Organic Chemistry Glossary
Glossary of Terms in Undergraduate Organic Chemistry & Their First Appearance Headings
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Abbreviation, Term, Symbol, Unit | Class | Database Headings |
Δ; ↑↓ | LAB | heat; reflux |
(+) (dextrorotatory) | I | Stereochemistry |
(-) (levorotatory) | I | Stereochemistry |
1,2-addition (direct addition) | I | Electrophilic Addition |
[1,2]-hydride shift | I | Carbocations |
[1,2]-alkyl shift | I | Carbocations |
1º, 2º, 3º, 4º | I | Classifying Carbons, C-Substituents |
[1,3] migration | II | Pericyclic reactions |
1,4-addition (conjugate addition); Michael rxn | II | Michael addition |
[1,5] migration | II | Sigmatropic Rearrangements |
[1,7] migration | II | Sigmatropic Rearrangements |
[2+2] cycloaddition | II | Pericyclic Reactions |
[3+2] cycloaddition | II | Pericyclic Reactions |
[4+2] cycloaddition | I | Pericyclic Reactions |
9-BBN | I | Electrophilic Addition |
absolute (pure, neat) | LAB | |
absolute configuration | I | Stereochemistry |
absorbance spectrum | I | IR, UV-Vis Spectroscopy |
acetal | II | Aldehydes and Ketones |
Acetoacetic Ester synthesis | II | Named Reactions |
acetylene | I | Alkynes |
acetylide Anion | I | Alkynes |
achiral | I | Stereochemistry |
acid anhydride | II | Carboxylic Acid Derivatives |
acid-catalyzed | I | Electrophilic Addition |
acid halide (also Acyl halide) | II | Carboxylic Acid Derivatives |
acid ionization constant (Ka) | I | Acids and Bases |
activated charcoal (Norit); decolorizer | LAB | |
activation energy | GEN | Kinetics vs. Thermodynamics |
activating group (EDG) | II | Reactions of Benzene |
actual yield (% yield) | LAB | |
acyl group (also acetyl when = ‘Ac’) | II | Carboxylic Acid Derivatives |
acylation reactions | II | Reactions of Benzene |
acylium ion | II | Reactions of Benzene |
Adenine (A) | II | Nucleic Acids |
Adenosine | II | Nucleic Acids |
addition reactions | I | Electrophilic Addition |
adsorption | LAB | |
Alanine (Ala or A) | II | Peptides and Proteins |
alcohol (ROH) | I | Alcohols, Ethers, Epoxides |
alcoholysis | II | Carboxylic Acid Derivatives |
aldehyde | II | Ketones and Aldehydes |
aldohexose | II | Sugars |
Aldol reaction | II | Ketones and Aldehydes II |
Aldol condensation | II | Ketones and Aldehydes II |
aldose sugar | II | Sugars |
alkali metal | GEN | |
alkaline | GEN | Acids & Bases |
Alkaline Earth Metals | GEN | The Periodic Table |
alkaloid | II | Amines; Natural Products |
alkane | I | Alkanes |
alkene | I | Alkenes |
alkyne | I | Alkynes |
alkoxide (-OR) | I | Substitution |
alkyl group/substituent | I | Nomenclature |
alkyl halide (R-X) | I | Nomenclature |
allene (1,2- or cumulated diene) | I | Dienes; Stereochemistry |
allyl group/position | I | Resonance |
allylic carbocations | I | Resonance |
allylic position | I | Resonance |
amino acid | II | Peptides and Proteins |
α-anomer or epimer (internal acetal-axial bond) | II | Sugars |
α-carbon (a carbon attached to functionality) | II | Functional groups |
alpha-helix | II | Peptides and Proteins |
anisotropy | I | NMR Spectroscopy |
amalgam | II | Redox Reactions |
ambident | II | Carbonyl Compounds |
amide | II | Carboxylic Acid Derivatives |
amine | I | Amines I & II |
amine oxide (N-oxide) | I | Elimination |
amu (Dalton) | GEN | |
angle strain | I | Conformational Analysis |
anhydrides, of acids | II | Carboxylic Acid Derivatives |
anhydrous | LAB | |
anion | GEN | |
annealing | II | Nucleic Acids |
anomer / anomeric | II | Sugars; Stereochemistry |
anomeric carbon | II | Sugars |
anomeric effect (negative hyperconjugation) | II | Electron Delocalization |
anti conformation | I | Stereochemistry |
anti addition | I | Electrophilic Addition |
anti-Markovnikov Addition/regiochemistry | I | Regiochemistry |
antiperiplanar | I | Conformational Isomerism |
anti-aromaticity | II | Aromaticity |
antibiotic | II | Drugs and Enzymes |
anti-bonding molecular orbital | I | Molecular Orbital Theory |
aprotic (solvent) | I | Solvents |
aqueous | I | Solvents |
arenium ion/intermediate | I | Aromatic Substitution |
Arginine (Arg or R) | II | Amino Acids and Proteins |
Arrhenius equation/constant/acid-base | I | Kinetics vs. Thermodynamics |
aryl or Ar- (aromatic substituent) | I | Nomenclature |
aryl halide (Ar-X) | II | Functional Groups |
Asparigine (Asn or Q) | II | Amino Acids and Proteins |
Aspartic Acid/Aspartate (Asp or E) | II | Amino Acids and Proteins |
asymmetric (chiral) | I | Stereochemistry |
asymmetric stretch/bend/wag | I | IR Spectroscopy |
atomic mass | GEN | The Periodic Table |
atomic number | GEN | The Periodic Table |
atomic orbital (s, p, d, f) | GEN | Covalent Bonding |
atomic radius | GEN | The Periodic Table |
ATP (adenosine triphosphate) | II | Nucleic Acids |
Avagadro’s Number (6.022 x 10-23) | GEN | Stoichiometry |
axial | I | Conformational Analysis |
