Glossary of abbreviations and terms

Plain-language explanations of the abbreviations, reagents, solvents, protecting groups and concepts that appear in reaction mechanisms. In the interactive app, these are explained next to the step where they appear.

Symbols (12)

Ar / Ar′: Aryl group. Any aromatic ring substituent such as phenyl.
B: / B⁻: Base. A proton acceptor.
EDG: Electron-donating group. A substituent (OR, NR₂, alkyl) that pushes electron density in, stabilising cations and activating rings toward electrophiles.
EWG: Electron-withdrawing group. A substituent (C=O, NO₂, CN…) that pulls electron density away, stabilising anions and activating electrophiles.
E+ / E⁺: Electrophile. An electron-poor species that accepts an electron pair.
HA: Generic acid. A proton donor.
X: Halogen / leaving group. Cl, Br or I (sometimes any leaving group).
LG: Leaving group. The group that departs with the bonding electrons (good ones are weak bases: I⁻, Br⁻, TsO⁻…).
L / Ln: Ligand. A Lewis-base group (often a phosphine) bound to a metal centre.
M: Metal. A generic metal centre.
Nu / Nu:: Nucleophile. An electron-rich species that donates an electron pair to form a new bond.
R / R′: R group. Any carbon substituent (alkyl, aryl…) whose identity does not matter for the mechanism.

Groups (29)

OAc: Acetoxy. –OC(=O)CH₃, an acetate group.
Ac: Acetyl. –C(=O)CH₃.
Bz: Benzoyl. –C(=O)C₆H₅.
Bn: Benzyl. –CH₂C₆H₅.
Bu / n-Bu: Butyl. –(CH₂)₃CH₃.
Cy: Cyclohexyl. –C₆H₁₁.
Cp: Cyclopentadienyl. A five-carbon aromatic ring ligand (C₅H₅⁻) that binds metals through all five carbons.
OEt: Ethoxy. –OCH₂CH₃.
Et: Ethyl. –CH₂CH₃.
i-Pr / iPr: Isopropyl. –CH(CH₃)₂.
Mes: Mesityl. 2,4,6-trimethylphenyl, a bulky aryl group.
Ms: Mesyl. Methanesulfonyl (CH₃SO₂–).
OMs: Mesylate. Methanesulfonate ester – an excellent leaving group.
OMe: Methoxy. –OCH₃.
Me: Methyl. –CH₃.
Cp*: Pentamethylcyclopentadienyl. A bulkier, more electron-rich Cp ligand (C₅Me₅).
Ph: Phenyl. –C₆H₅.
Pr / n-Pr: Propyl. –CH₂CH₂CH₃.
t-Bu / tBu: tert-Butyl. –C(CH₃)₃, a bulky group.
TBS / TBDMS: tert-Butyldimethylsilyl. A robust silyl protecting group for alcohols.
TBDPS: tert-Butyldiphenylsilyl. A very robust silyl protecting group.
Tol: Tolyl. Methyl-substituted phenyl.
Ts: Tosyl. p-Toluenesulfonyl (p-CH₃C₆H₄SO₂–).
OTs: Tosylate. p-Toluenesulfonate ester – an excellent leaving group.
TES: Triethylsilyl. –SiEt₃ silyl protecting group.
OTf: Triflate. Trifluoromethanesulfonate – among the best leaving groups.
Tf: Triflyl. Trifluoromethanesulfonyl (CF₃SO₂–).
TIPS: Triisopropylsilyl. A very bulky silyl protecting group.
TMS: Trimethylsilyl. –Si(CH₃)₃; a small silicon group used to protect or activate.

Protecting groups (9)

Troc: 2,2,2-Trichloroethoxycarbonyl. Amine protecting group removed with zinc.
SEM: 2-(Trimethylsilyl)ethoxymethyl. Protecting group removed with fluoride.
Alloc: Allyloxycarbonyl. Amine protecting group removed with Pd(0).
Cbz: Carboxybenzyl. Amine protecting group removed by hydrogenolysis.
Fmoc: Fluorenylmethoxycarbonyl. Base-labile amine protecting group (removed with piperidine).
MOM: Methoxymethyl. Acetal-type alcohol protecting group removed with acid.
PMB: p-Methoxybenzyl. Benzyl-type protecting group removable by oxidation (DDQ/CAN).
Boc: tert-Butoxycarbonyl. Acid-labile amine protecting group (removed with TFA).
THP: Tetrahydropyranyl. Acetal-type alcohol protecting group removed with mild acid.

