Table of Contents
Cover
Title page
Copyright page
PREFACE
ACKNOWLEDGMENTS
PART I: BACKGROUND
CHAPTER 1 An Introduction to Structure and Bonding
A. THE SOURCES OF CARBON COMPOUNDS
B. MORE ABOUT HYDROCARBONS
C. ON THE NATURE OF THE CHEMICAL BOND
NOTICE TO THE STUDENT
ADDITIONAL PROBLEMS
CHAPTER 2 An Introduction to Spectroscopy and Selected Spectroscopic Methods in Organic Chemistry
A. GENERAL INTRODUCTION
B. X-RAY CRYSTALLOGRAPHY
C. PHOTON SPECTROSCOPY
D. MS
ADDITIONAL PROBLEMS
CHAPTER 3 Structure: The Nomenclature of Hydrocarbons and the Shape of Things to Come
A. INTRODUCTION
B. NOMENCLATURE AND SPECTROSCOPY
C. PHYSICAL AND CHEMICAL PROPERTIES; OXIDATION AND REDUCTION OF HYDROCARBONS
ADDITIONAL PROBLEMS
CHAPTER 4 An Introduction to Dynamics
A. INTRODUCTION
B. REVIEW OF SOME ENERGY CONSIDERATIONS
C. THE BARRIER BETWEEN REACTANTS AND PRODUCTS
D. MORE ABOUT THE TRANSITION STATE
E. ROTATION ABOUT SIGMA (σ) BONDS IN ACYCLIC ALKANES, ALKENES, ALKYNES, AND ALKYL-SUBSTITUTED ARENES
F. CONFORMATIONAL ANALYSIS OF MEDIUM-RING CYCLIC ALKANES
G. THE CONSERVATION OF SYMMETRY DURING REACTIONS
H. THE MEASUREMENT OF CHIRALITY
ADDITIONAL PROBLEMS
CHAPTER 5 Classes of Organic Compounds—A Survey: An Introduction to Solvents and to Acids and Bases and to Computational Chemistry
A. INTRODUCTION
B. GENERAL CHARACTERISTICS OF FUNCTIONAL GROUP PLACEMENT
C. THE FUNCTIONAL GROUPS AND THEIR NAMES
D. AN INTRODUCTION TO SOLVENTS
E. ACIDS AND BASES
F. COMPUTATIONAL METHODS
ADDITIONAL PROBLEMS
PART II: MIDDLEGROUND
CHAPTER 6 The Reactions of Hydrocarbons: Oxidation, Reduction, Substitution, Addition, Elimination, and Rearrangement
A. INTRODUCTION
B. ALKANES
C. ALKENES
D. ALKYNES
E. ARENES AND AROMATICITY: SPECIAL INTRODUCTION
ADDITIONAL PROBLEMS
CHAPTER 7 The Reactions of Alkyl, Alkenyl, and Aryl Halides: Oxidation, Reduction, Substitution, Addition, Elimination, and Rearrangement
A. INTRODUCTION
B. FLUOROCARBONS
C. OXIDATION
D. REDUCTION OF ALKYL, ALKENYL, AND ARYL HALIDES
E. NUCLEOPHILIC SUBSTITUTION
F. ADDITION REACTIONS
G. ELIMINATION REACTIONS OF ALKYL AND ALKENYL HALIDES
H. REARRANGEMENT REACTIONS OF ALKYL AND ALKENYL HALIDES
ADDITIONAL PROBLEMS
CHAPTER 8 Part I. The Reactions of Alcohols, Enols, and Phenols: Oxidation, Reduction, Substitution, Addition, Elimination, and Rearrangement Part II. Ethers Part III. Selected Reactions of Alkyl and Aryl Thiols and Thioethers
SPECIAL INTRODUCTION TO CHAPTER 8
PART I. ALCOHOLS, ENOLS, AND PHENOLS
A. ACIDITY AND BASICITY
B. OXIDATION OF ALCOHOLS, ENOLS, AND PHENOLS
C. REDUCTION OF ALCOHOLS, ENOLS, AND PHENOLS
D. SUBSTITUTION REACTIONS OF ALCOHOL, ENOLS, AND PHENOLS