azeotrope; azeotropic mixture | LAB | |
azide anion | I | Substitution |
aziridine | I | Amines; Heterocycles |
Azimuthal Quantum Number | I | Electron Configuration |
diazo coupling | II | Reactions of Benzene |
backside attack | I | Nucleophilic Substitution |
Baeyer-Villiger Oxidation | II | Aldehydes and Ketones |
banana bonds (Walsh cyclopropane) | I | Cycloalkanes |
base (Brønsted or Lewis) | I | Acids and Bases |
base-catalyzed | I | Catalysis |
base pairing | II | Nucleic Acids |
Bond Dissociation Energy (BDE) | I | Covalent Bonds; Radicals |
bending mode (IR) | I | IR Spectroscopy |
benzylic carbocation | I | Carbocations |
benzyl group (PhCH2-) | I | Nomenclature |
benzylic position | I | Resonance |
Benzyne | II | Reactions of Benzene |
ß-anomer | II | Sugars |
ß-carbon | I | Elimination, Conjugate addition |
ß-elimination | I | Elimination |
betaine | II | Aldehydes and Ketones |
ß-pleated sheet | II | Peptides and Proteins |
bicyclic (bridged or spiro-) | II | Nomenclature |
bimolecular (2nd order) | I | Elimination, Substitution |
biosynthesis | II | Synthetic Strategy |
boat conformation | I | Conformational Analysis |
boiling point (BP) | I | Alkanes |
bond angle | I | Bonding & Hybridization |
bond dipole | I | Bonding and Hybridization |
bond length | I | Representing Organic Compounds |
bond order | GEN | |
bond rotation | I | Conformational Analysis |
bond stretch | I | IR Spectroscopy |
bond-line structure | I | Representing Organic Structures |
Bonding Molecular Orbital (σ or π) | I | Molecular Orbital theory |
borane | I | Electrophilic Addition |
branching | I | Alkanes; Nomenclature |
bridged | I | Polycyclic Compounds |
bromination | I | Electrophilic Addition & Substitution |
Brønsted Acid-Base Theory/Definition | I | Acids and Bases |
butyl- | I | Nomenclature |
Cahn-Ingold-Prelog (C-I-P) Rules | I | Nomenclature; Stereochemistry |
carbanion | II | Carbanions; Reactive intermediates |
carbocation or carbenium | I | Carbocations |
carbohydrate (CH2O)n | II | Sugars |
Carbon-13 NMR | I | NMR Spectroscopy |
carbonyl (C=O) | II | Ketones and Aldehydes |
carboxylate (-CO<2) | II | Carboxylic Acid Derivatives |
carboxylic acid (-CO2H) | II | Carboxylic Acid Derivatives |
carboxylic acid derivative | II | Carboxylic Acid Derivatives |
canonical form (or mesomer) | I | Resonance |
catalyst | I | Kinetics & Thermodynamics |
catalytic hydrogenation | I | Redox Reactions; Addition |
chain initiation (of radical reactions) | I | Radicals |
chain propagation (of radical reactions) | I | Radicals |
chain termination (of radical reactions) | I | Radicals |
chair conformations | I | Conformational Analysis |
chair flip (cyclohexane) | I | Conformational Analysis |
chemical shift (δ) [ppm] | I | NMR Spectroscopy |
chiral | I | Stereochemistry |
chirality (or asymmetric) center | I | Stereochemistry |
chlorination | I,II | Electrophilic Addition |
cholesterol | II | Fats & Lipids |
chromatography (several kinds) | LAB | Chemical Separation |
cis– | I | Stereochemistry |
Claisen condensation | II | Reactions at the α-carbon |
Claisen rearrangement | II | Pericyclic Reactions |
Clemmensen reduction | II | Redox Reactions |
combustion | I | Alkanes |
concerted (synchronous) reaction | I | Substitution |
condensation reaction | II | Condensation Reactions |
condensed formula (space-saving) | I | Representing Organic Compounds |
configuration (absolute and relative) | I | Stereochemistry |
configurational (stereo-) isomers | I | Stereochemistry |
conformation | I | Isomerism |
conformational isomers (conformers) | I | Isomerism |
conformers | I | Isomerism |
conjugate acid | I | Acids and Bases |
conjugate base | I | Acids and Bases |
conjugation | I | Resonance |
constitutional (“structural”) isomers | I | Isomerism |
coordination compounds | I | Organotransition Metal Chemistry |
coupling | I | NMR Spectroscopy |
coupling constant (J) [Hz] | I | NMR Spectroscopy |
covalent bond | I | Atoms and Molecules |
crown ethers (#C-cr-#O) | I | Alcohols, Ethers, Epoxides |
cuprates | I,II | Organometallic Compounds |
curved arrow formalism | I | Arrow pushing and Mechanism |
cycloaddition reaction | I | Pericyclic Reactions |
cycloalkane | I | Alkanes, Nomenclature |
cyclobutadiene | II | Aromaticity |
cyclooctatetraene | II | Aromaticity |
cyclopentadienyl anion | II | Aromaticity |
cyclopentadienyl cation | II | Aromaticity |
cyclopropane | I | Cycloalkanes |
cyclopropenyl cation | II | Aromaticity |
Cysteine (Cys or C) | II | Peptides and Proteins |
cystine bridge (Cys-Cys) | II | Peptides and Proteins |
Cytosine (C) | II | Nucleic Acids |
d- (same as (+)) | I | Stereochemistry |
D- (dextrorotatory) | I | Stereochemistry |
Dalton [Da] or [amu] | GEN | (an atomic mass unit) |
deactivating group | II | Reactions of Benzene |
deactivator | II | Reactions of Benzene |
decarboxylation | II | Condensation Reactions |
