Organic Chemistry

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Chemistry
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Contents

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  1. 00: Front Matter
  2. TitlePage
  3. InfoPage
  4. Table of Contents
  5. Licensing
  6. 1: Introduction and Review
  7. 1.1: The Origins of Organic Chemistry
  8. 1.2: Principles of Atomic Structure (Review)
  9. 1.3: Electronic Structure (Review)
  10. 1.4: Electron Configurations
  11. 1.5: Octet Rule - Ionic and Covalent Bonding (Review)
  12. 1.6: Lewis Structures
  13. 1.7: Common Bonding Patterns for Organic Chemistry
  14. 1.8: Structural Formulas - Lewis, Kekule, Bond-line, Condensed,
  15. 1.9: Electronegativity and Bond Polarity (Review)
  16. 1.10: Resonance
  17. 1.11: Arrhenius Acids and Bases (Review)
  18. 1.12: Brønsted-Lowry Acids and Bases (Review)
  19. 1.13: Lewis Acids and Bases
  20. 1.14: Distinguishing between pH and pKa
  21. 1.15: Predicting Relative Acidity
  22. 1.16: Molecular Formulas and Empirical Formulas (Review)
  23. 1.17: Additional Exercises
  24. 1.18: Solutions to Additional Exercises
  25. 2: Structure and Properties of Organic Molecules
  26. 2.1: Pearls of Wisdom
  27. 2.2: Molecular Orbital (MO) Theory (Review)
  28. 2.3: Hybridization and Molecular Shapes (Review)
  29. 2.4: 2.4 Conjugated Pi Bond Systems
  30. 2.5: Lone Pair Electrons and Bonding Theories
  31. 2.6: Bond Rotation
  32. 2.7: Isomerism Introduction
  33. 2.8: Hydrocarbons
  34. 2.9: Organic Functional Groups
  35. 2.10: Intermolecular Forces (IMFs) - Review
  36. 2.11: Intermolecular Forces
  37. 2.12: Intermolecular Forces
  38. 2.13: Additional Practice Problems
  39. 2.14: Organic Functional Groups: H-bond donors
  40. 2.15: Additional Exercises
  41. 2.16: 2.15 Solutions to Additional Exercises
  42. 3: Structure and Stereochemistry of Alkanes
  43. 3.1: Hydrocarbon Functional Groups
  44. 3.2: Physical Properties of Alkanes
  45. 3.3: Structure and Conformations of Alkanes
  46. 3.4: Conformations of Butane
  47. 3.5: Conformations of Higher Alkanes
  48. 3.6: Cycloalkanes and Ring Strain
  49. 3.7: Cyclohexane Conformations
  50. 3.8: Conformations of Monosubstituted Cyclohexanes
  51. 3.9: Cis-trans Isomerism in Cycloalkanes
  52. 3.10: Conformations of Disubstituted Cyclohexanes
  53. 3.11: Joined Rings
  54. 3.12: Uses and Sources of Alkanes
  55. 3.13: Reactions of Alkanes - a Brief Overview
  56. 3.14: Additional Exercises
  57. 3.15: Solutions to Additional Exercises
  58. 4: Stereochemistry at Tetrahedral Centers
  59. Front Matter
  60. TitlePage
  61. InfoPage
  62. 4.1: Chirality
  63. 4.2: Fischer Projections to communicate Chirality
  64. 4.3: Absolute Configuration and the (R) and (S) System
  65. 4.4: Diastereomers - more than one chiral center
  66. 4.5: Meso Compounds
  67. 4.6: Isomerism Summary Diagram
  68. 4.7: Optical Activity and Racemic Mixtures
  69. 4.8: 6.8 Resolution (Separation) of Enantiomers
  70. 4.9: Stereochemistry of Molecules with Three or More Asymmetric Carbons
  71. 4.10: Absolute and Relative Configuration - the distinction
