Key textbook & class topics are below and emphasized in Bold Red. Webassign, Worksheet, and ACS problems will serve as examples for many of the types of questions that will be on exams and quizzes.
(In-chapter textbook problems are also important and relate to pre-class preparation and i-clicker in-class questions. Attempting end of chapter problems is encouraged as your time allows.)
Webassign Homework . All assignments are to be done individually. Due dates are embedded on line and these homework problems should be your main focus along with the collaborative/group Worksheets.
ORGANIC CHEMISTRY (Carey 7th ed)CHAPTER 11
Arenes and Aromaticity 420
11.1 Benzene 421
11.2 Kekulé and the Structure of Benzene 422
11.3 A Resonance Picture of Bonding in Benzene 424
11.4 The Stability of Benzene 424
11.5 An Orbital Hybridization View of Bonding in Benzene 426
11.6 The Pi Molecular Orbitals of Benzene 427
11.7 Substituted Derivatives of Benzene and Their Nomenclature 428
11.8 Polycyclic Aromatic Hydrocarbons 430
11.9 Physical Properties of Arenes 431
Carbon Clusters, Fullerenes, and Nanotubes 432
11.10 Reactions of Arenes: A Preview 432
11.11 The Birch Reduction 433
11.12 Free-Radical Halogenation of Alkylbenzenes 436
11.13 Oxidation of Alkylbenzenes 438
11.14 Sn1 Reactions of Benzylic Halides 440
11.15 Sn2 Reactions of Benzylic Halides 441
11.16 Preparation of Alkenylbenzenes 442
11.17 Addition Reactions of Alkenylbenzenes 443
11.18 Polymerization of Styrene 445
11.19 Cyclobutadiene and Cyclooctatetraene 446
11.20 Hückel’s Rule 448
11.21 Annulenes 450
11.22 Aromatic Ions 452
11.23 Heterocyclic Aromatic Compounds 455
11.24 Heterocyclic Aromatic Compounds and Hückel’s Rule 457
11.25 Summary 459
Problems 462
Descriptive Passage and Interpretive Problems 11: The Hammett Equation 466
CHAPTER 12
Reactions of Arenes: Electrophilic Aromatic Substitution 470
12.1 Representative Electrophilic Aromatic Substitution Reactions of Benzene 471
12.2 Mechanistic Principles of Electrophilic Aromatic Substitution 472
12.3 Nitration of Benzene 474
12.4 Sulfonation of Benzene 476
12.5 Halogenation of Benzene 477
12.6 Friedel–Crafts Alkylation of Benzene 478
12.7 Friedel–Crafts Acylation of Benzene 481
12.8 Synthesis of Alkylbenzenes by Acylation–Reduction 483
12.9 Rate and Regioselectivity in Electrophilic Aromatic Substitution 484
12.10 Rate and Regioselectivity in the Nitration of Toluene 485
12.11 Rate and Regioselectivity in the Nitration of (Trifluoromethyl)benzene 488
12.12 Substituent Effects in Electrophilic Aromatic Substitution: Activating Substituents 490
12.13 Substituent Effects in Electrophilic Aromatic Substitution: Strongly Deactivating Substituents 493
12.14 Substituent Effects in Electrophilic Aromatic Substitution: Halogens 496
12.15 Multiple Substituent Effects 498
12.16 Regioselective Synthesis of Disubstituted Aromatic Compounds 499
12.17 Substitution in Naphthalene 502
12.18 Substitution in Heterocyclic Aromatic Compounds 502
12.19 Summary 504
Problems 507
Descriptive Passage and Interpretive Problems 12: Nucleophilic Aromatic Substitution 512
CHAPTER 13
Spectroscopy 516
13.1 Principles of Molecular Spectroscopy: Electromagnetic Radiation 518
13.2 Principles of Molecular Spectroscopy: Quantized Energy States 519
13.3 Introduction to 1 H NMR Spectroscopy 519
13.4 Nuclear Shielding and 1 H Chemical Shifts 521
13.5 Effects of Molecular Structure on 1 H Chemical Shifts 524
Ring Currents: Aromatic and Antiaromatic 529
13.6 Interpreting 1 H NMR Spectra 530
13.7 Spin–Spin Splitting in 1 H NMR Spectroscopy 532
13.8 Splitting Patterns: The Ethyl Group 534
13.9 Splitting Patterns: The Isopropyl Group 536
13.10 Splitting Patterns: Pairs of Doublets 536
13.11 Complex Splitting Patterns 538
13.12 1 H NMR Spectra of Alcohols 539
Magnetic Resonance Imaging (MRI) 540
13.13 NMR and Conformations 540
13.14 13 C NMR Spectroscopy 541
13.15 13 C Chemical Shifts 543
13.16 13 C NMR and Peak Intensities 545
13.17 13 C 1 H Coupling 546
13.18 Using DEPT to Count Hydrogens Attached to 13 C 546
13.19 2D NMR: COSY and HETCOR 547
13.20 Introduction to Infrared Spectroscopy 550
Spectra by the Thousands 551
13.21 Infrared Spectra 552
13.22 Characteristic Absorption Frequencies 554
13.23 Ultraviolet-Visible (UV-VIS) Spectroscopy 557
13.24 Mass Spectrometry 559
13.25 Molecular Formula as a Clue to Structure 563
Gas Chromatography, GC/MS, and MS/MS 564
13.26 Summary 566
Problems 569
Descriptive Passage and Interpretive Problems 13: Calculating Aromatic 13 C Chemical Shifts 575CHAPTER 16
Ethers, Epoxides, and Sulfides 662
16.1 Nomenclature of Ethers, Epoxides, and Sulfides 663
16.2 Structure and Bonding in Ethers and Epoxides 664
16.3 Physical Properties of Ethers 665
16.4 Crown Ethers 667
16.5 Preparation of Ethers 668
Polyether Antibiotics 669
16.6 The Williamson Ether Synthesis 670
16.7 Reactions of Ethers: A Review and a Preview 671
16.8 Acid-Catalyzed Cleavage of Ethers 672
16.9 Preparation of Epoxides: A Review and a Preview 674
16.10 Conversion of Vicinal Halohydrins to Epoxides 675
16.11 Reactions of Epoxides: A Review and a Preview 676
16.12 Nucleophilic Ring Opening of Epoxides 677
16.13 Acid-Catalyzed Ring Opening of Epoxides 679
16.14 Epoxides in Biological Processes 682
16.15 Preparation of Sulfides 682
16.16 Oxidation of Sulfides: Sulfoxides and Sulfones 683
16.17 Alkylation of Sulfides: Sulfonium Salts 684
16.18 Spectroscopic Analysis of Ethers, Epoxides, and Sulfides 685
16.19 Summary 688
Problems 692
Descriptive Passage and Interpretive Problems 16: Epoxide Rearrangements and the NIH Shift 697
CHAPTER 17
Aldehydes and Ketones: Nucleophilic Addition to the Carbonyl Group 700
17.1 Nomenclature 701
17.2 Structure and Bonding: The Carbonyl Group 704
17.3 Physical Properties 706
17.4 Sources of Aldehydes and Ketones 707
17.5 Reactions of Aldehydes and Ketones: A Review and a Preview 710
17.6 Principles of Nucleophilic Addition: Hydration of Aldehydes and Ketones 711
17.7 Cyanohydrin Formation 715
17.8 Acetal Formation 718
17.9 Acetals as Protecting Groups 721
17.10 Reaction with Primary Amines: Imines 722
Imines in Biological Chemistry 725
17.11 Reaction with Secondary Amines: Enamines 727
17.12 The Wittig Reaction 728
17.13 Planning an Alkene Synthesis via the Wittig Reaction 730
17.14 Stereoselective Addition to Carbonyl Groups 732
17.15 Oxidation of Aldehydes 733
17.16 Baeyer–Villiger Oxidation of Ketones 734
