Mcmurry15253 0495015253 01.01_toc

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Structures of Common CoenzymesThe reactive parts of the molecules are darkened, while nonreactive parts are ghosted.

+

CONH2

N

H3C

H3C

N N

NN

O

O–

P–O O

O

O–

P O OCH2

O

O–

P

O

OH

Flavin adenine dinucleotide—FAD (oxidation/reduction)

Nicotinamide adenine dinucleotide—NAD+ (oxidation/reduction)

Coenzyme A (acyl transfer)

Adenosine triphosphate—ATP (phosphorylation)

OH

HO CHCHCHCH2OPOPOCH2

O

O–

OOH

O–CH2

HSCH2CH2NHCCH2CH2NHCCHCCH2OPOPOCH2

O

O–

O

O–HO CH3

CH3OO

HO

O

OH OH (OPO32–)

(NADP+)

CH2OPOPOCH2

O

O–

O

O–

O

O

H

2–O3PO

O

OH

OOH HO

O

OH OH

NH2

N N

NN

NH2

N N

NN

NH2

N N

NN

NH2

N N

NN

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Copyright 2007 Thomson Learning, Inc. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part.

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S-Adenosylmethionine (methyl transfer)

Lipoic acid (acyl transfer)

Thiamin diphosphate

(decarboxylation)

Pyridoxal phosphate

(amino acid metabolism)

Tetrahydrofolate (transfer of C1 units)

CH2–OCCHCH2CH2

CH2CH2CH2CH2CO2–

S+

+NH3

O CH3

O

OHOH

H2N N

N

N

N

H

N

H

H

O

O

HH

NHCHCH2CH2C O–

1–5

OCO2–

S S CH2OPO32–

CH3

CHO

OHN

H+

H

CH3–OPOPOCH2CH2

N+

S

NH2

CH3

N

N

O

O–

O

O–

Biotin (carboxylation)

NN HH

O

S

HH

H

CH2CH2CH2CH2CO2–

NH2

N N

NN

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All royalties from Organic Chemistry: A Biological Approach will be donated to the Cystic Fibrosis (CF) Foundation. Thisbook and donation are dedicated to the author’s eldest son and to the thousands of others who daily fight this disease.To learn more about CF and the programs and services provided by the CF Foundation, please visit http://www.cff.org/.

Dear Colleague:

All of us who teach organic chemistry know that most of the students in our courses, even

the chemistry majors, are interested primarily in the life sciences rather than in pure

chemistry. Because we are teaching so many future biologists, biochemists, and doctors

rather than younger versions of ourselves, more and more of us are questioning why we

continue to teach the way we do. Why do we spend so much time discussing the details of

reactions that are of interest to research chemists but have little connection to biology? Why

don’t we instead spend more time discussing the organic chemistry of living organisms?

There is still much to be said for teaching organic chemistry in the traditional way, but it is

also true that until now there has been no real alternative for those instructors who want to

teach somewhat differently. And that is why I wrote Organic Chemistry: A Biological

Approach. As chemical biology continues to gain in prominence, I suspect that more and

more faculty will be changing their teaching accordingly.

Make no mistake: this is still a textbook on organic chemistry. But my guiding principle in

deciding what to include and what to leave out has been to focus almost exclusively on

those reactions that have a direct counterpart in biological chemistry. The space saved by

leaving out nonbiological reactions has been put to good use, for almost every reaction

discussed is followed by a biological example and approximately 25% of the book is devoted

entirely to biomolecules and the organic chemistry of their biotransformations. In addition,

Organic Chemistry: A Biological Approach is nearly 200 pages shorter than standard texts,

making it possible for faculty to cover the entire book in a typical two-semester course.

Organic Chemistry: A Biological Approach is different from any other text; I believe that it

is ideal for today’s students.Sincerely,

John McMurry

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Australia • Brazil • Canada • Mexico • Singapore • SpainUnited Kingdom • United States

Organic ChemistryA B I O L O G I C A L A P P R O A C H

J O H N M C M U R R YCornell University

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Organic Chemistry: A Biological ApproachJohn McMurry

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vv

1 Structure and Bonding 1

2 Polar Covalent Bonds; Acids and Bases 35

3 Organic Compounds: Alkanes and Their Stereochemistry 75

4 Organic Compounds: Cycloalkanes and Their Stereochemistry 111

5 An Overview of Organic Reactions 141

6 Alkenes and Alkynes 179

7 Reactions of Alkenes and Alkynes 221

8 Aromatic Compounds 267

9 Stereochemistry 319

10 Alkyl Halides: Nucleophilic Substitutions and Eliminations 363

11 Structure Determination:

Mass Spectrometry, Infrared Spectroscopy, and Ultraviolet Spectroscopy 415

12 Structure Determination: Nuclear Magnetic Resonance Spectroscopy 455

13 Alcohols, Phenols, and Thiols; Ethers and Sulfides 497

A Preview of Carbonyl Chemistry 547

14 Aldehydes and Ketones: Nucleophilic Addition Reactions 557

15 Carboxylic Acids and Nitriles 601

16 Carboxylic Acid Derivatives: Nucleophilic Acyl Substitution Reactions 633

17 Carbonyl Alpha-Substitution and Condensation Reactions 681

18 Amines and Heterocycles 735

19 Biomolecules: Amino Acids, Peptides, and Proteins 777

20 Amino Acid Metabolism 817

21 Biomolecules: Carbohydrates 851

22 Carbohydrate Metabolism 891

23 Biomolecules: Lipids and Their Metabolism 927

24 Biomolecules: Nucleic Acids and Their Metabolism 979

25 Secondary Metabolites: An Introduction to Natural Products Chemistry*

*Chapter 25 is available as an Adobe Acrobat PDF file at http://www.thomsonedu.com

Key to Sequence of Topics (chapter numbers are color coded as follows):• Traditional foundations of organic chemistry• Organic reactions and their biological counterparts• The organic chemistry of biological molecules and pathways

Brief Contents

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vi

Contents

1 Structure and Bonding 1

1.1 Atomic Structure: The Nucleus 3

1.2 Atomic Structure: Orbitals 4

1.3 Atomic Structure: Electron Configurations 5

1.4 Development of Chemical Bonding Theory 6

1.5 The Nature of Chemical Bonds: Valence Bond Theory 10

1.6 sp3 Hybrid Orbitals and the Structure of Methane 11

1.7 sp3 Hybrid Orbitals and the Structure of Ethane 13

1.8 sp2 Hybrid Orbitals and the Structure of Ethylene 14

1.9 sp Hybrid Orbitals and the Structure of Acetylene 17

1.10 Hybridization of Nitrogen, Oxygen, Phosphorus, and Sulfur 19

1.11 The Nature of Chemical Bonds: Molecular Orbital Theory 21

1.12 Drawing Chemical Structures 22

Lagniappe: Chemicals, Toxicity, and Risk 26

Summary 26

Exercises 28

2 Polar Covalent Bonds; Acids and Bases 35

2.1 Polar Covalent Bonds: Electronegativity 35

2.2 Polar Covalent Bonds: Dipole Moments 38

2.3 Formal Charges 40

2.4 Resonance 43

2.5 Rules for Resonance Forms 45

2.6 Drawing Resonance Forms 47

2.7 Acids and Bases: The Brønsted–Lowry Definition 50

2.8 Acid and Base Strength 51

2.9 Predicting Acid–Base Reactions from pKa Values 53

2.10 Organic Acids and Organic Bases 55

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2.11 Acids and Bases: The Lewis Definition 58

2.12 Noncovalent Interactions between Molecules 62

Lagniappe: Alkaloids: Naturally Occurring Bases 65

Summary 66

Exercises 67

3 Organic Compounds: Alkanes and Their Stereochemistry 75

3.1 Functional Groups 75

3.2 Alkanes and Alkane Isomers 82

3.3 Alkyl Groups 86

3.4 Naming Alkanes 89

3.5 Properties of Alkanes 95

3.6 Conformations of Ethane 96

3.7 Conformations of Other Alkanes 98

Lagniappe: Gasoline 103

Summary 104

Exercises 104

4 Organic Compounds: Cycloalkanes and Their Stereochemistry 111

4.1 Naming Cycloalkanes 112

4.2 Cis–Trans Isomerism in Cycloalkanes 115

4.3 Stability of Cycloalkanes: Ring Strain 118

4.4 Conformations of Cycloalkanes 119

4.5 Conformations of Cyclohexane 121

4.6 Axial and Equatorial Bonds in Cyclohexane 123

4.7 Conformations of Monosubstituted Cyclohexanes 126

4.8 Conformations of Disubstituted Cyclohexanes 128

4.9 Conformations of Polycyclic Molecules 131

Lagniappe: Molecular Mechanics 133

Summary 133

Exercises 134

5 An Overview of Organic Reactions 141

5.1 Kinds of Organic Reactions 141

5.2 How Organic Reactions Occur: Mechanisms 143

5.3 Radical Reactions 144

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5.4 Polar Reactions 147

5.5 An Example of a Polar Reaction: Addition of H2O to Ethylene 151

5.6 Using Curved Arrows in Polar Reaction Mechanisms 154

5.7 Describing a Reaction: Equilibria, Rates, and Energy Changes 157

5.8 Describing a Reaction: Bond Dissociation Energies 161

5.9 Describing a Reaction: Energy Diagrams and Transition States 163

5.10 Describing a Reaction: Intermediates 166

5.11 A Comparison between Biological Reactions and Laboratory Reactions 168

Lagniappe: Where Do Drugs Come From? 171

Summary 172

Exercises 173

6 Alkenes and Alkynes 179

6.1 Calculating a Degree of Unsaturation 180

6.2 Naming Alkenes and Alkynes 182

6.3 Cis–Trans Isomerism in Alkenes 185

6.4 Sequence Rules: The E,Z Designation 187

6.5 Stability of Alkenes 192

6.6 Electrophilic Addition Reactions of Alkenes 195

6.7 Orientation of Electrophilic Addition: Markovnikov’s Rule 198

6.8 Carbocation Structure and Stability 201

6.9 The Hammond Postulate 204

6.10 Carbocation Rearrangements 206

Lagniappe: Terpenes: Naturally Occurring Alkenes 209

Summary 210

Exercises 211

7 Reactions of Alkenes and Alkynes 221

7.1 Preparation of Alkenes: A Preview of Elimination Reactions 222

7.2 Halogenation of Alkenes 224

7.3 Halohydrins from Alkenes 226

7.4 Hydration of Alkenes 227

7.5 Reduction of Alkenes 232

7.6 Oxidation of Alkenes: Epoxidation 235

7.7 Oxidation of Alkenes: Hydroxylation 236

7.8 Radical Additions to Alkenes: Alkene Polymers 239

7.9 Biological Additions of Radicals to Alkenes 243

7.10 Conjugated Dienes 244

7.11 Reactions of Conjugated Dienes 248

7.12 Reactions of Alkynes 251

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C O N T E N T S ix

Lagniappe: Natural Rubber 253

Summary 254

Summary of Reactions 255

Exercises 258

8 Aromatic Compounds 267

8.1 Naming Aromatic Compounds 268

8.2 Structure and Stability of Benzene 270

8.3 Aromaticity and the Hückel 4n � 2 Rule 273

8.4 Aromatic Heterocycles 275

8.5 Polycyclic Aromatic Compounds 278

8.6 Reactions of Aromatic Compounds: Electrophilic Substitution 281

8.7 Alkylation and Acylation of Aromatic Rings 288

8.8 Substituent Effects in Electrophilic Substitutions 292

8.9 Oxidation and Reduction of Aromatic Compounds 298

8.10 An Introduction to Organic Synthesis: Polysubstituted Benzenes 300

Lagniappe: Combinatorial Chemistry 306

Summary 307


Exercises 310

9 Stereochemistry 319

9.1 Enantiomers and the Tetrahedral Carbon 320

9.2 The Reason for Handedness in Molecules: Chirality 321

9.3 Optical Activity 325

9.4 Pasteur’s Discovery of Enantiomers 327

9.5 Sequence Rules for Specifying Configuration 328

9.6 Diastereomers 333

9.7 Meso Compounds 335

9.8 Racemates and the Resolution of Enantiomers 338

9.9 A Brief Review of Isomerism 340

9.10 Stereochemistry of Reactions: Addition of H2O to an Achiral Alkene 342

9.11 Stereochemistry of Reactions: Addition of H2O to a Chiral Alkene 343

9.12 Chirality at Nitrogen, Phosphorus, and Sulfur 345

9.13 Prochirality 346

9.14 Chirality in Nature 349

Lagniappe: Chiral Drugs 351

Summary 352

Exercises 353

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10 Alkyl Halides: Nucleophilic Substitutions and Eliminations 363

10.1 Naming Alkyl Halides 364

10.2 Preparing Alkyl Halides 365

10.3 Reactions of Alkyl Halides: Grignard Reagents 367

10.4 Discovery of the Nucleophilic Substitution Reaction 368

10.5 The SN2 Reaction 371

10.6 Characteristics of the SN2 Reaction 374

10.7 The SN1 Reaction 381

10.8 Characteristics of the SN1 Reaction 385

10.9 Biological Substitution Reactions 390

10.10 Elimination Reactions: Zaitsev’s Rule 392

10.11 The E2 Reaction 394

10.12 The E1 and E1cB Reactions 398

10.13 Biological Elimination Reactions 400

10.14 A Summary of Reactivity: SN1, SN2, E1, E1cB, and E2 401

Lagniappe: Naturally Occurring Organohalides 402

Summary 403


Exercises 406

11Structure Determination: Mass Spectrometry, Infrared Spectroscopy, and Ultraviolet Spectroscopy 415

11.1 Mass Spectrometry of Small Molecules: Magnetic-Sector Instruments 415

11.2 Interpreting Mass Spectra 417

11.3 Mass Spectrometry of Some Common Functional Groups 422

11.4 Mass Spectrometry in Biological Chemistry: Time-of-Flight (TOF) Instruments 424

11.5 Spectroscopy and the Electromagnetic Spectrum 425

11.6 Infrared Spectroscopy 428

11.7 Interpreting Infrared Spectra 430

11.8 Infrared Spectra of Some Common Functional Groups 433

11.9 Ultraviolet Spectroscopy 438

11.10 Interpreting Ultraviolet Spectra: The Effect of Conjugation 441

11.11 Conjugation, Color, and the Chemistry of Vision 442

Lagniappe: Chromatography: Purifying Organic Compounds 444

Summary 445

Exercises 446

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12 Structure Determination: Nuclear Magnetic Resonance Spectroscopy 455

12.1 Nuclear Magnetic Resonance Spectroscopy 455

12.2 The Nature of NMR Absorptions 457

12.3 Chemical Shifts 460

12.4 13C NMR Spectroscopy: Signal Averaging and FT-NMR 462

12.5 Characteristics of 13C NMR Spectroscopy 464

12.6 DEPT 13C NMR Spectroscopy 467

12.7 Uses of 13C NMR Spectroscopy 469

12.8 1H NMR Spectroscopy and Proton Equivalence 470

12.9 Chemical Shifts in 1H NMR Spectroscopy 473

12.10 Integration of 1H NMR Absorptions: Proton Counting 475

12.11 Spin–Spin Splitting in 1H NMR Spectra 476

12.12 More Complex Spin–Spin Splitting Patterns 482

12.13 Uses of 1H NMR Spectroscopy 484

Lagniappe: Magnetic Resonance Imaging (MRI) 485

Summary 485

Exercises 486

13 Alcohols, Phenols, and Thiols; Ethers and Sulfides 497

13.1 Naming Alcohols, Phenols, and Thiols 499

13.2 Properties of Alcohols, Phenols, and Thiols 501

13.3 Preparation of Alcohols from Carbonyl Compounds 504

13.4 Reactions of Alcohols 512

13.5 Oxidation of Alcohols and Phenols 516

13.6 Preparation and Reactions of Thiols 520

13.7 Ethers and Sulfides 522

13.8 Preparation of Ethers 523

13.9 Reactions of Ethers 525

13.10 Preparation and Reactions of Sulfides 527

13.11 Spectroscopy of Alcohols, Phenols, and Ethers 529

Lagniappe: Ethanol: Chemical, Drug, and Poison 532

Summary 532


Exercises 536

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A Preview of Carbonyl Chemistry 547

I. Kinds of Carbonyl Compounds 547

II. Nature of the Carbonyl Group 549

III. General Reactions of Carbonyl Compounds 550

IV. Summary 555

14 Aldehydes and Ketones: Nucleophilic Addition Reactions 557

14.1 Naming Aldehydes and Ketones 558

14.2 Preparation of Aldehydes and Ketones 560

14.3 Oxidation of Aldehydes 561

14.4 Nucleophilic Addition Reactions of Aldehydes and Ketones 562

14.5 Nucleophilic Addition of H2O: Hydration 564

14.6 Nucleophilic Addition of Grignard and Hydride Reagents: Alcohol Formation 567

14.7 Nucleophilic Addition of Amines: Imine and Enamine Formation 568

14.8 Nucleophilic Addition of Alcohols: Acetal Formation 572

14.9 Nucleophilic Addition of Phosphorus Ylides: The Wittig Reaction 575

14.10 Biological Reductions 579

14.11 Conjugate Nucleophilic Addition to �,�-Unsaturated Aldehydes and Ketones 580

14.12 Spectroscopy of Aldehydes and Ketones 583

Lagniappe: Enantioselective Synthesis 587

Summary 588


Exercises 590

15 Carboxylic Acids and Nitriles 601

15.1 Naming Carboxylic Acids and Nitriles 602

15.2 Structure and Properties of Carboxylic Acids 605

15.3 Biological Acids and the Henderson–Hasselbalch Equation 608

15.4 Substituent Effects on Acidity 609

15.5 Preparation of Carboxylic Acids 611

15.6 Reactions of Carboxylic Acids: An Overview 613

15.7 Chemistry of Nitriles 614

15.8 Spectroscopy of Carboxylic Acids and Nitriles 617

Lagniappe: Vitamin C 618

Summary 620


Exercises 622

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C O N T E N T S xiii

16 Carboxylic Acid Derivatives: Nucleophilic Acyl Substitution Reactions 633

16.1 Naming Carboxylic Acid Derivatives 634

16.2 Nucleophilic Acyl Substitution Reactions 637

16.3 Nucleophilic Acyl Substitution Reactions of Carboxylic Acids 642

16.4 Chemistry of Acid Halides 648

16.5 Chemistry of Acid Anhydrides 652

16.6 Chemistry of Esters 653

16.7 Chemistry of Amides 659

16.8 Chemistry of Thioesters and Acyl Phosphates: Biological Carboxylic Acid Derivatives 661

16.9 Polyamides and Polyesters: Step-Growth Polymers 663

16.10 Spectroscopy of Carboxylic Acid Derivatives 666

Lagniappe: �-Lactam Antibiotics 668

Summary 669


Exercises 672

17 Carbonyl Alpha-Substitution and Condensation Reactions 681

17.1 Keto–Enol Tautomerism 682

17.2 Reactivity of Enols: �-Substitution Reactions 685

17.3 Acidity of � Hydrogen Atoms: Enolate Ion Formation 688

17.4 Alkylation of Enolate Ions 691

17.5 Carbonyl Condensations: The Aldol Reaction 701

17.6 Dehydration of Aldol Products 705

17.7 Intramolecular Aldol Reactions 707

17.8 The Claisen Condensation Reaction 708

17.9 Intramolecular Claisen Condensations 711

17.10 Conjugate Carbonyl Additions: The Michael Reaction 713

17.11 Carbonyl Condensations with Enamines: The Stork Reaction 716

17.12 Some Biological Carbonyl Condensation Reactions 718

Lagniappe: X-Ray Crystallography 720

Summary 721


Exercises 724

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18 Amines and Heterocycles 735

18.1 Naming Amines 736

18.2 Properties of Amines 739

18.3 Basicity of Amines 740

18.4 Basicity of Arylamines 743

18.5 Biological Amines and the Henderson–Hasselbalch Equation 745

18.6 Synthesis of Amines 746

18.7 Reactions of Amines 751

18.8 Heterocyclic Amines 755

18.9 Fused-Ring Heterocycles 759

18.10 Spectroscopy of Amines 762

Lagniappe: Green Chemistry 764

Summary 765


Exercises 768

19 Biomolecules: Amino Acids, Peptides, and Proteins 777

19.1 Structures of Amino Acids 778

19.2 Isoelectric Points 783

19.3 Synthesis of Amino Acids 784

19.4 Peptides and Proteins 787

19.5 Amino Acid Analysis of Peptides 789

19.6 Peptide Sequencing: The Edman Degradation 790

19.7 Peptide Synthesis 792

19.8 Protein Structure 797

19.9 Enzymes and Coenzymes 800

19.10 How Do Enzymes Work? Citrate Synthase 804

Lagniappe: The Protein Data Bank 807

Summary 808


Exercises 810

20 Amino Acid Metabolism 817

20.1 An Overview of Metabolism and Biochemical Energy 818

20.2 Catabolism of Amino Acids: Deamination 822

20.3 The Urea Cycle 827

20.4 Catabolism of Amino Acids: The Carbon Chains 831

20.5 Biosynthesis of Amino Acids 838

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C O N T E N T S xv

Lagniappe: Visualizing Enzyme Structures 844

Summary 845

Exercises 846

21 Biomolecules: Carbohydrates 851

21.1 Classification of Carbohydrates 852

21.2 Depicting Carbohydrate Stereochemistry: Fischer Projections 853

21.3 D,L Sugars 858

21.4 Configurations of the Aldoses 859

21.5 Cyclic Structures of Monosaccharides: Anomers 862

21.6 Reactions of Monosaccharides 866

21.7 The Eight Essential Monosaccharides 872

21.8 Disaccharides 873

21.9 Polysaccharides and Their Synthesis 876

21.10 Cell-Surface Carbohydrates and Carbohydrate Vaccines 879

Lagniappe: Sweetness 880

Summary 881

Exercises 882

22 Carbohydrate Metabolism 891

22.1 Hydrolysis of Complex Carbohydrates 892

22.2 Catabolism of Glucose: Glycolysis 893

22.3 Conversion of Pyruvate to Acetyl CoA 901

22.4 The Citric Acid Cycle 905

22.5 Biosynthesis of Glucose: Gluconeogenesis 912

Lagniappe: Avian Flu 920

Summary 921

Exercises 921

23 Biomolecules: Lipids and Their Metabolism 927

23.1 Waxes, Fats, and Oils 928

23.2 Soap 931

23.3 Phospholipids 933

23.4 Catabolism of Triacylglycerols: The Fate of Glycerol 934

23.5 Catabolism of Triacylglycerols: �-Oxidation 937

23.6 Biosynthesis of Fatty Acids 943

23.7 Prostaglandins and Other Eicosanoids 948

23.8 Terpenoids 950

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23.9 Steroids 959

23.10 Biosynthesis of Steroids 964

Lagniappe: Saturated Fats, Cholesterol, and Heart Disease 970

Summary 971

Exercises 971

24 Biomolecules: Nucleic Acids and Their Metabolism 979

24.1 Nucleotides and Nucleic Acids 979

24.2 Base Pairing in DNA: The Watson–Crick Model 982

24.3 Replication of DNA 985

24.4 Transcription of DNA 986

24.5 Translation of RNA: Protein Biosynthesis 987

24.6 DNA Sequencing 990

24.7 DNA Synthesis 992

24.8 The Polymerase Chain Reaction 995

24.9 Catabolism of Nucleotides 997

24.10 Biosynthesis of Nucleotides 1003

24.11 Some Final Comments on Metabolism 1008

Lagniappe: DNA Fingerprinting 1010

Summary 1011

Exercises 1012

25 Secondary Metabolites: An Introduction to Natural Products Chemistry25.1 Classification of Natural Products25.2 Biosynthesis of Pyridoxal Phosphate25.3 Biosynthesis of Morphine25.4 Biosynthesis of Erythromycin

Lagniappe: Bioprospecting: Hunting for Natural Products

SummaryExercises

AppendicesA Nomenclature of Polyfunctional Organic Compounds A-1

B Acidity Constants for Some Organic Compounds A-9

C Glossary A-11

D Answers to In-Text Problems A-31

Index I-1

Chapter 25 is available as an Adobe Acrobat PDF file athttp://www.thomsonedu.com

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Preface

IntroductionI’ve taught organic chemistry many times over many years, and it has oftenstruck me what a disconnect there is between the interests and expectationsof me, the teacher, and the interests and expectations of those being taught,my students. I love the logic and beauty of organic chemistry, and I want topass that feeling on to others. My students, however, seem to worry primarilyabout getting into medical school. Yes, of course that’s a simplification, butthere is truth in it. All of us who teach organic chemistry know that a largemajority of students in our courses—perhaps 80% or more, and includingmany chemistry majors—are interested primarily in the life sciences.

But if we are teaching future biologists, biochemists, physicians, and oth-ers in the life sciences, why do we continue to teach the way we do? Why dowe spend so much time discussing the details of reactions that are of interestto research chemists but have no connection to the biological sciences?Wouldn’t the limited amount of time we have be better spent paying moreattention to the organic chemistry of living organisms and less to the organicchemistry of the research laboratory? I believe so, and I have written thisbook, Organic Chemistry: A Biological Approach, to encourage others whomight also be thinking that the time has come to try something new.

OrganizationMake no mistake, this is still a textbook on Organic Chemistry, but the guid-ing principle in deciding what to include and what to leave out has been tofocus on those organic reactions that have a direct counterpart in biologicalchemistry. When looking through the text, three distinct groups of chaptersare apparent. The first group (Chapters 1–5, 9, 11, and 12) covers the tradi-tional foundations of organic chemistry that are essential in building thebackground necessary for further understanding of the science. The secondgroup (Chapters 6–8, 10, and 13–18) provides coverage of common laboratoryreactions that have biological counterparts (of which there are many morethan you might think). As each laboratory reaction is discussed, a biologicalexample is also shown. The inclusion of these biological reactions makes thematerial much more relevant for students, who might, for example, be more

“All of us who teach organic chemistryknow that the large majority of students in our courses are interested primarily in the life sciences.” John McMurry

“Make no mistake, this is still a textbook on Organic Chemistry.” John McMurry

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interested in reading about trans fatty acids when they’re learning about cat-alytic hydrogenation than when they’re learning about lipids. The thirdgroup of chapters (19–24) is unique to this text. These chapters deal exclu-sively with the main classes of biomolecules—amino acids and proteins,carbohydrates, lipids, and nucleic acids—and show how deeply organicchemistry and biochemistry are intertwined. Following an introduction to each class, the major metabolic pathways for that class are discussed from the perspective of mechanistic organic chemistry. See, for example, Sections 20.2 to 20.5 on amino acid metabolism.

Content ChoicesMany organic chemists might be surprised to find that such topics as carbenechemistry, acetylide alkylation, allylic bromination, and Diels–Alder reactionsare not included in this text. The decision not to cover these topics was not takenlightly, but the space saved by leaving out some nonbiological reactions hasbeen put to good use. Practically all reactions covered are immediately illus-trated with biological examples, and approximately 25% of the book is devotedentirely to biomolecules and the organic chemistry of their biotransformations.Furthermore, the deletion of some nonbiological reactions has resulted in ashorter text that many professors will have time to cover in its entirety.

There is more than enough organic chemistry in this text. My hope is thatthe students we teach, including those who worry about medical school, willcome to agree that there is also logic and beauty here.

Features

Reaction Mechanisms The innovative vertical presentation of reaction mechanisms that has been sowell received in my other texts is retained in Organic Chemistry: A BiologicalApproach. Mechanisms in this format have the reaction steps printed verti-cally while the changes taking place in each step are explained next to thereaction arrow. Students can see what is occurring at each step in a reactionwithout having to jump back and forth between structures and text.

VisualizationI want students to see that the mechanisms of biological reactions are thesame as those of laboratory organic reactions. Toward this end, and to let stu-dents more easily visualize the changes occurring in large biomolecules, thisbook introduces an innovative method for focusing on the reactive parts inlarge molecules by ghosting the nonreacting parts. In addition, consistentcolor, with clearly labeled numbered steps, is used in mechanisms through-out the text to show the progress of the reactions more clearly.

More Features• The reaction from students and colleagues to my previous texts has been

very gratifying, and I have made every effort to keep the writing in thistext as lucid and succinct as possible.

“Writing Organic Chemistry: ABiological Approach has been awonderful learning experience for me. I hope that both you and your studentswill enjoy and benefit from this text,and I would be very interested inhearing your questions and opinions.” John McMurry

“The innovative vertical presentationof reaction mechanisms that has been so well received in my othertexts is retained in Organic Chemistry:A Biological Approach.”John McMurry

“I want students to see that themechanisms of biological reactionsare the same as those of laboratoryorganic reactions.” John McMurry

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• Why do we have to learn this? I’ve been asked this question so manytimes by students that I thought that it would be appropriate to begin eachchapter with the answer. Why This Chapter? is a short paragraph at theend of the introduction to every chapter that tells students why the mate-rial about to be covered is important and explains how the organic chem-istry of each chapter relates to biochemistry.

• Worked Examples are titled to give students a frame of reference. EachWorked Example includes a Strategy and a worked-out Solution and isfollowed by Problems for students to try on their own.

• Lagniappe (a Creole word meaning “something extra”) boxes at the end ofeach chapter are provided to relate real-world concepts to students’ lives.

• The Visualizing Chemistry Problems that conclude each chapter offerstudents an opportunity to see chemistry in a different way by visualiz-ing molecules rather than by simply interpreting structural formulas.

• Thorough media integration with Organic ChemistryNow™ and OrganicOWL is provided to help students practice and test their knowledge of theconcepts. The Organic ChemistryNow online assessment program isenhanced with biochemical coverage especially for biology and premedstudents. Icons throughout the book direct students to the Organic Chem-istryNow website. An access code is required to enter Organic Chem-istryNow. Visit http://www.thomsonedu.com to register.

• A number of the figures are animated in Organic ChemistryNow. Thesefigures are designated as Active in the figure legends.

• Summaries and Key Word lists help students by outlining the key con-cepts of the chapter.

• Summaries of Reactions bring together the key reactions from the chapterin one complete list.

• An overview entitled “A Preview of Carbonyl Chemistry” follows Chap-ter 13 and highlights the idea that studying organic chemistry requiresboth summarizing and looking ahead.

• Current IUPAC nomenclature rules, as updated in 1993, are used to namecompounds in this text.

Companions to This TextSupporting instructor materials are available to qualified adopters. Pleaseconsult your local Thomson Brooks/Cole representative for details.

Visit http://www.thomsonedu.com to:

• Locate your local representative• Download electronic files of text art and ancillaries• Request a desk copy

For Students Study Guide and Solutions Manual By Susan McMurry. Provides answersand explanations to all in-text and end-of-chapter exercises. ISBN: 0-495-01530-x

To further student understanding, the text features sensi-ble media integration through the Organic ChemistryNow website, a power-ful online learning companion that helps students determine their unique

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study needs and provides them with individualized resources. This dynamicinteractive resource combines with the text to provide students with a seam-less, integrated learning system. A code is required to access Organic ChemistryNow and may be packaged with a new copy of the text or pur-chased separately. Visit http://www.thomsonedu.com to register for access to Organic ChemistryNow.

OWL for Organic Chemistry The most widely used online chemistry masteryhomework system in the world! Developed at the University of Massachusetts,Amherst, class-tested by thousands of students, and used by more than 200institutions and 50,000 students, OWL is the most widely used system provid-ing fully class-tested content in an easy-to-use system that has proved reliablefor tens of thousands of students. OWL is also customizable, cross-platform, andavailable for introductory/preparatory chemistry, general chemistry, organicchemistry, liberal arts chemistry, and allied health/GOB. The OWL Online Web-based Learning system provides students with instant analysis and feedback onhomework problems, modeling questions, and animations to accompany selectThomson Brooks/Cole texts. This powerful system maximizes each student’slearning experience and, at the same time, reduces faculty workload and helpsfacilitate instruction. OWL’s organic chemistry content takes advantage of thelatest technological advances in online computer modeling using Jmol and MarvinSketch. Jmol, an interactive molecule viewer, enables students to rotatemolecules, to change the display mode (ball and stick, space fill, etc.), and tomeasure bond distances and angles. MarvinSketch, a Java applet for drawingchemical structures, enables OWL to grade chemical structures that the studentsdraw. A fee-based code is required for access to the specific OWL databaseselected. OWL is available for use only within North America.

Pushing Electrons: A Guide for Students of Organic Chemistry, third editionBy Daniel P. Weeks. A workbook designed to help students learn techniques ofelectron pushing. Its programmed approach emphasizes repetition and activeparticipation. ISBN: 0-03-020693-6

Spartan Model Electronic Modeling Kit A set of easy-to-use builders allowfor the construction and 3-D manipulation of molecules of any size or com-plexity. This kit includes the SpartanModel software on CD-ROM, an exten-sive molecular database, 3-D glasses, and a Tutorial and Users Guide thatincludes a wealth of activities to help you get the most out of your course.ISBN: 0-495-01793-0

For InstructorsJoinIn™ on Turning Point® Organic Chemistry Book-specific JoinIn con-tent for Response Systems tailored to Organic Chemistry: A BiologicalApproach allows you to transform your classroom and assess your students’progress with instant in-class quizzes and polls. Our exclusive agreement tooffer TurningPoint software lets you pose book-specific questions and displaystudents’ answers seamlessly within the Microsoft® PowerPoint® slides ofyour own lecture, in conjunction with the “clicker” hardware of your choice.Enhance how your students interact with you, your lecture, and one another.Contact your local Thomson Brooks/Cole representative to learn more.

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Multimedia Manager CD-ROM The Multimedia Manager is a dual-platformdigital library and presentation tool that provides art and tables from themain text in a variety of electronic formats that are easily exported into othersoftware packages. This enhanced CD-ROM also contains simulations,molecular models, and QuickTime movies to supplement lectures as well aselectronic files of various print supplements. Slides use the full power ofMicrosoft PowerPoint and incorporate videos, animations, and other assetsfrom Organic ChemistryNow. Instructors can customize their lecture presen-tations by adding their own slides or by deleting or changing existing slides.

Test Bank By Thomas Lectka, Johns Hopkins University. Hundreds of questions and answers organized to correspond to the main text.

iLrn Testing This easy-to-use software, containing questions and problemsauthored specifically for the text, allows professors to create, deliver, andcustomize tests in minutes.

WebCT/Now Integration Instructors and students enter Organic Chem-istryNow through their familiar Blackboard or WebCT environment withoutthe need for a separate user name or password and can access all ofthe Organic ChemistryNow assessments and content.

The Organic Chemistry of Biological Pathways By John McMurry andTadhg Begley. Intended for advanced undergraduates and graduate studentsin all areas of chemistry and biochemistry, The Organic Chemistry of Biolog-ical Pathways provides an accurate treatment of the major biochemical path-ways from the perspective of mechanistic organic chemistry. Roberts andCompany Publishers, ISBN: 0-9747077-1-6

Organic Chemistry Laboratory Manuals Thomson Brooks/Cole is pleasedto offer you a choice of organic chemistry laboratory manuals catered to fityour needs. Visit http://www.thomsonedu.com. Customizable laboratorymanuals also can be assembled. Go to http://cerlabs.brookscole.com/ andhttp://outernetpublishing.com/ for more information.

AcknowledgmentsI thank all the people who helped to shape this book and its message. AtThomson Brooks/Cole they include David Harris, publisher; Sandra Kiselica,senior development editor; Julie Conover, executive marketing manager; LisaWeber, senior production project manager; Ellen Bitter, assistant editor; andSuzanne Kastner at Graphic World Inc. Many thanks to John R. Scheffer, University of British Columbia; Eric Kantorowski, California PolytechnicState University; and Jacquelyn Gervay-Hague, University of California,Davis, for serving as the accuracy reviewers. They carefully read and checkedthe page proofs for this text before publication.

I am grateful to colleagues who reviewed the manuscript for this bookand participated in a survey about its approach. They include:

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Manuscript ReviewersHelen E. Blackwell, University of Wisconsin

Joseph Chihade, Carleton College

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Eric Kantorowski, California Polytechnic State University

Thomas Lectka, Johns Hopkins University

Paul Martino, Flathead Valley Community College

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Organic ChemistryA B I O L O G I C A L A P P R O A C H

J O H N M C M U R R YCornell University

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A-1

AppendixNomenclature of Polyfunctional

Organic Compounds

A

With more than 26 million organic compounds now known and several thou-sand more being created daily, naming them all is a real problem. Part of theproblem is due to the sheer complexity of organic structures, but part is alsodue to the fact that chemical names have more than one purpose. For Chemi-cal Abstracts Service (CAS), which catalogs and indexes the worldwidechemical literature, each compound must have only one correct name. Itwould be chaos if half the entries for CH3Br were indexed under “M” formethyl bromide and half under “B” for bromomethane. Furthermore, a CASname must be strictly systematic so that it can be assigned and interpreted bycomputers; common names are not allowed.

People, however, have different requirements than computers. For people—which is to say chemists in their spoken and written communications—it’s bestthat a chemical name be pronounceable and that it be as easy as possible toassign and interpret. Furthermore, it’s convenient if names follow historicalprecedents, even if that means a particularly well-known compound might havemore than one name. People can readily understand that bromomethane andmethyl bromide both refer to CH3Br.

As noted in the text, chemists overwhelmingly use the nomenclature sys-tem devised and maintained by the International Union of Pure and AppliedChemistry, or IUPAC. Rules for naming monofunctional compounds weregiven throughout the text as each new functional group was introduced, anda list of where these rules can be found is given in Table A.1.

Naming a monofunctional compound is reasonably straightforward, buteven experienced chemists often encounter problems when faced with nam-ing a complex polyfunctional compound. Take the following compound, for instance. It has three functional groups, ester, ketone, and C�C, but how should it be named? As an ester with an -oate ending, a ketone with an -one ending, or an alkene with an -ene ending? It’s actually named methyl 3-(2-oxocyclohex-6-enyl)propanoate.

O

COCH3

Methyl 3-(2-oxocylohex-6-enyl)propanoate

Double bond

EsterKetoneO

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A-2 A P P E N D I X A: N O M E N C L AT U R E O F P O LY F U N C T I O N A L O R G A N I C C O M P O U N D S

The name of a polyfunctional organic molecule has four parts—suffix,parent, prefixes, and locants—which must be identified and expressed in theproper order and format. Let’s look at each of the four.

Name Part 1. The Suffix: Functional-Group PrecedenceAlthough a polyfunctional organic molecule might contain several differentfunctional groups, we must choose just one suffix for nomenclature purposes.It’s not correct to use two suffixes. Thus, keto ester 1 must be named either as aketone with an -one suffix or as an ester with an -oate suffix but can’t be namedas an -onoate. Similarly, amino alcohol 2 must be named either as an alcohol (-ol)or as an amine (-amine) but can’t be named as an -olamine or -aminol.

The only exception to the rule requiring a single suffix is when namingcompounds that have double or triple bonds. Thus, the unsaturated acidH2CUCHCH2CO2H is but-3-enoic acid, and the acetylenic alcoholHCqCCH2CH2CH2OH is pent-5-yn-1-ol.

How do we choose which suffix to use? Functional groups are dividedinto two classes, principal groups and subordinate groups, as shown in TableA.2. Principal groups can be cited either as prefixes or as suffixes, while sub-ordinate groups are cited only as prefixes. Within the principal groups, anorder of priority has been established, with the proper suffix for a given com-pound determined by choosing the principal group of highest priority. Forexample, Table A.2 indicates that keto ester 1 should be named as an ester

CH3CCH2CH2COCH3

OO1.

CH3CHCH2CH2CH2NH2

2. OH

Functional group Text section Functional group Text section

Acid anhydrides 16.1 Aromatic compounds 8.1

Acid halides 16.1 Carboxylic acids 15.1

Acyl phosphates 16.1 Cycloalkanes 4.1

Alcohols 13.1 Esters 16.1

Aldehydes 14.1 Ethers 13.7

Alkanes 3.4 Ketones 14.1

Alkenes 6.2 Nitriles 15.1

Alkyl halides 10.1 Phenols 13.1

Alkynes 6.2 Sulfides 13.7

Amides 16.1 Thiols 13.1

Amines 18.1 Thioesters 16.1

Table A.1 Nomenclature Rules for Functional Groups

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Functional group Name as suffix Name as prefix

Principal groups

Carboxylic acids -oic acid carboxy-carboxylic acid

Acid anhydrides -oic anhydride —-carboxylic anhydride

Esters -oate alkoxycarbonyl-carboxylate

Thioesters -thioate alkylthiocarbonyl-carbothioate

Acid halides -oyl halide halocarbonyl-carbonyl halide

Amides -amide carbamoyl-carboxamide

Nitriles -nitrile cyano-carbonitrile

Aldehydes -al oxo-carbaldehyde

Ketones -one oxo

Alcohols -ol hydroxy

Phenols -ol hydroxy

Thiols -thiol mercapto

Amines -amine amino

Imines -imine imino

Ethers ether alkoxy

Sulfides sulfide alkylthio

Disulfides disulfide —

Alkenes -ene —

Alkynes -yne —

Alkanes -ane —

Subordinate groups

Azides — azido

Halides — halo

Nitro compounds — nitro

aPrincipal groups are listed in order of decreasing priority; subordinate groups have no priority order.

