Mcmurry PDF

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Structures of Common Coenzymes

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Copyright 2007 Thomson Learning, Inc. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part.
Tetrahydrofolate (transfer of C1 units)
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s, even
Dear Colleague: t of th e st ud en ts in our course
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true th at un ti l now there has hy I w ro te O rg anic Chemistry: more and
also
ha t di ff er en tly. And that is
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teach som ew continues to ga in
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ta ke : th is is still a textbook s be en to focus almost ex
Make no m is e ou t ha saved by
t to in cl ud e and what to leav ol og ic al ch em istry. The space
deciding w ha counterpart in bi every reaction
on s th at have a direct to go od use, for almost voted
thos e re ac ti
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iolo ple and approx addition,
leaving out nonb by a biological exam bi ot ra nsformations. In
fo ll ow ed istr y of th ei r rd texts,
discussed is es an d the organic chem ge s sh orter than standa
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he m is tr y: A B iological Appro bo ok in a ty pi
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m ak ing it po ss ib
ff er en t fr om an y other text; I be
Approach is di
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Org
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is ideal for toda Sincerely,
John McMurry
All royalties from Organic Chemistry: A Biological Approach will be donated to the Cystic Fibrosis (CF) Foundation. This
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To learn more about CF and the programs and services provided by the CF Foundation, please visit http://www.cff.org/.
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Changing the way the world learns
Organic Chemistry
A BIOLO GICAL APPROACH
J O H N M CM U RRY
Cornell University
Australia Brazil Canada Mexico Singapore Spain

United Kingdom United States
Organic Chemistry: A Biological Approach

John McMurry
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Printed in the United States of America

1 2 3 4 5 6 7 00 09 08 07 06
Library of Congress Control Number: 2006920388
Student Edition: ISBN 0-495-01525-3
Brief Contents
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
v
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 BrnstedLowry Definition 50
2.8 Acid and Base Strength 51
2.9 Predicting AcidBase Reactions from pKa Values 53
vi 2.10 Organic Acids and Organic Bases 55
CONTENTS vii
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 CisTrans 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
viii CONTENTS
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 CisTrans 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: Markovnikovs 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
CONTENTS 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 Hckel 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 Pasteurs 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
x CONTENTS
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: Zaitsevs 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
Structure Determination: Mass

11 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
CONTENTS xi
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
13
12.4 C 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
1
12.8 H 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 SpinSpin Splitting in 1H NMR Spectra 476
12.12 More Complex SpinSpin 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
xii CONTENTS
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 HendersonHasselbalch 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
CONTENTS 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 KetoEnol 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
xiv CONTENTS
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 HendersonHasselbalch 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
CONTENTS 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
xvi CONTENTS
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 WatsonCrick 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 Chemistry
25.1 Classification of Natural Products
Chapter 25 is available as an 25.2 Biosynthesis of Pyridoxal Phosphate
Adobe Acrobat PDF file at
http://www.thomsonedu.com 25.3 Biosynthesis of Morphine
25.4 Biosynthesis of Erythromycin
Lagniappe: Bioprospecting: Hunting for Natural Products
Summary
Exercises
Appendices
A 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
Preface
Introduction
Ive taught organic chemistry many times over many years, and it has often
struck me what a disconnect there is between the interests and expectations
of 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 to
pass that feeling on to others. My students, however, seem to worry primarily
about getting into medical school. Yes, of course thats a simplification, but
there is truth in it. All of us who teach organic chemistry know that a large
majority of students in our coursesperhaps 80% or more, and including
many chemistry majorsare interested primarily in the life sciences.
But if we are teaching future biologists, biochemists, physicians, and oth- All of us who teach organic chemistry
ers in the life sciences, why do we continue to teach the way we do? Why do know that the large majority of
we spend so much time discussing the details of reactions that are of interest students in our courses are
to research chemists but have no connection to the biological sciences? interested primarily in the life
Wouldnt the limited amount of time we have be better spent paying more sciences.
attention to the organic chemistry of living organisms and less to the organic John McMurry
chemistry of the research laboratory? I believe so, and I have written this
book, Organic Chemistry: A Biological Approach, to encourage others who
might also be thinking that the time has come to try something new.
Organization
Make no mistake, this is still a textbook on Organic Chemistry, but the guid- Make no mistake, this is still a
ing principle in deciding what to include and what to leave out has been to textbook on Organic Chemistry.
focus on those organic reactions that have a direct counterpart in biological John McMurry
chemistry. When looking through the text, three distinct groups of chapters
are apparent. The first group (Chapters 15, 9, 11, and 12) covers the tradi-
tional foundations of organic chemistry that are essential in building the
background necessary for further understanding of the science. The second
group (Chapters 68, 10, and 1318) provides coverage of common laboratory
reactions that have biological counterparts (of which there are many more
than you might think). As each laboratory reaction is discussed, a biological
example is also shown. The inclusion of these biological reactions makes the
material much more relevant for students, who might, for example, be more xvii
xviii P R E FA C E
interested in reading about trans fatty acids when theyre learning about cat-
alytic hydrogenation than when theyre learning about lipids. The third
group of chapters (1924) is unique to this text. These chapters deal exclu-
sively with the main classes of biomoleculesamino acids and proteins,
carbohydrates, lipids, and nucleic acidsand show how deeply organic
chemistry 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 Choices
Writing Organic Chemistry: A Many organic chemists might be surprised to find that such topics as carbene
Biological Approach has been a chemistry, acetylide alkylation, allylic bromination, and DielsAlder reactions
wonderful learning experience for me. are not included in this text. The decision not to cover these topics was not taken
I hope that both you and your students lightly, but the space saved by leaving out some nonbiological reactions has
will enjoy and benefit from this text, been put to good use. Practically all reactions covered are immediately illus-
and I would be very interested in trated with biological examples, and approximately 25% of the book is devoted
hearing your questions and opinions. entirely to biomolecules and the organic chemistry of their biotransformations.
John McMurry Furthermore, the deletion of some nonbiological reactions has resulted in a
shorter 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 that
the students we teach, including those who worry about medical school, will
come to agree that there is also logic and beauty here.
Features
Reaction Mechanisms
The innovative vertical presentation The innovative vertical presentation of reaction mechanisms that has been so
of reaction mechanisms that has well received in my other texts is retained in Organic Chemistry: A Biological
been so well received in my other Approach. Mechanisms in this format have the reaction steps printed verti-
texts is retained in Organic Chemistry: cally while the changes taking place in each step are explained next to the
A Biological Approach. reaction arrow. Students can see what is occurring at each step in a reaction
John McMurry without having to jump back and forth between structures and text.
Visualization
I want students to see that the I want students to see that the mechanisms of biological reactions are the
mechanisms of biological reactions same as those of laboratory organic reactions. Toward this end, and to let stu-
are the same as those of laboratory dents more easily visualize the changes occurring in large biomolecules, this
organic reactions. book introduces an innovative method for focusing on the reactive parts in
John McMurry large molecules by ghosting the nonreacting parts. In addition, consistent
color, 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 this
text as lucid and succinct as possible.
P R E FA C E xix
Why do we have to learn this? Ive been asked this question so many
times by students that I thought that it would be appropriate to begin each
chapter with the answer. Why This Chapter? is a short paragraph at the
end 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. Each
Worked Example includes a Strategy and a worked-out Solution and is
followed by Problems for students to try on their own.
Lagniappe (a Creole word meaning something extra) boxes at the end of
each chapter are provided to relate real-world concepts to students lives.
The Visualizing Chemistry Problems that conclude each chapter offer
students 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 Organic
OWL is provided to help students practice and test their knowledge of the
concepts. The Organic ChemistryNow online assessment program is
enhanced with biochemical coverage especially for biology and premed
students. 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. These
figures are designated as Active in the figure legends.
Summaries and Key Word lists help students by outlining the key con-
cepts of the chapter.
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in one complete list.
An overview entitled A Preview of Carbonyl Chemistry follows Chap-
ter 13 and highlights the idea that studying organic chemistry requires
both summarizing and looking ahead.
Current IUPAC nomenclature rules, as updated in 1993, are used to name
compounds in this text.
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measure bond distances and angles. MarvinSketch, a Java applet for drawing
chemical structures, enables OWL to grade chemical structures that the students
draw. A fee-based code is required for access to the specific OWL database
selected. OWL is available for use only within North America.
Pushing Electrons: A Guide for Students of Organic Chemistry, third edition