  72. 4.11: Chirality at Nitrogen, Phosphorus, and Sulfur
  73. 4.12: Biochemistry of Enantiomers
  74. 4.13: 6.13 The Discovery of Enantiomers
  75. 4.14: Additional Exercises
  76. 4.15: Solutions to Additional Exercises
  77. Back Matter
  78. Index
  79. 5: An Introduction to Organic Reactions using Free Radical Halogenation of Alkanes
  80. 5.1: Types of Organic Reactions
  81. 5.2: 5.2 Reaction Mechanism Notation and Symbols
  82. 5.3: the Dance of the Nucleophile and Electrophile
  83. 5.4: Describing a Reaction - Equilibrium and Free Energy Changes
  84. 5.5: Homolytic Cleavage and Bond Dissociation Energies
  85. 5.6: Reaction Energy Diagrams and Transition States
  86. 5.7: 5.7 Reactive Intermediates - Carbocations
  87. 5.8: 5.8 Reactive Intermediates - Radicals
  88. 5.9: Reactive Intermediates: Carbanions and Carbon Acids
  89. 5.10: The Free-Radical Halogenation of Alkanes
  90. 5.11: Reactivity and Selectivity
  91. 5.12: A Comparison between Biological Reactions and Laboratory Reactions
  92. 5.13: Additional Exercises
  93. 5.14: Solutions to Additional Exercises
  94. 6: Alkyl Halides: Nucleophilic Substitution and Elimination
  95. 6.1: 7.1 Alkyl Halides - Structure and Physical Properties
  96. 6.2: Common Uses of Alkyl Halides
  97. 6.3: Preparation of Alkyl Halides
  98. 6.4: Reactions of Alkyl Halides: Substitution and Elimination
  99. 6.5: The Sₙ2 Reaction
  100. 6.6: Characteristics of the Sₙ2 Reaction
  101. 6.7: Stereochemistry of the SN2 Reaction
  102. 6.8: The Sₙ1 Reaction
  103. 6.9: Characteristics of the Sₙ1 Reaction
  104. 6.10: Rearrangements of the Carbocation and Sₙ1 Reactions
  105. 6.11: The Hammond Postulate and Transition States
  106. 6.12: Comparison of SN1 and SN2 Reactions
  107. 6.13: Characteristics of the E2 Reaction
  108. 6.14: Zaitsev's Rule
  109. 6.15: Characteristics of the E1 Reaction
  110. 6.16: E2 Regiochemistry and Cyclohexane Conformations
  111. 6.17: The E2 Reaction and the Deuterium Isotope Effect
  112. 6.18: Comparison of E1 and E2 Reactions
  113. 6.19: Comparing Substitution and Elimination Reactions
  114. 6.20: Biological Substitution Reactions
  115. 6.21: Biological Elimination Reactions
  116. 6.22: Additional Exercises
  117. 6.23: Solutions to Additional Exercises
  118. 7: Structure and Synthesis of Alkenes
  119. 7.1: Alkene Structure
  120. 7.2: Physical Properties and Important Common Names
  121. 7.3: The Alkene Double Bond and Stereoisomerism
  122. 7.4: Degrees of Unsaturation
  123. 7.05: The E
  124. Z System (when cis
  125. 7.5: The E/Z System (when cis/trans does not work)
  126. 7.6: Stability of Alkenes
  127. 7.7: Alkene Synthesis by Elimination of Alkyl Halides
  128. 7.8: Alkene Synthesis by Dehydration of Alcohols
  129. 7.9: Uses
  130. 7.10: Additional Exercises
  131. 7.11: Solutions to Additional Exercises
  132. 8: Reactions of Alkenes
  133. 8.1: Electrophilic Addition Reactions (EARs)
  134. 8.2: Addition of Hydrogen Halides to Symmetrical Alkenes
  135. 8.3: Alkene Asymmetry and Markovnikov's Rule
  136. 8.4: Hydration: Acid Catalyzed Addition of Water
  137. 8.5: Hydration: Oxymercuration-Demercuration