Table A.2 Classification of Functional Groupsa

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rather than as a ketone because an ester functional group is higher in prioritythan a ketone. Similarly, amino alcohol 2 should be named as an alcoholrather than as an amine. Thus, the name of 1 is methyl 4-oxopentanoate, andthe name of 2 is 5-aminopentan-2-ol. Further examples are shown:

Name Part 2. The Parent: Selecting the Main Chain or RingThe parent, or base, name of a polyfunctional organic compound is usuallyeasy to identify. If the principal group of highest priority is part of an openchain, the parent name is that of the longest chain containing the largest num-ber of principal groups. For example, compounds 6 and 7 are isomeric alde-hydo amides, which must be named as amides rather than as aldehydesaccording to Table A.2. The longest chain in compound 6 has six carbons, andthe substance is therefore named 5-methyl-6-oxohexanamide. Compound 7also has a chain of six carbons, but the longest chain that contains both prin-cipal functional groups has only four carbons. The correct name of 7 is 4-oxo-3-propylbutanamide.

If the highest-priority principal group is attached to a ring, the parentname is that of the ring system. Compounds 8 and 9, for instance, are isomericketo nitriles and must both be named as nitriles according to Table A.2. Sub-stance 8 is named as a benzonitrile because the –CN functional group is a substituent on the aromatic ring, but substance 9 is named as an acetonitrilebecause the –CN functional group is on an open chain. The correct names are

6. 5-Methyl-6-oxohexanamide

HCCHCH2CH2CH2CNH2

OO

CH3

7. 4-Oxo-3-propylbutanamide

CH3CH2CH2CHCH2CNH2

OCHO

1. Methyl 4-oxopentanoate

(an ester with a ketone group)2. 5-Aminopentan-2-ol

(an alcohol with an amine group)

CH3CCH2CH2COCH3

OO

CH3CHCH2CH2CH2NH2

OH

3. Methyl 5-methyl-6-oxohexanoate

(an ester with an aldehyde group)

CH3CHCH2CH2CH2COCH3

OCHO

4. 5-Carbamoyl-4-hydroxypentanoic acid

(a carboxylic acid with amide and alcohol groups)

O OH

H2NCCH2CHCH2CH2COH

O

CHO

O

5. 3-Oxocyclohexanecarbaldehyde

(an aldehyde with a ketone group)

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2-acetyl-(4-bromomethyl)benzonitrile (8) and (2-acetyl-4-bromophenyl)-acetonitrile (9). As further examples, compounds 10 and 11 are both ketoacids and must be named as acids, but the parent name in (10) is that of a ringsystem (cyclohexanecarboxylic acid) and the parent name in (11) is that of anopen chain (propanoic acid). The full names are trans-2-(3-oxopropyl)cyclo-hexanecarboxylic acid (10) and 3-(2-oxocyclohexyl)propanoic acid (11).

Name Parts 3 and 4. The Prefixes and LocantsWith parent name and suffix established, the next step is to identify and givenumbers, or locants, to all substituents on the parent chain or ring. These sub-stituents include all alkyl groups and all functional groups other than the onecited in the suffix. For example, compound 12 contains three different func-tional groups (carboxyl, keto, and double bond). Because the carboxyl groupis highest in priority and because the longest chain containing the functionalgroups has seven carbons, compound 12 is a heptenoic acid. In addition, themain chain has a keto (oxo) substituent and three methyl groups. Numberingfrom the end nearer the highest-priority functional group, compound 12 isnamed (E)-2,5,5-trimethyl-4-oxohept-2-enoic acid. Look back at some of theother compounds we’ve named to see other examples of how prefixes andlocants are assigned.

Writing the NameOnce the name parts have been established, the entire name is written out.Several additional rules apply:

1. Order of prefixes When the substituents have been identified, the mainchain has been numbered, and the proper multipliers such as di- and tri-have been assigned, the name is written with the substituents listed in

O CH3

CH3H3C

CCCCH3CH2 C

H

CO2H12. (E)-2,5,5-Trimethyl-4-oxohept-2-enoic acid

O

CCH3

CN

BrCH2

O

CCH3

CH2CN

Br

O

CO2HCHO

CO2H

H

H

8. 2-Acetyl-(4-bromomethyl)benzonitrile 9. (2-Acetyl-4-bromophenyl)acetonitrile

10. trans-2-(3-oxopropyl)cyclo-

hexanecarboxylic acid

11. 3-(2-Oxocyclohexyl)propanoic acid

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alphabetical, rather than numerical, order. Multipliers such as di- and tri-are not used for alphabetization purposes, but the prefix iso- is used.

2. Use of hyphens; single- and multiple-word names The general rule is todetermine whether the parent is itself an element or compound. If it is,then the name is written as a single word; if it isn’t, then the name is writ-ten as multiple words. Methylbenzene is written as one word, forinstance, because the parent—benzene—is itself a compound. Diethylether, however, is written as two words because the parent—ether—is aclass name rather than a compound name. Some further examples follow:

3. Parentheses Parentheses are used to denote complex substituents whenambiguity would otherwise arise. For example, chloromethylbenzenehas two substituents on a benzene ring, but (chloromethyl)benzene hasonly one complex substituent. Note that the expression in parentheses isnot set off by hyphens from the rest of the name.

18. p-Chloromethylbenzene

20. 2-(1-Methylpropyl)pentanedioic acid

HOCCHCH2CH2COH

O O

CH3CHCH2CH3

CH3

Cl

19. (Chloromethyl)benzene

CH2Cl

15. Isopropyl 3-hydroxypropanoate

(two words, because “propanoate”is not a compound)

14. Dimethylmagnesium

(one word, becausemagnesium is an element)

16. 4-(Dimethylamino)pyridine

(one word, because pyridineis a compound)

HOCH2CH2COCHCH3

O

CH3

Mg CH3H3C

N

CH3

CH3

N

17. Methyl cyclopentanecarbothioate

(two words, because “cyclopentane-carbothioate” is not a compound)

C

O

SCH3

OH

CH3

H2NCH2CH2CHCHCH3 13. 5-Amino-3-methylpentan-2-ol

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ADDITIONAL READING

Further explanations of the rules of organic nomenclature can be foundonline at http://www.acdlabs.com/iupac/nomenclature/ and in the followingreferences:

1. “A Guide to IUPAC Nomenclature of Organic Compounds,” CRC Press,Boca Raton, FL, 1993.

2. “Nomenclature of Organic Chemistry, Sections A, B, C, D, E, F, and H,”International Union of Pure and Applied Chemistry, Pergamon Press,Oxford, 1979.

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AppendixAcidity Constants for Some

Organic Compounds

B

Compound pKa

CH3SO3H �1.8

CH(NO2)3 0.1

0.3

CCl3CO2H 0.5

CF3CO2H 0.5

CBr3CO2H 0.7

HO2CCmCCO2H 1.2; 2.5

HO2CCO2H 1.2; 3.7

CHCl2CO2H 1.3

CH2(NO2)CO2H 1.3

HCmCCO2H 1.9

Z HO2CCHUCHCO2H 1.9; 6.3

2.4

CH3COCO2H 2.4

NCCH2CO2H 2.5

CH3CmCCO2H 2.6

CH2FCO2H 2.7

CO2H

NO2

OH

NO2

NO2

O2N

Compound pKa

CH2ClCO2H 2.8

HO2CCH2CO2H 2.8; 5.6

CH2BrCO2H 2.9

3.0

3.0

CH2ICO2H 3.2

CHOCO2H 3.2

3.4

3.5

HSCH2CO2H 3.5; 10.2

CH2(NO2)2 3.6

CH3OCH2CO2H 3.6

CH3COCH2CO2H 3.6

HOCH2CO2H 3.7

HCO2H 3.7

CO2HO2N

O2N

CO2HO2N

CO2H

OH

CO2H

Cl

Compound pKa

3.8

4.0

CH3BrCH2CO2H 4.0

4.1

4.2

H2CUCHCO2H 4.2

HO2CCH2CH2CO2H 4.2; 5.7

HO2CCH2CH2CH2CO2H 4.3; 5.4

4.5

H2CUC(CH3)CO2H 4.7

CH3CO2H 4.8

OH

Cl

Cl

Cl

Cl

Cl

CO2H

OH

O2N NO2

CO2HCl

CO2H

Cl

A–9(Continued)

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A–10 A P P E N D I X B: AC I D I T Y C O N S TA N T S F O R S O M E O R G A N I C C O M P O U N D S

Compound pKa

CH3CH2CO2H 4.8

(CH3)3CCO2H 5.0

CH3COCH2NO2 5.1

5.3

O2NCH2CO2CH3 5.8

5.8

6.2

6.6

HCO3H 7.1

7.2

(CH3)2CHNO2 7.7

7.8

CH3CO3H 8.2

8.5

CH3CH2NO2 8.5

8.7

An acidity list covering more than 5000 organic compounds has been published: E.P. Serjeant and B. Dempsey (eds.), “Ionization Constants ofOrganic Acids in Aqueous Solution,” IUPAC Chemical Data Series No. 23, Pergamon Press, Oxford, 1979.

OHF3C

Cl

OH

OH

Cl

Cl

OH

NO2

SH

OH

Cl

Cl

Cl

O

CHO

O

O

Compound pKa

CH3COCH2COCH3 9.0

9.3; 11.1

9.3; 12.6

9.4

9.9; 11.5

9.9

CH3COCH2SOCH3 10.0

10.3

CH3NO2 10.3

CH3SH 10.3

CH3COCH2CO2CH3 10.6

CH3COCHO 11.0

CH2(CN)2 11.2

CCl3CH2OH 12.2

Glucose 12.3

(CH3)2CUNOH 12.4

CH2(CO2CH3)2 12.9

CHCl2CH2OH 12.9

CH2(OH)2 13.3

HOCH2CH(OH)CH2OH 14.1

CH2ClCH2OH 14.3

15.0

OH

CH3

OH

OH

HO

CH2SH

OH

OH

HO OH

Compound pKa

15.4

CH3OH 15.5

H2CUCHCH2OH 15.5

CH3CH2OH 16.0

CH3CH2CH2OH 16.1

CH3COCH2Br 16.1

16.7

CH3CHO 17

(CH3)2CHCHO 17

(CH3)2CHOH 17.1

(CH3)3COH 18.0

CH3COCH3 19.3

23

CH3CO2CH2CH3 25

HCmCH 25

CH3CN 25

CH3SO2CH3 28

(C6H5)3CH 32

(C6H5)2CH2 34

CH3SOCH3 35

NH3 36

CH3CH2NH2 36

(CH3CH2)2NH 40

41

43

H2CUCH2 44

CH4 �60

CH3

O

CH2OH

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AppendixGlossary

C

A-11

Absolute configuration (Section 9.5): The exact three-dimensional structure of a chiral molecule. Absolute con-figurations are specified verbally by the Cahn–Ingold–Prelog R,S convention.

Absorbance (Section 11.9): In optical spectroscopy, thelogarithm of the intensity of the incident light divided bythe intensity of the light transmitted through a sample;A � log I0/I.

Absorption spectrum (Section 11.5): A plot of wave-length of incident light versus amount of light absorbed.Organic molecules show absorption spectra in both theinfrared and the ultraviolet regions of the electro-magnetic spectrum.

Acetal (Section 14.8): A functional group consisting oftwo –OR groups bonded to the same carbon, R2C(OR�)2.Acetals are often used as protecting groups for ketonesand aldehydes.

Acetoacetic ester synthesis (Section 17.4): The synthesisof a methyl ketone by alkylation of an alkyl halide, fol-lowed by hydrolysis and decarboxylation.

Acetyl group (Section 14.1): The CH3CO– group.

Acetylide anion (Section 7.12): The anion formed byremoval of a proton from a terminal alkyne.

Achiral (Section 9.2): Having a lack of handedness. Amolecule is achiral if it has a plane of symmetry and isthus superimposable on its mirror image.

Acid anhydride (Chapter 16 Introduction): A functionalgroup with two acyl groups bonded to a common oxygenatom, RCO2COR�.

Acid halide (Chapter 16 Introduction): A functional groupwith an acyl group bonded to a halogen atom, RCOX.

Acidity constant, Ka (Section 2.8): A measure of acidstrength in water. For any acid HA, the acidity constant is

given by the expression Ka � Keq[H2O] � .

Activating group (Section 8.8): An electron-donatinggroup such as hydroxyl (–OH) or amino (–NH2) thatincreases the reactivity of an aromatic ring towardelectrophilic aromatic substitution.

Activation energy, �G‡ (Section 5.9): The difference inenergy between ground state and transition state in a reac-tion. The amount of activation energy determines the rateat which the reaction proceeds. Most organic reactionshave activation energies of 40–100 kJ/mol.

Active site (Sections 5.11, 19.10): The pocket in an enzymewhere a substrate is bound and undergoes reaction.

Acyl group (Sections 8.7, 14.1): A –COR group.

Acyl phosphate (Chapter 16 Introduction): A functionalgroup with an acyl group bonded to a phosphate,RCOPO3

2�.

Acylation (Section 8.7): The introduction of an acylgroup, –COR, onto a molecule. For example, acylation ofan alcohol yields an ester, acylation of an amine yields anamide, and acylation of an aromatic ring yields an alkylaryl ketone.

Adams catalyst (Section 7.5): The PtO2 catalyst used foralkene hydrogenations.

1,2-Addition (Sections 7.11, 14.11): The addition of areactant to the two ends of a double bond.

1,4-Addition (Sections 7.11, 14.11): Addition of a reactantto the ends of a conjugated � system. Conjugated dienesyield 1,4-adducts when treated with electrophiles such as

[H3O�][A�]

[HA]

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Alkylation (Sections 8.7, 17.4): Introduction of an alkylgroup onto a molecule. For example, aromatic rings canbe alkylated to yield arenes, and enolate anions can bealkylated to yield �-substituted carbonyl compounds.

Alkyne (Chapter 6 Introduction): A hydrocarbon that con-tains a carbon–carbon triple bond, RCmCR.

Allyl group (Section 6.2): A H2CUCHCH2X substituent.

Allylic (Section 7.11): The position next to a double bond.For example, H2CUCHCH2Br is an allylic bromide.

�-Amino acid (Section 19.1): A difunctional compoundwith an amino group on the carbon atom next to a car-boxyl group, RCH(NH2)CO2H.

� Anomer (Section 21.5): The cyclic hemiacetal form of asugar that has the hemiacetal –OH group on the side of thering opposite the terminal –CH2OH.

� Helix (Section 19.8): A coiled secondary structure of aprotein.

� Position (Chapter 17 Introduction): The position next toa carbonyl group.

�-Substitution reaction (Section 17.2): The substitutionof the � hydrogen atom of a carbonyl compound by reac-tion with an electrophile.

Amide (Chapter 16 Introduction): A compound contain-ing the –CONR2 functional group.

Amidomalonate synthesis (Section 19.3): A method forpreparing an �-amino acid by alkylation of diethyl amido-malonate with an alkyl halide.

Amine (Chapter 18 Introduction): A compound contain-ing one or more organic substituents bonded to a nitrogenatom, RNH2, R2NH, or R3N.

Amino acid (See �-Amino acid; Section 19.1)

Amino sugar (Section 21.7): A sugar with one of its –OHgroups replaced by –NH2.

Amphiprotic (Section 19.1): Capable of acting either as anacid or as a base. Amino acids are amphiprotic.

Amplitude (Section 11.5): The height of a wave measuredfrom the midpoint to the maximum. The intensity of radiantenergy is proportional to the square of the wave’s amplitude.

Anabolism (Section 20.1): The group of metabolic path-ways that build up larger molecules from smaller ones.

Androgen (Section 23.9): A male steroid sex hormone.

Angle strain (Section 4.3): The strain introduced into amolecule when a bond angle is deformed from its idealvalue. Angle strain is particularly important in small-ring

HCl. Conjugated enones yield 1,4-adducts when treatedwith nucleophiles such as amines.

Addition reaction (Section 5.1): The reaction that occurswhen two reactants add together to form a single newproduct with no atoms “left over.”

Adrenocortical hormone (Section 23.9): A steroid hor-mone secreted by the adrenal glands. There are two types of adrenocortical hormones: mineralocorticoidsand glucocorticoids.

Alcohol (Chapter 13 Introduction): A compound with an–OH group bonded to a saturated, alkane-like carbon,ROH.

Aldaric acid (Section 21.6): The dicarboxylic acid result-ing from oxidation of an aldose.

Aldehyde (Chapter 14 Introduction): A compound con-taining the –CHO functional group.

Alditol (Section 21.6): The polyalcohol resulting fromreduction of the carbonyl group of a sugar.

Aldol reaction (Section 17.5): The carbonyl condensationreaction of an aldehyde or ketone to give a �-hydroxycarbonyl compound.

Aldonic acid (Section 21.6): The monocarboxylic acidresulting from oxidation of the aldehyde group of an aldose.

Aldose (Section 21.1): A carbohydrate with an aldehydefunctional group.

Alicyclic (Section 4.1): An aliphatic cyclic hydrocarbonsuch as a cycloalkane or cycloalkene.

Aliphatic (Section 3.2): A nonaromatic hydrocarbon suchas a simple alkane, alkene, or alkyne.

Alkaloid (Chapter 2 Lagniappe): A naturally occurringorganic base, such as morphine.

Alkane (Section 3.2): A compound of carbon and hydro-gen that contains only single bonds.

Alkene (Chapter 6 Introduction): A hydrocarbon that con-tains a carbon–carbon double bond, R2CUCR2.

Alkoxide ion (Section 13.2): The anion RO� formed bydeprotonation of an alcohol.

Alkyl group (Section 3.3): The partial structure thatremains when a hydrogen atom is removed from an alkane.

Alkyl halide (Chapter 10 Introduction): A compound witha halogen atom bonded to a saturated, sp3-hybridizedcarbon atom.

Alkylamine (Section 18.1): An amino-substituted alkane,RNH2, R2NH, or R3N.

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cycloalkanes, where it results from compression of bondangles to less than their ideal tetrahedral values.

Anomeric center (Section 21.5): The hemiacetal carbonatom in the cyclic pyranose or furanose form of a sugar.

Anomers (Section 21.5): Cyclic stereoisomers of sugarsthat differ only in their configuration at the hemiacetal(anomeric) carbon.

Anti conformation (Section 3.7): The geometric arrange-ment around a carbon–carbon single bond in which thetwo largest substituents are 180° apart as viewed in aNewman projection.

Anti periplanar (Section 10.11): Describing a stereochem-ical relationship whereby two bonds on adjacent carbonslie in the same plane at an angle of 180°.

Anti stereochemistry (Section 7.2): The opposite of syn.An anti addition reaction is one in which the two ends ofthe double bond are attacked from different sides. An antielimination reaction is one in which the two groups leavefrom opposite sides of the molecule.

Antiaromatic (Section 8.3): Describing a planar, appar-ently conjugated molecule with 4n � electrons. Delocal-ization of the � electrons leads to an increase in energy.

Antibonding MO (Section 1.11): A molecular orbital thatis higher in energy than the atomic orbitals from which itis formed.

Anticodon (Section 24.5): A sequence of three bases ontRNA that reads the codons on mRNA and brings the cor-rect amino acids into position for protein synthesis.

Antisense strand (Section 24.4): The template strand ofdouble-helical DNA that does not contain the gene.

Arene (Section 8.1): An alkyl-substituted benzene.

Aromatic (Chapter 8 Introduction): The special character-istics of cyclic conjugated molecules, including unusualstability and a tendency to undergo substitution reactionsrather than addition reactions on treatment with electro-philes. Aromatic molecules are planar, cyclic, conjugatedspecies that have 4n � 2 � electrons.

Arylamine (Section 18.1): An amino-substituted aromaticcompound, ArNH2.

Atomic mass (Section 1.1): The average mass number ofthe atoms of an element.

Atomic number, Z (Section 1.1): The number of protonsin the nucleus of an atom.

ATZ derivative (Section 19.6): An anilinothiazolinone,formed from an amino acid during Edman degradation.

Axial position (Section 4.6): A bond to chair cyclohexanethat lies along the ring axis perpendicular to the roughplane of the ring.

Backbone (Section 19.4): The continuous chain of atomsrunning the length of a protein or other polymer.

Base peak (Section 11.1): The most intense peak in a massspectrum.

Basicity constant, Kb (Section 18.3): A measure of basestrength in water. For any base B, the basicity constant is

given by the expression Kb � .

Bent bonds (Section 4.4): The bonds in small rings such ascyclopropane that bend away from the internuclear lineand overlap at a slight angle, rather than head-on. Bentbonds are highly strained and highly reactive.

Benzoyl group (Section 14.1): The C6H5CO– group.

Benzyl group (Section 8.1): The C6H5CH2– group.

Benzylic (Section 8.9): The position next to an aromatic ring.

� Anomer (Section 21.5): The cyclic hemiacetal form of asugar that has the hemiacetal –OH group on the same sideof the ring as the terminal –CH2OH.

� Diketone (Section 17.3): A 1,3-diketone.

�-Keto ester (Section 17.3): A 3-keto ester.

�-Oxidation pathway (Section 23.5): The metabolic path-way for degrading fatty acids.

�-Pleated sheet (Section 19.8): A type of secondary struc-ture of a protein.

Bimolecular reaction (Section 10.5): A reaction whoserate-limiting step occurs between two reactants.

Boat cyclohexane (Section 4.5): A conformation of cyclo-hexane that bears a slight resemblance to a boat. Boatcyclohexane has no angle strain but has a large number ofeclipsing interactions that make it less stable than chaircyclohexane.

Boc derivative (Section 19.7): A butyloxycarbonyl N-protected amino acid.

Bond angle (Section 1.6): The angle formed between twoadjacent bonds.

Bond dissociation energy, D (Section 5.8): The amount ofenergy needed to break a bond and produce two radicalfragments.

Bond length (Section 1.5): The equilibrium distancebetween the nuclei of two atoms that are bonded to eachother.

[BH�][OH�][B]

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Bond strength (Section 1.5): An alternative name for bonddissociation energy.

Bonding MO (Section 1.11): A molecular orbital that islower in energy than the atomic orbitals from which it isformed.

Branched-chain alkane (Section 3.2): An alkane that con-tains a branching connection of carbons as opposed to astraight-chain alkane.

Bridgehead atom (Section 4.9): An atom that is shared bymore than one ring in a polycyclic molecule.

Bromohydrin (Section 7.3): A 1,2-disubstituted bromo-alcohol; obtained by addition of HOBr to an alkene.

Bromonium ion (Section 7.2): A species with a divalent,positively charged bromine, R2Br�.

Brønsted–Lowry acid (Section 2.7): A substance thatdonates a hydrogen ion (proton; H�) to a base.

Brønsted–Lowry base (Section 2.7): A substance thataccepts H� from an acid.

C-terminal amino acid (Section 19.4): The amino acidwith a free –CO2H group at the end of a protein chain.

Cahn–Ingold–Prelog sequence rules (Sections 6.4, 9.5): Aseries of rules for assigning relative priorities to sub-stituent groups on a double-bond carbon atom or on a chi-rality center.

Cannizzaro reaction (Section 14.10): The disproportiona-tion reaction of an aldehyde to yield an alcohol and a car-boxylic acid on treatment with base.

Carbanion (Sections 13.3, 14.6): A carbon anion, or sub-stance that contains a trivalent, negatively charged carbonatom (R3C:�). Carbanions are sp3-hybridized and have eightelectrons in the outer shell of the negatively charged carbon.

Carbinolamine (Section 14.7): A molecule that containsthe R2C(OH)NH2 functional group. Carbinolamines areproduced as intermediates during the nucleophilic addi-tion of amines to carbonyl compounds.

Carbocation (Sections 5.5, 6.8): A carbon cation, or sub-stance that contains a trivalent, positively charged carbonatom having six electrons in its outer shell (R3C�).

Carbohydrate (Chapter 21 Introduction): A polyhydroxyaldehyde or ketone. Carbohydrates can be either simplesugars, such as glucose, or complex sugars, such as cellulose.

Carbonyl condensation reaction (Section 17.5): A reactionthat joins two carbonyl compounds together by a combina-tion of �-substitution and nucleophilic addition reactions.

Carbonyl group (Preview of Carbonyl Chemistry): TheC�O functional group.

Carboxyl group (Section 15.1): The –CO2H functionalgroup.

Carboxylation (Section 15.5): The addition of CO2 to amolecule.

Carboxylic acid (Chapter 15 Introduction): A compoundcontaining the –CO2H functional group.

Carboxylic acid derivative (Chapter 16 Introduction): Acompound in which an acyl group is bonded to an electro-negative atom or substituent that can act as a leavinggroup in a substitution reaction. Esters, amides, and acidhalides are examples.

Catabolism (Section 20.1): The group of metabolic path-ways that break down larger molecules into smaller ones.

Cation radical (Section 11.1): A species typically formedin a mass spectrometer, having both a positive charge andan odd number of electrons.

Chain-growth polymer (Sections 7.8, 16.9): A polymerwhose bonds are produced by chain reactions. Poly-ethylene and other alkene polymers are examples.

Chain reaction (Section 5.3): A reaction that, once initi-ated, sustains itself in an endlessly repeating cycle ofpropagation steps. The radical chlorination of alkanes isan example of a chain reaction that is initiated by irradia-tion with light and then continues in a series of propaga-tion steps.

Chair conformation (Section 4.5): A three-dimensionalconformation of cyclohexane that resembles the roughshape of a chair. The chair form of cyclohexane is the lowest-energy conformation of the molecule.

Chemical shift (Section 12.3): The position on the NMRchart where a nucleus absorbs. By convention, the chemi-cal shift of tetramethylsilane (TMS) is set at zero, and allother absorptions usually occur downfield (to the left onthe chart). Chemical shifts are expressed in delta units, �, where 1 � equals 1 ppm of the spectrometer operatingfrequency.

Chiral (Section 9.2): Having handedness. Chiral mole-cules are those that do not have a plane of symmetry andare therefore not superimposable on their mirror image. Achiral molecule thus exists in two forms, one right-handed and one left-handed. The most common cause ofchirality in a molecule is the presence of a carbon atomthat is bonded to four different substituents.

Chirality center (Section 9.2): An atom (usually carbon)that is bonded to four different groups.

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Chromatography (Chapter 11 Lagniappe, Section 19.5): Atechnique for separating a mixture of compounds intopure components. Different compounds adsorb to a sta-tionary support phase and are then carried along it at dif-ferent rates by a mobile phase.

Cis–trans isomers (Sections 4.2, 6.3): Stereoisomers thatdiffer in their stereochemistry about a double bond orring.

Citric acid cycle (Section 22.4): The metabolic pathwayby which acetyl CoA is degraded to CO2.

Claisen condensation reaction (Section 17.8): Thecarbonyl condensation reaction of an ester to give a �-ketoester product.

Coding strand (Section 24.4): The strand of double-helical DNA that contains the gene.

Codon (Section 24.5): A three-base sequence on a messen-ger RNA chain that encodes the genetic information nec-essary to cause a specific amino acid to be incorporatedinto a protein. Codons on mRNA are read by complemen-tary anticodons on tRNA.

Coenzyme (Section 19.9): A small organic molecule thatacts as a cofactor.

Cofactor (Section 19.9): A small nonprotein part of anenzyme that is necessary for biological activity.

Combinatorial chemistry (Chapter 8 Lagniappe): A tech-nique for preparing anywhere from a few dozen to severalhundred thousand substances simultaneously.

Complex carbohydrate (Section 21.1): A carbohydratethat is made of two or more simple sugars linked together.

Condensed structure (Sections 1.12, 3.2): A shorthandway of writing structures in which C–H and C–C bondsare understood rather than shown explicitly. Propane, forexample, has the condensed structure CH3CH2CH3.

Configuration (Section 9.5): The three-dimensionalarrangement of atoms bonded to a chirality center.

Conformation (Section 3.6): The three-dimensional shapeof a molecule at any given instant, assuming that rotationaround single bonds is frozen.

Conformational analysis (Section 4.8): A means of assess-ing the energy of a substituted cycloalkane by totaling thesteric interactions present in the molecule.

Conjugate acid (Section 2.7): The product that resultsfrom protonation of a Brønsted–Lowry base.

Conjugate addition (Section 14.11): Addition of a nucleo-phile to the � carbon atom of an �,�-unsaturated carbonylcompound.

Conjugate base (Section 2.7): The anion that results fromdeprotonation of a Brønsted–Lowry acid.

Conjugation (Section 7.10): A series of overlapping p orbitals, usually in alternating single and multiplebonds. For example, buta-1,3-diene is a conjugated diene,but-3-en-2-one is a conjugated enone, and benzene is acyclic conjugated triene.

Constitutional isomers (Sections 3.2, 9.9): Isomers that havetheir atoms connected in a different order. For example,butane and 2-methylpropane are constitutional isomers.

Coupled reactions (Section 20.1): Two reactions thatshare a common intermediate so that the energy releasedin the favorable step allows the unfavorable step to occur.

Coupling constant, J (Section 12.11): The magnitude(expressed in hertz) of the interaction between nucleiwhose spins are coupled.

Covalent bond (Section 1.4): A bond formed by sharingelectrons between atoms.

Cyanohydrin (Section 15.7): A compound with an –OHgroup and a –CN group bonded to the same carbon atom;formed by addition of HCN to an aldehyde or ketone.

Cycloalkane (Section 4.1): An alkane that contains a ringof carbons.

D Sugar (Section 21.3): A sugar whose hydroxyl group atthe chirality center farthest from the carbonyl grouppoints to the right when drawn in Fischer projection.

d,l form (Section 9.8): The racemic form of a chiral compound.

Deactivating group (Section 8.8): An electron-withdrawingsubstituent that decreases the reactivity of an aromatic ringtoward electrophilic aromatic substitution.

Deamination (Section 20.2): The removal of an aminogroup from a molecule, as occurs with amino acids duringmetabolic degradation.

Decarboxylation (Section 17.4): The loss of carbon diox-ide from a molecule. �-Keto acids decarboxylate readilyon heating.

Degree of unsaturation (Section 6.1): The number of ringsand/or multiple bonds in a molecule.

Dehydration (Sections 7.1, 13.4): The loss of water froman alcohol to yield an alkene.

Dehydrohalogenation (Sections 7.1, 10.10): The loss ofHX from an alkyl halide. Alkyl halides undergo dehydro-halogenation to yield alkenes on treatment with strongbase.

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Delocalization (Section 7.10): A spreading out of electrondensity over a conjugated � electron system. For exam-ple, allylic cations and allylic anions are delocalizedbecause their charges are spread out over the entire � electron system.

Delta scale (Section 12.3): An arbitrary scale used to cali-brate NMR charts. One delta unit (�) is equal to 1 part permillion (ppm) of the spectrometer operating frequency.

Denatured (Section 19.8): The physical changes thatoccur in a protein when secondary and tertiary structuresare disrupted.

Deoxy sugar (Section 21.7): A sugar with one of its –OHgroups replaced by an –H.

Deoxyribonucleic acid, DNA (Section 24.1): The biopolymerconsisting of deoxyribonucleotide units linked togetherthrough phosphate–sugar bonds. Found in the nucleus ofcells, DNA contains an organism’s genetic information.

DEPT-NMR (Section 12.6): An NMR method for distin-guishing among signals due to CH3, CH2, CH, and quater-nary carbons. That is, the number of hydrogens attachedto each carbon can be determined.

Deshielding (Section 12.2): An effect observed in NMRthat causes a nucleus to absorb downfield (to the left) oftetramethylsilane (TMS) standard. Deshielding is causedby a withdrawal of electron density from the nucleus.

Deuterium isotope effect (Section 10.11): A tool used inmechanistic investigations to establish whether a C–Hbond is broken in the rate-limiting step of a reaction.

Dextrorotatory (Section 9.3): A word used to describe anoptically active substance that rotates the plane of polar-ization of plane-polarized light in a right-handed (clock-wise) direction.

Diastereomers (Section 9.6): Non–mirror-image stereo-isomers; diastereomers have the same configuration at oneor more chirality centers but differ at other chirality centers.

Diastereotopic (Section 12.8): Two hydrogens in a mole-cule whose replacement by some other group leads to dif-ferent diastereomers.

1,3-Diaxial interaction (Section 4.7): The strain energycaused by a steric interaction between axial groups threecarbon atoms apart in chair cyclohexane.

Dideoxy method (Section 24.6): A biochemical methodfor sequencing DNA strands.

Dieckmann cyclization reaction (Section 17.9): Anintramolecular Claisen condensation reaction to give acyclic �-keto ester.

Digestion (Section 20.1): The first stage of catabolism, inwhich food is broken down by hydrolysis of ester, glyco-side (acetal), and peptide (amide) bonds to yield fattyacids, simple sugars, and amino acids.

Dihedral angle (Section 3.6): The angle between C–Hbonds on front and back carbons as viewed end-on.

Dipole moment, � (Section 2.2): A measure of the netpolarity of a molecule. A dipole moment arises when thecenters of mass of positive and negative charges within amolecule do not coincide.

Disaccharide (Section 21.8): A carbohydrate formed bylinking two simple sugars through an acetal bond.

Disulfide (Section 13.6): A compound of the generalstructure RSSR�.

DNA (See Deoxyribonucleic acid; Section 24.1)

Double helix (Section 24.2): The structure of DNA inwhich two polynucleotide strands coil around each other.

Doublet (Section 12.11): A two-line NMR absorptioncaused by spin–spin splitting when the spin of thenucleus under observation couples with the spin of aneighboring magnetic nucleus.

Downfield (Section 12.3): Referring to the left-hand por-tion of the NMR chart.

E geometry (Section 6.4): A term used to describe the stereo-chemistry of a carbon–carbon double bond. The two groupson each carbon are assigned priorities according to theCahn–Ingold–Prelog sequence rules, and the two carbons arecompared. If the high-priority groups on each carbon are onopposite sides of the double bond, the bond has E geometry.

E1 reaction (Section 10.12): A unimolecular eliminationreaction in which the C–X bond breaks before the C–Hbond, giving a carbocation intermediate.

E1cB reaction (Section 10.12): A unimolecular elimina-tion reaction in which the C–H bond breaks before theC–X bond, giving a carbanion intermediate.

E2 reaction (Section 10.11): A bimolecular eliminationreaction in which C–H and C–X bond cleavage aresimultaneous.

Eclipsed conformation (Section 3.6): The geometricarrangement around a carbon–carbon single bond inwhich the bonds to substituents on one carbon are paral-lel to the bonds to substituents on the neighboring carbonas viewed in a Newman projection.

Edman degradation (Section 19.6): A method for N-terminalsequencing of peptide chains.

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Eicosanoid (Section 23.7): A class of compounds consist-ing of prostaglandins, thromboxanes, and leukotrienes,which are derived biologically from arachidonic acid.

Electromagnetic spectrum (Section 11.5): The range ofelectromagnetic energy, including infrared, ultraviolet,and visible radiation.

Electron configuration (Section 1.3): A list of the orbitalsoccupied by electrons in an atom.

Electron-dot structure (Section 1.4): A representation of amolecule showing valence electrons as dots.

Electron-transport chain (Section 20.1): The final stage ofcatabolism in which ATP is produced.

Electronegativity, EN (Section 2.1): The ability of an atomto attract electrons in a covalent bond. Electronegativityincreases across the periodic table from right to left andfrom bottom to top.

Electrophile (Section 5.4): An “electron-lover,” or sub-stance that accepts an electron pair from a nucleophile ina polar bond-forming reaction.

Electrophilic addition reaction (Section 6.6): The additionof an electrophile to an alkene to yield a saturated product.

Electrophilic aromatic substitution reaction (Section 8.6):A reaction in which an electrophile (E�) reacts with an aromatic ring and substitutes for one of the ringhydrogens.

Electrophoresis (Sections 19.2, 24.6): A technique usedfor separating charged organic molecules, particularlyproteins and DNA fragments. The mixture to be separatedis placed on a buffered gel or paper, and an electric poten-tial is applied across the ends of the apparatus. Negativelycharged molecules migrate toward the positive electrode,and positively charged molecules migrate toward the neg-ative electrode.

Electrostatic potential map (Section 2.1): A molecularrepresentation that uses color to indicate the charge dis-tribution in the molecule as derived from quantum-mechanical calculations.

Elimination reaction (Section 5.1): What occurs when asingle reactant splits into two products.

Elution (Chapter 11 Lagniappe): The removal of a sub-stance from a chromatography column.

Embden–Meyerhof pathway (Section 22.2): An alterna-tive name for glycolysis.

Enamine (Section 14.7): A compound with theR2NXCRUCR2 functional group.

Enantiomers (Section 9.1): Stereoisomers of a chiral sub-stance that have a mirror-image relationship. Enantiomershave opposite configurations at all chirality centers.

Enantioselective synthesis (Chapter 14 Lagniappe, Sec-tion 19.3): A method of synthesis from an achiral precur-sor that yields only a single enantiomer of a chiralproduct.

Enantiotopic (Section 12.8): Two hydrogens in a moleculewhose replacement by some other group leads to differentenantiomers.

3� End (Section 24.1): The end of a nucleic acid chain witha free hydroxyl group at C3�.

5� End (Section 24.1): The end of a nucleic acid chain witha free hydroxyl group at C5�.

Endergonic (Section 5.7): A reaction that has a positivefree-energy change and is therefore nonspontaneous. In areaction energy diagram, the product of an endergonicreaction has a higher energy level than the reactants.

Endothermic (Section 5.7): A reaction that absorbs heatand therefore has a positive enthalpy change.

Enol (Section 17.1): A vinylic alcohol that is in equilib-rium with a carbonyl compound.

Enolate ion (Section 17.1): The anion of an enol,CUCXO�.

Enthalpy change, �H (Section 5.7): The heat of reaction.The enthalpy change that occurs during a reaction is ameasure of the difference in total bond energy betweenreactants and products.

Entropy change, �S (Section 5.7): The change in amountof molecular disorder. The entropy change that occursduring a reaction is a measure of the difference in disorderbetween reactants and products.

Enzyme (Sections 5.11, 19.9): A biological catalyst.Enzymes are large proteins that catalyze specific bio-chemical reactions.

Epimers (Section 9.6): Diastereomers that differ in config-uration at only one chirality center but are the same at allothers.

Epoxide (Section 7.6): A three-membered-ring ether func-tional group.

Equatorial position (Section 4.6): A bond to cyclohexanethat lies along the rough equator of the ring.

ESI (Section 11.4): Electrospray ionization, a “soft” ion-ization method used for mass spectrometry of biologicalsamples of very high molecular weight.

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Essential amino acid (Section 20.5): One of nine aminoacids that are biosynthesized only in plants and micro-organisms and must be obtained by humans in the diet.

Essential oil (Chapter 6 Lagniappe): The volatile oilobtained by steam distillation of a plant extract.

Ester (Chapter 16 Introduction): A compound containingthe –CO2R functional group.

Estrogen (Section 23.9): A female steroid sex hormone.

Ether (Chapter 13 Introduction): A compound that hastwo organic substituents bonded to the same oxygenatom, ROR�.

Exergonic (Section 5.7): A reaction that has a negativefree-energy change and is therefore spontaneous. On areaction energy diagram, the product of an exergonic reac-tion has a lower energy level than that of the reactants.

Exon (Section 24.4): A section of DNA that containsgenetic information.

Exothermic (Section 5.7): A reaction that releases heatand therefore has a negative enthalpy change.

Fat (Section 23.1): A solid triacylglycerol derived from ananimal source.

Fatty acid (Section 23.1): A long, straight-chain car-boxylic acid found in fats and oils.

Fatty acid–derived substance (Section 25.1): A naturalproduct biosynthesized from a fatty acid. Eicosanoids areexamples.*

Fibrous protein (Section 19.8): A protein that consists ofpolypeptide chains arranged side by side in long threads.Such proteins are tough, insoluble in water, and used innature for structural materials such as hair, hooves, andfingernails.

Fingerprint region (Section 11.7): The complex region ofthe infrared spectrum from 1500 to 400 cm�1.

First-order reaction (Section 10.7): A reaction whose rate-limiting step is unimolecular and whose kinetics there-fore depend on the concentration of only one reactant.

Fischer esterification reaction (Section 16.3): The acid-catalyzed reaction of an alcohol with a carboxylic acid toyield an ester.

Fischer projection (Section 21.2): A means of depictingthe absolute configuration of a chiral molecule on a flatpage. A Fischer projection uses a cross to represent thechirality center. The horizontal arms of the cross repre-

sent bonds coming out of the plane of the page, and thevertical arms of the cross represent bonds going back intothe plane of the page.

Fmoc derivative (Section 19.7): A fluorenylmethyloxy-carbonyl N-protected amino acid.

Formal charge (Section 2.3): The difference in the num-ber of electrons owned by an atom in a molecule and bythe same atom in its elemental state.

Formyl group (Section 14.1): A –CHO group.

Frequency, � (Section 11.5): The number of electro-magnetic wave cycles that travel past a fixed point in agiven unit of time. Frequencies are expressed in units ofcycles per second, or hertz.

Friedel–Crafts reaction (Section 8.7): An electrophilicaromatic substitution reaction to alkylate or acylate anaromatic ring.

FT-NMR (Section 12.4): Fourier-transform NMR; a rapidtechnique for recording NMR spectra in which all mag-netic nuclei absorb at the same time.

Functional group (Section 3.1): An atom or group ofatoms that is part of a larger molecule and that has a char-acteristic chemical reactivity.

Furanose (Section 21.5): The five-membered-ring form ofa simple sugar.

Gauche conformation (Section 3.7): The conformation ofbutane in which the two methyl groups lie 60° apart asviewed in a Newman projection. This conformation has3.8 kJ/mol steric strain.

Geminal (Section 14.5): Referring to two groups attachedto the same carbon atom. For example, a 1,1-diol is a gem-inal diol.