decomposition | LAB | |
degenerate | I | Resonance Structures |
delocalization | I | Resonance Structures |
Deoxyribonucleic Acid | II | Nucleic Acids |
deprotection / deblocking | II | Ketones and Aldehydes |
deprotonate/deprotonation | I | Acids & Bases |
DEPT | II | NMR spectroscopy |
deshielded (downfield) | I | NMR spectroscopy |
desolvation or dissolution | I | Solvents and Solutions |
destructive interference | I | MO theory; NMR spectroscopy |
detergent | II | Fats and Lipids |
detonation | LAB | |
deuterium (“heavy” hydrogen) 2H | I | Mass Spectrometry |
Dewar benzene | I | Benzene & Aromatics |
dextrorotatory (D or d or +) | I | Stereochemistry |
dextrose (D-glucose) | I | Sugars |
diastereomer | I | Stereochemistry |
diatomic (A2) | GEN | |
diaxial interaction | I | Conformational Analysis |
diazonium ion | II | Reactions of Benzene |
diazonium salt | II | Reactions of Benzene |
diazotization | II | Reactions of Benzene |
DIBAL or DIBAL-H | II | Redox Reactions |
dichloromethane (methylene chloride) | LAB | Solvents (Chart) |
dichromate | I | Redox Reactions |
Dieckmann Condensation | II | Condensation Reactions |
dielectric constant | I | Solvents |
Diels-Alder Reaction; [4+2] cycloaddition | I | Dienes, Pericyclic Reactions |
diene | I | Dienes, Conjugation |
dieneophile | I | Dienes, Pericyclic Reactions |
diethyl ether (Et2O | I | Ethers; Solvents |
diffraction | I | Refractive Index |
diffraction pattern | I | Refractive Index |
dihedral angle | I | Conformational Analysis |
dimer | I | Intermolecular forces |
dimethylformamide (DMF) | I | Solvents |
dimethyl sulfide (DMS) | I | Solvents |
dimethyl sulfoxide (DMSO) | I | Solvents |
diol | I | Redox Reactions |
dipeptide | I | Peptides and Proteins |
dipoles | I | Bonding and Hybridization |
dipole moment | GEN | Covalent Bonds |
disproportionation | II | Redox Reactions |
diprotic acid | GEN | |
diradical, triplet state | II | Alkenes, aromatization |
directing group | I | Reactions of Benzene |
disaccharide | II | Sugars |
Dispersion Force (London Force) | I | Intermolecular Forces |
distillation | LAB | |
di-substituted | I | Nomenclature |
disulfide -SS- | I | Peptides and Proteins |
disulfide bridge -cys-S-S-cys- | I | Peptides and Proteins |
divalent anions and cations | I | Formal Charge |
double or (π) bond | I | Alkenes |
Double Bond Equivalent (DBE) IU or IHD | I | Index of Unsaturation/IU/IHD |
double-headed arrow (→) | I | Arrow Pushing and Mechanism |
double helix | II | Nucleic Acids |
doublet (d) | I | NMR Spectroscopy |
downfield (de-shielded) | I | NMR Spectroscopy |
drug | II | Drugs, Enzymes, and Activation |
ε (electrical permittivity) | I | Solvents |
E (Ger. entgegen) | I | Stereochemistry |
E1 Mechanism | I | Elimination |
E1 Reaction | I | Elimination |
E1CB Mechanism | I | Elimination |
E2 Mechanism | I | Elimination |
E2 Reaction | I | Elimination |
Ea | I | Kinetics & Thermodynamics |
early (reactant-like) transition state | I | Kinetics & Thermodynamics |
eclipsed | I | Conformational Analysis |
% ee (enantiomeric excess) | I | Stereochemistry |
election configuration | I | Electron Configuration |
electron delocalization | I | Resonance; Conjugation |
Electron Donating Group (EDG) | I | Dienes |
electron pair repulsion | I | Structure and Bonding |
electron-sea (‘sea-of-electrons’) | I | Special Topic |
Electron Withdrawing Group (EWG) | I | Dienes |
electronegative | GEN | Covalent Bonds |
electronegativity | GEN | Covalent Bonds |
electroneutral (non-polar) | GEN | Covalent Bonds |
electrophile | I | Reactions |
Electrophilic Addition Reaction | I | Alkenes |
Electrophilic Aromatic Substitution | II | Reactions of Benzene |
electropositive | GEN | Covalent Bonds |
elimination reaction (e.g. | I | Eliminations |
emulsion | II, LAB | Fats and Lipids |
enamines | II | Ketones and Aldehydes; Amines |
enantiomeric excess (% ee) | I | Stereochemistry |
enantiomers | I | Stereochemistry, Chirality |
endergonic (+ΔG) | I | Kinetics and Thermodynamics |
endothermic (+ΔH) | I | Kinetics and Thermodynamics |
energy profile or Reaction Coordinate Diagram | I | Kinetics and Thermodynamics |
enols | I | Tautomerization |
enolates | II | Reactivity at the α-Carbon |
enolization | II | Reactivity at the α-Carbon |
enone | II | Enones and Enoates |
enthalpy (heat) of combustion | I | Kinetics and Thermodynamics |
enthalpy of formation | I | Kinetics and Thermodynamics |
enthalpy of hydrogenation | I | Kinetics and Thermodynamics |
enzyme | II | Kinetics and Thermodynamics |
epoxides | I | Alcohols, ethers, epoxides |
equations of state | GEN | |
equilibrium | GEN | |
equilibrium constant (Keq) | GEN | |
equatorial | I | Conformational analysis |
equivalent (equimolar or stiochiometric) | I | Lab |
ester | II | Carboxylic Acid Derivatives |
Et- (ethyl) | I | Nomenclature |
ether (R-O-R’) | I | Alcohols, Ethers, Epoxides |
