Organic Mechanisms

Preface Chapter 1 Fundamental Principles 1.1 - Reaction mechanisms and their importance 1.2 - Elementary (concerted) and stepwise reactions 1.3 - Molecularity 1.3.1 - Unimolecular reactions 1.3.2 - Bimolecular reactions 1.4 - Kinetics 1.4.1 - Rate-laws for elementary (concerted) reactions 1.4.2 - Reactive intermediates and the steady-state assumption 1.4.3 - Rate-laws for stepwise reactions 1.5 - Thermodynamics 1.5.1 - Enthalpy, entropy, and free energy 1.5.2 - Reversible and irreversible reactions 1.5.3 - Chemical equilibrium 1.6 - The transition state 1.6.1 - The transition state 1.6.2 - The Hammond postulate 1.6.3 - The Bell-Evans-Polanyi principle 1.7 - Electronic effects and Hammett equation 1.7.1 - Electronic effects of substituents 1.7.2 - Hammett equation 1.8 - The molecular orbital theory 1.8.1 - Formation of molecular orbitals from atomic orbitals 1.8.2 - Molecular orbital diagrams 1.8.3 - Resonance stabilization 1.8.4 - Frontier molecular orbitals 1.9 - Electrophiles/nucleophiles versus acids/bases 1.9.1 - Common electrophiles 1.9.2 - Common nucleophiles 1.10 - Isotope labeling 1.11 - Enzymes: Biological catalysts 1.12 - The green chemistry methodology Problems References Chapter 2 The Aliphatic C-H Bond Functionalization 2.1 - Alkyl radicals: Bonding and their relative stability 2.2 - Radical halogenations of the C-H bonds on sp3-hybridized carbons: Mechanism and nature of the transition states 2.3 - Energetics of the radical halogenations of alkanes and their regioselectivity 2.3.1 - Energy profiles for radical halogenation reactions of alkanes 2.3.2 - Regioselectivity for radical halogenation reactions 2.4 - Kinetics of radical halogenations of alkanes 2.5 - Radical initiators 2.6 - Transition-metal-compounds catalyzed alkane C-H bond activation and functionalization 2.6.1 - The C-H bond activation via agostic bond 2.6.2 - Mechanisms for the C-H bond oxidative functionalization 2.7 - Superacids catalyzed alkane C-H bond activation and functionalization 2.8 - Nitration of aliphatic C-H bonds via the nitronium NO2+ ion 2.9 - Photochemical and thermal C-H bond activation by the oxidative uranyl UO22+(VI) cation 2.10 - Enzyme catalyzed alkane C-H bond activation and functionalization: Biochemical methods Problems References Chapter 3 Functionalization of the Alkene C=C Bond by Electrophilic Additions 3.1 - Markovnikov additions via intermediate carbocations 3.1.1 - Protonation of the alkene C=C p bond by strong acids to form carbocations 3.1.2 - Additions of hydrogen halides (HCl, HBr, and HI) to alkenes: Mechanism, regiochemistry, and stereochemistry 3.1.3 - Acid and transition-metal catalyzed hydration of alkenes and its applications 3.1.4 - Acid catalyzed additions of alcohols to alkenes 3.1.5 - Special electrophilic additions of the alkene C=C bond: Mechanistic and synthetic aspects 3.1.6 - Electrophilic addition to the C C triple bond via a vinyl cation intermediate 3.2 - Electrophilic addition of hydrogen halides to conjugated dienes 3.3 - Non-Markovnikov radical addition 3.4 - Hydroboration: Concerted, non-Markovnikov syn-addition 3.4.1 - Diborane (B2H6): Structure and properties 3.4.2 - Concerted, non-Markovnikov syn-addition of borane (BH3) to the alkene C=C bond: Mechanism, regiochemisty and stereochemistry 3.4.3 - Synthesis of special hydroborating reagents 3.4.4 - Reactions of alkenes with special hydroborating reagents: Regiochemistry, stereochemistry and their applications in chemical