Gibbs free-energy change, �G (Section 5.7): The free-energy change that occurs during a reaction, given by theequation �G � �H � T�S. A reaction with a negative free-energy change is spontaneous, and a reaction with a posi-tive free-energy change is nonspontaneous.

Globular protein (Section 19.8): A protein that is coiledinto a compact, nearly spherical shape. These proteins,which are generally water-soluble and mobile within thecell, are the structural class to which enzymes belong.

Glucogenic amino acid (Section 20.4): An amino acid thatis metabolized either to pyruvate or to an intermediate ofthe citric acid cycle.


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Gluconeogenesis (Section 22.5): The anabolic pathway bywhich organisms make glucose from simple three-carbonprecursors.

Glycal (Section 21.9): An unsaturated sugar with a C1–C2double bond.

Glycal assembly method (Section 21.9): A method for link-ing monosaccharides together to synthesis polysaccharides.

Glycerophospholipid (Section 23.3): A lipid that containsa glycerol backbone linked to two fatty acids and a phos-phoric acid.

Glycoconjugate (Section 21.6): A molecule in which acarbohydrate is linked through its anomeric center toanother biological molecule such as a lipid or protein.

Glycol (Section 7.7): A diol, such as ethylene glycol,HOCH2CH2OH.

Glycolysis (Section 22.2): A series of ten enzyme-catalyzed reactions that break down glucose into 2 equiv-alents of pyruvate, CH3COCO2

�.

Glycoside (Section 21.6): A cyclic acetal formed by reac-tion of a sugar with another alcohol.

Green chemistry (Chapter 18 Lagniappe): The design andimplementation of chemical products and processes thatreduce waste and attempt to eliminate the generation ofhazardous substances.

Grignard reagent (Section 10.3): An organomagnesiumhalide, RMgX.

Ground state (Section 1.3): The most stable, lowest-energy electron configuration of a molecule or atom.

Halogenation (Sections 7.2, 8.6): The reaction of halogenwith an alkene to yield a 1,2-dihalide addition product or with an aromatic compound to yield a substitutionproduct.

Halohydrin (Section 7.3): A 1,2-disubstituted haloalcohol,such as that obtained on addition of HOBr to an alkene.

Hammond postulate (Section 6.9): A postulate statingthat we can get a picture of what a given transition statelooks like by looking at the structure of the nearest stablespecies. Exergonic reactions have transition states thatresemble reactant; endergonic reactions have transitionstates that resemble product.

Heat of hydrogenation (Section 6.5): The amount of heat released when a carbon–carbon double bond ishydrogenated.

Heat of reaction (Section 5.7): An alternative name for theenthalpy change in a reaction, �H.

Hemiacetal (Section 14.8): A functional group consistingof one –OR and one –OH group bonded to the samecarbon.

Hemithioacetal (Section 22.2): The sulfur analog of anacetal, resulting from nucleophilic addition of a thiol to aketone or aldehyde.

Henderson–Hasselbalch equation (Sections 15.3, 18.5):An equation for determining the extent of deprotonationof a weak acid at various pH values.

Hertz, Hz (Section 11.5): A measure of electromagneticfrequency, the number of waves that pass by a fixed pointper second.

Heterocycle (Sections 8.4, 18.8): A cyclic molecule whosering contains more than one kind of atom. For example,pyridine is a heterocycle that contains five carbon atomsand one nitrogen atom in its ring.

High-energy compound (Section 5.8): A term used in bio-chemistry to describe substances such as ATP thatundergo highly exothermic reactions.

Hofmann elimination reaction (Section 18.7): The elimi-nation reaction of an amine to yield an alkene by reactionwith iodomethane, followed by heating with Ag2O.

HOMO (Section 11.9): The highest occupied molecularorbital.

Homotopic (Section 12.8): Hydrogens that give the identi-cal structure on replacement by X and thus show identicalNMR absorptions.

Hormone (Section 23.9): A chemical messenger that issecreted by an endocrine gland and carried through thebloodstream to a target tissue.

HPLC (Chapter 11 Lagniappe): High-pressure liquid chro-matography; a variant of column chromatography usinghigh pressure to force solvent through very smallabsorbent particles.

Hückel’s rule (Section 8.3): A rule stating that monocyclicconjugated molecules having 4n � 2 � electrons (n � aninteger) are aromatic.

Hund’s rule (Section 1.3): If two or more empty orbitals ofequal energy are available, one electron occupies each,with their spins parallel, until all are half-full.

Hybrid orbital (Section 1.6): An orbital derived from a combination of atomic orbitals. Hybrid orbitals, such as the sp3, sp2, and sp hybrids of carbon, are stronglydirected and form stronger bonds than atomic orbitals do.

Hydration (Section 7.4): Addition of water to a molecule,such as occurs when alkenes are treated with aqueous sul-furic acid to give alcohols.

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Hydride shift (Section 6.10): The shift of a hydrogen atomand its electron pair to a nearby cationic center.

Hydroboration (Section 7.4): Addition of borane (BH3) oran alkylborane to an alkene. The resultant trialkylboraneproducts can be oxidized to yield alcohols.

Hydrocarbon (Section 3.2): A compound that containsonly carbon and hydrogen.

Hydrogen bond (Sections 2.12, 13.2): A weak attractionbetween a hydrogen atom bonded to an electronegativeatom and an electron lone pair on another electro-negative atom.

Hydrogenation (Section 7.5): Addition of hydrogen to adouble or triple bond to yield a saturated product.

Hydrogenolysis (Section 19.7): Cleavage of a bond byreaction with hydrogen. Benzylic ethers and esters, forinstance, are cleaved by hydrogenolysis.

Hydrophilic (Sections 2.12, 23.2): Water-loving; attractedto water.

Hydrophobic (Sections 2.12, 23.2): Water-fearing; notattracted to water.

Hydroquinone (Section 13.5): A 1,4-dihydroxybenzene.

Hydroxylation (Section 7.7): Addition of two –OH groupsto a double bond.

Hyperconjugation (Section 6.5): An interaction thatresults from overlap of a vacant p orbital on one atom witha neighboring C–H � bond. Hyperconjugation is impor-tant in stabilizing carbocations and in stabilizing substi-tuted alkenes.

Imine (Section 14.7): A compound with the R2CUNRfunctional group; also called a Schiff base.

Inductive effect (Sections 2.1, 6.8, 8.8): The electron-attracting or electron-withdrawing effect transmittedthrough � bonds. Electronegative elements have an electron-withdrawing inductive effect.

Infrared (IR) spectroscopy (Section 11.6): A kind of opti-cal spectroscopy that uses infrared energy. IR spec-troscopy is particularly useful in organic chemistry fordetermining the kinds of functional groups present inmolecules.

Initiator (Section 5.3): A substance with an easily brokenbond that is used to initiate a radical chain reaction. Forexample, radical chlorination of alkanes is initiatedwhen light energy breaks the weak Cl–Cl bond to form Cl·radicals.

Integration (Section 12.10): A technique for measuringthe area under an NMR peak to determine the relative

number of each kind of proton in a molecule. Integratedpeak areas are superimposed over the spectrum as a “stair-step” line, with the height of each step proportional to thearea underneath the peak.

Intermediate (Section 5.10): A species that is formed dur-ing the course of a multistep reaction but is not the finalproduct. Intermediates are more stable than transitionstates but may or may not be stable enough to isolate.

Intramolecular, intermolecular (Section 17.7): A reac-tion that occurs within the same molecule is intramolec-ular; a reaction that occurs between two molecules isintermolecular.

Intron (Section 24.4): A section of DNA that does not con-tain genetic information.

Ion pair (Section 10.7): A loose complex between twoions in solution. Ion pairs are implicated as intermediatesin SN1 reactions to account for the partial retention ofstereochemistry that is often observed.

Isoelectric point, pI (Section 19.2): The pH at which thenumber of positive charges and the number of negativecharges on a protein or an amino acid are equal.

Isomers (Section 3.2): Compounds that have the samemolecular formula but different structures.

Isoprene rule (Chapter 6 Lagniappe): An observation tothe effect that terpenoids appear to be made up of isoprene(2-methylbuta-1,3-diene) units connected head-to-tail.

Isotopes (Section 1.1): Atoms of the same element thathave different mass numbers.

IUPAC system of nomenclature (Section 3.4): Rules fornaming compounds, devised by the International Unionof Pure and Applied Chemistry.

Kekulé structure (Section 1.4): A method of representingmolecules in which a line between atoms indicates a bond.

Keto–enol tautomerism (Section 17.1): The rapid equili-bration between a carbonyl form and vinylic alcohol formof a molecule.

Ketogenic amino acid (Section 20.4): An amino acid thatis metabolized into an intermediate that can enter fatty-acid biosynthesis.

Ketone (Chapter 14 Introduction): A compound with twoorganic substituents bonded to a carbonyl group, R2CUO.

Ketone body (Section 20.4): One of the substances aceto-acetate, �-hydroxybutyrate, or acetone resulting fromamino acid catabolism.

Ketose (Section 21.1): A carbohydrate with a ketone func-tional group.

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Kinetics (Section 10.5): Referring to reaction rates.Kinetic measurements are useful for helping to determinereaction mechanisms.

Krebs cycle (Section 22.4): An alternative name for thecitric acid cycle, by which acetyl CoA is degraded to CO2.

Lagniappe: A word in the Creole dialect of southernLouisiana meaning an extra benefit or a little somethingextra. See the Lagniappes at the end of each chapter.

L Sugar (Section 21.3): A sugar whose hydroxyl group atthe chirality center farthest from the carbonyl grouppoints to the left when drawn in Fischer projection.

Lactam (Section 16.7): A cyclic amide.

Lactone (Section 16.6): A cyclic ester.

LD50 (Chapter 1 Lagniappe): The amount of a substanceper kilogram body weight that is lethal to 50% of test animals.

Leaving group (Section 10.5): The group that is replacedin a substitution reaction.

Levorotatory (Section 9.3): An optically active substancethat rotates the plane of polarization of plane-polarizedlight in a left-handed (counterclockwise) direction.

Lewis acid (Section 2.11): A substance with a vacant low-energy orbital that can accept an electron pair from a base.All electrophiles are Lewis acids.

Lewis base (Section 2.11): A substance that donates an elec-tron lone pair to an acid. All nucleophiles are Lewis bases.

Lewis structure (Section 1.4): A representation of a mole-cule showing valence electrons as dots.

Lindlar catalyst (Section 7.12): A hydrogenation catalystused to convert alkynes to cis alkenes.

Line-bond structure (Section 1.4): A representation of amolecule showing covalent bonds as lines between atoms.

134 Link (Section 21.8): An acetal link between the C1–OH group of one sugar and the C4 –OH group of anothersugar.

Lipid (Chapter 23 Introduction): A naturally occurring sub-stance isolated from cells and tissues by extraction with anonpolar solvent. Lipids belong to many different struc-tural classes, including fats, terpenes, prostaglandins, andsteroids.

Lipid bilayer (Section 23.3): The ordered lipid structurethat forms a cell membrane.

Lipoprotein (Chapter 23 Lagniappe): A complex moleculewith both lipid and protein parts that transports lipidsthrough the body.

Lone-pair electrons (Section 1.4): Nonbonding valence-shell electron pairs. Lone-pair electrons are used bynucleophiles in their reactions with electrophiles.

LUMO (Section 11.9): The lowest unoccupied molecularorbital.

Magnetic resonance imaging, MRI (Chapter 12 Lagniappe):A medical diagnostic technique based on nuclear magneticresonance.

Major groove (Section 24.2): The larger of two grooves inthe DNA double helix.

MALDI (Section 11.4): Matrix-assisted laser desorptionionization, a “soft” ionization method used for mass spec-trometry of biological samples of very high molecularweight.

Malonic ester synthesis (Section 17.4): The synthesis of acarboxylic acid by alkylation of an alkyl halide, followedby hydrolysis and decarboxylation.

Markovnikov’s rule (Section 6.7): A guide for determin-ing the regiochemistry (orientation) of electrophilic addi-tion reactions. In the addition of HX to an alkene, thehydrogen atom bonds to the alkene carbon that has feweralkyl substituents.

Mass number, A (Section 1.1): The total of protons plusneutrons in an atom.

Mass spectrometry (Section 11.1): A technique for mea-suring the mass, and therefore the molecular weight(MW), of ions.

McLafferty rearrangement (Section 11.3): A mass-spectral fragmentation pathway for carbonyl compounds.

Mechanism (Section 5.2): A complete description of howa reaction occurs. A mechanism must account for all start-ing materials and all products and must describe thedetails of each individual step in the overall reactionprocess.

Mercapto group (Section 13.1): An alternative name forthe thiol group, –SH.

Meso compound (Section 9.7): A compound that containschirality centers but is nevertheless achiral because itcontains a symmetry plane.

Messenger RNA (Section 24.2): A kind of RNA formed bytranscription of DNA and used to carry genetic messagesfrom DNA to ribosomes.

Meta, m- (Section 8.1): A naming prefix used for 1,3-disubstituted benzenes.

Metabolism (Section 20.1): A collective name for the manyreactions that go on in the cells of living organisms.

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Methylene group (Section 6.2): A –CH2– or �CH2 group.

Micelle (Section 23.2): A spherical cluster of soaplikemolecules that aggregate in aqueous solution. The ionicheads of the molecules lie on the outside, where they aresolvated by water, and the organic tails bunch together onthe inside of the micelle.

Michael reaction (Section 17.10): The conjugate additionreaction of an enolate ion to an unsaturated carbonyl compound.

Minor groove (Section 24.2): The smaller of two groovesin the DNA double helix.

Molar absorptivity (Section 11.9): A quantitative measureof the amount of UV light absorbed by a sample.

Molecular ion (Section 11.1): The cation produced in themass spectrometer by loss of an electron from the parentmolecule. The mass of the molecular ion corresponds tothe molecular weight of the sample.

Molecular mechanics (Chapter 4 Lagniappe): A computer-based method for calculating the minimum-energy confor-mation of a molecule.

Molecular orbital (MO) theory (Section 1.11): A descrip-tion of covalent bond formation as resulting from a math-ematical combination of atomic orbitals (wave functions)to form molecular orbitals.

Molecule (Section 1.4): A neutral collection of atoms heldtogether by covalent bonds.

Monomer (Section 7.8): The simple starting unit fromwhich a polymer is made.

Monosaccharide (Section 21.1): A simple sugar.

Monoterpene (Chapter 6 Lagniappe): A ten-carbon lipid.

Multiplet (Section 12.11): A pattern of peaks in an NMRspectrum that arises by spin–spin splitting of a singleabsorption because of coupling between neighboringmagnetic nuclei.

Mutarotation (Section 21.5): The change in optical rota-tion observed when a pure anomer of a sugar is dissolvedin water. Mutarotation is caused by the reversible openingand closing of the acetal linkage, which yields an equilib-rium mixture of anomers.

n � 1 rule (Section 12.11): A hydrogen with n otherhydrogens on neighboring carbons shows n � 1 peaks inits 1H NMR spectrum.

N-terminal amino acid (Section 19.4): The amino acidwith a free –NH2 group at the end of a protein chain.

Natural gas (Chapter 3 Lagniappe): A naturally occurringhydrocarbon mixture consisting chiefly of methane, alongwith smaller amounts of ethane, propane, and butane.

Natural product (Chapter 5 Lagniappe; Chapter 25): Acatchall term generally taken to mean a small moleculefound in bacteria, plants, or other living organisms.*

Neopentyl group (Section 10.6): The 2,2-dimethylpropylgroup, (CH3)3CCH2–.

Neuraminidase (Chapter 22 Lagniappe): An enzyme pres-ent on the surface of viral particles that cleaves the bondholding the newly formed viral particles to host cells.

New molecular entity, NME (Chapter 5 Lagniappe): A new biologically active chemical substance approved forsale as a drug by the U.S. Food and Drug Administration.

Newman projection (Section 3.6): A means of indicatingstereochemical relationships between substituent groupson neighboring carbons. The carbon–carbon bond isviewed end-on, and the carbons are indicated by a circle.Bonds radiating from the center of the circle are attachedto the front carbon, and bonds radiating from the edge ofthe circle are attached to the rear carbon.

Nitration (Section 8.6): The substitution of a nitro grouponto an aromatic ring.

Nitrile (Section 15.1): A compound containing the C�Nfunctional group.

Nitrogen rule (Section 18.10): A compound with an oddnumber of nitrogen atoms has an odd-numbered molecu-lar weight.

Node (Section 1.2): A surface of zero electron densitywithin an orbital. For example, a p orbital has a nodalplane passing through the center of the nucleus, perpen-dicular to the axis of the orbital.

Nonbonding electrons (Section 1.4): Valence electronsthat are not used in forming covalent bonds.

Noncovalent interaction (Section 2.12): One of a varietyof nonbonding interactions between molecules, such asdipole–dipole forces, dispersion forces, and hydrogenbonds.

Nonessential amino acid (Section 20.5): One of the elevenamino acids that are biosynthesized by humans.

Nonribosomal polypeptide (Section 25.1): A peptidelikecompound biosynthesized from an amino acid withoutdirect RNA transcription. The penicillins are examples.*

Normal alkane (Section 3.2): A straight-chain alkane, asopposed to a branched alkane. Normal alkanes aredenoted by the suffix n, as in n-C4H10 (n-butane).


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Nuclear magnetic resonance, NMR (Chapter 12 Intro-duction): A spectroscopic technique that provides infor-mation about the carbon–hydrogen framework of amolecule. NMR works by detecting the energy absorp-tion accompanying the transition between nuclear spinstates that occurs when a molecule is placed in a strongmagnetic field and irradiated with radiofrequencywaves.

Nucleophile (Section 5.4): A “nucleus-lover,” or speciesthat donates an electron pair to an electrophile in a polarbond-forming reaction. Nucleophiles are also Lewisbases.

Nucleophilic acyl substitution reaction (Section 16.2): Areaction in which a nucleophile attacks a carbonyl com-pound and substitutes for a leaving group bonded to thecarbonyl carbon.

Nucleophilic addition reaction (Section 14.4): A reactionin which a nucleophile adds to the electrophilic carbonylgroup of a ketone or aldehyde to give an alcohol.

Nucleophilic substitution reaction (Section 10.4): A reac-tion in which one nucleophile replaces another attachedto a saturated carbon atom.

Nucleoside (Section 24.1): A nucleic acid constituent,consisting of a sugar residue bonded to a heterocyclicpurine or pyrimidine base.

Nucleotide (Section 24.1): A nucleic acid constituent,consisting of a sugar residue bonded both to a hetero-cyclic purine or pyrimidine base and to a phosphoricacid. Nucleotides are the monomer units from whichDNA and RNA are constructed.

Nylon (Section 16.9): A synthetic polyamide step-growthpolymer.

Olefin (Chapter 6 Introduction): An alternative name foran alkene.

Optical isomers (Section 9.4): An alternative name forenantiomers. Optical isomers are isomers that have a mirror-image relationship.

Optically active (Section 9.3): A substance that rotates theplane of polarization of plane-polarized light.

Orbital (Section 1.2): A wave function, which describesthe volume of space around a nucleus in which an elec-tron is most likely to be found.

Organic chemistry (Chapter 1 Introduction): The study ofcarbon compounds.

Organophosphate (Section 1.10): A compound that con-tains a phosphorus atom bonded to four oxygens, withone of the oxygens also bonded to carbon.

Ortho, o- (Section 8.1): A naming prefix used for 1,2-disub-stituted benzenes.

Oxidation (Section 7.6): A reaction that causes a decreasein electron ownership by carbon, either by bond forma-tion between carbon and a more electronegative atom(usually oxygen, nitrogen, or a halogen) or by bond break-ing between carbon and a less electronegative atom (usu-ally hydrogen).

Oxidative deamination (Section 20.2): The conversion ofa primary amine into a ketone by oxidation to an iminefollowed by hydrolysis.

Oxidative decarboxylation (Section 22.3): A decarboxy-lation reaction, usually of an �-keto acid, that is accom-panied by a change in oxidation state of the carbonylcarbon from that of a ketone to that of a carboxylic acid orester.

Oxirane (Section 7.6): An alternative name for an epoxide.

Oxymercuration (Section 7.4): A method for double-bondhydration using aqueous mercuric acetate as the reagent.

Para, p- (Section 8.1): A naming prefix used for 1,4-disub-stituted benzenes.

Paraffin (Section 3.5): A common name for alkanes.

Parent peak (Section 11.1): The peak in a mass spectrumcorresponding to the molecular ion. The mass of the par-ent peak therefore represents the molecular weight of thecompound.

Pauli exclusion principle (Section 1.3): No more than twoelectrons can occupy the same orbital, and those two musthave spins of opposite sign.

Peptide (Chapter 19 Introduction): A short amino acidpolymer in which the individual amino acid residues arelinked by amide bonds.

Peptide bond (Section 19.4): An amide bond in a peptidechain.

Periplanar (Section 10.11): A conformation in whichbonds to neighboring atoms have a parallel arrangement.In an eclipsed conformation, the neighboring bonds aresyn periplanar; in a staggered conformation, the bonds are anti periplanar.

Peroxyacid (Section 7.6): A compound with the –CO3Hfunctional group.

Petroleum (Chapter 3 Lagniappe): A complex mixture ofnaturally occurring hydrocarbons derived from thedecomposition of plant and animal matter.

Phenol (Chapter 13 Introduction): A compound with an–OH group directly bonded to an aromatic ring, ArOH.

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Phenoxide ion (Section 13.2): The anion of a phenol, ArO�.

Phenyl group (Section 8.1): The name for the –C6H5 unitwhen the benzene ring is considered as a substituent. Aphenyl group is abbreviated as –Ph.

Phosphite (Section 24.7): A compound with the structureP(OR)3.

Phospholipid (Section 23.3): A lipid that contains a phos-phate residue. For example, glycerophospholipids con-tain a glycerol backbone linked to two fatty acids and aphosphoric acid.

Phosphoramidite (Section 24.7): A compound with thestructure R2NP(OR)2.

Phosphoric acid anhydride (Section 20.1): A substancethat contains PO2PO link, analogous to the CO2CO link incarboxylic acid anhydrides.

Physiological pH (Section 15.3): The pH of 7.3 that existsinside cells.

Pi (�) bond (Section 1.8): The covalent bond formed bysideways overlap of atomic orbitals. For example,carbon–carbon double bonds contain a � bond formed bysideways overlap of two p orbitals.

PITC (Section 19.6): Phenylisothiocyanate, used in theEdman degradation of proteins.

pKa (Section 2.8): The negative common logarithm of theKa; used to express acid strength.

Plane of symmetry (Section 9.2): A plane that bisects amolecule such that one half of the molecule is the mirrorimage of the other half. Molecules containing a plane ofsymmetry are achiral.

Plane-polarized light (Section 9.3): Ordinary light thathas its electromagnetic waves oscillating in a single planerather than in random planes. The plane of polarization isrotated when the light is passed through a solution of achiral substance.

Plasticizer (Section 16.6): A small organic molecule addedto polymers to act as a lubricant between polymer chains.

Polar aprotic solvent (Section 10.6): A polar solvent thatcan’t function as a hydrogen ion donor. Polar aprotic solvents such as dimethyl sulfoxide (DMSO) anddimethylformamide (DMF) are particularly useful in SN2reactions because of their ability to solvate cations.

Polar covalent bond (Section 2.1): A covalent bond inwhich the electron distribution between atoms is unsym-metrical.

Polar reaction (Section 5.2): A reaction in which bondsare made when a nucleophile donates two electrons to an

electrophile and in which bonds are broken when onefragment leaves with both electrons from the bond.

Polarity (Section 2.1): The unsymmetrical distribution ofelectrons in a molecule that results when one atomattracts electrons more strongly than another.

Polarizability (Section 5.4): The measure of the change ina molecule’s electron distribution in response to changingelectric interactions with solvents or ionic reagents.

Polycyclic compound (Section 4.9): A compound thatcontains more than one ring.

Polycyclic aromatic compound (Section 8.5): A com-pound with two or more benzene-like aromatic ringsfused together.

Polyketide (Section 25.1): A natural product biosynthe-sized from simple acyl precursors such as acetyl CoA,propionyl CoA, and methylmalonyl CoA by a large multi-functional enzyme complex.*

Polymer (Section 7.8): A large molecule made up of repeat-ing smaller units. For example, polyethylene is a syntheticpolymer made from repeating ethylene units, and DNA is abiopolymer made of repeating deoxyribonucleotide units.

Polymerase chain reaction, PCR (Section 24.8): A methodfor amplifying small amounts of DNA to produce largeramounts.

Polysaccharide (Section 21.9): A carbohydrate that is madeof many simple sugars linked together by acetal bonds.

Polyunsaturated fatty acid (Section 23.1): A fatty acidcontaining two or more double bonds.

Primary, secondary, tertiary, quaternary (Section 3.3):Terms used to describe the substitution pattern at a specificsite. A primary site has one organic substituent attached toit, a secondary site has two organic substituents, a tertiarysite has three, and a quaternary site has four.

Carbo-Carbon cation Hydrogen Alcohol Amine

Primary RCH3 RCH2� RCH3 RCH2OH RNH2

Secondary R2CH2 R2CH� R2CH2 R2CHOH R2NH

Tertiary R3CH R3C� R3CH R3COH R3N

Quaternary R4C

Primary structure (Section 19.8): The amino acid sequencein a protein.

pro-R configuration (Section 9.13): One of two identicalatoms in a compound, whose replacement leads to an R chirality center.


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pro-S configuration (Section 9.13): One of two identicalatoms in a compound whose replacement leads to an S chirality center.

Prochiral (Section 9.13): A molecule that can be converted from achiral to chiral in a single chemical step.

Prochirality center (Section 9.13): An atom in a com-pound that can be converted into a chirality center bychanging one of its attached substituents.

Propagation step (Section 5.3): The step or series of stepsin a radical chain reaction that carry on the chain. Thepropagation steps must yield both product and a reactiveintermediate.

Prostaglandin (Section 23.7): A lipid derived from arachi-donic acid. Prostaglandins are present in nearly all bodytissues and fluids, where they serve many important hor-monal functions.

Protecting group (Sections 19.7, 21.9): A group that isintroduced to protect a sensitive functional group towardreaction elsewhere in the molecule. After serving its pro-tective function, the group is removed.

Protein (Chapter 19 Introduction): A large peptide con-taining 50 or more amino acid residues. Proteins serveboth as structural materials and as enzymes that controlan organism’s chemistry.

Protein Data Bank (Chapter 19 Lagniappe): A worldwideonline repository of X-ray and NMR structural data forbiological macromolecules. To access the Protein DataBank, go to http://www.rcsb.org/pdb/.

Protic solvent (Section 10.6): A solvent such as water oralcohol that can act as a proton donor.

Pyramidal inversion (Section 18.2): The rapid inversionof configuration of an amine.

Pyranose (Section 21.5): The six-membered-ring form of asimple sugar.

Quartet (Section 12.11): A set of four peaks in an NMRspectrum, caused by spin–spin splitting of a signal bythree adjacent nuclear spins.

Quaternary (see Primary)

Quaternary structure (Section 19.8): The highest level ofprotein structure, involving a specific aggregation of indi-vidual proteins into a larger cluster.

Quinone (Section 13.5): A cyclohexa-2,5-diene-1,4-dione.

R group (Section 3.3): A generalized abbreviation for anorganic partial structure.

R configuration (Section 9.5): The configuration at a chi-rality center as specified using the Cahn–Ingold–Prelogsequence rules.

Racemate (Section 9.8): A mixture consisting of equalparts (�) and (�) enantiomers of a chiral substance.

Radical (Section 5.2): A species that has an odd number ofelectrons, such as the chlorine radical, Cl·.

Radical reaction (Section 5.2): A reaction in which bondsare made by donation of one electron from each of tworeactants and in which bonds are broken when each frag-ment leaves with one electron.

Rate constant (Section 10.5): The constant k in a rateequation.

Rate equation (Section 10.5): An equation that expressesthe dependence of a reaction’s rate on the concentration ofreactants.

Rate-limiting step (Section 10.7): The slowest step in amultistep reaction sequence. The rate-limiting step acts asa kind of bottleneck in multistep reactions.

Re face (Section 9.13): One of two faces of a planar, sp2-hybridized atom.

Reaction energy diagram (Section 5.9): A representationof the course of a reaction, in which free energy is plottedas a function of reaction progress. Reactants, transitionstates, intermediates, and products are represented, andtheir appropriate energy levels are indicated.

Reaction intermediate (See Intermediate; Section 5.10)

Reaction mechanism (See Mechanism; Section 5.2)

Rearrangement reaction (Section 5.1): What occurs whena single reactant undergoes a reorganization of bonds andatoms to yield an isomeric product.

Reducing sugar (Section 21.6): A sugar that reduces silverion in the Tollens test or cupric ion in the Fehling or Bene-dict tests.

Reduction (Section 7.5): A reaction that causes an increaseof electron ownership by carbon, either by bond breakingbetween carbon and a more electronegative atom or by bondformation between carbon and a less electronegative atom.

Reductive amination (Sections 18.6, 19.3): A method forpreparing an amine by reaction of an aldehyde or ketonewith ammonia and a reducing agent.

Refining (Chapter 3 Lagniappe): The process by whichpetroleum is converted into gasoline and other usefulproducts.

Regiospecific (Section 6.7): A term describing a reactionthat occurs with a specific regiochemistry to give a singleproduct rather than a mixture of products.

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Replication (Section 24.3): The process by which double-stranded DNA uncoils and is replicated to produce twonew copies.

Replication fork (Section 24.3): The point of unravelingin a DNA chain where replication occurs.

Residue (Section 19.4): An amino acid in a protein chain.

Resolution (Section 9.8): The process by which a racemicmixture is separated into its two pure enantiomers.

Resonance form (Section 2.4): An individual Lewis struc-ture of a resonance hybrid.

Resonance effect (Section 8.8): The donation or with-drawal of electrons through orbital overlap with neigh-boring � bonds. For example, an oxygen or nitrogensubstituent donates electrons to an aromatic ring by over-lap of the O or N orbital with the aromatic ring p orbitals.

Resonance hybrid (Section 2.4): A molecule, such as ben-zene, that can’t be represented adequately by a singleKekulé structure but must instead be considered as anaverage of two or more resonance structures. The reso-nance structures themselves differ only in the positions oftheir electrons, not their nuclei.

Restriction endonuclease (Section 24.6): An enzyme thatis able to cleave a DNA molecule at points in the chainwhere a specific base sequence occurs.

Retrosynthetic (Section 8.10): Planning an organic synthe-sis by working backward from product to starting material.

Ribonucleic acid, RNA (Section 24.1): The biopolymerfound in cells that serves to transcribe the genetic infor-mation found in DNA and uses that information to directthe synthesis of proteins.

Ribosomal RNA (Section 24.4): A kind of RNA used in thephysical makeup of ribosomes.

Ring-flip (Section 4.6): A molecular motion that convertsone chair conformation of cyclohexane into another chairconformation. The effect of a ring-flip is to convert anaxial substituent into an equatorial substituent.

RNA (See Ribonucleic acid; Section 24.1)

S configuration (Section 9.5): The configuration at a chi-rality center as specified using the Cahn–Ingold–Prelogsequence rules.

Saccharide (Section 21.1): A sugar.

Salt bridge (Section 19.8): The ionic attraction betweentwo oppositely charged groups in a protein chain.

Sanger dideoxy method (Section 24.6): A biochemicalmethod for sequencing DNA strands.

Saponification (Section 16.6): An old term for the base-induced hydrolysis of an ester to yield a carboxylic acid salt.

Saturated (Section 3.2): A molecule that has only singlebonds and thus can’t undergo addition reactions. Alkanesare saturated, but alkenes are unsaturated.

Sawhorse structure (Section 3.6): A manner of represent-ing stereochemistry that uses a stick drawing and gives aperspective view of the conformation around a single bond.

Schiff base (Section 22.2): An alternative name for animine, R2CUNR�, used primarily in biochemistry.

Second-order reaction (Section 10.5): A reaction whoserate-limiting step is bimolecular and whose kinetics are therefore dependent on the concentration of tworeactants.

Secondary (see Primary)

Secondary metabolite (Chapter 25 Introduction): A smallnaturally occurring molecule that is not essential to thegrowth and development of the producing organism andis not classified by structure.*

Secondary structure (Section 19.8): The level of proteinsubstructure that involves organization of chain sectionsinto ordered arrangements such as �-pleated sheets or �-helices.

Semiconservative replication (Section 24.3): The processby which DNA molecules are made containing one strandof old DNA and one strand of new DNA.

Sense strand (Section 24.4): The coding strand of double-helical DNA that contains the gene.

Sequence rules (Sections 6.4, 9.5): A series of rules forassigning relative priorities to substituent groups on adouble-bond carbon atom or on a chirality center.

Sesquiterpene (Chapter 6 Lagniappe): A 15-carbon lipid.

Sharpless epoxidation (Chapter 14 Lagniappe): A methodfor enantioselective synthesis of a chiral epoxide bytreatment of an allylic alcohol with tert-butyl hydro-peroxide, (CH3)3CXOOH, in the presence of titaniumtetraisopropoxide and diethyl tartrate.

Shell (electron) (Section 1.2): A group of an atom’s elec-trons with the same principal quantum number.

Shielding (Section 12.2): An effect observed in NMR thatcauses a nucleus to absorb toward the right (upfield) sideof the chart. Shielding is caused by donation of electrondensity to the nucleus.


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Si face (Section 9.13): One of two faces of a planar, sp2-hybridized atom.

Side chain (Section 19.1): The substituent attached to the� carbon of an amino acid.

Sigma (�) bond (Section 1.5): A covalent bond formed byhead-on overlap of atomic orbitals.

Silyl ether (Section 21.9): A substance with the structureR3SiXOXR. The silyl ether acts as a protecting group foralcohols.

Simple sugar (Section 21.1): A carbohydrate that cannotbe broken down into smaller sugars by hydrolysis.

Skeletal structure (Section 1.12): A shorthand way ofwriting structures in which carbon atoms are assumed tobe at each intersection of two lines (bonds) and at the endof each line.

SN1 reaction (Section 10.7): A unimolecular nucleophilicsubstitution reaction.

SN2 reaction (Section 10.5): A bimolecular nucleophilicsubstitution reaction.

Solid-phase synthesis (Section 19.7): A technique of syn-thesis whereby the starting material is covalently bound toa solid polymer bead and reactions are carried out on thebound substrate. After the desired transformations havebeen effected, the product is cleaved from the polymer.

Solvation (Section 10.6): The clustering of solvent mole-cules around a solute particle to stabilize it.

sp Hybrid orbital (Section 1.9): A hybrid orbital derivedfrom the combination of an s and a p atomic orbital. Thetwo sp orbitals that result from hybridization are orientedat an angle of 180° to each other.

sp2 Hybrid orbital (Section 1.8): A hybrid orbital derivedby combination of an s atomic orbital with two p atomicorbitals. The three sp2 hybrid orbitals that result lie in aplane at angles of 120° to each other.

sp3 Hybrid orbital (Section 1.6): A hybrid orbital derivedby combination of an s atomic orbital with three p atomicorbitals. The four sp3 hybrid orbitals that result aredirected toward the corners of a regular tetrahedron atangles of 109° to each other.

Specific rotation, [�]D (Section 9.3): The optical rotationof a chiral compound under standard conditions.

Sphingomyelin (Section 23.3): A phospholipid that hassphingosine as its backbone.

Spin–spin splitting (Section 12.11): The splitting of anNMR signal into a multiplet because of an interactionbetween nearby magnetic nuclei whose spins are cou-pled. The magnitude of spin–spin splitting is given by thecoupling constant, J.

Staggered conformation (Section 3.6): The three-dimensional arrangement of atoms around a carbon–carbonsingle bond in which the bonds on one carbon bisect thebond angles on the second carbon as viewed end-on.

Step-growth polymer (Section 16.9): A polymer in whicheach bond is formed independently of the others. Poly-esters and polyamides (nylons) are examples.

Stereochemistry (Section 3.6; Chapters 3, 4, and 9): The branch of chemistry concerned with the three-dimensional arrangement of atoms in molecules.

Stereoisomers (Section 4.2): Isomers that have their atoms connected in the same order but have differentthree-dimensional arrangements. The term stereoisomerincludes both enantiomers and diastereomers.

Steric strain (Sections 3.7, 4.7): The strain imposed on amolecule when two groups are too close together and tryto occupy the same space. Steric strain is responsible bothfor the greater stability of trans versus cis alkenes and forthe greater stability of equatorially substituted versus axi-ally substituted cyclohexanes.

Steroid (Section 23.9): A lipid whose structure is based on atetracyclic carbon skeleton with three 6-membered and one5-membered ring. Steroids occur in both plants and animalsand have a variety of important hormonal functions.

Stork enamine reaction (Section 17.11): The conjugateaddition of an enamine to an �,�-unsaturated carbonyl com-pound, followed by hydrolysis to yield a 1,5-dicarbonylproduct.

STR loci (Chapter 24 Lagniappe): Short, tandem repeatsequences of noncoding DNA that are unique to everyindividual and allow DNA fingerprinting.

Straight-chain alkane (Section 3.2): An alkane whosecarbon atoms are connected without branching.

Substitution reaction (Section 5.1): What occurs whentwo reactants exchange parts to give two new products.SN1 and SN2 reactions are examples.

Sulfide (Chapter 13 Introduction): A compound that has twoorganic substituents bonded to the same sulfur atom, RSR�.

Sulfonation (Section 8.6): The substitution of a sulfonicacid group onto an aromatic ring.

Sulfone (Section 13.10): A compound of the general struc-ture RSO2R�.

Sulfoxide (Section 13.10): A compound of the generalstructure RSOR�.

Symmetry plane (Section 9.2): A plane that bisects a mol-ecule such that one half of the molecule is the mirrorimage of the other half. Molecules containing a plane ofsymmetry are achiral.

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Syn periplanar (Section 10.11): Describing a stereochem-ical relationship in which two bonds on adjacent carbonslie in the same plane and are eclipsed.

Syn stereochemistry (Section 7.4): The opposite of anti. Asyn addition reaction is one in which the two ends of thedouble bond react from the same side. A syn eliminationis one in which the two groups leave from the same side ofthe molecule.

Tautomer (Section 17.1): Isomers that are rapidly interconverted.

Template strand (Section 24.4): The strand of double-helical DNA that does not contain the gene.

Terpenoid (Chapter 6 Lagniappe, Section 23.8): A lipidthat is formally derived by head-to-tail polymerization ofisoprene units.

Tertiary (see Primary)

Tertiary structure (Section 19.8): The level of proteinstructure that involves the manner in which the entireprotein chain is folded into a specific three-dimensionalarrangement.

Thioester (Chapter 16 Introduction): A compound withthe RCOSR� functional group.

Thiol (Chapter 13 Introduction): A compound containingthe –SH functional group.

TMS (Section 12.3): Tetramethylsilane, used as an NMRcalibration standard.

TOF (Section 11.4): A time-of-flight mass spectrometer.

Tollens’ reagent (Section 21.6): A solution of Ag2O inaqueous ammonia; used to oxidize aldehydes to car-boxylic acids.

Torsional strain (Section 3.6): The strain in a moleculecaused by electron repulsion between eclipsed bonds.Torsional strain is also called eclipsing strain.

Tosylate (Section 10.4): A p-toluenesulfonate ester.

Transamination (Section 20.2): The exchange of an aminogroup and a keto group between reactants.

Transimination (Section 20.2): The exchange of an aminogroup and an imine group between reactants.

Transcription (Section 24.4): The process by which thegenetic information encoded in DNA is read and used tosynthesize RNA in the nucleus of the cell. A small portionof double-stranded DNA uncoils, and complementaryribonucleotides line up in the correct sequence for RNAsynthesis.

Transfer RNA (Section 24.4): A kind of RNA that trans-ports amino acids to the ribosomes, where they are joinedtogether to make proteins.

Transition state (Section 5.9): An activated complexbetween reactants, representing the highest energy pointon a reaction curve. Transition states are unstable com-plexes that can’t be isolated.

Translation (Section 24.5): The process by which thegenetic information transcribed from DNA onto mRNA isread by tRNA and used to direct protein synthesis.

Tree diagram (Section 12.12): A diagram used in NMR tosort out the complicated splitting patterns that can arisefrom multiple couplings.

Triacylglycerol (Section 23.1): A lipid, such as that foundin animal fat and vegetable oil, that is a triester of glycerolwith long-chain fatty acids.

Tricarboxylic acid cycle (Section 22.4): An alternativename for the citric acid cycle by which acetyl CoA isdegraded to CO2.

Triplet (Section 12.11): A symmetrical three-line splittingpattern observed in the 1H NMR spectrum when a protonhas two equivalent neighbor protons.

Turnover number (Section 19.9): The number of substratemolecules acted on by an enzyme per unit time.

Twist-boat conformation (Section 4.5): A conformation ofcyclohexane that is somewhat more stable than a pureboat conformation.

Ultraviolet (UV) spectroscopy (Section 11.9): An opticalspectroscopy employing ultraviolet irradiation. UV spec-troscopy provides structural information about the extentof � electron conjugation in organic molecules.

Unimolecular reaction (Section 10.7): A reaction thatoccurs by spontaneous transformation of the startingmaterial without the intervention of other reactants. Forexample, the dissociation of a tertiary alkyl halide in theSN1 reaction is a unimolecular process.

Unsaturated (Section 6.1): A molecule that has one ormore multiple bonds.

Upfield (Section 12.3): The right-hand portion of the NMRchart.