ethyl acetate (EtOAc) | I | Solvents |
ethyl ether (Et2O) | I | Solvents |
ethyne (acetylene or HCCH) | I | Alkynes |
evaporation | GEN | Lab also Vaporization |
excess of reagent (“xs“); a non-limiting qnty. | I | Lab |
excited state (*) | I | Molecular Orbitals |
exergonic (-ΔG) | I | Kinetics and Thermodynamics |
exothermic (-ΔH) | I | Kinetics and Thermodynamics |
expanded octet/shell | I | Trends in the Periodic Table |
extinction coefficient (e) | I | Spectroscopy |
fatty acid | II | Fats and Lipids |
fingerprint region | I | IR Spectroscopy |
first-order coupling | I | NMR Spectroscopy |
first order splitting | I | NMR Spectroscopy |
Fischer esterification | II | Carboxylic Acid Derivatives |
Fischer Projection | I,II | Representing Compounds; Stereochemistry |
Five Zone Analysis | II | Drug Formulation Medicinal Chem. |
fluorination | II | Reactions of Benzene |
formal charge | I | Bonding and Hybridization |
fractional distillation | LAB | |
fragment Ion (formerly “daughter” ion) | I | Mass Spectrometry |
fragmentation reaction | I | Mass Spectrometry |
free radical | I | Radicals |
Friedel-Crafts acylation | II | Reactions of Benzene |
Friedel-Crafts alkylation | II | Reactions of Benzene |
front-side attack | II | |
fullerenes | II | Allotropes of Carbon |
functional groups | I | Functional Groups |
fused | II | Polycyclic Ring Systems |
Gas Chromatography (GC) | LAB | |
gauche | I | Conformational Analysis |
GC | LAB | |
GC-MS | LAB | |
geminal or (1,1) | I | Nomenclature |
‘geometric’ isomers (obsolete referring to E/Z) | I | Isomerism, Nomenclature |
Gibbs Free Energy (G) | I | Kinetics and Thermodynamics |
Gibbs-Helmholtz equation | I | Kinetics and Thermodynamics |
Gilman reagent (R)2CuLi (lithium dialkyl cuprate) | I | Organometallics; Cuprates |
glucose | II | Sugars |
glutamic acid (Glu or E) | II | Peptides and Proteins |
glutamine | II | Peptides and Proteins |
glycerol (1,2,3-propanetriol) | II | Fats and Lipids |
Glycine (Gly or G) | II | Peptides and Proteins |
glycosidic bond/linkage | II | Sugars |
Grignard Reaction | II | Carbonyl Compounds |
Grignard Reagent, R-MgX | I | Organometallics |
Grob Fragmentation | II | Named Reactions |
ground state (GS) | I | Reaction Coordinate Diagrams |
Guanine (G) | II | Nucleic Acids |
1,2-hydride [1,2-H] shift | I | Carbocations |
1H-NMR | I | NMR Spectroscopy |
hv (Plank’s constant⋅wavelength) | GEN | Energy of a photon |
H-Bond (hydrogen bond) | I | Intermolecular interactions |
halide (Group VIIA substituent) | I | Functional Groups |
haloalkanes (alkyl halides. R-X) | I | Functional Groups |
haloarene (aryl halide, Ar-X) | I | Functional Groups |
halogen | I | Trends in the Periodic Table |
halogenation | I,II | Addition, Substitution |
Hammond Postulate | I | Transition State Theory; RCD |
Hard/Soft-Acid/Base (HSAB) Theory | I | Polar Reactions |
Haworth projection (“hay-worth”) | II | Sugars |
heat (enthalpy) of combustion | I | Kinetics and Thermodynamics |
heat (enthalpy) of formation, Hf | I | Kinetics and Thermodynamics |
heats of hydrogenation | I | Kinetics and Thermodynamics |
hemiacetal (or hemiketal) | II | Ketones and Aldehydes |
Henderson-HasselBalch equation | GEN | Acids and Bases |
Henry’s Law | GEN | Partial Pressures |
Hess’s Law | GEN | Heat summation |
HETCOR | LAB | Advanced Spectroscopy |
heteroatom | I | Functional Groups |
heterocycle | I | Functional Groups |
heterogeneous | I | Catalysis |
heterolysis | I | Covalent Bonding |
heterolytic bond cleavage | I | Transition State Theory |
Highest Occupied Molecular Orbital (HOMO) | I | Molecular Orbitals |
Histidine (His or H) | II | Amino Acids and Proteins |
HMQC | II | NMR (Advanced) |
HOAc = AcOH = acetic acid | I | Nomenclature |
Hofmann degradation | II | Named Reactions |
Hofmann elimination (anti-Zaitzev) | II | Named Reactions |
Hofmann’s Rule (anti-Zaitzev) | I | Elimination |
HOMO-LUMO Gap/energy | I | Molecular Orbitals |
homogeneous | I | catalysis |
homolysis | I | Covalent Bonds; Transition States |
homolytic bond cleavage (homolysis) | I | Transition States |
Hooke’s Law | GEN | |
Hückel’s Rule (4n+2) | II | Aromaticity |
hybridization (of orbitals) | I | Bonding and Hybridization |
hydration | I | Electrophilic Addition |
hydride (H:– anion) | I | Redox Reactions |
hydroboration | I | Electrophilic Addition |
hydroboration-oxidation | I | Electrophilic Addition |
hydrolysis | II | Carboxylic Acid Derivatives |
hydronium ion, H3O+ | I | Acids and Bases |
hydrophilic | GEN | Solvents |
hydrophobic | GEN | Solvents |
hydrophobic Effect | GEN | Solvents |
hygroscopic | LAB | |
hyperconjugation | I | Electron Delocalization |
I or spin quantum number (±½) | I | Electron Configuration |
imidazole (imid.) | II | Aromatics; Heterocycles |
imine | II | Aldehydes and Ketones |
immiscible | I | Solvent and Solutions |
