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1 The Basics

BONDING AND MOLECULAR STRUCTURE 1

1.1 Life and the Chemistry of Carbon CompoundsWe are Stardust 2

1.2 Atomic Structure 3

1.3 Chemical Bonds: The Octet Rule 5

1.4 HOW TO Write Lewis Structures 7

1.5 Formal Charges and HOW TO Calculate Them 12

1.6 Isomers: Different Compounds that Have the Same Molecular Formula
14

1.7 HOW TO Write and Interpret Structural Formulas 15

1.8 Resonance Theory 22

1.9 Quantum Mechanics and Atomic Structure 27

1.10 Atomic Orbitals and Electron Configuration 28

1.11 Molecular Orbitals 30

1.12 The Structure of Methane and Ethane: sp3 Hybridization 32

1.13 The Structure of Ethene (Ethylene): sp2 Hybridization 36

1.14 The Structure of Ethyne (Acetylene): sp Hybridization 40

1.15 A Summary of Important Concepts That Come from Quantum


Mechanics 43
1.16 HOW TO Predict Molecular Geometry: The Valence Shell Electron
Pair Repulsion Model 44

1.17 Applications of Basic Principles 47

2 Families of Carbon Compounds

FUNCTIONAL GROUPS, INTERMOLECULAR FORCES, AND INFRARED


(IR) SPECTROSCOPY 55

2.1 Hydrocarbons: Representative Alkanes, Alkenes, Alkynes, and


Aromatic Compounds 56

2.2 Polar Covalent Bonds 59

2.3 Polar and Nonpolar Molecules 61

2.4 Functional Groups 64

2.5 Alkyl Halides or Haloalkanes 65

2.6 Alcohols and Phenols 67

2.7 Ethers 69

2.8 Amines 70

2.9 Aldehydes and Ketones 71

2.10 Carboxylic Acids, Esters, and Amides 73

2.11 Nitriles 75

2.12 Summary of Important Families of Organic Compounds 76

2.13 Physical Properties and Molecular Structure 77


2.14 Summary of Attractive Electric Forces 85

2.15 Infrared Spectroscopy: An Instrumental Method for Detecting


Functional Groups 86

2.16 Interpreting IR Spectra 90

2.17 Applications of Basic Principles 97

3 Acids and Bases

AN INTRODUCTION TO ORGANIC REACTIONS AND THEIR


MECHANISMS 104

3.1 AcidBase Reactions 105

3.2 HOW TO Use Curved Arrows in Illustrating Reactions 107

3.3 Lewis Acids and Bases 109

3.4 Heterolysis of Bonds to Carbon: Carbocations and Carbanions 111

3.5 The Strength of BrønstedLowry Acids and Bases: Ka and pKa 113

3.6 HOW TO Predict the Outcome of AcidBase Reactions 118

3.7 Relationships Between Structure and Acidity 120

3.8 Energy Changes 123

3.9 The Relationship Between the Equilibrium Constant and the Standard
Free-Energy Change, ?G° 125

3.10 Acidity: Carboxylic Acids versus Alcohols 126

3.11 The Effect of the Solvent on Acidity 130


3.12 Organic Compounds as Bases 130

3.13 A Mechanism for an Organic Reaction 132

3.14 Acids and Bases in Nonaqueous Solutions 133

3.15 AcidBase Reactions and the Synthesis of Deuterium- and Tritium-


Labeled Compounds 134

3.16 Applications of Basic Principles 135

4 Nomenclature and Conformations of Alkanes and Cycloalkanes 142

4.1 Introduction to Alkanes and Cycloalkanes 143

4.2 Shapes of Alkanes 144

4.3 HOW TO Name Alkanes, Alkyl Halides, and Alcohols: The IUPAC
System 146

4.4 HOW TO Name Cycloalkanes 153

4.5 HOW TO Name Alkenes and Cycloalkenes 156

4.6 HOW TO Name Alkynes 158

4.7 Physical Properties of Alkanes and Cycloalkanes 159

4.8 Sigma Bonds and Bond Rotation 162

4.9 Conformational Analysis of Butane 164

4.10 The Relative Stabilities of Cycloalkanes: Ring Strain 167

4.11 Conformations of Cyclohexane: The Chair and the Boat 168

4.12 Substituted Cyclohexanes: Axial and Equatorial Hydrogen Groups 171


4.13 Disubstituted Cycloalkanes: CisTrans Isomerism 175

4.14 Bicyclic and Polycyclic Alkanes 179

4.15 Chemical Reactions of Alkanes 180

4.16 Synthesis of Alkanes and Cycloalkanes 180

4.17 HOW TO Gain Structural Information from Molecular Formulas and


the Index of Hydrogen Deficiency 182

4.18 Applications of Basic Principles 184

5 Stereochemistry

CHIRAL MOLECULES 191

5.1 Chirality and Stereochemistry 192

5.2 Isomerism: Constitutional Isomers and Stereoisomers 193

5.3 Enantiomers and Chiral Molecules 195

5.4 Molecules Having One Chirality Center are Chiral 196

5.5 More about the Biological Importance of Chirality 199

5.6 HOW TO Test for Chirality: Planes of Symmetry 201

5.7 Naming Enantiomers: The R,S-System 202

5.8 Properties of Enantiomers: Optical Activity 206

5.9 The Origin of Optical Activity 211

5.10 The Synthesis of Chiral Molecules 213


5.11 Chiral Drugs 215

