Structure & Reactivity in Organic, Biological and Inorganic Chemistry



Acidity AB1; in amino acids, AB15; Bronsted acids, AB7, AB8; buffers, AB18; dative bonding, AB4, AB5; equilibrium, AB14, AB17; Lewis acids, AB3; pH, AB18; pKa as index of proton donor strength, AB9; pKa table, AX; solvent effects, AB16; structural effects, AB10, AB11, AB12.

Aromatic substitution, electrophilic AR, AR1; activation and deactivation, AR4; directing effects, AR5; electrophile formation, AR3; mechanism, AR2.

Atoms AT; developments up to the nineteenth century, AT1; early twentieth century development, AT2; electron configuration, AT5;  periodic table, AT1, AX; periodic trends, AT6; quantum numbers, AT4.

Basicity factors affecting Bronsted basicity AB13; Lewis bases AB2.

Biomolecules  common classes, IM13, IB; representations of protein structure, IM14; table of amino acids, AX.

Carbonyl functional groups in biology, CO1; as electrophiles, CO2; formation via oxidation, CO20.

Catalytic hydrogenation, OA5.

Conformational analysis CA; acyclic compounds, CA3; bicyclic systems, CA11; computational basis set, CA4; cyclic systems, CA6; in cyclohexanes, CA7, CA9, CA10; diamond lattice drawings, CA8; eclipsed conformation, CA2; heterocycles, CA12; molecular modeling, CA5; planar rings, CA12; staggered conformation, CA2; steric strain, CA3; torsional strain, CA2.

Coordination complexes  AB6; chelation, TM4, CC4; electron counting, TM3, CC3; formation constants, CC2; geometry, TM7; hapticity, CC6; hard and soft acid-base CC7; isomerism, TM5; Jahn-Teller distortion, CC12; lability, CC10; Lewis acid-base interaction, CC1; ligands, TM2, ligand table, AX; ligand field stabilisation energy, CC9; ligand field theory, CC8; ligand substitution, LS; metal ions, TM2; metal-ligand multiple bonds, CC13; naming, TM6; pi coordination (π-coordination) CC5; spectrochemical series, CC10; square bracket notation, TM1.

Covalent bonding IM1.

Electrophilic addition to alkenes EA, EA1; boranes, EA6; bromine and bromonium ions, EA4; carbenes and cyclopropanation, EA9; cationic intermediates, EA2; epoxidation, EA8; mercuration, EA5; oxidations, EA10; polymerization, EA11; solvent participation, EA3;

Electron transfer inner sphere, RO10;  outer sphere, RO9.

Elimination in organic compounds NS12; factors influencing mechanism, NS15; regiochemistry, NS13; stereochemistry, NS14.

Enzyme catalysis EZ; general overview, EZ1; inhibition, reversible vs. irreversible, EZ4;  kinetics, MK5, MK6; post-translational modification, EZ6; strategies for catalysis, EZ3; substrate binding, EZ2; reversible inhibitors, EZ5.

Fatty acid metabolism FA; enzyme catalysis in, FA3; pathway overview, FA1; steps compared to standard organic transformations, FA2.

Functional groups FG; alkyl halides, FG5; aromatics, FG6; carbonyl groups, FG3; carboxyloids FG4; hydrocarbons FG1; simple heteroatom groups FG2.

Hess' Law and reduction potential RO5.

Intermolecular forces or attractions and changes of state, SP2; dipole-dipole interactions, SP5; hydrogen bond acceptors, SP11; hydrogen bonding, SP6; induced dipole-induced dipole or London interactions, SP4; ionic attractions, SP7; and isomers, SP7; and kinetic molecular theory, SP3; in protein structure, SP13; solubility and miscibility, SP9, SP12; solubility of ions, SP10; in water, SP1.

Ionic compounds anions and cations, IC1; counterions, IC2; naming, IC7; physical properties, IC3; solubility, IC4; unit cells, IC5;

Glycolysis GL; and energy storage, GL1; enzyme catalysis in phase one, GL5; enzyme catalysis in phase two, GL7; overview, GL2; steps compared to standard organic transformations, phase one, GL3, GL4; steps compared to standard organic transformations, phase two, GL6; thermodynamics, GL8.

Kinetics and activation parameters, RK3MK1; of aliphatic nucleophilic substitutions, NS3; and elementary reactions, RK7, MK4; in enzymes, MK5, MK6; general, RK, MK; of ligand substitution in transition metal complexes, LS3, LS4, LS5; rate laws, RK6, MK2.

Lewis structures IM2, IM3, IM4; formal charge, IM5; geometry, IM9, IM10; line drawings in organic structures, IM8; molecular ions, IM7; resonance structures, IM6.