By Daniel P. Weeks. A workbook designed to help students learn techniques of
electron pushing. Its programmed approach emphasizes repetition and active
participation. ISBN: 0-03-020693-6
Spartan Model Electronic Modeling Kit A set of easy-to-use builders allow

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ISBN: 0-495-01793-0
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P R E FA C E xxi
Multimedia Manager CD-ROM The Multimedia Manager is a dual-platform

digital library and presentation tool that provides art and tables from the
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electronic files of various print supplements. Slides use the full power of
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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.
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authored specifically for the text, allows professors to create, deliver, and
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Tadhg Begley. Intended for advanced undergraduates and graduate students
in all areas of chemistry and biochemistry, The Organic Chemistry of Biolog-
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ways from the perspective of mechanistic organic chemistry. Roberts and
Company Publishers, ISBN: 0-9747077-1-6
Organic Chemistry Laboratory Manuals Thomson Brooks/Cole is pleased

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Acknowledgments
I thank all the people who helped to shape this book and its message. At
Thomson Brooks/Cole they include David Harris, publisher; Sandra Kiselica,
senior development editor; Julie Conover, executive marketing manager; Lisa
Weber, senior production project manager; Ellen Bitter, assistant editor; and
Suzanne Kastner at Graphic World Inc. Many thanks to John R. Scheffer,
University of British Columbia; Eric Kantorowski, California Polytechnic
State University; and Jacquelyn Gervay-Hague, University of California,
Davis, for serving as the accuracy reviewers. They carefully read and checked
the page proofs for this text before publication.
I am grateful to colleagues who reviewed the manuscript for this book
and participated in a survey about its approach. They include:
xxii P R E FA C E
Manuscript Reviewers
Helen E. Blackwell, University of Wisconsin
Joseph Chihade, Carleton College
Robert S. Coleman, Ohio State University
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Thomas Lectka, Johns Hopkins University
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Organic Chemistry
A BIOLO GICAL APPROACH
J O H N M CM U RRY
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Organic Chemistry: A Biological Approach

John McMurry
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Appendix A
Nomenclature of Polyfunctional
Organic Compounds
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 the
problem is due to the sheer complexity of organic structures, but part is also
due to the fact that chemical names have more than one purpose. For Chemi-
cal Abstracts Service (CAS), which catalogs and indexes the worldwide
chemical literature, each compound must have only one correct name. It
would be chaos if half the entries for CH3Br were indexed under M for
methyl bromide and half under B for bromomethane. Furthermore, a CAS
name must be strictly systematic so that it can be assigned and interpreted by
computers; common names are not allowed.
People, however, have different requirements than computers. For people
which is to say chemists in their spoken and written communicationsits best
that a chemical name be pronounceable and that it be as easy as possible to
assign and interpret. Furthermore, its convenient if names follow historical
precedents, even if that means a particularly well-known compound might have
more than one name. People can readily understand that bromomethane and
methyl 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 Applied
Chemistry, or IUPAC. Rules for naming monofunctional compounds were
given throughout the text as each new functional group was introduced, and
a list of where these rules can be found is given in Table A.1.
Naming a monofunctional compound is reasonably straightforward, but
even 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 CC, 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? Its actually named methyl
3-(2-oxocyclohex-6-enyl)propanoate.
Ketone Ester
O O
C
OCH3 Methyl 3-(2-oxocylohex-6-enyl)propanoate
Double bond A-1
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
Table A.1
Nomenclature Rules for Functional Groups
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
The name of a polyfunctional organic molecule has four partssuffix,

parent, prefixes, and locantswhich must be identified and expressed in the
proper order and format. Lets look at each of the four.
Name Part 1. The Suffix: Functional-Group Precedence

Although a polyfunctional organic molecule might contain several different
functional groups, we must choose just one suffix for nomenclature purposes.
Its not correct to use two suffixes. Thus, keto ester 1 must be named either as a
ketone with an -one suffix or as an ester with an -oate suffix but cant be named
as an -onoate. Similarly, amino alcohol 2 must be named either as an alcohol (-ol)
or as an amine (-amine) but cant be named as an -olamine or -aminol.
1. O O 2. OH
CH3CCH2CH2COCH3 CH3CHCH2CH2CH2NH2
The only exception to the rule requiring a single suffix is when naming
compounds that have double or triple bonds. Thus, the unsaturated acid
H2CUCHCH2CO2H is but-3-enoic acid, and the acetylenic alcohol
HCqCCH2CH2CH2OH is pent-5-yn-1-ol.
How do we choose which suffix to use? Functional groups are divided
into two classes, principal groups and subordinate groups, as shown in Table
A.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, an
order of priority has been established, with the proper suffix for a given com-
pound determined by choosing the principal group of highest priority. For
example, Table A.2 indicates that keto ester 1 should be named as an ester
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 A-3
Table A.2
Classification of Functional Groupsa
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.
rather than as a ketone because an ester functional group is higher in priority

than a ketone. Similarly, amino alcohol 2 should be named as an alcohol
rather than as an amine. Thus, the name of 1 is methyl 4-oxopentanoate, and
the name of 2 is 5-aminopentan-2-ol. Further examples are shown:
O O OH
CH3CCH2CH2COCH3 CH3CHCH2CH2CH2NH2
1. Methyl 4-oxopentanoate 2. 5-Aminopentan-2-ol

(an ester with a ketone group) (an alcohol with an amine group)
CHO O O OH O
CH3CHCH2CH2CH2COCH3 H2NCCH2CHCH2CH2COH
3. Methyl 5-methyl-6-oxohexanoate 4. 5-Carbamoyl-4-hydroxypentanoic acid

(an ester with an aldehyde group) (a carboxylic acid with amide and alcohol groups)
CHO
5. 3-Oxocyclohexanecarbaldehyde
(an aldehyde with a ketone group)
Name Part 2. The Parent: Selecting the Main Chain or Ring