in silico | GEN | (in glass) |
in situ | I | (during the reaction) |
in vitro | I | (in a model system) |
in vivo | I | (in a living system) |
indole | II | Aromatics; Alkaloids; Heterocycles |
inductive effects | I | Electron Delocalization |
Infrared spectroscopy | I | IR Spectroscopy |
infrared spectrum | I | IR Spectroscopy |
inhibitor | II | Radical Reactions |
initiation | I | Radical Reactions |
initiator | I | Radical Reactions |
integration | I | NMR Spectroscopy |
intermediate | I | Reactive Intermediates |
intermolecular | I | Reaction Dynamics |
internal alkene | I | Alkenes |
internal alkyne | I | Alkynes |
intramolecular | I | Reaction Dynamics |
inversion of stereochemistry/configuration | I | Stereochemistry |
iodination | I | Electrophilic Addition & Substitution |
Iodoform reaction | II | Ketones and Aldehydes |
ion | GEN | |
ionic bond | GEN | Bonding and Hybridization |
ionization | I | Bonding and Hybridization |
i-Pr (isopropyl) | I | Nomenclature |
ipso substitution | II | (Nucleophilic) Aromatic Substitution |
IR (infrared) | I | IR Spectroscopy |
isoelectronic | I | Organometallic Chemistry |
isoleucine (Ile or I) | I | Amino Acids and Proteins |
isomer | I | Isomerism |
isomerization | I | Isomerism |
isotope | I | Mass Spectrometry |
IUPAC (Int’l Union of Pure & Applied Chemistry) | I | Nomenclature |
Jahn-Teller Effect | I | Advanced Organic |
Joule (J) or kilojoule (kJ) | GEN | |
Jones Reagent (acidic dichromate) | II | Redox Reactions |
Ka (acid dissociation constant) | I | Acids and Bases |
kcal / kilocalorie or Calorie (C = 1000cal) | I | Equilibrium |
kJ / kilojoule | I | Equilibrium |
Kekulé structure | I | Representing Organic Compounds |
Keq (equilibrium constant) | GEN | Equilibrium |
keto isomer form | I | Tautomerism/Tautomerization |
ketone | II | Ketones and Aldehydes |
ketose | II | Sugars |
ketoxime | II | Sugars |
Kinetic Control/Product | I | Kinetics & Thermodynamics |
l- (prefix) | I | Stereochemistry |
L- (prefix) | I | Stereochemistry |
lactam | II | Carboxylic Acid Derivatives |
lactone | II | Carboxylic Acid Derivatives |
late transition state | I | The Transition State |
LDA (lithium diisopropylamide) | II | Ketones and aldehydes |
Le Chateliér’s Principle | GEN | |
leaving group | I | Substitution; Elimination |
Leucine (Leu or L) | II | Peptides and Proteins |
levorotatory (L or l or -) | I | Stereochemistry |
Lewis acids & bases; definition | I | Acids and Bases |
Lewis dot structure | I | Bonding and Hybridization |
Lewis structure | I | Bonding and Hybridization |
ligand | I | Hybridization; Organometallics |
limiting reagent | LAB | |
lipid | II | Fats and Lipids |
lipophilic (aliphatic) | II | Fats and Lipids |
lipophobic (hydrophilic) | II | Fats and Lipids |
London (dispersion) forces | I | Intermolecular Forces |
lone pair (electrons) | I | Bonding and Hybridization |
long-range coupling | I | NMR Spectroscopy |
Lowest Unoccupied Molecular Orbital (LUMO) | I | Molecular Orbital Theory |
Lysine (Lys or K) | II | Amino Acids and Proteins |
µ (mu) | I | Dipole Moment |
M+ (molecular ion) | I | Mass Spectrometry |
M+1 | I | Mass Spectrometry |
M+2 | I | Mass Spectrometry |
m/z (units of Mass Spectrometry) | I | Mass Spectrometry |
main group elements (A group) | I | Trends in the Periodic Table |
major groove | II | Nucleic Acids |
Markovnikov Regiochemistry | I | Electrophilic Addition |
Markovnikov’s Rule | I | Electrophilic Addition |
mass spectrum | I | Mass Spectrometry |
mass spectrometry | I | Mass Spectrometry |
McLafferty Rearrangement | I | Mass Spectrometry |
mCPBA | I | Redox Reactions |
Me- (methyl) | I | Nomenclature |
mechanism (re reactions) | I | Arrow Pushing and Mechanism |
medicinal chemistry | II | Medicinal Chemistry |
melting point (MP) | LAB | |
mercaptan (thiol) | I | Sulfur Compounds |
meso compound/diastereomer | I | Stereochemistry |
mesomerism (see resonance) | I | Stereochemistry |
mesylate (-OMs) | I | Substitution |
meta- (1,3-) | I | Reactions of Benzene |
meta director/directing | II | Reactions of Benzene |
metals and metalloids | I | The Periodic Table |
metabolism | II | Biochemistry |
methanesulfonate | I | Substitution |
methanesulfonic acid | I | Substitution |
methine proton R3C-H | I | NMR Spectroscopy |
Methionine (Met or M) | II | Peptides and Proteins |
methylene group R2CH2 | I | NMR Spectroscopy |
microscopic reversibility, principle of | I | Rxn Coord Diagrams |
mineral acid | I | Acids and Bases |
minor groove | II | Nucleic Acids |
miscible | I | Solutions & Solvents |
moiety | I | Functional Groups |
mol | Gen | mole |
molar mass / molecular weight | Gen | |
mole (Avagadro’s Number of species) | Gen | |
molecular formula (CnHm….) | Gen | Alkanes |
molecular ion (M+); formerly “mother” ion | I | Mass Spectrometry |
molecular model kit | I | Blog; Adjusting to organic chemistry |
molecular sieve (MS) (3Å-4Å) | LAB | |
