Preface rganic chemistry as an exciting and vitally morizing a multitude of facts.I have organized this book around shared features and uniryin y aven prncpes that can be applied again and agan want dens daily lives. Preparing Students for Future Study in a Variety of Scientific Disciplines first (other tha nds can be divided into families and that all members of a family react in the same way.And to make things even easier,each family can be put into one of four groups,and all the families in a group react in What We know about organic cher they have been and where they are gongas they proceed though ech of the four groups.It also encourages them to remember the fundamental reason behind the reactions of all organic compounds:electrophiles react with nucleophiles.When students finis ar group.they are given e opportunity to rev iew the group and understan the following order.(However.the book is written to be modular.so thecoud be coveredin any order.) witl carbo rbon double and triple bonds The therefore.react electrophil Group II:Compounds with electron-withdrawing atoms or groups attached to sp> carbons.These compounds are electrophiles and.therefore.react with nucleophiles undergo hmination reactions roi and,there and nucleophilic addition-limination reactions.Because of the"acidityof theaon can become a nucleophile and,therefore,react with electrophiles. omatic ds are nucleophiles and,there -an The organization discourages rote memorization and allows students to learn reactions based on their pa attern of reactivity.It is only after th e patterns of reactivity are understood that a deep and predict gives them a strong foundation to bring to their subsequent study of science.regardless of the discipline. AS StU s procee ugh come across ciate a box on the experimental drug used to treat Ebola.and they don't have to be preparing for a career in engineering to appreciate a box on the properties that a polymer used for dental impressions must have
xxii The guiding principle behind this book is to present organic chemistry as an exciting and vitally important science. To counter the impression that the study of organic chemistry consists primarily of memorizing a multitude of facts, I have organized this book around shared features and unifying concepts, while emphasizing principles that can be applied again and again. I want students to apply what they have learned to new settings and to learn how to reason their way to solutions. I also want them to see that organic chemistry is a fascinating discipline that is integral to their daily lives. Preparing Students for Future Study in a Variety of Scientific Disciplines This book organizes the functional groups around mechanistic similarities. When students see their first reaction (other than an acid–base reaction), they are told that all organic compounds can be divided into families and that all members of a family react in the same way. And to make things even easier, each family can be put into one of four groups, and all the families in a group react in similar ways. “Organizing What We Know About Organic Chemistry” is a feature based on these statements. It lets students see where they have been and where they are going as they proceed through each of the four groups. It also encourages them to remember the fundamental reason behind the reactions of all organic compounds: electrophiles react with nucleophiles. When students finish studying a particular group, they are given the opportunity to review the group and understand why the families came to be members of that particular group. The four groups are covered in the following order. (However, the book is written to be modular, so they could be covered in any order.) • Group I: Compounds with carbon-carbon double and triple bonds. These compounds are nucleophiles and, therefore, react with electrophiles—undergoing electrophilic addition reactions. • Group II: Compounds with electron-withdrawing atoms or groups attached to sp3 carbons. These compounds are electrophiles and, therefore, react with nucleophiles— undergoing nucleophilic substitution and elimination reactions. • Group III: Carbonyl compounds. These compounds are electrophiles and, therefore, react with nucleophiles—undergoing nucleophilic acyl substitution, nucleophilic addition, and nucleophilic addition-elimination reactions. Because of the “acidity” of the a-carbon, a carbonyl compound can become a nucleophile and, therefore, react with electrophiles. • Group IV: Aromatic compounds. Some aromatic compounds are nucleophiles and, therefore, react with electrophiles—undergoing electrophilic aromatic substitution reactions. Other aromatic compounds are electrophiles and, therefore, react with nucleophiles—undergoing nucleophilic aromatic substitution reactions. The organization discourages rote memorization and allows