Index

Two layers: a terse chapter-by-chapter overview (for navigation), then an alphabetical subject index (for lookup).

Part 1 — Chapter Overview

Part I — Foundations

Ch 1 — What is organic chemistry? Carbon's uniqueness. Aspirin/ibuprofen/acetaminophen introduced.
Ch 2 — Lewis structures, hybridization (sp³/sp²/sp), MOs, resonance, electronegativity, formal charge.
Ch 3 — pKa, ARIO factors, conjugate acid/base, equilibrium direction, Lewis acids.
Ch 4 — Functional groups, IUPAC nomenclature, common names, priority.
Ch 5 — Alkanes, Newman, chair, A-values, thermodynamics/kinetics, Hammond, Arrhenius.
Ch 6 — IR, MS, degrees of unsaturation, nitrogen rule, McLafferty.

Part II — Stereochemistry

Ch 7 — Chirality, R/S, E/Z, enantiomers, diastereomers, meso, atropisomerism, resolution.
Ch 8 — Reaction stereochemistry: inversion/retention/racemization, syn/anti, Felkin-Anh, thalidomide.
Ch 9 — NMR ¹H, ¹³C, multiplicity, Karplus, DEPT, COSY, HSQC, HMBC, NOESY.

Part III — Substitution and Elimination

Ch 10 — SN2 mechanism, kinetics, stereochemistry (inversion), Walden, Williamson.
Ch 11 — SN1, carbocation, rearrangement, hyperconjugation, solvolysis.
Ch 12 — E2 (anti-periplanar), E1, Zaitsev/Hofmann, cyclohexane constraints.
Ch 13 — SN/E decision framework.
Ch 14 — Synthesis workshop 1 (aspirin); retrosynthesis introduced.

Part IV — Addition Reactions

Ch 15 — Alkene structure, stability, Markovnikov, bromonium ion, rearrangements.
Ch 16 — Alkene toolkit: HX, hydration, X₂, BH₃, OsO₄, mCPBA, O₃, H₂; Sharpless AE.
Ch 17 — Alkynes, sp acidity, Lindlar/Na-NH₃, alkynides, Sonogashira preview.
Ch 18 — Radicals, chain mechanism, halogenation, NBS, autoxidation, antioxidants.
Ch 19 — Conjugation, 1,2 vs 1,4 addition, Diels-Alder, endo rule, FMO theory.

Part V — Aromatic Chemistry

Ch 20 — Aromaticity, Hückel 4n+2, heteroaromatics, NICS, DNA bases, graphene.
Ch 21 — EAS: halogenation, nitration, sulfonation, FC alkylation/acylation; ibuprofen BHC process.
Ch 22 — Substituent effects, o/p vs meta, Hammett, halogen exception, Sandmeyer/diazonium.
Ch 23 — SNAr, Meisenheimer, benzyne, Birch reduction, benzylic chemistry.

Part VI — Carbonyl Chemistry

Ch 24 — Carbonyl reactivity, electronic/steric/LG factors.
Ch 25 — Nucleophilic addition: acetals, imines, enamines, Grignard, Wittig, reductive amination.
Ch 26 — Nucleophilic acyl substitution; aspirin/COX, polyamides, β-lactams.
Ch 27 — Enols, enolates, α-acidity, LDA, α-halogenation/alkylation, thalidomide α-stereolability.
Ch 28 — Aldol, Claisen, Dieckmann; fatty acid biosynthesis, citric acid cycle.
Ch 29 — Conjugate (Michael) addition, Robinson annulation; steroid synthesis, covalent drugs (ibrutinib).
Ch 30 — Amines, basicity, Gabriel, reductive amination, Hofmann, diazonium.
Ch 31 — Synthesis workshop 2: retrosynthesis (atorvastatin); AI retrosynthesis.

Part VII — Bioorganic

Ch 32 — Carbohydrates: anomers, glycosidic bonds, polysaccharides, HbA1c.
Ch 33 — Amino acids, peptide bond, SPPS, protein folding, AlphaFold.
Ch 34 — Lipids, terpenes, cholesterol biosynthesis, statins.
Ch 35 — Drug design: SAR, Lipinski, bioisosteres, PROTACs; thalidomide arc closes.