The parent, or base, name of a polyfunctional organic compound is usually
easy to identify. If the principal group of highest priority is part of an open
chain, 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 aldehydes
according to Table A.2. The longest chain in compound 6 has six carbons, and
the substance is therefore named 5-methyl-6-oxohexanamide. Compound 7
also 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.
O O CHO O
HCCHCH2CH2CH2CNH2 CH3CH2CH2CHCH2CNH2
CH3
6. 5-Methyl-6-oxohexanamide 7. 4-Oxo-3-propylbutanamide
If the highest-priority principal group is attached to a ring, the parent

name is that of the ring system. Compounds 8 and 9, for instance, are isomeric
keto 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 acetonitrile
because the CN functional group is on an open chain. The correct names are
2-acetyl-(4-bromomethyl)benzonitrile (8) and (2-acetyl-4-bromophenyl)-

acetonitrile (9). As further examples, compounds 10 and 11 are both keto
acids and must be named as acids, but the parent name in (10) is that of a ring
system (cyclohexanecarboxylic acid) and the parent name in (11) is that of an
open chain (propanoic acid). The full names are trans-2-(3-oxopropyl)cyclo-
hexanecarboxylic acid (10) and 3-(2-oxocyclohexyl)propanoic acid (11).
O O
BrCH2 C Br C
CH3 CH3
CN CH2CN
8. 2-Acetyl-(4-bromomethyl)benzonitrile 9. (2-Acetyl-4-bromophenyl)acetonitrile
CO2H O
H
CHO CO2H
H
10. trans-2-(3-oxopropyl)cyclo- 11. 3-(2-Oxocyclohexyl)propanoic acid

hexanecarboxylic acid
Name Parts 3 and 4. The Prefixes and Locants

With parent name and suffix established, the next step is to identify and give
numbers, 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 one
cited in the suffix. For example, compound 12 contains three different func-
tional groups (carboxyl, keto, and double bond). Because the carboxyl group
is highest in priority and because the longest chain containing the functional
groups has seven carbons, compound 12 is a heptenoic acid. In addition, the
main chain has a keto (oxo) substituent and three methyl groups. Numbering
from the end nearer the highest-priority functional group, compound 12 is
named (E)-2,5,5-trimethyl-4-oxohept-2-enoic acid. Look back at some of the
other compounds weve named to see other examples of how prefixes and
locants are assigned.
O CH3
CH3CH2 C C 12. (E)-2,5,5-Trimethyl-4-oxohept-2-enoic acid

C C CO2H
H3C CH3 H
Writing the Name

Once 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 main
chain has been numbered, and the proper multipliers such as di- and tri-
have been assigned, the name is written with the substituents listed in
alphabetical, rather than numerical, order. Multipliers such as di- and tri-
are not used for alphabetization purposes, but the prefix iso- is used.
OH
H2NCH2CH2CHCHCH3 13. 5-Amino-3-methylpentan-2-ol
CH3
2. Use of hyphens; single- and multiple-word names The general rule is to

determine whether the parent is itself an element or compound. If it is,
then the name is written as a single word; if it isnt, then the name is writ-
ten as multiple words. Methylbenzene is written as one word, for
instance, because the parentbenzeneis itself a compound. Diethyl
ether, however, is written as two words because the parentetheris a
class name rather than a compound name. Some further examples follow:
O
H3C Mg CH3 HOCH2CH2COCHCH3
CH3
14. Dimethylmagnesium 15. Isopropyl 3-hydroxypropanoate

(one word, because (two words, because propanoate
magnesium is an element) is not a compound)
CH3
O
N
CH3 C
SCH3
N
16. 4-(Dimethylamino)pyridine 17. Methyl cyclopentanecarbothioate

(one word, because pyridine (two words, because cyclopentane-
is a compound) carbothioate is not a compound)
3. Parentheses Parentheses are used to denote complex substituents when

ambiguity would otherwise arise. For example, chloromethylbenzene
has two substituents on a benzene ring, but (chloromethyl)benzene has
only one complex substituent. Note that the expression in parentheses is
not set off by hyphens from the rest of the name.
CH3 CH2Cl
Cl
18. p-Chloromethylbenzene 19. (Chloromethyl)benzene
O O
HOCCHCH2CH2COH
CH3CHCH2CH3
20. 2-(1-Methylpropyl)pentanedioic acid
ADDITIONAL READING
Further explanations of the rules of organic nomenclature can be found

online at http://www.acdlabs.com/iupac/nomenclature/ and in the following
references:
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.
Appendix B
Acidity Constants for Some
Organic Compounds
Compound pKa Compound pKa Compound pKa
CH3SO3H 1.8 CH2ClCO2H 2.8 Cl

CH(NO2)3 0.1 HO2CCH2CO2H 2.8; 5.6
NO2 CH2BrCO2H 2.9 CO2H 3.8
CO2H
O2N OH 0.3 3.0
Cl CO2H 4.0
Cl
NO2 CO2H CH3BrCH2CO2H 4.0
CCl3CO2H 0.5 3.0
O2N NO2
CF3CO2H 0.5 OH 4.1
CBr3CO2H 0.7 CH2ICO2H 3.2
OH
HO2CCmCCO2H 1.2; 2.5 CHOCO2H 3.2
CO2H
HO2CCO2H 1.2; 3.7
4.2
CHCl2CO2H 1.3 O2N CO2H 3.4
CH2(NO2)CO2H 1.3
O2N H2CUCHCO2H 4.2
HCmCCO2H 1.9
HO2CCH2CH2CO2H 4.2; 5.7
Z HO2CCHUCHCO2H 1.9; 6.3
O2N CO2H 3.5 HO2CCH2CH2CH2CO2H 4.3; 5.4
CO2H
Cl Cl
2.4 HSCH2CO2H 3.5; 10.2
NO2 CH2(NO2)2 3.6 Cl OH 4.5
CH3COCO2H 2.4 CH3OCH2CO2H 3.6
NCCH2CO2H 2.5 CH3COCH2CO2H 3.6 Cl Cl
CH3CmCCO2H 2.6 HOCH2CO2H 3.7 H2CUC(CH3)CO2H 4.7
CH2FCO2H 2.7 HCO2H 3.7 CH3CO2H 4.8
(Continued)
A9
A10 A P P E N D I X B : A C 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 Compound pKa Compound pKa
CH3CH2CO2H 4.8 CH3COCH2COCH3 9.0

CH2OH 15.4
(CH3)3CCO2H 5.0 HO OH
CH3COCH2NO2 5.1 9.3; 11.1
CH3OH 15.5
O
H2CUCHCH2OH 15.5
OH
5.3 9.3; 12.6 CH3CH2OH 16.0
CH3CH2CH2OH 16.1
OH
O CH3COCH2Br 16.1
CH2SH
O2NCH2CO2CH3 5.8 9.4
O 16.7
O
5.8 OH CH3CHO 17
CHO 9.9; 11.5
(CH3)2CHCHO 17
Cl HO (CH3)2CHOH 17.1
OH (CH3)3COH 18.0
Cl OH 6.2 9.9
CH3COCH3 19.3
Cl
CH3COCH2SOCH3 10.0 23
OH
SH 6.6
10.3 CH3CO2CH2CH3 25
HCO3H 7.1 CH3 HCmCH 25
NO2 CH3NO2 10.3 CH3CN 25
7.2 CH3SO2CH3 28
CH3SH 10.3
OH CH3COCH2CO2CH3 10.6 (C6H5)3CH 32
(CH3)2CHNO2 7.7 CH3COCHO 11.0 (C6H5)2CH2 34
CH2(CN)2 11.2 CH3SOCH3 35