students to learn reactions based on their pattern of reactivity. It is only after these patterns of reactivity are understood that a deep understanding of organic chemistry can begin. As a result, students achieve the predictive capacity that is the beauty of studying science. A course that teaches students to analyze, classify, explain, and predict gives them a strong foundation to bring to their subsequent study of science, regardless of the discipline. As students proceed through the book, they come across ~200 interest boxes that connect what they are studying to real life. Students don’t have to be preparing for a career in medicine to appreciate a box on the experimental drug used to treat Ebola, and they don’t have to be preparing for a career in engineering to appreciate a box on the properties that a polymer used for dental impressions must have. Preface
Preface xxii The Organization Ties Together Reactivity and Synthesis ra a e another.Instead,when I discuss a functional group's reactivity.I cover the synthesis of compound that are formed as having students design syntheses. Chapter alkanes,etc.-the compounds formed when alkenes react.The synthesis of alkenes is not covered until the reactions of alkyl halides and alcohols are discussed-compounds whose reactions lead to the synthesis of a gether the reactivity of a functional g roup and the ts the student fro It also results in a certain economy of presentation,allowing more material to be covered in less time Although memorizing different ways a particular functional group can be prepared can be counterprod cuive to enjoying organic stry.It is ful to have suc a10n0 reacti ndix In the come to appreciate the importance of reactions that change the carbon skeleton of a molecule:these reactions are compiled in Appendix IV. Helping Students Learn and Study Organic Chemistry tivity and small"bites"of information,I have revisited this edition to make it more compatible with em to stu ds with a set of problems that students to work through to find out if they are ready to go on to the next section.or if they need to reviewthe section they thought they had just mastered.This allows the book to work well in a"flipped classroom. An enhanced art program with new and exnanded annotations nrovides key informatio to students so that they can review important parts of the chapter with the support of the visual program.Margin notes throughout the book succinctly repeat key points and help students review ant chapters to help students master essential skills 。Acids and Rase Using Molecular Models awing ve butors Drawing Curved Arrows in Radical Systems .Synthesis and Retrosynthetic analysis Organizational Changes Using the E.Z system to distinguish alkene stereoisomers was moved to Chapter 4,so now it appears immediately after using cis and trans to distinguish alkene stereoisomers. yc hydrogenation and the relative stabilities of alkenes was moved from Chapter Chapter5(ther 5430 an be use onlreaction of alkenes that does not have a well-defined mechanism.all the remaining reactions
The Organization Ties Together Reactivity and Synthesis Many organic chemistry textbooks discuss the synthesis of a functional group and the reactivity of that group sequentially, but these two groups of reactions generally have little to do with one another. Instead, when I discuss a functional group’s reactivity, I cover the synthesis of compounds that are formed as a result of that reactivity, often by having students design syntheses. In Chapter 6, for example, students learn about the reactions of alkenes, but they do not learn about the synthesis of alkenes. Instead, they learn about the synthesis of alkyl halides, alcohols, ethers, epoxides, alkanes, etc.—the compounds formed when alkenes react. The synthesis of alkenes is not covered until the reactions of alkyl halides and alcohols are discussed—compounds whose reactions lead to the synthesis of alkenes. This strategy of tying together the reactivity of a functional group and the synthesis of compounds resulting from its reactivity prevents the student from having to memorize lists of unrelated reactions. It also results in a certain economy of presentation, allowing more material to be covered in less time. Although memorizing different ways a particular functional group can be prepared can be counterproductive to enjoying organic chemistry, it is useful to have such a compilation of reactions when designing multistep syntheses. For this reason, lists of reactions that yield a particular functional group are compiled in Appendix III. In the course of learning how to design syntheses, students come to appreciate the importance of reactions that change the carbon skeleton of a molecule; these reactions are compiled in Appendix IV. Helping Students Learn and Study Organic Chemistry As each student generation