Part VIII — Advanced and Synthesis

Ch 36 — Oxidation/reduction: NADH/FADH₂, Sharpless AD.
Ch 37 — Organometallics: Pd cross-coupling, metathesis, Ziegler-Natta, C-H activation.
Ch 38 — Total synthesis: artemisinin, strychnine, classics.
Ch 39 — Pericyclic reactions, Woodward-Hoffmann, sigmatropic, electrocyclic, vitamin D.
Ch 40 — Green chemistry, flow, biocatalysis, photoredox, electrochemistry, AI synthesis.

Appendices

Glossary; Answers to selected; Bibliography; Index
App A — Periodic table and atomic data
App B — pKa reference table
App C — Common reaction summary
App D — Spectroscopy reference (IR, NMR, MS, UV)
App E — Computational chemistry setup
App F — Named reactions
App G — Retrosynthesis disconnections
App H — Nomenclature quick reference
App I — Reagents and solvents
App J — Laboratory safety
App K — Careers and graduate school

Part 2 — Alphabetical Subject Index

A

A-value — Ch 5
Acetal — Chs 25, 31 (protecting group); see App F
Acetic acid — Chs 3, 26
Acetylcholinesterase — Ch 35
Acetyl-CoA — Chs 28, 34
Activating groups — Ch 22
Activation energy — Ch 5
Acyl substitution — Ch 26
Adamantane — Ch 5; App H
Adenine — Ch 20 (heteroaromatic), Ch 33
Aldol reaction — Ch 28; App F
AlphaFold — Chs 33, 38, 40
Alkaloids — Ch 30
Alkenes — Chs 15, 16
Alkynes — Ch 17
Allyl cation — Chs 11, 18, 19
Ambident nucleophile — Ch 27
Amides — Chs 24, 26
Amines — Ch 30
Amino acids — Ch 33
Anchimeric assistance — Ch 11
Anhydride — Chs 24, 26
Anomers — Ch 32
Antibiotics — Chs 26 (β-lactams), 35
Antioxidants — Ch 18
Anti-periplanar — Ch 12
Aromaticity — Ch 20
Arrhenius equation — Ch 5
Artemisinin — Ch 38
Aryl — Chs 20, 22
Aspirin — Chs 1, 14, 21, 26, 35 (mechanism on COX)
Asymmetric synthesis — Chs 8, 16, 31, 36, 38
Atactic — Ch 37
Atom economy — Ch 40
Atomic orbital — Ch 2
Atorvastatin — Ch 31, 34
Autoxidation — Ch 18
Axial / equatorial — Ch 5
Azide — Chs 30, 39, 40 (click)

B

Beer-Lambert law — Ch 6
Benzene — Ch 20
Benzyl — Ch 23
Benzylic radical — Ch 23
Benzyne — Ch 23
Bertozzi, Carolyn — Chs 38, 40 (Nobel 2022, click in living systems)
β-Oxidation — Ch 34
Bicycle / bridgehead — Ch 5
BINOL — Ch 7
Biocatalysis — Ch 40
Birch reduction — Ch 23
Boc protecting group — Ch 31, 33
Bond dissociation energy — Ch 2, 18
Brønsted-Lowry — Ch 3
Bromonium ion — Ch 15
Buchwald-Hartwig amination — Chs 30, 37
Butane — Ch 5

C

Cahn-Ingold-Prelog (CIP) — Ch 7
Cannizzaro — Ch 25
Carbanion — Ch 27
Carbene — Chs 18, 37
Carbocation — Chs 11, 15, 21 (arenium)
Carbohydrates — Ch 32
Carbonyl group — Ch 24
Carboxylic acid — Chs 24, 26
Cellulose — Ch 32
Cereblon — Ch 35
C-H activation — Ch 37
Chemical shift — Ch 9
Chirality — Ch 7
Chiral pool — Ch 31
Cholesterol — Ch 34
Chromatography — App J
CIP rules — Ch 7
Cis/trans — Ch 7
Claisen condensation — Ch 28
Claisen rearrangement — Ch 39
Clemmensen reduction — Ch 21
Click chemistry — Chs 39, 40
Color — Ch 19 (conjugation)
Combinatorial chemistry — Ch 35
Common name vs IUPAC — Ch 4
Conformational analysis — Ch 5
Conjugate addition (Michael) — Ch 29
Conjugation — Ch 19
Corey, E. J. — Ch 31 (LCB), Ch 38
COSY — Ch 9
COX (cyclooxygenase) — Chs 26, 35
Cross-coupling — Ch 37
Crown ether — Ch 10
Curtius rearrangement — Ch 30
Cyclohexane — Ch 5
Cyclopentadienyl anion — Ch 20

