Common Sense Organic Chemistry

Glossary – Explanations of Terms in Organic Chemistry

Glossary of Terms

Organic Chemistry Glossary

Glossary of Terms

Δ – heat applied temperature not otherwise specified. Also, thermal pericyclic reaction (in contrast to photochemical).

↑↓ – reflux; reaction run at the boiling point of solvent using a condenser to prevent loss of solvent

(+)   (also dextrorotatory) – the absolute stereochemistry of a molecule; the direction a molecule rotates the plane of polarized light to the right

(-)    (also levorotatory) – the absolute stereochemistry of a molecule; the direction a molecule rotates the plane of polarized light to the left

1,2-addition (direct addition) –  the addition of an electrophile to a conjugated diene that results  in a kinetic product; the addition of a (usually hard) nucleophile to the carbonyl carbon of a Michael acceptor or (enone/enoate).

[1,2]-hydride shift – the rapid and energetically favorable movement of a hydrogen atom and two electrons into the bonding orbital of a carbocation to create a more stable (highly substituted) carbocation

[1,2]-alkyl shift – Similar to a [1,2]-hydride shift, instead of carbon, a neighboring carbon migrates. Also known as a Wagner-Meerwein Rearrangement

1º, 2º, 3º, 4º – primary, secondary, tertiary, quaternary. Here, this is the amount of substitution a carbon has to other carbons.

[1,3] migration

1,4-addition (conjugate addition)

[1,5] migration

[1,7] migration

[2+2] cycloaddition

[3+2] cycloaddition

[4+2] cycloaddition – the Diels-Alder reaction – the reaction of a diene and a dienophile to form a cyclohexene by a thermal pericyclic reaction.

9-BBN – an easier to handle and more selective form of BH3, borane; often used to make vinyl boranes

absolute – pure, neat, without solvent or solute

absolute configuration – the natural stereochemistry of a chiral biologically active substance; also the designation of R and S to stereogenic centers

absorbance spectrum

acetal – doubly RO-substituted aldehydes and ketones

Acetoacetic Ester Synthesis

acetylene

acetylide

Anion

achiral

acid anhydride

acid-catalyzed

acid halide (also Acyl halide)

acid

ionization constant (Ka)

Activated Charcoal (Norit); decolorizer

activation energy

activating group (EDG)

actual yield (% yield)

acyl group    (also acetyl when = ‘Ac’)

acylation reactions

acylium ion

Adenine (A)

Adenosine

Addition Reaction

adsorption

Alanine (ala or A)

alcohol (ROH)

alcoholysis

aldehyde

aldohexose

Aldol reaction

Aldol condensation

aldose

alkali metal

alkaline

Alkaline Earth Metal

alkaloid

alkane

alkene

alkyne

alkoxides

alkyl group/substituent

alkyl halide (R-X)

allene (1,2- or cumulated diene)

allyl group/position

allylic carbocations

allylic position

amino acid

α-anomer or epimer

α-carbon (carbon attacked to functionality)

alpha-helix

anisotropy

amalgam

ambident

amide

amine

amine oxide

amu (Dalton)angle strain

anhydrides, of acids

anhydrous

anion

annealing

anomer

anomeric carbon

anomeric effect (negative hyperconjugation)

anti

anti addition

Anti-Markovnikov Addition/regiochemistry

anti-periplanar

anti-aromaticity

antibiotic

anti-bonding molecular orbital

aprotic (solvent)

aqueous

arenium ion/intermediate

Arginine (Arg or R)

Arrhenius Equation/Constant/Acid-Base

Aryl or Ar- (aromatic substituent)

Aryl halide (Ar-X)

Asparigine (Asn or Q)

Aspartic Acid/Aspartate (Asp or E)

asymmetric (chiral)

asymmetric stretch/bend

Atomic Mass

Atomic Number

atomic orbital

atomic radius

ATP (adenosine triphosphate)

Avagadro’s Number (6.022 x 10-23)

axial

azeotrope

azide

aziridine

Azimuthal Quantum Number

diazo coupling

backside attack

Baeyer-Villiger Oxidation

banana bonds (Walsh cyclopropane)base (Brønsted or Lewis)

base-catalyzed

base pairing

Bond Dissociation Energy (BDE)

bending mode (IR)

benzylic carbocation

Benzyl group (PhCH2-)