  138. 8.6: Hydration: Hydroboration-Oxidation
  139. 8.7: Stereochemistry of Reactions - Hydration of Achiral Alkenes
  140. 8.8: Stereochemistry of Reactions - Hydration of Chiral Alkenes
  141. 8.9: Addition of Halogens
  142. 8.10: Formation of Halohydrins
  143. 8.11: Reduction of Alkenes - Catalytic Hydrogenation
  144. 8.12: Oxidation of Alkenes - Epoxidation
  145. 8.13: Dihydroxylation of Alkenes
  146. 8.14: Opening of Epoxides - Acidic versus Basic Conditions
  147. 8.15: Oxidative Cleavage of Alkenes
  148. 8.16: Addition of Carbenes to Alkenes - Cyclopropane Synthesis
  149. 8.17: Radical Chain-Growth Polymerization
  150. 8.18: 9.18 Biological Additions of Radicals to Alkenes
  151. 8.19: Additional Exercises
  152. 8.20: Solutions to Additional Exercises
  153. 9: Alkynes
  154. 9.1: Structure and Physical Properties
  155. 9.2: 10.2 Synthesis of Alkynes - Elimination Reactions of Dihalides
  156. 9.3: Reactions of Alkynes - Addition of HX and X₂
  157. 9.4: Hydration of Alkynes for Markovnikov Products
  158. 9.5: Hydration of Alkynes for Anti-Markovnikov Products
  159. 9.6: 10.6 Reduction of Alkynes
  160. 9.7: Oxidation of Alkynes
  161. 9.8: Acidity of Terminal Alkynes
  162. 9.9: Synthesis of Larger Alkynes from Acetylides
  163. 9.10: An Introduction to Multiple Step Synthesis
  164. 9.11: Additional Exercises
  165. 9.12: Solutions to Additional Exercises
  166. 10: Reactions of Alcohols
  167. 10.1: 14.1 Reactions of Alcohols with Hydrohalic Acids
  168. 10.2: Reactions with Phosphorus Halides
  169. 10.3: Alcohol conversion to Esters - Tosylate and Carboxylate
  170. 10.4: Dehydration Reactions of Alcohols
  171. 10.5: Oxidation States of Alcohols and Related Functional Groups
  172. 10.6: Oxidation Reactions of Alcohols
  173. 10.7: Determining Alcohol Classifications in the Lab - alternate reactions
  174. 10.8: Protection of Alcohols
  175. 10.9: Cleavage of Diols
  176. 10.10: Reactions of Alkoxides
  177. 10.11: Biological Oxidation - an introduction
  178. 10.12: Additional Exercises
  179. 10.13: Solutions to Additional Exercises
  180. 11: Structure and Synthesis of Alcohols
  181. 11.1: Introduction to Structure and Synthesis of Alcohols
  182. 11.2: Classification of Alcohols
  183. 11.3: Physical Properties of Alcohols
  184. 11.4: Spectroscopy of Alcohols
  185. 11.5: Acidity of Alcohols and Phenols
  186. 11.6: Synthesis of Alcohols - Review
  187. 11.7: Reduction of the Carbonyl Group - Synthesis of 1º and 2º Alcohols
  188. 11.8: Organometallic Reagents
  189. 11.9: Organometallic Reagents in Alcohol Synthesis
  190. 11.10: Thiols (Mercaptans)
  191. 11.11: Commercially Important Alcohols
  192. 11.12: 13.12 Additional Exercises
  193. 11.13: Solutions to Additional Exercises
  194. 12: Infrared Spectroscopy and Mass Spectrometry
  195. 12.1: The Electromagnetic Spectrum
  196. 12.2: Infrared (IR) Spectroscopy
  197. 12.3: IR-Active and IR-Inactive Vibrations
  198. 12.4: Interpretting IR Spectra
  199. 12.5: Infrared Spectra of Some Common Functional Groups
  200. 12.6: Summary and Tips to Distinguish between Carbonyl Functional Groups
  201. 12.7: Mass Spectrometry - an introduction