evolves and becomes increasingly diverse, we are challenged as teachers to support the unique ways students acquire knowledge, study, practice, and master a subject. In order to support contemporary students who are often visual learners, with preferences for interactivity and small “bites” of information, I have revisited this edition to make it more compatible with their learning style by streamlining the narrative and using organizing bullets and subheads. This will allow them to study more efficiently with the text. The book is written much like a tutorial. Each section ends with a set of problems that students need to work through to find out if they are ready to go on to the next section, or if they need to review the section they thought they had just mastered. This allows the book to work well in a “flipped classroom.” For those who teach organic chemistry after one semester of general chemistry, Chapter 5 and Appendix II contain material on thermodynamics and kinetics, so those topics can be taught in the organic course. An enhanced art program with new and expanded annotations provides key information to students so that they can review important parts of the chapter with the support of the visual program. Margin notes throughout the book succinctly repeat key points and help students review important material at a glance. Tutorials follow relevant chapters to help students master essential skills: • Acids and Bases • Using Molecular Models • Interconverting Structural Representations • Drawing Curved Arrows • Drawing Resonance Contributors • Drawing Curved Arrows in Radical Systems • Synthesis and Retrosynthetic analysis MasteringChemistry includes additional online tutorials on each of these topics that can be assigned as homework or for test preparation. Organizational Changes Using the E,Z system to distinguish alkene stereoisomers was moved to Chapter 4, so now it appears immediately after using cis and trans to distinguish alkene stereoisomers. Catalytic hydrogenation and the relative stabilities of alkenes was moved from Chapter 6 to Chapter 5 (thermodynamics), so it can be used to illustrate how ΔH° values can be used to determine relative stabilities. Moving this has another advantage—because catalytic hydrogenation is the only reaction of alkenes that does not have a well-defined mechanism, all the remaining reactions Preface xxiii
xxiv Preface the first step is aly carbon bonded to the most hydrogens. Chapter 8 starts by discussing the structure of benzene because it is the ideal compound to use ocalized electrons.This chapter also includes a discussion on aromaticity addition the reactions they just finished studying. Traditionally.electronic effects are taught so students can understand the activating and directing rings. NOW that most of the chemistry of benzene follows car get to ben chemis pK values of phenols,benzoic acids,and anilinium ions.Electronic effects are then reviewed in the chapter on ben ers in the prev s editi n tha itution and elimina ing that alkyl halides do not undergo S solvolysis reactions has allowed this material to be greatly simplified,so now it fits nicely into one chapter. carbonyl before the chemistry of aromatic compounds(a for my p unds are prob they should have.In addition.the curent location of the chemistry of benzene allows it and the chemistry of aromatic heterocyclic compounds to be taught sequentially. eo chaper on coy chemstry soud be l ao hoeer bonyl chemistry beco of the chapter.Therefore.the lipid material was removed and pter:The Organic Chemistry of Lipids.The discussion of terpenes from the metabolism chapter has also been moved into this chapter,and some some new material has been included. Modularity/Spectroscopy be covered in any order. Sixty spectroscopy problems and their answers in addition to-170 spectroscopy problems in the tex found in the Study 3a Guide and Solur ons Manual.The spectroscopy chapters 、teach at any time du ourse.F An Early and Consistent Emphasis on Organic Synthesis Students are introduced to synthetic chemistry and retrosynthetic analysis early in the book 7.respectively).so the can stant d s early in the course examples of complicated multistep syntheses from the literature. Example 2 tarting with ethyne,how could you make 2-bromopentane? HC=CH7 CHCH.CH-CHCH, ye-Pene 2-bromopentane prepared from
