Organic chemistry/ T.W. Graham Solomons

BONDING AND MOLECULAR STRUCTURE:The Basics l
Molecular Graphic: Glycine, an organic molecule found :n space 1
1.1 Organic Chemistry and Life 2
1.2 The Structural Theory of Organic Chemistry 3
1.3 Isomers: The Importance of Structural Formulas 4
1.4 Chemical Bonds: The Octet Rule 5
1.5 Wr.ting Lewis Structures 7
1.6 Exceptions to the Octet Rule 9
1.7 Formal Charge 10
1.8 Resonance Theory 13
1.9 Quantum Mechanics and Atomic Structure 18
1.10 Atomic Orbitals and Electron Configuration 20
1.11 Molecular Orbitals 21
1.12 The Structure of Methane and Ethane:sp^ Hybridization 24
THE CHEMISTRY OF... Calculated Molecular Models: Electron Density Surfaces 28
1.13 The Structure ofEthene(Ethylene):sp^ Hybridization 28
1.14 The Structure of Ethyne(Acetylene):sp Hybridization 33
1.15 A Summary of important Concepts that Come from Quantum Mechanics 35
1.16 Molecular Geometry: The Valence Shell Electron Pair Repulsion Model 36
1.17 Representation of Structural Formulas 39
1.18 Applications of Basic Principles 44
FUNCTIONAL GROUPS,INTERMOLECULAR FORCES,AND
INFRARED(IR)SPECTROSCOPY 51
Structure and Function: Organic Chemistry, Nanotechnology,and Bioengineering/
Molecular Graphic: A molecular template for bone growth 51
2.1 Carbon-Carbon Covalent Bonds 52
2.2 Hydrocarbons: Representative Alkanes, Alkenes, Alkynes,and Aromatic
Compounds 52
2.3 Polar Covalent Bonds55
THE CHEMISTRY OF...Calculated Molecular Models: Maps of Electrostatic Potential
2.4 Polar and Nonpolar Molecules 56
Functional Groups 59
AlkyI Halides or Haloalkanes 60
Alcohols 61
Ethers 63
Amines 63
Aldehydes and Ketones 65
Carboxylic Acids, Esters,and Amides 65
Nitrites 67
Summary of important Families organic Compounds 68
Physical Properties and Molecular Structure 68
Summary of attractive Electric Forces 75
the CHEMISTRY OF...Organic Templates Engineered to Mimic Bone Growth 75
2.16 Infrared Spectroscopy:An Instrumental Method for Detecting Functional Groups
2.17 Applications of basic Principles 84
ACIDS AND BASES:An Introduction to
Organic Reactions and Their Mechanisms 91
Shuttling of Protons/Molecular Graphic: Diamox, a drug that prevents altitude
sickness 91
3.1 Reactions and Their Mechanisms 92
3.2 Acid-Base Reactions 94
THE CHEMISTRY OF...HOMOsand LUMOs in Reactions 97

3.3 Hcterolysis of Bondfi to C.irhnn Cofb<Ho!: .ttid C.irixtmofi'. 97
3.4 The Uio of Curved Arrows
3.5 The Strength of acids a
3.6 Predicting the Outcome of Acid-Base Reactions 103
3.7 The Relationship between Sinjcturo and Ac-dry 105
3.8 Energy Changes 108
3.9 The Relationship between the ('equilibrium Constant
Change.SG" 110
3.10 The Acidity of Carboxylic Acids 111
3.11 The Effect of the Solvent on Aadity 115
3.12 Organic Compounds as Bases 116
3.13 A Mechanism for an Organic Reaction 117
THE CHEMISTRY OF . Carbonic Anhydrase 118
3.14 Acids and Bases m Nonaqueous Solutions 119
3.15 Acid-Base Reactions and the Synthesis of Deuterium- and
Tritium-Labeled Compounds 120
3.16 Applications of Basic Principles 121
NOMENCLATURE AND CONFORMATIONS
OF ALKANES 129
7b Be Flexible or Inflexible - Molecular Structure Makes the Difference/ Molecular
Graphic: A portion of the structure of diamond,an exceptionally rigid molecule 129
4.1 Introduction to Alkanes and Cycloalkanes 130
^ THE CHEMISTRY OF... Petroleum Refining 130
4.2 Shapes ofAlkanes 132
4.3 IUPAC Nomenclature of alkanes. AlkyI Hades. and Alcohols 134
4.4 Nomenclature ofCycloalkanes 141
4.5 Nomenclature of Alkenes and Cycloalkenes 143
4.6 Nomenclature ofAlkynes 145
4.7 Physical Properties of alkanes and Cycloalkanes 146
'THE CHEMISTRY OF... Pheromones:Communication by Means of Chemicals 148
4.8 Sigma Bonds and Bond Rotation 148
4.9 Conformational Analysis of Butane 151