E. ADDITION REACTIONS OF ALCOHOLS, ENOLS, AND PHENOLS
F. ELIMINATION REACTIONS OF ALCOHOLS, ENOLS, AND PHENOLS
G. REARRANGEMENT REACTIONS OF ALCOHOLS, ENOLS, AND PHENOLS
PART II. ETHERS
A. INTRODUCTION
B. THE REACTIONS OF ETHERS
PART III. THIOLS, THIOETHERS, AND SOME PRODUCTS OF THEIR OXIDATION
ADDITIONAL PROBLEMS
CHAPTER 9 Part I. The Reactions of Aldehydes and Ketones: Oxidation, Reduction, Addition, Substitution, and Rearrangement Part II. The Reactions of Carboxylic Acids and Their Derivatives: Oxidation, Reduction, Addition, Substitution, Elimination, and Rearrangement
A. INTRODUCTION
PART I. ALDEHYDES AND KETONES
A. OXIDATION OF ALDEHYDES AND KETONES
B. REDUCTION OF ALDEHYDES AND KETONES
C. ADDITION TO ALDEHYDES AND KETONES
D. SUBSTITUTION REACTIONS PRODUCING ALDEHYDES AND KETONES
E. REARRANGEMENT REACTION OF ALDEHYDES AND KETONES
PART II. CARBOXYLIC ACIDS AND THEIR DERIVATIVES
A. GENERAL INTRODUCTION
B. OXIDATION
C. REDUCTION
D. SUBSTITUTION: ADDITION AND ELIMINATION
E. ADDITIONAL REACTIONS AND REARRANGEMENTS OF ESTERS AND β-DICARBONYL COMPOUNDS
ADDITIONAL PROBLEMS
CHAPTER 10 Part I. The Reactions of Amines: Oxidation, Reduction, Addition, Substitution, and Rearrangement Part II. Some Organophosphorus Chemistry Part III. Some Organosilicon Chemistry
PART I. THE REACTIONS OF AMINES
A. INTRODUCTION
B. SOME COMMENTS ON THE PREPARATION OF AMINES
C. OXIDATION OF AMINES
D. REDUCTION OF AMINES
E. ADDITION AND SUBSTITUTION REACTIONS OF AMINES
F. ADDITION AND REARRANGEMENT REACTIONS OF AMINES
PART II. SOME ORGANOPHOSPHORUS CHEMISTRY
PART III. SOME ORGANOSILICON CHEMISTRY
ADDITIONAL PROBLEMS
PART III: FOREGROUND
CHAPTER 11 An Introduction to Carbohydrates, Acetogenins, and Steroids
A. INTRODUCTION
B. THE CALVIN CYCLE
C. CARBOHYDRATES
D. ACETOGENINS
ADDITIONAL PROBLEMS
CHAPTER 12 An Introduction to Amino Acids, Peptides and Proteins, Enzymes, Coenzymes, and Metabolic Processes
A. INTRODUCTION
B. AMINO ACIDS
C. PEPTIDES AND PROTEINS—INTRODUCTION
D. THE COENZYMES
CHAPTER 13 An Introduction to Alkaloids and Some Other Heterocyclic Compounds
A. INTRODUCTION
B. TROPANE ALKALOIDS
C. MORPHINE (AND CODEINE AND THEBAINE)
D. VINBLASTINE
E. CAFFEINE
CHAPTER 14 Part I. On the Genetic Code: Unity and Diversity Part II. The Tetrapyrrolic Cofactors: Unity and Diversity
PART I. ON THE GENETIC CODE: UNITY AND DIVERSITY
A. INTRODUCTION (THE GENETIC CODE)
B. PART A
C. PART B
PART II. THE TETRAPYRROLIC COFACTORS: UNITY AND DIVERSITY
A. THE TETRAPYRROLIC COFACTORS
Epilogue
APPENDIX I: The Schrödinger Equation
APPENDIX II: The Literature
Index
To my family . . .
who have, for so long, and with such good grace,
tolerated the attention I have paid to Chemistry.
