged carbon, sp³ hybridised, pyramidal geometry) are destabilised by the same factors. The most electron-withdrawing substituents on the carbanion make it more stable. Stability order for simple carbanions: methyl > 1° > 2° > 3° — exactly opposite to carbocations.

Free radicals (neutral species with an unpaired electron, sp² hybridised, planar) are stabilised by: resonance (allylic, benzylic), hyperconjugation, and delocalisation. Stability order: benzyl/allyl > 3° > 2° > 1° > methyl.

Nucleophilicity vs Basicity:

• Basicity: The affinity of a species for a proton (H⁺). Measured by the equilibrium constant for protonation in water. Strong bases have high proton affinity.
• Nucleophilicity: The affinity of a species for an electrophile (electron-deficient carbon). Measured by the rate of substitution reactions.

In aprotic solvents (acetone, DMSO, DMF): nucleophilicity parallels basicity — larger, more polarisable species are better nucleophiles. $I^- > Br^- > Cl^- > F^-$

In protic solvents (water, alcohols): nucleophilicity decreases down a group because the solvent molecules hydrogen-bond to the nucleophile, reducing its ability to attack the electrophile. $F^- > Cl^- > Br^- > I^-$ in protic solvents.

Electrophiles and Nucleophiles:

Electrophiles (electron-loving): $H^+$, $NO_2^+$ (nitronium ion, from HNO₃ + H₂SO₄), $SO_3H^+$, $AlCl_3$ (Lewis acid), $BF_3$, $Cu^{2+}$, carbocations ($R^+$). Electrophiles accept an electron pair.

Nucleophiles (nucleus-loving): $OH^-$, $CN^-$, $RO^-$, $NH_3$, $R-NH_2$, carbanions, halide ions. Nucleophiles donate an electron pair.

Reaction Intermediates — Shapes and Properties:

Intermediate	Hybridisation	Shape	Geometry
Carbocation	sp²	Planar	Trigonal planar
Carbanion	sp³	Pyramidal	Tetrahedral with lone pair
Free radical	sp²	Planar	Trigonal planar
Carbene (:CH₂) singlet	sp²	Planar	Triangular, lone pair + empty p
Carbene (:CH₂) triplet	sp	Linear	Linear, two unpaired electrons

Carbocation Rearrangements:

1,2-hydride shifts and 1,2-methyl shifts occur when a more stable carbocation can be formed. The migrating group moves with its bonding electrons to the electron-deficient carbon, creating a more stable carbocation intermediate. This is why the product of an SN1 reaction may differ from the expected substitution product — rearrangements are common.

⚡ Standard MDCAT Strategy: When you see a carbocation intermediate in a reaction mechanism, always ask: “Can this rearrange to a more stable carbocation?” If yes, the rearrangement usually occurs and the major product reflects the more stable intermediate. For example, a secondary carbocation adjacent to a tertiary carbon will rearrange via a 1,2-hydride shift to become a tertiary carbocation.

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🔴 Extended — Deep Study (3mo+)

Comprehensive coverage for students on a longer study timeline.

Advanced Resonance Concepts:

Cross-conjugation occurs in systems like 1,3-butadiene and vinyl ethers where a pi system is conjugated to two other pi systems but those two pi systems are not conjugated to each other. In 1,3-butadiene ($CH_2=CH-CH=CH_2$), each terminal carbon contributes one pi electron pair to delocalisation, making each carbon approximately $sp^2$ hybridised.

Hückel’s 4n+2 Rule for Aromaticity:

A planar cyclic conjugated system is aromatic if it contains $(4n+2)$ pi electrons, where $n = 0, 1, 2, 3…$

• Benzene ($n=1$): 6 π electrons, highly aromatic, exceptionally stable (resonance energy ~150 kJ/mol)
• Cyclopentadienyl anion ($n=1$): 6 π electrons, aromatic despite being negatively charged
• Tropylium cation ($n=1$): 6 π electrons, aromatic despite being positively charged
• Cyclobutadiene ($n=1$): 4 π electrons, antiaromatic (destabilised), highly reactive
• Cyclooctatetraene ($n=2$): 8 π electrons, adopts a tub conformation to avoid antiaromaticity

Stereochemistry — R/S and E/Z:

For assigning R/S (Cahn-Ingold-Prelog priority):

1. Identify the chiral centre (usually carbon with four different substituents)
2. Assign priorities 1-4 based on atomic number of directly attached atoms
3. If the lowest priority (4) is on a dashed bond (pointing away), and priority decreases 1→2→3 clockwise, the centre is R (Rectus, clockwise)
4. If the lowest priority is pointing away and priority decreases anticlockwise, the centre is S (Sinister, anticlockwise)
5. If the lowest priority is on a wedge (pointing towards), reverse the R/S assignment

E/Z for Alkenes:

• E (Entgegen, “opposite”): higher priority groups on opposite sides of the double bond
• Z (Zusammen, “together”): higher priority groups on the same side

For a double bond C=C where each carbon has two different substituents: Z has the two higher-priority groups on the same side; E has them on opposite sides.

SN1 vs SN2 — The Deciding Factors:

SN1 (two steps, unimolecular rate-determining step):

• Rate = k[substrate] only
• Favoured by: stable carbocation (3° > 2° > 1°), polar protic solvent, weak nucleophile, poor leaving group ability
• Stereochemistry: racemic mixture (loss of chirality at the reaction centre)

SN2 (one step, bimolecular, Walden inversion):

• Rate = k[substrate][nucleophile]
• Favoured by: less hindered substrate (methyl > 1° > 2°), aprotic polar solvent, strong nucleophile, good leaving group
• Stereochemistry: inversion of configuration (backside attack)

⚡ Extended MDCAT Note: In elimination reactions, E1 (unimolecular elimination) competes with SN1 when a carbocation intermediate forms — 3° substrates in polar protic solvents give mixed SN1/E1 products. E2 (bimolecular elimination) is a concerted one-step process requiring anti-periplanar geometry — the leaving group and the hydrogen being removed must be on opposite sides of the C-C bond. E2 gives the more substituted alkene (Saytzeff product) with normal bases, but bulky bases (like t-butoxide) favour the less substituted alkene (Hofmann product).

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