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Che 333 Organic Chemistry Iii OIT: CHE 333 ORGANIC CHEMISTRY III Travis Lund Oregon Institute of Technology Oregon Institute of Technology OIT: CHE 333 Organic Chemistry III Travis Lund This text is disseminated via the Open Education Resource (OER) LibreTexts Project (https://LibreTexts.org) and like the hundreds of other texts available within this powerful platform, it freely available for reading, printing and "consuming." Most, but not all, pages in the library have licenses that may allow individuals to make changes, save, and print this book. Carefully consult the applicable license(s) before pursuing such effects. Instructors can adopt existing LibreTexts texts or Remix them to quickly build course-specific resources to meet the needs of their students. Unlike traditional textbooks, LibreTexts’ web based origins allow powerful integration of advanced features and new technologies to support learning. 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This text was compiled on 09/26/2021 TABLE OF CONTENTS 1: REACTIONS AT THE Α-CARBON, PART II 1.1: PRELUDE TO REACTIONS AT THE Α-CARBON, PART II 1.2: DECARBOXYLATION 1.3: AN OVERVIEW OF FATTY ACID METABOLISM 1.4: CLAISEN CONDENSATION 1.5: CONJUGATE ADDITION AND ELIMINATION 1.6: CARBOXYLATION 1.7: REACTIONS AT THE Α-CARBON, PART II (EXERCISES) 1.8: REACTIONS AT THE Α-CARBON, PART II (SUMMARY) 2: RETROSYNTHETIC ANALYSIS AND METABOLIC PATHWAY PREDICTION 2.1: PATHWAY PREDICTION PRACTICE PROBLEMS 3: ELECTROPHILIC REACTIONS 3.1: PRELUDE TO ELECTROPHILIC REACTIONS 3.2: ELECTROPHILIC ADDITION TO ALKENES 3.3: ELIMINATION BY THE E1 MECHANISM 3.4: ELECTROPHILIC ISOMERIZATION 3.5: ELECTROPHILIC SUBSTITUTION 3.6: CARBOCATION REARRANGEMENTS 3.7: ELECTROPHILIC REACTIONS (EXERCISES) 3.8: ELECTROPHILIC REACTIONS (SUMMARY) 4: OXIDATION AND REDUCTION REACTIONS 4.1: PRELUDE TO OXIDATION AND REDUCTION REACTIONS 4.2: OXIDATION AND REDUCTION OF ORGANIC COMPOUNDS - AN OVERVIEW 4.3: OXIDATION AND REDUCTION IN THE CONTEXT OF METABOLISM 4.4: HYDROGENATION OF CARBONYL AND IMINE GROUPS 4.5: HYDROGENATION OF ALKENES AND DEHYDROGENATION OF ALKANES 4.6: MONITORING HYDROGENATION AND DEHYDROGENATION REACTIONS BY UV SPECTROSCOPY 4.7: REDOX REACTIONS OF THIOLS AND DISULFIDES 4.8: FLAVIN-DEPENDENT MONOOXYGENASE REACTIONS - HYDROXYLATION, EPOXIDATION, AND THE BAEYER-VILLIGER OXIDATION 4.9: HYDROGEN PEROXIDE IS A HARMFUL - REACTIVE OXYGEN SPECIES 4.10: OXIDATION AND REDUCTION REACTIONS (EXERCISES) 4.11: OXIDATION AND REDUCTION REACTIONS (SUMMARY) 5: RADICAL REACTIONS 5.1: PRELUDE TO RADICAL REACTIONS 5.2: OVERVIEW OF SINGLE-ELECTRON REACTIONS AND FREE RADICALS 5.3: RADICAL CHAIN REACTIONS 5.4: USEFUL POLYMERS FORMED BY RADICAL CHAIN REACTIONS 5.5: DESTRUCTION OF THE OZONE LAYER BY A RADICAL CHAIN REACTION 5.6: OXIDATIVE DAMAGE TO CELLS, VITAMIN C, AND SCURVY 5.7: FLAVIN AS A ONE-ELECTRON CARRIER 5.8: RADICAL REACTIONS (EXERCISES) 5.9: RADICAL REACTIONS (SUMMARY) 6: THE ORGANIC CHEMISTRY OF VITAMINS 6.1: PRELUDE TO THE ORGANIC CHEMISTRY OF VITAMINS 6.2: PYRIDOXAL PHOSPHATE (VITAMIN B6) 6.3: THIAMINE DIPHOSPHATE (VITAMIN B1) 1 9/26/2021 6.4: THIAMINE DIPHOSPHATE, LIPOAMIDE AND THE PYRUVATE DEHYDROGENASE REACTION 6.5: FOLATE 6.6: THE OGANIC CHEMISTRY OF VITAMINS (EXERCISES) 6.7: THE OGANIC CHEMISTRY OF VITAMINS (SUMMARY) 7: INDEX OF ENZYMATIC REACTIONS BY PATHWAY 7.1: AMINO ACID BIOSYNTHESIS 7.2: AMINO ACID CATABOLISM 7.3: CITRIC ACID CYCLE 7.4: FATTY ACID METABOLISM 7.5: GLYCOLYSIS, GLUCONEOGENESIS, FERMENTATION 7.6: ISOPRENOID BIOSYNTHESIS 7.7: NUCLEOSIDE BIOSYNTHESIS 7.8: NUCLEOTIDE CATABOLISM 7.9: PENTOSE PHOSPHATE PATHWAY, CALVIN CYCLE 8: INDEX OF LABORATORY SYNTHESIS REACTIONS BACK MATTER INDEX GLOSSARY 2 9/26/2021 CHAPTER OVERVIEW 1: REACTIONS AT THE Α-CARBON, PART II 1.1: PRELUDE TO REACTIONS AT THE Α-CARBON, PART II 1.2: DECARBOXYLATION 1.3: AN OVERVIEW OF FATTY ACID METABOLISM 1.4: CLAISEN CONDENSATION 1.5: CONJUGATE ADDITION AND ELIMINATION 1.6: CARBOXYLATION 1.7: REACTIONS AT THE Α-CARBON, PART II (EXERCISES) 1.8: REACTIONS AT THE Α-CARBON, PART II (SUMMARY) 1 9/26/2021 1.1: Prelude to Reactions at the α-Carbon, Part