synthesis 3.5 - Transition-metal catalyzed hydrogenation of the alkene C=C bond (syn-addition) 3.5.1 - Mechanism and stereochemistry 3.5.2 - Synthetic applications 3.5.3 - Biochemically related applications: Hydrogenated fats (oils) 3.6 - Halogenation of the alkene C=C bond (Anti-addition): Mechanism and its stereochemistry Problems References Chapter 4 Functionalization of the Alkene C=C Bond by Cycloaddition Reactions 4.1 - Cycloadditions of the alkene C=C bond to form three-membered rings 4.1.1 - Epoxidation 4.1.2 - Cycloadditions via carbenes and related species 4.2 - Cycloadditions to form four-membered rings 4.3 - Deals-Alder cycloadditions of the alkene C=C bond to form six-membered rings 4.3.1 - Frontier molecular orbital interactions 4.3.2 - Substituent effects 4.3.3 - Other Diels-Alder reactions 4.4 - 1,3-Dipolar cycloadditions of the C=C and other multiple bonds to form five- membered rings 4.4.1 - Oxidation of alkenes by ozone (O3) and osmium tetraoxide (OsO4) via cycloadditions 4.4.2 - Cycloadditions of nitrogen-containing 1,3-dipoles to alkenes 4.4.3 - Cycloadditions of the dithionitronium (NS2+) ion to alkenes, alkynes, and nitriles: Making CNS-containing aromatic heterocycles 4.5 - Other pericyclic reactions 4.6 - Deals-Alder cycloadditions in water: The green chemistry methods 4.7 - Biological applications 4.7.1 - Photochemical synthesis of Vitamin D2 via a cyclic transition state 4.7.2 - Ribosome-catalyzed peptidyl transfer via a cyclic transition state: Biosynthesis of proteins Problems References Chapter 5 The Aromatic C-H bond Functionalization and Related Reactions 5.1 - Aromatic nitration: All reaction intermediates and full mechanism for the aromatic C-H bond substitution by nitronium (NO2+) and related electrophiles 5.1.1 - Charge-transfer complex [ArH, NO2+] between arene and nitronium 5.1.2 - Ion-radical pair [ArH+.,NO2.] 5.1.3 - Arenium [Ar(H)NO2]+ ion 5.1.4 - Full mechanism for aromatic nitration 5.2 - Mechanisms and synthetic utility for aromatic C-H bond substitutions by other related electrophiles 5.3 - The iron (III) catalyzed electrophilic aromatic C-H bond substitution 5.4 - The electrophilic aromatic C-H bond substitution reactions via SN1 and SN2 mechanisms 5.4.1 - Reactions involving SN1 steps 5.4.2 - Reactions involving SN2 steps 5.5 - Substituent effects on the electrophilic aromatic substitution reactions 5.5.1 - Ortho- and para-directors 5.5.2 - Meta-directors 5.6 - Isomerizations effected by the electrophilic aromatic substitution reactions 5.7 - Electrophilic substitution reactions on the aromatic carbon-metal bonds: Mechanisms and synthetic applications 5.7.1 - Aryl Grignard and aryllithium compounds 5.7.2 - Ortho-metallation-directing groups (MDGs): Mechanism and synthetic applications 5.8 - Nucleophilic aromatic substitution via a benzyne (aryne) intermediate: Functional group transformations on aromatic rings 5.9 - Nucleophilic aromatic substitution via an anionic Meisenheimer complex 5.10 - Biological applications of functionalized aromatic compounds Problems References Chapter 6 Nucleophilic Substitutions on sp3-Hybridized Carbons: Functional Group Transformations 6.1 - Nucleophilic substitution on mono-functionalized sp3-hybridized carbon 6.2 - Functional groups which are good and poor leaving groups 6.3 - Good and poor nucleophiles 6.4 - SN2 reactions: Kinetics, mechanism, and stereochemistry 6.4.1 - Mechanism and stereochemistry for SN2 reactions 6.4.2 - Steric hindrance on SN2 reactions. 