molecular weight (MW or M) or molar mass | GEN | |
molozonide | I | Redox reactions; Alkenes |
molecular orbital (MO) | I | Molecular Orbitals |
monosubstituted | I | Alkenes |
multiplet (m) | I | NMR Spectroscopy |
mutarotation | II | Sugars; Epimerization |
N-bromosuccinimide (NBS) | I | Electrophilic Addition, Radicals |
N-chlorosuccinimide (NCS) | I | Electrophilic Addition |
N-iodosuccinimide (NIS) | I | Electrophilic Addition, Radicals |
n- (normal or unbranched) | I | Nomenclature |
n-BuLi | I | Alkanes; Organometallics |
n+1 rule | I | NMR Spectroscopy |
4n rule | II | Aromaticity |
4n+2 (Hückel’s rule) | II | Aromaticity |
NaBH4 | I | Redox Reactions |
NaH | I | Substitution; Alcohols |
Named Reaction | I | Named Reactions |
Natural Product (Organic I, Intro to Synthesis) | II | Organic Subdivisions; Synthesis |
Newman Projection | I | Conformational Analysis |
nitration (-NO2) | II | Reactions of Benzene |
nitrile | II | Carboxylic Acid Derivatives |
nitro compounds/groups | II | Reactions of Benzene, Amines |
nitrogen/amine (Walden) inversion | I | Stereochemistry |
“Nitrogen Rule” | I | Mass Spectrometry |
NMR | I | Nuclear Magnetic Resonance |
node or nodal surface | I | Atoms and Orbitals |
nomenclature | I | IUPAC Nomenclature |
Non-first Order Coupling | I | NMR Spectroscopy |
Non-first Order Splitting | I | NMR Spectroscopy |
non-aromatic | II | Aromaticity |
non-bonded electron pair | I | Mass Spectrometry |
non-decoupled | II | C NMR Spectroscopy |
nonpolar nolvent | II | Solvents |
non-spontaneous reaction | I | Kinetics vs. Thermodynamics |
nonsuperimposable (unmappable on itself) | I | Chirality |
Nu: (nucleophile) | I | Reaction Mechanism, Lewis Bases |
nuclear spin flip | I | NMR Spectroscopy |
nucleic acids | II | Nucleic Acids |
nucleophile | I | Reaction Mechanisms |
Nucleophilic Aromatic Substitution | II | Reactions of Benzene II |
nucleophilicity | I | Reaction Mechanism |
nucleoside | II | Nucleic Acids |
nucleotide | II | Nucleic Acids |
Octet Rule (second row elements) | I | Bonding and Hybridization |
olefin (alkene) | I | Alkenes |
one equivalent (1 equiv.) (1eq.) | LAB | |
One-Molecule-Rule | I | |
optical activity | I | Chirality & Stereochemistry |
optically inactive | I | Chirality & Stereochemistry |
organometallic (organotransition metals) | I | Organotransition metal compounds |
organolithium Reagent, RLi | I | Organometallics |
ortho– (o-) | II | Reactions of Benzene |
ortho/para directing group | II | Reactions of Benzene |
-OMs (mesylate) | I | Alcohols |
-OTf (triflate) | I | Alcohols; Amines, Oximes |
-OTs (tosylate) | I | Alcohols |
oxaphosphetaine | II | Ketones & Aldehydes |
oxidant/oxidizing agent | I,II | Redox Reactions |
oxidation | I,II | Electrophilic Addition, Redox |
oxime | II | Ketones and Aldehydes |
oxonium ion; oxocarbenium ion | II | Alkenes, Ketones and Aldehydes |
oxyanion | I | Substitution |
ozone (O3) | I | Redox Reactions, Alkenes, Alkynes |
ozonolysis (Harries Reaction) | I | Redox Reactions, Alkenes, Alkynes |
pi-(π) bond | I | Bonding and Hybridization |
pi-(π) molecular orbital | I | Bonding and Hybridization |
pi* (π*) molecular orbital | I | Bonding and Hybridization |
p orbital / p character | I | Bonding and Hybridization |
para- (1,4-) | II | Reactions of Benzene |
paraffin | I | Alkanes |
pentet | I | NMR Spectroscopy |
peptide | II | Amino Acids and Proteins |
peptide (amide) bond | II | Amino Acids and Proteins |
peracetic acid (RCO3H) | I | Redox Reactions |
peracid | I | Redox Reactions |
percent (%) yield (Actual Yield) | LAB | |
permanganate | I | Redox Reactions |
peroxide (ROOR), peracid (RCO3H) | I | Radical Reactions |
pH | I | Acids and Bases |
pKa | I | Acids and Bases |
pharmacology; pharacokinetics | II | Drugs and Enzymes |
phenol (Organic II, Reactions of Benzene) | II | Alcohols; Reactions of Benzene |
phenyl group (Ph-) | I | Nomenclature |
Phenylalanine (Phe, F) | II | AminoAcids and Proteins |
phospholipid | II | Fats and Lipids |
phosphodiester | II | Nucleic Acids |
photochemistry | II | Pericyclic Reactions |
photolysis | II | Radical Reactions |
photon (E = hv) | Gen | |
pi-cation interaction | II | Secondary Spatial Effects |
π-stacking | II | Secondary Spatial Effects |
piperidine | II | Heterocycles |
pKa | I | Acids and Bases |
pKb | I | Acids and Bases |
plane-polarized light | I | Chirality |
polar covalent bond | I | Bonding and Hybridization |
polar polvent | I | Solvents |
polarimetry | I | Chirality |
polarizability | GEN | |
polypeptide | II | Peptides and Proteins |
polysaccharide | II | Sugars |
potential energy | I | Kinetics and Thermodynamics |
ppm | I | NMR Spectroscopy |
Pr- (propyl substituent) | I | Nomenclature |
precipitate | LAB | |
primary (1o) | I | Classifying Carbons |
pro-drug | II | Drugs and Enzymes |
product | I | Mechanism |