in Chapter 6 now have well-defined mechanisms, all following the general rule that applies to all electrophilic addition reactions: the first step is always the addition of the electrophile to the sp2 carbon bonded to the most hydrogens. Chapter 8 starts by discussing the structure of benzene because it is the ideal compound to use to explain delocalized electrons. This chapter also includes a discussion on aromaticity, so a short introduction to electrophilic aromatic substitution reactions is now included. This allows students to see how aromaticity causes benzene to undergo electrophilic substitution rather than electrophilic addition—the reactions they just finished studying. Traditionally, electronic effects are taught so students can understand the activating and directing effects of substituents on benzene rings. Now that most of the chemistry of benzene follows carbonyl chemistry, students need to know about electronic effects before they get to benzene chemistry (so they are better prepared for spectroscopy and carbonyl chemistry). Therefore, in this edition electronic effects are discussed in Chapter 8 and used to teach students how substituents affect the pKa values of phenols, benzoic acids, and anilinium ions. Electronic effects are then reviewed in the chapter on benzene. The two chapters in the previous edition that covered the substitution and elimination reactions of alkyl halides have been combined into one chapter (Chapter 9). The recent compelling evidence showing that alkyl halides do not undergo SN1 solvolysis reactions has allowed this material to be greatly simplified, so now it fits nicely into one chapter. I have found that teaching carbonyl chemistry before the chemistry of aromatic compounds (a change made in the last edition) has worked well for my students. Carbonyl compounds are probably the most important organic compounds, and moving them forward gives them the prominence they should have. In addition, the current location of the chemistry of benzene allows it and the chemistry of aromatic heterocyclic compounds to be taught sequentially. The focus of the first chapter on carbonyl chemistry should be all about how a tetrahedral intermediate partitions. If students understand this, then carbonyl chemistry becomes relatively easy. I found that the lipid material that had been put into this chapter detracted from the main message of the chapter. Therefore, the lipid material was removed and put into a new chapter: The Organic Chemistry of Lipids. The discussion of terpenes from the metabolism chapter has also been moved into this chapter, and some some new material has been included. Modularity/Spectroscopy The book is designed to be modular, so the four groups (Group I—Chapters 6, 7, 8; Group II—Chapters 9 and 10; Group III—Chapters 15, 16, 17; Group IV—Chapters 18 and 19) can be covered in any order. Sixty spectroscopy problems and their answers—in addition to ~170 spectroscopy problems in the text—can be found in the Study Guide and Solutions Manual. The spectroscopy chapters (Chapters 13 and 14) are written so that they can be covered at any time during the course. For those who prefer to teach spectroscopy before all the functional groups have been introduced—or in a separate laboratory course—there is a table of functional groups at the beginning of Chapter 13. An Early and Consistent Emphasis on Organic Synthesis Students are introduced to synthetic chemistry and retrosynthetic analysis early in the book (Chapters 6 and 7, respectively), so they can start designing multistep syntheses early in the course. Seven special sections on synthesis design, each with a different focus, are introduced at appropriate intervals. There is also a tutorial on synthesis and retrosynthetic analysis that includes some examples of complicated multistep syntheses from the literature. 308 xxiv CHAPTER 7 Preface The Reactions of Alkynes • An Introduction to Multistep Synthesis Designing a Synthesis The following examples will give you an idea of the type of thinking required to design a successful synthesis. Problems of this kind will appear repeatedly throughout the book, because s olving them is fun and is a good way to learn organic chemistry. Example 1 Starting with 1-butyne, how could you make the ketone shown here? You can use any reagents you need. CH3CH2C C CH H3CH2CCH2CH2CH3 O ? 1-butyne Many chemists find that the easiest way to design a synthesis is to work backward. Instead of looking at the reactant and deciding how to do the first step of the synthesis, look at the product and decide how to do the last step. The product of the synthesis is a ketone. Now you need to remember all the reactions you have learned that form a ketone. We will use the acid-catalyzed addition of water to an alkyne. (You also could use hydroboration–oxidation.) If the alkyne used in the reaction has identical substituents on both sp carbons, only one ketone will be obtained. Thus, 3-hexyne is the alkyne that should be used for the synthesis of the desired ketone. CH3CH2C CCH2CH3 CH3CH2C CHCH2CH3 CH3CH2CCH2CH2CH3 OH O H2O H2SO4 3-hexyne 3-Hexyne can be obtained from the starting material (1-butyne) by removing the proton from its sp carbon, followed by alkylation. To produce the desired six-carbon product, a two-carbon alkyl halide must be used in the alkylation reaction. CH3CH2C CH