Urea cycle (Section 20.3): The metabolic pathway for con-verting ammonia into urea.

Uronic acid (Section 21.6): The monocarboxylic acidformed by oxidizing the –CH2OH end of a sugar withoutaffecting the –CHO end.

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Valence bond theory (Section 1.5): A bonding theory thatdescribes a covalent bond as resulting from the overlap oftwo atomic orbitals.

Valence shell (Section 1.4): The outermost electron shellof an atom.

Van der Waals forces (Section 2.12): Intermolecularforces that are responsible for holding molecules togetherin the liquid and solid states.

Vegetable oil (Section 23.1): A liquid triacylglycerolderived from a plant source.

Vinyl group (Section 6.2): An H2CUCHX substituent.

Vinyl monomer (Section 7.8): A substituted alkenemonomer used to make chain-growth polymers.

Vinylic (Section 8.7): A term that refers to a substituent ata double-bond carbon atom. For example, chloroethyleneis a vinylic chloride.

Virion (Chapter 22 Lagniappe): A viral particle.

Vitamin (Section 19.9): A small organic molecule thatmust be obtained in the diet and is required in traceamounts for proper growth and function.

Vulcanization (Chapter 7 Lagniappe): A technique forcross-linking and hardening a diene polymer by heatingwith a few percent by weight of sulfur.

Walden inversion (Section 10.4): The inversion of configu-ration at a chirality center that accompanies an SN2 reaction.

Wave equation (Section 1.2): A mathematical expressionthat defines the behavior of an electron in an atom.

Wave function (Section 1.2): A solution to the wave equa-tion for defining the behavior of an electron in an atom.The square of the wave function defines the shape of anorbital.

Wavelength, � (Section 11.5): The length of a wave frompeak to peak. The wavelength of electromagnetic radia-

tion is inversely proportional to frequency and inverselyproportional to energy.

Wavenumber, �� (Section 11.6): The reciprocal of thewavelength in centimeters.

Wax (Section 23.1): A mixture of esters of long-chain car-boxylic acids with long-chain alcohols.

Williamson ether synthesis (Section 13.8): A method forsynthesizing ethers by SN2 reaction of an alkyl halidewith an alkoxide ion.

Wittig reaction (Section 14.9): The reaction of a phospho-rus ylide with an aldehyde or ketone to yield an alkene.

X-ray crystallography (Chapter 17 Lagniappe): A tech-nique using X rays to determine the structure of molecules.

Ylide (Sections 14.9, 22.3): A neutral species with adja-cent � and � charges, such as the phosphoranes used inWittig reactions.

Z geometry (Section 6.4): A term used to describe thestereochemistry of a carbon–carbon double bond. The twogroups on each carbon are assigned priorities according tothe Cahn–Ingold–Prelog sequence rules, and the two car-bons are compared. If the high-priority groups on eachcarbon are on the same side of the double bond, the bondhas Z geometry.

Zaitsev’s rule (Section 10.10): A rule stating that E2 elim-ination reactions normally yield the more highly substi-tuted alkene as major product.

Zwitterion (Section 19.1): A neutral dipolar molecule in which the positive and negative charges are not adjacent. For example, amino acids exist as zwitterions,H3N�XCHRXCO2

�.

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A-31

AppendixAnswers to In-Text Problems

D

The following answers are meant only as a quickcheck while you study. Full answers for all prob-lems are provided in the accompanying StudyGuide and Solutions Manual.

CHAPTER 11.1 (a) 1s2 2s2 2p4 (b) 1s2 2s2 2p6 3s2 3p3

(c) 1s2 2s2 2p6 3s2 3p4

1.2 (a) 2 (b) 2 (� 7) (c) 6

1.3

1.4

1.5 (a) CH2Cl2 (b) CH3SH (c) CH3NH2

1.6

1.7 C2H7 has too many hydrogens for a compoundwith 2 carbons.

1.8

CHC

H All bond angles arenear 109°.

H H

C

H H

H H

C

Cl(a)

Cl

Cl S

H

H

C

H

H H

H N H

HClCH Cl

HS H

Cl

HCH HNH H

(b)

(c)

H

H

C

H H

HH

C

C

H

Cl ClCl

1.9

1.10 The CH3 carbon is sp3; the double-bond carbonsare sp2; the C�C–C and C�C–H bond angles areapproximately 120°; other bond angles are near109°.

1.11 All carbons are sp2, and all bond angles are near120°.

1.12 All carbons except CH3 are sp2.

1.13 The CH3 carbon is sp3, the triple-bond carbons aresp; the C�C–C and H–C�C bond angles areapproximately 180°.

CHH

H

H

C C

H

C

C

C

C

C

C

H

H

H

C H

CH3C

O

O

O

O

H H

CC

H H

HC H

C

C

H

C

H

HH

H H

C

C

H

H HC

H

H

H

C

H

C

H

C

H

H

H

C

H

H

H

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A-32 A P P E N D I X D: A N S W E R S TO I N -T E X T P R O B L E M S

1.14

1.15

1.16 There are numerous possibilities, such as:

1.17

C

H2N

O

OH

C5H12(a)

C2H7N(b)

C3H6O H2C CHCH2OH(c)

C4H9Cl

CH3CH2CH2CH2CH3

CH3CH2CHCH3

CH3CH2NH2 CH3NHCH3

CH3CH

CH3

CH3CH2CH2CH2Cl

CH3CH2CHCH3

(d)

O

Cl

H2C CHOCH3

CH3CCH3

CH3

CH3

CH3CHCH2Cl

CH3

HO

HO

OH(a)

(b)

NHCH3

O

HO

1 H

1 H

1 H

1 H

1 H

1 H

1 H

1 H

0 H

0 H

0 H

0 H

0 H

0 H

0 H2 H

2 H

2 H

2 H

2 H

2 H2 H

3 H

Adrenaline—C9H13NO3

Estrone—C18H22O2

OHC

HC

H HH(a)

(c)

(b)

(d)

H

SCH2CH2CHCOH

N

P

CH3

NH2

H3C

H3C

H3C

sp3—tetrahedral

sp3—tetrahedral

sp3—tetrahedral

sp3—tetrahedral

HHH

O

CHAPTER 22.1 (a) H (b) Br (c) Cl (d) C

2.2

2.3 H3CXOH � H3CXMgBr � H3CXLi �

H3CXF � H3CXK

2.4 The nitrogen is electron-rich, and the carbon iselectron-poor.

2.5 The two C–O dipoles cancel because of the sym-metry of the molecule:

2.6

2.7 (a) For carbon: FC � 4 � 8/2 � 0 � 0; for themiddle nitrogen: FC � 5 � 8/2 � 0 � �1; for the end nitrogen: FC � 5 � 4/2 � 4 � –1

(b) For nitrogen: FC � 5 � 8/2 � 0 � �1; for oxygen: FC � 6 � 2/2 � 6 � �1

(c) For nitrogen: FC � 5 � 8/2 � 0 � �1; for the end carbon: FC � 4 � 6/2 � 2 � �1

CH

No dipolemoment

HHHC

CHH

ClClC

C

H(a) (b)

(c) (d)

Cl ClCl

C

Cl

H ClH

H H

H H

CHO C

OH

C

NH2

H HH �+

�–

�+ �–ClH3C

�+ �–

�+ �–

NH2H3C�– �+

HH2N

SH

(a) (b) (c)

(d) (e) (f)H3C

Carbon and sulfurhave identicalelectronegativities.

MgBrH3C�– �+

FH3C

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A P P E N D I X D: A N S W E R S TO I N -T E X T P R O B L E M S A-33

2.8

2.9

2.10

2.11 Phenylalanine is stronger.

2.12 Water is a stronger acid.

2.13 Neither reaction will take place.

2.14 Reaction will take place.

2.15 Ka � 4.9 � 10�10

+ +NO3H NH3 NH4+NO3

–

Acid Base Conjugatebase

Conjugateacid

O(a)

(b)

(c)

(d)

–O

– O

–O

O

CH3OP

–O

– O

O

OCH3OP

–O

–O

OCH3O

P

N

–

++O

–– O–

OON

+O

–O

N

H2C CH CH2 H2C CH CH2

CO

O

–

CO

–

CO

O–

CO

O–

O

+ +

O

H

H C

H

O

O

P

O

0

-1

2.16

2.17

H

H

HH

More basic (red)(a)

(b)

Most acidic (blue)

ImidazoleNN

H

H

HH

NN

H

H

H

HH

NN

HA

+

H

H

H

HH

NN +

H

H

HH

NN B

H

HH

N

H

HH

N–

N

–N

CH3CH2OH + H Cl

(a)

(b)

H

CH3CH2OH + Cl–

HN(CH3)2 HN(CH3)2+ H Cl

H+

+

+ Cl–

P(CH3)3 P(CH3)3+ H Cl H+

–

+ Cl–

HO +CH3 CH3+�

HO

HO B(CH3)3 B(CH3)3+�

HO

–HO MgBr2 MgBr2+

�HO

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2.18 Vitamin C is water-soluble (hydrophilic); vitamin Ais fat-soluble (hydrophilic).

CHAPTER 33.1 (a) Sulfide, carboxylic acid, amine

(b) Aromatic ring, carboxylic acid

(c) Ether, alcohol, aromatic ring, amide, C�Cbond

3.2

3.3

3.4

3.5 Part (a) has nine possible answers.

3.6 (a) Two (b) Four (c) Four

CH3CH2CH2COCH3

CH3CH2SSCH2CH3 CH3SSCH2CH2CH3 CH3SSCHCH3

O(a)

(b)

CH3CH2COCH2CH3

O

CH3COCHCH3

O CH3

CH3

CH3CHCH2CH2CH3

CH3

CH3CCH2CH3

CH3

CH3

CH3

CH3CHCHCH3

CH3

CH3CH2CHCH2CH3

CH3

CH3CH2CH2CH2CH2CH3

CO

CH3H3C

O

Amine

Ester

N

Double bond

C8H13NO2

CH3OH

CH3COH

(a)

CH3NH2(d)

(b) (c)

(f)

CH3 O

CH3CCH2NH2

(e) O

3.7

3.8

3.9 Primary carbons have primary hydrogens, sec-ondary carbons have secondary hydrogens, andtertiary carbons have tertiary hydrogens.

3.10

3.11 (a) Pentane, 2-methylbutane, 2,2-dimethylpropane

(b) 3,4-Dimethylhexane

(c) 2,4-Dimethylpentane

(d) 2,2,5-Trimethylheptane

3.12

CH3

CH3CH2CH2CH2CH2CHCHCH2CH3

CH3(a)

CH3CCH2CH3

CH3

CH3

CH3

CH3CHCHCH3

CH3(a)

CH3CH2CHCH2CH3

CH3CHCH3(b)

(c)

CH3CHCH2 C

CH3

CH3

CH3

CH3

p

p p

p p

p

p

pt s s p p

pqp

t

t

s s

t s

CH3CHCH2CH2CH3

CH3(a)

CH3CH2CHCH2CH3

CH3CHCH3(b)

(c)

CH3CH2CH2CH2CH2

CH3

CH3

CH3CHCH2CH2

CH3

CH3

CH3CH2C

CH3

CH3

CH3CCH2

CH3

CH3

CH3CHCH

CH3CH2CH2CH

CH3

CH3CH2CHCH2

CH2CH3

CH3CH2CH

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3.13 Pentyl, 1-methylbutyl, 1-ethylpropyl, 2-methyl-butyl, 3-methylbutyl, 1,1-dimethylpropyl, 1,2-dimethylpropyl, 2,2-dimethylpropyl

3.14

3.15

3.16

0° 60° 120° 180° 240° 300° 360°

16 kJ/mol

6.0 kJ/mol4.0 kJ/mol

H H

CH3(b)CH3

CH3 CH3

H

HHH

HH

En

erg

y

(a)

(c), (d)

0° 60° 120° 180°

Angle of rotation

240° 300° 360°

14 kJ/mol

H HH

H3CH

H

H3C

H HH

HH

H HH

H3CH

H

H3C

H HH

HH

H HH

H3CH

H H HH

H3CH

H

H3C

H HH

HH

En

erg

y

3,3,4,5-Tetramethylheptane

CH3CH2CH2C

CH3 CH2CH3

CH3

CHCH2CH3

CH3CH2CH2CH2CHCH2C(CH3)3

CH2CH2CH3

(b)

CH3CHCH2CCH3

CH3

CH3

CH3(d)

(c)

3.17

3.18

CHAPTER 44.1 (a) 1,4-Dimethylcyclohexane

(b) 1-Methyl-3-propylcyclopentane

(c) 3-Cyclobutylpentane

(d) 1-Bromo-4-ethylcyclodecane

(e) 1-Isopropyl-2-methylcyclohexane

(f) 4-Bromo-1-tert-butyl-2-methylcycloheptane

4.2

4.3 3-Ethyl-1,1-dimethylcyclopentane

4.4 (a) trans-1-Chloro-4-methylcyclohexane

(b) cis-1-Ethyl-3-methylcycloheptane

4.5 (b)(a)

(c)

Br

HH3C

H

CH2CH3

CH3

H

H

CH3

H

C(CH3)3H

CH3

CH3

CH3

Cl

Cl

(b)

BrBr

(a)

(c) (d)

CH33.8 kJ/mol

3.8 kJ/mol

3.8 kJ/mol Total: 11.4 kJ/molCH3CH3

CH3

H

H

CH3

CH3CH3

H3C

H

H

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4.6 The two hydroxyl groups are cis. The two sidechains are trans.

4.7 (a) cis-1,2-Dimethylcyclopentane

(b) cis-1-Bromo-3-methylcyclobutane

4.8 Six interactions; 21% of strain

4.9 The cis isomer is less stable because the methylgroups eclipse each other.

4.10 Ten eclipsing interactions; 40 kJ/mol; 35% isrelieved.

4.11 Conformation (a) is more stable because themethyl groups are farther apart.

4.12

4.13

4.14 Before ring-flip, red and blue are equatorial andgreen is axial. After ring-flip, red and blue areaxial and green is equatorial.

4.15 4.2 kJ/mol

4.16 Cyano group points straight up.

4.17 (a) 2.0 kJ/mol (b) 11.4 kJ/mol

(c) 2.0 kJ/mol (d) 8.0 kJ/mol

4.18

4.19 trans-Decalin is more stable because it has no 1,3-diaxial interactions.

CHAPTER 55.1 (a) Substitution (b) Elimination (c) Addition

5.2 1-Chloro-2-methylpentane, 2-chloro-2-methyl-pentane, 3-chloro-2-methylpentane, 2-chloro-4-methylpentane, 1-chloro-4-methylpentane

a

a

eCH3 Less stable chair form

CH3

Cl

a

a

e

e

CH3

CH3

CH3

H3C

OHa e

OH

5.3

5.4 (a) Carbon is electrophilic.

(b) Sulfur is nucleophilic.

(c) Nitrogens are nucleophilic.

(d) Oxygen is nucleophilic; carbon is electrophilic.

5.5

5.6 Cyclohexanol (hydroxycyclohexane)

5.7

5.8

5.9

CH

C

CO2–

CO2–

CO2–CH2

–O2C–O2C

CH2CO2–H2O+

H H

C

H

C

H

H

O+

H

H

O

NH3+ClCl(a)

(c)

ClNH3+ + Cl–

+ Cl–

CH3O + BrH3C(b) CH3OCH3 + Br–

�

�O O

H3C OCH3C

H3CCl

CH3C

CH3H3C

CH3

C+

Electrophilic;vacant p orbital

F F

F

B

H

O

OCO2H

H

CO2H

H

H

O

O

H

H

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5.10 Negative �G° is more favored.

5.11 Larger Keq is more exergonic.

5.12 Lower �G‡ is faster.

5.13

CHAPTER 66.1 (a) 2 (b) 3 (c) 3 (d) 5 (e) 5 (f) 3

6.2 (a) 1 (b) 2 (c) 2

6.3 C16H13ClN2O

6.4 (a) 3,4,4-Trimethylpent-1-ene

(b) 3-Methylhex-3-ene

(c) 4,7-Dimethylocta-2,5-diene

(d) 6-Ethyl-7-methylnon-4-ene

(e) 1,2-Dimethylcyclohexene

(f) 4,4-Dimethylcycloheptene

(g) 3-Isopropylcyclopentene

6.5

H2C CHCH2CH2C CH2

(a)

(b)

(c)

CH3CH2CH2CH

CH3CH CHCH3

CH3CH CHCH3

CC(CH3)3

CH2CH3

CH3

CH3CH CHCH CHC C CH2

CH3

CH3

CH3

(d)

C C

CH3

CH3CH3

CH3

Intermediate

Product

Reactant�G�

�G‡

Reaction progress

En

erg

y

6.6 (a) 2,5-Dimethylhex-3-yne

(b) 3,3-Dimethylbut-1-yne

(c) 3,3-Dimethyloct-4-yne

(d) 2,5,5-Trimethylhept-3-yne

(e) 6-Isopropylcyclodecyne

6.7

6.8 Compounds (c), (e), and (f) have cis–trans isomers.

6.9 (a) cis-4,5-Dimethylhex-2-ene

(b) trans-6-Methylhept-3-ene

6.10 (a) –Br (b) –Br (c) –CH2CH3

(d) –OH (e) –CH2OH (f) –CH�O

6.11 (a) –Cl, –OH, –CH3, –H

(b) –CH2OH, –CH�CH2, –CH2CH3, –CH3

(c) –CO2H, –CH2OH, –C�N, –CH2NH2

(d) –CH2OCH3, –C�N, –C�CH, –CH2CH3

6.12 (a) Z (b) E (c) Z (d) E

6.13

6.14 (a) 2-Methylpropene is more stable than but-1-ene.

(b) trans-Hex-2-ene is more stable than cis-hex-2-ene.

(c) 1-Methylcyclohexene is more stable than 3-methylcyclohexene.

6.15 (a) Chlorocyclohexane

(b) 2-Bromo-2-methylpentane

(c) 2-Hydroxy-4-methylpentane

(d) 1-Bromo-1-methylcyclohexane

6.16 (a) Cyclopentene

(b) 1-Ethylcyclohexene or ethylidenecyclohexane

(c) Hex-3-ene (d) Cyclohexylethylene

6.17CH2CH3CH3CH2CCH2CHCH3

CH3(a) (b) +

+

CH3

CO2CH3

CH2OHZ

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6.18 In the conformation shown, only the methyl-group C–H that is parallel to the carbocation p orbital can show hyperconjugation.

6.19 The second step is exergonic; the transition stateresembles the carbocation.

6.20

CHAPTER 77.1 2-Methylbut-2-ene and 2-methylbut-1-ene

7.2 Five

7.3 trans-1,2-Dichloro-1,2-dimethylcyclohexane

7.4

7.5 Markovnikov orientation

7.6 (a) Oxymercuration: 2-methylpentan-2-ol; hydroboration: 2-methylpentan-3-ol

(b) Oxymercuration: 1-ethylcyclohexanol; hydroboration: 1-cyclohexylethanol

7.7 (a) From 3-methylbut-1-ene by hydroboration

(b) From 2-methylbut-2-ene by hydroboration orfrom 3-methylbut-1-ene by oxymercuration

(c) From methylenecyclohexane by hydroboration

7.8 CH3

H3C

H

OH

H

H

and

CH3

H3C

HOH

H

H

CH3Cl

CH3H

ClCH3

CH3

and

H

CCH2

HH

H Br

HH

+

Br

Br H H

+

�

7.9 (a) 2-Methylpentane

(b) 1,1-Dimethylcyclopentane

7.10

7.11 (a) 1-Methylcyclohexene

(b) 2-Methylpent-2-ene (c) Buta-1,3-diene

7.12 (a) H2CUCHOCH3 (b) ClCHUCHCl

7.13

7.14 1,2-Addition: 4-chloropent-2-ene, 3-chloropent-1-ene

1,4-Addition: 4-chloropent-2-ene, 1-chloropent-1-ene

7.15 1,2-Addition: 6-bromo-1,6-dimethylcyclohexene

1,4-Addition: 3-bromo-1,2-dimethylcyclohexene

7.16 (a) 1,1,2,2-Tetrachloropentane

(b) 1-Bromo-1-cyclopentylethylene

(c) 2-Bromohept-2-ene and 3-bromohept-2-ene

CHAPTER 88.1 (a) Meta (b) Para (c) Ortho

8.2 (a) m-Bromochlorobenzene

(b) (3-Methylbutyl)benzene

(c) p-Bromoaniline

(d) 2,5-Dichlorotoluene

(e) 1-Ethyl-2,4-dinitrobenzene

(f) 1,2,3,5-Tetramethylbenzene

8.3

NH2H3C

CH3

Br

Cl(a)

Br

CH3

ClH3C

(b)

(c) (d)

CH2CH2 +

CH2CH3

CH CH2

+ CH CH2

H

H3C CH3

O

H HC C cis-2,3-Epoxybutane

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8.4 Pyridine has an aromatic sextet of electrons.

8.5 Cyclodecapentaene is not flat because of stericinteractions.

8.6 The thiazolium ring has six � electrons.

8.7

8.8 The three nitrogens in double bonds each con-tribute one; the remaining nitrogen contributestwo.

8.9 o-, m-, and p-Bromotoluene

8.10 o-Xylene: 2; m-xylene: 3; p-xylene: 1

8.11 D� does electrophilic substitutions on the ring.

8.12 No rearrangement: (a), (b), (e)

8.13 tert-Butylbenzene

8.14 (a) (CH3)2CHCOCl (b) PhCOCl

8.15 (a) Phenol Toluene Benzene Nitrobenzene

(b) Phenol Benzene Chlorobenzene

Benzoic acid

(c) Aniline Benzene Bromobenzene

Benzaldehyde

8.16 (a) Methyl m-nitrobenzoate

(b) m-Bromonitrobenzene

(c) o- and p-Chlorophenol

(d) o- and p-Bromoaniline

NR+

S

RR

H

N

H H

H H

H Pyridine

8.17

8.18 (a) m-Chlorobenzonitrile

(b) o- and p-Bromochlorobenzene

8.19 (a) m-Nitrobenzoic acid

(b) p-tert-Butylbenzoic acid

8.20 1. PhCOCl, AlCl3; 2. H2/Pd

8.21 (a) 1. HNO3, H2SO4; 2. Cl2, FeCl3

(b) 1. CH3COCl, AlCl3; 2. Cl2, FeCl3; 3. H2, Pd

(c) 1. CH3CH2COCl, AlCl3; 2. H2, Pd; 3. Cl2, FeCl3

(d) 1. CH3Cl, AlCl3; 2. SO3, H2SO4; 3. Br2, FeBr3

NO2

H

Cl+

NO2

Ortho intermediate:

H

Cl

+

NO2

H

Cl+

NO2

H

Cl

+

NO2

H

+

NO2

Para intermediate:

H

Cl

+

Cl

ClCl

NO2

H

+

NO2

H

+

NO2

H

+

NO2

Meta intermediate:

HCl

+

Cl

Cl

NO2

H

+

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8.22 (a) The Friedel–Crafts reaction in step 1 will nottake place on a cyano-substituted benzene.

(b) The Friedel–Crafts reaction will occur with acarbocation rearrangement, and the wrongisomer will be obtained on chlorination.

CHAPTER 99.1 Chiral: screw, beanstalk, shoe

9.2

9.3

9.4

9.5 Levorotatory

9.6 �16.1

9.7 (a) –OH, –CH2CH2OH, –CH2CH3, –H

(b) –OH, –CO2CH3, –CO2H, –CH2OH

(c) –NH2, –CN, –CH2NHCH3, –CH2NH2

(d) –SSCH3, –SH, –CH2SCH3, –CH3

9.8 (a) S (b) R (c) S

9.9 (a) S (b) S (c) R

9.10

C

H

HO CH2CH2CH3H3C

CC

CC

OHO

HO H

* **

H OHHH

H(a) (b)

CC

OC

HH

F F

ClF

F F

C andH CH3

CO2H

H2N

CH3C H

CO2H

NH2

(a) (b)

(c)

N

*

*

**

* **

H

CH2CH2CH3 CH3

CH3O

HO

H

HH

N CH3H

9.11 S

9.12 (a) R,R (b) S,R (c) R,S (d) S,S

Compounds (a) and (d) are enantiomers and arediastereomeric with (b) and (c).

9.13 S,S

9.14 Five chirality centers; 32 stereoisomers

9.15 Compounds (a) and (d) are meso.

9.16 Compounds (a) and (c) have meso forms.

9.17

9.18 The product retains its S stereochemistry.

9.19 Two diastereomeric salts are formed: (R)-lacticacid plus (S)-1-phenylethylamine and (S)-lacticacid plus (S)-1-phenylethylamine.

9.20 (a) Constitutional isomers (b) Diastereomers

9.21 An optically inactive, non-50�50 mixture of tworacemic pairs: (2R,4R) � (2S,4S) and (2R,4S) �

(2S,4R)

9.22 Non-50�50 mixture of two racemic pairs:(1S,3R) � (1R,3S) and (1S,3S) � (1R,3R)

9.23

9.24

9.25 (S)-Lactate

OH3C

CH2OHC

Re face(a)

Si face

CH3C

H

HCH2OH

C

Re face

Si face

(b)

CHOHO

HH(a) pro-S pro-R

HHO

CO2–

H3C

HH

HH3N

(b) pro-R pro-S

+

H3C

OH

CH3

Meso

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9.26 The –OH adds to the Re face of C2, and –H adds tothe Re face of C3. The overall addition has antistereochemistry.

CHAPTER 1010.1 (a) 1-Iodobutane (b) 1-Chloro-3-methylbutane

(c) 1,5-Dibromo-2,2-dimethylpentane

(d) 1,3-Dichloro-3-methylbutane

(e) 1-Chloro-3-ethyl-4-iodopentane

(f) 2-Bromo-5-chlorohexane

10.2 (a) CH3CH2CH2C(CH3)2CH(Cl)CH3

(b) CH3CH2CH2C(Cl)2CH(CH3)2

(c) CH3CH2C(Br)(CH2CH3)2

10.3 (a) 2-Methylpropan-2-ol � HCl

(b) 4-Methylpentan-2-ol � PBr3

(c) 5-Methylpentan-1-ol � PBr3

(d) 2,4-Dimethylhexan-2-ol � HCl

10.4 Both reactions occur.

10.5 React Grignard reagent with D2O.

10.6 (R)-1-Methylpentyl acetate,CH3CO2CH(CH3)CH2CH2CH2CH3

10.7 (S)-Butan-2-ol

CH3CH2CH2CH2CH2CHCH2CHCH3

CH3CHCH2CH3

Cl

Br

Br(d)

(e)

(f)

Br

Br

10.8

10.9 (a) 1-Iodobutane (b) Butan-1-ol

(c) Butylammonium bromide

10.10 (a) (CH3)2N� (b) (CH3)3N (c) H2S

10.11 CH3OTos CH3Cl (CH3)2CHCl CH3NH2

10.12 Similar rate to protic solvents because the transi-tion state is not stabilized

10.13 Racemic 1-ethyl-1-methylhexyl acetate

10.14 Racemic 2-phenylbutan-2-ol

10.15 H2CUCHCH(Br)CH3 �

(CH3)3CBr CH3CH(Br)CH3 H2CUCHBr

10.16 The same allylic carbocation intermediate isformed in both reactions.

10.17 (a) SN1 (b) SN2

10.18

10.19 (a) Major: 2-methylpent-2-ene; minor: 4-methylpent-2-ene

(b) Major: 2,3,5-trimethylhex-2-ene; minor: 2,3,5-trimethylhex-3-ene and 2-isopropyl-4-methylpent-1-ene

(c) Major: ethylidenecyclohexane; minor: cyclohexylethylene

10.20 (a) 1-Bromo-3,6-dimethylheptane

(b) 4-Bromo-1,2-dimethylcyclopentane

10.21 (Z)-1-Bromo-1,2-diphenylethylene

OPP PPi

H Base

Linalyl diphosphate

Limonene

+

+

(R) CH3CHCH2CHCH3

SCH3

(S)-2-Bromo-4-methylpentane

CH3

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10.22 (Z)-3-Methylpent-2-ene

10.23 The cis isomer reacts faster because the bromineis axial.

10.24 (a) SN2 (b) E2 (c) SN1 (d) E1cB

CHAPTER 1111.1 C19H28O2

11.2 (a) 2-Methylpent-2-ene (b) Hex-2-ene

11.3 (a) 43, 71 (b) 82 (c) 58 (d) 86

11.4 102 (M�), 84 (dehydration), 87 (alpha cleavage),59 (alpha cleavage)

11.5 X-ray energy is higher. � � 9.0 � 10�6 m is higher in energy.

11.6 (a) 2.4 � 106 kJ/mol (b) 4.0 � 104 kJ/mol

(c) 2.4 � 103 kJ/mol (d) 2.8 � 102 kJ/mol

(e) 6.0 kJ/mol (f) 4.0 � 10�2 kJ/mol

11.7 (a) Ketone or aldehyde (b) Nitro compound

(c) Carboxylic acid

11.8 (a) CH3CH2OH has an –OH absorption.

(b) Hex-1-ene has a double-bond absorption.

(c) CH3CH2CO2H has a very broad –OH absorption.

11.9 (a) 1715 cm�1 (b) 1730, 2100, 3300 cm�1

(c) 1720, 2500–3100 cm�1, 3400–3650 cm�1

11.10 1690, 1650, 2230 cm�1

11.11 300–600 kJ/mol; UV energy is greater than IR energy.

11.12 1.46 � 10�5 M

11.13 All except (a) have UV absorptions.

CHAPTER 1212.1 7.5 � 10�5 kJ/mol for 19F;

8.0 � 10�5 kJ/mol for 1H

(CH3)3C

Br

H

12.2 The vinylic C–H protons are nonequivalent.

12.3 (a) 7.27 � (b) 3.05 � (c) 3.46 � (d) 5.30 �

12.4 (a) 420 Hz (b) 2.1 � (c) 1050 Hz

12.5 (a) 4 (b) 7 (c) 4 (d) 5 (e) 5 (f) 7

12.6 (a) 1,3-Dimethylcyclopentene

(b) 2-Methylpentane

(c) 1-Chloro-2-methylpropane

12.7 –CH3, 9.3 �; –CH2–, 27.6 �, C�O, 174.6 �, –OCH3, 51.4 �

12.8

12.9

12.10

12.11 A DEPT-90 spectrum would show two absorp-tions for the non-Markovnikov product(RCHUCHBr) but no absorptions for theMarkovnikov product (RBrCUCH2).

12.12 (a) Enantiotopic (b) Diastereotopic

(c) Diastereotopic (d) Diastereotopic

(e) Diastereotopic (f) Homotopic

12.13 (a) 2 (b) 4 (c) 3 (d) 4 (e) 5 (f) 3

12.14 4

C CH3

CH3

CH3

CH2

C

O

O

CH2 CH3

DEPT-135 (+)DEPT-135 (–)

H3CDEPT-135 (+)

H3CDEPT-135 (+) H DEPT-90, DEPT-135 (+)

C

C

OH23, 26 �

132 �124 �

39 �24 �

68 �18 �

C

Hb

c

a

H Cl

C

CH3

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12.15 (a) 1.43 � (b) 2.17 � (c) 7.37 �

(d) 5.30 � (e) 9.70 � (f) 2.12 �

12.16 Seven kinds of protons

12.17 Two peaks; 3�2 ratio

12.18 (a) –CHBr2, quartet; –CH3, doublet

(b) CH3O–, singlet; –OCH2–, triplet; –CH2Br, triplet

(c) ClCH2–, triplet; –CH2–, quintet

(d) CH3–, triplet; –CH2–, quartet; –CH–, septet; (CH3)2, doublet

(e) CH3–, triplet; –CH2–, quartet; –CH–, septet; (CH3)2, doublet

(f) �CH, triplet, –CH2–, doublet; aromatic C–H, two multiplets

12.19 (a) CH3OCH3 (b) CH3CH(Cl)CH3

(c) ClCH2CH2OCH2CH2Cl

(d) CH3CH2CO2CH3 or CH3CO2CH2CH3

12.20 CH3CH2OCH2CH3

12.21 J1–2 � 16 Hz; J2–3 � 8 Hz

12.22 1-Chloro-1-methylcyclohexane has a singletmethyl absorption; 1-chloro-2-methylcyclohexanehas a doublet.

CHAPTER 1313.1 (a) 5-Methylhexane-2,4-diol

(b) 2-Methyl-4-phenylbutan-2-ol

(c) 4,4-Dimethylcyclohexanol

(d) trans-2-Bromocyclopentanol

(e) 2-Methylheptane-4-thiol

(f) Cyclopent-2-ene-1-thiol

CH2Br

J1–2 = 16 Hz

J2–3 = 8 Hz

C

H

H2

3

1

C

13.2

13.3 (a) p-Methylphenol � Phenol �

p-(Trifluoromethyl)phenol

(b) Benzyl alcohol � Phenol �

p-Hydroxybenzoic acid

13.4 The electron-withdrawing nitro group stabilizesan alkoxide ion, but the electron-donatingmethoxyl group destabilizes the anion.

13.5 Thiophenol is more acidic because the anion isresonance-stabilized.

13.6 (a) Benzaldehyde or benzoic acid (or ester)

(b) Acetophenone

(c) Cyclohexanone

(d) 2-Methylpropanal or 2-methylpropanoic acid(or ester)

13.7 (a) 1-Methylcyclopentanol

(b) 3-Methylhexan-3-ol

13.8 (a) Acetone � CH3MgBr, or ethyl acetate� 2 CH3MgBr

(b) Cyclohexanone � CH3MgBr

(c) Butan-2-one � PhMgBr, or ethyl phenylketone � CH3MgBr, or acetophenone� CH3CH2MgBr

(e) Formaldehyde � PhMgBr

13.9 Cyclohexanone � CH3CH2MgBr

13.10 (a) 2-Methylpent-2-ene

(b) 3-Methylcyclohexene

(c) 1-Methylcyclohexene

OHCH3CH

CH2CH3

C

CH2OH(a)

(c)

(e)

(b)

(d)

(f)

CH3CHCH2CH2CH2SH

SHH

H OHCl

CH3

OH

H3C

OH

CH2CH2OH

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13.11 (a) 1-Phenylethanol (b) 2-Methylpropan-1-ol

(c) Cyclopentanol

13.12 (a) Hexanoic acid, hexanal (b) Hexan-2-one

(c) Hexanoic acid, no reaction

13.13 1. LiAlH4; 2. PBr3; 3. (H2N)2CUS; 4. H2O, NaOH

13.14 (a) Diisopropyl ether

(b) Cyclopentyl propyl ether

(c) p-Bromoanisole or 4-bromo-1-methoxybenzene

(d) 1-Methoxycyclohexene

(e) Benzyl methyl sulfide

(f) Allyl methyl sulfide

13.15 A mixture of diethyl ether, dipropyl ether, andethyl propyl ether is formed in a 1�1�2 ratio.

13.16 (a) CH3CH2CH2O� � CH3Br

(b) PhO� � CH3Br

(c) (CH3)2CHO� � PhCH2Br

(d) (CH3)3CCH2O� � CH3CH2Br

13.17 (a) Bromoethane 2-Bromopropane

Bromobenzene

(b) Bromoethane Chloroethane

1-Iodopropene

13.18

13.19 Protonation of the oxygen atom, followed by E1 reaction

PREVIEW OF CARBONYL CHEMISTRY1. Acetyl chloride is more electrophilic than acetone.

2.

3. (a) Nucleophilic acyl substitution

(b) Nucleophilic addition

(c) Carbonyl condensation

H3C CH3

O

C C

O–

H3C CNH3C

C

OH

H3C CNH3C

–CN H3O+

CH3CH2CH2Br+CH3CH2CHOH

CH3(b)

CH3OH+

(a)

Br

CHAPTER 1414.1 (a) 2-Methylpentan-3-one

(b) 3-Phenylpropanal

(c) Octane-2,6-dione

(d) trans-2-Methylcyclohexanecarbaldehyde

(e) Hex-4-enal

(f) cis-2,5-Dimethylcyclohexanone

14.2

14.3 (a) 1. CH3COCl, AlCl3; 2. Br2, FeBr3

(b) 1. Mg; 2. CH3CHO, then H3O�; 3. PCC

(c) 1. BH3, then H2O2, NaOH; 2. PCC

14.4

14.5 The electron-withdrawing nitro group in p-nitrobenzaldehyde polarizes the carbonylgroup.

14.6 CCl3CH(OH)2

14.7 Labeled water adds reversibly to the carbonylgroup.

14.8

14.9 The steps are the exact reverse of the forwardreaction.

14.10

N(CH2CH3)2(CH3CH2)2NH+O

NCH2CH3

and

N(CH2CH3)2

OH

CN

CH3CHCH2CHO

CH3(a) (b)

(c) (d)

(e) (f)

CH3CHCH2CCH3

Cl O

H2C CCH2CHO

CH3

CH3CH2CHCH2CH2CHCHO

CH3 CH3CHCl

CH2CHO HCHO

H(CH3)3C

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14.11 The mechanism is identical to that between aketone and 2 equivalents of a monoalcohol (seeFigure 14.10, p. 573).

14.12

14.13 (a) Cyclohexanone � CH3CHUP(Ph)3

(b) Cyclohexanecarbaldehyde � H2CUP(Ph)3

(c) Acetone � CH3CH2CH2CHUP(Ph)3

(d) Acetone � PhCHUP(Ph)3

(e) Acetophenone � PhCHUP(Ph)3

(f) Cyclohex-2-enone � H2CUP(Ph)3

14.14

14.15 Addition of the pro-R hydrogen of NADH takesplace on the Re face of pyruvate.

14.16 The –OH group adds to the Re face at C2, and –H adds to the Re face at C3, to yield (2R,3S)-isocitrate.

14.17

14.18 Look for the presence or absence of a saturatedketone absorption in the product.

14.19 (a) 1715 cm�1 (b) 1685 cm�1

(c) 1750 cm�1 (d) 1705 cm�1

(e) 1715 cm�1 (f) 1705 cm�1

14.20 (a) Different peaks due to McLafferty rearrangement

(b) Different peaks due to � cleavage and McLafferty rearrangement

(c) Different peaks due to McLafferty rearrangement

14.21 IR: 1750 cm�1; MS: 140, 84

CNO

2

CHOCH3O2C

CH3OH

CH3

+

CHAPTER 1515.1 (a) 3-Methylbutanoic acid

(b) 4-Bromopentanoic acid

(c) 2-Ethylpentanoic acid

(d) cis-Hex-4-enoic acid

(e) 2,4-Dimethylpentanenitrile

(f) cis-Cyclopentane-1,3-dicarboxylic acid

15.2

15.3 Dissolve the mixture in ether, extract with aque-ous NaOH, separate and acidify the aqueous layer,and extract with ether.

15.4 43%

15.5 (a) 82% dissociation (b) 73% dissociation

15.6 Lactic acid is stronger because of the inductiveeffect of the –OH group.

15.7 The dianion is destabilized by repulsion betweencharges.

15.8 More reactive

15.9 (a) 1. Mg; 2. CO2, then H3O�

(b) 1. Mg; 2. CO2, then H3O� or 1. NaCN; 2. H3O� with heat

15.10 1. NaCN; 2. H3O�; 3. LiAlH4 or Grignard carboxylation, then LiAlH4

15.11 1. H3O� with heat; 2. LiAlH4

15.12 A carboxylic acid has a very broad –OH absorp-tion at 2500–3300 cm�1.

15.13 4-Hydroxycyclohexanone: H–C–O absorption near4 � in 1H spectrum and C�O absorption near 210 � in 13C spectrum. Cyclopentanecarboxylicacid: –CO2H absorption near 12 � in 1H spectrumand –CO2H absorption near 170 � in 13C spectrum.

CO2H

(c)

(e)

CO2H

H

H

CO2H

(d) CO2H

OH

CH3CH2CH2CHCHCO2H

CH3(a) H3C

CH3CH2CH CHCN(f)

CH3CHCH2CH2CO2H

CH3(b)

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CHAPTER 1616.1 (a) 4-Methylpentanoyl chloride

(b) Cyclohexylacetamide

(c) Isopropyl 2-methylpropanoate

(d) Benzoic anhydride

(e) Isopropyl cyclopentanecarboxylate

(f) Cyclopentyl 2-methylpropanoate

(g) N-Methylpent-4-enamide

(h) (R)-2-Hydroxypropanoyl phosphate

(i) Ethyl 2,3-Dimethylbut-2-enethioate

16.2

16.3

16.4 The electron-withdrawing trifluoromethyl grouppolarizes the carbonyl carbon.

COCH3OCH3

O Cl

CCl

O

COCH3

O

�

�

(h)COBr

CH3

H

H

(d)

CO2CH3

CH3

C6H5CO2C6H5(a)

(g)

CH3CH2CH2CON(CH3)CH2CH3(b)

(CH3)2CHCH2CH(CH3)COCl(c)

(e) (f)O

CH3CH2CCH2COCH2CH3

O

CSCH3

Br

O

O

OH CH2CH3C C

O

16.5 (a) CH3CO2� Na� (b) CH3CONH2

(c) CH3CO2CH3 � CH3CO2� Na�

(d) CH3CONHCH3

16.6

16.7 (a) Acetic acid � butan-1-ol

(b) Butanoic acid � methanol

16.8

16.9 (a) Propanoyl chloride � methanol

(b) Acetyl chloride � ethanol

(c) Benzoyl chloride � ethanol

16.10 Benzoyl chloride � cyclohexanol

16.11 This is a typical nucleophilic acyl substitutionreaction, with morpholine as the nucleophile andchloride as the leaving group.