Ligand substitution in coordination complexes LS; activation parameters, LS5; associative pathway, LS3; comparative mechanisms, LS2; dissociative pathway, LS4; factors influencing mechanism, LS6; kinetics as evidence of a mechanism, LS3; trans effect, LS7.

Ligands for coordination complexes TM2, TM4; and spectrochemical series, CC10AX; table of ligands, AX.

Macromolecules MM; biomacromolecules, IM13; condensation polymers, CX8; definition, MM1; general synthesis, MM6; glass transition temperature, MM3; living cationic polymerization, EA12; living radical polymerization, RR10; microphase separation, MM5; molecular weight, MM7; olefin or alkene polymerization, EA11; peptide synthesis, CX9; polymer architecture, MM4; radical polymerization, RR9; ring-opening metathesis polymerization, OC10; ring-opening trans-esterification polymerization, CX8b; supramolecular assemblies, MM8; viscosity, MM2; Ziegler-Natta polymerization, EA13.

Metabolic pathways (at Biochemistry Online) MP; anabolic pathways, MP2; catabolic pathways, MP1; cell tutorial, CT0; regulation, MP4, MP5.

Metal ions in biology charge, effect on reduction potential, MB2; environment, effect on reduction potential, MB3; hard & soft acid & base, effect on reduction potential, MB5;  magnetism as evidence of oxidation state, MB7; in nitrogen fixation, NF3; in oxidative phosphorylation, OP; pH, effect on reduction potential, MB4.

Metals close packing, ME3; hexagonal layers, ME2; properties, ME1; unit cells, ME3.

Molecular orbitals MO; in aromatics, MO16; diatomic molecules,  MO6a, MO6b; diatomic hydrogen, MO2b, MO3; diatomics with heteroatoms, MO9; delocalization, MO14, MO15; experimental evidence for, MO7;  frontier orbitals, MO18; geometry and hybridization, MO11, MO12; heteroaromatics, MO17; more complex molecules, MO13; pi bonding (π-bonding), MO5; s and p mixing, MO10; sigma bonding (σ-bonding), MO4; symmetry, MO8; wave behaviour, MO2a.

Network solids NW; aluminosilicates, NW4; cyclosilicates, NW3; diamond, NW1; graphite, NW2; inosilicates, NW3; nesosilicates, NW3; phyllosilicates, NW4; silicates, NW3; sorosilicates, NW3; tectosilicates, NW4.

Nitrogen reduction NF; in the Haber-Bosch process, NF2; model studies for binding, NF4; nitrogenase, NF3; significance on earth, NF1;

Nucleophilic addition to carbonyls CA; activation, CO13; addition of nucleophile, CO7; aldol reaction & condensation, CO12; anomeric center, CO18; arrow conventions in mechanisms, CO4; carbohydrates, furanose and pyranose forms, CO17; conjugate addition, CO22, CO23; elementary steps in mechanism, CO25; molecular orbital picture, CO5; nature of nucleophiles, CO9; neutral nucleophiles (oxygen, nitrogen, sulfur), CO3b, CO14; overall reactivity pattern, CO3; pi donation (π-donation), CO16; proton transfers during, CO8, CO15; reductions in biology, CO19; relative reactivities, CO6; role of solvent, CO10; semi-anionic nucleophiles (metal alkyls and complex hydrides), CO11; in organic synthesis, CO24; ylides, CO21.

Nucleophilic substitution, aliphatic NS;  amine formation, NS17; enolate nucleophiles, NS9; in epoxides, NS11; ether formation, NS16;  formation of oxygen leaving groups, NS10; mechanistic options, NS2; rate laws, NS3; regiochemistry, NS5; relative nucleophilicity, NS8; silicon analogue, NS18; solvent effects, NS7; stereochemistry, NS4; structural factors, NS6;

Nucleophilic substitution, at carboxyloids or carboxylic acid derivatives CX, CX1, CX2; Claisen condensation, CX7; condensation polymers, CX8; formation of acid chlorides, CX5;  interconversion of carboxylic acid derivatives, CX4; peptide synthesis, CX9; protein acetylation, CX10; ring-opening polymerization, CX8b; semi-anionic nucleophiles (metal alkyls and hydrides), CX6; thermodynamic "ski-hill", CX3, CX4, CX5.

Olefin metathesis OC10.

Orbital control, reactions under OC; alkene oxidations, OC8; Claisen and Cope rearrangement, OC2; decarboxylation, OC9; Diels-Alder reaction, OC3, OC4, OC5, OC7; olefin metathesis, OC10; photochemically-induced cycloaddition, OC6.