5.12 Molecules with More than One Chirality Center 217

5.13 Fischer Projection Formulas 223

5.14 Stereoisomerism of Cyclic Compounds 225

5.15 Relating Configurations through Reactions in which No Bonds to the


Chirality Center Are Broken 227

5.16 Separation of Enantiomers: Resolution 231

5.17 Compounds with Chirality Centers Other than Carbon 232

5.18 Chiral Molecules That Do Not Possess a Chirality Center 232

6 Ionic Reactions

NUCLEOPHILIC SUBSTITUTION AND ELIMINATION REACTIONS OF


ALKYL HALIDES 239

6.1 Alkyl Halides 240

6.2 Nucleophilic Substitution Reactions 241

6.3 Nucleophiles 243

6.4 Leaving Groups 245

6.5 Kinetics of a Nucleophilic Substitution Reaction: An SN2 Reaction


245

6.6 A Mechanism for the SN2 Reaction 246

6.7 Transition State Theory: Free-Energy Diagrams 248


6.8 The Stereochemistry of SN2 Reactions 251

6.9 The Reaction of Tert-Butyl Chloride with Water: An SN1 Reaction


253

6.10 A Mechanism for the SN1 Reaction 254

6.11 Carbocations 256

6.12 The Stereochemistry of SN1 Reactions 258

6.13 Factors Affecting the Rates of SN1 and SN2 Reactions 261

6.14 Organic Synthesis: Functional Group Transformations Using SN2


Reactions 271

6.15 Elimination Reactions of Alkyl Halides 275

6.16 The E2 Reaction 276

6.17 The E1 Reaction 278

6.18 HOW TO Determine Whether Substitution or Elimination Is Favored


280

6.19 Overall Summary 282

7 Alkenes and Alkynes I

PROPERTIES AND SYNTHESIS. ELIMINATION REACTIONS OF


ALKYL HALIDES 291

7.1 Introduction 292

7.2 The (E)(Z) System for Designating Alkene Diastereomers 292

7.3 Relative Stabilities of Alkenes 293


7.4 Cycloalkenes 296

7.5 Synthesis of Alkenes via Elimination Reactions 296

7.6 Dehydrohalogenation of Alkyl Halides 297

7.7 Acid-Catalyzed Dehydration of Alcohols 303

7.8 Carbocation Stability and the Occurrence of Molecular


Rearrangements 309

7.9 The Acidity of Terminal Alkynes 313

7.10 Synthesis of Alkynes by Elimination Reactions 314

7.11 Terminal Alkynes Can Be Converted to Nucleophiles for CarbonCarbon


Bond Formation 316

7.12 Hydrogenation of Alkenes 318

7.13 Hydrogenation: The Function of the Catalyst 320

7.14 Hydrogenation of Alkynes 321

7.15 An Introduction to Organic Synthesis 323

8 Alkenes and Alkynes II

ADDITION REACTIONS 337

8.1 Addition Reactions of Alkenes 338

8.2 Electrophilic Addition of Hydrogen Halides to Alkenes: Mechanism


and Markovnikovs Rule 340

8.3 Stereochemistry of the Ionic Addition to an Alkene 345


8.4 Addition of Water to Alkenes: Acid-Catalyzed Hydration 346

8.5 Alcohols from Alkenes through OxymercurationDemercuration:


Markovnikov Addition 349

8.6 Alcohols from Alkenes through HydroborationOxidation: Anti-


Markovnikov Syn Hydration 352

8.7 Hydroboration: Synthesis of Alkylboranes 353

8.8 Oxidation and Hydrolysis of Alkylboranes 355

8.9 Summary of Alkene Hydration Methods 358

8.10 Protonolysis of Alkylboranes 359

8.11 Electrophilic Addition of Bromine and Chlorine to Alkenes 359

8.12 Stereospecific Reactions 363

8.13 Halohydrin Formation 364

8.14 Divalent Carbon Compounds: Carbenes 366

8.15 Oxidation of Alkenes: Syn 1,2-Dihydroxylation 368

8.16 Oxidative Cleavage of Alkenes 371

8.17 Electrophilic Addition of Bromine and Chlorine to Alkynes 374

8.18 Addition of Hydrogen Halides to Alkynes 374

8.19 Oxidative Cleavage of Alkynes 375

8.20 HOW TO Plan a Synthesis: Some Approaches and Examples 376

9 Nuclear Magnetic Resonance and Mass Spectrometry


TOOLS FOR STRUCTURE DETERMINATION 391

9.1 Introduction 392

9.2 Nuclear Magnetic Resonance (NMR) Spectroscopy 392

9.3 HOW TO Interpret Proton NMR Spectra 398

9.4 Nuclear Spin: The Origin of the Signal 401

9.5 Detecting the Signal: Fourier Transform NMR Spectrometers 403

9.6 The Chemical Shift 405

9.7 Shielding and Deshielding of Protons 406

9.8 Chemical Shift Equivalent and Nonequivalent Protons 408

9.9 Signal Splitting: SpinSpin Coupling 411

9.10 Proton NMR Spectra and Rate Processes 420

9.11 Carbon-13 NMR Spectroscopy 422

9.12 Two-Dimensional (2D) NMR Techniques 428

9.13 An Introduction to Mass Spectrometry 431

9.14 Formation of Ions: Electron Impact Ionization 432

9.15 Depicting the Molecular Ion 432

9.16 Fragmentation 433

9.17 Isotopes in Mass Spectra 440

9.18 GC/MS Analysis 443


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