Proline (Pro or P) | II | Peptides and Proteins |
propagation | I | Radical Reactions |
progargylic position | I | Resonance |
Protection, Functional Group | I | Ketones and aldehydes |
protecting groups | II | Protecting Groups |
protein | II | Peptides and Proteins |
protic solvent (H-bonding solvent) | I | Solvents |
proton (H+) | I | Atoms and Molecules |
proton 1H NMR | I | NMR Spectroscopy |
protonation | I | Catalysis |
p-toluenesulfonate | I | Substitution/Elimination |
p-TsCl (para-toluenesulfonyl chloride) | I | Substitution/Elimination |
p-TsOH (para-toluenesulfonic acid) | I | Substitution/Elimination |
purine | II | Nucleic Acids |
pyran | II | Alcohols, Ethers & Epoxides |
pyridine (pyr.) | II | Aromatics |
pyrimidine | II | Nucleic Acids |
pyrrole | II | Aromaticity; Heterocycles |
pyrrolidine | II | Heterocycles; Amines |
QSAR (quantitative structure-activity relationships) | I | Electron Configuration |
quantum numbers | I | Electron Configuration |
quartet (q) | I | NMR Spectroscopy |
quaternary Carbon (4o) | I | Classifying Carbon |
quaternary structure | I | Peptides & Proteins; Enzymes |
quintet | I | NMR Spectroscopy |
R = Universal Descriptor | I | Nomenclature |
R- Group (often alkyl) | I | Nomenclature |
racemic | I | Stereochemistry |
racemic mixture (racemate) | I | Stereochemistry |
radical or free radical | I | Radicals |
radical cation | I | Mass Spectrometry |
rate-determining or rate-limiting or slow | I | Rxn Coord Diagrams |
reactant | I | Mechanism |
reaction coordinate diagram | I | Rxn Coord Diagrams |
reaction coordinate (surface) | I | Mechanism |
reaction mechanism | I | Organic Reactions |
reactive oxygen species (ROS) | I | Radicals |
reactivity-selectivity principle | I | Kinetics & Thermodynamics |
rearrangements (as reactions) | I, II | Carbocations |
reducing agent or reductant | I | Redox Reactions |
reduction (reaction) | I | Redox Reactions |
regioselectivity, regioselection | I | Regiochemistry |
resolution – chiral; kinetic | I | Stereochemistry |
resonance | I | Resonance I |
resonance contributor/structure/mesomer | I | Resonance I |
resonance forms, prioritization of | I | Resonance I |
Retro-aldol | II | Ketones & Aldehydes |
Retro Diels-Alder ([4+2] cycloreversion) | I | Dienes |
Retrosynthetic Analysis/Retrosynthesis | I | Introduction to Synthesis |
Ribonucleic Acid | II | Nucleic Acids |
ribose | II | Nucleic Acids |
Ring Flip – Chair-Boat-Chair Interconversion | I | Conformational Analysis |
Ring Strain: Baeyer, Pitzer, Transannular | I | Conformational Analysis |
RNA – ribonucleic acid | II | Nucleic Acids |
sigma (σ) bond | I | Bonding and Hybridization |
s orbital | I | Bonding and Hybridization |
σ and σ* orbitals | I | Bonding and Hybridization |
S (Lat. sinister) configuration | I | Stereochemistry |
s-cis (s = single-bond) | I | Dienes |
s-BuLi (s=sec) | II | Carbon Bases |
s-trans (s = single-bond) | I | Dienes |
Sanger’s Reagent | II | Nucleic Acid (Sequencing) |
saponification (ester hydrolysis) | II | Carboxylic Acid Derivatives |
saturated | I | Alkanes |
sawhorse projection | I | Representing Organic Compounds |
Saytseff’s Rule (Zaitzev’s Rule) | I | Elimination |
Schiff Base (akylamine) | II | Ketones and Aldehydes |
sec-butyl group | I | Nomenclature |
secondary structure | II | Peptides and Proteins, Nucleic Acids |
Serine (ser or S) | II | Peptides and Proteins |
sextet | I | NMR Spectroscopy |
side chain | I | Nomenclature |
shielded (upfield), chemically | I | NMR Spectroscopy |
single bond | I | Bonding and Hybridization |
singlet (s) | I | NMR Spectroscopy |
skeletal formula (line-angle) | I | Representing Organic Compounds |
SN1 limiting mechanism | I | Substitution |
SN2 limiting mechanism; SN2′ mechanism | I | Substitution |
sodium borohydride (NaBH4) | I | Redox Reactions |
sodium hydride (NaH) | I | Bases |
solubility | I | Solvents |
solute | I | Solvents |
solvent | I | Solvents |
solvent cage | I | Solvents |
solvolysis/solvolytic | I | SN1 and E1 |
sp orbitals/atoms | I | Hybridization |
sp2 orbitals/atoms | I | Orbital Hybridization |
sp3 orbitals/atoms | I | Orbital Hybridization |
space-filling model | I | Representing Organic Compounds |
specific rotation [αo] | I | Chirality |
spectrometry | I | Structural Elucidation |
spectroscopy | I | Structural Elucidation |
spin quantum number | I | Electron Configuration |
spin-spin coupling | I | Spectroscopy |
spirocyclic ring | II | Polycyclic rings systems |
splitting, nuclear (multiplicity in signals) | I | NMR Spectroscopy |
spontaneous change/reaction | I | Thermodynamics |
squiggly line bond | I | Representing organic compounds |
staggered conformation | I | Newman Projections |
starting material (substrate beginning a synthesis) | I | Reactions |
stereocenter or stereogenic center | I | Chirality |
stereochemistry | I | Stereochemistry |
stereoselective | I | Chirality |
