SynthLab Academy · Organic Chemistry

Master Reactions & Mechanisms

A complete reference for organic chemistry — functional groups, reaction types, electron flow, and step-by-step mechanisms with interactive diagrams. Built for students and researchers.

Mechanism Types

50+

Reactions Covered

20+

Named Reactions

Quiz Sections

Fundamentals

Electron Flow & Curved Arrows

All organic reactions are the movement of electrons. Curved arrows are the language used to show where electrons come from and where they go.

Core principle: A curved arrow always points from electrons (nucleophile / lone pair / π bond) to where they are going (electrophile / new bond).

Full-headed vs. Half-headed Arrows

Nucleophile → Electrophile Pattern

Every ionic reaction follows the same logic: an electron-rich species (nucleophile) donates electrons to an electron-poor species (electrophile). Identify these two partners and you can predict the product.

Common nucleophiles: H₂O, NH₃, OH⁻, CN⁻, Br⁻, I⁻, alkenes (π electrons), carbonyl enolates.

Common electrophiles: H⁺, carbocations (R₃C⁺), Lewis acids (AlCl₃, BF₃), polarised halogens (Br–Br near π bonds), carbonyl carbons (C=O).

Fundamentals

Brønsted–Lowry & Lewis Acids

Acid–base concepts underpin nearly every organic mechanism. pKₐ values let you predict the direction of every proton transfer.

Brønsted–Lowry: An acid is a proton donor; a base is a proton acceptor. The stronger acid/base side is always favoured (equilibrium towards weaker).

Lewis: An acid accepts an electron pair; a base donates an electron pair. This covers reactions with no proton transfer (e.g. AlCl₃ + alkyl halides).

Key pKₐ Values to Memorise

Compound / Bond	pKₐ	Conjugate Base	Strength
HI	−10	I⁻	Very Strong Acid
H₂SO₄	−3	HSO₄⁻	Strong
H₃O⁺	−1.7	H₂O	Strong
CH₃COOH	4.7	CH₃COO⁻	Weak
H₂O	15.7	OH⁻	Very Weak
EtOH	16	EtO⁻	Very Weak
R–C≡C–H	25	R–C≡C⁻	Extremely Weak
NH₃	38	NH₂⁻	Barely Acidic
R–H (alkane)	50	R⁻	Not Acidic

Golden Rule: A reaction goes from the stronger acid to the weaker acid. If pKₐ(product acid) > pKₐ(starting acid), equilibrium lies on the left (reactant side).

Fundamentals

Resonance

When electrons can be delocalized over multiple atoms, the molecule is more stable than any single Lewis structure suggests. Resonance structures are a tool — the real molecule is the weighted average.

Rules for Drawing Resonance Structures

1. Move electrons, not atoms. Only electrons (lone pairs or π bonds) move; the atomic framework stays fixed.

2. Arrows flow toward positive charge or adjacent π systems.

3. Never exceed octets for second-row elements (C, N, O, F). Octet-expanding structures with N or O bearing positive charge while lacking full valence are minor contributors.

4. Equivalent structures contribute equally; structures with more covalent bonds and less charge separation are major contributors.

Fundamentals

Stability & Reaction Energy

Thermodynamics tells you whether a reaction will happen; kinetics tells you how fast. Understanding both lets you predict and control outcomes.

Carbocation Stability

Order: 3° > 2° > 1° > methyl (> vinyl / phenyl in some contexts). More substituents stabilise via hyperconjugation and inductive donation.

Carbanion Stability

Order: Opposite of carbocations — methyl > 1° > 2° > 3°. Stabilised by EWG (CN, C=O), resonance, and sp hybridisation.

Radical Stability

Radicals follow the same order as carbocations: 3° > 2° > 1° (hyperconjugation), but allylic and benzylic radicals are exceptionally stable due to resonance delocalization.

Alkene Stability (Degree of Substitution)

Alkene	Example	Relative Stability
Tetrasubstituted	(CH₃)₂C=C(CH₃)₂	Most stable
Trisubstituted	(CH₃)₂C=CHCH₃	Very stable
Disubstituted (trans)	CH₃CH=CHCH₃	Stable
Monosubstituted	CH₂=CHCH₃	Less stable
Ethene	CH₂=CH₂	Least stable

Functional Groups

Alkanes

Saturated hydrocarbons — all C–C and C–H single bonds. Generally unreactive toward ionic reagents; react via radical halogenation and combustion.