  202. 12.8: Fragmentation Patterns in Mass Spectrometry
  203. 12.9: Useful Patterns for Structure Elucidation
  204. 12.10: Determination of the Molecular Formula by High Resolution Mass Spectrometry
  205. 13: Nuclear Magnetic Resonance Spectroscopy
  206. 13.1: Theory of Nuclear Magnetic Resonance (NMR)
  207. 13.2: NMR Spectra - an introduction
  208. 13.3: Chemical Shifts and Shielding
  209. 13.4: ¹H NMR Spectroscopy and Proton Equivalence
  210. 13.5: Functional Groups and Chemical Shifts in ¹H NMR Spectroscopy
  211. 13.6: Integration of ¹H NMR Absorptions: Proton Counting
  212. 13.7: Spin-Spin Splitting in ¹H NMR Spectra
  213. 13.8: More Complex Spin-Spin Splitting Patterns
  214. 13.9: Uses of ¹H NMR Spectroscopy
  215. 13.10: ¹³C NMR Spectroscopy
  216. 13.11: Chemical Shifts and Interpreting ¹³C NMR Spectra
  217. 13.12: ¹³C NMR Spectroscopy
  218. 13.13: Uses of ¹³C NMR Spectroscopy
  219. 13.14: More NMR Examples
  220. 13.15: Sample NMR Spectra
  221. 14: Ethers, Epoxides and Thioethers
  222. 14.1: Physical Properties of Ethers
  223. 14.2: Spectroscopy of Ethers
  224. 14.3: The Williamson Ether Synthesis
  225. 14.4: Alkoxymercuration-Demercuration Synthesis of Ethers
  226. 14.5: Acidic Cleavage of Ethers
  227. 14.6: Autoxidation of Ethers
  228. 14.7: Synthesis of Epoxides
  229. 14.8: Opening of Epoxides
  230. 14.9: Reactions of Epoxides with Grignard and Organolithium Reagents
  231. 14.10: Crown Ethers
  232. 14.11: Epoxy Resins: The Advent of Modern Glues
  233. 14.12: Thioethers (Sulfides) and Silyl Ethers
  234. 14.13: Additional Exercises
  235. 14.14: Solutions to Additional Exercises
  236. 15: Conjugated Systems, Orbital Symmetry, and Ultraviolet Spectroscopy
  237. 15.1: Stability of Conjugated Dienes - Molecular Orbital Theory
  238. 15.2: Allylic Cations
  239. 15.3: Electrophilic Additions to Conjugated Dienes
  240. 15.4: Kinetic versus Thermodynamic Control
  241. 15.5: SN2 Reactions of Allylic Halides and Tosylates
  242. 15.6: The Diels-Alder (4 2) Cycloaddition Reaction
  243. 15.7: Diels-Alder Stereochemistry
  244. 15.8: Diene Polymers - Natural and Synthetic Rubbers
  245. 15.9: Structure Determination in Conjugated Systems - Ultraviolet Spectroscopy
  246. 15.10: Interpreting Ultraviolet Spectra - The Effect of Conjugation
  247. 15.11: 16.11:Conjugation, Color, and the Chemistry of Vision
  248. 15.12: Additional Exercises
  249. 15.13: Solutions to Additional Exercises
  250. 16: Aromatic Compounds
  251. 16.1: Introduction: The Discovery of Benzene
  252. 16.2: The Structure and Properties of Benzene and its Derivatives
  253. 16.3: Resonance and the Molecular Orbitals of Benzene
  254. 16.4: The Molecular Orbital Picture of Cyclobutadiene
  255. 16.5: Aromaticity and Huckel's Rule
  256. 16.6: Aromatic Ions - a closer look
  257. 16.7: Heterocyclic Aromatic Compounds - a closer look
  258. 16.8: Polycyclic Aromatic Hydrocarbons
  259. 16.9: Spectroscopy of Aromatic Compounds
  260. 16.10: Additional Exercises
  261. 16.11: Solutions to Additional Exercises
  262. 17: Reactions of Aromatic Compounds
  263. 17.1: Electrophilic Aromatic Substitution (EAS)