17.17 Spectroscopic Analysis of Aldehydes and Ketones 736
17.18 Summary 738
Problems 742
Descriptvie Passage and Interpretive Problems 17: Alcohols, Aldehydes, and Carbohydrates 749
CHAPTER 18
Enols and Enolates 752
18.1 The -Hydrogen and Its pKa 753
18.2 The Aldol Condensation 757
18.3 Mixed Aldol Condensations 761
18.4 Alkylation of Enolate Ions 763
18.5 Enolization and Enol Content 764
18.6 Stabilized Enols 766
18.7 Halogenation of Aldehydes and Ketones 768
18.8 Mechanism of Halogenation of Aldehydes and Ketones 768
18.9 The Haloform Reaction 770
18.10 Some Chemical and Stereochemical Consequences of Enolization 772
The Haloform Reaction and the Biosynthesis of Trihalomethanes 773
18.11 Effects of Conjugation in ,-Unsaturated Aldehydes and Ketones 774
18.12 Conjugate Addition to ,-Unsaturated Carbonyl Compounds 775
18.13 Addition of Carbanions to ,-Unsaturated Ketones: The Michael Reaction 778
18.14 Conjugate Addition of Organocopper Reagents to ,-Unsaturated Carbonyl Compounds 778
18.15 Summary 779
Problems 782
Descriptive Passage and Interpretive Problems 18: Enolate Regiochemistry and Stereochemistry 787
CHAPTER 19
Carboxylic Acids 790
19.1 Carboxylic Acid Nomenclature 791
19.2 Structure and Bonding 793
19.3 Physical Properties 794
19.4 Acidity of Carboxylic Acids 794
19.5 Salts of Carboxylic Acids 797
19.6 Substituents and Acid Strength 799
19.7 Ionization of Substituted Benzoic Acids 801
19.8 Dicarboxylic Acids 802
19.9 Carbonic Acid 802
19.10 Sources of Carboxylic Acids 803
19.11 Synthesis of Carboxylic Acids by the Carboxylation of Grignard Reagents 806
19.12 Synthesis of Carboxylic Acids by the Preparation and Hydrolysis of Nitriles 806
19.13 Reactions of Carboxylic Acids: A Review and a Preview 807
19.14 Mechanism of Acid-Catalyzed Esterification 808
19.15 Intramolecular Ester Formation: Lactones 811
19.16 Alpha Halogenation of Carboxylic Acids: The Hell–Volhard–Zelinsky Reaction 813
19.17 Decarboxylation of Malonic Acid and Related Compounds 815
19.18 Spectroscopic Analysis of Carboxylic Acids 817
19.19 Summary 818
Problems 821
Descriptive Passage and Interpretive Problems 19: Lactonization Methods 825
CHAPTER 20
Carboxylic Acid Derivatives: Nucleophilic Acyl Substitution 825
20.1 Nomenclature of Carboxylic Acid Derivatives 830
20.2 Structure and Reactivity of Carboxylic Acid Derivatives 831
20.3 General Mechanism for Nucleophilic Acyl Substitution 834
20.4 Nucleophilic Acyl Substitution in Acyl Chlorides 836
20.5 Nucleophilic Acyl Substitution in Carboxylic Acid Anhydrides 839
20.6 Sources of Esters 842
20.7 Physical Properties of Esters 842
20.8 Reactions of Esters: A Review and a Preview 844
20.9 Acid-Catalyzed Ester Hydrolysis 844
20.10 Ester Hydrolysis in Base: Saponification 848
20.11 Reaction of Esters with Ammonia and Amines 851
20.12 Amides 852
20.13 Hydrolysis of Amides 857
20.14 Lactams 861
-Lactam Antibiotics 861
20.15 Preparation of Nitriles 862
20.16 Hydrolysis of Nitriles 863
20.17 Addition of Grignard Reagents to Nitriles 864
20.18 Spectroscopic Analysis of Carboxylic Acid Derivatives 866
20.19 Summary 867
Problems 870
Descriptive Passage and Interpretive Problems 20: Thioesters 876
CHAPTER 21
Ester Enolates 880
21.1 Ester Hydrogens and Their pKa ’s 881
21.2 The Claisen Condensation 883
21.3 Intramolecular Claisen Condensation: The Dieckmann Reaction 886
21.4 Mixed Claisen Condensations 886
21.5 Acylation of Ketones with Esters 887
21.6 Ketone Synthesis via -Keto Esters 888
21.7 The Acetoacetic Ester Synthesis 889
21.8 The Malonic Ester Synthesis 892
21.9 Michael Additions of Stabilized Anions 894
21.10 Reactions of LDA-Generated Ester Enolates 895
21.11 Summary 897
Problems 899
Descriptive Passage and Interpretive Problems 21: The Enolate Chemistry of Dianions 903
CHAPTER 22
Amines 908
22.1 Amine Nomenclature 909
22.2 Structure and Bonding 911
22.3 Physical Properties 913
22.4 Basicity of Amines 914
Amines as Natural Products 919
22.5 Tetraalkylammonium Salts as Phase-Transfer Catalysts 921
22.6 Reactions That Lead to Amines: A Review and a Preview 922
22.7 Preparation of Amines by Alkylation of Ammonia 923
22.8 The Gabriel Synthesis of Primary Alkylamines 924
22.9 Preparation of Amines by Reduction 926
22.10 Reductive Amination 928
22.11 Reactions of Amines: A Review and a Preview 929
22.12 Reaction of Amines with Alkyl Halides 931
22.13 The Hofmann Elimination 931
22.14 Electrophilic Aromatic Substitution in Arylamines 932
22.15 Nitrosation of Alkylamines 935
22.16 Nitrosation of Arylamines 937
22.17 Synthetic Transformations of Aryl Diazonium Salts 938
22.18 Azo Coupling 942
From Dyes to Sulfa Drugs 943
22.19 Spectroscopic Analysis of Amines 944
22.20 Summary 947
Problems 953
Descriptive Passage and Interpretive Problems 22: Synthetic Applications of Enamines 960
CHAPTER 23
Aryl Halides 964
23.1 Bonding in Aryl Halides 965
23.2 Sources of Aryl Halides 966
23.3 Physical Properties of Aryl Halides 966
23.4 Reactions of Aryl Halides: A Review and a Preview 966
23.5 Nucleophilic Substitution in Nitro-Substituted Aryl Halides 968
23.6 The Addition–Elimination Mechanism of Nucleophilic Aromatic Substitution 971
23.7 Related Nucleophilic Aromatic Substitution Reactions 973
23.8 The Elimination–Addition Mechanism of Nucleophilic Aromatic Substitution: Benzyne 974
23.9 Diels–Alder Reactions of Benzyne 978
23.10 m-Benzyne and p-Benzyne 979
23.11 Summary 980
Problems 982
Descriptive Passage and Interpretive Problems 23: The Heck Reaction 986
CHAPTER 24
Phenols 990
24.1 Nomenclature 991
24.2 Structure and Bonding 992
24.3 Physical Properties 993
24.4 Acidity of Phenols 994
24.5 Substituent Effects on the Acidity of Phenols 995
24.6 Sources of Phenols 996
24.7 Naturally Occurring Phenols 998
24.8 Reactions of Phenols: Electrophilic Aromatic Substitution 999
24.9 Acylation of Phenols 1001
24.10 Carboxylation of Phenols: Aspirin and the Kolbe–Schmitt Reaction 1002
24.11 Preparation of Aryl Ethers 1004
Agent Orange and Dioxin 1005
24.12 Cleavage of Aryl Ethers by Hydrogen Halides 1006
24.13 Claisen Rearrangement of Allyl Aryl Ethers 1006
24.14 Oxidation of Phenols: Quinones 1007
24.15 Spectroscopic Analysis of Phenols 1009
24.16 Summary 1010
Problems 1013
Descriptive Passage and Interpretive Problems 24: Directed Metalation of Aryl Ethers 1018
CHAPTER 25
Carbohydrates 1022
25.1 Classification of Carbohydrates 1023
25.2 Fischer Projections and D–L Notation 1024
25.3 The Aldotetroses 1025