Name	Formula	BP (°C)	Key Property
Methane	CH₄	−161	Gas; major component of natural gas
Ethane	CH₃CH₃	−89	Gas; free rotation around C–C bond
Propane	CH₃CH₂CH₃	−42	LPG fuel
Butane	CH₃(CH₂)₂CH₃	−1	Lighter fuel; gauche/anti conformations
Cyclohexane	C₆H₁₂	81	Chair/boat conformations; axial/equatorial

Free Radical Halogenation

Radical3 stages

CH₄ + Cl₂ —hν/Δ→ CH₃Cl + HCl

Initiation: Light or heat homolytically cleaves Cl₂ → 2 Cl• radicals. Energy input: ~242 kJ/mol.

Propagation (×n): Cl• abstracts H from CH₄ → HCl + CH₃•. Then CH₃• + Cl₂ → CH₃Cl + Cl•. The radical is regenerated — chain continues.

III

Termination: Two radicals combine: Cl•+Cl• → Cl₂, CH₃•+Cl• → CH₃Cl, CH₃•+CH₃• → C₂H₆. Chain ends.

Exothermic ΔH ≈ −105 kJ/mol

Conditions: hν or 300°C

Functional Groups

Alkenes

Contain a C=C π bond — the most reactive unit in most synthesis plans. π electrons are high-energy and readily attacked by electrophiles.

The π bond (HOMO) donates electrons into the LUMO of an electrophile. This defines electrophilic addition — the defining reaction of alkenes.

Reagent	Product	Selectivity	Mechanism
H₂ / Pd,Pt	Alkane	Syn addition	Heterogeneous cat.
HX (HBr, HCl)	Haloalkane	Markovnikov	Via carbocation
Br₂ / CCl₄	1,2-Dibromide	Anti addition	Via bromonium ion
H₂O / H⁺	Alcohol	Markovnikov	Via carbocation
cold KMnO₄	Diol (syn)	Syn dihydroxylation	Cyclic MnO ester
O₃ then Zn/H₂O	2 Carbonyls	Cleaves C=C	Ozonolysis
mCPBA	Epoxide	Syn (retention)	Peracid epoxidation

Mechanism: HBr Addition (Markovnikov)

Step 1: Protonation

Step 2: Carbocation

Step 3: Br⁻ Attack

Step 1 of 3

Protonation of the π bond

The alkene π bond (HOMO) donates electrons to the electrophilic proton (H⁺) from HBr. The proton adds to the less-substituted carbon (Markovnikov's rule), generating the more stable, more-substituted carbocation.

Markovnikov's Rule: The electrophile (H⁺) adds to the carbon bearing more hydrogens, because this places positive charge on the more substituted, more stable carbon.

1 / 3

Functional Groups

Alkynes

Triple bond (C≡C) — contains one σ and two π bonds. The terminal alkyne C–H is surprisingly acidic (pKₐ ≈ 25) due to the high s-character of the sp carbon.

Reagent	Product	Notes
H₂ / Lindlar's cat.	cis-Alkene	Syn addition; Pd/CaCO₃ + Pb(OAc)₂
H₂ / Pd, excess	Alkane	Over-reduction
Na / NH₃ (liq.)	trans-Alkene	Birch / dissolving metal; anti addition
HX (1 equiv.)	Vinyl halide	Markovnikov
HX (2 equiv.)	Gem-dihalide	Double Markovnikov
H₂O / H⁺ / Hg²⁺	Ketone	Markovnikov; vinyl alcohol → ketone tautomerism
BH₃ / H₂O₂,OH⁻	Aldehyde	Anti-Markovnikov; hydroboration-oxidation
NaNH₂ / R–X	Internal alkyne	Terminal alkyne alkylation (SN2)

Acidity of terminal alkynes: The sp C–H bond (pKₐ 25) is much more acidic than sp² C–H (pKₐ 44) or sp³ C–H (pKₐ 50), making terminal alkynes deprotonatable with NaNH₂ or n-BuLi to form acetylide anions — powerful C-nucleophiles for alkylation.

Functional Groups

Alcohols

The –OH group makes alcohols amphoteric (both acid and base), nucleophilic, and oxidizable. They are the most versatile functional group in synthesis.

Reactions Overview

Reaction	Conditions	Product
Dehydration	H₂SO₄, 170°C	Alkene (Zaitsev product)
Oxidation (1°)	KMnO₄ or CrO₃	Aldehyde → Carboxylic acid
Oxidation (2°)	PCC or Jones	Ketone
Oxidation (3°)	Not oxidizable	No reaction
Esterification	RCOOH / H⁺ cat.	Ester + H₂O (Fischer)
HX substitution	HBr or SOCl₂	Alkyl halide
Tosylation	TsCl / pyridine	Tosylate (good LG)
Mitsunobu	PPh₃, DIAD	Inversion of configuration

Functional Groups

Ethers (R–O–R′)

Generally inert solvents, but can be cleaved by strong acids (HI or HBr at high temperatures). Epoxides are cyclic ethers with exceptional reactivity.