Cl OH 7.8 NH3 36
CCl3CH2OH 12.2
Glucose 12.3 CH3CH2NH2 36
Cl
(CH3)2CUNOH 12.4 (CH3CH2)2NH 40
CH3CO3H 8.2
CH2(CO2CH3)2 12.9 CH3
OH 41
CHCl2CH2OH 12.9
8.5
CH2(OH)2 13.3
Cl
HOCH2CH(OH)CH2OH 14.1
CH3CH2NO2 8.5 43
CH2ClCH2OH 14.3
F3C OH 8.7 15.0 H2CUCH2 44

CH4 60
An acidity list covering more than 5000 organic compounds has been published: E.P. Serjeant and B. Dempsey (eds.), Ionization Constants of
Organic Acids in Aqueous Solution, IUPAC Chemical Data Series No. 23, Pergamon Press, Oxford, 1979.
Appendix C
Glossary
Absolute configuration (Section 9.5): The exact three- Acidity constant, Ka (Section 2.8): A measure of acid
dimensional structure of a chiral molecule. Absolute con- strength in water. For any acid HA, the acidity constant is
figurations are specified verbally by the CahnIngold [H3O][A]
Prelog R,S convention. given by the expression Ka Keq[H2O] .
[HA]
Absorbance (Section 11.9): In optical spectroscopy, the Activating group (Section 8.8): An electron-donating
logarithm of the intensity of the incident light divided by group such as hydroxyl (OH) or amino (NH2) that
the intensity of the light transmitted through a sample; increases the reactivity of an aromatic ring toward
A log I0/I. electrophilic aromatic substitution.
Absorption spectrum (Section 11.5): A plot of wave- Activation energy, G (Section 5.9): The difference in
length of incident light versus amount of light absorbed. energy between ground state and transition state in a reac-
Organic molecules show absorption spectra in both the tion. The amount of activation energy determines the rate
infrared and the ultraviolet regions of the electro- at which the reaction proceeds. Most organic reactions
magnetic spectrum. have activation energies of 40100 kJ/mol.
Acetal (Section 14.8): A functional group consisting of Active site (Sections 5.11, 19.10): The pocket in an enzyme
two OR groups bonded to the same carbon, R2C(OR)2. where a substrate is bound and undergoes reaction.
Acetals are often used as protecting groups for ketones
Acyl group (Sections 8.7, 14.1): A COR group.
and aldehydes.
Acyl phosphate (Chapter 16 Introduction): A functional
Acetoacetic ester synthesis (Section 17.4): The synthesis
group with an acyl group bonded to a phosphate,
of a methyl ketone by alkylation of an alkyl halide, fol-
RCOPO32.
lowed by hydrolysis and decarboxylation.
Acylation (Section 8.7): The introduction of an acyl
Acetyl group (Section 14.1): The CH3CO group.
group, COR, onto a molecule. For example, acylation of
Acetylide anion (Section 7.12): The anion formed by an alcohol yields an ester, acylation of an amine yields an
removal of a proton from a terminal alkyne. amide, and acylation of an aromatic ring yields an alkyl
aryl ketone.
Achiral (Section 9.2): Having a lack of handedness. A
molecule is achiral if it has a plane of symmetry and is Adams catalyst (Section 7.5): The PtO2 catalyst used for
thus superimposable on its mirror image. alkene hydrogenations.
Acid anhydride (Chapter 16 Introduction): A functional 1,2-Addition (Sections 7.11, 14.11): The addition of a
group with two acyl groups bonded to a common oxygen reactant to the two ends of a double bond.
atom, RCO2COR.
1,4-Addition (Sections 7.11, 14.11): Addition of a reactant
Acid halide (Chapter 16 Introduction): A functional group to the ends of a conjugated system. Conjugated dienes
with an acyl group bonded to a halogen atom, RCOX. yield 1,4-adducts when treated with electrophiles such as
A-11
A-12 A P P E N D I X C: G LO S S A RY
HCl. Conjugated enones yield 1,4-adducts when treated Alkylation (Sections 8.7, 17.4): Introduction of an alkyl
with nucleophiles such as amines. group onto a molecule. For example, aromatic rings can
be alkylated to yield arenes, and enolate anions can be
Addition reaction (Section 5.1): The reaction that occurs
alkylated to yield -substituted carbonyl compounds.
when two reactants add together to form a single new
product with no atoms left over. Alkyne (Chapter 6 Introduction): A hydrocarbon that con-
tains a carboncarbon triple bond, RCmCR.
Adrenocortical hormone (Section 23.9): A steroid hor-
mone secreted by the adrenal glands. There are two Allyl group (Section 6.2): A H2CUCHCH2X substituent.
types of adrenocortical hormones: mineralocorticoids
Allylic (Section 7.11): The position next to a double bond.
and glucocorticoids.
For example, H2CUCHCH2Br is an allylic bromide.
Alcohol (Chapter 13 Introduction): A compound with an
-Amino acid (Section 19.1): A difunctional compound
OH group bonded to a saturated, alkane-like carbon,
with an amino group on the carbon atom next to a car-
ROH.
boxyl group, RCH(NH2)CO2H.
Aldaric acid (Section 21.6): The dicarboxylic acid result-
Anomer (Section 21.5): The cyclic hemiacetal form of a
ing from oxidation of an aldose.
sugar that has the hemiacetal OH group on the side of the
Aldehyde (Chapter 14 Introduction): A compound con- ring opposite the terminal CH2OH.
taining the CHO functional group.
Helix (Section 19.8): A coiled secondary structure of a
Alditol (Section 21.6): The polyalcohol resulting from protein.
reduction of the carbonyl group of a sugar.
Position (Chapter 17 Introduction): The position next to
Aldol reaction (Section 17.5): The carbonyl condensation a carbonyl group.
reaction of an aldehyde or ketone to give a -hydroxy
-Substitution reaction (Section 17.2): The substitution
carbonyl compound.
of the hydrogen atom of a carbonyl compound by reac-
Aldonic acid (Section 21.6): The monocarboxylic acid tion with an electrophile.
resulting from oxidation of the aldehyde group of an aldose.
Amide (Chapter 16 Introduction): A compound contain-
Aldose (Section 21.1): A carbohydrate with an aldehyde ing the CONR2 functional group.
functional group.
Amidomalonate synthesis (Section 19.3): A method for
Alicyclic (Section 4.1): An aliphatic cyclic hydrocarbon preparing an -amino acid by alkylation of diethyl amido-
such as a cycloalkane or cycloalkene. malonate with an alkyl halide.
Aliphatic (Section 3.2): A nonaromatic hydrocarbon such Amine (Chapter 18 Introduction): A compound contain-
as a simple alkane, alkene, or alkyne. ing one or more organic substituents bonded to a nitrogen
atom, RNH2, R2NH, or R3N.
Alkaloid (Chapter 2 Lagniappe): A naturally occurring
organic base, such as morphine. Amino acid (See -Amino acid; Section 19.1)
Alkane (Section 3.2): A compound of carbon and hydro- Amino sugar (Section 21.7): A sugar with one of its OH
gen that contains only single bonds. groups replaced by NH2.
Alkene (Chapter 6 Introduction): A hydrocarbon that con- Amphiprotic (Section 19.1): Capable of acting either as an
tains a carboncarbon double bond, R2CUCR2. acid or as a base. Amino acids are amphiprotic.
Alkoxide ion (Section 13.2): The anion RO formed by Amplitude (Section 11.5): The height of a wave measured
deprotonation of an alcohol. from the midpoint to the maximum. The intensity of radiant
energy is proportional to the square of the waves amplitude.
Alkyl group (Section 3.3): The partial structure that
remains when a hydrogen atom is removed from an alkane. Anabolism (Section 20.1): The group of metabolic path-
ways that build up larger molecules from smaller ones.
Alkyl halide (Chapter 10 Introduction): A compound with
a halogen atom bonded to a saturated, sp3-hybridized Androgen (Section 23.9): A male steroid sex hormone.