  264. 17.2: Halogenation of Benzene (an EAS Reaction)
  265. 17.3: Nitration of Benzene (an EAS Reaction)
  266. 17.4: Sulfonation of Benzene (an EAS Reaction)
  267. 17.5: Alkylation and Acylation of Benzene - The Friedel-Crafts EAS Reactions
  268. 17.6: Substituent Effects on the EAS Reaction
  269. 17.7: Side-Chain Reactions of Benzene Derivatives
  270. 17.8: Synthetic Strategies for Di-substituted Benzenes
  271. 17.9: Trisubstituted Benzenes - Effects of Multiple Substituents
  272. 17.10: Nucleophilic Aromatic Substitution - The Addition-Elimantion Mechanism
  273. 17.11: NAS Reactions - the Elimination-Addition (Benzyne) Mechanism
  274. 17.12: Reduction of Aromatic Compounds
  275. 17.13: Additional Exercises
  276. 17.14: Solutions to Additional Exercises
  277. 18: Ketones and Aldehydes
  278. 18.1: Carbonyl Compound Structure and Properties
  279. 18.2: Spectroscopy of Ketones and Aldehydes
  280. 18.3: Review of Ketone and Aldehyde Synthesis
  281. 18.4: 19.4 New Synthesis of Aldehydes and Ketones
  282. 18.5: Nucleophilic Addition Reactions of Ketones and Aldehydes
  283. 18.6: Nucleophilic Addition of Water (Hydration)
  284. 18.7: Nucleophilic Addition of Cyanide and Acetylide
  285. 18.8: Nucleophilic Addition of Grignards
  286. 18.9: Nucelophilic Addition of Amines (Imine and Enamine Formation)
  287. 18.10: Nucleophilic Addition of Hydrazine (Wolff-Kishner Reaction)
  288. 18.11: Nucelophilic Addition of Alcohols (Acetal Formation)
  289. 18.12: Acetals as Protecting Groups
  290. 18.13: Nucelophilic Addition of Phosphorus Ylides (The Wittig Reaction)
  291. 18.14: Oxidation of Aldehydes
  292. 18.15: Reductions of Ketones and Aldehydes
  293. 18.16: Additional Exercises
  294. 18.17: Solutions to Additional Exercises
  295. 19: Carboxylic Acids
  296. 19.1: Structure and Properties of Carboxylic Acids and their Salts
  297. 19.2: Acidity of Carboxylic Acids
  298. 19.3: Spectroscopy of Carboxylic Acids
  299. 19.4: Synthesis of Carboxylic Acids
  300. 19.5: Reactions of Carboxylic Acids Overview
  301. 19.6: Condensation of Acids with Alcohols: The Fischer Esterification
  302. 19.7: Methyl Ester Synthesis Using Diazomethane
  303. 19.8: Condensation of Acids with Amines
  304. 19.9: Reduction of Carboxylic Acids
  305. 19.10: Biochemically Interesting Carboxylic Acids
  306. 19.11: Additional Exercises
  307. 19.12: Solutions to Additional Exercises
  308. 20: Carboxylic Acid Derivatives and Nitriles
  309. 20.1: Structure and Physical Properties of Acid Derivatives
  310. 20.2: Spectroscopy of Carboxylic Acid Derivatives
  311. 20.3: Interconversion of Acid Derivatives by Nucleophilic Acyl Substitution
  312. 20.4: Acid Halide Chemistry
  313. 20.5: Acid Anhydride Chemistry
  314. 20.6: Ester Chemistry
  315. 20.7: Amide Chemistry
  316. 20.8: Nitrile Chemistry
  317. 20.9: Thioesters: Biological Carboxylic Acid Derivatives
  318. 20.10: Polyamides and Polyesters: Step-Growth Polymers
  319. 20.11: Beta-Lactams: An Application
  320. 20.12: Biological Acylation Reactions
  321. 20.13: Additional Exercises
  322. 20.14: Solutions to Additional Exercises
