1 A Review of General Chemistry: Electrons, Bonds, and Molecular Properties 1

1.1 Introduction to Organic Chemistry 2

1.2 The Structural Theory of Matter 3

1.3 Electrons, Bonds, and Lewis Structures 4

1.4 Identifying Formal Charges 7

1.5 Induction and Polar Covalent Bonds 8

1.6 Reading Bond- Line Structures 11

1.7 Atomic Orbitals 14

1.8 Valence Bond Theory 17

1.9 Molecular Orbital Theory 18

1.10 Hybridized Atomic Orbitals 20

1.11 Predicting Molecular Geometry: VSEPR Theory 26

1.12 Dipole Moments and Molecular Polarity 30

1.13 Intermolecular Forces and Physical Properties 33

WorldLinks Biomimicry and Gecko Feet 37

BioLinks Drug- Receptor Interactions 38

1.14 Solubility 39

BioLinks Propofol: The Importance of Drug Solubility 40

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2 Molecular Representations 49

2.1 Molecular Representations 50

2.2 Bond- Line Structures 52

2.3 Identifying Functional Groups 54

BioLinks Marine Natural Products 55

2.4 Carbon Atoms with Formal Charges 57

2.5 Identifying Lone Pairs 57

2.6 Three- Dimensional Bond- Line Structures 60

BioLinks The Opioids 61

2.7 Introduction to Resonance 62

2.8 Curved Arrows 64

2.9 Formal Charges in Resonance Structures 66

2.10 Drawing Resonance Structures via Pattern Recognition 68

2.11 Assessing the Relative Importance of Resonance Structures 73

2.12 The Resonance Hybrid 77

2.13 Delocalized and Localized Lone Pairs 79

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3 Acids and Bases 91

3.1 Introduction to Brønsted- Lowry Acids and Bases 92

3.2 Flow of Electron Density: Curved- Arrow Notation 92

BioLinks Antacids and Heartburn 94

3.3 Brønsted- Lowry Acidity: Quantitative Perspective 95

BioLinks Drug Distribution and pK a 101

3.4 Brønsted- Lowry Acidity: Qualitative Perspective 102

3.5 Brønsted- Lowry Acidity: Assessing the Relative Acidity of Cationic Acids 113

3.6 Position of Equilibrium and Choice of Reagents 118

3.7 Leveling Effect 121

3.8 Solvating Effects 122

3.9 Counterions 123

WorldLinks Baking Soda versus Baking Powder 123

3.10 Lewis Acids and Bases 124

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4 Alkanes and Cycloalkanes 137

4.1 Introduction to Alkanes 138

4.2 Nomenclature of Alkanes 138

WorldLinks Pheromones: Chemical Messengers 142

BioLinks Naming Drugs 150

4.3 Constitutional Isomers of Alkanes 151

4.4 Relative Stability of Isomeric Alkanes 152

4.5 Sources and Uses of Alkanes 153

WorldLinks An Introduction to Polymers 155

4.6 Drawing Newman Projections 155

4.7 Conformational Analysis of Ethane and Propane 157

4.8 Conformational Analysis of Butane 159

BioLinks Drugs and Their Conformations 163

4.9 Cycloalkanes 163

BioLinks Cyclopropane as an Inhalation Anesthetic 165

4.10 Conformations of Cyclohexane 166

4.11 Drawing Chair Conformations 167

4.12 Monosubstituted Cyclohexane 169

4.13 Disubstituted Cyclohexane 171

4.14 cis-trans Stereoisomerism 175

4.15 Polycyclic Systems 176

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5 Stereoisomerism 187

5.1 Overview of Isomerism 188

5.2 Introduction to Stereoisomerism 189

WorldLinks The Sense of Smell 194

5.3 Designating Configuration Using the Cahn-Ingold-Prelog System 194

BioLinks Chiral Drugs 199

5.4 Optical Activity 200

5.5 Stereoisomeric Relationships: Enantiomers and Diastereomers 206

5.6 Symmetry and Chirality 209

5.7 Fischer Projections 213

5.8 Conformationally Mobile Systems 215

5.9 Chirality without a Chiral Center 216

5.10 Resolution of Racemic Mixtures 217

5.11 Asymmetric Synthesis: Stereoselective and Stereospecific Reactions 219

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6 Chemical Reactivity and Mechanisms 229