carbon atom.
Angle strain (Section 4.3): The strain introduced into a
Alkylamine (Section 18.1): An amino-substituted alkane, molecule when a bond angle is deformed from its ideal
RNH2, R2NH, or R3N. value. Angle strain is particularly important in small-ring
A P P E N D I X C: G LO S S A RY A-13
cycloalkanes, where it results from compression of bond Axial position (Section 4.6): A bond to chair cyclohexane
angles to less than their ideal tetrahedral values. that lies along the ring axis perpendicular to the rough
plane of the ring.
Anomeric center (Section 21.5): The hemiacetal carbon
atom in the cyclic pyranose or furanose form of a sugar.
Anomers (Section 21.5): Cyclic stereoisomers of sugars Backbone (Section 19.4): The continuous chain of atoms
that differ only in their configuration at the hemiacetal running the length of a protein or other polymer.
(anomeric) carbon. Base peak (Section 11.1): The most intense peak in a mass
Anti conformation (Section 3.7): The geometric arrange- spectrum.
ment around a carboncarbon single bond in which the Basicity constant, Kb (Section 18.3): A measure of base
two largest substituents are 180 apart as viewed in a strength in water. For any base B, the basicity constant is
Newman projection. [BH][OH]
given by the expression Kb .
[B]
Anti periplanar (Section 10.11): Describing a stereochem-
ical relationship whereby two bonds on adjacent carbons Bent bonds (Section 4.4): The bonds in small rings such as
lie in the same plane at an angle of 180. cyclopropane that bend away from the internuclear line
and overlap at a slight angle, rather than head-on. Bent
Anti stereochemistry (Section 7.2): The opposite of syn. bonds are highly strained and highly reactive.
An anti addition reaction is one in which the two ends of
the double bond are attacked from different sides. An anti Benzoyl group (Section 14.1): The C6H5CO group.
elimination reaction is one in which the two groups leave Benzyl group (Section 8.1): The C6H5CH2 group.
from opposite sides of the molecule.
Benzylic (Section 8.9): The position next to an aromatic ring.
Antiaromatic (Section 8.3): Describing a planar, appar-
ently conjugated molecule with 4n electrons. Delocal- Anomer (Section 21.5): The cyclic hemiacetal form of a
ization of the electrons leads to an increase in energy. sugar that has the hemiacetal OH group on the same side
of the ring as the terminal CH2OH.
Antibonding MO (Section 1.11): A molecular orbital that
Diketone (Section 17.3): A 1,3-diketone.
is higher in energy than the atomic orbitals from which it
is formed. -Keto ester (Section 17.3): A 3-keto ester.
Anticodon (Section 24.5): A sequence of three bases on -Oxidation pathway (Section 23.5): The metabolic path-
tRNA that reads the codons on mRNA and brings the cor- way for degrading fatty acids.
rect amino acids into position for protein synthesis. -Pleated sheet (Section 19.8): A type of secondary struc-
Antisense strand (Section 24.4): The template strand of ture of a protein.
double-helical DNA that does not contain the gene. Bimolecular reaction (Section 10.5): A reaction whose
Arene (Section 8.1): An alkyl-substituted benzene. rate-limiting step occurs between two reactants.
Boat cyclohexane (Section 4.5): A conformation of cyclo-
Aromatic (Chapter 8 Introduction): The special character-
hexane that bears a slight resemblance to a boat. Boat
istics of cyclic conjugated molecules, including unusual
cyclohexane has no angle strain but has a large number of
stability and a tendency to undergo substitution reactions
eclipsing interactions that make it less stable than chair
rather than addition reactions on treatment with electro-
cyclohexane.
philes. Aromatic molecules are planar, cyclic, conjugated
species that have 4n 2 electrons. Boc derivative (Section 19.7): A butyloxycarbonyl
N-protected amino acid.
Arylamine (Section 18.1): An amino-substituted aromatic
compound, ArNH2. Bond angle (Section 1.6): The angle formed between two
adjacent bonds.
Atomic mass (Section 1.1): The average mass number of
the atoms of an element. Bond dissociation energy, D (Section 5.8): The amount of
energy needed to break a bond and produce two radical
Atomic number, Z (Section 1.1): The number of protons fragments.
in the nucleus of an atom.
Bond length (Section 1.5): The equilibrium distance
ATZ derivative (Section 19.6): An anilinothiazolinone, between the nuclei of two atoms that are bonded to each
formed from an amino acid during Edman degradation. other.
Bond strength (Section 1.5): An alternative name for bond Carbonyl group (Preview of Carbonyl Chemistry): The
dissociation energy. CO functional group.
Bonding MO (Section 1.11): A molecular orbital that is Carboxyl group (Section 15.1): The CO2H functional
lower in energy than the atomic orbitals from which it is group.
formed.
Carboxylation (Section 15.5): The addition of CO2 to a
Branched-chain alkane (Section 3.2): An alkane that con- molecule.
tains a branching connection of carbons as opposed to a
straight-chain alkane. Carboxylic acid (Chapter 15 Introduction): A compound
containing the CO2H functional group.
Bridgehead atom (Section 4.9): An atom that is shared by
more than one ring in a polycyclic molecule. Carboxylic acid derivative (Chapter 16 Introduction): A
compound in which an acyl group is bonded to an electro-
Bromohydrin (Section 7.3): A 1,2-disubstituted bromo- negative atom or substituent that can act as a leaving
alcohol; obtained by addition of HOBr to an alkene. group in a substitution reaction. Esters, amides, and acid
Bromonium ion (Section 7.2): A species with a divalent, halides are examples.
positively charged bromine, R2Br. Catabolism (Section 20.1): The group of metabolic path-
BrnstedLowry acid (Section 2.7): A substance that ways that break down larger molecules into smaller ones.
donates a hydrogen ion (proton; H) to a base.
Cation radical (Section 11.1): A species typically formed
BrnstedLowry base (Section 2.7): A substance that in a mass spectrometer, having both a positive charge and
accepts H from an acid. an odd number of electrons.
Chain-growth polymer (Sections 7.8, 16.9): A polymer
whose bonds are produced by chain reactions. Poly-
C-terminal amino acid (Section 19.4): The amino acid
ethylene and other alkene polymers are examples.
with a free CO2H group at the end of a protein chain.
CahnIngoldPrelog sequence rules (Sections 6.4, 9.5): A Chain reaction (Section 5.3): A reaction that, once initi-
series of rules for assigning relative priorities to sub- ated, sustains itself in an endlessly repeating cycle of
stituent groups on a double-bond carbon atom or on a chi- propagation steps. The radical chlorination of alkanes is
rality center. an example of a chain reaction that is initiated by irradia-
tion with light and then continues in a series of propaga-
Cannizzaro reaction (Section 14.10): The disproportiona- tion steps.
tion reaction of an aldehyde to yield an alcohol and a car-
boxylic acid on treatment with base. Chair conformation (Section 4.5): A three-dimensional
conformation of cyclohexane that resembles the rough
Carbanion (Sections 13.3, 14.6): A carbon anion, or sub- shape of a chair. The chair form of cyclohexane is the
stance that contains a trivalent, negatively charged carbon lowest-energy conformation of the molecule.