25.4 Aldopentoses and Aldohexoses 1026
25.5 A Mnemonic for Carbohydrate Configurations 1028
25.6 Cyclic Forms of Carbohydrates: Furanose Forms 1029
25.7 Cyclic forms of Carbohydrates: Pyranose Forms 1032
25.8 Mutarotation and the Anomeric Effect 1035
25.9 Ketoses 1037
25.10 Deoxy Sugars 1038
25.11 Amino Sugars 1039
25.12 Branched-Chain Carbohydrates 1040
25.13 Glycosides 1040
25.14 Disaccharides 1042
25.15 Polysaccharides 1044
How Sweet It Is! 1045
25.16 Reactions of Carbohydrates 1047
25.17 Reduction of Monosaccharides 1047
25.18 Oxidation of Monosaccharides 1047
25.19 Cyanohydrin Formation and Chain Extension 1049
25.20 Epimerization, Isomerization, and Retro-Aldol Cleavage 1050
25.21 Acylation and Alkylation of Hydroxyl Groups 1052
25.22 Periodic Acid Oxidation 1053
25.23 Summary 1054
Problems 1057
Descriptive Passage and Interpretive Problems 25: Emil Fischer and the Structure of (+)-Glucose 1061
CHAPTER 26
Lipids 1064
26.1 Acetyl Coenzyme A 1066
26.2 Fats, Oils, and Fatty Acids 1067
26.3 Fatty Acid Biosynthesis 1070
26.4 Phospholipids 1073
26.5 Waxes 1075
26.6 Prostaglandins 1076
Nonsteroidal Antiinflammatory Drugs (NSAIDS) and COX-2 Inhibitors 1078
26.7 Terpenes: The Isoprene Rule 1079
26.8 Isopentenyl Pyrophosphate: The Biological Isoprene Unit 1082
26.9 Carbon–Carbon Bond Formation in Terpene Biosynthesis 1082
26.10 The Pathway from Acetate to Isopentenyl Diphosphate 1086
26.11 Steroids: Cholesterol 1087
26.12 Vitamin D 1090
Good Cholesterol? Bad Cholesterol? What’s the Difference? 1091
26.13 Bile Acids 1092
26.14 Corticosteroids 1092
26.15 Sex Hormones 1093
26.16 Carotenoids 1093
Anabolic Steroids 1094
Crocuses Make Saffron from Carotenes 1095
26.17 Summary 1096
Problems 1098
Descriptive Passage and Interpretive Problems 26: Polyketides 1101
CHAPTER 27
Amino Acids, Peptides, and Proteins 1106
27.1 Classification of Amino Acids 1108
27.2 Stereochemistry of Amino Acids 1113
27.3 Acid–Base Behavior of Amino Acids 1114
27.4 Synthesis of Amino Acids 1117
Electrophoresis 1117
27.5 Reactions of Amino Acids 1119
27.6 Some Biochemical Reactions of Amino Acids 1120
27.7 Peptides 1127
27.8 Introduction to Peptide Structure Determination 1130
27.9 Amino Acid Analysis 1130
27.10 Partial Hydrolysis of Peptides 1131
27.11 End Group Analysis 1132
27.12 Insulin 1133
27.13 The Edman Degradation and Automated Sequencing of Peptides 1134
Peptide Mapping and MALDI Mass Spectrometry 1136
27.14 The Strategy of Peptide Synthesis 1137
27.15 Amino Group Protection 1138
27.16 Carboxyl Group Protection 1140
27.17 Peptide Bond Formation 1141
27.18 Solid-Phase Peptide Synthesis: The Merrifield Method 1143
27.19 Secondary Structures of Peptides and Proteins 1145
27.20 Tertiary Structure of Polypeptides and Proteins 1148
27.21 Coenzymes 1152
Oh NO! It’s Inorganic! 1153
27.22 Protein Quaternary Structure: Hemoglobin 1153
27.23 Summary 1154
Problems 1156
Descriptive Passage and Interpretive Problems 27: Amino Acids in Enantioselective Synthesis 1159
CHAPTER 28
Nucleosides, Nucleotides, and Nucleic Acids 1162
28.1 Pyrimidines and Purines 1163
28.2 Nucleosides 1166
28.3 Nucleotides 1167
28.4 Bioenergetics 1170
28.5 ATP and Bioenergetics 1170
28.6 Phosphodiesters, Oligonucleotides, and Polynucleotides 1172
28.7 Nucleic Acids 1173
28.8 Secondary Structure of DNA: The Double Helix 1174
“It Has Not Escaped Our Notice . . .” 1175
28.9 Tertiary Structure of DNA: Supercoils 1177
28.10 Replication of DNA 1178
28.11 Ribonucleic Acids 1180
28.12 Protein Biosynthesis 1183
RNA World 1184
28.13 AIDS 1184
28.14 DNA Sequencing 1185
28.15 The Human Genome Project 1187
28.16 DNA Profiling and the Polymerase Chain Reaction 1188
28.17 Summary 1191
Problems 1194
Descriptive Passage and Interpretive Problems 28: Oligonucleotide Synthesis 1195
CHAPTER 29
Synthetic Polymers 1200
29.1 Some Background 1201
29.2 Polymer Nomenclature 1202
29.3 Classification of Polymers: Reaction Type 1203
29.4 Classification of Polymers: Chain-Growth and Step-Growth 1204
29.5 Classification of Polymers: Structure 1205
29.6 Classification of Polymers: Properties 1207
29.7 Addition Polymers: A Review and a Preview 1209
29.8 Chain Branching in Free-Radical Polymerization 1211
29.9 Anionic Polymerization: Living Polymers 1214
29.10 Cationic Polymerization 1216
29.11 Polyamides 1217
29.12 Polyesters 1218
29.13 Polycarbonates 1219
29.14 Polyurethanes 1220
29.15 Copolymers 1221
29.16 Summary 1223
Problems 1225
Descriptive Passage and Interpretive Problems 29: Chemical Modification of Polymers 1227
Activity 5 (Worksheet) - Aromaticity .pdf
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Activity 6 (Worksheet) - Electrophilic
Aromatic Substitution .pdf.
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Activity 7 (Worksheet) - 1H & 13C NMRs
/ Electrophilic Aromatic Substitution Worksheet .pdf
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Library Research / Calibrated Peer Review (CPR)
LABORATORY
NOTE: Worksheets are in pdf format. You will need Adobe Acrobat Reader to view and print them which can be downloaded for free at: http://www.adobe.com/products/acrobat/readstep2.html
IR (Infrared) / UV Spectrosopy & Mass Spectrometry
IR (Infrared) / UV Spectrosopy & Mass Spectrometry (MS) Lab Worksheet .pdf1H NMR Spectrosopy
1H NMR Spectrosopy: Interpretation / Prediction & Reactions Lab Worksheet .pdf13C NMR Spectrosopy
13C NMR Spectrosopy: Interpretation / Prediction & Reactions Lab Worksheet .pdfAromaticity .pdf
Electrophilic Aromatic Substitution .pdf
1H & 13C NMRs / Electrophilic Aromatic Substitution Worksheet .pdfAldehydes & Ketones: Synthesis and Nucleophilic Addition .pdf
Aldehyde & Ketone Syntheses .pdf
Synthesis and Reactions of Dicarbonyl Compounds .pdf
Carboxylic Acids .pdf
Carboxylic Acid Derivatives: Nucleophilic Acyl Substitutions .pdf
Exploration 3-form .pdf
Nucleophilic Aromatic Substitution .pdf
Amines .pdf
Carbohydrates .pdf
Halides-Tosylates I .pdf
Halides-Tosylates II .pdf
Halides-Tosylates Synthesis .pdfMolecular Modeling / Resonance .pdf
Review .pdf
NOTE: Check List must be completed as part of the pre-lab before you may start any lab experiment. You should be able to describe each skill that is to be used in the lab to Dr. R.. Upon completion of the lab experiment you should be able to demonstrate and to teach someone the skills that you acquired.
Tentative Lab Schedule: (Refer to the course calendar for more exact details and for Due dates.)