stereospecific | I | Stereochemistry |
steric effects | I | Stereoelectronics |
steric hindrance | I | Conformational Analysis |
steric number | I | Conformational Analysis |
steric strain | I | Conformational Analysis |
steroids | II | Lipids and Fats |
stoichiometry | GEN | |
stretching frequency [cm-1] | I | IR Spectroscopy |
sublimation | GEN | (s) → (g) |
substituent (any replacement for hydrogen) | I | Nomenclature |
substitution Reaction (displacement) | I | Classes of reaction |
substrate (reactant) | I | Mechanism |
sucrose (disaccharide) | II | Sugars |
suicide inhibitor/inhibition | II | Drugs, Enzymes, & Kinetics |
sulfide (R-S-R) | I | Functional Groups |
sulfonamide (-S(O2)ONR2) | II | Functional Groups |
sulfonate ester (RSO3R) | I | Functional Groups |
sulfonate anion (-RSO3-) | I | Functional Groups |
sulfonic acid (RSO3H) | I | Functional Groups |
sulfonation | II | Reactions of Benzene |
sulfone (R-SO2R) | I | Functional Groups |
sulfonic Acid | II | Functional Groups |
sulfonyl chloride (thionyl chloride) | II | Substitution |
sulfoxide (R-S(O)R) | I | Functional Groups |
superimposable (superposable or mappable onto itself) | I | Chirality |
suspension | GEN | |
symmetric stretch | I | IR spectroscopy |
syn or erythro configuration (rings or chains) | I | Modes of Addition |
syn addition | I | Modes of Addition |
syn-periplanar | I | Dihedral geometry |
synthesis | I | Chemical Synthesis |
t-BuLi | II | Organometallics |
tautomer | I | Tautomerization |
tautomerization | I | Tautomerization |
t-Bu | I | tert-butyl |
t-BuOH | I | t-butyl alcohol |
terminal alkene | I | Alkenes |
terminal alkyne | I | Alkynes |
termination, of a chain reaction | I | Radical Reactions |
termolecular (3rd order) | I | Electrophilic Addition |
tertiary (3o | I | Classifying carbon |
tetrahedral carbon (sp3 | I | Classifying carbon |
tetrahedral intermediate | I | Carboxylic Acid Derivatives |
tetrahydrofuran (THF) | I | Solvents |
tetramethylsilane (TMS) | I | NMR Spectroscopy |
tetrasubstituted | I | Alkene stability |
theoretical yield | GEN | Lab |
thermodynamic control/product | I | Kinetics vs. Thermodynamics |
thioester | I | Functional Groups |
thioether (sulfide, R-S-R’) | I | Functional Groups |
thiol (thioalcohol; RSH; mercaptan) | I | Functional Groups |
thiolate anion; RS– | I | Functional Groups |
thiophene | I | Heterocycles |
Threonine (Thr or T) | II | Peptides and Proteins |
Thymine (T) | II | Nucleic Acids |
titration | I | Acids and Bases |
toluene (tol.) | I | Aromaticity |
torsional strain | I | Conformational Analysis |
tosylate (-OTs) | I | Substitution |
trans– | I | Stereochemistry |
transesterification | II | Carboxylic Acid Derivatives |
transition metals | II | Organometallics |
transition state | I | Reaction Mechanism |
tricyclic | I | Polycyclic compounds |
triflate (-OTf) | I | Super Leaving groups |
triflic acid (HOTf, TfOH) | I | Substitution |
triglyceride (Triacylglycerol) | II | Fats and Lipids |
triose | II | Sugars |
triple bond | I | Alkynes |
triplet (t) | I | NMR Spectroscopy |
triplet of doublets (td) | I | NMR Spectroscopy |
trisubstituted | I | Alkenes |
Tritium 3H | I | Mass Spectrometry |
Tryptophan (Trp or W) | II | Peptides and Proteins |
Two-Dimensional NMR | II | NMR spectroscopy |
Tyrosine (Tyr or Y) | I | Peptides and Proteins |
unimolecular kinetics | I | Kinetics |
unsaturated / unsaturation | I | Fats and Lipids |
upfield, chemically (shielded) | I | NMR Spectroscopy |
Uracil (U) | II | Nucleic Acids |
valence | I | Trends in the Periodic Table |
Valence Bond Theory | I | Theory |
valence electrons | I | Electron Configuration |
valence shell | I | Electron Configuration |
Valine (Val or V) | I | Peptides and Proteins |
Van der Waals Forces | I | Intermolecular Interactions |
Van ’t Hoff Rule | I | Stereochemistry |
vapor pressure | LAB | |
vaporization | GEN | |
vicinal (1,2 or vic) | I | Nomenclature |
vinyl group | I | Nomenclature |
vinylic Position | I | Nomenclature |
vitamin | II | Enzymes and Co-factors |
VSEPR Guidelines | GEN | |
Walden Inversion | I | Stereochemistry |
Watson-Crick Base Pair | II | Nucleic Acids |
wavenumber (cm-1) | I | IR Spectroscopy |
wavy line (ambiguous configuration) | I | Representing Organic Compounds |
wedge | I | Representing Organic Compounds |
Williamson Ether Synthesis | I | Named Reactions |
Wittig Reaction | II | Ketones and Aldehydes |
Wolff-Kischner Reduction | II | Redox Reactions |
% percent yield (actual yield) | LAB | |
ylide (or ylid) | II | Ketones and Aldehydes |
Z (Ger. Zussamen) olelins, esters, enolates | I | Stereochemistry |
Zaitsev’s Rule | I | Elimination |
zig-zag Structure (see line-angle) | I | Drawing Organic Structures |
zwitterion (‘w’ pronounced as ‘v’) | II | Peptides and Proteins |
Organic-ese Organic Chemistry
Glossary
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