Bioorganic synthesis : an introduction

Content: Note continued: Study Problems --
Why We Synthesize Organic Compounds --
Synthetic Challenges: Total Synthesis --
Synthetic Challenges: Semisynthesis --
Synthetic Challenges: Biomimetic Synthesis --
Synthetic Challenges: Structural Revision or Confirmation --
Synthetic Challenges: Formal Synthesis --
Synthetic Challenges: Stereoselective Synthesis of Optically Pure Compounds --
Resolution of Enantiomers to Obtain Optically Pure Compounds --
Use of Chiral Pool Compounds for Synthesis of Optically Pure Natural Products --
Use of Chiral Reagents for Synthesis of Optically Pure Compounds --
Use of Chiral Substrate Control for Stereoselective Synthesis --
Use of Chiral Auxiliaries for Synthesis of Optically Pure Compounds --
Use of Chiral Catalysis for Synthesis of Optically Pure Compounds --
Use of Enzymes for Synthesis of Optically Pure Compounds: Biocatalysis --
Some Final Thoughts --
Study Problems. Machine generated contents note: The Unique Role of Carbon --
Distinguishing Primary Versus Secondary Metabolism --
Secondary Metabolites and Natural Products --
Natural Products in Organic Chemistry and Medicine --
The Organic Chemistry of Biosynthesis --
Goals and Structure of This Book --
Review of Functional Groups, Stereochemistry, and Conformational Analysis --
Prochiral Relationships: One Step from Chirality --
Prochiral it-Systems: "Two-Faced" Reaction Centers --
Diastereotopic Atoms and Groups: One Step from a Diasteroeomer --
Monosubstituted Cyclohexanes: Favoring Equatorial Positions --
Disubstituted Cyclohexanes: Equivalent and Nonequivalent Combinations --
Bicyclic Systems: Joining of Rings --
Heterocyclic Ring Systems: One Atom Makes All the Difference --
Bond Making and Breaking: Have Pair, Will Share
 Need Two from You --
Bronsted Acid-Base Reactions: Proton Donors Gladly Accepted --
Acidity Trends: Why that Proton Is or Isn't Acidic --
Carbocations: Three Bonds to Carbon Can Be a Plus --
Radicals: Odd and Reactive --
Elimination Reactions: Introducing the Carbon-Carbon n-Bond --
Carbocations: Rearrangements and Fates --
Electrophilic Additions: n-Bonds as Nucleophilic Agents --
Nucleophilic Substitutions and Alkylations: Make or Break for C-X Bonds --
Nucleophilic Carbonyl Addition Reactions: C=O n-Bond under Attack --
Imine Formation: Making the Essential C=N Linkage --
Nucleophilic 1,4-(Conjugate) Addition Reactions: Remote Attack on Conjugated Carbonyls --
Nucleophilic Acyl Substitution Reactions: Turning One Acyl Compound into Another --
Looking Ahead --
Study Problems --
Enzymes: The Catalysts of Biological Organic Chemistry --
Cofactors: Enzyme Assistants in Bioorganic Reactions --
NADH/NADPH: Nature's Version of Sodium Borohydride for Carbonyl Reduction --
NAD+/NADP+: Nature's Version of PCC for Alcohol Oxidation --
FAD: Another Hydride Acceptor for Dehydrogenations --
Monooxygenases: Special Delivery of One 0 atom from 02 --
Dioxygenases: Delivering Both 0 Atoms from 02 --
Other Oxidations: Hydroquinone and Catechol Oxidations --
Amine Oxidations: From Imines to Carbonyl Compounds and Beyond --
PLP: Transamination and Decarboxylation of Amino Acids --
Other Important Decarboxylations: 13-Keto Acids, o- and p-Hydroxybenzoic Acids --
Thiamine Diphosphate (TPP) and Lipoic Acid: Decarboxylation and Acyl Transfer --
Biotin: The CO2 Carrier, Transport, and Transfer Agent --
SAM: A C1 Fragment for Methyl Groups --
DMAPP: An Allylic C, Fragment for Structure Building --
Other Essential Structural Fragments: Putting it All Together --