Skills & Operations: Exercises / Activities / Experiments
1. Use & Care of Tapered Glassware.
2. Weighing Techniques: Tare & Care
3. Transferring Liquids.
4. Care, Handling & Storage of Chemicals.
5. Chemical Hygiene & Waste Disposal
6. Temperature: Measurement & Control.
7. Heating Methods.
8. Reflux.
9. Cooling Methods.
10. Methods of Addition (s, l, & g).
11. Filtration (Gravity).
12. Filtration (Vacuum/Aspirator).
13. Extraction.
14. Evaporation.
15. Rotevap: Recovery of Solvents.
16. Column Chromatography.
17. Thin-Layer Chromatography.
18. Gas Chromatography.
19. Washing Liquids.
20. Drying Liquids.
21. Drying Solids.
22. Drying and Trapping Gases.
23. Recrystallization.
24. Sublimation.
25. Steam Distillation.
26. Simple Distillation.
27. Vacuum Distillation.
28. Fractional Distillation.
29. Melting Point Determination.
30. Boiling Point Determination.
31. Refractive Index Determination.
32. Polarimetry: Optical Rotation.
33. IR: Infrared Spectrometry.
34. NMR: Nuclear Magnetic Resonance.
35. Ultraviolet-Visible Spectrometry.
36. Mass Spectrometry.
Safety:
SAFETY: General Regulations & Lab Guidelines
Safety Quiz Sheet & AcknowledgmentMolecular Modeling / WebMO
Electrophilic Aromatic Substitution / Friedel Crafts Acylation (Handouts)
Chiral Compounds and Green Chemistry: Reduction of a ketone by sodium borohydride and baker's yeast (Handouts)
Hydrolysis Rate of Esters (Handouts)
Insect Repellant: Deet Synthesis-Explorations 1, 2, 3Synthesis of a bioregulator: 1-phenyl-3-(4-diethylaminoethoxyphenyl)-2-(E)-propen-1-one (Handouts)
Chem 226 Experiments & Skills: (Previous Course)
Experiment #1: ExtractionExperiment #2: Recrystallization & Melting Point
Experiment #3: Thin Layer Chromatography (TLC)
TLC of Analgesic Drug Components
Experiment #4: Synthesis of Salicylic Acid from Wintergreen
Experiment #5: Gas Chromatography & Fractional Distillation
Experiment #6: Enantiomeric Separation/ Resolution (Ibuprofen)
Optical Activity /Polarimetry: Part I & Part II
Optical Rotation I .pdf; Optical Rotation II .pdf
Experiment #7: Bromination of Cinnamic AcidExperiment #8: Acetate Synthesis, Simple Distillation, Infrared Spectroscopy, GC
Experiment #9: Sn1 , Sn2 Reactions and Solvent EffectsExperiment #10: Essential Oils / Steam Distillation / Extraction
Experiment #11: Diels Alder reaction of maleic anhydride and furan
Experiment #12: Identification of TerpenoidsExperiment #13 : Colorful Grignard Reaction
Laboratory Techniques & Videos:
Laboratory Experiments These experiments have been adapted from standard types of experiments commonly performed in organic chemistry courses throughout North America. They are derived from the non-copyrighted, open Web source materials kindly made available by a large number of notable educators/professors who generously share their creativity, time, efforts, and excellent materials. Their institutions include: University of Colorado, Boulder; McMaster University; University of Alberta; University of Calgary; Reed College, Barnard University; Massachusettes Institute of Technology; University of California, Los Angeles; Dakota State University; Wellesley University; University of California, Berkeley; Mount Holyoke College, Manhattan College.
Exercises / Worksheets / Tutorials:
Spectroscopy 1: IR Spectroscopy: Handout [Group] & [Individual]
IR (Infrared) / UV Spectrosopy & Mass Spectrometry
Worksheet FORM: IR (Infrared) / UV Spectrosopy & Mass Spectrometry (MS) Lab Worksheet .pdf(MS data for the individual unknowns is provided by Dr. R. in response to your e-mail reply to the assignment from first class meeting.)
IR Resources:- Spectroscopy for the Organic Chemistry Student from Professor Paul R. Young: University of Illinois, Chicago Organic Chemistry OnLine: Spectroscopy
- Section VIa (IR Background): Infrared Spectroscopy
- Tutorial Problem Set ( Ten Problems):
- Infrared Spectroscopy Problem Set
Infrared Basic Tutorial with six practice problems California State University, Stanislaus
IR Wizard from Steffan (St.) Thomas, University of Potsdam, Germany. A query based tool in English and German. Useful in self-learning-testing applications. Supply a wave number (cm-1) and a table of possibilities is produced with chemical functions that have the value within their range of peak frequencies. Pages are cleanly designed and the built-in search engine works well.
NIST Chemistry Webbook
http://webbook.nist.gov/chemistry
Free government database that includes numerous compounds. Provides a variety of data: physical, thermodynamic and spectroscopic. IR and MS spectra available for a portion of the compounds in the data base. An excellent resource.Spectral Data Base System for Organic Compounds
http://www.aist.go.jp/RIODB/SDBS/
SDBS: Integrated Spectral Data Base System for Organic Compounds, a searchable database that contains: MS (ca 18,000 spectra), 13C NMR (ca 9,700 spectra), Compound Dictionary, 1H NMR (ca 10,100 spectra, 29,000 compounds) add IR and Raman.Interactive Tutorial: University of Alberta
http://www.chem.ualberta.ca/~orglabs/spectroscopy/specmaster.html
An excellent resource for practice in prediction and interpretation.
Mass Spectrometry:
Mass Spectrometer Animated Tutorial Dr. Thomas Poon, Colby College mass spectrometer Shockwave Interactive Tutorial: Instrument Function, Data Generation, Intrepretation and More. (127 kB)
- Spectroscopy for the Organic Chemistry Student from Professor Paul R. Young: University of Illinois, Chicago Organic Chemistry OnLine: Spectroscopy
- Section VIc (Background): Mass Spectroscopy
- Tutorial Problem Set (Five Problems)
- Mass Spectroscopy Problem Set
MS Fragment Wizard from Steffan (St.) Thomas, University of Potsdam, Germany. A query based tool in English and German. Useful in self-learning-testing applications. Supply m/e value and a list of possibilities for the fragment or mass loss fragment is produced with links to exact mass and isotope distribution calculators. Pages are cleanly designed and the built-in search engine works well.- SDBS Mass Spectrometry Database A collection of spectra for over 200 relatively simple organic compounds containing up to 30 carbon atoms
NIST Chemistry Webbook
http://webbook.nist.gov/chemistry
Free government database that includes numerous compounds. Provides a variety of data: physical, thermodynamic and spectroscopic. IR and MS spectra available for a portion of the compounds in the data base. An excellent resource.MRI Photos
http://www.simplyphysics.com/flying_objects.html
Spectroscopy 2: 1H NMR Spectroscopy
1H NMR Spectrosopy
Worksheet Form: 1H NMR Spectrosopy: Interpretation / Prediction & Reactions Lab Worksheet .pdf
Interactive Tutorial: University of Alberta
http://www.chem.ualberta.ca/~orglabs/spectroscopy/specmaster.html
An excellent resource for practice in prediction and interpretation.The Basics of NMR: Dr. Joseph Hornak http://www.cis.rit.edu/htbooks/nmr/nmr-main.htm
1 H and 13C NMRs :
Example compound: 1H nmr - example
Prediction & Interpretation: (Could also be Interpretation and Comparison.)
- Identify the protons as equivalent or diastereotopic or enantiotopic.
- Predict the chemical shifts and mutliplicities.
- Draw the spectrum.
- Compare to example.
1H nmr data for your individual unknown is to be generated using the department's 60 MHz FT-NMR spectrometer.
Spectroscopy 3: 13C NMR Spectroscopy
13C NMR Spectrosopy
Worksheet Form: 13C NMR Spectrosopy: Interpretation / Prediction & Reactions Lab Worksheet .pdf
The Basics of NMR: Dr. Joseph Hornak http://www.cis.rit.edu/htbooks/nmr/nmr-main.htm
1 H and 13C NMRs :
Example compound: 13C nmr - example
Prediction & Interpretation: (Could also be Interpretation and Comparison.)
- Identify the carbons as equivalent or different.
- Predict the chemical shifts and mutliplicities. (Decoupled)
- Draw the spectrum.
- Compare to example.
13C nmr data for your individual unknown is to be generated using the department's 60 MHz FT-NMR spectrometer.
13C nmr: Worksheet spectrum
NMR:
- Spectroscopy for the Organic Chemistry Student from Professor Paul R. Young: University of Illinois, Chicago Organic Chemistry OnLine: Spectroscopy
- Section VIb Background: 1H & 13C NMR
- Tutorial Problem Sets (Ten 1H & Five 13C Problems)
- 1H & 13C NMR Problem Set
Proton Chemical Shift Table California State University, StanislausProton NMR Wizardfrom Steffan (St.) Thomas, University of Potsdam, Germany. A query based nmr tool in English and German. Useful in self-learning/testing applications. Supply a chemical shift value and a table of possibilities is produced with ranges of chemical shifts. Pages are cleanly designed and the built-in search engine works well.
13C Chemical Shift Calculator University of Potsdam, Germany, Produces13C spectra for phenyls, biphenyls, pyridines and pyridazines.