Peroxide hazard: Diethyl ether forms explosive peroxides on prolonged storage. Always check for peroxides before distilling.

Reaction	Reagent	Product	Notes
Synthesis (Williamson)	R–O⁻ + R′–X	R–O–R′	SN2; requires 1° alkyl halide
Acid cleavage	HI (excess, Δ)	2 Alkyl iodides	More substituted side cleaved first
Epoxide + Nu⁻	OH⁻, CN⁻, RMgX	β-Hydroxy product	Attack at less hindered C (SN2)
Epoxide + H₃O⁺	H⁺, H₂O	Trans-diol	Attack at more substituted C (SN1-like)

Functional Groups

Aldehydes (RCHO)

The most electrophilic carbonyl — the terminal H provides no steric protection. Highly reactive toward nucleophilic addition.

Reaction	Reagent	Product
Nucleophilic addition	RMgX, RLi	2° Alcohol
Reduction	NaBH₄ or LiAlH₄	1° Alcohol
Oxidation	KMnO₄, Tollens, Fehling	Carboxylic acid
Acetal formation	ROH / H⁺ cat.	Acetal (protecting group)
Aldol condensation	NaOH	β-Hydroxy aldehyde
Wittig reaction	Ph₃P=CR₂	Alkene
Imine formation	RNH₂ / H⁺	Imine (Schiff base)

Tollens' test: Ag⁺ (ammoniacal) oxidises aldehydes → silver mirror. Fehling's test: Cu²⁺ → Cu₂O red precipitate. Both are negative for ketones.

Functional Groups

Ketones (RCOR′)

Two alkyl groups flanking the C=O. Less electrophilic and less oxidizable than aldehydes, but undergo the same nucleophilic addition reactions.

Reaction	Reagent	Product
Nucleophilic addition	RMgX, RLi	3° Alcohol
Reduction	NaBH₄	2° Alcohol
Baeyer–Villiger	mCPBA	Ester
Aldol condensation	NaOH or LDA	β-Hydroxy ketone
Mannich reaction	HCHO, RNH₂	β-Amino ketone
Enamine formation	R₂NH / Δ	Enamine
α-Halogenation	X₂ / H⁺	α-Haloketone

Functional Groups

Carboxylic Acids (RCOOH)

The –COOH group is the most acidic common organic functional group. The carboxylate anion is stabilised by two equivalent resonance structures.

Derivative	Reagent	Product	Mechanism
Esterification (Fischer)	ROH / H⁺, Δ	Ester	Acyl substitution
Acid chloride	SOCl₂ or PCl₅	RCOCl	Nucleophilic acyl sub.
Anhydride	RCOOH / Δ or Ac₂O	(RCO)₂O	Condensation
Amide	RNH₂ / Δ	RCONHR	Fischer amide syn.
Reduction	LiAlH₄	1° Alcohol	2 equiv. H⁻
Decarboxylation	Δ (β-keto acid)	Ketone + CO₂	Cyclic 6e⁻ TS
Hell–Volhard–Zelinskyl	Br₂/PBr₃	α-Bromo acid	Radical at α-C

Functional Groups

Esters (RCOOR′)

Fruity fragrance compounds and the backbone of fats and oils. Hydrolyze to give the acid + alcohol; react with nucleophiles via the tetrahedral intermediate.

Reaction	Conditions	Product
Saponification (base)	NaOH, H₂O, Δ	Carboxylate + alcohol
Hydrolysis (acid)	H₂O / H⁺, Δ	Acid + alcohol (reversible)
Reduction	LiAlH₄	2 Primary alcohols
Grignard addition	2 RMgX	Tertiary alcohol
Claisen condensation	NaOEt / base	β-Ketoester
Transesterification	ROH / H⁺ or base	New ester

Functional Groups

Amines (RNH₂, R₂NH, R₃N)

Strong nucleophiles and bases. Classification (1°/2°/3°) refers to carbons attached to N, not H atoms.

Reaction	Conditions	Product
Alkylation	RX (excess leads to over-alkylation)	2°, 3° amine, salt
Acylation	RCOCl / Et₃N	Amide
Diazotization	NaNO₂ / HCl, 0°C	Diazonium salt (ArN₂⁺)
Reductive amination	RCHO / NaBH₃CN	Amine
Gabriel synthesis	Phthalimide / base / RX	1° Amine (no over-alkylation)
Hofmann rearrangement	Br₂ / NaOH	1° Amine (shorter by 1C)

Mechanism Library

Electrophilic Addition (EA)

Alkenes and alkynes react with electrophiles in a two-stage process: the π bond attacks the electrophile (rate-limiting), then nucleophilic capture of the cationic intermediate.