Benzylic Position

Benzyne

ß-anomer

ß-carbon

ß-elimination

betaine

ß-pleated sheet

bicyclic (bridged or spiro-)bimolecular (2nd order)biosynthesis

boat conformation

boiling point (BP)bond angle

bond dipole

bond length

bond order

bond rotation

bond stretch

bond-line structure

Bonding Molecular Orbital (σ or π)

borane

branching

bridged

bromination

Brønsted Acid-Base Theory/Definition

butyl

Cahn-Ingold-Prelog (C-I-P) Rules

carbanion

carbocation or carbenium

carbohydrate (CH2O)nCarbon-13 NMR

carbonyl (C=O)carboxylate (-CO<2)carboxylic acid (-CO2H)carboxylic acid derivative

canonical form (or mesomer)

catalyst

catalytic hydrogenation

Chain Initiation

Chain Propagation

Chain Termination

Chair conformation

Chair flip (Cyclohexane(Chemical shift (δ) [ppm]

chirality

chiral (asymmetric) center

chlorination

cholesterol

chromatography

cis-Claisen CondensationClaisen Rearrangement

Clemmensen Reduction

combustion

concerted (synchronous) reaction

condensation reaction

condensed formula

configuration

configurational isomers

conformation

conformational isomers

conformer

conjugate acid

conjugate base

conjugation

constitutional isomers

coordination compounds

coupling

coupling constant (J) [Hz]

covalent bond

crown ethers

cuprates

curved arrow

Cycloaddition reaction

Cycloalkane

Cyclobutadiene

Cyclooctatetraene

Cyclopentadienyl anion

Cyclopentadienyl cation

Cyclopropane

Cyclopropenyl cation

Cysteine (Cys or C)

Cystine bridge (Cys-Cys)

Cytosine (C)d- (same as (+))D- (dextrorotatory)Dalton [Da] or [amu]deactivating group

deactivator

decarboxylation

decomposition

degenerate

delocalization

Deoxyribonucleic Acid

Deprotection / Deblocking

deprotonate/deprotonation

DEPT

deshielded (downfield)

desolvation or dissolution

destructive interference

detergent

detonation

Deuterium (“heavy” Hydrogen) 2H

Dewar Benzene

Dextrorotatory (D or d or +)

dextrose (D-glucose)

diastereomer

diatomic< A2/td>diaxial interaction

diazonium ion

diazonium salt

diazotization

DIBAL or DIBAL-H

dichloromethane  (methylene chloride)

dichromate

Dieckmann Condensation

dielectric constant

Diels-Alder Reaction; [4+2] cycloaddition

diene

dieneophile

diethyl ether (Et2O

diffraction

Diffraction Pattern

dihedral angle

dimer

dimethylformamide (DMF)

dimethyl sulfide (DMS)

dimethyl sulfoxide (DMSO)

diol

dipeptide

dipoles

dipole moment

disproportionation

diprotic acid

diradical, triplet state

directing group

disaccharide

Dispersion Force (London Force)

distillation

di-substituted

disulfide

disulfide Bridge

divalent Anions and Cations

double or (π) bond

Double Bond Equivalent (DBE)

double-headed Arrow

double helix

doublet (d)

downfield (de-shielded)

drug

ε (electrical permittivity)

E (Ger. entgegen)

E1 Mechanism

E1 Reaction

E1CB Mechanism

E2 Mechanism

E2 Reaction

Ea

early (reactant-like) transition state

eclipsed

%ee (enantiomeric excess)

election configuration

electron delocalization

Electron Donating Group (EDG)

electron pair repulsion

electron-sea (sea-of-electrons) model

Electron Withdrawing Group (EWG)

electronegative

electronegativity

electroneutral (non-polar)

electrophile

Electrophilic Addition Reaction

Electrophilic Aromatic Substitution

electropositive

Elimination Reaction

emulsion

enamines

enantiomeric excess (%ee)

enantiomers

endergonic (+ΔG)endothermic (+ΔH)energy profile or Reaction Coordinate DiagramenolsenolatesenolizationenoneEnthalpy (Heat) of CombustionEnthalpy of FormationEnthalpy of Hydrogenation