atom (R3C:). Carbanions are sp3-hybridized and have eight
electrons in the outer shell of the negatively charged carbon. Chemical shift (Section 12.3): The position on the NMR
chart where a nucleus absorbs. By convention, the chemi-
Carbinolamine (Section 14.7): A molecule that contains cal shift of tetramethylsilane (TMS) is set at zero, and all
the R2C(OH)NH2 functional group. Carbinolamines are other absorptions usually occur downfield (to the left on
produced as intermediates during the nucleophilic addi- the chart). Chemical shifts are expressed in delta units,
tion of amines to carbonyl compounds. , where 1 equals 1 ppm of the spectrometer operating
Carbocation (Sections 5.5, 6.8): A carbon cation, or sub- frequency.
stance that contains a trivalent, positively charged carbon
Chiral (Section 9.2): Having handedness. Chiral mole-
atom having six electrons in its outer shell (R3C).
cules are those that do not have a plane of symmetry and
Carbohydrate (Chapter 21 Introduction): A polyhydroxy are therefore not superimposable on their mirror image. A
aldehyde or ketone. Carbohydrates can be either simple chiral molecule thus exists in two forms, one right-
sugars, such as glucose, or complex sugars, such as handed and one left-handed. The most common cause of
cellulose. chirality in a molecule is the presence of a carbon atom
that is bonded to four different substituents.
Carbonyl condensation reaction (Section 17.5): A reaction
that joins two carbonyl compounds together by a combina- Chirality center (Section 9.2): An atom (usually carbon)
tion of -substitution and nucleophilic addition reactions. that is bonded to four different groups.
Chromatography (Chapter 11 Lagniappe, Section 19.5): A Conjugate base (Section 2.7): The anion that results from
technique for separating a mixture of compounds into deprotonation of a BrnstedLowry acid.
pure components. Different compounds adsorb to a sta-
Conjugation (Section 7.10): A series of overlapping
tionary support phase and are then carried along it at dif-
p orbitals, usually in alternating single and multiple
ferent rates by a mobile phase.
bonds. For example, buta-1,3-diene is a conjugated diene,
Cistrans isomers (Sections 4.2, 6.3): Stereoisomers that but-3-en-2-one is a conjugated enone, and benzene is a
differ in their stereochemistry about a double bond or cyclic conjugated triene.
ring.
Constitutional isomers (Sections 3.2, 9.9): Isomers that have
Citric acid cycle (Section 22.4): The metabolic pathway their atoms connected in a different order. For example,
by which acetyl CoA is degraded to CO2. butane and 2-methylpropane are constitutional isomers.
Claisen condensation reaction (Section 17.8): The Coupled reactions (Section 20.1): Two reactions that
carbonyl condensation reaction of an ester to give a -keto share a common intermediate so that the energy released
ester product. in the favorable step allows the unfavorable step to occur.
Coding strand (Section 24.4): The strand of double- Coupling constant, J (Section 12.11): The magnitude
helical DNA that contains the gene. (expressed in hertz) of the interaction between nuclei
whose spins are coupled.
Codon (Section 24.5): A three-base sequence on a messen-
ger RNA chain that encodes the genetic information nec- Covalent bond (Section 1.4): A bond formed by sharing
essary to cause a specific amino acid to be incorporated electrons between atoms.
into a protein. Codons on mRNA are read by complemen- Cyanohydrin (Section 15.7): A compound with an OH
tary anticodons on tRNA. group and a CN group bonded to the same carbon atom;
Coenzyme (Section 19.9): A small organic molecule that formed by addition of HCN to an aldehyde or ketone.
acts as a cofactor. Cycloalkane (Section 4.1): An alkane that contains a ring
Cofactor (Section 19.9): A small nonprotein part of an of carbons.
enzyme that is necessary for biological activity.
Combinatorial chemistry (Chapter 8 Lagniappe): A tech- D Sugar (Section 21.3): A sugar whose hydroxyl group at
nique for preparing anywhere from a few dozen to several the chirality center farthest from the carbonyl group
hundred thousand substances simultaneously. points to the right when drawn in Fischer projection.
Complex carbohydrate (Section 21.1): A carbohydrate d,l form (Section 9.8): The racemic form of a chiral
that is made of two or more simple sugars linked together. compound.
Condensed structure (Sections 1.12, 3.2): A shorthand Deactivating group (Section 8.8): An electron-withdrawing
way of writing structures in which CH and CC bonds substituent that decreases the reactivity of an aromatic ring
are understood rather than shown explicitly. Propane, for toward electrophilic aromatic substitution.
example, has the condensed structure CH3CH2CH3.
Deamination (Section 20.2): The removal of an amino
Configuration (Section 9.5): The three-dimensional group from a molecule, as occurs with amino acids during
arrangement of atoms bonded to a chirality center. metabolic degradation.
Conformation (Section 3.6): The three-dimensional shape Decarboxylation (Section 17.4): The loss of carbon diox-
of a molecule at any given instant, assuming that rotation ide from a molecule. -Keto acids decarboxylate readily
around single bonds is frozen. on heating.
Conformational analysis (Section 4.8): A means of assess- Degree of unsaturation (Section 6.1): The number of rings
ing the energy of a substituted cycloalkane by totaling the and/or multiple bonds in a molecule.
steric interactions present in the molecule.
Dehydration (Sections 7.1, 13.4): The loss of water from
Conjugate acid (Section 2.7): The product that results an alcohol to yield an alkene.
from protonation of a BrnstedLowry base.
Dehydrohalogenation (Sections 7.1, 10.10): The loss of
Conjugate addition (Section 14.11): Addition of a nucleo- HX from an alkyl halide. Alkyl halides undergo dehydro-
phile to the carbon atom of an ,-unsaturated carbonyl halogenation to yield alkenes on treatment with strong
compound. base.
Delocalization (Section 7.10): A spreading out of electron Digestion (Section 20.1): The first stage of catabolism, in
density over a conjugated electron system. For exam- which food is broken down by hydrolysis of ester, glyco-
ple, allylic cations and allylic anions are delocalized side (acetal), and peptide (amide) bonds to yield fatty
because their charges are spread out over the entire acids, simple sugars, and amino acids.
electron system.
Dihedral angle (Section 3.6): The angle between CH
Delta scale (Section 12.3): An arbitrary scale used to cali- bonds on front and back carbons as viewed end-on.
brate NMR charts. One delta unit () is equal to 1 part per Dipole moment, (Section 2.2): A measure of the net
million (ppm) of the spectrometer operating frequency. polarity of a molecule. A dipole moment arises when the
Denatured (Section 19.8): The physical changes that centers of mass of positive and negative charges within a
occur in a protein when secondary and tertiary structures molecule do not coincide.
are disrupted. Disaccharide (Section 21.8): A carbohydrate formed by
Deoxy sugar (Section 21.7): A sugar with one of its OH linking two simple sugars through an acetal bond.
groups replaced by an H. Disulfide (Section 13.6): A compound of the general
Deoxyribonucleic acid, DNA (Section 24.1): The biopolymer structure RSSR.