CH₂=CH₂

Ethene

HBr

25°C, no peroxides

CH₃CH₂Br

Bromoethane

Bromination: Anti-Addition via Bromonium Ion

AntiStereospecific

R–CH=CH–R′+Br₂—CCl₄→R–CHBr–CHBr–R′(anti)

π bond polarises Br₂: The electron-dense alkene π bond induces a dipole in the approaching Br₂ molecule (Brδ⁺–Brδ⁻). No reaction yet.

Bromonium ion formation: The π electrons attack Brδ⁺, ejecting Br⁻ and forming a 3-membered cyclic bromonium ion. This bridged cation blocks one face — the key to anti stereospecificity.

Anti attack by Br⁻: Br⁻ attacks one of the two carbons from the back side (opposite face), opening the ring. Anti addition gives the meso (or trans) vicinal dibromide.

ExothermicΔH ≈ −115 kJ/mol

CCl₄, 25°C, dark

Mechanism Library

SN1 — Unimolecular Nucleophilic Substitution

A two-step mechanism proceeding through a carbocation intermediate. The rate depends only on the substrate — not the nucleophile. Rate = k[R-X]

Favoured by: 3° substrates, polar protic solvents (H₂O, ROH, RCOOH), weak nucleophiles, and leaving groups that form stable anions (I⁻ > Br⁻ > Cl⁻).

SN1 Mechanism — tert-Butyl Bromide + H₂O

2 stepsRacemisation

(CH₃)₃CBr+ H₂O →(CH₃)₃COH+ HBr

Ionisation (rate-limiting): The C–Br bond breaks heterolytically. Br⁻ departs (good LG) and a tertiary carbocation forms. Polar protic solvent stabilises both ions by solvation. Energy barrier: ~100 kJ/mol.

Nucleophilic attack: H₂O (or any nucleophile) attacks the flat sp² carbocation from either face with equal probability → racemisation at the former stereocenter (if chiral). A proton is then lost to give the alcohol.

Exothermic overallEa (ionization) ≈ 100 kJ/mol

Polar protic solvent

Mechanism Library

SN2 — Bimolecular Nucleophilic Substitution

A concerted one-step mechanism. Nucleophile attacks the backside of the carbon bearing the leaving group simultaneously with LG departure. Rate = k[R-X][Nu]

Favoured by: 1° (or methyl) substrates, polar aprotic solvents (DMF, DMSO, acetone), strong nucleophiles (CN⁻, I⁻, RS⁻, RO⁻).

SN2: Methyl Bromide + OH⁻

ConcertedInversion

CH₃Br+ OH⁻ →CH₃OH+ Br⁻

Backside approach: OH⁻ approaches the carbon 180° from the C–Br bond (backside). The transition state has both Nu and LG partially bonded to the carbon (trigonal bipyramidal, pentacoordinate).

Walden inversion: As the Nu–C bond forms and the C–LG bond breaks, the three substituents on carbon flip through the plane — like an umbrella in wind. The product has inverted configuration (Walden inversion).

ExothermicConcerted TS

DMF or DMSO favoured

SN1 vs SN2 Summary

Feature	SN1	SN2
Rate law	k[RX]	k[RX][Nu]
Steps	2 (carbocation)	1 (concerted)
Best substrate	3°, benzylic, allylic	Methyl, 1°
Stereochemistry	Racemisation	Inversion (Walden)
Solvent	Polar protic	Polar aprotic
Nucleophile	Weak fine	Strong required
Rearrangement?	Yes (hydride/methyl shift)	No

Mechanism Library

E1 Elimination

A two-step elimination: ionisation of the leaving group forms a carbocation, then a base removes a β-hydrogen to give the alkene. Competes with SN1 under the same conditions.

Zaitsev's Rule: The more substituted (more stable) alkene is the major product in E1 and E2.

E1: 2-Bromobutane + EtOH / Δ

2-Butene (major)1-Butene (minor)

Ionisation: C–Br bond breaks; Br⁻ leaves (same as SN1 first step). A secondary carbocation forms at C2.

Proton loss: A base (solvent EtOH, or Br⁻) removes a β-H. Loss from C1 gives 1-butene (minor); loss from C3 gives 2-butene (major — Zaitsev).