Solvents (20)

DCE: 1,2-Dichloroethane. Higher-boiling chlorinated solvent.
DMPU: 1,3-Dimethyl-3,4,5,6-tetrahydro-2(1H)-pyrimidinone. A safer HMPA substitute that frees up anions.
AcOH / HOAc: Acetic acid. Weak acid and polar protic solvent.
MeCN / CH3CN: Acetonitrile. Polar aprotic solvent.
DCM / CH2Cl2: Dichloromethane. Common non-polar-ish solvent for reactions that need no nucleophilic or protic solvent.
Et2O / Et₂O: Diethyl ether. Low-boiling ether solvent, classic for Grignard reagents.
DMSO: Dimethyl sulfoxide. Polar aprotic solvent; also the oxidant in Swern/Kornblum-type reactions.
EtOH: Ethanol. Polar protic solvent.
EtOAc: Ethyl acetate. Moderately polar solvent.
TFE / HFIP: Fluorinated alcohols. Strongly H-bond-donating, non-nucleophilic solvents that stabilise cations.
HMPA: Hexamethylphosphoramide. Very strongly cation-solvating polar aprotic additive (carcinogenic; DMPU is a safer substitute).
MeOH: Methanol. Polar protic solvent (also a nucleophile in solvolysis).
MTBE: Methyl tert-butyl ether. A safer, peroxide-resistant ether solvent.
DMA / DMAc: N,N-Dimethylacetamide. High-boiling polar aprotic solvent.
DMF: N,N-Dimethylformamide. Polar aprotic solvent – dissolves ionic nucleophiles but does not H-bond to them, speeding SN2 and SNAr.
NMP: N-Methyl-2-pyrrolidone. High-boiling polar aprotic solvent.
py / pyr: Pyridine. Weak amine base / nucleophilic catalyst and solvent.
THF: Tetrahydrofuran. Cyclic ether solvent; its oxygen lone pairs solvate Li⁺/Mg²⁺ so organometallics stay dissolved and reactive.
PhMe: Toluene. Non-polar aromatic solvent.
TFA: Trifluoroacetic acid. A strong organic acid (pKa ≈ 0.5), used to remove Boc groups and protonate carbonyls.

Bases (25)