Copyright © 2011 by John Wiley & Sons, Inc. All rights reserved
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Library of Congress Cataloging-in-Publication Data:
Dalton, David R.
Foundations of organic chemistry : unity and diversity of structures, pathways, and reactions / by David R. Dalton.
p. cm.
ISBN 978-0-470-47908-7 (cloth)
1. Chemistry, Organic–Textbooks. I. Title.
QD251.3.D35 2011
547–dc22
2010043290
oBook ISBN: 978-1-118-00539-2
ePDF ISBN: 978-1-118-00537-8
ePub ISBN: 978-1-118-00538-5
Welcome! The study of organic chemistry can be filled with either the joy of discovery of one of the great ongoing intellectual efforts of human beings or the sad drudgery afforded a task seen only as a barrier to “getting on.” If you consider it the latter, you will lose the richness of what is offered and will have cheated yourself of a major inheritance.
The organizational tree of organic chemistry, built up over generations, has many branches. Some branches are rich with fruit that should be savored at length; others, fragrant with blossom, invite shorter pause. Still other limbs may be mostly deadwood, on which some new growth is seen, or may be new sprouts from the main trunk ready for a growth spurt. To appreciate this vibrant life takes time; plan now on budgeting enough.
You will probably find that you are expected to master sufficient material from lecture and text to be able to make predictions and to justify observations. Although it is true that you must discover for yourself (if you do not already know) what you must do to learn, the time-tested methods of reading, rereading, doing more problems than assigned, and, when you have thought it through and still cannot quite understand, asking your instructor will work here too. However, I hope you are not intimidated by hard work!
DAVID R. DALTON
Philadelphia, Pennsylvania
March 2011
It is clear that I cannot sufficiently acknowledge the contributions of my family, friends, and colleagues as well as all of the men and women from whom I have learned. However, there are some who, more than others, directly contributed to this volume.
The men and women with whom I worked at Clemson University and, in particular, John Huffman, Karl Dieter, and Melanie Cooper deserve an early mention as their perception of teaching played a significant role. Subsequently, colleagues and students at Temple University struggled with various portions of the manuscript over many revisions and years and the fortitude of Linda Mascavage (Arcadia University), Serge Jasmin (Temple University), Phil Sonnet (USDA, retired), Charlie DeBrosse (Temple University) and Harry Gottlieb (Temple University) in particular, was beyond what any reasonable person could expect.
The staff at John Wiley were left to cope with my efforts and that anything reasonable has come out clearly is the responsibility of Jonathan Rose, Lauren Hilger, Amanda Amunullah, Lisa Morano Van Horn and their colleague Stephanie Sakson.
Everything that you don’t like and the blunders and errors are mine alone!
D. R. D.
Nullius addictus iurare in verba magistri … (I am not bound to swear allegiance to the word of any master …)
—Horrace, Epistulae
INTRODUCTION TO PART I
As is generally true for established subjects, it is difficult to know exactly where to begin learning. If a linear historical route is taken, the advantages gained by subsequent organizational insights are lost. For example, the use of ethyl alcohol (ethanol, CH3CH2OH, 1) (Alcohols, Chapter 8) as an intoxicant from fermentation of sucrose containing plants (Carbohydrates, Chapter 11) is buried in antiquity, preceding the written record, and the substance we call morphine (2, below) (Alkaloids, Chapter 13) has a recorded history of at least 4000 years. Indeed, the use of the former is attributed to the gods themselves! The latter (albeit in crude form) was apparently obtained from the unripe seed pods (as is done today) of what may have been the opium poppy (Papaver somniferum L.) by the Sumerians, the early inhabitants of part of what was later called Babylonia and is currently called Iraq. These materials are still being actively studied, and a representation for each of them is shown below. However, to begin to study a well-organized subject with two such diverse materials whose major link appears to be some interesting physiological activity would deny the benefits of that organization.
