Structure & Reactivity in Organic, Biological and Inorganic Chemistry

Index

 

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.

 

 

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.

Creative Commons License
Structure & Reactivity in Organic, Biological and Inorganic Chemistry by Chris Schaller is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License

Send corrections to cschaller@csbsju.edu

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

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

 

Back to Structure & Reactivity Main Page

Back to CSB/SJU