6.4.3 - Effect of nucleophiles 6.4.4 - Solvent effect 6.4.5 - Effect of unsaturated groups attached to the functionalized electrophilic carbon 6.5 - Analysis of the SN2 mechanism using symmetry rules and molecular orbital theory 6.5.1 - The SN2 reactions of methyl and primary haloalkanes RCH2X (X =Cl, Br, or I; R = H or an Alkyl Group) 6.5.2 - Reactivity of Dichloromethane CH2Cl2 6.6 - SN1 reactions: Kinetics, mechanism, and product development 6.6.1 - The SN1 mechanism and rate law 6.6.2 - Solvent effect 6.6.3 - Effects of carbocation stability and quality of leaving group on the SN1 rates 6.6.4 - Product development for SN1 reactions 6.7 - Competitions between SN1 and SN2 reactions 6.8 - Some useful SN1 and SN2 reactions: Mechanisms and synthetic perspectives 6.8.1 - Nucleophilic substitution reactions effected by carbon nucleophiles. 6.8.2 - Synthesis of primary amines 6.8.3 - Synthetic utility of triphenylphosphine: A strong phosphorus nucleophile 6.8.4 - Neighboring group assisted SN1 reactions 6.8.5 - Nucleophilic substitution reactions of alcohols catalyzed by solid Bronsted acids: A green chemistry approach 6.9 - Biological applications of nucleophilic substitution reactions 6.9.1 - Biomedical applications 6.9.2 - Glycoside hydrolases: Enzymes catalyzing hydrolytic cleavage of the glycosidic bonds by the SN2-like reactions 6.9.3 - Biosynthesis involving nucleophilic substitution reactions 6.9.4 - An enzyme-catalyzed nucleophilic substitution of an haloalkane Problems References Chapter 7 Eliminations 7.1 - E2 Elimination: Bimolecular b-elimination of H/LG and its regiochemistry and stereochemistry 7.1.1 - Mechanism and regiochemistry 7.1.2 - E2 eliminations of functionalized cycloalkanes 7.1.3 - Stereochemistry 7.2 - Analysis of the E2 mechanism using symmetry rules and molecular orbital theory 7.2.1 - Chain-like haloalkanes 7.2.2 - Halocyclohexane 7.2.3 - Quantitative theoretical studies of E2 reactions 7.3 - Basicity versus nucleophilicity for various anions 7.4 - Competition of E2 and SN2 reactions 7.5 - E1 Elimination: Stepwise b-elimination of H/LG via an intermediate carbocation and its rate-law 7.5.1 - Mechanism and rate law 7.5.2 - E1 dehydration of alcohols 7.6 - Energy profiles for E1 reactions 7.6.1 - The Bell-Evens-Polanyi Principle 7.6.2 - The E1 dehydration of alcohols (ROH) 7.6.3 - The E1 dehydrohalogenation of haloalkanes (RX, X = Cl, Br, or I) 7.7 - The E1 elimination of ethers 7.8 - Intramolecular (unimolecular) eliminations via a cyclic transition state 7.8.1 - Concerted, syn-elimination of esters 7.8.2 - Selenoxide elimination 7.8.3 - Silyloxide elimination 7.8.4 - Unimolecular elimination of hydrogen halide from haloalkanes 7.9 - Mechanisms for reductive elimination of LG1/LG2 (two functional groups) on adjacent carbons 7.10 - The a-Elimination giving a carbene: A mechanistic analysis using symmetry rules and molecular orbital theory 7.10.1 - The bimolecular a-elimination of trichloromethane (CHCl3) giving dichlorocarbene (CCl2) 7.10.2 - Formation of a carbene by unimolecular a-elimination of a haloalkane and the subsequent rearrangement to an alkene via a C-H (C-D) bond elimination 7.11 - E1cb elimination 7.12 - Biological applications: Enzyme-catalyzed biological elimination reactions 7.12.1 - The enzyme-catalyzed b-oxidation of fatty acyl coenzyme A 7.12.2 - Elimination reactions involved in biosynthesis Problems References Chapter 8 Nucleophilic Additions and Substitutions on