EndothermicEa ~ 130 kJ/mol

Polar protic, high T

Mechanism Library

E2 Elimination

A concerted, one-step elimination. Base removes the β-H while the LG departs simultaneously. Strictly requires anti-periplanar geometry between H and LG. Rate = k[RX][B]

Anti-periplanar requirement: H and LG must be 180° dihedral — this means the E2 is trans-selective and can be used to determine or control stereochemistry.

Feature	E1	E2
Steps	2	1 (concerted)
Rate law	k[RX]	k[RX][B]
Base	Weak (solvent)	Strong (t-BuO⁻, NaOEt)
Geometry	No requirement	Anti-periplanar (180°)
Regioselectivity	Zaitsev	Zaitsev (or Hofmann with bulky base)
Stereospecificity	No	Yes — syn/anti selectivity

Mechanism Library

Electrophilic Aromatic Substitution (EAS)

Aromatic rings react with electrophiles to give substituted products — retaining aromaticity. The key intermediate is the arenium ion (σ-complex, Wheland intermediate).

General EAS Mechanism

2-stepAromaticity retained

σ-Complex (Wheland intermediate): The aromatic π system attacks E⁺. One carbon becomes sp³, breaking aromaticity. The positive charge is delocalised over the ring (3 resonance structures).

Deprotonation (rearomatisation): A base (commonly the conjugate base of the acid by-product) removes H⁺ from the sp³ carbon, restoring the aromatic system. This is thermodynamically driven — regaining aromaticity releases ~150 kJ/mol.

Directing Effects

Group	Effect on Ring	Directs to	Examples
–OH, –OR, –NH₂	Activating (strong)	ortho / para	Phenol nitration gives o- and p-nitrophenol
–R (alkyl)	Activating (weak)	ortho / para	Toluene → o- and p-xylene
–F, –Cl, –Br, –I	Deactivating (weak)	ortho / para	Halobenzenes — slow but ortho/para
–NO₂, –CN, –CHO, –COOH	Deactivating (strong)	meta	Nitrobenzene → m-dinitrobenzene

Mechanism Library

Radical Reactions

Reactions proceeding through species with one unpaired electron. Initiated by heat or light (homolysis). Chain reactions are the hallmark — one radical spawns thousands of product molecules.

Half-headed arrows (fishhook) are mandatory for radical mechanisms. Each moves one electron — never use full arrows here.

Reaction	Initiator	Regioselectivity	Notes
Radical halogenation	hν, Cl₂ or Br₂	Br: 3°>2°>1°; Cl: less selective	Chain mechanism (I/P/T)
Radical addition to alkenes	ROOR (peroxide)	Anti-Markovnikov	HBr + peroxide → Br at less-sub C
Allylic bromination	NBS, hν	Allylic position	Resonance-stabilised radical
Benzylic bromination	NBS, hν	Benzylic C–H	Resonance over ring

Mechanism Library

Nucleophilic Addition to Carbonyls

The C=O carbon is electrophilic (δ+). Nucleophiles attack it, breaking the π bond and forming a tetrahedral intermediate.

Grignard Reaction (RMgX + Carbonyl)

C–C Bond FormingIrreversible

RMgX+R′CHO→ [tetrahedral] → H₃O⁺ →R–CH(OH)–R′

Nucleophilic attack: The carbanion equivalent R⁻ (from RMgX) attacks the electrophilic C=O carbon. The π bond electrons shift to oxygen, giving a magnesium alkoxide.

Aqueous workup: Addition of H₃O⁺ protonates the alkoxide, releasing the alcohol product. No elimination — the C–O bond is preserved.

Mechanism Library

Nucleophilic Acyl Substitution

Acyl compounds (acid chlorides, esters, anhydrides, amides) react with nucleophiles via an addition-elimination mechanism: addition to C=O gives a tetrahedral intermediate, then the leaving group departs.

Reactivity order: Acid chloride > Anhydride > Ester > Amide. The better the leaving group, the more reactive the acyl compound.

Ester Hydrolysis (Saponification)

Irreversible in base

RCOOR′+ OH⁻ →RCOO⁻+ R′OH

Addition: OH⁻ attacks the electrophilic acyl carbon. The C=O π bond breaks and both electrons go to oxygen — tetrahedral intermediate forms (alkoxide).

Elimination: The alkoxide OR′ departs (LG), restoring the C=O. The carboxylate anion is the thermodynamic sink — irreversible in base.

Named Reactions

Named Reaction Library

Twenty-four essential named reactions — each with substrate, product, mechanism type, and conditions.

Test Yourself

Reaction Mechanism Quiz

Ten questions spanning mechanisms, functional groups, and named reactions. Instant feedback on every answer.