NMR Spectroscopy Problems On-Line:
Prof. Browne: University of Alberta
http://www.chem.ualberta.ca/~orglabs/spectroscopy/specmaster.htmlProf. Merlic, UCLA, WebSpectra
http://www.chem.ucla.edu/~webspectra/Prof. Smith, Notre Dame
www.nd.edu/~smithgrp/structure/workbook.html
INTEGRATED ANALYSES:Interpretation:
IR- example, 1H nmr - example, MS - example, table 13C nmr - example
Example compound:
Review the structural assignment of each of the on-line compounds reconciling any differences in earlier assignments and considering in toto: IR, MS
1H & 13C nmr data.Apply IR data , MS data (provided by Dr. R.), and 1H & 13C nmr data to your individual unknown. NMR data generated using the department's 60 MHz FT-NMR spectrometer. Be sure that the structural assignment is complete and accurate.
Integrated Quiz/ Problems:Spectroscopy for the Organic Chemistry Student from Professor Paul R. Young: University of Illinois, Chicago Organic Chemistry OnLine: Spectroscopy
Multiple Choice Quiz: Spectroscopy -----
Integrated Problems (Ten Problems}
Spectroscopy 4:
NMR Spectroscopy in Context (handouts)1) Integrated Spectroscopy and Reaction Chemistry: Analysis of a Draft for Publication - pdf
----- Spectra - pdf
----- Team Form - pdf
"Is Peer Review Broken?", The Scientist, Volume 20 | Issue 2 | Page 26, (February 2006)
http://www.the-scientist.com/article/display/23061/
2) Dehydration of 1-ethyl-2-methylcyclohexanol: NMR application to determine the respective distribution of kinetic and thermodynamic products. See:- NMRs of 1- and 3-methyl cyclopentene and their mixture.
- NMR QuickTime Movie (156Kb)
LABORATORY:
Synthesis Project: Electrophilic Aromatic Substitution / Friedel Crafts Acylation
1) Consult in-lab Team Project list for your Team members.
2) Refer to Team letter (A, B, C, etc.) for the list of starting aromatic compounds assigned to the Team.
3) If Team has less than 4 members, you may choose from the list which of those you will use. Read the project instructions. Select a starting material. Write up a pre-lab in lab notebook. Complete the Skills Check List for this experiment. Have pre-lab reviewed and initialed by Dr. R. before beginning. Complete the experiment.Project Instructions .pdf
Electrophilic Aromatic Substitution Worksheet .pdf
1H & 13C NMRs / Electrophilic Aromatic Substitution Worksheet .pdf
a) Nitration Quicktime Movie
b) Bromination Quicktime Movie
c) Acylation Quicktime MovieSummary Report (Group/Typed) to follow a common journal format, click here for an example , plus an abstract, and including:
1) Reactions and structures (Either drawn with a template [See Dr. R. if you plan this approach] or using ISIS Draw; a free/downloadable drawing program), or similar program drawing program, Marvin, etc.
2) Concise experimental procedures with % yield of each of the synthesis,
3) IR/NMR spectroscopy data,
4) Physical data: boiling point, index of refraction
5) Answers to the following questions
a) Name the major mono-nitration product of: 1) phenyl acetate, 2) 2,4-dinitrotoluene, 3) p-methoxybenzaldehyde
b) Beginning with benzene and 2,5-dichloro-2,5-dimethyl hexane, using any other necessary organic and inorganic reagents, outline a synthesis of versalide, which is a starting material for a class of aroma therapy compounds referred to as tetralin musks.c) The 13C NMR that was provided to you was taken from consolidated student samples for the reaction product(s) of your individual starting compound. The samples reportedly had all of the solvent removed, but this may not actually be the case. Draw structures on the NMR handout for all compounds that you believe present in the sample and assign the corresponding 13C NMR peaks to support your conclusion. Using your IR for the crude product briefly explain on your IR page if the IR agrees with your 13C NMR conclusion. Bonus: Download 1H 13C NMR fid files, assign signals/peaks to structures.
d) Find the boiling point for your individual product(s) from published sources. If you cannot find the exact structure select a compound that best approximates the product(s)' structure(s). Using a nomography determine what boiling point or boiling range would be expected at 4 torr. Include this information on your NMR handout including the reference you found for the boiling point.
e) Refer to the following list of criteria for "green chemistry". Identify those items in the list that relate to the reaction procedure that you just performed. For each item that you selected provide a recommendation for an improved alternative.
Green Chemistry: Science and Politics of Change
Martyn Poliakoff, J. Michael Fitzpatrick, Trevor R. Farren, Paul T. Anastas
Science, Volume 297, Number 5582, Issue of 2 Aug 2002, pp. 807-810.
Green Chemistry Principles
1. It is better to prevent waste than to treat or clean up waste after it is formed.
2. Synthetic methods should be designed to maximize the incorporation of all materials used in the process into the final product.
3. Wherever practicable, synthetic methodologies should be designed to use and generate substances that possess little or no toxicity to human health and the environment.
4. Chemical products should be designed to preserve efficacy of function while reducing toxicity.
5. The use of auxiliary substances (e.g., solvents, separation agents, and so forth) should be made unnecessary wherever possible and innocuous when used.
6. Energy requirements should be recognized for their environmental and economic impacts and should be minimized. Synthetic methods should be conducted at ambient temperature and pressure.
7. A raw material or feedstock should be renewable rather than depleting wherever technically and economically practicable.
8. Unnecessary derivatization (blocking group, protection/deprotection, temporary modification of physical/chemical processes) should be avoided whenever possible.
9. Catalytic reagents (as selective as possible) are superior to stoichiometric reagents.
10. Chemical products should be designed so that at the end of their function they do not persist in the environment and break down into innocuous degradation products.
11. Analytical methodologies need to be developed further to allow for real-time in-process monitoring and control before the formation of hazardous substances.
12. Substances and the form of a substance used in a chemical process should be chosen so as to minimize the potential for chemical accidents, including releases, explosions, and fires.6) Attach copies of each group members raw lab research notebook pages, which should be clearly and legibly written in the format described in the course syllabus to include title, name, date, etc.
7) a typed invoice for NSF that includes an itemized account of the costs per kg of each product broken down into their respective raw material costs (refer to chemical company catalogues for prices) and their relative labor costs: man/woman hours for each group member devoted to the syntheses, the total hours for the group, the $/hour charge that you think reasonable for re-imbursement. The complete package must be submitted by the deadline noted in the calendar. LATE submissions will not be accepted. All group members receive the same base grade for the project.
Individual RESULTS & Group Results:
(NOTE: Your individual grade will be subject to adjustment based on the results of a private, confidential survey within the group of each group members performance and contribution.)
Hydrolysis Rate of Esters in strong base: Click on the link and view the video. Work within your bioregulator teams following the procedure below. Turn in one completed lab form per group when due, consult the course calendar.
Procedure:
Place 2 mL of 50% ethanol, 2 drops of 1M NaOH, and 2 drops of universal indicator into each of 4 labeled test tubes. Stopper the tubes and shake each of them. Then, add 5 drops of one of the following esters: ethyl acetate, ethyl benzoate, ethyl butyrate, ethyl formate, to one of the labeled test tubes. Repeat for the remaining three esters and test tubes. Stpper and shake each until the ester dissolves. Record the color, and then heat the test tubes in a water bath to 50oC for a total of 30 minutes, recording the color every 10 minutes. Using a color chart convert the color to an approximate pH value.
See a similar mechanism to that used for the synthesis of dimedone. It is used in the preparation of oak moss odorant (an earthy odor): http://www.bojensen.net/Oakmoss/Oakmoss.htm (Courtesy of Bo Jensen)
It illustrates one method of synthesis for 2,4-dihydroxy-3,6-dimethylbenzoic acid methyl ester, the most important odour component in Oakmoss, Evernia prunastri (Usneaceae).
It has a very powerful odour: earthy, woody, like some lichens. It is used in perfumery in low concentrations.