D

Deactivating groups — Ch 22
Decarboxylation — Ch 28, 34
Degrees of unsaturation — Ch 6
DEPT — Ch 9
Deuterium — Ch 9
Dextrorotatory — Ch 7
DFT — App E
Diastereomer — Ch 7
Diazonium — Chs 22, 30
Dieckmann — Ch 28
Diels-Alder — Ch 19
Diol — Ch 16
Dipole moment — Ch 2
Disconnection (retrosynthesis) — Chs 14, 31; App G
DMSO — Ch 10
DNA bases — Ch 20

E

E1, E2 — Ch 12
E-factor — Ch 40
E/Z nomenclature — Ch 7
Eclipsed — Ch 5
Electrocyclic — Ch 39
Electronegativity — Ch 2
Electrophile — Ch 3
Enamine — Ch 25
Enantiomer — Ch 7
Enantiomeric excess — Ch 7
Endo rule — Ch 19
Enol / enolate — Ch 27
Enthalpy — Ch 5
Entropy — Ch 5
Enzyme — Chs 33, 40
Epoxide — Ch 16
Ester — Chs 24, 26
Ether — Ch 4
Ethylene — Ch 15

F

FAD/FADH₂ — Ch 36
Fats — Ch 34
Felkin-Anh — Ch 8
Fenton reaction — Ch 18
Fischer projection — Ch 7
Fischer esterification — Ch 26
Flow chemistry — Ch 40
Fluorination — Ch 35, 40
FMO theory — Chs 19, 39
Formal charge — Ch 2
Friedel-Crafts — Ch 21
Frontier orbitals — Chs 19, 39
Functional group — Ch 4
Furanose — Ch 32

G

Gabriel synthesis — Ch 30
Glucose — Chs 24, 32
Glycolysis — Ch 28
Glycosidic bond — Ch 32
Graphene — Ch 20
Green chemistry — Ch 40
Grignard reagent — Ch 25
Grubbs, Robert (Nobel 2005) — Ch 37 (metathesis)

H

Haloform reaction — Ch 27
Halogenation — Chs 18 (radical), 21 (EAS), 27 (α)
Halohydrin — Ch 16
Hammett equation — Ch 22
Hammond postulate — Ch 5
HBr peroxide effect — Ch 18
HbA1c — Ch 32
Heat of combustion — Ch 5
Heck reaction — Ch 37; App F
Hemiacetal — Ch 25, 32
Heteroaromatic — Ch 20
Hofmann elimination — Ch 30
Hofmann rule — Ch 12
HOMO — Chs 2, 19
HSQC, HMBC — Ch 9
Hückel rule — Ch 20
Hybridization — Ch 2
Hydration — Chs 15, 16
Hydride shift — Ch 11
Hydroboration — Chs 16, 17
Hydrogenation — Chs 16, 36
Hyperconjugation — Chs 11, 12

I

Ibrutinib — Ch 29 (Michael covalent inhibitor)
Ibuprofen — Chs 1, 21, 35; BHC process (Ch 21)
Imine — Ch 25
Inductive effect — Chs 3, 22
Inhibitors (enzyme) — Ch 35
Infrared spectroscopy — Ch 6; App D
Insulin — Ch 33
Inversion (Walden) — Ch 10
Iodination — Ch 21
Isoelectric point — Ch 33
Isoprene rule — Ch 34
IUPAC — Ch 4; App H

J

Jones reagent — Ch 36
Journals — Bibliography

K

Kekulé — Ch 20
Ketone — Chs 4, 24
Kinetic vs thermodynamic control — Chs 5, 19
Kolbe-Schmitt — Ch 14
Koshland induced-fit — Ch 33