CH3CH2C CCH2CH3 1. NaNH2 2. CH3CH2Br 1-butyne 3-hexyne Designing a synthesis by working backward from product to reactant is not just a technique taught to organic chemistry students. It is used so frequently by experienced synthetic chemists that it has been given a name: retrosynthetic analysis. Chemists use open arrows when they write retrosynthetic analyses to indicate they are working backward. Typically, the reagents needed to carry out each step are not specified until the reaction is written in the forward direction. For example, the ketone synthesis just discussed is arrived at by the following retrosynthetic analysis. CH3CH2CCH2CH2CH3 CH3CH2C CCH2CH3 CH3CH2C CH retrosynthetic analysis O Once the sequence of reactions is worked out by retrosynthetic analysis, the synthetic scheme can be written by reversing the steps and including the reagents required for each step. CH3CH2C CH CH3CH2C CCH2CH3 1. NaNH2 2. CH3CH2Br CH3CH2CCH2CH2CH3 O H2O H2SO4 synthesis Example 2 Starting with ethyne, how could you make 2-bromopentane? HC CH CH3CH2CH2CHCH3 ? ethyne 2-bromopentane Br 2-Bromopentane can be prepared from 1-pentene, which can be prepared from 1-pentyne. 1-Pentyne can be prepared from ethyne and an alkyl halide with three carbons. NOTE TO THE STUDENT • As the number of reactions that you know increases, you may find it helpful to consult Appendix III when designing syntheses; it lists the methods that can be used to synthesize each functional group
Preface xxv Problems,Solved Problems,and Problem-Solving Strategies The book contains more than 2,000 problems,many with multiple parts.This edition has many new problems,both in-chapter and end-of-chapter.They include new solved problems.new problem solving strategies,and new problems incorporating information from more than one chapter.I keep n my students have when they come to office hours.Many of the new problem The answers (and explanatio the problems are in the acco Guide/Solutions Manal,which I authored to ensure consistency in language with the text.The ohthn each chapter are primarily drill problems.They appear at the endh net o they a llow students to test thems students immediate feedback con ng their mastery of a skillo ond give Selected problems are accompanied by worked-out solutions to provide insight into problem oving techniquand min Sirategies teach students how top inds of pr ems.Ihese sh mnity to use the stra d These the first of such problms.are indicated in the margin by USE THE STRATEGY. The Study Guide/Solutions Manual has a practice test at the end of each chapter and contains Powerpoint ailable on Po Students Interested in The Biological Sciences and MCAT2015 chemistry chemistry course with a solid appreciation of organic mechanism and synthesis.But when they take b chemistry,they will never hear al ut Claisen condensations,Sx2 reactions,nuc. ougn chemistry they leam r eats itself in the biological world? Now that the MCAT is focusing almost exclusively on the organic chemistr y of living systems t is even more important that we provide our students w the b organ c bndge -the materi: hat provides】 ctions that n organic iochem stry.Student should see tha performed by nature inside a cell. The seven chapters(Chapters 20-26)that focus primarily on the organic chemistry of living e connection between the organic reactions that occur in the laboratory and occur in cells Each organic reaction that oc to the organic reaction with which the student is already familiar cond step is identical to the when they ydrate che in the citric acid cvele isan aldol addition followed by a nucleophilic acyl substitution reaction the second step is an E2 dehydration followed by the conjugate addition of water.the third step is oxidation of a secondary alcohol followed by decarboxylation of a 3-oxocarboxylate ion. ch students about halide and sulfonate leavi akm butnthstudentnorn to study biochemistry
Problems, Solved Problems, and Problem-Solving Strategies The book contains more than 2,000 problems, many with multiple parts. This edition has many new problems, both in-chapter and end-of-chapter. They include new solved problems, new problemsolving strategies, and new problems incorporating information from more than one chapter. I keep a list of questions my students have when they come to office hours. Many of the new problems were created as a result of these questions. The answers (and explanations, when needed) to all the problems are in the accompanying Study Guide/Solutions Manual, which I authored to ensure consistency in language with the text. The problems within each chapter are primarily drill problems. They appear at the end of each section, so they allow students to test themselves on material just covered before moving on to the next section. Short answers provided at the end of the book for problems marked with a diamond