16.12 (a) Propanoyl chloride � methylamine

(b) Benzoyl chloride � diethylamine

(c) Propanoyl chloride � ammonia

16.13 This is a typical nucleophilic acyl substitutionreaction, with p-hydroxyaniline as the nucleo-phile and acetate ion as the leaving group.

16.14 Monomethyl ester of benzene-1,2-dicarboxylicacid

16.15 Reaction of a carboxylic acid with an alkoxide iongives the carboxylate ion.

16.16 HOCH2CH2CH2CHO

16.17 (a) CH3CH2CH2CH(CH3)CH2OH

(b) PhOH � PhCH2OH

16.18 (a) H2O, NaOH (b) Product of (a), then LiAlH4

(c) LiAlH4

O

O

OCH3

–OCH3+

OH–

O

OH

O

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16.19 1. Mg; 2. CO2, then H3O�; 3. SOCl2; 4. (CH3)2NH; 5. LiAlH4

16.20

16.21

16.22

16.23 (a) Ester (b) Acid chloride (c) Carboxylic acid

(d) Aliphatic ketone or cyclohexanone

n

O O

NH CNH C

OCH2CH2CH2OCH2CH2CH2

O

(a)

O

OCH2CH2OC(CH2)6Cn

n

n

O O

NH(CH2)6NHC(CH2)4C

(b)

(c)

H3C O

O

CO Adenosine

RS HBase

O

P

O–

H3C S

O

C R

H3C OS

R

CO Adenosine

O

P

O–

–O+

O Adenosine

Acetyl CoA

O

P

O–

�O

16.24 (a) CH3CH2CH2CO2CH2CH3 and other possibilities

(b) CH3CON(CH3)2

(c) CH3CHUCHCOCl or H2CUC(CH3)COCl

CHAPTER 1717.1

17.2

17.3 (a) CH3CH2CHO (b) (CH3)3CCOCH3

(c) CH3CO2H (d) PhCONH2

(e) CH3CH2CH2CN (f) CH3CON(CH3)2

17.4 � CH2C N H2C �NC

O

O

O

O

OH

Equivalent;more stable

OH

O

O

OH

OH

Equivalent;less stable

(b)(a)

H2C CSCH3

OH

CH3CH COH

OH

PhCH CCH3 or

OH

PhCH2C CH2

OH

(c) (d)

(e)

H2C COCH2CH3

OH CH3CH CHOH

OH

(f)

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17.5 (a) 1. Na� �OEt; 2. PhCH2Br; 3. H3O�

(b) 1. Na� �OEt; 2. CH3CH2CH2Br; 3. Na� �OEt;4. CH3Br; 5. H3O�

(c) 1. Na� �OEt; 2. (CH3)2CHCH2Br; 3. H3O�

17.6 1. Na� �OEt; 2. (CH3)2CHCH2Br; 3. Na� �OEt; 4. CH3Br; 5. H3O�

17.7 (a) (CH3)2CHCH2Br (b) PhCH2CH2Br

17.8 None can be prepared.

17.9 1. 2 Na� �OEt; 2. BrCH2CH2CH2CH2Br; 3. H3O�

17.10 (a) Alkylate phenylacetone with CH3I

(b) Alkylate pentanenitrile with CH3CH2I

(c) Alkylate cyclohexanone with H2CUCHCH2Br

(d) Alkylate cyclohexanone with excess CH3I

(e) Alkylate C6H5COCH2CH3 with CH3I

(f) Alkylate methyl 3-methylbutanoate withCH3CH2I

17.11

17.12 The reverse reaction is the exact opposite of theforward reaction.

17.13

(b)(a)

(CH3)2CHCH2CH CCH

(c) O

CH(CH3)2

H

O

C

OCH3

CC

CH3CH2CH2CHCHCH

OH(a) O

(b)

(c)

CH2CH3

CH3

OOH

HOO

17.14

17.15 (a) Not an aldol product (b) Pentan-3-one

17.16 The CH2 position between the two carbonylgroups is so acidic that it is completely deproto-nated to give a stable enolate ion.

17.17

17.18

17.19 The cleavage reaction is the exact reverse of theforward reaction.

17.20

17.21 O

+CO2Et

H3C O

CO2Et

CH3

O

CO2EtH3C

CH3CHCH2CCHCOEt

CH3

CH(CH3)2

(a)O O

PhCH2CCHCOEt

Ph

(b)O O

C6H11CH2CCHCOEt

C6H11

(c)O O

O

CH3

H3C

O

CH3

H3C

and

O

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17.22

17.23

17.24

17.25 (a) Cyclopentanone enamine � propenenitrile

(b) Cyclohexanone enamine � methyl propenoate

CHAPTER 1818.1 (a) N-Methylethylamine

(b) Tricyclohexylamine

(c) N-Ethyl-N-methylcyclohexylamine

(d) N-Methylpyrrolidine

(e) Diisopropylamine

(f) Butane-1,3-diamine

18.2 [(CH3)2CH]3N(a)

NCH2CH3

CH3(d)

(b) (H2C CHCH2)2NH

NHCH(CH3)2(e)

NHCH3(c)

(f)CH2CH3N

(a) (b) OO

CH2CH2CO2Et

(c) O O

CH2CH2CHO

(a) (b)

(EtO2C)2CHCH2CH2CCH3

CO2Et

OO O

CH2CH2CCH3

(b) (CH3CO)2CHCH2CH2CN

O(a) CH(COCH3)2

(c)

(CH3CO)2CHCHCH2COEt

CH3

O

18.3

18.4 (a) CH3CH2NH2 (b) NaOH (c) CH3NHCH3

18.5 Propylamine is stronger; benzylamine pKb � 4.67;propylamine pKb � 3.29

18.6 (a) p-Nitroaniline � p-Aminobenzaldehyde �

p-Bromoaniline

(b) p-Aminoacetophenone � p-Chloroaniline �

p-Methylaniline

(c) p-(Trifluoromethyl)aniline �

p-(Fluoromethyl)aniline � p-Methylaniline

18.7 Pyrimidine is essentially 100% neutral (unprotonated).

18.8 (a) Propanenitrile or propanamide

(b) N-Propylpropanamide

(c) Benzonitrile or benzamide

(d) N-Phenylacetamide

18.9

18.10

18.11 (a) Oct-3-ene and oct-4-ene

(b) Cyclohexene

(c) Hept-3-ene

(d) Ethylene and cyclohexene

18.12 H2CUCHCH2CH2CH2N(CH3)2

18.13 1. HNO3, H2SO4; 2. H2/PtO2; 3. (CH3CO)2O; 4. HOSO2Cl; 5. aminothiazole; 6. H2O, NaOH

H3C

(CH3)2NH

CHO

+ NaBH4

HO CH2CH2Br

HO

or

NH3

HO CH2Br

HO

1. NaCN2. LiAlH4

N(CH3)2

(a) (b)

(c) (d)

CH3

H3C

N

CH3O

N

H

N

NH2N

N

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18.14 (a) 1. HNO3, H2SO4; 2. H2/PtO2; 3. 2 CH3Br

(b) 1. HNO3, H2SO4; 2. H2/PtO2; 3. (CH3CO)2O; 4. Cl2; 5. H2O, NaOH

(c) 1. HNO3, H2SO4; 2. Cl2, FeCl3; 3. Sn

18.15

18.16 4.1% protonated

18.17

N

Attack at C2:

E+

NE

H

+

NE

H

+

NE

H

+

N

Attack at C3:

E+

N

H

E

+

H

E

H

E

N+ N

+

N

Attack at C4:

E+

N

E H

+

E H E H

Unfavorable

Unfavorable

N+

N

+

N S

HH

H

18.18 The side-chain nitrogen is more basic than thering nitrogen.

18.19 Reaction at C2 is disfavored because the aroma-ticity of the benzene ring is lost

CHAPTER 1919.1 Aromatic: Phe, Tyr, Trp, His;

sulfur-containing: Cys, Met; alcohols: Ser, Thr; hydrocarbon side chains: Ala, Ile, Leu, Val, Phe

19.2 The sulfur atom in the –CH2SH group of cysteinemakes the side chain higher in priority than the–CO2H group.

19.3

19.4 Net positive at pH � 5.3; net negative at pH � 7.3

19.5 (CH3)2CHCH2Br(a)

N

N

H

CH2Br(b)

N

H

CH2Br(c) CH3SCH2CH2Br(d)

L-Threonine Diastereomers of L-threonine

CO2–

CH3

H3N+

H

HS

R OH

CO2–

CH3

H3N+

HO

HS

S H

CO2–

CH3

H+

H

NH3R

R OH

N

HN

E

H

+

H

N

E

H

+

H

N

E

H+

H

E+

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19.6

19.7 Val-Tyr-Gly (VYG), Tyr-Gly-Val (YGV), Gly-Val-Tyr (GVY), Val-Gly-Tyr (VGY), Tyr-Val-Gly (YVG), Gly-Tyr-Val (GYV)

19.8

19.9

19.10

19.11 Trypsin: Asp-Arg � Val-Tyr-Ile-His-Pro-Phe

Chymotrypsin: Asp-Arg-Val-Tyr � Ile-His-Pro-Phe

19.12 Methionine

19.13

19.14 This is a typical nucleophilic acyl substitutionreaction, with the amine of the amino acid as thenucleophile and tert-butyl carbonate as the leav-ing group. The tert-butyl carbonate then loses CO2 and gives tert-butoxide, which is protonated.

N

H

HC

CN

C

OC6H5

CH2CO2HS

–O

N (CH3)2CHCHO CO2 + +

O

O

O

NH3+

HOCCH2 SCH2CHCO–

O O

H3NCHC

CH3SCH2CH2

N

O

CH(CH3)2

CHC NHCHC NHCH2CO–

O O O+

C

(CH3)2CH

H

NHCOCH3

CO2H

C 1. H2, [Rh(DiPAMP)(COD)]+ BF4–

2. NaOH, H2O

CO2–

H3N H+

19.15 (1) Protect the amino group of leucine.

(2) Protect the carboxylic acid group of alanine.

(3) Couple the protected amino acids with DCC.

(4) Remove the leucine protecting group.

(5) Remove the alanine protecting group.

19.16 (a) Lyase (b) Hydrolase (c) Oxidoreductase

CHAPTER 2020.1

20.2 The mechanism is the reverse of that shown inFigure 20.2.

20.3 The Re face

20.4

20.5 The mechanism is the same as that shown in Figure 20.2.

20.6

20.7 The mechanism is essentially the same as that inProblem 20.6.

H2N+

+

H2O

H2O

CH3

CO2–C

H2N

+H2O

CH3

CO2–C

H3N

HO

CH3

CO2–C

O+

CH3

CO2–

+

+H3O+

NH3CH

O

CH3

CO2–C

N

NN

NH2

–O2CN

HH NH3

+NH2

+ OCH2O

OHOH

N

O P O

O–C

ADPATP

2–O3PO OHC

OO

OH–OC

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20.8

20.9 The nonenzymatic cyclization is an internalimine formation that occurs by nucleophilic addi-tion of the amine to the carbonyl group followedby loss of water. The enzymatic reduction is anucleophilic addition to the iminium ion:

CHAPTER 2121.1 (a) Aldotetrose (b) Ketopentose

(c) Ketohexose (d) Aldopentose

21.2 (a) S (b) R (c) S

21.3 A, B, and C are the same.

21.4

21.5 CHO

CH2OH

OHH

OH

R

RH

H

R

Cl

CH3HOCH2

HH

NH2C

O

N

H

N+

HH

CO2–

H

N

H

CO2–

CO2–

+

OPO32– PO4

3–+

HH

NH2C

O

N

H

NH2C

O

N+

CO

H NH3

CO2–

++

H

CO

H NH3

21.6 (a) L-Erythrose; 2S,3S (b) D-Xylose; 2R,3S,4R

(c) D-Xylulose; 3S,4R

21.7

21.8

21.9 16 D and 16 L aldoheptoses

21.10

21.11

21.12

OH

�-D-Fructopyranose

cis

OH

OH

CH2OH

CH2OH

HOCH2

HOHO

O

OOH

OH

�-D-Fructofuranose

�-D-Fructopyranose

trans

OHOH

CH2OH

OH

HOCH2* * *

*

HOHO

O

OCH2OH

OH

OH

�-D-Fructofuranose

HOCH2O

OH

H,OH

OH

D-Ribose

OHH

CH2OH

OHH

CHO

OHH

CHO

HHO

HHO

CH2OH

OHH

(a) CHO

HHO

OHH

CH2OH

HHO

OHH

(b) CHO

HHO

HHO

CH2OH

HHO

OHH

(c)

L-(+)-Arabinose

HHO

CH2OH

HHO

CHO

OHH

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21.13

21.14

21.15 �-D-Allopyranose (see Figure 21.3)

21.16

21.17 D-Galactitol has a plane of symmetry and is ameso compound, whereas D-glucitol is chiral.

21.18 The –CHO end of L-gulose corresponds to the–CH2OH end of D-glucose after reduction.

21.19 D-Allaric acid has a symmetry plane and is a mesocompound, but D-glucaric acid is chiral.

21.20 D-Allose and D-galactose yield meso aldaric acids;the others yield optically active aldaric acids.

21.21

COH

HCH3CONH

OHH

CH2OH

OHH

HHO

C O

CO2–

H2C H Base

HCH3CONH

OHH

CH2OH

OHH

HHO

OHH

C O

CO2–

CH2

CH3OCH2 OCH3O

OCH3OCH3

AcOCH2 OAcO

OAcOAc

OHOHHOCH2

HOHO

O

e

a

e

e

e

�-D-Galactopyranose

OH

OH

CH2OHee

e

e e

a

e e e

a

HO

O

HO

OH

�-D-Mannopyranose

HOCH2

HO

HO

O

OH21.22

CHAPTER 2222.1 Steps 7 and 10

22.2 Steps 1, 3: nucleophilic acyl substitutions atphosphorus; steps 2, 5, 7, 8, 10: isomerizations;step 4: retro-aldol reaction; step 6: oxidation and nucleophilic acyl substitution by phosphate;step 9: E1cB dehydration

22.3 pro-R

22.4

22.5 C1 and C6 of glucose become –CH3 groups; C3 and C4 become CO2.

22.6 Citrate and isocitrate

22.7 E1cB elimination of water, followed by conjugateaddition

22.8 pro-R; anti geometry

22.9 Re face; anti geometry

HH

CONH2

N

OH

O

CH2OH

HOHO O

OH

CH2OH

CH2OHHO

OHH

OH

O

CH2OH

HOHO O

OH

CH2OH

CO2HHO

OHH

OAc

O

CH2OAc

AcOAcO O

OAc

CH2OAc

OAcAcO

O

2. H2O

1. NaBH4(a)

H2O

Br2(b)

Cellobiose

Cellobiose

Cellobiosepyridine

CH3COCl(c)

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22.10 The reaction occurs by two sequential nucleo-philic acyl substitutions, the first by a cysteineresidue in the enzyme, with phosphate as leavinggroup, and the second by hydride donation fromNADH, with the cysteine residue as leaving group.

CHAPTER 2323.1 CH3(CH2)18CO2CH2(CH2)30CH3

23.2 Glyceryl tripalmitate is higher melting.

23.3 [CH3(CH2)7CHUCH(CH2)7CO2�]2 Mg2�

23.4 Glyceryl dioleate monopalmitate 88nGlycerol � 2 Sodium oleate � Sodium palmitate

23.5 Caprylyl CoA 88n Hexanoyl CoA 88nButyryl CoA 88n 2 Acetyl CoA

23.6 (a) 8 acetyl CoA; 7 passages

(b) 10 acetyl CoA; 9 passages

23.7 The dehydration is an E1cB reaction.

23.8 At C2, C4, C6, C8, and so forth

23.9 The Si face

23.10

23.11 The pro-S hydrogen is cis to the –CH3 group; thepro-R hydrogen is trans.

23.12

OPP(a)

–OPP+

+

+

�-Pinene

+

H

Base

H

HH

R SRR

OH OHH

CO2H

O

CH2

(b)

OPP

B H

�-Bisabolene

+

+CH2

+

+

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23.13

23.14

CHAPTER 2424.3 (5) ACGGATTAGCC (3)

24.4

24.5 (3) CUAAUGGCAU (5)

24.6 (5) ACTCTGCGAA (3)

24.7 (a) GCU, GCC, GCA, GCG

(b) UUU, UUC

(c) UUA, UUG, CUU, CUC, CUA, CUG

(d) UAU, UAC

24.8 Leu-Met-Ala-Trp-Pro-Stop

24.9 (5) TTA-GGG-CCA-AGC-CAT-AAG (3)

24.10 The cleavage is an SN1 reaction that occurs byprotonation of the oxygen atom followed by lossof the stable triarylmethyl carbocation.

24.11

RO O

O

OR

P CHC

H

NCH2

NH3

E2 reaction

HN

N

N

NN

N

H

NHO

O

H

H

CH3

CH3

OHe

H

CH3

CO2H

CH3e

H(a)

H CH3

a

H(b)

H

24.12 The mechanism was shown in Figure 20.2 onpage 823.

24.13

24.14 The mechanism occurs by (1) phosphorylation of inosine monophosphate by reaction with GTP,(2) acid-catalyzed nucleophilic addition of aspar-tate to an imine, and (3) loss of phosphate by anE1cB reaction.

24.15 The reaction is an E1cB elimination.

CHAPTER 25The answers to the problems in Chapter 25 can be down-loaded from the web at http://www.thomsonedu.com

CH3

CH3–O2C

CoASH

O

OH

O

O

O

CH3–O2C

HO

N

N

H

H

CH3

O

–O

H2N

CH3

O

O

N

N

H

H

–O

H2N

CH3

N

NADP+NADPH, H+

�-Ketoglutarate

Glutamate

H2ONH4

+

CO2

H2O

CoASHNAD+

NADH/H+

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The boldfaced references refer to pageswhere terms are defined.

�, see AlphaAbbreviated mechanism, nucleophilic

acyl substitution reactions, 840Absolute configuration, 330Absorbance, 440Absorption spectrum, 427Acesulfame-K, structure of, 881

sweetness of, 880Acetal(s), 572

from aldehydes, 572–574from ketones, 572–574hydrolysis of, 572–573mechanism of formation of, 572–573

Acetaldehyde, aldol reaction of, 701, 703bond angles in, 549bond lengths in, 549electrostatic potential map of, 54913C NMR absorptions of, 5851H NMR spectrum of, 584pKa of, 690

Acetamide, basicity of, 690electrostatic potential map of, 639, 673,

743Acetaminophen, molecular model of, 28

synthesis of, 652Acetanilide, electrophilic aromatic

substitution of, 753–754Acetate ion, electrostatic potential map

of, 44, 54, 57, 607resonance in, 43–44

Acetic acid, dimer of, 605dipole moment of, 39electrostatic potential map of, 54, 56hydrogen bonding in, 605pKa of, 52, 606properties of, 605protonation of, 60–61

Acetic acid dimer, electrostatic potentialmap of, 605

Acetic anhydride, electrostatic potentialmap of, 639

reaction with alcohols, 652

reactions with amines, 652synthesis of, 643

Acetoacetic ester, alkylation of, 695–696

ketones from, 695–696Acetoacetic ester synthesis, 695–696Acetoacetyl-CoA acetyltransferase, 952Acetone, enol content of, 683

hydrate of, 564pKa of, 688uses of, 557

Acetone anion, electrostatic potentialmap of, 56, 57, 80, 555

Acetonitrile, electrostatic potential mapof, 615

pKa of, 690Acetophenone, 13C NMR absorptions of,

585structure of, 559

Acetyl azide, electrostatic potential mapof, 673

Acetyl chloride, electrostatic potentialmap, 555, 639

pKa of, 690reaction with alcohols, 652reaction with amines, 652see also Acid chloride

Acetyl CoA, anion of, 46biosynthesis of, 662 carboxylation of, 945catabolism of, 905–910citric acid cycle and, 905–910Claisen condensation reactions of,

720fat catabolism and, 938–942fatty acids from, 943–947from acetyl dihydrolipoamide,

904–905from pyruvate, 901–905function of, 662–663reaction with glucosamine, 662–663reaction with oxaloacetate, 906–907structure of, 819thioester in, 662

Acetyl CoA anion, resonance in, 46

Acetyl coenzyme A, see Acetyl CoAAcetyl dihydrolipoamide, acetyl CoA

from, 904–905Acetyl group, 559N-Acetyl-D-neuraminic acid, structure

and function of, 872Acetylene, bond angles in, 18

bond lengths in, 18bond strengths in, 18molecular model of, 18pKa of, 252sp hybrid orbitals in, 17–18structure of, 18

N-Acetylglucosamine, biosynthesis of,662–663

structure and function of, 872Acetylide anion(s), 252

alkylation of, 412electrostatic potential map of, 253

N-Acetylmannosamine, structure andfunction of, 872

Achiral, 322Acid, Brønsted–Lowry, 50

Lewis, 58organic, 56–57strengths of, 51–53

Acid anhydride(s), 633amides from, 652electrostatic potential map of, 639esters from, 652from acid chlorides, 648from carboxylic acids, 643IR spectroscopy of, 667naming, 634NMR spectroscopy of, 667–668nucleophilic acyl substitution

reactions of, 652–653reaction with alcohols, 652reaction with amines, 652

Acid chloride(s), 633acid anhydrides from, 648alcoholysis of, 650amides from, 650–651aminolysis of, 650–651carboxylic acids from, 648

Index

I-1

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I-2 I N D E X

Acid chloride(s) (continued)electrostatic potential map of, 639esters from, 650from carboxylic acids, 642–643hydrolysis of, 648IR spectroscopy of, 667naming, 634NMR spectroscopy of, 667–668nucleophilic acyl substitution reactions

of, 648, 650–651pKa of, 690polarity of, 80reaction with alcohols, 650reaction with amines, 650–651reaction with ammonia, 650–651reaction with carboxylate ions, 648reaction with water, 648

Acid halide(s), 633naming, 634nucleophilic acyl substitution reactions

of, 648, 650–651reaction with alcohols, 650reaction with amines, 650–651see also, Acid chloride

Acidity, alcohols and, 501–503amines and, 743carbonyl compounds and, 689–690carboxylic acids and, 605–607phenols and, 501–503

Acidity constant (Ka), 51table of, 52

Acid–base reactions, prediction of, 53–54Aconitase, 907ACP, see Acyl carrier protein, 943ACP transacylase, 943Acrolein, structure of, 558Acrylic acid, pKa of, 606

structure of, 603Activating group (aromatic substitution),

294acidity and, 610explanation of, 294–295

Activation energy, 164magnitude of, 164–165reaction rate and, 164–165

Active site (enzyme), 169citrate synthase and, 805hexokinase and, 169urocanase and, 845

Acyl adenosyl phosphate, asparaginebiosynthesis and, 839–840

biological reactions of, 648–649fatty acid catabolism and, 937

Acyl adenylate, biological reactions of,648–649

see also Acyl adenosyl phosphateAcyl carrier protein (ACP), structure and

function of, 943Acyl cation, electrostatic potential map

of, 290Friedel–Crafts acylation reaction and,

290resonance in, 290

Acyl group, 290, 547, 559naming, 603

Acyl phosphate, 633naming, 636

Acyl-CoA dehydrogenase, 939Acyl-CoA synthetase, 937Acylation (aromatic), see Friedel–Crafts

reactionAdams catalyst, 2321,2-Addition (conjugated carbonyl), 5801,2-Addition (diene), 248–2491,4-Addition (conjugated carbonyl), 5801,4-Addition (diene), 248–249Addition reaction, 142Adenine, aromaticity of, 280

electrostatic potential map of, 983molecular model of, 68protection of, 993structure of, 980

Adenosine, biosynthesis of, 1006–1007catabolism of, 999–1000

Adenosine diphosphate (ADP), functionof, 819–820

structure of, 163Adenosine triphosphate (ATP), coupled

reactions and, 821energy rich bonds in, 162–163function of, 819–820hydrolysis of, 163reaction with alcohols, 819–820reaction with glucose, 821reaction with methionine, 528structure and function of, 163, 802

S-Adenosylhomocysteine, from S-adenosylmethionine, 390–391

metabolism of, 411S-Adenosylmethionine, biological

methylation with, 390–391from methionine, 528SN2 reactions of, 390–391stereochemistry of, 346structure and function of, 803

Adenylosuccinate synthetase, 1006Adipic acid, structure of, 603ADP, see Adenosine diphosphateAdrenaline, biosynthesis of, 390–391

molecular model of, 354Adrenocortical hormone, 963-al, aldehyde name ending, 558Alanine, biosynthesis of, 838

catabolism of, 833configuration of, 330electrostatic potential map of, 778molecular model of, 28, 777pyruvate from, 833structure and properties of, 780zwitterion of, 778

Alanine zwitterion, electrostatic potentialmap of, 778

Alcohol(s), 497acetals from, 572–574acidity of, 501–503aldehydes from, 516–517alkenes from, 223, 513–515alkoxide ions from, 501–503alkyl halides from, 365–366, 387,

512alpha cleavage of, 422biological dehydration of, 513–514biological oxidation of, 519carbonyl compounds from, 516–519

carbonyl nucleophilic additionreactions of, 572–574

carboxylic acids from, 516–517common names of, 500dehydration of, 222, 513–515electrostatic potential map of, 79esters from, 515–516ethers from, 523–524from aldehydes, 506,–507, 509–510,

567–568from alkenes, 227–230, 504–505from carbonyl compounds, 505–511from carboxylic acids, 507–508, 647from epoxides, 505from esters, 507–510, 657–658from ethers, 525–526from ketones, 506–507, 509–510,

567–568hydrogen bonds in, 501IR spectroscopy of, 436, 529ketones from, 516–517mass spectrometry of, 422, 531mechanism of dehydration of, 513–515mechanism of oxidation of, 518naming, 499–500NMR spectroscopy of, 530oxidation of, 516–519polarity of, 79primary, 499properties of, 501–503reaction with acid, 513–514reaction with acid anhydrides, 652reaction with acid chlorides, 650reaction with aldehydes, 572–574reaction with alkyl halides, 524reaction with ATP, 819–820reaction with carboxylic acids,

644–645reaction with CrO3, 517–518reaction with HX, 366, 512reaction with ketones, 572–574reaction with Na2Cr2O7, 517–518reaction with NaH, 503reaction with NaNH2, 503reaction with PBr3, 366, 512reaction with PCC, 517–518reaction with POCl3, 513–515reaction with potassium, 503reaction with SOCl2, 366, 512reactions of, 512–518secondary, 499synthesis of, 504–511tertiary, 499

Alcoholysis (nucleophilic acylsubstitution reaction), 640

Aldaric acid(s), 871from aldoses, 871

Aldehyde(s), 557acetals from, 572–574alcohols from, 506–507, 509–510,

567–568aldol reaction of, 702alkenes from, 575–577� bromination of, 686–687amines from, 748–750biological reduction of, 507, 580Cannizzaro reaction of, 579

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INDEX I-3

carbonyl condensation reactions of,701–706

carboxylic acids from, 561–562common names of, 558conjugate addition reactions of,

580–583enamines from, 568–571enols of, 682–684enones from, 705–706from alcohols, 516–517from esters, 560, 658Grignard reaction of, 509–510, 567hydrates of, 561, 565–566imines from, 568–569IR spectroscopy of, 436, 583–584mass spectrometry of, 422, 585–586McLafferty rearrangement of, 422mechanism of hydration of, 565–566naming, 558NMR spectroscopy of, 584–585oxidation of, 561–562pKa of, 690polarity of, 80reaction with alcohols, 572–574reaction with amines, 568–571reaction with Br2, 686–687reaction with CrO3, 561reaction with Grignard reagents,

509–510, 567reaction with H2O, 564–566reaction with LiAlH4, 506, 568reaction with NaBH4, 506 568reactivity of versus ketones, 563–564reduction of, 506–507, 568reductive amination of, 748–750Wittig reaction of, 575–577

Alditol(s), 868from monosaccharides, 868–869

Aldol reaction, 701–703biological, 718–719cyclohexenones from, 707–708cyclopentenones from, 707–708dehydration in, 705–706equilibrium in, 702glucose biosynthesis and, 719intramolecular, 707–708mechanism of, 702–703requirements for, 701–702reversibility of, 702steric hindrance to, 702

Aldolase, class I, 718–719, 897class II, 718–719, 897types of, 718

Aldonic acid(s), 870from aldoses, 870–871

Aldose(s), 853aldaric acids from, 871alditols from, 868–869aldonic acids from, 870–871Benedict’s test on, 870configurations of, 859–861Fehling’s test on, 870Fischer projections of, 854–856esters from, 866ethers from, 866glycosides of, 867–868names of, 860–861

oxidation of, 870–871reaction with Br2, 871reaction with HNO3, 871reduction of, 868–869see also Carbohydrate, Monosaccharidetable of, 860Tollens’ test on, 870uronic acids from, 871

Aldosterone, structure and function of,963

Algae, chloromethane from, 363Alicyclic, 112Aliphatic, 82Alitame, structure of, 881

sweetness of, 880Alkaloid, 65Alkane(s), 82

boiling points of, 96branched-chain, 83combustion of, 95conformations of, 101dispersion forces in, 62, 96from alkyl halides, 368from Grignard reagents, 368general formula of, 82IR spectroscopy of, 434isomers of, 82–83mass spectrometry of, 418–419melting points of, 96naming, 84–85, 89–93Newman projections of, 97normal (n), 83pKa of, 252properties of, 95–96reaction with chlorine, 95sawhorse representations of, 97straight-chain, 83

Alkene(s), 179alcohols from, 227–230, 504–505biological addition of radicals to,

243–244biological hydration of, 940biological reduction of, 234–235, 947bond rotation in, 186bromohydrins from, 226–227bromonium ion from, 224–225cis–trans isomerism in, 186–187common names of, 1841,2-dihalides from, 224–2251,2-diols from, 236–239electron distribution in, 152electrophilic addition reactions of,

195–196electrostatic potential map of, 79, 152epoxides from, 235–237E,Z configuration of, 188–190from alcohols, 223, 513–515from aldehydes, 575–577from alkyl halides, 222from alkynes, 251from amines, 751–752from ketones, 575–577general formula of, 180halohydrins from, 226–227hydration of, 227–230hydroboration of, 229–230hydrogenation of, 232–234

hydroxylation of, 236–239hyperconjugation in, 194IR spectroscopy of, 434Markovnikov’s rule and, 198–199naming, 182–184nucleophilicity of, 152organoboranes from, 229oxymercuration of, 228–229pKa of, 252polymerization of, 240–242reaction summary of, 221reaction with borane, 229–230reaction with Br2, 224–225reaction with Cl2, 224–225reaction with H2O, 151–154reaction with halogen, 224–225reaction with HBr, 195–196reaction with HCl, 195–196reaction with HI, 195–196reaction with hydrogen, 232–234reaction with mercuric ion, 229reaction with OsO4, 238–239reaction with peroxyacids, 235–236reaction with radicals, 240–242reduction of, 232–234Sharpless epoxidation of, 587stability of, 192–194steric strain in cis isomer, 192synthesis of, 222–223

Alkoxide ion, 501Alkoxy group, 522Alkyl group(s), 86

directing effect of, 294inductive effect of, 294–295naming, 86–87, 92–93orienting effect of, 294

Alkyl halide(s), 363alkenes from, 222amines from, 747–748amino acids from, 784–785carboxylic acids from, 611–612dehydrohalogenation of, 222electrostatic potential map of, 79ethers from, 524from alcohols, 365–366, 387, 512from ethers, 525–526Grignard reagents from, 367malonic ester synthesis with,

692–694naming, 364–365naturally occurring, 402–403phosphonium salts from, 575–576polarity of, 79polarizability of, 149reaction with alcohols, 524reaction with amines, 747–748reaction with carboxylate ions, 643reaction with HS�, 521reaction with sulfides, 527reaction with thiols, 527reaction with thiourea, 521reaction with triphenylphosphine,

575–576see also Organohalidesynthesis of, 365–366thiols from, 521uses of, 363

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Alkyl shift, carbocation rearrangementsand, 207–208

Alkylamine(s), 736basicity of, 740–743

Alkylation (aromatic), see Friedel–Craftsreaction

Alkylation (carbonyl), 288acetoacetic ester, 695–696biological, 700carbonyl compounds and, 691–699ester, 698ketone, 698malonic ester, 692–694nitrile, 699

Alkylbenzene(s), from aryl alkyl ketones,299–300

side-chain oxidation of, 298–299Alkylthio group, 523Alkyne(s), 179

acetylide anions from, 252–253acidity of, 252–253alkenes from, 251electrophilic addition reactions of,

196electrostatic potential map of, 79hydrogenation of, 251IR spectroscopy of, 434–435naming, 184pKa of, 252reaction with Br2, 251reaction with Cl2, 251reaction with HBr, 251reaction with HCl, 251reduction of, 251vinylic halides from, 251

Alkynyl group, 184Allene, heat of hydrogenation of, 214

structure of, 33Allinger, Norman Louis, 133Allose, configuration of, 860Allyl group, 184Allylic, 249Allylic carbocation, electrostatic

potential map of, 249, 385resonance in, 249SN1 reaction and, 385–386stability of, 249

Allylic halide, SN1 reaction and, 385–386SN2 reaction and, 386

Alpha amino acid, see Amino acid, 779Alpha anomer, 863Alpha cleavage, alcohol mass spectrum

and, 422, 531aldehyde mass spectrum and, 423, 585amine mass spectrum and, 422, 763ketone mass spectrum and, 423, 585

Alpha farnesene, structure of, 212Alpha-glycosidase, 877, 892Alpha helix, molecular model of, 798

secondary protein structure and, 798Alpha-keto acid, amino acids from, 785

reductive amination of, 785transamination of, 822–825

Alpha-ketoglutarate, from glutamate, 826from oxalosuccinate, 908glutamate from, 838oxidative decarboxylation of, 908

succinyl CoA from, 908transamination of, 825–826

Alpha pinene, structure of, 179Alpha position (carbonyl compounds,

681acidity of, 684

Alpha substitution reaction, 553, 681alkylation and, 691–700carbonyl condensation reactions and,

704enolate ions and, 691–699enols and, 685–686mechanism of, 685–686

Altrose, configuration of, 860Aluminum chloride, Friedel–Crafts

reaction and, 288–289Amantadine, structure of, 139Amide(s), 633

amines from, 660–661basicity of, 742–743carboxylic acids from, 659–660DCC for formation of, 646electrostatic potential map of, 639from acid anhydrides, 652from acid chlorides, 650–651from amines, 751from carboxylic acids, 646–647from esters, 657from nitriles, 616hydrolysis of, 659–660IR spectroscopy of, 667mechanism of hydrolysis of, 659–660mechanism of reduction of, 661naming, 635nitriles from, 615NMR spectroscopy of, 667–668nucleophilic acyl substitution reactions

of, 659–661peptide bond and, 787pKa of, 690polarity of, 80reaction with LiAlH4, 660–661reaction with SOCl2, 615reduction of, 660–661restricted rotation in, 788

Amidomalonate synthesis, 784–785-amine, name ending for amines, 736Amine(s), 735

acidity of, 743alkenes from, 751–752alpha cleavage of, 422amides from, 751basicity of, 740–745biological, 745–746carbonyl nucleophilic addition

reactions of, 568–571chirality of, 345, 739conjugate addition reactions to enones,

582electrostatic potential map of, 80from aldehydes, 748–750from amides, 660–661from ketones, 748–750from lactams, 661from nitriles, 616Henderson–Hasselbalch equation and,

745–746

heterocyclic, 738, 755–759Hofmann elimination of, 751–752hydrogen bonding in, 740IR spectroscopy of, 436, 762mass spectrometry of, 422, 763–764naming, 736–738nitrogen rule and, 763occurrence of, 735odor of, 740polarity of, 80primary, 736properties of, 739–740pyramidal inversion in, 739reaction with acid anhydrides, 652reaction with acid chlorides, 650–651reaction with aldehydes, 568–571reaction with alkyl halides, 747–748reaction with carboxylic acids and

DCC, 646reaction with enones, 582reaction with esters, 657reaction with ketones, 568–571secondary, 736SN2 reactions of, 747–748structure of, 739synthesis of, 746–750tertiary, 736uses of, 739

Amino acid(s), 777abbreviations for, 780–781acetoacetate from, 832acetyl CoA from, 832acidic, 782�-ketoglutarate from, 832amidomalonate synthesis of, 784–785amphiprotic behavior of, 778basic, 782biological precursors of, 839biosynthesis of, 838–844Boc derivatives of, 794C-terminal, 787catabolism of, 822–826, 831–838catabolism of carbon chains in,

831–838configuration of, 779, 782deamination of, 822–826electrophoresis of, 784enantioselective synthesis of, 785–786essential, 838esters of, 793Fmoc derivatives of, 796from �-keto acids, 785from alkyl halides, 784–785fumarate from, 832glucogenic, 832Henderson–Hasselbalch equation and,

746isoelectric points of, 780–781ketogenic, 832molecular weights of, 780–781N-terminal, 787neutral, 782nonessential, 838nonprotein, 779oxaloacetate from, 832pI’s of, 780–781pKa’s of, 780–781

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INDEX I-5

protecting groups for, 793–794, 796pyruvate from, 832reaction with di-tert-butyl dicarbonate,

794reaction with ninhydrin, 789succinyl CoA from, 832synthesis of, 784–786table of, 780–781transimination of, 824zwitterion form of, 778

Amino acid analysis, 789Amino acid analyzer, 789Amino group(s), 737

directing effect of, 294inductive effect of, 294–295orienting effect of, 294

Amino sugar, 873p-Aminobenzoic acid, molecular model

of, 25Aminolysis (nucleophilic acyl

substitution reaction), 640Aminotransferase, 822–824Ammonia, carbamoyl phosphate from,

827dipole moment of, 39electrostatic potential map of, 150elimination of in animals, 827hydrogen bond in, 63reaction with acid chlorides, 650–651reaction with carboxy phosphate, 827reaction with carboxylic acids and

DCC, 646urea cycle and, 827–831

Amphetamine, synthesis of, 748–749Amplitude, 426�-Amylase, 800, 892–893Amylopectin, structure of, 876–877Amylose, structure of, 876–877Anabolism, 818Androgen, 962

function of, 962Androstenedione, structure and function

of, 962Androsterone, structure and function of,

962-ane, alkane name ending, 86Angle strain, 118Angstrom, 3Anhydride, see Acid anhydrideAniline, basicity of, 743–745

electrostatic potential map of, 744from nitrobenzene, 285synthesis of, 285

Anilinium ion, electrostatic potentialmap of, 744

Anilinothiazolinone, Edman degradationand, 790–791

Anisole, electrostatic potential map of,623

Anomer, 862�-, 863�-, 863

Anomeric center, 862Anthracene, structure of, 278Anti conformation, 99Anti periplanar geometry, 396

molecular model of, 396

Anti stereochemistry, 224Antiaromaticity, 273Antibiotic(s), cephalosporins, 669

�-lactam, 668–669penicillins, 688–669sulfonamides, 285vancomycin, 403

Antibonding molecular orbital, 22Anticodon (tRNA), 988Antigenic determinants, blood groups

and, 879Antisense strand (DNA), 987Arabinose, configuration of, 860Arachidic acid, structure of, 929Arachidonic acid, cyclooxygenase

reaction of, 1–2prostaglandins from, 1–2, 243–244,

948–950radical reactions of, 146structure of, 929

Arecoline, molecular model of, 81Arene(s), 269

electrostatic potential map of, 79see also Aromatic compound

Arginase, 831Arginine, biosynthesis of, 828–831,

840–841from glutamate, 840–841ornithine from, 831structure and properties of, 781urea cycle and, 828–831

Argininosuccinate, arginine from,830–831

from citrulline, 828–830metabolism of, 413urea cycle and, 828–830

Argininosuccinate lyase, 830stereochemistry of, 830

Argininosuccinate synthetase, 828epi-Aristolochene, biosynthesis of, 218Aromatic compound(s), 267

alkylation of, 288–289biological hydroxylation of, 286–287bromination of, 282–284characteristics of, 273–275chlorination of, 283common names for, 268electrophilic substitution reactions of,

282–283Friedel–Crafts acylation of, 290Friedel–Crafts alkylation of, 288–289halogenation of, 282–284iodination of, 284IR spectroscopy of, 435naming, 268–270nitration of, 284–285oxidation of, 298–299reduction of, 299–300see also Aromaticitysulfonation of, 286trisubstituted, 300–302

Aromaticity, heterocycles and, 276–277Hückel 4n � 2 rule and, 273–275imidazole and, 276–277ions and, 315naphthalene and, 279pyridine and, 276–277

pyrimidine and, 276–277pyrrole and, 276–277requirements for, 273

Arrow, electron movement and, 45fishhook, 143See also Curved arrow

Arsenic trioxide, LD50 of, 26leukemia therapy and, 26

Aryl alkyl ketone, reduction of, 299–300Aryl halide, SN2 reaction and, 375–376Arylamine(s), 736

basicity of, 741, 743–745electrophilic aromatic substitution of,

753–754from nitroarenes, 747resonance in, 744synthesis of, 285

Ascorbic acid, see Vitamin C-ase, enzyme name ending, 801Asparagine, aspartate from, 834

biosynthesis of, 839–840catabolism of, 834from aspartate, 839–840fumarate from, 834oxaloacetate from, 834structure and properties of, 780