consisting of deoxyribonucleotide units linked together DNA (See Deoxyribonucleic acid; Section 24.1)
through phosphatesugar bonds. Found in the nucleus of
cells, DNA contains an organisms genetic information. Double helix (Section 24.2): The structure of DNA in
which two polynucleotide strands coil around each other.
DEPT-NMR (Section 12.6): An NMR method for distin-
Doublet (Section 12.11): A two-line NMR absorption
guishing among signals due to CH3, CH2, CH, and quater-
caused by spinspin splitting when the spin of the
nary carbons. That is, the number of hydrogens attached
nucleus under observation couples with the spin of a
to each carbon can be determined.
neighboring magnetic nucleus.
Deshielding (Section 12.2): An effect observed in NMR
Downfield (Section 12.3): Referring to the left-hand por-
that causes a nucleus to absorb downfield (to the left) of
tion of the NMR chart.
tetramethylsilane (TMS) standard. Deshielding is caused
by a withdrawal of electron density from the nucleus.
Deuterium isotope effect (Section 10.11): A tool used in E geometry (Section 6.4): A term used to describe the stereo-
mechanistic investigations to establish whether a CH chemistry of a carboncarbon double bond. The two groups
bond is broken in the rate-limiting step of a reaction. on each carbon are assigned priorities according to the
CahnIngoldPrelog sequence rules, and the two carbons are
Dextrorotatory (Section 9.3): A word used to describe an compared. If the high-priority groups on each carbon are on
optically active substance that rotates the plane of polar- opposite sides of the double bond, the bond has E geometry.
ization of plane-polarized light in a right-handed (clock-
wise) direction. E1 reaction (Section 10.12): A unimolecular elimination
reaction in which the CX bond breaks before the CH
Diastereomers (Section 9.6): Nonmirror-image stereo- bond, giving a carbocation intermediate.
isomers; diastereomers have the same configuration at one
or more chirality centers but differ at other chirality centers. E1cB reaction (Section 10.12): A unimolecular elimina-
tion reaction in which the CH bond breaks before the
Diastereotopic (Section 12.8): Two hydrogens in a mole- CX bond, giving a carbanion intermediate.
cule whose replacement by some other group leads to dif-
ferent diastereomers. E2 reaction (Section 10.11): A bimolecular elimination
reaction in which CH and CX bond cleavage are
1,3-Diaxial interaction (Section 4.7): The strain energy simultaneous.
caused by a steric interaction between axial groups three
carbon atoms apart in chair cyclohexane. Eclipsed conformation (Section 3.6): The geometric
arrangement around a carboncarbon single bond in
Dideoxy method (Section 24.6): A biochemical method which the bonds to substituents on one carbon are paral-
for sequencing DNA strands. lel to the bonds to substituents on the neighboring carbon
as viewed in a Newman projection.
Dieckmann cyclization reaction (Section 17.9): An
intramolecular Claisen condensation reaction to give a Edman degradation (Section 19.6): A method for N-terminal
cyclic -keto ester. sequencing of peptide chains.
Eicosanoid (Section 23.7): A class of compounds consist- Enantiomers (Section 9.1): Stereoisomers of a chiral sub-
ing of prostaglandins, thromboxanes, and leukotrienes, stance that have a mirror-image relationship. Enantiomers
which are derived biologically from arachidonic acid. have opposite configurations at all chirality centers.
Electromagnetic spectrum (Section 11.5): The range of Enantioselective synthesis (Chapter 14 Lagniappe, Sec-
electromagnetic energy, including infrared, ultraviolet, tion 19.3): A method of synthesis from an achiral precur-
and visible radiation. sor that yields only a single enantiomer of a chiral
product.
Electron configuration (Section 1.3): A list of the orbitals
occupied by electrons in an atom. Enantiotopic (Section 12.8): Two hydrogens in a molecule
whose replacement by some other group leads to different
Electron-dot structure (Section 1.4): A representation of a
enantiomers.
molecule showing valence electrons as dots.
3 End (Section 24.1): The end of a nucleic acid chain with
Electron-transport chain (Section 20.1): The final stage of
a free hydroxyl group at C3.
catabolism in which ATP is produced.
Electronegativity, EN (Section 2.1): The ability of an atom 5 End (Section 24.1): The end of a nucleic acid chain with
to attract electrons in a covalent bond. Electronegativity a free hydroxyl group at C5.
increases across the periodic table from right to left and Endergonic (Section 5.7): A reaction that has a positive
from bottom to top. free-energy change and is therefore nonspontaneous. In a
Electrophile (Section 5.4): An electron-lover, or sub- reaction energy diagram, the product of an endergonic
stance that accepts an electron pair from a nucleophile in reaction has a higher energy level than the reactants.
a polar bond-forming reaction. Endothermic (Section 5.7): A reaction that absorbs heat
Electrophilic addition reaction (Section 6.6): The addition and therefore has a positive enthalpy change.
of an electrophile to an alkene to yield a saturated product. Enol (Section 17.1): A vinylic alcohol that is in equilib-
Electrophilic aromatic substitution reaction (Section 8.6): rium with a carbonyl compound.
A reaction in which an electrophile (E) reacts with Enolate ion (Section 17.1): The anion of an enol,
an aromatic ring and substitutes for one of the ring CUCXO.
hydrogens.
Enthalpy change, H (Section 5.7): The heat of reaction.
Electrophoresis (Sections 19.2, 24.6): A technique used The enthalpy change that occurs during a reaction is a
for separating charged organic molecules, particularly measure of the difference in total bond energy between
proteins and DNA fragments. The mixture to be separated reactants and products.
is placed on a buffered gel or paper, and an electric poten-
tial is applied across the ends of the apparatus. Negatively Entropy change, S (Section 5.7): The change in amount
charged molecules migrate toward the positive electrode, of molecular disorder. The entropy change that occurs
and positively charged molecules migrate toward the neg- during a reaction is a measure of the difference in disorder
ative electrode. between reactants and products.
Electrostatic potential map (Section 2.1): A molecular Enzyme (Sections 5.11, 19.9): A biological catalyst.
representation that uses color to indicate the charge dis- Enzymes are large proteins that catalyze specific bio-
tribution in the molecule as derived from quantum- chemical reactions.
mechanical calculations. Epimers (Section 9.6): Diastereomers that differ in config-
Elimination reaction (Section 5.1): What occurs when a uration at only one chirality center but are the same at all
single reactant splits into two products. others.
Elution (Chapter 11 Lagniappe): The removal of a sub- Epoxide (Section 7.6): A three-membered-ring ether func-
stance from a chromatography column. tional group.
EmbdenMeyerhof pathway (Section 22.2): An alterna- Equatorial position (Section 4.6): A bond to cyclohexane
tive name for glycolysis. that lies along the rough equator of the ring.
Enamine (Section 14.7): A compound with the ESI (Section 11.4): Electrospray ionization, a soft ion-
R2NXCRUCR2 functional group. ization method used for mass spectrometry of biological