References:
1) Sonn A, Berichte 1929;62B:3012
2) Eur.Pat. 133,960 (Chem.Abstr 1986;105:226057x)
3) Bauer K, Garbe D, Surburg H (1990) Common fragrance and flavor materials. Preparation, properties and uses. 2'nd rev. ed. VCH Germany.Synthesis of Dimedone
General Procedure:
Add ~25 mmol of dimethylmalonate to a dry round bottom flask equipped with a condenser. After the addition is complete place a drying tube on top of the condenser. Mix in ~26 mmol of a solution of 25% NaOCH3 in methanol. Add a spin bar or boiling chips, then heat the reaction mixture to just boiling in a water bath. Any solids should be dissolved at this point. Remove the water bath, from the top of the condenser slowly add ~26 mmol of mesityl oxide (freshly distilled) in small portions over a period of ~ 3 min. Reflux the reaction mixture for ~ 1hr. Evaporate the methanol until a moist solid residue is obtained.Add 20. mL of a 3 M solution of NaOH, reinstall the condenser and heat to reflux (90-95ºC) for ~45 min. Pour the reaction mixture with stirring into a beaker containing 15 mL of 6 M HCl. Carefully boil the mixture in the beaker under a hood until gas is no longer evolved. Cool the reaction mixture and collect the crystals by vacuum filtration. At this point, either dry the crystals or recrystallize them with a 50% acetone/water solution. Using either the crude or recrystallized product, obtain a melting point, IR, 1H NMR, and 13C NMR. Turn in the sample in a labeled vial. Answer the Postlab questions.
Postlab Questions:
a) Explain how IR could be used to determine the enol content.
b) Using the nmr spectrum for dimedone that is provided from the link below, calculate the percent of the enol present in the sample.
Dimedone NMR
c) Using your value in question b) calculate the equilibrium constant K.
d) Complete the in--lab/postlab SLO questionaire.
Preparation of Aldol Condensation Products
(Individual Assignments)
1) Prepare a prelab report in your lab notebook for your assigned reactants: the aldehyde and a ketone from the link above, using Procedure A, which follows.
2) This must be done independently. (Including both prelab and post-lab questions): Complete the prelab questions in the handout & turn-in.
3) Have the prelab notebook pages initialed before beginning.
Procedure A:
Place 2 mmol of ketone in a test tube or centrifuge tube and dissolve in ~ 4 mL of 95% ethanol. Add 8 mmol of aldehyde and 3 mL of 1 M NaOH. Let the reaction mixture stand at room temperature for ~15 minutes with occasional shaking. If little or no precipitation is observed, heat the reaction mixture in a boiling water bath until there is no further precipitation. Cool the mixture in an ice bath for ~5-10 minutes. Collect the solid by vacuum filtration. Wash the crystals with 2 mL of 4% acetic acid/95% ethanol v/v followed by 2 mL of cold 95% ethanol. Dry the product.Procedure B:
Place 0.006 moles of aldehyde, 0.003 moles of ketone, and 3 mL of 95% ethanol in a conical test tube. Mix until completely dissolved. Add 1 mL of 10% sodium hydroxide solution. Mix the contents until precipitation is observed. Let the mixture stand for another 20 minutes with occasional shaking. After the 20-minute period is completed, cool the mixture in an ice bath for 10 minutes. Using a Pasteur pipet, remove the liquid from the conical test tube, leaving the solid behind. In order to assure that no solid product is transferred out of the test tube, you could take a very small piece of cotton, and plug up the tip of the pipet (from the outside), such that only liquids are transferred into the pipet. Wash the crystals with 2 portions of 2 mL ice-cold water. Recrystallize the solid product in the same conical test tube, using 95% ethanol. Collect the product via vacuum filtration and allow it to dry. Note that you may need to tare your filter paper if you have very little product. Weigh your product. Measure the melting point and the IR spectrum of your obtained product.4) Post-lab Questions (Attach answers to notebook pages.)
Three unknown compounds with a molecular formula of C12H16O, (A, B, and C), were all optically active, all had strong IR bands in the 1700 cm–1 region. When A was treated with NaOD/D2O, three hydrogens were exchanged for deuterium, and the deuterated product of A remained optically active. When A was treated with I2/aq. NaOH, a yellow precipitate formed (A positive iodoform tests as in the prelab.) Compounds B and C did not give a yellow precipitate with I2/aq. NaOH. Compound B exchanged only one H for D when treated with NaOD/D2O, and the monodeuterated product of B was optically inactive. When compound C was reacted with NaOD/D2O, four H's were exchanged for D's, and the deuterated product of C remained optically active.
1) Give possible, plausible structures for A–C consistent with the preceding information. (There may be more than one possible structure for each of them.)
2) Which of your 3 structures would be the best candidate to produce a single product when reacted with benzaldehyde in an aldol condensaton? Briefly explain your answer. Draw a structure for the product of the condensation that would form at low temperature.
3) A fourth aldehyde, trans-cinnamaldehyde was assigned in previous years, but in 2009 the condensation did not occur, and trans-cinnamaldehyde was eliminated from this year's reagents. Analyze the Spectroscopy Data for the "trans-cinnamaldehyde" from the bottle which was used in Spring 2009. Provide a brief explanation of why the reaction did not occur.
Synthesis of Dimedone Derivatives
Literature Research / Organic Synthesis
A Remembrance to HeatherPART I: Calibrated Peer Review (CPR) on-line writing assignment
CPR UsernamesDesign and Development of Drugs
http://cpr.molsci.ucla.edu/1) You will read an article from the Journal of Chemical Education about organic synthesis and the history of many drugs and medicines,
K.C. Nicolaou, et. al., JChemEd, 75, 1226-1258, (1998); pdf files: Reading-1.pdf; Reading-2.pdf.
2) Learn about the way that one drug (aspirin) was discovered and how chemists contributed to its improvement.
3) Learn to identify new synthetic methods necessary in drug synthesis and future drug development.
4) Learn about a widely used approach to the rapid development of new chemical compounds using Combinatorial Synthesis and how chemical libraries (in a non-traditional sense) are used.
5) Write an essay on-line explaining how aspirin was developed, the methods chemists currently use to develop new and better drugs, which can be applied to any area including nano-materials, and in new applications of organic synthesis.
6) Review and appraise 3 of your classmates essays, and then reconsider and appraise your own submission.PART II: Literature Research
You are to select a compound which interests you. The accompanying list includes a number of compounds for your consideration, eg. thienamycin. Everyone will have a different individual compound. You are to identify and report your target compound, its CAS number, its General Class, eg. b-lactam antibiotics, and include a set of related Keywords, eg. thienamycin, b-lactam antibiotics, penems, carbopenems, monobactams, penicillins, etc., to Dr. R. by e-mail on or before April 16th. The compound does not have to come from the accompanying list, but you must have your selection approved before you begin your research.
Using Google Scholar, http://scholar.google.com/schhp?hl=en, Google Patents, http://www.google.com/patents?hl=en, and ERIC: Educational Resources Information Center, http://www.eric.ed.gov/, you are to find literature references, evaluate them, and produce a bibliography with abstracts that includes one or more relevant non-primary background reference(s) [books, review articles, etc.] or primary literature references [peer reviewed journals], which describe the General Class of compounds, their use, educational importance, and value to society, plus citing a minimum of 5 primary literature references, which describe the following topics: 1) physical, stereochemical and spectroscopic related data, e.g., [a], m.p or b.p., IR, 1H NMR, 13C NMR, 2) biological mode of action/ pharmacology/ toxicology, 3) one or more total or partial syntheses of the selected compound and/or its analogs. (More than one primary reference per topic is acceptable.)
Your report is to be type-written with a complete bibliography (6 references minimum: 1 non-primary, 5 primary), patents are acceptable as primary references, and it must include respective abstracts. See: Thienamycin Example.pdf. The report is to be type-written and include an introductory narrative section on the general class of compounds, their use, importance, and history. The report is to include the CAS number of your compound and a clearly drawn structure as a cover page with a Title, your name, and course and section information. You are to use a chemical drawing program such as ISIS/Draw or marvin/Draw for the drawing, which are free to students and faculty (See course Web site for download links.) or they can be used directly on the PS 110 computers. (Cutting and pasting, or freehand/ stenciled drawings are unacceptable.)
Two copies of the report are to be submitted by 5:00PM on April 30th. Late reports will not be accepted.
Library Research / Organic Synthesis (Instructions)
A Remembrance to Heather
Library Research / Organic Synthesis
(Instructions)Calibrated Peer Review (CPR)
CPR UsernamesDesign and Development of Drugs
http://cpr.molsci.ucla.edu/1) You are to read an article from the Journal of Chemical Education about organic synthesis and the history of many drugs and medicines,
K.C. Nicolaou, et. al., JChemEd, 75, 1226-1258, (1998); pdf files: Reading-1.pdf; Reading-2.pdf.