enzymeepoxidesEquations of Stateequilibriumequilibrium constant (Keq)equatorialequivalent (equimolar unit)estersEt- (ethyl)ether (R-O-R’)ethyl acetate (EtOAc)ethyl ether (Et2O)ethyne (acetylene or HCCH)evaporationexcess of reagent (“xs“) is a non-limiting qty.excited state (*)exergonic (-ΔG)exothermic (-ΔH)expanded octet/shellextinction coefficient {efatty acidfingerprint regionfirst-order couplingfirst order splittingFischer esterificationFischer ProjectionFive Zone Analysisfluorinationformal chargefractional distillationfragment Ion (formerly “daughter” ion)fragmentation reactionfree radicalFriedel-Crafts acylationFriedel-Crafts alkylationFront-side Attackfullerenesfunctional groupsfusedGas ChromatographygaucheGCGC-MSgeminal or (1,1)geometric isomers (obsolete referring to E/Z)Gibbs Free Energy (G)Gibbs-Helmholtz EquationGilman Reagent  (R)2CuLiglucoseglutamic acid (Glu or E)glutamineglycerol (1,2,3-propanetriol)

Glycine (Gly or G)

glycosidic bond/linkageGrignard ReactionGrignard Reagent, R-MgXGrob FragmentationGround StateGuanine (G)1,2-hydride shift1H-NMRhvH-Bond (hydrogen bond)halide (Group VIIA substituent)haloalkanes (alkyl halides. R-X)haloarene (aryl halide, Ar-X)halogenhalogenationHammond PostulateHard/Soft-Acid/Base (HSAB) TheoryHaworth Projection (“hay-worth”)

Heat of Combustion

Heat of Formation, Hf

Heat of Hydrogenation

hemiacetal or hemiketal

Henderson-HasselBalch Equation

Henry’s LawHess’s Law

HETCOR

heteroatomheterocycle

heterogeneous

heterolysis

heterolytic bond cleavage

Highest Occupied Molecular Orbital (HOMO)Histidine (His or H)HMQCHOAc = AcOH = acetic acidHofmann DegradationHofmann Elimination (anti-Zaitzev)Hofmann’s Rule (anti-Zaitzev)HOMO-LUMO Gap/energy difference

homogeneous

homolysis

homolytic Bond Cleavage

Hooke’s Law

Hückel’s Rule (4n+2)

hybridization (of orbitals)

hydrationhydride (H: anion)

hydroboration

hydroboration-oxidation

hydrolysis

hydronium ion, H3O+

hydrophilic

hydrophobic

hydrophobic Effect

hygroscopic

hyperconjugation

I or spin quantum number (±½)

imidazole (imid.)

imine

immiscible

in silico

in situ

in vitro

in vivo

indole

inductive effects

Infrared Spectroscopy

infrared spectrum

inhibitor

initiation

initiator

integration

intermediate

intermolecular

internal alkene

internal alkyne

intramolecular

inversion of stereochemistry/configuration

iodination

Iodoform reaction

ion – a species whose electron count exceeds or falls below the group number of the element. Cation = positively charged ion (electron deficient); anion = negatively charged ion (electron-rich)

ionic bond – mutual attraction between two species of opposite charge by Coulombic force (electrostatic attraction) by atoms that differ in electronegativity by greater than 2.5

ionization

i-Pr (isopropyl)

ipso Substitution

IR

isoelectronic

isoleucine (Ile or I)

isomer – a compound that is related to another by many standards but at a minimum must have the same molecular formula

isomerization

isotope – an atom whose number of neutrons does not match that of other isotopes of that atom

IUPAC – the International Union of Pure and Applied Chemistry

Jahn-Teller Effect

Joule (J) or kilojoule (kJ)