Looking Ahead --
Study Problems --
What Makes a Carbohydrate? --
Cyclic Hemiacetals and Anomers --
C-2 Epimers and Enediols[—]Simple Conversion of One Carbohydrate into Another --
Other Important Monosaccharides: Deoxy and Amino Sugars --
The Significance of the Anomeric Carbon: Glycoside Formation --
UDP-Sugars and Glycoside Formation: SN2 Chemistry at Work --
Organic Reactions in Carbohydrate Chemistry: Overview of Glucose Metabolism --
Glycolysis: A 10-Step Program --
What Happens to the Pyruvic Acid from Glycolysis --
The Citric Acid Cycle: Another 10-Step Program --
The Pentose Phosphate Pathway: Seven Alternative Steps to Some Familiar Intermediates --
The Big Picture --
Amino Acids: More Important Primary Metabolite Building Blocks for Biosynthesis --
Biosynthesis of Serine: A Good Place to Start --
Peptides and Proteins: A Very Brief Review --
Putting Proteins and Carbohydrates Together: Glycoproteins Versus Protein Glycosylation --
Looking Ahead --
Study Problems --
Classification of Terpenes: How Many Isoprene Units? --
The Mevalonic Acid Route to DMAPP and IPP --
The Deoxyxylulose Phosphate Route to IPP and DMAPP --
Hemiterpenes: Just One Isoprene Unit --
Monoterpenes (C10) and Isoprene Linkage: Heads, IPP Wins
 Tails, DMAPP Loses --
Geranyl PP to Neryl PP via Linalyl PP: The Importance of Alkene Stereochemistry --
Some Acyclic Monoterpenes and Their Uses --
Mono- and Bicyclic Monoterpenes via Cationic Cyclizations and Wagner-Meerwein Shifts --
What's that Smell? Limonene Derivatives as Flavor and Fragrance Compounds --
Irregular Monoterpenes: If Not Head-to-Tail, then How? --
Iridoids: From Catnip to Alkaloids --
Sesquiterpenes (C15): Linking of Different Starter Units --
Some FPP Cyclizations in Sesquiterpene Biosynthesis --
Trichodiene and the Trichothecenes: How to Trace a Rearrangement Pathway --
Diterpenes (C20): Taking it to the Next Level of Molecular Complexity and Diversity --
Cyclic Diterpenes: From Baseball and Plant Hormones to Anticancer Drugs --
Sesterterpenes (C25): Less Common, More Complex --
Triterpenes and Steroids: Another Case of Irregular Linkage of Terpene Units --
Oxidosqualene and Steroid Biosynthesis: Cyclization to Lanosterol and Beyond --
Conversion of Lanosterol (C30) to Cholesterol (C27): Where Did the Carbons Go? --
Conversions of Cholesterol: Production of the Sex Hormones --
Dehydrocholesterol, Sunshine, and Vitamin D3 Biosynthesis --
Tetraterpenes and Carotenoids: Tail-to-Tail Linkage of C20 Units --
Looking Ahead --
Study Problems --
Fatty Acids: Multiples of Two Carbons, Saturated or Unsaturated --
Saturated Fatty Acid Biosynthesis: It All Starts with Acetyl-CoA --
Branched Fatty Acids: Different Routes and Different Results --
Mono- and Polyunsaturated Fatty Acids: Putting in the "Essential" Double Bonds --
Aerobic Versus Anaerobic Routes to Desaturation --
Further Desaturation of Fatty Acids: Triple Bonds and Rings --
Prostaglandins, Thromboxanes, and Leukotrienes: The Power of Oxygenated FAs --
Polyketide Biosynthesis: More Starter Units and Extender Units, but with a Twist --
Aromatic Polyketide Natural Products: Phenols and Related Structures --
Isotopic Labeling Studies: Biosynthetic Insights via 13C NMR --
Further Modification of Polyketides: Alkylations, Oxidations, Reductions, and Decarboxylations --
Other Oxidative Modifications of Aromatic Rings: Expansion or Cleavage Processes --
Oxidative Coupling of Phenols: Formation of Aryl-Aryl Bonds --
The Use of Other Starter Groups: From Cancer Drugs and Antibiotics to Poison Ivy --