4.10 The Relative Stabilities ofCycloalkanes: Ring Strain 153
4.11 The Origin offering Strain in Cyclopropane and Cyclobutane:
Angle Strain and Torsional Strain 155
4.12 Conformations ofCyclohexane 156
THE CHEMISTRY OF... Nanoscale Motors and Molecular Switches 159
4.13 Substituted Cyclohexanes:Axial and Equatorial Hydrogen Atoms 160
4.14 Disubstituted Cycloalkanes: Cis-Trans Isomerism 163
4.15 Bicyclic and Polycyclic Alkanes 166
THE CHEMISTRY OF...Elemental Carbon 167
4.16 Chemical Reactions of alkanes 168
4.17 Synthesis of alkanes and Cycloalkanes 168
4.18 Structural Information from Molecular Formulas and the Index of
Hydrogen Deficiency 169
4.19 NMR Spectroscopy-A Practical Introduction 171
4.20 Applications of basic Principles 175
STEREOCHEMISTRY:Enantiomers and Diastereomers 181
The Handedness ofLife/Molecular Graphic: The mirror-image stereoisomers of
alanine,a chiral amino acid 181
5.1 The Biological Significance ofChirality 182
5.2 Isomerism: Constitutional Isomers and Stereoisomers 183
5.3 Enantiomers and Chiral Molecules 184
5.4 More about the Biological Importance ofChirality 187
5.5 Historical Origin ofStereochemistry 1885.6 Tests for Chirality: Planes of Symmetry 189
5.7 Nomenclature of Enantiomers: The R.S-Syslcm 190
5.8 Properties of enantiomers: Optical Activity 194
5.9 The Origin of Optical Activity 198
5.10 The Synthesis of Chiral Molecules 200
5.11 Chiral Drugs 202
THE CHEMISTRY OF ... Selective Binding of Drug Enantiomers to Left- and
Rig fit-Handed Coiled DNA 203
5.12 Molecules With More than One Chirality Center 203
5.13 Fischer Projection Formulas 207
5.14 Stereoisomerism of Cyclic Compounds 209
5.15 Relating Configurations through Reactions in WIvch No Bonds to
the Chirality Center Are Broken 211
5.16 Separation of Enantiomers: Resolution 213
5.17 Compounds with Chirality Centers Other than Carbon 214
5.18 Chiral Molecules that Do Not Possess a Chirality Center 215
i:
REACTIONS OF ALKYL HALIDES:
Nucleophilic Substitution and Elimination 221
Breaking Bacterial Cell Walls with Organic Chemistry/ Molecular Graphic: Lysozyme 221
6.1 Organic Halides 222
6.2 Nucleophilic Substitution Reactions 224
6.3 Nucleophiles 224
6.4 Leaving Groups 225
6.5 Kinetics of a Nucleophilic Substitution Reaction: An Sf^2 Reaction 226
6.6 A Mechanism for the Sn2 Reaction 227
6.7 Transition State Theory: Free-Energy Diagrams 228
6.8 The Stereochemistry of Si\i2 Reactions 231
THE CHEMISTRY OF...Lysozyme 234
6.9 The Reaction after-Butyl Chloride with Hydroxide Ion:An Si^l Reaction 235
6.10 A Mechanism for the S^l Reaction 236
6.11 Carbocations 237
6.12 The Stereochemistry of SnI Reactions 239
6.13 Factors Affecting the Rates ofS^l and Sf^2 Reactions 241
. 6.14 Organic Synthesis: Functional Group Transformations Using Sn2 Reactions 250
^ THE CHEMISTRY OF...Biological Methylation:A Biological nucleophilic substitution
Reaction 251
6.15 Elimination Reactions ofAlky!Halides 253
6.16 The E2Reaction 255
6.17 The El Reaction 256
6.18 Substitution versus Elimination 257
6.19 Overall Summary 260
ALKENES AND ALKYNES-Part I:
Elimination Reactions of AlkyI Halides 269
Cell Membrane Fluidity/Molecular Graphic: cis-9-Octadecenoic acid, and unsaturated
fatty acid incorporated into cell membrane phospholipids 269
7.1 Introduction 270
7.2 The(EHZ)System for Designating Alkene Diastereomers 270
7.3 Relative Stabilities ofAlkenes 272
7.4 Cycloalkenes 274
7.5 Synthesis ofAlkenes via Elimination Reactions 274
7.6 Dehydrohalogenation ofAlkyI Halides 275
7.7 Acid-Catalyzed Dehydration of Alcohols 280
7.8 Carbocation Stability and the Occurrence ofMolecular Rearrangements 285
7.9 Synthesis ofAlkynes by Elimination Reactions 2887.10 The Acidity of Torm-nal Alkynrs 290