Carbonyl Groups 8.1 - Nucleophilic additions and substitutions of carbonyl compounds 8.2 - Nucleophilic additions of aldehydes and ketones and their biological applications 8.2.1 - Acid and base catalyzed hydration of aldehydes and ketones 8.2.2 - Acid catalyzed nucleophilic additions of alcohols to aldehydes and ketones 8.2.3 - Biological applications: Cyclic structures of carbohydrates 8.2.4 - Addition of sulfur nucleophile to aldehydes 8.2.5 - Nucleophilic addition of amines to ketones and aldehydes 8.2.6 - Nucleophilic additions of hydride donors to aldehydes and ketones: Organic reductions and mechanisms 8.3 - Biological hydride donors NAD(P)H and FADH2 8.4 - Activation of carboxylic acids via nucleophilic substitutions on the carbonyl carbons 8.4.1 - Reactions of carboxylic acids with thionyl chloride 8.4.2 - Esterification reactions, synthetic applications, and green chemistry methods 8.4.3 - Formation of anhydrides 8.4.4 - Nucleophilic addition to alkyllithium 8.5 - Nucleophilic substitutions of acyl derivatives and their biological applications 8.5.1 - Nucleophilic substitutions of acyl chlorides and anhydrides 8.5.2 - Hydrolysis and other nucleophilic substitutions of esters 8.5.3 - Biodiesel synthesis and reaction mechanism 8.5.4 - Biological applications: Mechanisms for serine-type hydrolases 8.6 - Reduction of acyl derivatives by hydride donors 8.7 - Kinetics of the Nucleophilic addition and substitution of acyl derivatives Problems References Chapter 9 Reactivity of the a-Hydrogen to Carbonyl Groups 9.1 - Formation of enolates and their nucleophilicity 9.1.1 - Formation of enolates 9.1.2 - Molecular orbitals and nucleophilicity of enolates 9.2 - Alkylation of carbonyl compounds (aldehydes, ketones, and esters) via enolates and hydrazones 9.2.1 - Alkylation via enolates 9.2.2 - Alkylation via hydrazones and enamines 9.3 - Aldol reactions 9.3.1 - Mechanism and synthetic utility 9.3.2 - Stereoselectivity 9.3.3 - Other synthetic applications 9.4 - Acylation reactions of esters via enolates: Mechanism and synthetic utility 9.5 - Biological applications: Roles of enolates in metabolic processes in living organisms 9.5.1 - The citric acid cycle and mechanism for citrate synthase 9.5.2 - Ketogenesis and thiolase Problems References Chapter 10 Rearrangements 10.1 - Major types of rearrangements 10.2 - Rearrangement of carbocations: 1,2-Shift 10.2.1 - 1,2-Shifts in carbocations produced from acyclic molecules 10.2.2 - 1,2-Shifts in carbocations produced from cyclic molecules - Ring expansion 10.2.3 - Resonance stabilization of carbocation - Pinacol rearrangement 10.2.4 - In vivo cascade carbocation rearrangements: Biological significance 10.2.5 - Acid catalyzed 1,2-shift in epoxides 10.2.6 - Anion initiated 1,2-shift 10.3 - Neighboring leaving group facilitated 1,2-rearrangement 10.3.1 - Beckmann rearrangement 10.3.2 - Hofmann rearrangement 10.3.3 - Baeyer-Villiger oxidation (rearrangement) 10.3.4 - Acid catalyzed rearrangement of organic peroxides 10.4 - Carbene rearrangement: 1,2-Rearrangement of hydrogen facilitated by a lone pair of electrons 10.5 - Claisen rearrangement 10.6 - Claisen rearrangement in water: The green chemistry methods 10.7 - Photochemical isomerization of alkenes and its biological applications 10.7.1 - Photochemical isomerization 10.7.2 - Biological relevance 10.8 - Rearrangement of carbon-nitrogen-sulfur containing heterocycles Problems References

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