Chemistry of carbon compounds: functional groups, hydrocarbons, aromaticity, stereochemistry, reaction mechanisms (SN1/SN2/E1/E2), and carbonyl chemistry. Organic chemistry is the substrate of biochemistry.
organic-chemistry
Functional group
A specific arrangement of atoms within an organic molecule responsible for its characteristic chemical behaviour (e.g. hydroxyl -OH,…
Hydrocarbon
Molecule composed exclusively of carbon and hydrogen. Divided into aliphatic (alkanes, alkenes, alkynes) and aromatic hydrocarbons. The…
Aromaticity (Hückel rule)
A cyclic, planar, fully-conjugated molecule with (4n+2) π electrons exhibits extra thermodynamic stability and a characteristic ring…
Stereochemistry
Study of the three-dimensional arrangement of atoms in molecules. Includes configurational isomerism (R/S, E/Z), chirality, and…
Chirality
Property of a molecule that is non-superposable on its mirror image. The two mirror-image forms are enantiomers; they share identical…
SN2 mechanism
Bimolecular nucleophilic substitution: a nucleophile attacks carbon from the opposite face of a leaving group in a single concerted step,…
Carbonyl chemistry
Chemistry of the C=O functional group (aldehydes, ketones, carboxylic-acid derivatives). The polarised C=O makes the carbon electrophilic,…
Retrosynthetic analysis
Corey's planning framework for organic synthesis: work backward from the target molecule by applying disconnections (bond breaks) to reveal…
Alcohol (-OH)
Carbon bearing a hydroxyl group. Classified primary/secondary/tertiary by substitution at the C. Substrate for oxidation to carbonyls and…
Ether (C-O-C)
Two carbon groups bonded through an oxygen. Chemically inert relative to alcohols/carbonyls; common solvents (diethyl ether, THF).
Ester (-COOR)
Carboxylic-acid derivative in which the acidic H is replaced by an alkyl/aryl group. Key linkage in fats, waxes, and biodegradable polymers.
Amide (-CONR₂)
Carboxylic-acid derivative with N replacing OH. Rotationally restricted C-N bond (partial-double-bond character). The backbone-forming…
Amine (-NR₂)
Nitrogen-centred functional group derived from ammonia. Primary/secondary/tertiary by substitution. Basic (lone pair on N), nucleophilic.
Carboxylic acid (-COOH)
Carbonyl bearing a hydroxyl — the most acidic common organic functional group (pKa ≈ 4-5). Parent of esters, amides, acid chlorides, and…
Thiol (-SH)
Sulfur analogue of alcohol. Strong nucleophile/reducing agent; forms disulfide bridges (-S-S-) crucial to protein tertiary structure.
Alkene C=C double bond
Carbon-carbon σ + π bond. Locus of addition reactions (Markovnikov, hydrogenation, halogenation) and of E/Z geometric isomerism.
Alkyne C≡C triple bond
Carbon-carbon σ + 2π triple bond. Linear geometry at the sp-hybridised carbons; terminal alkynes are weakly acidic (pKa ≈ 25).
Alkane (saturated hydrocarbon)
Acyclic saturated hydrocarbon with formula CₙH₂ₙ₊₂; every carbon sp³-hybridized, all bonds single (σ only). Homologous series: methane…
Isomerism
The phenomenon of two or more distinct compounds sharing the same molecular formula but differing in structure. Two broad families: (1)…
Retrosynthetic analysis
Corey's disconnection approach; synthons, FGIs; target-oriented synthesis planning; 1990 Nobel.
Protecting groups (TBS, Boc, benzyl, acetal)
Temporarily mask reactive FGs; orthogonal deprotection; Greene's handbook; standard practice in multi-step synthesis.
CIP priority & R/S nomenclature
Cahn-Ingold-Prelog: assign priorities by atomic number, then substituents; R clockwise, S counterclockwise; E/Z alkene geometry.
Prochirality and re/si faces
Prochiral center becomes chiral upon substitution; faces re/si by CIP; enzymes discriminate via stereogenic environment.
Cram/Felkin–Anh model
Predicts diastereoselectivity in nucleophilic addition to α-stereocenter; largest group antiperiplanar to incoming Nu.
Zimmerman–Traxler model (aldol)
Chair-like 6-membered TS predicts E/Z → syn/anti in aldol; Evans auxiliaries exploit it for ee.
Curtin–Hammett (stereo)
Product ratio from rapidly interconverting stereoisomers reflects ΔG‡, not populations; guides asymmetric catalysis.
Frontier molecular orbital theory
HOMO-LUMO interactions dominate reactivity; normal/inverse electron-demand DA; predicts regio/stereoselectivity; Fukui 1981 Nobel.
Baldwin rules for ring closure
Endo/exo-tet/trig/dig classification; favored vs disfavored ring closures by orbital alignment.
Markovnikov & anti-Markovnikov additions
HX adds to alkene via more-stable carbocation; radical HBr, hydroboration give anti-Markovnikov; regioselectivity rationale.
SN1/SN2/E1/E2 mechanisms
Concerted vs stepwise; Hammond, solvent effects, substrate/base strength govern which pathway dominates; kinetic signatures.
Stille/Suzuki/Negishi cross-couplings
Pd-catalyzed C-C coupling; Suzuki uses ArB(OH)₂, Stille ArSnR₃, Negishi ArZnX; 2010 Nobel.
Buchwald–Hartwig amination
Pd-cat aryl C-N bond formation from ArX + HNR₂ with base; bulky phosphines (BrettPhos, tBuXPhos); workhorse in medchem.
Olefin metathesis (Grubbs/Schrock)
Ru/Mo carbene catalysts interconvert C=C; cross, ring-closing, ring-opening variants; 2005 Nobel.
C–H activation & directing groups
Transition-metal-mediated selective C-H functionalization; pyridine, amide DGs; step-economical alternative to prefunctionalization.
Click chemistry (CuAAC)
Cu-cat azide-alkyne cycloaddition gives 1,4-triazoles; bioorthogonal; 2022 Nobel (Sharpless, Meldal, Bertozzi).
Asymmetric hydrogenation (Knowles/Noyori)
Rh/Ru with chiral phosphines (BINAP) reduce prochiral alkenes/ketones with >90% ee; L-DOPA synthesis; 2001 Nobel.
Sharpless asymmetric epoxidation
Ti(Oi-Pr)₄ + diethyl tartrate + TBHP epoxidizes allylic alcohols with high ee; mnemonic for face selection.
Organocatalysis (List, MacMillan)
Proline-cat aldol, enamine/iminium LUMO-lowering; 2021 Nobel; broad asymmetric C-C bond formation.
Photoredox in organic synthesis
Visible-light PC generates radicals for C-C, C-N bond formation; merger with Ni catalysis (metallaphotoredox) enabling.
Heck reaction (mechanism)
Pd(0) → oxidative addition ArX → syn insertion into alkene → β-hydride elimination → reductive elimination; 2010 Nobel.
Aldol reaction & Evans chiral auxiliary
Enolate + carbonyl → β-hydroxy carbonyl; kinetic/thermodynamic enolate control; Evans oxazolidinone auxiliary for syn/anti ee.
Mannich & Strecker reactions
Mannich: aldehyde+amine+enol → β-aminocarbonyl; Strecker: RCHO+NH₃+HCN → α-amino nitrile; amino-acid synthesis.
Wittig & McMurry olefinations
Wittig: Ph₃P=CR₂ + R'CHO → alkene; McMurry: TiCl₃/Zn pinacol coupling of ketones; both give defined C=C geometry.