Thus, we will take, as is usually done, a mixed approach—selectively using history to suit our needs.
Only about 2500 years ago, a Greek school led by Demokritos of Abdera (468–370 BCE) laid down ideas we interpret as similar to those of the atomic theory, reformulated in the first decade of the nineteenth century by the English schoolteacher and meteorologist John Dalton.*
The years between Demokritos and Dalton had seen advances in the arts of metallurgy, distillation (heating to cause vaporization followed by condensation of the vapors), wine making, and so on, which gradually advanced with the passing generations. In retrospect, the frustration of that slow pace and the absence of tools with which to accelerate it, to satisfy both curiosity and greed, clearly accompanied mankind’s plunge into the Dark Ages. That sad period saw the rise of magic and superstition, which still enslave some today, and the mad search for al-kimiya, the Philosopher’s Stone. While the alchemist practitioners did slowly advance the tools and techniques of manipulation of materials, that advance was sometimes justified as a search for the “true names” of things, so their transformations could be properly affected.
The progress that might have been anticipated following Dalton was not immediately forthcoming. As we shall see, being able to say how many atoms of any given element are present in a molecule is related to the structure of that molecule as the number of bricks in a pile is related to a building, which might be built with them. Thus, some 30 years after Dalton, we find the “father” of modern dye chemistry, W. H. Perkin,† apparently assuming (at age 18) that twice the number of atoms in p-N-allyltoluidine (C10H13N) (3, Chapter 10) plus oxygen (3/2 O2) should be equivalent to quinine (C20H24N2O2) (4, Alkaloids, Chapters 12 and 13) plus water (H2O). When he did the experiment, he treated the p-N-allyltoluidine (C10H13N), 3, with the known oxidizing agent potassium dichromate (K2Cr2O7), a dark brown material was obtained, which, although subsequently leading Perkin to dyestuffs (Chapter 10) for wool and cotton, was not the well-defined construction quinine (C20H24N2O2) (4).
These retrospective glimpses clearly require our carrying to them our current ideas and tools. Indeed, it can be argued that the development of tools, which confirmed some ideas and not others, has led to our present understandings. However, the tools of organic chemistry are the same as those used elsewhere, and so it is frequently suggested that the study of organic chemistry might begin with those things that distinguish it from other disciplines.
In that vein, historically, the subject of organic chemistry was divided from other branches of chemistry first by the idea that organic compounds were exclusive to living systems and that, somehow, such materials possessed special characteristics. Second, having disabused ourselves of that idea, the subject was considered as the domain, for the most part, of compounds of carbon and their interrelationships. Third, and most recently, organic chemistry has evolved into what it is that individuals who practice the art choose to call what they do. Nonetheless, it is still generally true that the distinguishing characteristic of the study of organic chemistry is the central role played by compounds containing carbon.
So it is, today, very important that you realize, first, that the enormous, yet incomplete, structure you face, which shares both praise and blame for our current way of life, did not leap into being full grown. The process was slow.
Second, it is continuing to grow. Indeed, the present increasing rate of accretion of information, in part due to a confluence of trends that include, most apparently, a major refinement of our tools as they are interfaced with microprocessors, an ever-increasing population of active workers, and rapid communication of results upon which new building can occur, is leading to a better understanding of our world and our place in it. Nonetheless, much of the early work remains important as it serves as the foundation of our present edifice, and it will serve as a starting place for us.
Notes
* John Dalton (1766–1844) was a teacher of “natural philosophy” in Manchester, England, where he studied chemistry and physics. He is known for his research into color blindness (called Daltonism) and atomic theory.
† William Henry Perkin, FRS (1838–1907), found, among other colors, “mauveine” (today sometimes called simply “mauve”) while working with aniline (vide infra, Chapter 10) and other aromatic amines.