2) Learn about the way that one drug (aspirin) was discovered and how chemists contributed to its improvement.
3) Learn to identify new synthetic methods necessary in drug synthesis and future drug development.
4) Learn about a widely used approach to the rapid development of new chemical compounds using Combinatorial Synthesis and how chemical libraries (in a non-traditional sense) are used.
5) Write an essay explaining how aspirin was developed, the methods chemists currently use to develop new and better drugs, which can be applied to any area including nano-materials, and the future of organic synthesis.Library Research
DVC Library
http://www.dvc.edu/library/
DVC On-line Databases
http://www.dvc.edu/library/databases.htmUC Berkeley Chemistry Library & Maps: Campus, Zoom in, Chem Library
Chem Library Homepage: http://www.lib.berkeley.edu/CHEM/
March 2006, UC Berkeley Chem Library Calendar Hours
UCB Pathfinder
http://sunsite2.berkeley.edu:8000/
UC Davis
http://www.lib.ucdavis.edu/
http://www.lib.ucdavis.edu/pse/databases/index.html
University of Texas
http://www.lib.utexas.edu/Libs/Chem/info/
ERIC: Educational Resources Information Center
http://www.eric.ed.gov/
Examples of Some past papers:
Ibogaine
Leinamycin
Ascorbic Acid
Gibberellic Acid
Synthetic Challenges: Earn $$$ for your knowledge and imagination!
For example:
INNOCENTIVE 861088
Substituted Propionic Acid
POSTED: APR 22, 2003
DEADLINE: JUL 30,
2003
$30,000 USD
Insect Repellants: Synthesis of DEET
(1) Read: Lab Instructions
(2) Complete the synthetic procedure, purify a portion for IR analysis of your product. Answer the post lab questions at the end of the instructions, plus the following NMR related questions.
IR Fraction #1(bp <120 oC @ 2 torr)
Click for larger image.
IR Fraction #2 (bp 128-29 oC @ 2 torr)
Click for larger image.
1H NMR.fid Fraction #2 (bp 128-29 oC @ 2 torr)Composite Sample's 1H NMR.fid
Composite Sample's 13C NMR.fid
NMR Postlab Questions-10 .pdf
Extra Credit:
See: http://chemconnections.org/organic/chem226/Labs/Smell/ChemComm.htmlRead the article "Love Molecules". Identify the structure of the elephant pheromone and outline a synthesis of the compound starting from heptanoic acid lactone, 1-bromopentane, acetic anhydride and any other reagents that you choose.
(3) Enzymes & biological activity
- Amino Acids: http://www.bio.cmu.edu/Courses/BiochemMols/AAViewer/AAVFrameset.htm
- Proteins: http://www.cryst.bbk.ac.uk/PPS2/course/index.html
Enzyme Docking (683K QuickTime Movie)
- Trypsin musically: Man or Mouse? http://chemconnections.org/music/
Enzyme catalyzed hydrolysis: Trypsin : p-nitrophenylacetate (498K, QuickTime Movie)
- Cholinesterase: http://www.rcsb.org/pdb/molecules/pdb54_1.html
- Acetylcholinesterase: http://chemconnections.org/Presentations/Columbia/ace1.html
- Hemoglobin / Sickle Cell: http://chemconnections.org/Presentations/Columbia/slide8-3.html
Separation and Identification of Unknown
High Resolution Masses for unknowns
Beynon Table:
http://www.chm.davidson.edu/java/beynon/beynon.html
Polymers: Slime and Gak (Silly Putty's Cousin)
Procedure .pdf
Report Form .pdfAmino Acids/Proteins, Beads and the Chemistry of Flour:
Amino acids chart .pdf
Amino Acids Jmol/Rasmol Colors
Primary protein bead stringing
“The Chemistry of Cereals” and “Wheat, Flour and the Action of Water” .pdf
Protein Chemistry: Amino Acids, Flour, Dough & Elasticity .pdf
- http://www.exploratorium.edu/cooking/bread/index.html
http://www.exploratorium.edu/cooking/bread/activity-gluten.html
http://members.lycos.nl/ClassoFoods/ukindex.htmlBread Recipes:
http://www.recipesource.com/baked-goods/breads/Molecular model of the spiral structure formed by the HMW subunits of glutenin. The model was developed by Drs. O. Parchment and D. Osguthorpe at the University of Bath, U.K. Peter Shewry, et. al., http://www.pbi.nrc.ca/bulletin/sept97/intro.html
Chiral Compounds and Green Chemistry: Reduction of a ketone by sodium borohydride and baker's yeast
Introduction .pdf
Procedure .pdf
Spectra .pdf:
1H & 13C NMRs, and IRs
Post Lab Questions.pdf
Carbohydrates, Glycoproteins and Related:
- Carbohydrates: Worksheet
- Carbohydrates (University of Akron): http://ull.chemistry.uakron.edu/genobc/Chapter_17/
- Carbohydrate Active Enzymes: http://afmb.cnrs-mrs.fr/;
http://afmb.cnrs-mrs.fr/rubrique117.html
Bio-Recognition: Saccharides, Proteins, Influenza, SARS, HIV
See Professor Carolyn Bertozzi’s related LBL / You Tube Presentation:
http://www.youtube.com/watch?v=VBwNMR3C0Ys&feature=PlayList&p=10F61E434B646DE1&index=1Viruses and influenza .pdf
Birds, Swine, Influenza & Us .pdf
"Why does the flu appear every year?" : A 4 act drama by Prof. Andy Mobley, Grinnell College
A Dramatic/Molecular Interpretation of the Influenza Virus's Life Cycle
- The Actors
A Parent Virus Group (Hemagglutinin Proteins)
A Cell Membrane Group
A Cell Cytoplasm Group
A Viral Progeny Group
A Neuraminidase Group (Sialidase Enzyme)
An Anti-influenza Group (Neuraminidase Inhibitors)
The Play
Scene 1: The Parent Virus recognizes The Cell Membrane and infects the cell
Scene 2: Viral RNA is transported into the cell and cellular machinery in the Cell Cytoplasm builds new virions
Scene 3: The Viral Progeny escape from the cell only to clump together
Scene 4: Neuraminidase cleaves frees Viral Progeny from clumping
Alternate Ending:
Scene 4: The Neuraminidase inhibitor keeps Neuraminidase from freeing Viral Progeny
Click on the links below the images for the 2010 Performances:
2010 Quicktime/AVI Movies:
M/W Production Team/ 59.5 Mb
T/Th Production Team/ 100.4Mb2009 Quicktime/AVI Movies:
T/Th Production Team/ 65 Mb; 8 Mb
M/W Production Team/ 39.7 Mb; 161 Mb
Click on the above image for the 2003 Performance:
http://chemconnections.org/organic/chem227/Flu-slides/index.html
Click on the above image for the 2006 Performances:
Influenza 2006 Performances: Movie (17MB)
- Flu Pandemic Monitoring: http://pandemicflu.gov/
- Flu Pandemics: http://chemconnections.org/ScanDbase/Flu-NYT-11-92.html
- SARS (Sudden Acute Respiratory Syndrone) http://www.who.int/csr/sars/en/
- Centers for Disease Control (CDC)
- http://www.promedmail.org
- http://www.nejm.com
- HIV
- HIV overcomes almost every antibody that attaches to its surface protein, gp120. The virus copies itself rapidly and mutates frequently, creating a staggering number of viral strains, which makes it a formidable challenge for antibodies to control. It has also evolved to effect the "primitive" innate immune system as well.
- HIV evolved to avoid 2 virus controlling enzymes in the innate immune system: Ref-1 & CEM 15
Synthesis of a bioregulator: 1-phenyl-3-(4-diethylaminoethoxyphenyl)-2-(E)-propen-1-one
Plant Hormones (phytohormones) are divided into five groups: cytokinins, abscisins, gibberellins, auxins, and ethylene. These groups interact and control the overall development of plant organs (eg. leaves, stems, roots, fruit) and effect plant behavior in relation to environmental conditions. Auxins control cell growth and are involved with plant functions such as phototropism (growing toward light), suppressing abscission (shedding: leaves, stalks, fruit, diseased parts), enhancing fruit production, and inhibiting growth. In this experiment you will prepare a synthetic auxin, which promotes the production of a carotenoid, lycopene. Carotenoids are highly conjugated and absorb ultraviolet radiation. They are colored and provide protection from sunlight and ultraviolet damage.