L

Lactam, lactone — Ch 26
LDA — Ch 27
Leaving group — Chs 3, 10
Levorotatory — Ch 7
Lewis acid/base — Ch 3
Lewis structure — Ch 2
Lindlar catalyst — Ch 17
Line-angle structure — Ch 1
Lipid bilayer — Ch 34
Lipinski rule of 5 — Ch 35
Lipitor — Chs 31, 34 (atorvastatin)
LUMO — Chs 2, 19

M

Magic acid — Ch 11
Markovnikov rule — Ch 15
Mass spectrometry — Ch 6; App D
McLafferty rearrangement — Ch 6
Meisenheimer complex — Ch 23
Mendeleev — Ch 2
Meso compound — Ch 7
Metathesis (olefin) — Ch 37
Methane — Chs 2, 5
Mevalonate — Ch 34
Michael addition — Ch 29
Molecular orbital — Ch 2
Monomer — Ch 37
Morphine — Ch 9 (NMR), Ch 30 (alkaloid)
Mutarotation — Ch 32

N

N-bromosuccinimide (NBS) — Chs 18, 23
NADH — Ch 36
Named reactions — App F
Naphthalene — Ch 20
Negishi cross-coupling — Ch 37
Newman projection — Ch 5
NICS — Ch 20
Nitration — Ch 21
Nitrogen rule — Ch 6
NMR spectroscopy — Ch 9; App D
NOE / NOESY — Ch 9
Nomenclature (IUPAC) — Ch 4; App H
Nucleophile — Ch 3
Nucleophilic addition (C=O) — Ch 25
Nucleophilic acyl substitution — Ch 26

O

Olah, George — Ch 11 (superacids)
Optical activity — Ch 7
Orbital symmetry — Ch 39
Organometallic — Ch 37
Ortho/para vs meta — Ch 22
Oxidation — Ch 36
Oxidation state — Ch 36
Oxidative addition — Ch 37
Ozonolysis — Ch 16

P

Palladium (Pd) catalysis — Ch 37
Penicillin — Ch 26
Peptide bond — Ch 33
Pericyclic reactions — Ch 39
pH and pKa — Ch 3; App B
Pharmaceuticals — Chs 31, 35
Phenol — Chs 3, 22
Photoredox catalysis — Ch 40
Pi bond — Ch 2
Pinacol rearrangement — Ch 11
PLP (pyridoxal phosphate) — Ch 27
Polyethylene — Chs 18, 37
Polymer — Chs 26, 37
Polysaccharide — Ch 32
Predictive policing — (not applicable)
PROTAC — Ch 35
Protecting group — Ch 31
Pyridine vs pyrrole — Ch 20
Pyrolysis — Ch 18

Q

Quantum chemistry — Ch 2; App E
Quaternary ammonium salt — Ch 30
Quinoline — Ch 17 (Lindlar)

R

R/S configuration — Ch 7
Racemate / racemization — Chs 7, 8
Radical reactions — Ch 18
Rate-determining step — Ch 5
Reaction coordinate — Ch 5
Reductive amination — Chs 25, 30
Reductive elimination — Ch 37
Regiochemistry — Chs 15, 22
Resonance — Ch 2
Resolution — Ch 7
Retrosynthesis — Chs 14, 31, 38; App G
Ribozyme — Ch 33
Robinson annulation — Ch 29
Roberts (benzyne) — Ch 23
Ru catalysts (Grubbs) — Ch 37

S

Sandmeyer — Chs 22, 30
Saponification — Ch 26
Sawhorse projection — Ch 5
Schrock metathesis — Ch 37
Sharpless asymmetric epoxidation — Chs 8, 16, 36
Sharpless dihydroxylation — Ch 36
Sharpless, K. Barry (Nobel 2001, 2022) — Chs 8, 16, 36, 40
Sigma bond — Ch 2
Sigmatropic rearrangement — Ch 39
Silyl ether — Ch 31
Singlet/triplet carbene — Ch 39
Sitagliptin (Januvia) — Chs 37, 40
SN1, SN2, SNAr — Chs 10, 11, 23
Solvent effects — Ch 10
Solvolysis — Ch 11
Sonogashira coupling — Ch 37
sp/sp²/sp³ — Ch 2
Specific rotation — Ch 7
Spectroscopy — Chs 6, 9; App D
Spiro compound — Ch 5
SPPS (solid-phase peptide synthesis) — Ch 33
Staggered — Ch 5
Statins — Chs 31, 34
Stereoisomerism — Ch 7
Stereoselectivity vs stereospecificity — Ch 8
Steroids — Ch 29 (Robinson), Ch 34
Stork enamine — Chs 25, 29
Strychnine — Ch 38 (Woodward)
Substituent effects — Ch 22
Sulfonation — Ch 21
Sulfur ylide — Ch 25
Suprafacial / antarafacial — Ch 39
Suzuki coupling — Ch 37
Swern oxidation — Ch 36
Synthesis workshops — Chs 14, 31, 38
Synthon — Ch 31; App G