Jones Reagent (acidic dichromate)Ka (acid dissociation constant)kcal / kilocalorie or Calorie (C = 1000cal)kJ / kilojouleKekulé structureKeq (equilibrium constant)keto isomer formketoneketoseketoximeKinetic Control/Productl- (prefix)L- (prefix)lactamlactonelate transition stateLDA (lithium diisopropylamide)Le Chateliér’s Principleleaving groupLeucine (Leu or L)levorotatory (L or l or -)Lewis Acids & BasesLewis Dot StructureLewis Structureligandlimiting reagentlipidlipophilic (aliphatic)lipophobic (hydrophilic)London (dispersion) Forcelone pair (electrons)long-range couplingLowest Unoccupied Molecular Orbital (LUMO)Lysine (Lys or K)µ (mu)M+ (molecular ion)M+1M+2m/z (units of Mass Spectrometry)main group elements (A group)major grooveMarkovnikov Addition/RegiochemistryMarkovnikov’s Rulemass spectrummass spectrometryMcLafferty RearrangementmCPBAMe- (methyl)mechanism (re reactions)Medicinal chemistrymelting point (MP)mercaptan (thiol)meso compound/diastereomermesomerism (see resonance)mesylate (-OMs)meta (1,3-)meta director/directingmetals and metalloidsmetabolismmethanesulfonatemethanesulfonic acidmethine proton R3C-HMethionine (Met or M)methylene group R2CH2Microscopic Reversibility, Principle ofmineral acidminor groovemisciblemoietymolMolar Mass / Molecular Weightmole (Avagadro’s Number of species)Molecular Formula (CnHn….)molecular ion (M+)molecular model kitMolecular Sieve (3Å-4Å MS)molecular weight (MW or M) or molar massmolozonidemolecular orbital (MO)monosubstitutedmultiplet (m)mutarotationN-bromosuccinimide (NBS)N-chlorosuccinimide (NCS)N-iodosuccinimide (NIS)n-  (normal or unbranched)n-BuLin+1 rule4n rule4n+2 (Hückel’s rule)NaBH4NaHNamed ReactionNatural Product  (Organic I, Intro to Synthesis)Newman Projectionnitration (-NO2)nitrilenitro compounds/groupsnitrogen/amine (Walden) inversion”Nitrogen Rule”NMRnode momenclatureNon-first Order CouplingNon-first Order SplittingNon-aromaticNon-bonded Electron PairNon-decouplednonpolar nolventnon-spontaneous reactionnonsuperimposableNu: (Nucleophile)Nuclear Spin FlipNucleic AcidsNucleophileNucleophilic Aromatic SubstitutionNucleophilicityNucleosideNucleotideOctet Rule (Second row elements)Olefin (alkene)One equivalent (1 equiv.) (1eq.)One Molecule RuleOptical ActivityOptically InactiveOrganometallic CompoundOrganolithium Reagent, RLi0rtho0rtho-para director/directing-OMs (mesylate)-OTf (triflate)-OTs (tosylate)OxaphosphetaineOxidant/Oxidizing agentOxidationOximeOxonium IonOxyanionOzone (O3Ozonolysis (Harries Reaction)pi (π) bondpi (π) orbitalpi* (π*) orbitalp-orbitalpara- (1,4-)paraffinpentetpeptidePeptide Bondperacetic acid (RCO3H)peracidPercent (%) Yield (Actual Yield)PermanganatePeroxide (ROOR)pHpKaPharmacologyPhenol  (Organic II, Reactions of Benzene)Phenyl Group (Ph-)Phenylalanine (Phe, F)PhospholipidPhosphodiesterPhotochemistryPhotolysisPhotonpi-cation interactionπ-stackingpiperidinepKapKbPlane Polarized LightPolar Covalent BondPolar SolventPolarimetryPolarizabilityPolypeptidePolysaccharidePotential EnergyppmPr- (propyl substituent)PrecipitationPrimary (1o)ProdrugProductProline (Pro or P)PropagationProgargylic positionProtection, Functional GroupProtecting GroupsProteinProtic Solvent (H-bonding)Proton (H+)Proton 1H NMRProtonationp-toluenesulfonatep-TsCl (para-toluenesulfonyl chloride)p-TsOH (para-toluenesulfonic acid)Purinepyranpyridine (pyr.)pyrimidinepyrrolepyrrolidineQuantum