DABCO: 1,4-Diazabicyclo[2.2.2]octane. Unhindered tertiary amine, a good nucleophilic catalyst (Baylis–Hillman).
DBN: 1,5-Diazabicyclo[4.3.0]non-5-ene. Amidine base similar to DBU.
DBU: 1,8-Diazabicyclo[5.4.0]undec-7-ene. Strong, non-nucleophilic amidine base (pKaH ≈ 12 in water, 24 in MeCN) used for E2.
DMAP: 4-Dimethylaminopyridine. Hypernucleophilic acyl-transfer catalyst – forms a very reactive N-acylpyridinium.
Cs2CO3 / Cs₂CO₃: Cesium carbonate. Mild, soluble inorganic base (the “cesium effect”).
LiTMP: Lithium 2,2,6,6-tetramethylpiperidide. An even bulkier lithium amide base.
LDA: Lithium diisopropylamide. Strong (pKa ≈ 36), bulky, non-nucleophilic base that makes kinetic enolates quantitatively.
LiHMDS: Lithium hexamethyldisilazide. Strong, bulky, non-nucleophilic base (pKa ≈ 26).
TMEDA: N,N,N′,N′-Tetramethylethylenediamine. Chelates Li⁺ and breaks up RLi aggregates, making them more reactive.
DIPEA / DIEA: N,N-Diisopropylethylamine (Hünig’s base). Hindered, non-nucleophilic amine base.
n-BuLi / BuLi: n-Butyllithium. Very strong base/nucleophile (pKa of butane ≈ 50); deprotonates alkynes and does lithium–halogen exchange.
K2CO3 / K₂CO₃: Potassium carbonate. Mild inorganic base.
KHMDS: Potassium hexamethyldisilazide. Strong, bulky base that favours more reactive (“naked”) enolates.
KH: Potassium hydride. Stronger/faster relative of NaH.
KOH: Potassium hydroxide. Strong aqueous/alcoholic base.
KOtBu / t-BuOK: Potassium tert-butoxide. Strong, bulky alkoxide base – favours elimination over substitution.
s-BuLi: sec-Butyllithium. Strong organolithium base.
NaNH2 / NaNH₂: Sodium amide. Very strong base (pKa of NH₃ ≈ 38); makes acetylides and arynes.
NaOEt / EtONa: Sodium ethoxide. Alkoxide base matched to ethyl esters (avoids transesterification).
NaHMDS: Sodium hexamethyldisilazide. Strong, bulky, non-nucleophilic base.
NaH: Sodium hydride. Insoluble, irreversible base: removes H⁺ and bubbles off H₂.
NaOH: Sodium hydroxide. Strong aqueous base and nucleophile.
NaOMe: Sodium methoxide. Alkoxide base matched to methyl esters.
t-BuLi: tert-Butyllithium. Extremely strong, pyrophoric organolithium.
Et3N / TEA: Triethylamine. Common tertiary-amine base that scavenges HCl.

Reducing agents (13)

9-BBN: 9-Borabicyclo[3.3.1]nonane. Bulky borane giving very regioselective hydroboration.
BH3 / BH₃: Borane. Electron-deficient Lewis acid that adds H–B across alkenes.
DIBAL-H / DIBAL: Diisobutylaluminium hydride. Bulky hydride; at –78 °C stops esters at the aldehyde stage.
H2 / H₂: Hydrogen gas. Reductant for catalytic hydrogenation.
LiAlH4 / LAH: Lithium aluminium hydride. Powerful hydride (H⁻) donor; reduces esters, acids, amides to alcohols/amines.
LiBH4: Lithium borohydride. Hydride donor that reduces esters, unlike NaBH₄.
Pd/C: Palladium on carbon. Heterogeneous hydrogenation catalyst.
SmI2 / SmI₂: Samarium diiodide. Mild one-electron reductant.
NaBH4: Sodium borohydride. Mild hydride donor; reduces aldehydes and ketones but not esters.
NaBH3CN: Sodium cyanoborohydride. Mild reductant stable at pH 3–6; reduces iminium ions selectively (reductive amination).
NaBH(OAc)3 / STAB: Sodium triacetoxyborohydride. Mild, selective hydride donor for reductive aminations.
Bu3SnH / Bu₃SnH: Tributyltin hydride. Radical H-atom donor (weak Sn–H bond).
Zn(Hg): Zinc amalgam. Reductant for the Clemmensen reduction.

Oxidants (19)