Asparagine synthetase, 839Aspartame, molecular model of, 29

structure of, 816, 881sweetness of, 880

Aspartate, asparagine from, 839–840biosynthesis of, 838catabolism of, 834from oxaloacetate, 828fumarate from, 834homoserine from, 842–843oxaloacetate from, 834partial reduction of, 842reaction with citrulline, 828–830threonine from, 842–844

Aspartate semialdehyde, from aspartate,842

Aspartic acid, structure and properties of,781

Asphalt, composition of, 103Aspirin, LD50 of, 26

molecular model of, 17synthesis of, 652

Asymmetric center, 322-ate, ester name ending, 635Atom, atomic mass of, 4

atomic number of, 4electron configurations of, 5–6electron shells in, 4–5isotopes of, 4orbitals in, 4–5quantum mechanical model of, 4–5size of, 3structure of, 3

Atomic mass, 4Atomic number (Z), 4Atomic weight, 4Atorvastatin, structure and function of,

1010ATP, see Adenosine triphosphateAtropine, structure proof of, 773ATZ, see Anilinothiazolinone, 790–791

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Aufbau principle, 5Avian flu, 920Axial bonds (cyclohexane), 123

drawing, 124

�, see BetaBackbone (protein), 787Backside displacement, SN2 reaction and,

372–373von Baeyer, Adolf, 118Baeyer strain theory, 118Banana, esters in, 653Base, Brønsted–Lowry, 50

Lewis, 58organic, 57strengths of, 51–53

Base pair (DNA), 982–984electrostatic potential maps of, 983hydrogen bonding in, 983

Base peak (mass spectrum), 416Basicity, alkylamines, 740–743

amides, 742–743amines, 740–745arylamines, 741, 743–745heterocyclic amines, 742nucleophilicity and, 377

Basicity constant (Kb), 741Beeswax, 928Benedict’s test, 870Bent bond, cyclopropane, 119–120Benzaldehyde, electrophilic aromatic

substitution of, 296–297electrostatic potential map of, 294IR spectrum of, 58413C NMR absorptions of, 585

Benzene, alkylation of, 288–289bond lengths in, 271bromination of, 282–284chlorination of, 283discovery of, 269electrostatic potential map of, 44, 271,

294Friedel–Crafts reactions of, 288–290heat of hydrogenation of, 271Hückel 4n � 2 rule and, 274–275iodination of, 284molecular orbitals of, 272–273nitration of, 284–285reaction with Br2, 282–283reaction with Cl2, 283reaction with HNO3, 284–285reaction with I2, 284resonance in, 44, 271stability of, 271structure of, 270–273sulfonation of, 285–286toxicity of, 267UV absorption of, 441

Benzenesulfonic acid, synthesis of, 286

Benzodiazepine, combinatorial library of, 306

Benzoic acid, 13C NMR absorptions in,618

pKa of, 606, 609substituent effects on acidity of, 609

Benzophenone, structure of, 559

Benzoquinone, electrostatic potentialmap of, 519

Benzoyl group, 559Benzoyl peroxide, ethylene

polymerization and, 240–241Benzo[a]pyrene, metabolism of, 238

structure of, 278Benzyl ester, hydrogenolysis of, 793Benzyl group, 269Benzylic carbocation, electrostatic

potential map of, 385resonance in, 385SN1 reaction and, 385–386

Benzylic halide, SN1 reaction and,385–386

SN2 reaction and, 386Benzylic radical, resonance in, 299Benzylpenicillin, discovery of, 668Beta anomer, 863Beta-carotene, structure of, 179, 951

industrial synthesis of, 577UV spectrum of, 442

Beta-diketone, Michael reactions and,715

Beta-keto acid, decarboxylation of, 693Beta-keto ester, alkylation of, 696

cyclic, 711–713decarboxylation of, 696Michael reactions and, 715pKa of, 690synthesis of, 708–710

Beta-lactam antibiotics, 668–669Beta-oxidation pathway, 938–942

mechanism of, 938–942Beta-pleated sheet, molecular model of,

798secondary protein structure and, 797

Bextra, prostaglandin synthesis and, 2structure of, 313

Bimolecular, 372Biodegradable polymers, 665–666Biological amine(s),

Henderson–Hasselbalch equationand, 745–746

protonation of, 745–746Biological carboxylic acid(s), dissociation

of, 608–609Henderson–Hasselbalch equation and,

608–609Biological mass spectrometry, 424–425Biological reactions

alcohol dehydration, 513–514aldol reaction, 718–719alkylation, 700benzylic oxidation, 299characteristics of, 168–170Claisen condensation reaction, 720comparison with laboratory reactions,

168–170conjugate nucleophilic addition

reaction, 582conventions for writing, 169, 197dehydration, 513–514elimination reaction, 400epoxidation, 236–237Friedel–Crafts alkylation, 290–291halogenation (alkene), 225

halohydrin formation, 227Hofmann elimination reaction, 752hydrolysis, thioester, 678hydroxylation (aromatic), 286–287iodination (aromatic), 284methylation, 390–391nucleophilic acyl substitution, 648–649oxidations with FAD, 939–940oxidations with NAD�, 519radical reaction, 146, 243–244energy diagram of, 167reductions ( alkene), 234–235reduction (aldehyde), 580reduction (ketone, 580reduction (thioester), 663reduction with NADH, 507reduction with NADPH, 507reductive amination, 750SN1 reaction, 390–391SN2 reaction, 390–391

Biot, Jean Baptiste, 325Biotin, carboxylation with, 913, 916, 945

mechanism of carboxylation with, 916,945

stereochemistry of, 356structure and function of, 803, 913,

916, 945bis, name prefix, 6621,3-Bisphosphoglycerate, from

glyceraldehyde 3-phosphate, 898reaction with ADP, 899

Blood groups, antigenic determinants in,879

compatibility of, 879types of, 879

Boc (tert-butoxycarbonyl amide), 794amino acid protection with, 794

Bombykol, 538Bond, covalent, 10–11

pi, 15sigma, 10

Bond angle, 13Bond dissociation energy (D), 161

table of, 162Bond length, 11Bond strength, 11Bonding molecular orbital, 22Borane, electrophilicity of, 229

reaction with alkenes, 229–230Borneol, rearrangement of, 977Boron trifluoride, electrostatic potential

map of, 59, 151Branched-chain alkane, 83Breathalyzer test, 532BRENDA enzyme database, 807Bridgehead atom, 131Broadband-decoupled NMR, 467Bromine, reaction with alkenes, 224–225

reaction with aromatic compounds,282–284

Bromo group, directing effect of, 294p-Bromoacetophenone, molecular model

of, 46513C NMR spectrum of, 465symmetry plane in, 465

Bromocyclohexane, molecular model of,125

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INDEX I-7

Bromoethane, 1H NMR spectrum of, 476

spin–spin splitting in, 476–478Bromohydrin(s), 226

from alkenes, 226–227mechanism of formation of, 226–227

Bromomethane, electrostatic potentialmap of, 150

Bromonium ion, 224electrostatic potential map of, 225from alkenes, 224

2-Bromopropane, 1H NMR spectrum of,478

spin–spin splitting in, 478Brønsted–Lowry acid, 50

conjugate base of, 50strengths of, 51–53

Brønsted–Lowry base, 50conjugate acid of, 50strengths of, 51–53

cis-But-2-ene, heat of hydrogenation of,194

molecular model of, 186, 192steric strain in, 192

trans-But-2-ene, heat of hydrogenation of,194

molecular model of, 186, 192But-3-en-2-one, electrostatic potential

map of, 581UV absorption of, 441

Buta-1,3-diene, 1,2 addition reactions of,248–249

1,4 addition reactions of, 248–249electrophilic addition reactions of,

248–249electrostatic potential map of, 248heat of hydrogenation of, 245molecular orbitals in, 247reaction with HBr, 248–249stability of, 245–247UV spectrum of, 440

Butan-1-ol, mass spectrum of, 531Butan-2-one, 13C NMR spectrum of, 465,

585Butane, anti conformation of, 99–100

bond rotation in, 99–100conformations of, 99–100gauche conformation of, 99–100molecular model of, 83

Butanoic acid, IR spectrum of, 617tert-Butoxycarbonyl amide, amino acid

protection with, 794Butter, composition of, 929tert-Butyl alcohol, pKa of, 502tert-Butyl carbocation, molecular model

of, 202Butyl group, 87Butyllithium, reaction with

alkyltriphenylphosphonium saltsreaction with diisopropylamine, 689

c (Speed of light), 426C-terminal amino acid, 787Cadaverine, odor of, 740Caffeine, structure of, 33Cahn–Ingold–Prelog sequence rules,

188–190, 328

Camphor, specific rotation of, 326structure of, 951

Cannizzaro reaction, 579mechanism of, 579

Capsaicin, structure of, 81-carbaldehyde, aldehyde name ending, 558Carbamoyl phosphate, biosynthesis of,

827reaction with ornithine, 828–829

Carbamoyl phosphate synthetase, 827Carbanion, 393, 567

stability of, 253Carbinolamine, 569Carbocation(s), 153

alkyl shift in, 207–208aromatic substitution and, 282E1 reaction and, 399electronic structure of, 202–203electrophilic addition reactions and,

153, 195–196Friedel–Crafts reaction and, 289Hammond postulate and, 204–206hydride shift in, 207–208hyperconjugation in, 202–203Markovnikov’s rule and, 199molecular orbital of, 203rearrangements of, 206–208, 289SN1 reactions and, 382–383solvation of, 388stability of, 202–203, 386steroid biosynthesis and, 968–969

Carbohydrate(s), 851anomers of, 863–864catabolism of, 893–900classification of, 853complex, 852Fischer projections of, 854–856glycosides of, 867–8681→4-links in, 874–875origin of name, 851photosynthesis of, 852see also Aldose, Monosaccharide

Carbon, ground-state electronconfiguration of, 6

Carbon atom, 3 dimensionality of, 7tetrahedral geometry of, 7

-carbonitrile, nitrile name ending, 604Carbonyl chemistry, overview of,

547–555Carbonyl compound(s), acidity of,

689–690alcohols from, 505–511alkylation of, 691–699classification of, 548–549electrophilicity of, 549electrostatic potential map of, 80, 150from alcohols, 516–519general reactions of, 550–555kinds of, 80mass spectrometry of, 422–423name endings for, 548polarity of, 80table of, 548

Carbonyl condensation reaction, 554, 681�-substitution reactions and, 704biological, 718–720mechanism of, 701

Carbonyl group(s), 547directing effect of, 294inductive effect of, 294–295orienting effect of, 294resonance effect of, 294–295

-carbothioate, thioester name ending, 635

-carboxamide, amide name ending, 635Carboxy phosphate, mechanism of

formation, 945reaction with ammonia, 827

Carboxylate ion, reaction with acidchlorides, 648

reaction with alkyl halides, 643resonance in, 607

Carboxylation, 612biological, 913, 916, 945

-carboxylic acid, name ending forcarboxylic acids, 602

Carboxylic acid(s), 601acid anhydrides from, 643acid chlorides from, 642–643acidity of, 605–607alcohols from, 507–508, 647amides from, 646–647biological, 608–609biological nucleophilic acyl

substitutions of, 647–648common names of, 603dimers of, 605dissociation of, 605–606dissociation of in cells, 608–609esters from, 643–645from acid halides, 648from alcohols, 516–517from aldehydes, 561–562from alkyl halides, 611–612, 692–694from amides, 659–660from esters, 654–656from Grignard reagents, 612from malonic ester, 692–694from nitriles, 611–612, 616Henderson–Hasselbalch equation and,

608–609hydrogen bonding in, 605inductive effects in, 609IR spectroscopy of, 617naming, 602–603NMR spectroscopy of, 618nucleophilic acyl substitution reactions

of, 642–645occurrence of, 601pKa table of, 606polarity of, 80properties of, 605protonation of in cells, 745–746reaction with alcohols, 644–645reaction with amines and DCC, 646reaction with ammonia and DCC, 646reaction with diazomethane, 677reaction with Grignard reagents, 510reaction with LiAlH4, 507–508, 647reaction with SOCl2, 642–643reactions of, 613reduction of, 507–508, 647substituent effects on acidity of, 609synthesis of, 611–612

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Carboxylic acid derivative(s), 663electrostatic potential maps of, 639interconversions of, 640IR spectroscopy of, 666–667kinds of, 663naming, 634–636NMR spectroscopy of, 667–668nucleophilic acyl substitution reactions

of, 640–641polarity of, 639relative reactivity of, 639–640

Cardiolipin, structure of, 973Carvone, structure of, 24Caryophyllene, structure of, 975Catabolism, 818

acetyl CoA, 905–910amino acids, 822–826, 831–838carbohydrates, 893–900fats, 934–942fatty acids, 937–942glucose, 893–900glycerol, 934–937nucleic acids, 997–1002pyruvate, 901–905triacylglycerols, 934–942

Catalytic cracking, 103Catalytic hydrogenation, see

HydrogenationCation radical, mass spectrometry and,

416Celebrex, prostaglandin synthesis and, 2Cell membrane, lipid bilayer in, 934Cellobiose, molecular model of, 874

mutarotation of, 874Cellulose, function of, 876

structure of, 876uses of, 876

Cellulose nitrate, 876Cephalexin, structure of, 669Cephalosporin, structure of, 669Chain, Ernst, 668Chain-growth polymer, 240–242, 664Chain reaction (radical), 145Chair conformation (cyclohexane), 122

drawing, 122molecular model of, 122see also Cyclohexane

Chemical Abstracts, 75Chemical reactions, conventions for

writing, 197Chemical shift (NMR), 461

13C NMR spectroscopy and, 4641H NMR spectroscopy and, 473–474

Chemical structure, drawing, 22–24Chemical waste, green chemistry and,

764–765Chiral, 321Chiral drugs, 351–352Chiral methyl group, 414Chirality, amines and, 345, 739

amino acids and, 782carbohydrates and, 858–859cause of, 322naturally occurring molecules and,

349–351phosphines and, 345, 785–786sulfonium salts and, 346

Chirality center, 322detection of, 323R,S configuration of, 328–330

Chloral hydrate, structure of, 566Chloramphenicol, structure of, 357Chlorine, reaction with alkanes, 95

reaction with alkenes, 224reaction with aromatic compounds, 283reaction with methane, 145

Chloro group, directing effect of, 294Chlorobenzene, electrostatic potential

map of, 294Chloroform, LD50 of, 26Chloromethane, dipole moment of, 39

electrostatic potential map of, 147natural sources of, 363

Chloronium ion, 224Chlorosulfite, 643

leaving group ability of, 378Cholestanol, structure of, 334Cholesterol, biosynthesis of, 964–969

heart disease and, 970molecular model of, 961specific rotation of, 326statin drugs and, 1009 –1010

Cholic acid, molecular model of, 602Choline, synthesis of, 772Chromate, alcohol oxidation and, 518Chromatography, 444

explanation of, 444–445high-pressure, 444liquid, 444

Chrysanthemic acid, structure of, 111Chymotrypsin, peptide cleavage with, 792trans-Cinnamaldehyde, 1H NMR

spectrum of, 482synthesis of, 729tree diagram for, 483

Cis–trans isomers, 116alkenes and, 186–187cycloalkanes and, 115–116requirements for, 187

Citrate, biosynthesis of, 804–805,906–907

Citrate synthase, active site in, 805function of, 804mechanism of, 806molecular model of, 805

Citric acid, molecular model of, 28Citric acid cycle, 819, 905–910

requirements for, 905result of, 910steps in, 906

Citrulline, argininosuccinate from,828–830

from ornithine, 828–829reaction with aspartate, 828–830

Claisen condensation reaction, 708–710�-oxidation and, 941biological, 718–719fatty acid biosynthesis and, 720intramolecular, 711–713mechanism of, 709–710requirements for, 709

Cocaine, specific rotation of, 327structure of, 735synthesis of, 733

Coconut oil, composition of, 929Coding strand (DNA), 987Codon (mRNA), 988

table of, 988Coenzyme, 170, 802

functions of, 802–803table of, 802–803

Coenzyme A, structure and function of,802

see also Acetyl CoACoenzyme Q, 520

function of, 1004Cofactor (enzyme), 802Color, perception of, 442–443

UV spectroscopy and, 442–443Combinatorial chemistry, 306–307

kinds of, 307Combinatorial library, 306Common cold, vitamin C and, 619Complex carbohydrate, 852

biological hydrolysis of, 892–893Concanavalin A, � sheet in, 798

ribbon model of, 798Condensed structure, 22

rules for drawing, 22–23Cone cells, vision and, 443Configuration, 328

assignment of, 328–330chirality centers and, 328–330Fischer projections and, 855inversion of, 368–370R, 329S, 329

Conformation (cyclohexane), 97calculating energy of, 133E2 reactions and, 397

Conformational analysis (cyclohexane),128–130

Coniine, molecular model of, 28Conjugate acid, 50Conjugate base, 50Conjugate nucleophilic addition reaction,

580–583biological, 582mechanism of, 581Michael reactions and, 713–715

Conjugated diene(s), 2451,2 addition reactions of, 248–2491,4 addition reactions of, 248–249allylic carbocations from, 249electrophilic addition reactions of,

248–249electrostatic potential map of, 248heats of hydrogenation of, 245molecular orbitals in, 247reaction with HBr, 248–249stability of, 245–248

Conjugation, 245ultraviolet spectroscopy and, 441

Constitutional isomers, 83kinds of, 84

Contraceptive, steroid, 963Copper(II) chloride, aromatic iodination

and, 284Coprostanol, structure of, 334Corn oil, composition of, 929Coronene, structure of, 278

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INDEX I-9

Cortisone, structure of, 111Couper, Archibald Scott, 6Coupled reactions, ATP and,

820–821Coupling (NMR), 477

see also Spin–spin splittingCoupling constant, 478

size of, 478use of, 478

Covalent bond, 8molecular orbital theory of, 21–22polar, 36rotation around, 115valence bond theory of, 10–20

COX-2, see CyclooxygenaseCOX-2 inhibitors, 2Crick, Francis H. C., 982Crotonaldehyde, structure of, 558Crotonic acid, 13C NMR absorptions in,

618Crum Brown, Alexander, 7Crystallization, fractional, 338Curved arrow, electron movement

and, 45guidelines for using, 154–156polar reactions and, 149, 154–156meaning of, 58–59

Cyanocobalamin, structure of, 1009Cyanocycline A, structure of, 614Cyanogenic glycoside, 614Cycloalkane(s), 112

angle strain in, 118Baeyer strain theory and, 118cis–trans isomerism in, 115–116naming, 112–114representation of, 112strain energies of, 118

Cycloalkene, naming, 183Cyclobutadiene, antiaromaticity of,

274electrostatic potential map of, 274Hückel 4n � 2 rule and, 274

Cyclobutane, angle strain in, 120conformation of, 120molecular model of, 120strain energy of, 118torsional strain in, 120

Cyclodecane, strain energy of, 118Cyclodecapentaene, molecular model of,

275Cycloheptane, strain energy of, 118Cycloheptatrienyl cation, aromaticity of,

315Cyclohexa-1,3-diene, heat of

hydrogenation of, 271UV absorption of, 441

Cyclohexane, axial bonds in, 123–125barrier to ring flip in, 125chair conformation of, 122–125conformational analysis of, 126–1301,3-diaxial interactions in, 126–128drawing chair form of, 122equatorial bonds in, 123–125IR spectrum of, 448ring-flip in, 125strain energy of, 118twist-boat conformation of, 123

Cyclohexanol, IR spectrum of, 52913C NMR spectrum of, 530

Cyclohexanone, aldol reaction of, 702enol content of, 683enolate ion of, 689IR spectrum of, 58413C NMR absorptions of, 585

Cyclohexene, heat of hydrogenation of,271

IR spectrum of, 449Cyclohexenones, from 1,5-diketones,

707–708Cyclohexylamine, IR spectrum of, 762Cyclohexylmethanol, 1H NMR spectrum

of, 484Cyclononane, strain energy of, 118Cyclooctane, strain energy of, 118Cyclooctatetraene dianion, aromaticity

of, 315electrostatic potential map of, 274Hückel 4n � 2 rule and, 274reactivity of, 274

Cyclooxygenase, 1–2function of, 948, 950types of, 948

Cyclooxygenase reaction, arachidonicacid and, 1–2

Cyclopenta-1,3-diene, electrostaticpotential map of, 756

Cyclopentadienyl anion, aromaticity of,315

Cyclopentane, angle strain in, 120–121conformation of, 120–121molecular model of, 121strain energy of, 118torsional strain in, 120–121

Cyclopentanone, IR absorption of, 583Cyclopentenones, from 1,4-diketones,

707–708Cyclopropane, angle strain in, 119–120

bent bonds in, 119–120bond strength in, 120molecular model of, 115, 119strain energy of, 118torsional strain in, 119–120

Cystathionine, cysteine from, 849Cysteine, biosynthesis of, 849

disulfide bridges from, 788structure and properties of, 780

Cytidine, biosynthesis of, 1006catabolism of, 1002

Cytosine, electrostatic potential map of,983

molecular model of, 68protection of, 993structure of, 980

D (Debye), 38D (Bond dissociation energy), 161D Sugar, 858

Fischer projections of, 858Dacron, structure of, 665DCC, see DicyclohexylcarbodiimideDeactivating group (aromatic

substitution), 294acidity and, 610explanation of, 294–295

Deamination, 822amino acids and, 822–826mechanism of, 823–825PLP and, 823–825

Debye (D), 38cis-Decalin, conformation of, 132

molecular model of, 132, 960trans-Decalin, conformation of, 132

molecular model of, 132, 960Decane, molecular model of, 101Decarboxylation, 693

acetoacetic ester synthesis and, 696malonic ester synthesis and, 693–694orotidine monophosphate and, 1005thiamin diphosphate and, 901–903

DEET, structure of, 677Degenerate orbitals, 273Degree of unsaturation, 180

calculation of, 180–181Dehydration, alcohols, 222

alcohol mass spectrum and, 531aldol reaction and, 705–706biological, 513–514

Dehydrohalogenation, 222Delocalization (electron), 248Delta scale (NMR), 461Denature (protein), 799Deoxy sugar, 873Deoxyguanosine, catabolism of, 997–1000Deoxyribonucleic acid (DNA), 979–982

antisense strand of, 987base-pairing in, 982–984bases in, 980cleavage of, 991coding strand of, 987double helix in, 982–9843’ end of, 9825’ end of, 982exons in, 987fingerprinting with, 1010–1011introns in, 987major groove in, 983–984minor groove in, 983–984polymerase chain reaction and,

995–997promotor sites in, 987replication fork in, 986replication of, 985–986sense strand of, 987sequencing of, 990–992size of, 980structure of, 981–984synthesis of, 992–995template strand of, 987transcription of, 986–987Watson–Crick model of, 982–984

Deoxyribonucleotide(s), structures of,981

2’-Deoxyribose, structure of, 9801-Deoxyxylulose 5-phosphate,

isopentenyl diphosphate from, 952DEPT-NMR, 467–468

uses of, 467–468DEPT-NMR spectrum, 6-methylhept-5-en-

2-ol, 468Detectors, mass spectrometry and, 416Detergent, structure of, 932

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Deuterium isotope effect, 395E1 reaction and, 399E2 reaction and, 395

Dextromethorphan, structure of, 324Dextrorotatory, 326Dialkyl phthalates, plasticizers and,

653–654Dialkylamine, pKa of, 690Diastereomers, 334

kinds of, 341Diastereotopic (NMR), 4721,3-Diaxial interactions, 126–128

table of, 128Diazepam, structure of, 182, 267, 283Diazomethane, reaction with carboxylic

acids, 677DIBAH, see Diisobutylaluminum hydrideDibromophosphite, leaving group ability

of, 378cis-1,2-Dichloroethylene, electrostatic

potential map of, 67trans-1,2-Dichloroethylene, electrostatic

potential map of, 67Dicyclohexylcarbodiimide (DCC), amide

bond formation with, 646peptide synthesis with, 794

Dideoxy DNA sequencing, 991–9922’,3’-Dideoxyribonucleotide, 991Dieckmann cyclization, 711–713

mechanism of, 711–712Diene, conjugated, 245Diene polymers, 253–254

vulcanization of, 254Diethyl ether, synthesis of, 523

uses of, 498Diethyl malonate, alkylation of, 692–694

carboxylic acids from, 692–694Michael reactions and, 715pKa of, 690

Diethyl propanedioate, see Diethylmalonate

Diffraction limit, light waves and, 720Digestion, 819Digitoxin, structure of, 868Dihedral angle, 98Dihydrogen phosphate ion, pKa of, 52Dihydrolipoamide, oxidation by FAD, 904Dihydroorotase, 1003Dihydroorotate dehydrogenase, 1004Dihydroxyacetone phosphate, fructose

1,6-bisphosphate from, 917–918isomerization of, 897–898

Diisobutylaluminum hydride, reactionwith esters, 560, 658

Diisopropylamine, pKa of, 690, 743reaction with butyllithium, 689

1,3-Diketone, pKa of, 690Dimethyl ether, electrostatic potential

map of, 59, 523Dimethyl sulfide, bond angle in, 20

molecular model of, 20sp3 hybrid orbitals in, 20structure of, 20

Dimethyl sulfoxide, electrostaticpotential map of, 41

formal charges in, 40–42skin penetration by, 528SN2 reaction and, 379

Dimethylallyl diphosphate (DMAPP),from isopentenyl diphosphate, 956

terpenoid biosynthesis and, 956–958Dimethylamine, electrostatic potential

map of, 740cis-1,2-Dimethylcyclohexane,

conformational analysis of, 128–130trans-1,2-Dimethylcyclohexane,

conformational analysis of, 128–130cis-1,2-Dimethylcyclopropane, molecular

model of, 116trans-1,2-Dimethylcyclopropane,

molecular model of, 116Dimethylformamide, SN2 reaction and,

3792,2-Dimethylpropane, mass spectrum of,

418molecular model of, 83

N,N-Dimethyltryptamine, molecularmodel of, 761

Diol, 236from alkenes, 236–239from epoxides, 236–238

DiPAMP ligand, amino acid synthesisand, 785–786

Dipole moment (�), 38polar covalent bonds and, 38–39table of, 39

Dipole–dipole forces, 62Disaccharide, 873–876

1→4-links in, 874–875synthesis of, 878

Disparlure, 543Dispersion forces, 62

alkanes and, 96Distortionless enhancement by

polarization transfer, see DEPT-NMRDisulfide, 521

electrostatic potential map of, 80from thiols, 521polarity of, 80reduction of, 521thiols from, 521

Disulfide bridge, peptides and, 788Diterpene, 209Diterpenoid, 951DMAPP, see Dimethylallyl diphosphate,

956DMF, see DimethylformamideDMSO, see Dimethyl sulfoxideDMT (dimethoxytrityl ether), 993DNA, see Deoxyribonucleic acidDNA fingerprinting, 1010–1011

reliability of, 1010–1011STR loci and, 1010–1011

DNA polymerase, 991Dopamine, molecular model of, 748Double bond, electronic structure of, 14–16

length of, 15–16molecular orbitals in, 22see also Alkenestrength of, 15–16

Double helix (DNA), 982–984Doublet (NMR), 478Downfield (NMR), 460Drugs, approval procedure for, 171

chiral, 351–352origin of, 171

E configuration, 188assignment of, 188–190

E1 reaction, 393, 398carbocations and, 399deuterium isotope effect and, 399kinetics of, 399mechanism of, 398–399rate-limiting step in, 399stereochemistry of, 399

E1cB reaction, 393, 400biological, 400carbanion intermediate in, 400mechanism of, 400rate-limiting step in, 400requirements for, 400

E2 reaction, 393, 394alcohol oxidation and, 518cyclohexane conformation and, 397deuterium isotope effect and, 395kinetics of, 395mechanism of, 394–395menthyl chloride and, 397neomenthyl chloride and, 397periplanar geometry of, 395–397rate law for, 395rate-limiting step in, 395stereochemistry of, 397

Ebonite, structure of, 254Eclipsed conformation, 97

molecular model of, 97Edman degradation, 790–792

mechanism of, 790–791Eicosanoid, 948–950

biosynthesis of, 948–950naming of, 948–949

Elaidic acid, structure of, 930Electromagnetic radiation, 425

amplitude of, 426characteristics of, 425–426energy of, 427frequency of, 426kinds of, 425speed of, 426wavelength of, 426

Electromagnetic spectrum, 425regions in, 425

Electron, delocalization of, 248lone-pair, 9nonbonding, 9spin of, 6

Electron configuration, ground state, 5

rules for assigning, 5–6Table of, 6

Electron-dot structure, 8Electron-impact mass spectrometry,

416–417Electron movement, curved arrows

and, 58–59Electron shell, 4Electron-transport chain, 819Electronegativity, 36

inductive effects and, 37polar covalent bonds and, 36–37table of, 36

Electrophile, 149–150characteristics of, 155curved arrows and, 154–156

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INDEX I-11

electrostatic potential maps of, 150examples of, 150

Electrophilic addition reaction, 195–196carbocation rearrangements in,

206–208energy diagram of, 164–167Hammond postulate and, 204–206intermediate in, 166Markovnikov’s rule and, 198–199mechanism of, 152–154, 195–196regiospecificity of, 198–199stereochemistry and, 342–344

Electrophilic aromatic substitutionreaction, 281

arylamines and, 753–754inductive effects in, 294–295kinds of, 281pyridine and, 758pyrrole and, 756–757resonance effects in, 294–295substituent effects in, 292–297

Electrophoresis, 784DNA sequencing and, 992

Electrospray ionization massspectrometry, see ESI massspectrometry

Electrostatic potential map, 37acetaldehyde, 549acetamide, 639, 673, 743acetate ion, 44, 54, 57, 607acetic acid, 54, 56acetic acid dimer, 605acetic anhydride, 639acetone, 56, 57, 80, 555acetone anion, 57acetonitrile, 615acetyl azide, 673acetyl chloride, 555, 639acetylide anion, 253acid anhydride, 639acid chloride, 639acyl cation, 290adenine, 983alanine, 778alanine zwitterion, 778alcohol, 79alkene, 79, 152alkyl halide, 79alkyne, 79allyl carbocation, 249, 385amide, 639amine, 80ammonia, 150aniline, 744anilinium ion, 744anisole, 623arene, 79benzaldehyde, 294benzene, 44, 271, 294benzoquinone, 519benzyl carbocation, 385boron trifluoride, 59, 151bromomethane, 150bromonium ion, 225but-3-en-2-one, 581buta-1,3-diene, 248carbonyl compound, 80, 150carboxylic acid derivatives, 639

chlorobenzene, 294chloromethane, 37, 147conjugated diene, 248cyclobutadiene, 274cyclooctatetraene, 274cyclopenta-1,3-diene, 756cytosine, 983cis-1,2-dichloroethylene, 67trans-1,2-dichloroethylene, 67dimethyl ether, 59, 523dimethyl sulfoxide, 41dimethylamine, 740disulfide, 80DNA base pairs, 983electrophiles, 150enamine, 716enol, 682, 685enolate ion, 688, 692ester, 639ethane, 152ether, 79ethoxide ion, 607ethylene, 78, 152fatty-acid carboxylate, 932formaldehyde, 173formate ion, 607Grignard reagent, 367guanine, 983histidine, 782HOSO2

�, 286hydrogen bond, 63, 501hydronium ion, 150hydroxide ion, 54, 150imidazole, 61, 276menthene, 78methanethiol, 173methanol, 37, 56, 57, 148, 501methoxide ion, 57methyl acetate, 639methyl anion, 253methyl thioacetate, 639methylamine, 38, 57, 743methyllithium, 37, 147methylmagnesium chloride, 567methylmagnesium iodide, 367naphthalene, 279nitronium ion, 285nucleophiles, 150nucleophilic addition reaction, 562penta-1,4-diene, 248phenol, 294phosphate, 79polar covalent bonds and, 37protonated methanol, 148purine, 761pyridine, 276pyrimidine, 276pyrrole, 276, 756pyrrolidine, 756SN2 reaction, 373sulfide, 80thioanisole, 623thioester, 639thiol, 80thymine, 983toluene, 311trifluoromethylbenzene, 311trimethylamine, 740

vinylic anion, 253water, 54, 150zwitterion, 778

Elimination reaction(s), 142mechanisms of, 393–400summary of, 401

Embden–Meyerhof pathway, 893–900see also Glycolysis

Enamido acid, amino acids from,785–786

Enamine, 568conjugate addition reactions of, 717electrostatic potential map of, 716from aldehydes, 568–571from ketones, 568–571mechanism of formation of, 570Michael reactions of, 717 nucleophilicity of, 716reaction with enones, 717

Enantiomeric excess, 587 Enantiomers, 320

discovery of, 327–328resolution of, 338–340

Enantioselective synthesis, 352, 587Enantiotopic (NMR), 471–472Endergonic reaction, 158

Hammond postulate and, 205Endothermic reaction, 159-ene, alkene name ending, 182Energy diagram, see also Reaction energy

diagram, 163–164Energy-rich bonds, explanation of,

161–162Enethiol, 497Enflurane, molecular model of, 325Enol, 497, 682

�-substitution reaction and, 685–686electrostatic potential map of, 682, 685from aldehydes, 682–684from ketones, 682–684mechanism of acid-catalyzed formation

of, 683mechanism of base-catalyzed formation

of, 684reactivity of, 685–687

Enolase, 900Enolate ion, 553, 684

alkylation of, 691–699electrostatic potential map of, 688, 692reactivity of, 691–692resonance in, 688

Enone, conjugate addition reactions ofamines, 582

conjugate addition reactions of water,582

from aldehydes, 705–706from aldol reaction, 705–706from ketones, 705–706IR absorption of, 583molecular orbitals of, 706reaction with amines, 582reaction with water, 582stability of, 705–706synthesis of, 688

Enoyl-CoA hydratase, 940Entgegen, E configuration and, 188Enthalpy change (�H), 159

explanation of, 159

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Entner–Douderoff pathway, 923Entropy change (�S), 160

explanation of, 160Enzyme, 168–169, 800–801

active site in, 169classification of, 801naming, 801rate enhancements in, 800specificity of, 800stereochemistry of reactions, 350–351substrates for, 800transition state stabilization by, 800turnover number of, 800visualization of, 844–845

Ephedrine, structure of, 65Epibatidine, molecular model of, 363Epimers, 334Epinephrine, biosynthesis of, 390–391Epoxide(s), 235

acid-catalyzed cleavage of, 236–238alcohols from, 505base-catalyzed cleavage of, 5261,2-diols from, 236–238from alkenes, 235–237from halohydrins, 236mechanism of cleavage of, 237–238reaction with acids, 236–238reaction with base, 526reaction with HCl, 378SN2 reactions of, 378synthesis of, 235–237

Equations, conventions for writing, 197Equatorial bonds (cyclohexane), 123

drawing, 124Equilibrium constant, Keq, 157

free-energy change and, 159Ergosterol, UV absorption of, 451Erlenmeyer, Emil, 7Erythronolide B, structure of, 355Erythrose, configuration of, 860ESI mass spectrometry, 424Essential amino acid, 838

biological precursors of, 839Essential monosaccharide, 872–873

biosynthesis of, 873Essential oil, 209Ester(s), 633

acid-catalyzed hydrolysis of, 655–656alcohols from, 507–510, 657–658aldehydes from, 560, 658alkylation of, 698amides from, 657aminolysis of, 657�-keto esters from, 711–713base-catalyzed hydrolysis of, 654–655carbonyl condensation reactions of,

708–710carboxylic acids from, 654–656electrostatic potential map of, 639from acid anhydrides, 652from acid chlorides, 650from alcohols, 515–516from carboxylate ions, 643from carboxylic acids, 643–645Grignard reaction of, 509–510, 658IR spectroscopy of, 436–437, 667mechanism of hydrolysis of, 654–656

mechanism of Grignard reaction of, 658mechanism of reduction of, 657naming, 635NMR spectroscopy of, 667–668nucleophilic acyl substitution reactions

of, 654–658occurrence of, 653partial reduction of, 560pKa of, 690polarity of, 80reaction with amines, 657reaction with DIBAH, 560, 658reaction with Grignard reagents,

509–510, 658reaction with LDA, 698reaction with LiAlH4, 507–508, 657reduction of, 507–508, 657–658saponification of, 654–655uses of, 653

Estradiol, structure and function of,962–963

Estrogen, 962–963function of, 962

Estrone, structure and function of,962–963

Ethane, bond angles in, 13–14bond lengths in, 13–14bond rotation in, 96–98bond strengths in, 13–14conformations of, 96–98eclipsed conformation of, 97electrostatic potential map of, 152molecular model of, 9, 14, 83rotational barrier in, 97sp3 hybrid orbitals in, 13–14staggered conformation of, 97structure of, 14torsional strain in, 97

Ethanol, from pyruvate, 923history of, 532industrial synthesis of, 227, 498IR spectrum of, 427LD50 of, 26metabolism of, 532physiological effects of, 532pKa of, 52, 502toxicity of, 532U.S. production of, 498

Ether(s), 497alcohols from, 525–526alkyl halides from, 525–526bond angles in, 523cleavage of with HI, 525–526cleavage of with trifluoroacetic acid,

526electrostatic potential map of, 79from alcohols, 523–524from alkyl halides, 524IR spectroscopy of, 529naming, 522NMR spectroscopy of, 530polarity of, 79properties of, 523reaction with HI, 525–526uses of, 498

Ethoxide ion, electrostatic potential mapof, 607

Ethyl acetate, ethyl acetoacetate from,709–710

1H NMR spectrum of, 667Ethyl acetoacetate, see Malonic esterEthyl acrylate, 13C NMR absorptions in,

466Ethyl alcohol, see EthanolEthyl benzoate, 13C NMR spectrum of,

492Ethyl cation, molecular orbital of, 203Ethyl group, 86Ethylcyclopentane, mass spectrum of,

420Ethylene, bond angles in, 15–16

bond lengths in, 15–16bond strengths in, 15–16electrostatic potential map of, 78, 152ethanol from, 227heat of hydrogenation of, 194hormonal activity of, 179molecular model of, 15molecular orbitals in, 22pKa of, 252polymerization of, 240–241reaction with H2O, 151–154sp2 hybrid orbitals in, 14–16structure of, 14–16

Ethylene dichloride, synthesis of, 224Ethylene glycol, acetals from, 574

manufacture of, 237uses of, 237

N-Ethylpropylamine, mass spectrum of,764

Ethynylestradiol, structure and functionof, 963

Exergonic reaction, 158Hammond postulate and, 205

Exon (DNA), 987Exothermic reaction, 159

FAD, see Flavin adenine dinucleotideFADH2, see Flavin adenine dinucleotide

(reduced),Faraday, Michael, 269Farnesyl diphosphate, biosynthesis of,

957–958squalene from, 957, 964

Farnesyl diphosphate synthase, 957Fat(s), 928

biological hydrolysis of, 656–657,934–937

catabolism of, 934–942energy content of, 928saponification of, 931table of, 929

Fatty acid(s), 928acetyl CoA from, 937–942biosynthesis of, 943–947catabolism of, 937–942Claisen reactions in biosynthesis of,

720fatty acyl CoAs from, 937mechanism of biosynthesis, 943–947melting point trends in, 930polyunsaturated, 928table of, 929trans, 234, 930

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INDEX I-13

Fatty acyl CoA, formation of, 649, 937Fatty acid biosynthesis, differences from

fatty acid catabolism, 943loading reaction in, 945overall result of, 947priming reactions in, 943–944

Fatty acid carboxylate, electrostaticpotential map of, 932

Fatty acid catabolism, differences fromfatty acid biosynthesis, 943

Fatty acid synthase, 943Favorskii reaction, 629Fehling’s test, 870Fenoprofen, synthesis of, 611Fibrous protein, 797Fingerprint region (IR), 430First-order reaction, 381Fischer, Emil, 853Fischer esterification reaction, 644–645

limitations of, 644mechanism of, 644–645

Fischer projection, 853–856carbohydrates and, 854–856D sugars, 858L, sugars, 858–859rotation of, 854–855R,S configuration of, 855conventions for, 854

Fishhook arrow, radical reactions and,143–144

Flavin adenine dinucleotide (FAD),mechanism of, 939–940

structure and function of, 803, 939Flavin adenine dinucleotide (reduced),

structure of, 939Flavin hydroperoxide, alkene

epoxidation with, 236–237, 965Flavin mononucleotide (FMN),

mechanism of, 1004Flavin mononucleotide (reduced),

function of, 1001, 1004Fleming, Alexander, 668Flexibilene, structure of, 975Florey, Howard, 668(S)-Fluoxetine, molecular model of,

350stereochemistry of, 350

FMN, see Flavin mononucleotideFmoc, amino acid protection with, 796

cleavage of, 813Food, catabolism of, 818–819Food and Drug Administration (FDA),

171Formal charge, 40–42

calculation of, 42summary table of, 42

Formaldehyde, dipole moment of, 39electrostatic potential map of, 173hydrate of, 565reaction with Grignard reagents,

509–510U.S. production of, 557uses of, 557

Formate ion, bond lengths in, 607electrostatic potential map of, 607

Formic acid, bond lengths in, 607pKa of, 606

N-Formiminoglutamate, reaction withtetrahydrofolate, 836–837

Formyl group, 559Fourier-transform NMR spectroscopy

(FT-NMR), 462–463Fractional crystallization, 338Fragmentation (mass spectrum), 417–420Free-energy change (�G), 158Free radical, 144Fremy’s salt, 519Frequency (�), 426Friedel–Crafts acylation reaction, 290

acyl cations in, 290arylamines and, 753–754mechanism of, 290

Friedel–Crafts alkylation reaction,288–289

arylamines and, 753–754carbocation rearrangements in, 289limitations of, 288–289mechanism of, 288