The synthesis involves two steps. The first is an aldol condensation of the enolate of acetophenone with p-hydroxybenzaldehyde. The resulting phenoxide that occurs in the reaction mixture is then directly used as a nucleophile and reacted with diethyl aminoethyl chloride.
The bioassay of the product measures its effectiveness by determining the mass percent of lycopene produced by carotogenesis over a period of several days through the Beer’s Law analysis of the lycopene concentration.
Organize into a group of four. Split the group in half: one half as Team A and the other Team B. Select which group will do the synthesis: Parts A & B, and which group will do the bioassay Parts: C & D. One report will be submitted per group and include the post lab questions.
The entire group is to answer all of the prelab questions before beginning. The individual Teams are to independently complete the Aldehyde & Ketone Synthesis Worksheet and Enolate Molecular Modeling exercise.
Reading / instructions: :
Flatulence-I.pdfExperimental Data / Questions:
Flatulence-II.pdf
Prelab form .pdf
Postlab form .pdfPatented Invention: (Click image to see patent.)
- Exercise to be done before doing the assigned reading:
Click on each of the birds in the following table one at a time. When opened you will see a page with a colored bird on the left and an empty cage on the right. Focus your eyes on the bird's eye and slowly count to twenty; then quickly shift your view to the center of the empty cage. Record what you observe for each bird and then refer to the color wheel in the Web-link below. Write a brief description relating your results to the color wheel, comparing pairs of colors and their relative locations on the wheel. Also refer to the MC2 emission and absorption spectrum simulation tools to vary colors. These can be linked from the MC2 Java Applets page.
Bird 1
Bird 2
Bird 3
Exercise adapted from the Exploratorium's Snacks: http://www.exploratorium.edu/snacks/bird_in_cage.html- Color Wheel
- MC2 Java Applets: http://mc2.cchem.berkeley.edu/Java/
- Assigned Background Reading:
- Genetech's Access Excellence: http://www.gene.com/ae/AE/AEC/CC/vision_background.html Collected Chemistry & Biochemistry: Adapted from various sources, including ChemFinder and Metabolic Pathways, Genome Project (Japan) http://www.genome.ad.jp/kegg/metabolism_menu.html : http://chemconnections.llnl.gov/organic/Chem227/Vision/chem-vision.html and others.
- Functional Properties of Rhodopsin:http://www.isat.jmu.edu/users/klevicca/isat280/DETAILS.HTM
Questions:
How many different types of cone cells are there in the eye that respond to color?What do you think the color of these cells might be if they were viewable to you?
Based on the experiment done in class,sketch the eye and illustrate where on the retina these cells are located.
Color Wave length (nm) Violet 390-455 Dark Blue 455-485 Light Blue 455-485 Green 505-550 Yellow-Green 550-575 Yellow 575-585 Orange 585-620 Red 620-760
- You will need Chime, beta ver. 2.0, or RasMol to answer the following questions. The above image is retinal bound to rhodopsin, a vision protein that occurs in rod cells. How many helices and how many beta-sheets are found in rhoposin? Is the retinal in the all trans form or cis form? (Hint, the command: select hetero will select the retinal). Rhodopsin.PDB Name three enzymes related to"rhodopsin" that are also involved with rods and human vision. List the enzymes respective uv/visible absorbtion maxima and what color you would expect each of them to be? Postulate in molecular terms a brief explanation of the "experimental bird-watching" results noting probable changes to cellular enzymes in the cones that relate to your observed color changes and what the uv/visible absorbtion maxima of the enzymes might be?
- What structural features common to retinoids and carotenes contribute to their importance in vision?
The Human Genome:http://www.wellcome.ac.uk/en/genome/index.html
1 GCA17 CUC33 GUG 49 GAU 2 CCC18 CUA34 AAU 50 GAC 3 GUU19 UUU35 AAC 51 CGU 4 CUU20 CUG36 CAG 52 UAG 5 UUG21 UAU37 UGU 53 AAG 6 AUG22 UAC38 CGC 54 UGG 7 CCU23 UAA39 GGU 55 AGG 8 GCC24 AAA40 GGC 56 GAG 9 GCU25 UGA41 GGA 57 GAA 10 UCG26 AGA42 GGG 58 CCG 11 AUA27 AGC43 CGA 59 UCC 12 UUA28 AGU44 CGG 60 ACC 13 UUC29 GCG45 UGC 61 ACU 14 AUC30 CCA46 CAA 62 UCU 15 UCA31 GUC47 CAC 63 AUU 16 ACG32 GUA48 CAU 64 ACA
(2003)
SARS: Genetic translation
1 HLKNGTCGLVELEKGVLPQLEQPYVFIKRSDALSTNHGHKVVELVAEMDGIQYGRSGI
2 TLGVLVPHVGETPIAYRNVLLRKNGNKGAGGHSYGIDLKSYDLGDELGTDPIEDYEQN
3 WNTKHGSGALRELTRELNGGAVTRYVDNNFCGPDGYPLDCIKDFLARAGKSMCTLSEQ
4 LDYIESKRGVYCCRDHEHEIAWFTERSDKSYEHQTPFEIKSAKKFDTFKGECPKFVFP
5 LNSKVKVIQPRVEKKKTEGFMGRIRSVYPVASPQECNNMHLSTLMKCNHCDEVSWQTC
6 DFLKATCEHCGTENLVIEGPTTCGYLPTNAVVKMPCPACQDPEIGPEHSVADYHNHSN
7 IETRLRKGGRTRCFGGCVFAYVGCYNKRAYWVPRASADIGSGHTGITGDNVETLNEDL
8 LEILSRERVNINIVGDFHLNEEVAIILASFSASTSAFIDTIKSLDYKSFKTIVESCGN
9 YKVTKGKPVKGAWNIGQQRSVLTPLCGFPSQAAGVIRSIFARTLDAANHSIPDLQRAA
10 VTILDGISEQSLRLVDAMVYTSDLLTNSVIIMAYVTGGLVQQTSQWLSNLLGTTVEKL
11 RPIFEWIEAKLSAGVEFLKDAWEILKFLITGVFDIVKGQIQVASDNIKDCVKCFIDVV
12 NKALEMCIDQVTIAGAKLRSLNLGEVFIAQSKGLYRQCIRGKEQLQLLMPLKAPKEVT
13 FLEGDSHDTVLTSEEVVLKNGELEALETPVDSFTNGAIVGTPVCVNGLMLLEIKDKEQ
14 YCALSPGLLATNNVFRLKGGAPIKGVTFGEDTVWEVQGYKNVRITFELDERVDKVLNE
15 KCSVYTVESGTEVTEFACVVAEAVVKTLQPVSDLLTNMGIDLDEWSVATFYLFDDAGE
16 ENFSSRMYCSFYPPDEEEEDDAECEEEEIDETCEHEYGTEDDYQGLPLEFGASAETVR
17 VEEEEEEDWLDDTTEQSEIEPEPEPTPEEPVNQFTGYLKLTDNVAIKCVDIVKEAQSA
18 NPMVIVNAANIHLKHGGGVAGALNKATNGAMQKESDDYIKLNGPLTVGGSCLLSGHNL
19 AKKCLHVVGPNLNAGEDIQLLKAAYENFNSQDILLAPLLSAGIFGAKPLQSLQVCVQT
20 VRTQVYIAVNDKALYEQVVMDYLDNLKPRVEAPKQEEPPNTEDSKTEEKSVVQKPVDV
21 KPKIKACIDEVTTTLEETKFLTNKLLLFADINGKLYHDSQNMLRGEDMSFLEKDAPYM
22 VGDVITSGDITCVVIPSKKAGGTTEMLSRALKKVPVDEYITTYPGQGCAGYTLEEAKT(2005-2006)
Will Bird Flu mutate and transfer from human to human? Where did SARS go?
(April 2009)
Will SwineFlu become pandemic nightmare?
High resolution MS Molecular ion data
- Prelab pdf
- Experiment pdf
- Report form pdf
End of Course Survey: (Anonymous survey)