TEMPO: 2,2,6,6-Tetramethylpiperidine N-oxyl. Stable nitroxyl radical used as a catalyst for alcohol oxidation.
DDQ: 2,3-Dichloro-5,6-dicyano-1,4-benzoquinone. Strong hydride-abstracting quinone oxidant.
IBX: 2-Iodoxybenzoic acid. Hypervalent-iodine oxidant.
AIBN: Azobisisobutyronitrile. Radical initiator: on heating releases N₂ and two 2-cyano-2-propyl radicals.
BPO: Benzoyl peroxide. Radical initiator that cleaves at the weak O–O bond.
CAN: Ceric ammonium nitrate. One-electron Ce(IV) oxidant.
DMP: Dess–Martin periodinane. Mild hypervalent-iodine oxidant for alcohols.
H2O2 / H₂O₂: Hydrogen peroxide. Oxidant; its anion HOO⁻ is an excellent nucleophile.
mCPBA: meta-Chloroperoxybenzoic acid. Peracid that transfers an electrophilic oxygen (epoxidation, Baeyer–Villiger).
NBS: N-Bromosuccinimide. Source of a low, steady concentration of Br₂/Br• for allylic/benzylic bromination.
NCS: N-Chlorosuccinimide. Electrophilic chlorine source.
NIS: N-Iodosuccinimide. Electrophilic iodine source.
NMO: N-Methylmorpholine N-oxide. Co-oxidant that reoxidises Os(VI) to Os(VIII).
OsO4 / OsO₄: Osmium tetroxide. Adds syn across alkenes to give diols (via a cyclic osmate ester).
KMnO4 / KMnO₄: Potassium permanganate. Strong oxidant: diols (cold, basic) or cleavage (hot).
Oxone: Potassium peroxymonosulfate. Inexpensive solid peracid-type oxidant.
PCC: Pyridinium chlorochromate. Mild Cr(VI) oxidant: alcohols stop at aldehydes/ketones.
PDC: Pyridinium dichromate. Mild Cr(VI) oxidant.
TBHP: tert-Butyl hydroperoxide. Oxidant/oxygen donor (Sharpless epoxidation).

Reagents (28)

CDI: 1,1′-Carbonyldiimidazole. Activates acids as acyl imidazoles; phosgene substitute.
HATU: 1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxide hexafluorophosphate. Highly efficient peptide-coupling reagent.
EDC / EDCI: 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide. Water-soluble carbodiimide coupling agent.
HOBt: 1-Hydroxybenzotriazole. Additive that suppresses racemisation in amide coupling.
Ac2O / Ac₂O: Acetic anhydride. Acetylating agent.
AlCl3 / AlCl₃: Aluminium chloride. Strong Lewis acid for Friedel–Crafts reactions.
BF3 / BF₃: Boron trifluoride. Lewis acid (usually as the Et₂O complex).
TMSCl: Chlorotrimethylsilane. Silylating agent.
DCU: Dicyclohexylurea. Insoluble by-product of DCC couplings.
DEAD: Diethyl azodicarboxylate. Mitsunobu oxidant: picks up PPh₃ to form a betaine.
DIAD: Diisopropyl azodicarboxylate. Mitsunobu oxidant, handier than DEAD.
HBr: Hydrobromic acid. Strong acid; bromide is a good nucleophile.
HCl: Hydrochloric acid / hydrogen chloride. Strong acid; chloride is the nucleophile in additions/substitutions.
FeBr3 / FeBr₃: Iron(III) bromide. Lewis acid catalyst for aromatic bromination.
Lewis acid: Lewis acid. Electron-pair acceptor (AlCl₃, BF₃, TiCl₄…) that activates carbonyls and halides.
MsCl: Methanesulfonyl chloride. Turns an alcohol OH into a good leaving group (mesylate).
DCC: N,N′-Dicyclohexylcarbodiimide. Dehydrating coupling agent: activates RCO₂H as an O-acylisourea; byproduct DCU precipitates.
TsOH / p-TsOH: p-Toluenesulfonic acid. Strong organic acid catalyst, soluble in organic solvents.
TsCl: p-Toluenesulfonyl chloride. Turns an alcohol OH into a good leaving group (tosylate).
PBr3 / PBr₃: Phosphorus tribromide. Converts alcohols to bromides by SN2.
POCl3 / POCl₃: Phosphoryl chloride. Dehydrating/chlorinating agent (Vilsmeier, Bischler–Napieralski).
H2SO4 / H₂SO₄: Sulfuric acid. Strong acid and dehydrating agent.
TBAF: Tetrabutylammonium fluoride. Soluble fluoride source; strong Si–F bond cleaves silyl ethers.
SOCl2 / SOCl₂: Thionyl chloride. Converts acids/alcohols to chlorides; byproducts SO₂ and HCl leave as gases.
TiCl4 / TiCl₄: Titanium tetrachloride. Strong, oxophilic Lewis acid that chelates carbonyls.
Tf2O / Tf₂O: Triflic anhydride. Powerful triflating agent.
PPh3 / PPh₃: Triphenylphosphine. Nucleophilic phosphine; forms very strong P=O bonds, driving Wittig, Appel and Mitsunobu reactions.
TPPO / Ph3P=O: Triphenylphosphine oxide. The thermodynamic sink of Wittig/Mitsunobu/Appel reactions.