T

Tautomer — Ch 27
Terpene — Ch 34
Tetrahedral intermediate — Chs 25, 26
Thalidomide — Chs 1, 7, 8, 27 (α-lability), 35 (PROTAC arc closes)
Thiol — Ch 4
Total synthesis — Ch 38
Tosylate — Ch 10
Trans/cis — Ch 7
Transition state — Ch 5
Triterpene — Ch 34
Tu, Youyou (Nobel 2015) — Ch 38 (artemisinin)

U

Umpolung — Ch 27
UV-Vis — Ch 6; App D

V

Vinyl — Ch 15
Vitamin C, E — Ch 18
Vitamin D photochemistry — Ch 39
VSEPR — Ch 2

W

Walden inversion — Ch 10
Wheland intermediate (arenium) — Ch 21
Williamson ether synthesis — Ch 10
Wittig reaction — Ch 25
Wöhler (urea synthesis 1828) — Ch 1
Wolff-Kishner reduction — Ch 21
Woodward, R. B. — Chs 19, 38, 39 (Nobel 1965)
Woodward-Hoffmann rules — Chs 19, 39

X

X-ray crystallography — Ch 7 (early stereochem proofs), Ch 33 (proteins)

Y

Yield — App J
Ylide — Ch 25 (Wittig)

Z

Zaitsev rule — Ch 12
Ziegler-Natta — Ch 37
Zwitterion — Ch 33

Part 3 — Key concepts and where to find them

Aspirin synthesis — Ch 14 (workshop), Ch 26 (mechanism on alcohol/anhydride), Ch 35 (drug action on COX), Ch 21 case study (industrial).

Thalidomide arc — Ch 1 (introduction), Ch 7 (stereochemistry), Ch 8 (in-vivo racemization), Ch 27 (α-acidity explains racemization), Ch 35 (PROTAC comeback closes arc).

SN/E decision — Chs 10-13 (building blocks), Ch 14 (first applications), used throughout.

Retrosynthetic analysis — Chs 14, 31, 38 (three workshops, ascending difficulty).

Spectroscopy — Chs 6 (IR/MS), 9 (NMR), applied throughout. See App D for reference.

Aromaticity — Ch 20 (theory), Ch 21-23 (reactions), and revisited in heterocycle natural products (Chs 30, 34, 35).

Carbonyl chemistry (the heart of organic synthesis) — Chs 24-29 plus revisits in 32-34, 36-38.

Asymmetric catalysis (2001 Nobel theme) — Chs 8, 16 (Sharpless AE), 31 (atorvastatin), 36 (Sharpless AD), 37 (Noyori hydrogenation, sitagliptin), 38 (modern total synthesis), 40 (biocatalysis).

Green chemistry metrics — Ch 40 (definitions), Ch 21 (ibuprofen BHC case), Ch 37 (sitagliptin asymmetric hydrogenation), Ch 40 (sitagliptin biocatalysis).

Biology-chemistry interface — Ch 26 (β-lactams), Ch 28 (fatty acid biosynthesis), Chs 32-34 (sugars, peptides, lipids), Ch 35 (drug design), Ch 40 (biocatalysis).

Use this index to navigate the book's ~415K words. Most concepts are mapped to a primary chapter and recur in 2-5 later chapters. Bold cross-references to appendices: glossary for definitions, App F for named reactions, App G for retrosynthesis disconnections, App B for pKa, App D for spectroscopy.