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The primary aim of this course, which is the second semester in a two-course sequence, is to continue the presentation of organic chemistry as a vigorous science based on a well-developed theory and to show its application in society. To attain this end, this course will:

• Include essential principles (such as nomenclature, molecular structure, functional groups) and simple reactions (such as those of aromatic hydrocarbons, aldehydes, ketones, carbohydrates, carboxylic acids and their derivatives, lipids, amines, alkaloids, amino acids, peptides and proteins and nucleic acids) so as to give the student a thorough training in the fundamentals of organic chemistry.
• Interpret organic reactions in terms of modern theories of electronic structure and geometry thereby enabling the student to recognize the fundamental mechanisms which relate the many types of organic reactions.
• Involve the student in laboratory sessions which are designed to complement the lecture material so that a more thorough understanding of organic chemistry is achieved at the same time that practical laboratory techniques are developed. Some of these include further drill in those techniques learned in the first semester such as infrared spectrophotometry, gas chromatography, polarimetry, refractometry, distillations, and other separation methods, and refluxing, and will be supplemented with training in paper chromatography, analyses of nuclear magnetic resonance spectra, recrystallizations, and qualitative analytical methods.

After completing this course the student will be able to:

1. Calculate heats of reaction from bond dissociation energies.
2. Compare the stabilities of free radicals.
3. Describe the mechanisms of various free radical reactions.
4. Compare the selectivity of halogens in free radical reactions.
5. Predict the products in free radical additions to alkenes: anti-Markovnikov additions to alkenes.
6. Describe free radical polymerizations of alkenes.
7. Understand conjugated unsaturated systems and the role of ultraviolet (UV) spectroscopy.
8. Describe the resonance and molecular orbital structure of benzene.
9. Predict aromaticity in ring compounds.
10. Draw structures of aromatic and substituted aromatic compounds.
11. Name aromatic and substituted aromatic compounds according to the IUPAC system given the structural formulas and vice versa. Do the same using common names.
12. Investigate and reproduce the steps involved in various electrophilic aromatic substitution reactions - including the role of catalysts - and also conversion reactions of aromatic molecules.
13. Predict the activity and orientation in electrophilic aromatic substitution reactions based on existing substituent groups.
14. Plan multistep syntheses.
15. Determine the structures of molecules from IR and NMR spectra.
16. Name aldehydes and ketones according to the IUPAC system given the structural formula and vice versa. Do the same using common names.
17. Draw the structures of the carbonyl group showing bond angles, resonance-contributing forms, dipoles and electron densities.
18. Contrast and predict physical properties of aldehydes and ketones.
19. Explain physical properties of aldehydes and ketones in terms of dipole-dipole interactions and hydrogen bonding.
20. Design and understand the mechanisms involved in the preparation of aldehydes and ketones.
21. Report on the sources and uses of aldehydes and ketones.
22. Investigate and reproduce the steps involved in various oxidation, reduction and additional reactions of aldehydes and ketones.
23. Describe the mechanisms of reactions involving the enolate ion including condensations.
24. Explain the optical activity in a molecule in terms of the molecule's geometric orientation in space - stereochemistry.
25. Calculate the specific rotation of a molecule given experimental data.
26. Define and classify carbohydrates according to the products of their hydrolysis, the number of carbons and their membership in the D- or L- family.
27. Describe mutarotation and the cyclic forms of sugars, and draw Haworth representations of sugars.
28. Investigate and reproduce the steps involved in the reactions of monosaccharides.
29. Describe the biochemical oxidation of sugars.
30. Discuss disaccharides and the nature of the glycosidic bond.
31. Differentiate between various polysaccharides - the glucosans.
32. Relate the uses of cellulose.
33. Name carboxylic acids according to the IUPAC system given the structural formula and vice versa. Do the same using common names.
34. Contrast and predict physical properties of carboxylic acids.
35. Explain the physical properties of carboxylic acids in terms of the hydrogen bonds between the molecules.
36. Contrast the acidity of various acids.
37. Use Ka and pKa to describe the acidity of a carboxylic acid.
38. Calculate the pH of a weak acid.
39. Describe buffer systems.
40. Use the Henderson-Hasselbach equation to calculate the pH of a buffer solution.