II Introduction We begin this chapter with the story of two men, and two chemical reactions. The two men couldn't be more different. One was an acclaimed scientist who lived and continued to work productively into his eighties. The other was struck down as a young boy by what was assumed at the time to be a fatal disease. With the heroic support of his parents and caregivers, though, he lived to his thirtieth birthday and provided the inspiration for development of a medical treatment that could potentially save thousands of lives. The two chemical reactions in this story are closely related, and both involve the metabolism of fats in the human body. One serves to build up fatty acid chains by repeatedly linking together two-carbon units, while the other does the reverse, progressively breaking off two-carbon pieces from a long chain fatty acid molecule. The life and work of the two men are inextricably linked to the two reactions, and while we will be learning all about the reactions in the main part of this chapter, we'll begin with the stories of the two men. On a Saturday in January of 2007, Dr. Hugo Moser passed away in the Johns Hopkins Hospital in Baltimore, succumbing to pancreatic cancer. He was 82 years old. A neurologist who had taught and researched for much of his career at Johns Hopkins, he was well known for his workaholic nature: he had signed off on his last grant application while on the way to the hospital for major surgery just a few months previously. Two days after his death, his wife and colleague Ann Moser was back in their lab, because, she said, “He gave us all a mandate to continue with the work”. Dr. Moser was a highly esteemed scientist who had devoted his life to understanding and eventually curing a class of devastating neurodegenerative diseases, most notably adrenoleukodystrophy, or ALD. In his work he was careful, rational, painstaking, and relentless – a classic scientist. But in the minds of many movie fans, he became a Hollywood villain. Only 17 months after the death of Dr. Moser, newspapers around the world published moving obituaries marking the passing, at age 30, of Lorenzo Odone. In one, written by his older sister and published in the British newspaper The Guardian, Lorenzo as a young boy is described as “lively and charming . .he displayed a precocious gift for languages as he mastered English, Italian and French. He was funny, articulate and favored opera over nursery rhymes.” But for more than 20 years leading up to his death, he had been confined to a wheelchair, blind, paralyzed, and unable to communicate except by blinking his eyes. Because he was unable to swallow, he needed an attendant to be with him around the clock to suction saliva from his mouth so he wouldn't choke. When he was he six years old, Lorenzo started to show changes in behavior: a shortening attention span, moodiness. More disturbing to his parents, Augusto and Michaela Odone, was their suspicion that he was having trouble hearing. They took him in to be examined, and although his hearing was fine, the doctors noticed other behavioral symptoms that concerned them, and so ordered more neurological tests. The results were a kick to the stomach: Lorenzo had a fatal neurodegenerative disease called adrenoleukodystrophy. There was no cure; his nervous system would continue to degenerate, and he would probably be dead within two years. Tim Soderberg 1.1.1 9/19/2021 https://chem.libretexts.org/@go/page/151244 What happened next became such a compelling story that it was eventually retold by director George Miller in the 1992 movie Lorenzo's Oil, starring Nick Nolte and Susan Sarandon as Augusto and Michaela Odone and Peter Ustinov as a character based on Dr. Hugo Moser. The Odones were unwilling to accept the death sentence for their son and, despite having no scientific or medical training, set about to learn everything they could about ALD. They found out that the cause of ALD is a mutation in a gene that plays an important role in the process by which saturated fatty acids of 26 or more carbons are broken down in the body.
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