Fructose, anomers of, 863–864furanose form of, 864phosphorylation of, 896pyranose form of, 864sweetness of, 880

Fructose 1,6-bisphosphatase, 918FT-NMR, 462–463L-Fucose, biosynthesis of, 926

structure and function of, 872Fumarase, 909Fumarate, from succinate, 909

malate from, 909Fumaric acid, structure of, 603Functional group(s), 75

carbonyl compounds and, 80electronegative atoms in, 79–80importance of, 78IR spectroscopy of, 430–437multiple bonds in, 78–79polarity patterns of, 148table of, 76–77

Furan, industrial synthesis of, 755Furanose, 863Fused-ring heterocycle, 759–761

�, see GammaGalactose, biosynthesis of, 923

configuration of, 860metabolism of, 543

Gamma-aminobutyric acid, structure of,779

Gamma rays, electromagnetic spectrumand, 425

Gasoline, composition of, 103octane number of, 103

Gatterman–Koch reaction, 317Gauche conformation, 99

steric strain in, 99Gel electrophoresis, DNA sequencing

and, 992Gem (geminal), 564Geminal (gem), 564Gene, 986

number of in humans, 1, 992Genome, human, 986Geraniol, biosynthesis of, 390–391

Geranyl diphosphate, biosynthesis of,957–958

terpenoids from, 958Gibbs free-energy change (�G), 158

equilibrium constant and, 159Globo H hexasaccharide, structure of, 880Globular protein, 797Glucitol, structure of, 869Glucocorticoid, 963Glucogenic amino acid, 832Gluconeogenesis, 913–919

comparison with glycolysis, 919steps in, 914–915summary of, 919

�-D-Glucopyranose, molecular model of,863

�-D-Glucopyranose, molecular model of,863

Glucosamine, biosynthesis of, 924Glucose, anomers of, 863

biosynthesis of, 912–919catabolism of, 893–900chair conformation of, 123configuration of, 860ethers from, 524Fischer projection of, 856from starch, 892–893glycosides of, 867isomerization of, 895–896molecular model of, 130mutarotation of, 863–864oxidation of, 870–871pentaacetyl ester of, 866pentamethyl ether of, 866phosphorylation of, 895pyranose form of, 863reaction with acetic anhydride, 866reaction with ATP, 821reaction with iodomethane, 866reduction of, 869sweetness of, 880Williamson ether synthesis with, 866

Glucose 6-phosphate, hydrolysis of, 918Glucose-6-phosphate isomerase, 895Glutamate, arginine from, 840–841

biosynthesis of, 838glutamine from, 840ornithine from, 841oxidative deamination of, 826partial reduction of, 840–841proline from, 841transamination and, 822–825

Glutamate dehydrogenase, 826Glutamate 5-semialdehyde, from

glutamate, 841proline from, 750

Glutamic acid, structure and propertiesof, 781

Glutamine, biosynthesis of, 839–840from glutamate, 840structure and properties of, 780

Glutamine synthetase, 839Glutaric acid, structure of, 603Glutathione, oxidation of, 522

prostaglandin biosynthesis and, 948,950

structure of, 522

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I-14 I N D E X

Glycal, 878Glycal assembly method, 878(–)-Glyceraldehyde, configuration of, 330(R)-Glyceraldehyde, Fischer projection

of, 854molecular model of, 855

Glyceraldehyde 3-phosphate, fromdihydroxyacetone phosphate,897–898

fructose 1,6-bisphosphate from,917–918

Glyceraldehyde-3-phosphatedehydrogenase, 917

Glyceric acid, structure of, 603Glycerol, biological oxidation of, 937

catabolism of, 934–937sn-Glycerol 3-phosphate, naming of, 937Glycerophospholipid, 933Glycine, structure and properties of, 780Glycoconjugate(s), 868

biosynthesis of, 868–869mechanism of formation of, 868–869

Glycogen, function of, 877structure of, 877–878

Glycol, 236Glycolic acid, pKa of, 606

structure of, 603Glycolipid(s), 868Glycolysis, 893–900

comparison with gluconeogenesis, 919steps in, 894–895summary of, 900

Glycoprotein(s), 868biosynthesis of, 868–869

Glycosidase, 800, 877, 892�-, 877, 892mechanism of, 892–893

Glycoside, 867hydrolysis of, 868naming, 868occurrence of, 868–869

Glyoxalate cycle, 922GMP synthetase, 1007GPP, see Geranyl diphosphateGreen chemistry, 764–765

principles of, 764–765Grignard, François Auguste Victor, 367Grignard reaction, aldehydes and,

509–510, 567esters and, 509–510, 658formaldehyde and, 509–510ketones and, 509–510, 567mechanism of, 567strategy for using, 511

Grignard reagent, 367alkanes from, 368carboxylation of, 612carboxylic acids from, 612electrostatic potential map of, 367from alkyl halides, 367reaction with acids, 368reaction with aldehydes, 509–510, 567reaction with carboxylic acids, 510reaction with CO2, 612reaction with esters, 509–510, 658reaction with formaldehyde, 509–510reaction with ketones, 509–510, 567

Griseofulvin, synthesis of, 732Guanine, aromaticity of, 280

biological hydrolysis of, 999catabolism of, 997–1000electrostatic potential map of, 983phosphorolysis of, 998protection of, 993structure of, 980xanthine from, 997–998

Guanine deaminase, 998Guanosine, biosynthesis of, 1007–1008

catabolism of, 997–1000Gulose, configuration of, 860Guncotton, 876

H5N1 virus, 920Halo group, inductive effect of, 294–295Haloalkane, see Alkyl halideHalogen, directing effect of, 294

inductive effect of, 294–295orienting effect of, 294resonance effect of, 294–295

Halohydrin(s), 226epoxides from, 236reaction with base, 236

Haloperoxidase, biological halogenationswith, 225

biological halohydrin formation with,227

Hammond postulate, 204–206SN1 reaction and, 385

Handedness, 319–320HDL, heart disease and, 970Heart disease, cholesterol and, 970Heat of hydrogenation, 193

table of, 194Heat of reaction, 159Helminthogermacrene, structure of, 972Heme, cyclooxygenase reaction and, 1–2

structure of, 755Hemiacetal, 572Hemithioacetal, 898Henderson–Hasselbalch equation,

608–609carboxylic acids and, 608–609amines and, 745–746

Hertz (Hz), 426Heterocycle, 275

aromatic, 275–277fused-ring, 759–761

Heterocyclic amine, 738, 755–759basicity of, 742names of, 738

HETPP, see Hydroxyethylthiamindiphosphate

Hevea brasieliensis, rubber from, 253Hex-1-ene, IR spectrum of, 432Hex-2-ene, mass spectrum of, 421Hex-1-yne, IR spectrum of, 432Hexa-1,3,5-triene, UV absorption of, 441Hexane, IR spectrum of, 432

mass spectrum of, 419molecular model of, 14

Hexokinase, 895active site in, 169function of, 169molecular model of, 169

High-pressure liquid chromatography, 445Highest occupied molecular orbital

(HOMO), 439UV spectroscopy and, 439

Histidine, basicity of, 757catabolism of, 835–837electrostatic potential map of, 782structure and properties of, 781trans-urocanate from, 835–836

Histidine ammonia lyase, 835HMG-CoA, see 3-Hydroxy-3-

methylglutaryl CoA, 954HMG-CoA reductase, cholesterol

biosynthesis and, 1009Hoffmann-LaRoche Co., vitamin C

synthesis and, 619Hofmann elimination reaction, 414,

751–752biological, 752mechanism of, 752regiochemistry of, 752Zaitsev’s rule and, 752

HOMO, see Highest occupied molecularorbital, 439

homo-, as naming prefix, 842Homocysteine, structure of, 779Homoserine, biosynthesis of, 842–843

from aspartate, 842–843threonine from, 843–844

Homotopic (NMR), 471Honey, sugars in, 875Hormone, 962

adrenocortical, 963sex, 962–963

HPLC, 445Hückel, Erich, 273Hückel 4n � 2 rule, 273–275

cyclobutadiene and, 274cycloheptatrienyl cation and, 315cyclooctatetraene and, 274cyclopentadienyl anion and, 315explanation of, 274–275imidazole and, 276–277molecular orbitals and, 274–275pyridine and, 276–277pyrimidine and, 276–277pyrrole and, 276–277

Hughes, Edward Davies, 372Human fat, composition of, 929Human genome, size of, 986, 992Humulene, structure of, 209Hund’s rule, 6Hybrid orbitals, 12–20

sp, 17–18sp2, 15sp3, 12–14

Hydrate (carbonyl), 561from aldehydes, 564–566from ketones, 564–566

Hydration (alkene), 227–230Hydride shift, carbocation

rearrangements and, 207–208Hydroboration, 229–230

mechanism of, 229–230regiochemistry of, 229–230, 484stereochemistry of, 229–230

Hydrocarbon, 82

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INDEX I-15

Hydrochloric acid, pKa of, 52Hydrocortisone, structure and function

of, 963Hydrocyanic acid, pKa of, 52Hydrogen bond, 63

alcohols and, 501amines and, 740ammonia and, 63carboxylic acids and, 605DNA and, 63DNA base pairs and, 983electrostatic potential map, 63, 501phenols and, 501water and, 63

Hydrogen iodide, ether cleavage with,525–526

Hydrogen molecule, bond length in, 11bond strength in, 11molecular orbitals in, 21–22

Hydrogen peroxide, reaction withorganoboranes, 229–230

Hydrogenation, 232alkenes and, 232–234alkyne, 251catalysts for, 232mechanism of, 232–233stereochemistry of, 232–233trans fatty acids and, 234, 930vegetable oil, 930

Hydrolase, 801Hydrolysis (nucleophilic acyl

substitution reaction), 640amides, 659–660esters, 654–656fats, 656–657nitriles, 616proteins, 660

Hydronium ion, electrostatic potentialmap of, 150

Hydrophilic, 64Hydrophobic, 64Hydroquinone, 519

from quinones, 519–520Hydroxide ion, electrostatic potential

map of, 54, 1503-Hydroxy-3-methylglutaryl-CoA,

reduction of, 9543-Hydroxy-3-methylglutaryl-CoA

reductase, 9543-Hydroxy-3-methylglutaryl-CoA

synthase, 954Hydroxyacetic acid, pKa of, 606L-3-Hydroxyacyl-CoA dehydrogenase,

mechanism of, 940Hydroxyethylthiamin diphosphate, from

pyruvate, 903reaction with lipoamide, 904

Hydroxyl group, directing effect of,294–296

inductive effect of, 294–295orienting effect of, 294–296resonance effect of, 294–295

Hydroxylation, alkene, 237–239Hydroxylation, aromatic, 286–287Hyperconjugation, 194

alkenes and, 194carbocation stability and, 202–203

Hypoxanthine, biological oxidation of,1000

from adenosine, 1000

Ibuprofen, chirality and, 352green synthesis of, 765molecular model of, 352stereochemistry of, 352

Idose, configuration of, 860Imidazole, aromaticity of, 276–277

basicity of, 742, 757electrostatic potential map of, 61,

276Hückel 4n � 2 rule and, 276–277

Imidazolone 5-propionate, from trans-urocanate, 836–837

hydrolysis of, 836Imine(s), 568

from aldehydes, 568–569from ketones, 568–569mechanism of formation of, 569Schiff base and, 897

IMP dehydrogenase, 1007IND, see Investigational new drug, 171Indole, aromaticity of, 279

electrophilic substitution reaction of,761

structure of, 760Indolmycin, biosynthesis of, 700Inductive effect, 37, 294–295

carboxylic acid strength and, 609electronegativity and, 37electrophilic aromatic substitution and,

294–295Influenza pandemics, 920Influenza virus, spread of, 920Infrared radiation, electromagnetic

spectrum and, 425–426energy of, 428–429frequencies of, 429wavelengths of, 429

Infrared spectroscopy, 428–429acid anhydrides, 667acid chlorides, 667alcohols, 436, 529aldehydes, 436, 583–584alkanes, 434alkenes, 434alkynes, 434–435amides, 667amines, 436, 762aromatic compounds, 435bond stretching in, 429carbonyl compounds, 436–437carboxylic acid derivatives, 666–667carboxylic acids, 617esters, 436–437, 667ethers, 529explanation of, 429fingerprint region in, 430ketones, 436, 583–584molecular motions in, 429nitriles, 617phenols, 529regions in, 430table of absorptions in, 431vibrations in, 429

Infrared spectrum, benzaldehyde, 584butanoic acid, 617cyclohexane, 448cyclohexanol, 529cyclohexanone, 584cyclohexene, 449cyclohexylamine, 762ethanol, 427hex-1-ene, 432hex-1-yne, 432hexane, 432interpretation of, 430–437phenol, 529phenylacetaldehyde, 437toluene, 435

Ingold, Christopher Kelk, 372Initiation step (radical), 145Inosine, biosynthesis of, 1006–1007Inosine monophosphate, oxidation of,

1007–1008Integration (1H NMR), 476Intermediate, See Reaction intermediateIntoxilyzer test, 532Intramolecular aldol reaction, 707–708

mechanism of, 707–708Intramolecular Claisen reaction, 711–713

mechanism of, 711–712Intron (DNA), 987Invert sugar, 875Investigational new drug (IND), 171Iodination (aromatic), 284

thyroxine biosynthesis and, 284Iodoform reaction, 680Ion pair, 384

SN1 reaction and, 384Ionic bond, 8Ionization sources, mass spectrometry

and, 416IPP, see Isopentenyl diphosphate, 951IPP isomerase, 956IR, see InfraredIron, reaction with nitroarenes, 747Iron(III) bromide, aromatic bromination

and, 282Iron sulfate, LD50 of, 26Isoamyl group, 93Isoborneol, structure of, 976Isobutane, molecular model of, 83Isobutyl group, 87Isocitrate, from citrate, 906–907

oxalosuccinate from, 908oxidation of, 908

Isocitrate dehydrogenase, 908Isoelectric point (pI), 783

calculation of, 783Isoleucine, metabolism of, 728

molecular model of, 335structure and properties of, 780

Isomerase, 801Isomers, 83

alkanes, 82–83cis–trans, 116, 186–187constitutional, 83epimers, 334kinds of, 341review of, 340–342stereoisomers, 116

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I-16 I N D E X

Isonitrile, 412Isopentenyl diphosphate, biosynthesis of,

952–955dimethylallyl diphosphate from, 956mevalonate pathway for, 952–955terpenoids from, 956–958

Isoprene, heat of hydrogenation of, 245structure of, 184

Isoprene rule, terpenes and, 209–210Isopropyl group, 87Isoquinoline, aromaticity of, 279

electrophilic substitution reaction of,760

Isotope, 4Isoxazole, aromaticity of, 313IUPAC system of nomenclature, 89

J, see Coupling constant, 478Jefferson, Thomas, DNA fingerprinting

and, 1010–1011

Ka (acidity constant), 51Kb, basicity constant, 741Keq (equilibrium constant), 157KEGG biosynthesis database, 807Kekulé, Friedrich August, 6Kekulé structure, 8Kelp, chloromethane from, 403Kerosene, composition of, 103Ketal, see Acetal, 572�-Keto acid, transamination of,

822–825Keto–enol tautomerism, 682–684�-Keto thioester reductase, 946�-Ketoacyl-CoA thiolase, mechanism of,

941Ketogenic amino acid, 832�-Ketoglutarate, from glutamate, 826

from oxalosuccinate, 908glutamate from, 838oxidative decarboxylation of, 908succinyl CoA from, 908transamination of, 825–826

Ketone(s), 557� bromination of, 686–687acetals from, 572–574acidity of, 690alcohols from, 506–507, 509–510,

567–568aldol reaction of, 702alkenes from, 575–577alkylation of, 698amines from, 748–750biological reduction of, 507, 580carbonyl condensation reactions of,

701–706common names of, 559conjugate addition reactions of,

580–583enamines from, 568–571enols of, 682–684enones from, 705–706from acetoacetic ester, 695–696from alcohols, 516–517Grignard reaction of, 509–510, 567hydrates of, 564–566imines from, 568–569

IR spectroscopy of, 436, 583–584mass spectrometry of, 422, 585–586McLafferty rearrangement of, 422,

585–586naming, 559NMR spectroscopy of, 584–585pKa of, 690polarity of, 80reaction with alcohols, 572–574reaction with amines, 568–571reaction with Br2, 686–687reaction with Grignard reagents,

509–510, 567reaction with H2O, 564–566reaction with LDA, 698reaction with LiAlH4, 506, 568reaction with NaBH4, 506, 568reactivity versus aldehydes, 563–564reduction of, 299–300, 506–507, 568reductive amination of,748–750Wittig reaction of, 575–577

Ketone bodies, 832Ketose, 853Kiliani–Fischer reaction, 887Kilojoule (kJ), 11Kinetics, 371

E1 reaction and, 399E2 reaction and, 395SN1 reaction and, 381–382SN2 reaction and, 371–372

Knowles, William S., 587, 786Krebs, Hans Adolf, 905Krebs cycle, see Citric acid cycle

L Amino acid, 779, 782L Sugar, 858

Fischer projections of, 858–859Labetalol, structure of, 739

synthesis of, 739Laboratory reactions, comparison with

biological reactions, 168–170Lactam(s), 661

cyclic amines from, 661reaction with LiAlH4, 661

Lactic acid, configuration of (–)enantiomer, 330

configuration of (�) enantiomer, 330

enantiomers of, 320–321molecular model of, 321resolution of, 338–340

Lactone(s), 654alkylation of, 698reaction with LDA, 698

Lactose, molecular model of, 875occurrence of, 875structure of, 875sweetness of, 880

Lanosterol, biosynthesis of, 964–969Lard, composition of, 929Latex, rubber from, 253–254Lauric acid, structure of, 929LD50, 26

table of, 26LDA, see Lithium diisopropylamideLDL, heart disease and, 970Le Bel, Joseph Achille, 7

Leaving group, 372reactivity of, 377–378SN1 reaction and, 386–387SN2 reactions and, 377–378

LeBlanc process, 931Leucine, biosynthesis of, 731

metabolism of, 728structure and properties of, 780

Leukotriene, naming of, 948–949Levorotatory, 326Lewis acid, 58

examples of, 59reactions of, 58–59

Lewis base, 58examples of, 60reactions of, 59–61

Lewis structure, 8resonance and, 43–44

Lidocaine, molecular model of, 104Ligase, 801Light, plane-polarized, 325

speed of, 426Limit dextrin, from starch, 892Limonene, biosynthesis of, 218, 958

molecular model of (–) enantiomer, 349molecular model of (�) enantiomer,

349odor of, 349

Linalyl diphosphate, biosynthesis of, 958Lindlar catalyst, 251Line-bond structure, 81→4-Link, 874Linoleic acid, structure of, 929Linolenic acid, molecular model of, 930

structure of, 929Lipase, 934

mechanism of, 935Lipid, 927

classification of, 927Lipid bilayer, 934

structure of, 934Lipitor, structure and function of, 1010Lipoamide, structure and function of, 904Lipoic acid, structure and function of,

803, 904Lipoprotein, heart disease and, 970Liquid chromatography, 444Lithium aluminum hydride, danger of,

506reaction with carboxylic acids, 647reaction with ketones and aldehydes,

506, 567Lithium diisopropylamide (LDA),

formation of, 689properties of, 689reaction with cyclohexanone, 689reaction with esters, 698reaction with ketones, 698reaction with lactones, 698reaction with nitriles, 699

Lithocholic acid, structure of, 628, 962Loading reaction, fatty acid biosynthesis

and, 945Locant (nomenclature), 91

position of in chemical names, 183Lone-pair electrons, 9Loratidine, structure of, 213

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INDEX I-17

Lotaustralin, structure of, 614Lowest unoccupied molecular orbital

(LUMO), 439LUMO, see Lowest unoccupied molecular

orbital, 439Lyase, 801Lysine, catabolism of, 849

saccharopine from, 849structure and properties of, 781

Lysozyme, isoelectric point of, 784MALDI-TOF mass spectrum of, 425

Lyxose, configuration of, 860

Magnetic field, NMR spectroscopy and,456–457

Magnetic resonance imaging, 485uses of, 485

Major groove (DNA), 983–984Malate, oxaloacetate from, 910

oxidation of, 910Malate dehydrogenase, 910MALDI–TOF mass spectrometry, 424–425MALDI-TOF mass spectrum, lysozyme,

425Maleic acid, structure of, 603Malic acid, structure of, 603

Walden inversion of, 368–369Malonic ester, carboxylic acids from,

692–694decarboxylation of, 693pKa of, 690

Malonic ester synthesis, 692–694intramolecular, 694

Malonyl CoA, from acetyl CoA, 945Maltose, molecular model of, 874

mutarotation of, 874Maltotriose, from starch, 892Mannich reaction, 733Mannose, biosynthesis of, 924

configuration of, 860molecular model of, 130

Margarine, manufacture of, 930Markovnikov, Vladimir Vassilyevich, 198Markovnikov’s rule, 198–199

alkyne additions and, 251carbocation stability and, 199hydroboration and, 229–230oxymercuration and, 229

Mass analyzers, mass spectrometry and,416

Mass number (A), 4Mass spectrometer, detectors in, 416

double-focusing, 418exact mass measurement in, 418ionization sources in, 416kinds of, 416mass analyzers in, 416operation of, 416–417soft ionization in, 418, 424–425

Mass spectrometry (MS), 415alcohols, 422, 531aldehydes, 422–423, 585–586alkanes and, 418–419alpha cleavage of alcohols in, 422, 531alpha cleavage of aldehydes in, 423,

585alpha cleavage of amines in, 422, 763

alpha cleavage of ketones in, 423, 585amines, 422, 763–764base peak in, 416biological, 424–425carbonyl compounds and, 422–423cation radicals in, 416dehydration of alcohols in, 422electron-impact, 416–417ESI source in, 424fragmentation in, 417–420ketones, 422–423, 585–586MALDI source in, 424–425McLafferty rearrangement in, 422molecular ion in, 417nitrogen rule and, 447, 763parent peak in, 417time-of-flight, 424–425

Mass spectrum, 416butan-1-ol, 5312,2-dimethylpropane, 418ethylcyclopentane, 420hex-2-ene, 421hexane, 419lysozyme, 425methylcyclohexane, 4202-methylpent-2-ene, 4212-methylpentan-2-ol, 4232-methylpentane, 4475-methylhexan-2-one, 586N-ethylpropylamine, 764propane, 417

Matrix-assisted laser-desorptionionization mass spectrometry, seeMALDI

Maxam–Gilbert DNA sequencing, 991McLafferty rearrangement, 422, 585Mechanism (reaction), 143

acetal formation, 572–573acid-catalyzed enol formation, 683acid-catalyzed epoxide cleavage,

237–238, 526acid-catalyzed ester hydrolysis,

655–656alcohol dehydration with acid,

513–514alcohol dehydration with POCl3,

513–515alcohol oxidation, 518aldehyde hydration, 565–566aldehyde oxidation, 561–562aldol reaction, 702–703alkene epoxidation, 236alkene hydration, 227alkene polymerization, 240–241� bromination of aldehydes, 686–687� bromination of ketones, 686–687�-substitution reaction, 685–686amide hydrolysis, 659–660amide reduction, 661amide synthesis with DCC, 646aromatic bromination, 282–283aromatic chlorination, 283aromatic iodination, 284aromatic nitration, 285aromatic sulfonation, 286�-oxidation pathway, 938–942base-catalyzed enol formation, 684

base-catalyzed epoxide cleavage, 526base-catalyzed ester hydrolysis,

654–655biological alkene epoxidation, 236–237biological alkene reductions with

NADPH, 234–235biological epoxidation, 964–965biological hydroxylation of aromatic

compounds, 286–287biological carbonyl reduction with

NADH, 507biological carbonyl reduction with

NADPH, 507biotin-mediated carboxylation, 945bromohydrin formation, 226–227bromonium ion formation, 224Cannizzaro reaction, 579carbonyl condensation reaction, 701citric acid cycle, 905–910Claisen condensation reaction,

709–710conjugate nucleophilic additions to

enones, 581deamination, 823–825Dieckmann cyclization reaction,

711–712DNA replication, 985–986DNA transcription, 986–987E1 reaction, 399E1cB reaction, 400E2 reaction, 394–395Edman degradation, 790–791electrophilic addition reaction,

152–154, 195–196electrophilic aromatic substitution,

282–283enamine formation, 570ester reduction, 657ether cleavage with HI, 525–526FAD reactions, 939–940fat hydrolysis, 934–937fatty acid biosynthesis, 943–947fatty acyl CoA biosynthesis, 649, 937Fischer esterification reaction, 644–645Friedel–Crafts acylation reaction, 290Friedel–Crafts alkylation reaction, 288geranyl diphosphate biosynthesis,

957–958glycoconjugate biosynthesis, 868–869glycolysis, 894–895Grignard carboxylation, 612Grignard reaction, 567Hofmann elimination reaction, 752hydroboration, 229–230hydrogenation, 232–233imine formation, 569intramolecular aldol reaction, 707–708isopentenyl diphosphate biosynthesis,

952–955ketone hydration, 565–566lipase, 935mevalonate decarboxylation, 955Michael reaction, 714mutarotation, 863–864nitrile hydrolysis, 616nucleophilic acyl substitution reaction,

637–638

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Mechanism (reaction) (continued)nucleophilic addition reaction, 562orotidine monophosphate

decarboxylase, 1005oxidative deamination, 826oxymercuration, 229phosphorylation with ATP, 820pyruvate decarboxylation, 901–903reductive amination, 749saponification, 654–655SN1 reaction, 382, 387SN2 reaction, 372–373steroid biosynthesis, 964–969Stork enamine reaction, 717transamination, 823–825transimination, 824Williamson ether synthesis, 524Wittig reaction, 575–576

Meerwein–Ponndorf–Verley reaction, 595Menthene, electrostatic potential map of,

78functional groups in, 78

Menthol, molecular model of, 121structure of, 324

Menthyl chloride, E2 reaction of, 397Mercapto group, 500Mercurinium ion, 229Merrifield solid-phase synthesis, 794–796

Fmoc protecting group in, 796PAM resin in, 796steps in, 795–796Wang resin in, 796

Meso compound, 336plane of symmetry in, 336

Messenger RNA, 986codons in, 988translation of, 987–989

Mestranol, structure of, 261Meta (m), 269Meta-directing group, 293Metabolic cycle, reasons for, 910–911Metabolic pathways, kinds of, 910Metabolism, 818

overview of, 818Methandrostenolone, structure and

function of, 963Methane, bond angles in, 13

bond lengths in, 13bond strengths in, 13molecular model of, 7, 13, 83pKa of, 252reaction with Cl2, 145sp3 hybrid orbitals in, 12–13structure of, 13

Methanethiol, bond angle in, 20dipole moment of, 39electrostatic potential map of, 173molecular model of, 20pKa of, 502sp3 hybrid orbitals in, 20structure of, 20

Methanol, bond angle in, 19dipole moment of, 39electrostatic potential map of, 37, 56,

57, 148, 501industrial synthesis of, 497molecular model of, 19

pKa of, 502polar covalent bond in, 36–37sp3 hybrid orbitals in, 19structure of, 19toxicity of, 497U.S. production of, 497uses of, 497

Methionine, biosynthesis of, 593molecular model of, 333reaction with ATP, 528S-adenosylmethionine from, 528structure and properties of, 780

Methoxide ion, electrostatic potentialmap of, 57

p-Methoxybenzoic acid, pKa of, 609p-Methoxypropiophenone, 1H NMR

spectrum of, 480Methyl acetate, electrostatic potential

map of, 63913C NMR spectrum of, 4581H NMR spectrum of, 458pKa of, 690

Methyl anion, electrostatic potential mapof, 253

Methyl 2,2-dimethylpropanoate, 1H NMRspectrum of, 475

Methyl group, 86chiral, 414directing effect of, 294inductive effect of, 294–295orienting effect of, 294

Methyl phosphate, bond angle in, 20molecular model of, 20sp3 hybrid orbitals in, 20structure of, 20

Methyl propanoate, 13C NMR spectrumof, 466

Methyl thioacetate, electrostatic potentialmap of, 639

pKa of, 690Methylamine, bond angles in, 19

dipole moment of, 39electrostatic potential map of, 38, 57,

743molecular model of, 19sp3 hybrid orbitals in, 19structure of, 19

2-Methylbutan-2-ol, 1H NMR spectrumof, 481

2-Methylbutane, molecular model of, 83Methylcyclohex-1-ene, 13C NMR

spectrum of, 470Methylcyclohexane, conformations of,

126–1271,3-diaxial interactions in, 126–127mass spectrum of, 420molecular model of, 323

1-Methylcyclohexanol, 1H NMRspectrum of, 484

2-Methylcyclohexanone, chirality of, 323molecular model of, 323

N-Methylcyclohexylamine, 13C NMRspectrum of, 763

1H NMR spectrum of, 763Methylene group, 1846-Methylhept-5-en-2-ol, DEPT-NMR

spectra of, 468

5-Methylhexan-2-one, mass spectrum of,586

4-Methylideneimidazol-5-one, formationof, 836

histidine catabolism and, 835–836Methyllithium, electrostatic potential

map of, 37, 147polar covalent bond in, 37

Methylmagnesium chloride, electrostaticpotential map of, 567

Methylmagnesium iodide, electrostaticpotential map of, 367

2-Methylpent-2-ene, mass spectrum of,421

2-Methylpentan-3-ol, mass spectrum of,423

2-Methylpentane, mass spectrum of, 447p-Methylphenol, pKa of, 5022-Methylpropane, molecular model of, 832-Methylpropene, heat of hydrogenation

of, 194Mevaldehyde, biosynthesis of, 663Mevalonate, biosynthesis of, 952–954

decarboxylation of, 954–955isopentenyl diphosphate from,

952–955Mevalonate-5-diphosphate

decarboxylase, 955Mevalonate kinase, 955Micelle, 932Michael reaction, 713–715

acceptors in, 715donors in, 715mechanism of, 714Stork enamine reaction and, 717

Microwaves, electromagnetic spectrumand, 425

Mineralocorticoid, 963Minor groove (DNA), 983–984MIO, see 4-Methylideneimidazol-5-one,

836Mobile phase, chromatography and, 444Molar absorptivity, 440Molecular ion (M�), 417Molecular mechanics, 133Molecular model, � helix, 798

acetaminophen, 28acetylene, 18adenine, 68adrenaline, 354alanine, 28, 777p-aminobenzoic acid, 25anti periplanar geometry, 396arecoline, 81aspartame, 29aspirin, 17�-D-glucopyranose, 863�-D-glucopyranose, 863p-bromoacetophenone, 465bromocyclohexane, 125butane, 83cis-but-2-ene, 186trans-but-2-ene, 186cellulose, 874chair cyclohexane, 122cholesterol, 961cholic acid, 602

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INDEX I-19

citrate synthase, 805citric acid, 28coniine, 28cyclobutane, 120cyclodecapentaene, 275cyclohexane ring flip, 125cyclopentane, 121cyclopropane, 115, 119cytosine, 68cis-decalin, 132, 960trans-decalin, 132, 960decane, 101dimethyl sulfide, 20cis-1,2-dimethylcyclopropane, 116trans-1,2-dimethylcyclopropane, 116dimethylpropane, 83N,N-dimethyltryptamine, 761dopamine, 748eclipsed ethane conformation, 97enflurane, 325epibatidine, 363ethane, 9, 14, 83ethylene, 15(S)-fluoxetine, 350glucose, 130(R)-glyceraldehyde, 855hexane, 14(S)-ibuprofen, 352isobutane, 83isoleucine, 335lactic acid, 321lactose, 875lidocaine, 104(–)-limonene, 349(�)-limonene, 349linolenic acid, 930maltose, 874mannose, 130menthol, 121meso-tartaric acid, 336methane, 7, 13, 83methanethiol, 20methanol, 19methionine, 333methyl phosphate, 20methylamine, 192-methylbutane, 832-methylcyclohexanone, 323methylcyclohexane, 3232-methylpropane, 83naphthalene, 61Newman projections, 97oseltamivir, 133pentane, 83phenylalanine, 104piperidine, 753pleated sheet, 798propane, 83propane conformations, 98pseudoephedrine, 354staggered ethane conformation, 97stearic acid, 929steroid, 960sucrose, 876syn periplanar geometry, 396Tamiflu, 133tert-butyl carbocation, 202

testosterone, 132threose, 325trimethylamine, 739twist-boat cyclohexane, 123vitamin C, 619

Molecular orbital, 21antibonding, 22bonding, 22buta-1,3-diene, 247

Molecular orbital (MO) theory, 21–22benzene and, 272–275conjugated dienes and, 246–247Hückel 4n � 2 rule and, 274–275

Molecular weight, determination of, 418

Molecule, 8electron-dot structures of, 8–9lone-pair electrons in, 9

Monomer, 239Monosaccharide(s), 852

aldaric acids from, 871alditols from, 868–869aldonic acids from, 870–871anomers of, 863–864configurations of, 859–861cyclic forms of, 863–864essential, 872–873esters of, 866ethers of, 866Fischer projections of, 854–856glycosides of, 867–868hemiacetal forms of, 863–864osazones from, 888oxidation of, 870–871phosphorylation of, 868reaction with acetic anhydride, 866reaction with iodomethane, 866reaction with NaBH4, 868–869reactions of, 866–871reduction of, 868–869see also Aldoseuronic acids from, 871

Monoterpene, 209Monoterpenoid, 951Morphine, specific rotation of, 326

structure of, 65MRI, see Magnetic resonance imaging,

485mRNA, see Messenger RNAMS, see Mass spectrometryMullis, Kary Banks, 995Multiplet (NMR), 476

table of, 479Mutarotation, 864

glucose and, 863–864mechanism of, 863–864

Mycomycin, stereochemistry of, 361Mylar, structure of, 665myo-Inositol, structure of, 138Myoglobin, � helix in, 798

ribbon model of, 798Myrcene, structure of, 209Myristic acid, catabolism of, 942

structure of, 929

n- (normal), 84n � 1 rule (NMR), 478

N-terminal amino acid, 787NADH, see Nicotinamide adenine

dinucleotide (reduced)NADPH, see Nicotinamide adenine

dinucleotide phosphate (reduced)Naming, acid anhydrides, 634

acid chlorides, 634acid halides, 634acyl groups, 603acyl phosphates, 636alcohols, 499–500aldehydes, 558aldoses, 860–861alkanes, 89–93alkenes, 182–184alkyl groups, 86–87, 92–93alkyl halides, 364–365alkynes, 184alphabetization and, 93amides, 635amines, 736–738aromatic compounds, 268–270carboxylic acid derivatives,

634–636carboxylic acids, 602–603cycloalkanes, 112–114cycloalkenes, 183eicosanoids, 948–949enzymes, 801esters, 635ethers, 522heterocyclic amines, 738ketones, 559leukotrienes, 948–949nitriles, 604phenols, 500prostaglandins, 948–949sulfides, 523thioesters, 635thiols, 500thromboxanes, 948–949

Naphthalene, aromaticity of, 279electrostatic potential map of, 279Hückel 4n � 2 rule and, 279molecular model of, 67orbitals of, 279reaction with Br2, 279resonance in, 278

Natural gas, composition of, 103thiols in, 521

Natural products, drugs from, 171Natural rubber, structure of, 254NDA, see New drug application, 171Neomenthyl chloride, E2 reaction of, 397Neopentyl group, 93

SN2 reaction and, 375Neuraminic acid, biosynthesis of, 873Neuraminidase, influenza virus and, 920New drug application (NDA), 171New molecular entity (NME), number of,

171Newman projection, 97

molecular model of, 97Nicotinamide adenine dinucleotide

(NAD�), biological oxidations with,518

mechanism of oxidation with, 518

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Nicotinamide adenine dinucleotide(reduced), biological reductionswith, 507, 580

mechanism of reduction with, 507, 580structure of, 170, 507

Nicotinamide adenine dinucleotidephosphate (reduced), biologicalreductions with, 235, 507

mechanism of reduction with, 235, 507Nicotine, structure of, 30, 735Ninhydrin, reaction with amino acids,

789Nitration (aromatic), 284–285Nitric acid, pKa of, 52Nitrile(s), 604

alkylation of, 699amides from, 616amines from, 616carboxylic acids from, 611–612, 616from amides, 615hydrolysis of, 611–612, 616IR spectroscopy of, 617mechanism of hydrolysis of, 616naming, 604naturally occurring, 614NMR spectroscopy of, 618nucleophilic additions to, 615pKa of, 690reaction with LDA, 699reaction with LiAlH4, 616reactions of, 615–616reduction of, 616synthesis of, 615

Nitrile group, directing effect of, 294inductive effect of, 294–295orienting effect of, 294resonance effect of, 294–295

Nitro group, directing effect of, 294inductive effect of, 294–295orienting effect of, 294resonance effect of, 294–295

Nitroarene, arylamines from, 747catalytic reduction of, 747reaction with iron, 747reaction with tin, 747reduction of, 747

Nitrobenzene, aniline from, 285reduction of, 285synthesis of, 285

p-Nitrobenzoic acid, pKa of, 609Nitrogen rule (mass spectrometry), 447,

763Nitronium ion, 284–285

electrostatic potential map of, 285p-Nitrophenol, pKa of, 502p-Nitrophenoxide ion, resonance in, 503NME, see New molecular entity, 171NMR, see Nuclear magnetic resonanceNode, 5Nomenclature, see NamingNonbonding electrons, 9Noncovalent interaction(s), 62

dipole–dipole forces and, 62dispersion forces and, 62hydrogen bonds and, 63kinds of, 62–64van der Waals forces and, 62

Nonequivalent protons, spin–spinsplitting and, 482–483

tree diagram in NMR of, 483Nonessential amino acid, 838

biological precursors of, 839Norepinephrine, biosynthesis of, 299Norethindrone, structure and function of,

963Normal (n) alkane, 83Noyori, Ryoji, 587Nuclear magnetic resonance

spectrometer, field strength of, 456operation of, 459

Nuclear magnetic resonance spectroscopy(NMR), 455

acid anhydrides, 667–668acid chlorides, 667–668alcohols, 530aldehydes, 584–585amides, 667–668amines, 762–76313C chemical shifts in, 464calibration peak for, 461carboxylic acids, 618carboxylic acid derivatives, 667–668chart of absorptions in, 461coupling constants in, 478delta scale for, 461DEPT-NMR and, 467–468diastereotopic protons and, 472enantiotopic protons and, 471–472energy levels in, 456–457esters, 667–668ethers, 530field strength and, 456–457FT-NMR and, 462–463H chemical shifts in, 473–474homotopic protons and, 471integration of 1H spectra, 475–476ketones, 584–585multiplets in, 478–479n � 1 rule and, 478nitriles, 618overlapping signals in, 482peak assigning in 13C spectra, 464,

467–468peak size in 13C spectra, 465peak size in 1H spectra, 475–476phenols, 531principle of, 455–457proton equivalence and, 470–472radiofrequency energy and, 456–457shielding in, 458signal averaging in, 462–463spin-flips in, 456spin–spin splitting in, 476–480time scale of, 460uses of 13C spectra in, 469–470uses of 1H spectra in, 484

13C Nuclear magnetic resonancespectrum, acetaldehyde, 585

acetophenone, 585benzaldehyde, 585benzoic acid, 618p-bromoacetophenone, 465butan-2-one, 465, 585crotonic acid, 618

cyclohexanol, 530cyclohexanone, 585ethyl benzoate, 492methyl acetate, 458methyl propanoate, 4661-methylcyclohexene, 470N-methylcyclohexylamine, 763pentan-1-ol, 463propanenitrile, 618propanoic acid, 618propionic acid, 618

1H Nuclear magnetic resonancespectrum, acetaldehyde, 584

bromoethane, 4762-bromopropane, 478trans-cinnamaldehyde, 482cyclohexylmethanol, 484ethyl acetate, 667methyl acetate, 458methyl 2,2-dimethylpropanoate, 4752-methylbutan-2-ol, 4811-methylcyclohexanol, 484N-methylcyclohexylamine, 763p-methoxypropiophenone, 480phenylacetic acid, 618propan-1-ol, 530toluene, 482

Nuclear spin, common nuclei and, 457

NMR and, 455–457Nuclease, 997Nucleic acid, 979–982

biosynthesis of, 1003–1008catabolism of, 997–1002hydrolysis of, 997see also Deoxyribonucleic acid,

Ribonucleic acidstructure of, 981–982

Nucleophile, 149–150characteristics of, 155curved arrows and, 154–156electrostatic potential maps of, 150examples of, 150SN1 reaction and, 387SN2 reaction and, 376–377

Nucleophilic acyl substitution reaction,552, 637–638

abbreviated mechanism for, 840acid anhydrides, 652–653acid chlorides, 648, 650–651acid halides, 648, 650–651amides, 659–661biological, 648–649carboxylic acids and, 642–645esters, 654–658kinds of, 640–641mechanism of, 637–638reactivity in, 639–640

Nucleophilic carbonyl addition reaction,550–551, 562

acid catalysis of, 565–566base catalysis of, 565electrostatic potential map of, 562kinds of, 563mechanism of, 562steric hindrance in, 563trajectory of, 563–564

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Nucleophilic substitution reaction, 369biological examples of, 390–391summary of, 401