More on Polyketide Synthase (PKS) Systems: Increasing Product Diversity --
Modular Type I PKS Complexes and Macrolide Antibiotics: Erythromycin Biosynthesis --
Genetic Manipulation of Modular PKS Systems: Rational Drug Modification --
Some Final PKS Products of Medicinal Importance --
Looking Ahead --
Study Problems --
What Is Shikimic Acid? --
Shikimic, Chorismic, and Prephenic Acids at the Heart of the Pathway --
The Claisen Rearrangement: Allyl Vinyl Ethers in a Chair --
Conversion of Chorismic Acid to Prephenic Acid --
Conversion of Prephenic Acid to Phenylalanine or Tyrosine --
More Uses for Chorismic Acid --
Shikimic Acid Pathway Products from Phenylalanine and Tyrosine: An Overview --
Phenylpropanoids: A Large Family of Phenyl C3 Compounds --
Phenylpropanoids: Reduction of Acids to Phenyl C3 Aldehydes and Alcohols --
Reduction of Phenyl C3 Alcohols to Phenylpropenes --
Lignans and Lignin: Oxidative Phenolic Coupling with a Twist --
Coniferyl Alcohol Oxidative Coupling: Allyl C-Radical + Allyl C-Radical --
Coniferyl Alcohol Oxidative Coupling: Ortho C-Radical + Allyl C-Radical --
Coniferyl Alcohol Oxidative Coupling: O-Radical + Allyl C-Radical --
Lignin: A Plant Polymer and Major Source of Carbon --
Podophyllotoxin Biosynthesis: Aryltetralin Lignans from the American Mayapple --
Cleavage of Cinnamic Acids to Phenyl Cl Compounds: Different Routes, Similar Outcomes --
Coumarins: Sweet-Smelling Benzopyrones --
Mixed Products: Combining the Shikimate, Polyketide, and Terpenoid Pathways --
Kavalactones: Natural Sedatives from the South Pacific --
Flavonoids: Structurally Diverse Plant Polyphenolics --
The Chalcone-to-Flavanone-to-Flavone Sequence: Formation of Apigenin --
The Flavanone-to-Dihydroflavonol-to-Anthocyanin Sequence: Formation of Pelargonidin --
The Flavanone-to-Isoflavanone-to-Isoflavone Sequence: Formation of Genistein --
Isoflavanoid Structural Modifications: Production of Antimicrobial Phytoalexins --
Rotenoids: Fish Poisons from Isoflavones --
Looking Ahead --
Study Problems --
Alkaloid Structure: The Importance of N-Heterocycles --
Alkaloids Not Derived from Amino Acids: Amination Reactions, Poisons, and Venoms --
Amino Acids and Mannich Reactions: Important Keys to Alkaloid Biosynthesis --
Alkaloids from Ornithine: Tropanes via the Mannich Reaction in Action --
Pyrrolizidine Alkaloids: Poison Plants and Insect Defense --
Piperidine-Type Alkaloids Derived from Lysine --
Quinolizidine Alkaloids: Livestock Poisons from Cadaverine --
Alkaloids from Phenylalanine: From Neurotransmitters to Decongestants and Narcotics --
Alkaloids from Tyrosine: The Pictet-Spengler Reaction in Alkaloid Biosynthesis --
(S)-Reticuline: A Versatile Pictet-Spengler-Derived Benzyltetrahydroisoquinoline --
Oxidative Coupling in Alkaloid Biosynthesis: Biosynthesis of Corytuberine and Morphine --
The Morphine Rule --
Alkaloids from Tryptophan: Adventures in Indole Alkaloid Structural Complexity --
Pictet-Spengler-Type Reactions of Tryptamine: p-Carbolines and Indole Terpene Alkaloids --
Alkaloids from Nicotinic Acid: Toxic Addictive Derivatives of a Common Nutrient --
Alkaloids from Anthranilic Acid: From Tryptophan to Quinolines and Acridines --
Alkaloids from Histidine: From Simple Amides to Glaucoma Drugs --
Purine Alkaloids: Addictive Stimulants in our Coffee, Tea, and Chocolate --
Cyclic and Macrocyclic Peptides: From Sweeteners to Antibiotics and Beyond --
Penicillins, Cephalosporins, and Carbapenums: The Essential p-Lactam Antibiotics --
A Final Look Ahead