give students immediate feedback concerning their mastery of a skill or concept. Selected problems are accompanied by worked-out solutions to provide insight into problemsolving techniques, and the many Problem-Solving Strategies teach students how to approach various kinds of problems. These skill-teaching problems are indicated by LEARN THE STRATEGY in the margin. These strategies are followed by one or more problems that give students the opportunity to use the strategy just learned. These problems, or the first of a group of such problems, are indicated in the margin by USE THE STRATEGY. The Study Guide/Solutions Manual has a practice test at the end of each chapter and contains Special Topics Sections on molecular orbital theory and how to solve problems on pH, pKa, and buffer solutions. Powerpoint All the art in the text is available on PowerPoint slides. I created the PowerPoint lectures so they would be consistent with the language and philosophy of the text. Students Interested in The Biological Sciences and Mcat2015 I have long believed that students who take organic chemistry also should be exposed to bioorganic chemistry—the organic chemistry that occurs in biological systems. Students leave their organic chemistry course with a solid appreciation of organic mechanism and synthesis. But when they take biochemistry, they will never hear about Claisen condensations, SN2 reactions, nucleophilic acyl substitution reactions, etc., although these are extremely important reactions in cells. Why are students required to take organic chemistry if they are not going to be taught how the organic chemistry they learn repeats itself in the biological world? Now that the MCAT is focusing almost exclusively on the organic chemistry of living systems, it is even more important that we provide our students with the “bioorganic bridge”—the material that provides the bridge between organic chemistry and biochemistry. Students should see that the organic reactions that chemists carry out in the laboratory are in many ways the same as those performed by nature inside a cell. The seven chapters (Chapters 20–26) that focus primarily on the organic chemistry of living systems emphasize the connection between the organic reactions that occur in the laboratory and those that occur in cells. Each organic reaction that occurs in a cell is explicitly compared to the organic reaction with which the student is already familiar. For example, the first step in glycolysis is an SN2 reaction, the second step is identical to the enediol rearrangement that students learn when they study carbohydrate chemistry, the third step is another SN2 reaction, the fourth step is a reverse aldol addition, and so on. The first step in the citric acid cycle is an aldol addition followed by a nucleophilic acyl substitution reaction, the second step is an E2 dehydration followed by the conjugate addition of water, the third step is oxidation of a secondary alcohol followed by decarboxylation of a 3-oxocarboxylate ion, and so on. We teach students about halide and sulfonate leaving groups. Adding phosphate leaving groups takes little additional time but introduces the students to valuable information if they are going on to study biochemistry. Preface xxv
xxvi Preface RNA.But how many of these students are ever told that the reason for the difference in the bases in DNA and RNA is tautomerization and imine hydrolysis? enough time.I have organized the book in a way that allows some"traditional"chapters to be omit students can be prepared for biochemistry and/or the MCAT organic cours The Bioorganic Bridge students that organic le elect sit and nucleophilicity affect the reactions of simple organic compo nds.they can appreciate how these the reactions of organic compounds in cells. nc ma and to the las instructor to introduce bioorganic tonics into the course for exam nple.after hydrogen bonding s introduced in Chapter 3.hydrogen boding in proteins in DNA is discussed:after catalysis is intro duced in Chapter sby enzymes is discussed;after the stereochemistry of organic reaction er afte halide or an methods chemists use to activate carboxync a ing groups)inChapter 15,the methods cells us toactivate these same acid (by givingu ate,or tion reactions are shown In addition.seven chapters in the last part of the book (Chapters 20-26)focus on the organic ne cor ing panf mistry text. ploved in oreanic reactions and then shows that they are identical to the modes of students to understand the lightning-fast rates of Coenz ds Derve rom vitamin s)emph dies the oound that transfers a carb and describes how the many different reactions of vitamin B have common mechanisms. -with the first step always being imine formation.Chapter 24 (The Organic Chemistry of Metabolic Pathways) ns the chem nd shows ts that the reactions enc molecules in RNA catalyzes its hydrolysis and that is why DNA.which has to stay intact for the life of the cell,does not have 2'. OH gr ps.Students also see that the synthesis of proteins in cell r example of a nuc apters in the biological world