Catalysts (9)

CuI: Copper(I) iodide. Co-catalyst for Sonogashira, Ullmann and click chemistry.
CuAAC: Copper-catalysed azide–alkyne cycloaddition. The copper-catalysed “click” reaction giving 1,4-triazoles.
dba: Dibenzylideneacetone. Weakly bound alkene ligand on Pd(0).
Grubbs: Grubbs catalyst. Ruthenium carbene catalyst for olefin metathesis.
NHC: N-Heterocyclic carbene. A strongly σ-donating carbene ligand/organocatalyst (e.g. in the Stetter and Breslow chemistry).
Pd(OAc)2 / Pd(OAc)₂: Palladium(II) acetate. Pd(II) pre-catalyst, reduced in situ to Pd(0).
Pd(PPh3)4 / Pd(PPh₃)₄: Tetrakis(triphenylphosphine)palladium(0). Classic Pd(0) pre-catalyst for cross-coupling.
Pd2(dba)3 / Pd₂(dba)₃: Tris(dibenzylideneacetone)dipalladium(0). Air-stable source of Pd(0).
Wilkinson / Wilkinson’s: Wilkinson’s catalyst, RhCl(PPh₃)₃. Homogeneous hydrogenation catalyst.

Ligands (9)

dppf: 1,1′-Bis(diphenylphosphino)ferrocene. Bidentate phosphine with a large bite angle.
dppe: 1,2-Bis(diphenylphosphino)ethane. Bidentate phosphine ligand.
COD: 1,5-Cyclooctadiene. Labile diene ligand.
bipy / bpy: 2,2′-Bipyridine. Bidentate N,N-ligand.
BINAP: 2,2′-Bis(diphenylphosphino)-1,1′-binaphthyl. Chiral bidentate phosphine for asymmetric catalysis.
acac: Acetylacetonate. Bidentate O,O-chelating ligand.
CO: Carbon monoxide (carbonyl ligand). σ-donor / strong π-acceptor ligand; also a C1 building block.
L2 / Ln: Ligand set. Spectator ligands on the metal that tune its reactivity.
PPh3 / PPh₃: Triphenylphosphine. A common phosphine ligand (σ-donor, π-acceptor).

Concepts (39)