Organotransition metal reactions MI, OA; beta-elimination (β-elimination) and 1,2-insertion at coordinated alkenes, MI4EA6; carbon monoxide binding, MI2; catalytic coupling reactions, OA6; catalytic hydrogenation, OA5; concerted mechanism of oxidative addition, OA4;  insertions, general,  MI1; migratory insertion, MI3; oxidative addition and reductive elimination,  OA1, OA2; stepwise mechanism of oxidative additions, OA3.

Oxidation of alcohols, CO20; of alkenes, EA10.

Oxidation levels RO12.

Oxidation states RO1, TM2.

Oxidative phosphorylation OP; electron transfer, OP2, OP3, OP4, OP5; proton pumping, OP2, OP4, OP5; ATP synthesis, OP6.

Oxygen reduction OR; metal-binding steps, OR2; metal oxo species, OR4; in oxidative phosphorylation, OP5; reduction steps, OR3.

Periodic table  AT1, AX.

Periodic trends  AT6.

Photochemistry PC; absorbance, PC1; fluorescence & phosphorescence, PC3; in the ozone cycle, PC5; photolysis of transition metal complexes, PC4; photoredox catalysis, PC6, PC7; selection rules, PC2.

Photosynthesis PS; and ATP production, PS7; carbon capture and carbohydrate synthesis, PS8; electron transfer, PS3; location in the plant cell, PS1; oxygen production, PS4; photosystem I, PS6; photosystem II, PS2; proton pump, PS5.

Polymers see macromolecules.

Quantum mechanics early twentieth century development, AT2; quantum numbers, AT4.

Radicals RR; addition to alkenes, RR8; detection by electron paramagnetic resonance (EPR), RR11; initiation through bond homolysis, RR2; initiation through single electron transfer, RR4; in polymerisation, RR9, RR10; propagation, in chain reactions, RR5; singlet and triplet diradicals, RR1; stability of organic radicals, RR3; structure, RR1; substitution in hydrocarbons, RR7; termination steps in chain reactions, RR6.

Rate laws see kinetics.

Rearrangements ER; Baeyer-Villiger, ER3; Beckmann, ER4; Pinacol, ER2; Wolff, ER5.

Reduction and oxidation (redox) RO; in batteries, RO7; charge, effect on reduction potential, MB2; in conversion of ores to metals, RO6; cyclic voltammetry, RO11; electron transfer, inner sphere, RO10; electron transfer, outer sphere, RO9; environment, effect on reduction potential, MB3; hard & soft acid & base, effect on reduction potential, MB5; Hess' Law and RO5; magnetism as evidence of oxidation state, MB7; of metal ions in biology, MB; in organic chemistry, RO12; oxidation levels, RO12; oxidation states, RO1, TM2; oxidative addition and reductive elimination,  OA1, OA2; in oxidative phosphorylation, OP2, OP3, OP4; pH, effect on reduction potential, MB4; redox reactions, RO2, RO8; reduction potentials, RO3, RO4, RO5, RO11.

Spectroscopy fluorescence, PC3; infrared, IR; nuclear magnetic resonance, NMR; structure determination using, SD; two-dimensional NMR, NMR2D;  tables for spectral interpretation, AX; ultraviolet-visible, UV, CC10, PC1, PC2. Related topic: mass spectrometry, MS.

Stereochemistry SC; in alkenes, SC15, SC16; alpha helix, SC13; in amino acids, SC12; in carbohydrates, SC8, SC9; SC11; chiral induction in catalysis, SSC19; chiral resolution, SC14cis and trans in octahedral complexes, SC17; cis and trans in square planar complexes, SC2; diastereomers, SC9, SC10; enantiomers, SC3; in octahedral coordination complexes, SC18; optical activity and polarimetry, SC6, SC7R and S configuration, SC4, SC5.

Supramolecular assemblies see macromolecules.

Thermodynamics TD; le Chatelier's principle, TD5; enthalpy, TD2; entropy, TD3; equilibrium and pKa, TD7; free energy, TD4; free energy and equilibrium, TD6; Hess' Law, TD8; relationship to bond-breaking, TD1.

Transition metal complexes see coordination complexes.

Tricarboxylic acid cycle TC; enzyme catalysis in, TC3; overview, TC1; steps compared to standard organic transformations, TC2.

UV-visible spectroscopy UV; absorbance UV1, PC1; metal ions & coordination complexes UV2, CC10; organic compounds UV3; selection rules  PC2.


This site is written and maintained by Chris P. Schaller, Ph.D., College of Saint Benedict / Saint John's University (with contributions from other authors as noted).  It is freely available for educational use.

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This material is based upon work supported by the National Science Foundation under Grant No. 1043566.

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