Students who study organic chemistry learn about tautomerization and imine hydrolysis, and students who study biochemistry learn that DNA has thymine bases in place of the uracil bases in RNA. But how many of these students are ever told that the reason for the difference in the bases in DNA and RNA is tautomerization and imine hydrolysis? Colleagues have asked how they can find time to fit the “bioorganic bridge” into their organic chemistry courses. I found that tying together reactivity and synthesis (see p. xxiii) frees up a lot of time. (This is the organization I adopted many years ago when I was trying to figure out how to incorporate the bioorganic bridge into my course.) And if you find that this still does not give you enough time, I have organized the book in a way that allows some “traditional” chapters to be omitted (Chapters 12, 18, 19, and 28), so students can be prepared for biochemistry and/or the MCAT without sacrificing the rigor of the organic course. The Bioorganic Bridge Bioorganic chemistry is found throughout the text to show students that organic chemistry and biochemistry are not separate entities but rather are closely related on a continuum of knowledge. Once students learn how, for example, electron delocalization, leaving-group propensity, electrophilicity, and nucleophilicity affect the reactions of simple organic compounds, they can appreciate how these same factors influence the reactions of organic compounds in cells. In Chapters 1–19, the bioorganic material is limited mostly to “interest boxes” and to the last sections of the chapters. Thus, the material is available to the curious student without requiring the instructor to introduce bioorganic topics into the course. For example, after hydrogen bonding is introduced in Chapter 3, hydrogen boding in proteins in DNA is discussed; after catalysis is introduced in Chapter 5, catalysis by enzymes is discussed; after the stereochemistry of organic reactions is presented in Chapter 6, the stereochemistry of enzyme-catalyzed reactions is discussed; after sulfonium ions are discussed in Chapter 10, a biological methylation reaction using a sulfonium ion is examined and the reason for the use of different methylating agents by chemists and cells is explained; after the methods chemists use to activate carboxylic acids are presented (by giving them halide or anhydride leaving groups) in Chapter 15, the methods cells use to activate these same acids are explained (by giving them phosphoanhydride, pyrophosphate, or thiol leaving groups); and after condensation reactions are discussed in Chapter 17, the mechanisms of some biological condensation reactions are shown. In addition, seven chapters in the last part of the book (Chapters 20–26) focus on the organic chemistry of living systems. These chapters have the unique distinction of containing more chemistry than is typically found in the corresponding parts of a biochemistry text. Chapter 22 (Catalysis in Organic Reactions and in Enzymatic Reactions), for example, explains the various modes of catalysis employed in organic reactions and then shows that they are identical to the modes of catalysis found in reactions catalyzed by enzymes. All of this is presented in a way that allows students to understand the lightning-fast rates of enzymatic reactions. Chapter 23 (The Organic Chemistry of the Coenzymes, Compounds Derived from Vitamins) emphasizes the role of vitamin B1 in electron delocalization, vitamin K as a strong base, vitamin B12 as a radical initiator, biotin as a compound that transfers a carboxyl group by means of a nucleophilic acyl substitution reaction, and describes how the many different reactions of vitamin B6 have common mechanisms—with the first step always being imine formation. Chapter 24 (The Organic Chemistry of Metabolic Pathways) explains the chemical function of ATP and shows students that the reactions encountered in metabolism are just additional examples of reactions that they already have mastered. In Chapter 26 (The Chemistry of the Nucleic Acids), students learn that 2′-OH group on the ribose molecules in RNA catalyzes its hydrolysis and that is why DNA, which has to stay intact for the life of the cell, does not have 2′-OH groups. Students also see that the synthesis of proteins in cells is just another example of a nucleophilic acyl substitution reaction. Thus, these chapters do not replicate what will be covered in a biochemistry course; they provide a bridge between the two disciplines, allowing students to see how the organic chemistry that they have learned is repeated in the biological world. xxvi Preface