pKa: Acid-dissociation constant (–log). Lower pKa = stronger acid; used to judge which proton a base removes.
anti-Markovnikov: Anti-Markovnikov. The opposite regiochemistry (radical HBr addition, hydroboration).
ATRP: Atom-transfer radical polymerisation. Controlled polymerisation via reversible halogen-atom transfer to Cu(I).
E2: Bimolecular elimination. Concerted base removal of β-H and loss of the leaving group (anti-periplanar).
SN2: Bimolecular nucleophilic substitution. One concerted step with backside attack and inversion; rate = k[RX][Nu].
CMD: Concerted metalation–deprotonation. C–H activation where a carboxylate shuttles the proton as the C–M bond forms.
dr: Diastereomeric ratio. Ratio of diastereomers formed.
EAS: Electrophilic aromatic substitution. An electrophile replaces H on an arene via a Wheland intermediate.
E1cB / E1cb: Elimination, unimolecular conjugate base. Deprotonation first to a carbanion, then loss of the leaving group.
ee: Enantiomeric excess. How much more of one enantiomer than the other is present.
FMO: Frontier molecular orbital. HOMO/LUMO analysis of which orbitals interact.
HSAB: Hard–soft acid–base. Soft nucleophiles prefer soft electrophilic sites (1,4-addition); hard ones prefer hard sites (1,2-addition).
Δ: Heat. Reaction is run at elevated temperature.
HOMO: Highest occupied molecular orbital. The orbital that donates electrons in a reaction.
Hofmann: Hofmann product/rule. Elimination giving the less substituted alkene (bulky base or leaving group).
HAT: Hydrogen-atom transfer. A radical abstracts H• from a C–H or X–H bond.
hν: Light. Photochemical activation.
LUMO: Lowest unoccupied molecular orbital. The orbital that accepts electrons in a reaction.
Markovnikov: Markovnikov’s rule. In HX addition, H goes to the carbon with more H’s so the more stable cation forms.
Meisenheimer: Meisenheimer complex. The anionic cyclohexadienyl intermediate of SNAr stabilised by electron-withdrawing groups.
SNAr: Nucleophilic aromatic substitution. Addition–elimination at an electron-poor arene via a Meisenheimer complex.
OA: Oxidative addition. A metal inserts into a bond (e.g. Ar–X), raising its oxidation state by two.
π*: Pi antibonding orbital. The empty orbital of a C=O or C=C that accepts nucleophiles.
PCET: Proton-coupled electron transfer. Concerted transfer of an electron and a proton.
RE: Reductive elimination. Two groups on a metal couple and leave, lowering the oxidation state by two.
RAFT: Reversible addition–fragmentation chain transfer. Controlled radical polymerisation with thiocarbonylthio agents.
RCM: Ring-closing metathesis. Intramolecular olefin metathesis forming a ring.
ROMP: Ring-opening metathesis polymerisation. Polymerisation of strained cycloalkenes with a metal carbene.
rt: Room temperature. About 20–25 °C.
σ*: Sigma antibonding orbital. The empty orbital an incoming nucleophile attacks in SN2 (the back lobe of C–LG).
SET: Single-electron transfer. Movement of one electron (not a pair), generating radicals/radical ions.
SOMO: Singly occupied molecular orbital. The half-filled orbital of a radical.
SN2′: SN2-prime (allylic). Nucleophile attacks the alkene terminus with allylic transposition.
TS / TS‡: Transition state. The highest-energy point on the pathway between two minima; it cannot be isolated.
TM: Transmetalation. Transfer of an organic group from one metal (B, Sn, Zn, Cu) to another (Pd).
E1: Unimolecular elimination. Carbocation forms first, then a base removes a β-H.
SN1: Unimolecular nucleophilic substitution. Two steps: leaving group departs (rate-determining) to give a carbocation, then nucleophile attacks.
Wheland / σ-complex: Wheland intermediate (arenium ion). The cyclohexadienyl cation formed when an electrophile adds to a benzene ring.
Zaitsev / Zaitsev’s: Zaitsev’s rule. Elimination usually gives the more substituted (more stable) alkene.

Biochemistry (17)

ADP: Adenosine diphosphate. ATP after losing one phosphate.
ATP: Adenosine triphosphate. The cell’s energy currency; transfers phosphate groups.
Asp: Aspartate. Acidic amino acid.
CoA / CoA-SH: Coenzyme A. Thiol carrier that forms high-energy thioesters (acetyl-CoA).
dNTP: Deoxynucleoside triphosphate. DNA building block.
DNA: Deoxyribonucleic acid. The genetic polymer.
FAD / FADH2: Flavin adenine dinucleotide. Two-electron/one-electron redox coenzyme.
GAPDH: Glyceraldehyde-3-phosphate dehydrogenase. Glycolytic enzyme oxidising G3P with NAD⁺.
His: Histidine. Amino acid whose imidazole acts as acid/base catalyst.
Lys: Lysine. Basic amino acid with a nucleophilic –NH₂.
NADP / NADPH: NADP⁺ / NADPH. Phosphorylated NAD cousin used mainly in biosynthetic reductions.
NAD+ / NAD⁺: Nicotinamide adenine dinucleotide (oxidised). Hydride-accepting coenzyme in oxidations.
NADH: Nicotinamide adenine dinucleotide (reduced). Hydride-donating coenzyme.
PFK-1: Phosphofructokinase-1. The key regulated, committed step of glycolysis.
RNase: Ribonuclease. Enzyme that cleaves RNA.
RNA: Ribonucleic acid. Single-stranded nucleic acid.
Ser: Serine. Amino acid with a nucleophilic –OH.