MechanicsQuantum NumbersQuartet (q)Quaternary Carbon (4o)Quaternary StructureQuintetR  = Universal DescriptorR- GroupRacemicRacemic Mixture (racemate)Radical or Free RadicalRadical CationRate-Determining or Limiting StepReactantReaction CoordinateReaction MechanismReaction ProductReactive Oxygen Species (ROS)Reactivity-Selectivity PrincipleRearrangement ReactionsReducing Agent or ReductantReduction reactionRegioselectivityResolutionResonanceResonance Contributor/StructureResonance Forms, Prioritization ofRetro-aldolRetro Diels-Alder ([4+2] cycloreversion)Retrosynthetic Analysis/RetrosynthesisRibonucleic AcidRiboseRing FlipRing StrainRNAsigma (σ) bonds orbitalσ* orbitalS (Lat. sinister)s-cis   (s = single-bond)s-BuLi (s=sec)s-trans (s = single-bond)Sanger’s ReagentSaponification (ester hydrolysis)saturatedSawhorse ProjectionSaytseff’s Rule (Zaitzev’s Rule)Schiff Base (akylamine)sec-butyl groupSecondary StructureSerine (ser or S)SextetSide ChainShielded (upfield)Single bondSinglet (s)Skeletal Formula (line-angle)SN1 MechanismSN2 MechanismSodium Borohydride (NaBH4)Sodium Hydride (NaH)SolubilitySoluteSolventSolvent CageSolvolysis/solvolyticsp orbitalsp2 orbitalsp3 orbitalSpace-Filling ModelSpecific Rotation [αo]SpectrometrySpectroscopySpin Quantum NumberSpin-Spin CouplingSpirocyclicSplitting (multiplicity in signals)Spontaneous ChangeSquiggly LineStaggered conformationStarting Material (substrate or reactant)Stereocenter or Stereogenic CenterStereochemistryStereoselectiveStereospecificSteric EffectsSteric HindranceSteric NumberSteric StrainSteroidsStoichiometryStretching FrequencysublimationSubstituent (any replacement for hydrogen)Substitution Reaction (displacement)Substrate (reactant)Sucrose (disaccharide)Suicide InhibitorSulfide (R-S-R)Sulfonamide (-S(O2)ONR2)Sulfonate Ester (RSO3R)Sulfonate Anion (-RSO4<4+Sulfonic acid (RSO3HSulfonationSulfone (R-SO2R)Sulfonic AcidSulfonyl Chloride (thionyl chloride)Sulfoxide (R-S(O)R)Superimposable (superposable)suspensionsymmetric stretchsyn or erythrosyn additionsyn-periplanarsynthesist-BuLitautomertautomerizationt-But-BuOHterminal alkeneterminal alkynetermination, of a chain reactiontermolecular (3rd order)tertiary (3otetrahedral carbon (sp3tetrahedral intermediatetetrahydrofuran (THF)tetramethylsilane (TMS)TetrasubstitutedTheoretical YieldThermodynamic Control/Productthioesterthioether (sulfide, R-S-R’)thiol (thioalcohol; RSH; mercaptan)thiolate anion; RSthiopheneThreonine (Thr or T)Thymine (T)TitrationToluene (tol.)Torsional StrainTosylate (-OTs)transtransesterificationtransition metalstransition statetricyclictriflate (-OTf)Triflic Acid (HOTf, TfOH)Triglyceride (Triacylglycerol)TrioseTriple BondTriplet (t)Triplet of doublets (td)trisubstitutedTritium 3HTryptophan (Trp or W)Two-Dimensional NMRTyrosine (Tyr or Y)UnimolecularUnsaturatedUpfieldUracil (U)ValenceValence Bond TheoryValence ElectronValence ShellValine (Val or V)Van der Waals ForcesVan’t Hoff RuleVapor PressureVaporizationVicinal (1,2 or vic)Vinyl groupVinylic PositionVitaminVSEPRWalden InversionWatson-Crick Base PairWavenumber (cm-1)Wavy Line (ambiguous configuration)WedgeWilliamson Ether SynthesisWittig ReactionWolff-Kischner Reduction% Percent YieldYlide (or ylid) Z (Ger. Zussamen)Zaitsev’s RuleZig-Zag Structure (see line-angle) Zwitterion (‘w’ pronounced as ‘v’)

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