6.1 Enthalpy 230

6.2 Entropy 233

6.3 Gibbs Free Energy 235

WorldLinks Explosives 236

WorldLinks Do Living Organisms Violate the Second Law of Thermodynamics? 238

6.4 Equilibria 238

6.5 Kinetics 240

BioLinks Nitroglycerin: An Explosive with Medicinal Properties 243

WorldLinks Beer Making 244

6.6 Energy Diagrams 245

6.7 Nucleophiles and Electrophiles 248

6.8 Mechanisms and Arrow Pushing 252

6.9 Combining the Patterns of Arrow Pushing 257

6.10 Drawing Curved Arrows 259

6.11 Carbocation Rearrangements 262

6.12 Reversible and Irreversible Reaction Arrows 264

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7 Substitution Reactions 277

7.1 Introduction to Substitution Reactions 278

7.2 Alkyl Halides 279

7.3 Possible Mechanisms for Substitution Reactions 283

7.4 The S N 2 Mechanism 285

BioLinks Pharmacology and Drug Design 291

7.5 Nucleophilic Strength in S N 2 Reactions 293

BioLinks S N 2 Reactions in Biological Systems-Methylation 293

7.6 The S N 1 Mechanism 295

7.7 Solvent Effects in Substitution Reactions 301

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8 Alkenes: Structure and Preparation via Elimination Reactions 313

8.1 Introduction to Elimination Reactions 314

8.2 Stereoisomerism in Alkenes 314

BioLinks Phototherapy Treatment for Neonatal Jaundice 317

8.3 Stability of Alkenes and Cycloalkenes 319

8.4 Possible Mechanisms for Elimination Reactions 321

8.5 The E2 Mechanism 323

8.6 Regiochemical and Stereochemical Outcomes for E2 Reactions 325

8.7 The E1 Mechanism 335

8.8 Predicting Products: Substitution vs. Elimination 342

8.9 Substitution and Elimination Reactions with Other Substrates 348

8.10 Synthesis Strategies - Substitution and Elimination 352

BioLinks Radiolabeled Compounds in Diagnostic Medicine 356

SpecialTopic Kinetic Isotope Effects 361

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9 Addition Reactions of Alkenes 371

9.1 Introduction to Addition Reactions 372

9.2 Alkenes in Nature and in Industry 373

WorldLinks Pheromones to Control Insect Populations 373

9.3 Nomenclature of Alkenes 374

9.4 Addition vs. Elimination: A Thermodynamic Perspective 376

9.5 Hydrohalogenation 377

WorldLinks Cationic Polymerization and Polystyrene 384

9.6 Acid-Catalyzed Hydration 385

9.7 Oxymercuration-Demercuration 389

9.8 Hydroboration-Oxidation 390

9.9 Catalytic Hydrogenation 396

WorldLinks Partially Hydrogenated Fats and Oils 401

9.10 Halogenation and Halohydrin Formation 402

9.11 Anti Dihydroxylation 406

9.12 Syn Dihydroxylation 409

9.13 Oxidative Cleavage 411

9.14 Predicting the Products of an Addition Reaction 413

9.15 Synthesis Strategies 415

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10 Alkynes 431

10.1 Introduction to Alkynes 432

BioLinks The Role of Molecular Rigidity 434

WorldLinks Conducting Organic Polymers 435

10.2 Nomenclature of Alkynes 435

10.3 Acidity of Acetylene and Terminal Alkynes 437

10.4 Preparation of Alkynes 440

10.5 Reduction of Alkynes 442

10.6 Hydrohalogenation of Alkynes 445

10.7 Hydration of Alkynes 447

10.8 Halogenation of Alkynes 453

10.9 Ozonolysis of Alkynes 453

10.10 Alkylation of Terminal Alkynes 454

10.11 Synthesis Strategies 456

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11 Radical Reactions 467

11.1 Radicals 468

11.2 Common Patterns in Radical Mechanisms 473

11.3 Chlorination of Methane 476

11.4 Thermodynamic Considerations for Halogenation Reactions 480

11.5 Selectivity of Halogenation 482

11.6 Stereochemistry of Halogenation 485

11.7 Allylic Bromination 487

11.8 Atmospheric Chemistry and the Ozone Layer 490

WorldLinks Fighting Fires with Chemicals 492

11.9 Autooxidation and Antioxidants 493

BioLinks Why Is an Overdose of Acetaminophen Fatal? 495

11.10 Radical Addition of HBr: Anti-Markovnikov Addition 496

11.11 Radical Polymerization 500

11.12 Radical Processes in the Petrochemical Industry 502

11.13 Halogenation as a Synthetic Technique 502

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12 Systematic Approach to Synthesis 511

12.1 One-Step Syntheses 512

12.2 Functional Group Transformations 513

12.3 Reactions That Change the Carbon Skeleton 517

BioLinks Vitamins 519

12.4 How to Approach a Synthesis Problem 520

BioLinks The...