41. Discuss the resonance structures of the carboxylate ion and their significance in determining the acid's acidity.
42. Discuss the inductive effect in substituted carboxylic acids and its significance in determining the acid's acidity.
43. Describe the mechanisms of reactions involved in the syntheses of carboxylic acids using various methods.
44. Investigate and reproduce the steps involved in various reactions of carboxylic acids.
45. Name derivatives of carboxylic acids (acyl halides, anhydrides, esters, and amides) according to the IUPAC system given the structural formula and vice versa. Do the same using common names.
46. Describe the mechanisms of reactions involved in the syntheses of acyl halides, anhydrides, esters and amides using various methods.
47. Investigate and reproduce the steps involved in various reactions of acyl halides, anhydrides, esters and amides.
48. Report on the sources and uses of important carboxylic acids and derivatives of carboxylic acids.
49. Contrast and predict physical properties of acyl halides, anhydrides, esters and amides.
50. Differentiate among the different lipids: fatty acids, triglycerides, waxes, phospholipids, glycolipids, steroids, fat soluble vitamins and prostoglandins.
51. Name amines according to the IUPAC system given the structural formula and vice versa. Do the same using common names.
52. Classify amines as primary, secondary or tertiary.
53. Draw the structure of an amine showing bond angles and electron densities.
54. Contrast and predict physical properties of the amines.
55. Contrast the basicity of various amines.
56. Discuss the resonance structures and inductive effects in substituted ammonium ions and their significance in determining the base's basicity.
57. Describe the mechanisms involved in the syntheses of amines using various methods.
58. Investigate and reproduce the steps involved in various reactions of amines.
59. Investigate the effects of biogenic amines and alkaloids including: psychomimetic drugs, neurotransmitters, amphetamines, acetylcholine, dopamine, barbiturates, and hallucinogens.
60. Draw the structure of an amino acid.
61. Understand the ionic properties of amino acids, the nature of the zwitterion and the isoelectric point.
62. Describe electrophoresis and ion-exchange chromatography as a method for separating and analyzing amino acid mixtures.
63. Describe the mechanisms involved in the syntheses of amino acids.
64. Reproduce the steps involved in the reactions of amino acids.
65. Classify peptides, and describe the peptide bond.
66. Follow the steps in the structural determination of peptides.
67. . Follow the steps in the syntheses of peptides.
68. Compare the common properties of proteins, peptides and amino acids.
69. Investigate the specific properties of proteins.
70. Identify the primary, secondary, tertiary and quaternary structures of proteins.
71. Demonstrate the structural relationship between an enzyme and a substrate.
72. Describe the metabolism of proteins.
73. Determine the structure of the components in nucleosides, nucleotides, and nucleic acids.
74. Investigate the roles of some nucleotides.
75. Investigate the three-dimensional structure of DNA and the importance of the hydrogen bond.
76. Relate the replication procedure in DNA.
77. Demonstrate the role of DNA and RNA in the synthesis of a protein.
78. Recrystallize an impure solid.
79. Decolorize using charcoal.
80. Perform a hot gravity filtration with a short-stemmed funnel using fluted filter paper.
81. Perform a vacuum filtration.
82. Operate a Fisher melting point apparatus.
83. Perform an aromatic substitution reaction.
84. Reflux a liquid.
85. Operate a Fourier transform infrared (FT-IR) spectrometer and use it to identify a solid product.
86. Determine the theoretical, actual, and percent yield of a product.
87. Perform an aldol reaction.
88. Induce crystallization using special techniques.
89. Conduct an esterification.
90. Wash a product using a separatory funnel.
91. Confirm the identity of a liquid product using refractometry.
92. Operate a Fourier transform nuclear magnetic resonance (FT-NMR) spectrometer and analyze the ¹H and ¹³C NMR spectra of a synthesized product.
93. Operate a Fourier transform infrared (FT-IR) spectrometer and use it to identify a liquid product.
94. Operate an ultraviolet-visible (UV-Vis) spectrophotometer and use it to identify a chromophore.
95. Prepare NYLON 610 and collect it as a rope. Test its physical properties.
96. Conduct a qualitative analysis to determine whether an unknown is an aldehyde, a ketone (methyl or otherwise), a carboxylic acid, an amine (primary, secondary or tertiary), an ester, or an amide.
97. Operate a polarimeter to determine the optical activity of a sugar solution and to follow the mutarotation of glucose.
98. Experimentally investigate the properties of proteins.
99. Perform a paper chromatographic separation of amino acids formed by the hydrolysis of gelatin. Measure the Rf values and compare them to tabulated values.