Nucleophilicity, 377basicity and, 377table of, 376trends in, 377

Nucleosidase, 997Nucleoside, 979–982Nucleoside phosphorylase, 998Nucleotidase, 997Nucleotide, 979–982

biosynthesis of, 1003–1008catabolism of, 997–10023’ end of, 9825’ end of, 982

Nucleus, size of, 3Nylon, 664

naming, 664uses of, 664

Nylon 6, structure of, 664Nylon 66, structure of, 664

Ocimene, structure of, 212Octane number (fuel), 103Octet rule, 7-oic acid, name ending for carboxylic

acids, 602-ol, alcohol name ending, 499Olefin, 179Oleic acid, structure of, 929Oligonucleotide, 992

synthesis of, 992–995Olive oil, composition of, 929-one, ketone name ending, 559-onitrile, nitrile name ending, 604Optical activity, measurement of,

325–326Optical isomers, 328Optically active, 325Orbital, 4

energies of, 5hybridization of, 12–20shapes of, 4–5

d Orbital, shape of, 4p Orbital, lobes of, 5

nodes in, 5shape of, 4–5

s Orbital, shape of, 4Organic chemicals, elements found

in, 3number of, 75size of, 2toxicity of, 26

Organic chemistry, 2foundations of, 2

Organic molecule, polar covalent bondsin, 147–149

Organic reactions, conventions forwriting, 197

kinds of, 142–143stereochemistry and, 342–344

Organic synthesis, enantioselective, 587strategy for, 300–306

Organodiphosphate, Friedel-Craftsreactions and, 290–291

SN1 reactions and, 390–391

Organoborane, from alkenes, 229reaction with H2O2, 229–230

Organohalide(s), biological uses of,402–403

function of, 403naturally occurring, 402–403

Organometallic compound, 367polarity of, 147

Organophosphate, sp3 hybrid orbitals in,20

structure of, 20Ornithine, biosynthesis of, 841

citrulline from, 828–829from arginine, 831reaction with carbamoyl phosphate,

828–829urea cycle and, 828

Ornithine transcarbamoylase, 828Orotate, biosynthesis of, 1003–1006Orotate phosphoribosyltransferase, 1004Orotidine, biosynthesis of, 1003–1005Orotidine monophosphate,

decarboxylation of, 1005Orotidine monophosphate decarboxylase,

1005rate acceleration in, 1005

Ortho (m), 269Ortho- and para-directing group, 293,

295–296Osazone, 888-ose, carbohydrate name ending, 853Oseltamivir, molecular model of, 133Oseltamivir phosphate, mechanism of,

920-oside, glycoside name ending, 868Osmium tetroxide, reaction with alkenes,

238–239Oxalic acid, structure of, 603Oxaloacetate, aspartate from, 828, 838

decarboxylation of, 913from malate, 910from pyruvate, 913, 916phosphoenolpyruvate from, 913reaction with acetyl CoA, 906–907

Oxaloacetic acid, structure of, 603Oxalosuccinate, decarboxylation of, 908

from isocitrate, 908Oxidation, alcohols and, 516–519

aldehydes, 561–562FAD and, 939–949NAD� and, 519organic, 235phenols, 519

Oxidative deamination, 826mechanism of, 826

Oxidative decarboxylation, 901Oxidoreductase, 801Oxidosqualene : lanosterol cyclase, 965Oxirane, 235Oxo group, 559Oxymercuration, 228

mechanism of, 229regiochemistry of, 229

Oxytocin, structure of, 815

Palmitic acid, structure of, 929Palmitoleic acid, structure of, 929

PAM resin, peptide synthesis and, 796Para (m), 269Paraffin, 95Parallel synthesis, 307Parent peak (mass spectrum), 417Partial charge, 36Pasteur, Louis, 327

enantiomers and, 327–328Patchouli alcohol, structure of, 951Pauli exclusion principle, 6Pauling, Linus Carl, 12PCC, see Pyridinium chlorochromatePCR, see Polymerase chain reaction,

995–997PDB, see Protein Data BankPeanut oil, composition of, 929Penicillin, discovery of, 668Penicillin V, specific rotation of, 326

stereochemistry of, 351Penta-1,4-diene, electrostatic potential

map of, 248Pentan-1-ol, 13C NMR spectrum of, 463Pentane, molecular model of, 83Pentane-2,4-dione anion, resonance

forms of, 47–48pKa of, 690

Pentose phosphate pathway, 924, 925PEP, see PhosphoenolpyruvatePepsin, isoelectric point of, 784Peptide, 777

amino acid analysis of, 789backbone of, 787covalent bonding in, 788disulfide bonds in, 788Edman degradation of, 790–792reaction with phenylisothiocyanate,

790–791sequencing of, 790–792solid-phase synthesis of, 794–796synthesis of, 793–796

Peptide bond, 787DCC formation of, 794restricted rotation in, 788

Periplanar geometry, 395E2 reactions and, 395–397

Perlon, structure of, 664Peroxyacid, 235

reaction with alkenes, 235–236Petroleum, catalytic cracking of, 103

composition of, 103gasoline from, 103refining of, 103

Pfu DNA polymerase, 996PGA, see Polyglycolic acid, 665–666PGH synthase, 948Pharmaceuticals, approval procedure for,

171origin of, 171

PHB, see Polyhydroxybutyrate, 665–666Phenol(s), 497

acidity of, 501–503electrophilic aromatic substitution of,

295–296electrostatic potential map of, 294hydrogen bonds in, 501IR spectroscopy of, 529IR spectrum of, 529

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Phenol(s) (continued)naming, 500NMR spectroscopy of, 531oxidation of, 519phenoxide ions from, 501–503pKa of, 502, 606properties of, 501–503quinones from, 519uses of, 498

Phenoxide ion, 501resonance in, 503

Phenyl group, 269Phenylacetaldehyde, aldol reaction of,

702IR spectrum of, 437

Phenylacetic acid, 1H NMR spectrum of,618

Phenylalanine, molecular model of, 104structure and properties of, 780

Phenylisothiocyanate, Edmandegradation and, 790–791

Phenylthiohydantoin, Edmandegradation and, 790–791

Phosphate, electrostatic potential map of,79

polarity of, 79Phosphatidic acid, structure of, 933Phosphatidylcholine, structure of, 933Phosphatidylethanolamine, structure of,

933Phosphatidylserine, structure of, 933Phosphine(s), chirality of, 345Phosphite, 994

oxidation of, 994Phosphoenolpyruvate (PEP), from

2-phosphoglycerate, 900from oxaloacetate, 9132-phosphoglycerate from, 915pyruvate from, 900

Phosphoenolpyruvate carboxykinase, 913

Phosphofructokinase, 8962-Phosphoglycerate, from

phosphoenolpyruvate, 915from 3-phosphoglycerate, 899

3-Phosphoglycerate, from 1,3-bisphosphoglycerate, 899

isomerization of, 899Phosphoglycerate kinase, 899Phosphoglycerate mutase, 899Phosphohomoserine, elimination

reaction of, 844Phospholipid, 933–934

abundance of, 934classification of, 933

Phosphopantetheine, structure of, 662,819

Phosphoramidite, 994Phosphorane, 575Phosphoric acid, pKa of, 52Phosphoric acid anhydride, 819Phosphorus, ground-state electron

configuration of, 6Phosphorus oxychloride, alcohol

dehydration with, 513–515Phosphorus tribromide, reaction with

alcohols, 366, 512

Phosphorylation, ATP and, 819–820mechanism of, 820

Photon, 426energy of, 427

Photosynthesis, 852Phthalic acid, structure of, 603Phylloquinone, biosynthesis of, 291Physiological pH, 608Pi (�) bond, 15

acetylene and, 17–18ethylene and, 14–16molecular orbitals in, 22

Picometer, 3Pinacol rearrangement, 542Pineapple, esters in, 653Piperidine, molecular model of, 753PITC, see Phenylisothiocyanate, 790–791pKa, 52

table of, 52PLA, see Polylactic acid, 665–666Plane of symmetry, 321–322

meso compounds and, 336Plane-polarized light, 325Plasmalogen, structure of, 972Plasticizer, 653–654Plexiglas, 263Plocamium cartilagineum, alkyl halides

in, 225PLP, see Pyridoxal phosphatePMP, see Pyridoxamine phosphatePoison ivy, urushiols in, 498Polar aprotic solvent, 379

SN1 reaction and, 388SN2 reaction and, 379

Polar covalent bond, 36dipole moments and, 38–39electronegativity and, 36–37electrostatic potential maps and, 37

Polar reaction, 144characteristics of, 147–150curved arrows in, 149, 154–156electrophiles in, 149–150example of, 151–154nucleophiles in, 149–150

Polarimeter, 325Polarizability, 149Poly(vinyl pyrrolidone), 263Polyamide, 664Polycyclic aromatic compound,

278–280Polycyclic compound(s), 131

conformations of, 131–132Polyester, 664

uses of, 665Polyethylene, synthesis of, 240–241Polyglycolic acid, 665–666Polyhydroxybutyrate, 665–666Polylactic acid, 665–666Polymer, 239

biodegradable, 665–666biological, 239–240chain-growth, 240–242, 664step-growth, 664

Polymerase chain reaction (PCR),995–997

amplification factor in, 997taq DNA polymerase in, 996

Polymerization, mechanism of, 240–241radical, 240–242

Polysaccharide(s), 852, 876–878synthesis of, 878

Polyunsaturated fatty acid, 928Porphobilinogen, biosynthesis of, 772Potassium nitrosodisulfonate, reaction

with phenols, 519Preeclampsia, Viagra and, 171Prelaureatin, biosynthesis of, 264Priestley, Joseph, 253Primary alcohol, 499Primary amine, 736Primary carbon, 88Primary hydrogen, 88Primary protein structure, 797Priming reaction, fatty acid biosynthesis

and, 943–944pro-R prochirality center, 347pro-S prochirality center, 347Problems, how to work, 27Procaine, structure of, 32Prochirality, 346–348

assignment of, 346–348biological reactions and, 348Re descriptor for, 346Si descriptor for, 347structure and function of, 962–963

Prochirality center, 347pro-R, 347pro-S, 347

Progestin, 962–963function of, 962

Proline, biosynthesis of, 750, 840–841catabolism of, 848from glutamate, 841structure and properties of, 780

Promotor site (DNA), 987Propagation step (radical), 145Propan-1-ol, 1H NMR spectrum of, 530Propane, bond rotation in, 98

molecular model of, 98conformations of, 98mass spectrum of, 417molecular model of, 83

Propanenitrile, 13C NMR absorptions in,618

Propanoic acid, 13C NMR absorptions in,618

Propionic acid, 13C NMR absorptions in,618

Propionyl CoA, catabolism of, 942Propyl group, 87Propylene, heat of hydrogenation of, 194Prostaglandin(s), 948

biological activity of, 2, 948biosynthesis of, 1–2, 243–244structure of, 1, 117, 948–949functions of, 948naming of, 948–949number of, 948

Prostaglandin H2, biosynthesis of, 1–2,146

structure of, 1Protein(s), 777

� helix in, 798backbone of, 787

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INDEX I-23

biosynthesis of, 987–989classification of, 797denaturing, 799electrophoresis of, 784fibrous, 797globular, 797hydrolysis of, 660, 789isoelectric point of, 784number of in humans, 817primary structure of, 797purification of, 784quaternary structure of, 797secondary structure of, 797see also Peptidetertiary structure of, 797X-ray crystallography of, 721

Protein Data Bank, 807uses of, 807visualizing enzyme structures and,

844–845X-ray crystallographic structures in,

721Protic solvent, SN1 reaction and, 388

SN2 reaction and, 379Proton equivalence, 1H NMR

spectroscopy and, 470–472Protonated methanol, electrostatic

potential map of, 148Protosteryl cation, steroid biosynthesis

and, 968Prozac, structure of, 350PRPP synthetase, 1005Pseudoephedrine, molecular model of,

354PTH, see Phenylthiohydantoin, 790–791PUFA, see Polyunsaturated fatty acid,

928Purification, organic compounds,

444–445Purine, aromaticity of, 279

basicity of, 761biosynthesis of, 1006–1008catabolism of, 997–1000electrostatic potential map of, 761

Purine nucleoside phosphorylase, 998Pyramidal inversion, amines and, 739

energy barrier to, 739Pyran, structure of, 863Pyranose, 862Pyridine, aromaticity of, 276–277

basicity of, 742, 758bond lengths in, 758dipole moment of, 759electrophilic substitution reactions of,

758electrostatic potential map of, 276Hückel 4n � 2 rule and, 276–277

Pyridinium chlorochromate, reactionwith alcohols, 517–518

Pyridoxal phosphate, 803deamination and, 823–825from PMP, 825–826imine formation from, 568, 824

Pyridoxamine phosphate, structure of,825

transamination of, 825–826Pyridoxine, structure of, 822

Pyrimidine, aromaticity of, 276–277basicity of, 742, 759biosynthesis of, 1003–1006catabolism of, 1000–1002electrostatic potential map of, 276Hückel 4n � 2 rule and, 276–277

Pyrrole, aromaticity of, 276–277, 756basicity of, 742, 756electrophilic substitution reactions of,

756–757electrostatic potential map of, 276, 756Hückel 4n � 2 rule and, 276–277industrial synthesis of, 755

Pyrrolidine, electrostatic potential mapof, 756

Pyrrolysine, structure of, 779Pyruvate, acetyl CoA from, 901–905

alanine from, 838carboxylation of, 913, 916catabolism of, 901–905decarboxylation of, 901–903ethanol from, 923from alanine, 833from phosphoenolpyruvate, 900from serine, 833–834oxaloacetate from, 913, 916reaction with thiamine diphosphate,

901–903Pyruvate carboxylase, 913Pyruvate dehydrogenase complex, 901Pyruvate kinase, 900Pyruvic acid, structure of, 603

Quantum mechanical model, 4–5Quartet (NMR), 476Quaternary ammonium salt, 736

Hofmann elimination of, 751–752Quaternary carbon, 88Quaternary protein structure, 797Quinine, structure of, 280, 760Quinoline, aromaticity of, 279

electrophilic substitution reaction of, 760Quinone, 519

from phenols, 519hydroquinones from, 519–520reduction of, 519–520

R configuration, 329assignment of, 328–330

R group, 88Racemate, 338Racemic mixture, 338Radical, 144

addition reactions of, 144biological addition reactions of,

243–244reaction with alkenes, 240–242reactivity of, 144–146substitution reactions of, 144–145

Radical polymerization, 240–242Radical reaction, 144–146

biological, 146characteristics of, 144–146fishhook arrows and, 143–144initiation steps in, 145propagation steps in, 145termination steps in, 145

Radio waves, electromagnetic spectrumand, 425

Radiofrequency energy, NMRspectroscopy and, 456–457

Rate equation, 372Rate-determining step, 381Rate-limiting step, 381Rayon, 876Re prochirality, 346Reaction (polar), 144, 147–150Reaction (radical), 144–146Reaction coordinate, 163Reaction energy diagram, 163–164

biological reactions and, 167electrophilic addition reactions and,

164–167endergonic reactions and, 165exergonic reactions and, 165intermediates and, 166–167

Reaction intermediate, 166Reaction mechanism, 143Reaction rate, activation energy and,

164–165Rearrangement reaction, 142Reducing sugar, 870Reduction, aldehydes, 506–507, 568

alkenes, 232–234alkynes, 251amides, 660–661aromatic compounds and,

299–300carboxylic acids, 507–508esters, 507–508, 657–658ketones, 506–507, 568lactams, 661nitriles, 616organic, 232quinones, 519–520

Reductive amination, 748–750biological, 750mechanism of, 749

Refining (petroleum), 103Regiospecific, 198Replication (DNA), 985–986Replication fork (DNA), 986Reserpine, structure of, 65Residue (protein), 787Resolution (enantiomers), 338–340Resonance, acetate ion and, 43–44

acetyl CoA anion and, 46acyl cations and, 290allylic carbocations and, 249arylamines and, 744benzene and, 271, 44benzylic carbocation and, 385benzylic radical and, 299carboxylate ions and, 607enolate ions and, 688naphthalene and, 278p-nitrophenoxide ion and, 503pentane-2,4-dione anion and,

47–48phenoxide ion and, 503see also Resonance form,

Resonance effect, 294–295electrophilic aromatic substitution

and, 294–295

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I-24 I N D E X

Resonance form, 44drawing, 47–49electron movement and, 45rules for, 45–46stability of, 46three-atom groupings in, 47–49

Resonance hybrid, 44Restriction endonuclease, 991Retinal, vision and, 443–444Rhodopsin, isomerization of,

443–444vision and, 443–444

Ribavirin, structure of, 313Ribonucleic acid, 979–982

bases in, 980biosynthesis of, 986–987catabolism of, 997–10023’ end of, 9825’ end of, 982kinds of, 986messenger, 986ribosomal, 986size of, 980structure of, 981–982transfer, 986translation of, 987–989

Ribonucleotide, biosynthesis of,1003–1008

catabolism of, 997–1002structures of, 981

Ribose, configuration of, 860Ribosomal RNA, 986

function of, 987–989Ricinoleic acid, structure of, 929Ring-flip (cyclohexane), 125

energy barrier to, 125molecular model of, 125

Risk, chemicals and, 26RNA, see Ribonucleic acidRod cells, vision and, 443rRNA, see Ribosomal RNARubber, history of, 253–254

vulcanization of, 254

S configuration, 329assignment of, 328–330

Saccharin, structure of, 881sweetness of, 880

Saccharopine, from lysine, 849SAH, see S-AdenosylhomocysteineSalt bridge (protein), 799SAM, see S-AdenosylmethionineSanger, Frederick, 991Sanger dideoxy DNA sequencing,

991–992Saponification, 654 931

mechanism of, 654–655Saturated, 82Sawhorse representation, 97Schiff base, 897

see also ImineScurvy, vitamin C and, 619sec-Butyl group, 87Second-order reaction, 372Secondary alcohol, 499Secondary amine, 736Secondary carbon, 88

Secondary hydrogen, 88Secondary protein structure, 797

� helix in, 798� sheet in, 798

Selenocysteine, structure of, 779Semiconservative replication (DNA),

985Sense strand (DNA), 987Sequence rules, 188–190, 328

alkenes and, 188–190enantiomers and, 328–330

Serine, catabolism of, 833–834, 847pyruvate from, 833–834structure and properties of, 781

Serine dehydratase, 833Serum lipoprotein, table of, 970Sesquiterpene, 209Sesquiterpenoid, 951Sex hormone, 962–963Sharpless, K. Barry, 587Sharpless epoxidation, 587Shell (electron), 4

capacity of, 5Shielding (NMR), 458Si prochirality, 347Sialic acid, 873Side chain (amino acid), 779Sigma (�) bond, 10

cylindrical symmetry of, 10Signal averaging, FT-NMR spectroscopy

and, 462–463Sildenafil, structure of, 755

see also ViagraSilver oxide, Hofmann elimination

reaction and, 752Simple sugar, 852Simvastatin, structure and function of,

1010Single bond, electronic structure of,

13–14length of, 13–14see also Alkanestrength of, 13–14

Skeletal structure, 23rules for drawing, 23–24

Skunk scent, cause of, 520sn-, naming prefixSN1 reaction, 381

allylic halides in, 385–386benzylic halides in, 385–386biological, 390–391carbocation stability and, 385–386characteristics of, 385–389energy diagram for, 383ion pairs in, 384kinetics of, 381–382leaving groups in, 386–387mechanism of, 382, 387nucleophiles and, 387racemization in, 382–384rate law for, 381rate-limiting step in, 381–382solvent effects on, 388stereochemistry of, 382–384substrate structure and, 385–386summary of, 388–389epoxide cleavage and, 526

SN2 reaction, 372allylic halides in, 386amines and, 747–748benzylic halides in, 386biological, 390–391characteristics of, 374–380electrostatic potential maps of, 373inversion of configuration in, 372–373kinetics of, 371–372leaving groups and, 377–378mechanism of, 372–373nucleophiles in, 376–377rate law for, 372solvent effects and, 379stereochemistry of, 372–373steric hindrance in, 374–375substrate structure and, 374–376summary of, 380table of, 376Williamson ether synthesis and, 524epoxide cleavage and, 526

Soap, 931–932history of, 931manufacture of, 931mechanism of action of, 932micelles in, 932

Sodium amide, reaction with alcohols,503

Sodium bisulfite, osmate reduction with,238–239

Sodium borohydride, reaction withaldehydes, 506, 568

reaction with ketones, 506, 568reaction with organomercury

compounds, 229reductive amination with, 749

Sodium chloride, dipole moment of, 39Sodium cyclamate, LD50 of, 26Sodium hydride, reaction with alcohols,

503Solid-phase synthesis, DNA, 992–995

peptides, 794–796see also, Merrifield, 794–796

Solvation, 379carbocations and, 388SN2 reaction and, 379

Solvent, polar aprotic, 379SN1 reaction and, 388SN2 reaction and, 379

Soot, carcinogenic compounds in, 238Sorbitol, structure of, 869Specific rotation, 326

table of, 326Sphingomyelin, 933–934Sphingosine, structure of, 934Spin-flip, NMR spectroscopy and, 456Spin–spin splitting, 477

alcohols and, 530bromoethane and, 476–4782-bromopropane and, 478n � 1 rule and, 47813C NMR spectroscopy and, 4801H NMR spectroscopy and, 476–480nonequivalent protons and, 478–479origin of, 477–478rules for, 479tree diagrams and, 483

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INDEX I-25

Split synthesis, 307Squalene, biological epoxidation of,

236–237, 964–965from farnesyl diphosphate, 964steroid biosynthesis and, 964–969

Squalene epoxidase, 964Staggered conformation, 97

molecular model of, 97Standard state, biological, 159

thermodynamic, 159Starch, digestion of, 877

glucose from, 892–893hydrolysis of, 892–893maltotriose from, 892structure of, 876–877

Statins, mechanism of, 1010Stationary phase, chromatography and,

444Stearic acid, molecular model of, 929

structure of, 929Step-growth polymer, 664Stereochemistry, 96

absolute configuration and, 330alkene addition reactions and, 342–344cis–trans isomers and, 115–116,

186–187cycloalkenes and, 188–190diastereomers and, 334E1 reaction and, 399E2 reactions and, 397enantiomers and, 320–322epimers and, 334R,S configuration and, 328–330SN1 reaction and, 382–384SN2 reactions and, 372–373

Stereogenic center, 322Stereoisomers, 116

cis–trans isomers and, 115–116,186–187

diastereomers and, 334enantiomers and, 320–322epimers and, 334kinds of, 341properties of, 336

Stereospecific numbering (sn-), 937Steric hindrance, SN2 reaction and,

374–375Steric strain, 99

cis alkenes and, 192substituted cyclohexanes and, 126–128

Steroid(s), 959–969adrenocortical, 963anabolic, 963biosynthesis of, 964–969classification of, 962conformations of, 132, 960–961hormones and, 962–963molecular model of, 960numbering of, 960shape of, 960synthetic, 963

Stork enamine reaction,717mechanism of, 717

STR loci, DNA fingerprinting and,1010–1011

Straight-chain alkane, 83Strecker synthesis, 775

Structure, condensed, 22electron-dot, 8Kekulé, 8Lewis, 8line-bond, 8skeletal, 23

Strychnine, LD50 of, 26Substituent effect, additivity of,

301–302electrophilic aromatic substitution and,

292–297summary of, 297

Substitution reaction, 142Substrate (enzyme), 800Succinate, dehydrogenation of, 909

from succinyl CoA, 908–909fumarate from,909

Succinate dehydrogenase, 909Succinic acid, structure of, 603Succinyl CoA, from �-ketoglutarate,

908succinate from, 908–909

Succinyl CoA synthetase, 908Sucralose, structure of, 881

sweetness of, 880Sucrose, molecular model of, 876

specific rotation of, 326structure of, 876sweetness of, 880

Sugar, D, 858L, 858simple, 852see also Aldose, Carbohydrate,

MonosaccharideSulfa drugs, 754

synthesis of, 285Sulfanilamide, structure of, 285

synthesis of, 754Sulfathiazole, structure of, 754Sulfide(s), 497

electrostatic potential map of, 80from thiols, 527naming, 523occurrence of, 498oxidation of, 528polarity of, 80reaction with alkyl halides, 527sp3 hybrid orbitals in, 20structure of, 20sulfoxides from, 528

Sulfonamides, synthesis of, 285Sulfonation (aromatic), 285–286Sulfone(s), 528

from sulfoxides, 528Sulfonium salt(s), 346

chirality of, 346Sulfoxide(s), 528

from sulfides, 528oxidation of, 528

Sutures, absorbable, 666Sweeteners, synthetic, 880–881Symmetry plane, 321–322Syn periplanar geometry, 395–396

molecular model of, 396Syn stereochemistry, 229Synthesis, trisubstituted aromatic

compounds, 300–306

Table sugar, see SucroseTalose, configuration of, 860Tamiflu, avian flu virus and, 920

mechanism of, 920molecular model of, 133

Tamoxifen, synthesis of, 595Taq DNA polymerase, PCR and, 996Tartaric acid, stereoisomers of, 335–336meso-Tartaric acid, molecular model of,

336Tautomer, 682Tautomerism, 682Template strand (DNA), 987Termination step (radical), 145Terpene, 209, 950

biosynthesis of, 209–210Terpene cyclase, 957Terpenoid, 209, 950–958

biosynthesis of, 951–958classification of, 951occurrence of, 951

�-Terpineol, biosynthesis of, 959tert-Amyl group, 93tert-Butyl group, 87Tertiary alcohol, 499Tertiary amine, 736Tertiary carbon, 88Tertiary hydrogen, 88Tertiary protein structure, 797

hydrophilic interactions in, 799hydrophobic interactions in, 799noncovalent interactions in, 799salt bridges in, 799

Testosterone, conformation of, 132molecular model of, 132structure and function of, 962

Tetrahedral geometry, conventions fordrawing, 7

Tetrahydrofolate, histidine catabolismand, 836–837

structure and function of, 803, 837Tetrahydrofuran, as reaction solvent, 223Tetramethylsilane, NMR spectroscopy

and, 461Tetraterpenoid, 951Tetrazole, DNA synthesis and, 994Thermodynamic quantities, 160Thermodynamic standard state, 159Thiamin, aromaticity of, 278

basicity of, 757Thiamin diphosphate, decarboxylations

with, 901–903pKa of, 903reaction with pyruvate, 901–903structure and function of, 803, 903ylide from, 903

Thiazole, basicity of, 757Thiazolium ring, aromaticity of, 278

pKa of, 901Thioacetal, synthesis of, 594Thioanisole, electrostatic potential map

of, 623-thioate, thioester name ending, 635Thioester(s), 633

biological hydrolysis of, 678biological reactivity of, 662biological reduction of, 663

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I-26 I N D E X

Thioester(s) (continued)electrostatic potential map of, 639naming, 635pKa of, 690polarity of, 80

Thiol(s), 497acidity of, 502disulfides from, 521electrostatic potential map of, 80from alkyl halides, 521naming, 500occurrence of, 498odor of, 520oxidation of, 521polarity of, 80polarizability of, 149reaction with alkyl halides, 527reaction with Br2, 521reaction with NaH, 527sp3 hybrid orbitals in, 20structure of, 20sulfides from, 527thiolate ions from, 527

-thiol, thiol name ending, 500Thionyl chloride, reaction with alcohols,

366, 512reaction with amides, 615reaction with carboxylic acids,

642–643Thiophene, aromaticity of, 277Thiophenol, 497Thiourea, reaction with alkyl halides, 521Threonine, biosynthesis of, 842–844

catabolism of, 847from aspartate, 842–844from homoserine, 843–844stereoisomers of, 333structure and properties of, 781

Threonine synthase, 843Threose, configuration of, 860

molecular model of, 325Thromboxane, naming of, 948–949Thymidine, catabolism of, 1002Thymine, electrostatic potential map of,

983structure of, 980

Thyroxine, biosynthesis of, 284structure of, 779

Time-of-flight (TOF) mass spectrometry,424–425

sensitivity of, 424Tin, reaction with nitroarenes, 747TMS, see Tetramethylsilane, 461Tollens’ test, 870Toluene, electrostatic potential map of,

311IR spectrum of, 4351H NMR spectrum of, 482

Torsional strain, 97Tosylate, 369Toxicity, chemicals and, 26TPP, see, Thiamin diphosphateTrans fatty acid, formation of, 234

from hydrogenation of fats, 930Transamination, 822

PMP and, 825–826

Transcription (DNA), 986–987Transfer RNA, 986

anticodons in, 988–989function of, 988–989shape of, 989

Transferase, 801Transimination, 824

amino acids and, 824mechanism of, 824

Transition state, 164Hammond postulate and, 204–206

Translation (RNA), 988–989Tree diagram (NMR), 483Triacylglycerol, 928

catabolism of, 934–942Trialkylsulfonium salt, alkylations with,

528from sulfides, 527–528

1,2,4-Triazole, aromaticity of, 313Tricarboxylic acid cycle, see Citric acid

cycleTrichodiene, biosynthesis of, 978Trifluoroacetic acid, ether cleavage with,

526pKa of, 606

Trifluoromethylbenzene, electrostaticpotential map of, 311

Triglyceride, see Triacylglycerol, 928Trimethylamine, bond angles in, 739

electrostatic potential map of, 740molecular model of, 739

Trimetozine, synthesis of, 651Triose phosphate isomerase, 898Triphenylphosphine, reaction with alkyl

halides, 575–576Triple bond, electronic structure of,

17–18length of, 18see also Alkynestrength of, 18

Triplet (NMR), 476Trisubstituted aromatic compound,

synthesis of, 300–306Triterpenoid, 951tRNA, see Transfer RNATrypsin, peptide cleavage with, 792Tryptophan, structure and properties of,

781Tswett, Mikhail, 444Turnover number, enzyme, 800Twist-boat conformation, cyclohexane, 123

molecular model of, 123Tyrosine, biological iodination of, 284

biosynthesis of, 514catabolism of, 848structure and properties of, 781

Ubiquinones, function of, 520structure of, 520

Ultraviolet light, electromagneticspectrum and, 425

wavelength of, 438–439Ultraviolet spectroscopy, 438–440

absorbance and, 440conjugation and, 441HOMO–LUMO transition in, 439

interpretation of, 441molar absorptivity and, 440

Ultraviolet spectrum, benzene, 441�-carotene, 442but-3-en-2-one, 441buta-1,3-diene, 440cyclohexa-1,3-diene, 441ergosterol, 451hexa-1,3,5-triene, 441

Unimolecular, 381Unsaturated, 180Unsaturated aldehyde, conjugate addition

reactions of, 580–583Unsaturated ketone, conjugate addition

reactions of, 580–583Unsaturation, degree of, 180Upfield (NMR), 460Uracil, biological reduction of, 1001

catabolism of, 1001–1002structure of, 980

Urea, from ammonia, 827–831Urea cycle, 828–831

steps in, 829Uric acid, from xanthine, 999

pKa of, 625structure of, 625, 827

Uridine, biosynthesis of, 1003–1006catabolism of, 1000–1002from orotidine, 1005phosphorolysis of, 1000–1001

Uridine phosphorylase, 1001Uridine triphosphate, glycoconjugate

biosynthesis and, 868–869Urocanase, active site of, 845

histidine catabolism and, 835ribbon model of, 844

trans-Urocanate, from histidine, 835–836hydration of, 836–837imidazolone 5-propionate from,

836–837Uronic acid, 871

from aldoses, 871Urushiols, structure of, 498UV, see Ultraviolet

Valence bond theory, 10–20orbital hybridization and, 12–20

Valence shell, 7Valine, structure and properties of, 781Valium, see DiazepamVan der Waals forces, 62

alkanes and, 96Vancomycin, structure of, 403

uses of, 403van’t Hoff, Jacobus Hendricus, 7Vasopressin, structure of, 788Vegetable oil, 928

hydrogenation of, 233–234, 930table of, 929

Vent DNA polymerase, 996Viagra, structure of, 755

preeclampsia and, 171Vinyl group, 184Vinyl monomer, 241Vinylic anion, electrostatic potential map

of, 253

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INDEX I-27

Vinylic halide, SN2 reaction and,375–376

Vioxx, prostaglandin synthesis and, 2Visible light, electromagnetic spectrum

and, 425Vision, chemistry of, 443–444

retinal and, 443–444Vitamin, 802

chromatography of, 445coenzymes from, 802

Vitamin B6, structure of, 822Vitamin B12, structure of, 1009Vitamin C, history of, 618

industrial synthesis of, 619molecular model of, 619scurvy and, 619uses of, 618

Vitamin K1, biosynthesis of, 291VLDL, heart disease and, 970Volcano, chloromethane from, 363Vulcanization, 254

Walden, Paul, 368Walden inversion, 368–370Wang resin, peptide synthesis and, 796Water, acid–base behavior of, 50–51

conjugate addition reactions to enones,582

dipole moment of, 39

electrophilicity of, 150electrostatic potential map of, 54, 150hydrogen bond in, 63nucleophilic addition reactions of,

564–566nucleophilicity of, 150pKa of, 52reaction with aldehydes, 564–566reaction with enones, 582reaction with ketones, 564–566

Watson, James Dewey, 982Watson–Crick DNA model, 982–984Wave equation, 4Wave function, 4

molecular orbitals and, 21–22Wavelength (), 426Wavenumber, 428Wax, 928Whale blubber, composition of, 929Williamson ether synthesis, 524

Ag2O in, 524carbohydrates and, 866mechanism of, 524

Wittig reaction, 575–577mechanism of, 575–576uses of, 577ylides in 575–576

Wohl degradation, 887Wood alcohol, 497

X rays, electromagnetic spectrum and, 425X-ray crystallography, 720–721X-ray diffractometer, 721Xanthine, biological oxidation of, 999

from guanine, 998–999Xanthine oxidase, 999Xanthosine, biosynthesis of, 1007–1008Xylose, configuration of, 860

Yeast alcohol dehydrogenase,stereochemistry of, 348

-yl, alkyl group name ending, 86Ylide, 575

synthesis of, 575–576-yne, alkyne name ending, 184

Z configuration, 188assignment of, 188–190

Zaitsev, Alexander M., 392Zaitsev’s rule, 392

alcohol dehydration and, 513Hofmann elimination and, 752NMR proof for, 470

Zocor, structure and function of, 1010Zusammen, Z configuration and, 188Zwitterion, 778

amino acids and, 778Zwitterion, electrostatic potential map of,

778

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1 HH

ydro

gen

1.00

79

3 Li

Lith

ium

6.94

1

4 Be

Ber

ylliu

m

9.01

22

79 Au

Gol

d

196.

9665

1A (1)

2A (2)

3B (3)

3A (13)

4A (14)

5A (15)

6A (16)

7A (17)

8A (18)

4B (4)

5B (5)

6B (6)

7B (7)

8B (8)

8B (9)

8B (10)

1B (11)

2B (12)

11 Na

Sod

ium

22.9

898

12 Mg

Mag

nesi

um

24.3

050

19 KPo

tass

ium

39.0

983

20 Ca

Cal

cium

40.0

78

21 Sc

Sca

ndiu

m

44.9

559

22 Ti

Tita

nium

47.8

8

23 VV

anad

ium

50.9

415

24 Cr

Chr

omiu

m

51.9

961

25 Mn

Man

gane

se

54.9

380

26 Fe

Iron

55.8

47

2 He

Hel

ium

4.00

26

7 NN

itrog

en

14.0

067

8 OO

xyge

n

15.9

994

15 PPh

osph

orus

30.9

738

16 SS

ulfu

r

32.0

66

29 Cu

Cop

per

63.5

46

30 Zn

Zinc

65.3

9

31 Ga

Gal

lium

69.7

23

32 Ge

Ger

man

ium

72.6

1

33 As

Ars

enic

74.9

216

34 Se

Sel

eniu

m

78.9

6

35 Br

Bro

min

e

79.9

04

36 Kr

Kyr

pton

83.8

0

9 FFl

uorin

e

18.9

984

10 Ne

Neo

n

20.1

797

17 Cl

Chl

orin

e

35.4

527

18 Ar

Arg

on

39.9

48

27 Co

Cob

alt

58.9

332

28 Ni

Nic

kel

58.6

93

5 BB

oron

10.8

11

6 CC

arbo

n

12.0

11

13 Al

Alu

min

um

26.9

815

14 Si

Sili

con

28.0

855

37 Rb

Rub

idiu

m

85.4

678

38 Sr

Str

ontiu

m

87.6

2

39 YY

ttriu

m

88.9

059

40 Zr

Zirc

oniu

m

91.2

24

41 Nb

Nio

bium

92.9

064

42 Mo

Mol

ybde

num

95.9

4

43 Tc

Tech

netiu

m

(98)

44 Ru

Rut

heni

um

101.

07

47 Ag

Silv

er

107.

8682

48 Cd

Cad

miu

m

112.

411

49 InIn

dium

114.

82

50 Sn

Tin

118.

710

51 Sb

Ant

imon

y

121.

757

52 Te

Tellu

rium

127.

60

53 IIo

dine

126.

9045

54 Xe

Xen

on

131.

29

45 Rh

Rho

dium

102.

9055

46 Pd

Palla

dium

106.

42

55 Cs

Ces

ium

132.

9054

56 Ba

Bar

ium

137.

327

57 La

Lant

hanu

m

138.

9055

72 Hf

Haf

nium

178.

49

104

Rf

Rut

herf

ordi

um

(261

)

73 Ta

Tant

alum

180.

9479

74 WTu

ngst

en

183.

85

75 Re

Rhe

nium

186.

207

76 Os

Osm

ium

190.

2

79 Au

Gol

d

196.

9665

80 Hg

Mer

cury

200.

59

81 Tl

Thal

lium

204.

3833

82 Pb

Lead

207.

2

83 Bi

Bis

mut

h

208.

9804

84 Po

Polo

nium

(209

)

85 At

Ast

atin

e

(210

)

86 Rn

Rad

on

(222

)

77 IrIri

dium

192.

22

109

Mt

Mei

tner

ium

(266

)

78 Pt

Plat

inum

195.

08

87 Fr

Fran

cium

(223

)

88 Ra

Rad

ium

227.

0278

89 Ac

Act

iniu

m

(227

)

58 Ce

Cer

ium

140.

115

105

Db

Dub

nium

(262

)

59 Pr

Pras

eody

miu

m

140.

9076

106

Sg

Sea

borg

ium

(263

)

60 Nd

Neo

dym

ium

144.

24

107

Bh

Boh

rium

(262

)

61 Pm

Prom

ethi

um

(145

)

108

Hs

Has

sium

(265

)

64 Gd

Gad

oliu

m

157.

25

111

Rg

Roe

ntge

nium

(272

)

65 Tb

Terb

ium

158.

9253

66 Dy

Dys

pros

ium

162.

50

67 Ho

Hol

miu

m

164.

9303

68 Er

Erbi

um

167.

26

69 Tm

Thul

ium

168.

9342

70 Yb

Ytte

rbiu

m

173.

04

71 Lu

Lute

tium

174.

967

62 Sm

Sam

ariu

m

150.

36

63 Eu

Euro

pium

151.

965

110

Ds

Dar

mst

adtiu

m

(269

)

90 Th

Thor

ium

232.

0381

91 Pa

Prot

actin

ium

231.

0359

92 UU

rani

um

238.

0028

9

93 Np

Nep

tuni

um

(237

)

96 Cm

Cur

ium

(247

)

97 Bk

Ber

keliu

m

(247

)

98 Cf

Cal

iforn

ium

(251

)

99 Es

Eins

tein

ium

(252

)

100

Fm

Ferm

ium

(257

)

101

Md

Men

dele

vium

(258

)

102

No

Nob

eliu

m

(259

)

103

Lr

Law

renc

ium

(260

)

94 Pu

Plut

oniu

m

(244

)

95 Am

Am

eric

ium

(243

)

1 2 3 4 5 6 7

6 7

6 771 2 3 4 5 6

Lant

hani

des

Act

inid

es

Met

als

Ato

mic

nu

mb

erS

ymb

ol

Nam

eA

tom

ic m

ass

An

ele

men

t

Nu

mb

ers

in p

aren

thes

esar

e m

ass

nu

mb

ers

of

rad

ioac

tive

iso

top

es.

Gro

up

nu

mb

er,

U.S

. sys

tem

IUP

AC

sys

tem

Per

iod

n

um

ber

Key

Sem

imet

als

No

nm

etal

s

Perio

dic

Tabl

e of

the

Elem

ents

01525_30_EP6-EP7 2/2/06 6:04 PM Page EP6


Licensed to:

Structures of Some Common Functional Groups

Name Structure Name ending

Alkene(double bond)

Alkyne(triple bond)

Arene(aromatic ring)

Halide

Alcohol

Ether

Monophosphate

Amine

Imine(Schiff base)

Nitrile

Thiol

-ene

-yne

None

None

-ol

ether

phosphate

-amine

None

-nitrile

-thiol

XCmCX

(X � F, Cl, Br, I)

XCmN

CSH

C C

N

C

CN

CO O–P

O

O–

CO

C

COH

CX

CC

Name Structure Name ending

Sulfide

Disulfide

Sulfoxide

Aldehyde

Ketone

Carboxylic acid

Ester

Thioester

Amide

Acid chloride

sulfide

disulfide

sulfoxide

-al

-one

-oic acid

-oate

-thioate

-amide

-oyl chloride

C Cl

O

C

C

O

CN

C S

O

C C

C O

O

C C

C OH

O

C

C C

O

C

H

O

C

CS+

O–

C

CS C

S

CS

C

01525_30_EP6-EP7 2/2/06 6:04 PM Page EP7


Mcmurry15253 0495015253 01.01_toc

Engineering

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