  323. 21: Alpha Substitutions and Condensations of Carbonyl Compounds
  324. 21.1: Relative Acidity of alpha-Hydrogens
  325. 21.2: Enols, Enolate Ions and Tautomerization
  326. 21.3: Reaction Overview
  327. 21.4: Alpha Halogenation of Carbonyls
  328. 21.5: Bromination of Acids: The HVZ Reaction
  329. 21.6: Alkylation of the alpha-Carbon via the LDA pathway
  330. 21.7: Alkylation of the Alpha-Carbon via the Enamine Pathway
  331. 21.8: The Aldol Reaction and Condensation of Ketones and Aldehydes
  332. 21.9: The Claisen Condensation Reactions of Esters
  333. 21.10: Conjugate Additions: The Michael Reaction
  334. 21.11: Decarboxylation Reactions
  335. 21.12: Additional Exercises
  336. 21.13: Solutions to Additional Exercises
  337. 22: Amines
  338. 22.1: Structure and Physical Properties of Amines
  339. 22.2: Basicity of Amines and Ammonium Salt Formation
  340. 22.3: Spectroscopy of Amines
  341. 22.4: Synthesis of Amines
  342. 22.5: Synthesis of Primary Amines
  343. 22.6: Reactions of Amines
  344. 22.7: Reactions of Arylamines
  345. 22.8: The Hofmann Elimination: Amines as Leaving Groups
  346. 22.9: Oxidation of Amines - The Cope Elimination
  347. 22.10: Sulfa Drugs - a closer look
  348. 22.11: Additional Exercises
  349. 22.12: Solutions to Additional Exercises
  350. 23: Carbohydrates
  351. 23.1: Introduction
  352. 23.2: Classification of Carbohydrates
  353. 23.3: Fischer Projections
  354. 23.4: D and L Sugars
  355. 23.5: Configuration of Aldoses
  356. 23.6: Cyclic Structures of Monosaccharides
  357. 23.7: Reactions of Monosaccharides
  358. 23.8: Disaccharides and Glycosidic Bonds
  359. 23.9: Polysaccharides
  360. 23.10: Other Important Carbohydrates
  361. 23.11: Cell Surface Carbohydrates and Influenza Viruses
  362. 24: Amino Acids, Peptides, and Proteins
  363. 24.1: Introduction
  364. 24.2: Structure and Stereochemistry of the Amino Acids
  365. 24.3: Isoelectric Points and Electrophoresis
  366. 24.4: Synthesis of Amino Acids
  367. 24.5: Peptides and Proteins
  368. 24.6: Amino Acid Analysis of Peptides
  369. 24.7: Peptide Sequencing: The Edman Degradation
  370. 24.8: Peptide Synthesis
  371. 24.9: Automated Peptide Synthesis: The Merrifield Solid-Phase Technique
  372. 24.10: Levels of Protein Structure
  373. 24.11: Enzymes and Coenzymes
  374. 24.12: How do enzymes work?
  375. 25: Lipids
  376. 25.1: Introduction
  377. 25.2: Waxes, Fats, and Oils
  378. 25.3: Saponification of Fats and Oils; Soaps and Detergents
  379. 25.4: Phospholipids
  380. 25.5: Prostaglandins and other Eicosanoids
  381. 25.6: Terpenes and Terpenoids
  382. 25.7: Steroids
  383. 25.8: Biosynthesis of Steroids
  384. 26: Nucleic Acids
  385. 26.1: Nucleotides and Nucleic Acids
  386. 26.2: DNA Base Pairs
  387. 26.3: DNA Replication
  388. 26.4: Transcription of DNA
  389. 26.5: Translation of RNA: Protein Biosynthesis
  390. 26.6: DNA Sequencing
  391. 26.7: Polymerase Chain Reactions
  392. 27: Front Matter
  393. 27.1: Table of Contents
  394. 28: Back Matter
  395. Front Matter
  396. Table of Contents
  397. Back Matter
  398. Index
  399. Glossary
  400. Detailed Licensing