samples of very high molecular weight.
Essential amino acid (Section 20.5): One of nine amino sent bonds coming out of the plane of the page, and the
acids that are biosynthesized only in plants and micro- vertical arms of the cross represent bonds going back into
organisms and must be obtained by humans in the diet. the plane of the page.
Essential oil (Chapter 6 Lagniappe): The volatile oil Fmoc derivative (Section 19.7): A fluorenylmethyloxy-
obtained by steam distillation of a plant extract. carbonyl N-protected amino acid.
Ester (Chapter 16 Introduction): A compound containing Formal charge (Section 2.3): The difference in the num-
the CO2R functional group. ber of electrons owned by an atom in a molecule and by
Estrogen (Section 23.9): A female steroid sex hormone. the same atom in its elemental state.
Ether (Chapter 13 Introduction): A compound that has Formyl group (Section 14.1): A CHO group.
two organic substituents bonded to the same oxygen Frequency, (Section 11.5): The number of electro-
atom, ROR. magnetic wave cycles that travel past a fixed point in a
Exergonic (Section 5.7): A reaction that has a negative given unit of time. Frequencies are expressed in units of
free-energy change and is therefore spontaneous. On a cycles per second, or hertz.
reaction energy diagram, the product of an exergonic reac- FriedelCrafts reaction (Section 8.7): An electrophilic
tion has a lower energy level than that of the reactants. aromatic substitution reaction to alkylate or acylate an
Exon (Section 24.4): A section of DNA that contains aromatic ring.
genetic information.
FT-NMR (Section 12.4): Fourier-transform NMR; a rapid
Exothermic (Section 5.7): A reaction that releases heat technique for recording NMR spectra in which all mag-
and therefore has a negative enthalpy change. netic nuclei absorb at the same time.
Functional group (Section 3.1): An atom or group of
atoms that is part of a larger molecule and that has a char-
Fat (Section 23.1): A solid triacylglycerol derived from an
acteristic chemical reactivity.
animal source.
Furanose (Section 21.5): The five-membered-ring form of
Fatty acid (Section 23.1): A long, straight-chain car-
a simple sugar.
boxylic acid found in fats and oils.
Fatty acidderived substance (Section 25.1): A natural
product biosynthesized from a fatty acid. Eicosanoids are Gauche conformation (Section 3.7): The conformation of
examples.* butane in which the two methyl groups lie 60 apart as
Fibrous protein (Section 19.8): A protein that consists of viewed in a Newman projection. This conformation has
polypeptide chains arranged side by side in long threads. 3.8 kJ/mol steric strain.
Such proteins are tough, insoluble in water, and used in Geminal (Section 14.5): Referring to two groups attached
nature for structural materials such as hair, hooves, and to the same carbon atom. For example, a 1,1-diol is a gem-
fingernails. inal diol.
Fingerprint region (Section 11.7): The complex region of Gibbs free-energy change, G (Section 5.7): The free-
the infrared spectrum from 1500 to 400 cm1. energy change that occurs during a reaction, given by the
First-order reaction (Section 10.7): A reaction whose rate- equation G H TS. A reaction with a negative free-
limiting step is unimolecular and whose kinetics there- energy change is spontaneous, and a reaction with a posi-
fore depend on the concentration of only one reactant. tive free-energy change is nonspontaneous.
Fischer esterification reaction (Section 16.3): The acid- Globular protein (Section 19.8): A protein that is coiled
catalyzed reaction of an alcohol with a carboxylic acid to into a compact, nearly spherical shape. These proteins,
yield an ester. which are generally water-soluble and mobile within the
cell, are the structural class to which enzymes belong.
Fischer projection (Section 21.2): A means of depicting
the absolute configuration of a chiral molecule on a flat Glucogenic amino acid (Section 20.4): An amino acid that
page. A Fischer projection uses a cross to represent the is metabolized either to pyruvate or to an intermediate of
chirality center. The horizontal arms of the cross repre- the citric acid cycle.
Gluconeogenesis (Section 22.5): The anabolic pathway by Hemiacetal (Section 14.8): A functional group consisting
which organisms make glucose from simple three-carbon of one OR and one OH group bonded to the same
precursors. carbon.
Glycal (Section 21.9): An unsaturated sugar with a C1C2 Hemithioacetal (Section 22.2): The sulfur analog of an
double bond. acetal, resulting from nucleophilic addition of a thiol to a
ketone or aldehyde.
Glycal assembly method (Section 21.9): A method for link-
ing monosaccharides together to synthesis polysaccharides. HendersonHasselbalch equation (Sections 15.3, 18.5):
An equation for determining the extent of deprotonation
Glycerophospholipid (Section 23.3): A lipid that contains
of a weak acid at various pH values.
a glycerol backbone linked to two fatty acids and a phos-
phoric acid. Hertz, Hz (Section 11.5): A measure of electromagnetic
frequency, the number of waves that pass by a fixed point
Glycoconjugate (Section 21.6): A molecule in which a
per second.
carbohydrate is linked through its anomeric center to
another biological molecule such as a lipid or protein. Heterocycle (Sections 8.4, 18.8): A cyclic molecule whose
ring contains more than one kind of atom. For example,
Glycol (Section 7.7): A diol, such as ethylene glycol,
pyridine is a heterocycle that contains five carbon atoms
HOCH2CH2OH.
and one nitrogen atom in its ring.
Glycolysis (Section 22.2): A series of ten enzyme-
High-energy compound (Section 5.8): A term used in bio-
catalyzed reactions that break down glucose into 2 equiv-
chemistry to describe substances such as ATP that
alents of pyruvate, CH3COCO2.
undergo highly exothermic reactions.
Glycoside (Section 21.6): A cyclic acetal formed by reac-
Hofmann elimination reaction (Section 18.7): The elimi-
tion of a sugar with another alcohol.
nation reaction of an amine to yield an alkene by reaction
Green chemistry (Chapter 18 Lagniappe): The design and with iodomethane, followed by heating with Ag2O.
implementation of chemical products and processes that
HOMO (Section 11.9): The highest occupied molecular
reduce waste and attempt to eliminate the generation of
orbital.
hazardous substances.
Homotopic (Section 12.8): Hydrogens that give the identi-
Grignard reagent (Section 10.3): An organomagnesium
cal structure on replacement by X and thus show identical
halide, RMgX.
NMR absorptions.
Ground state (Section 1.3): The most stable, lowest-
Hormone (Section 23.9): A chemical messenger that is
energy electron configuration of a molecule or atom.
secreted by an endocrine gland and carried through the
bloodstream to a target tissue.
Halogenation (Sections 7.2, 8.6): The reaction of halogen HPLC (Chapter 11 Lagniappe): High-pressure liquid chro-
with an alkene to yield a 1,2-dihalide addition product matography; a variant of column chromatography using
or with an aromatic compound to yield a substitution high pressure to force solvent through very small
product. absorbent particles.
Halohydrin (Section 7.3): A 1,2-disubstituted haloalcohol, Hckels rule (Section 8.3): A rule stating that monocyclic
such as that obtained on addition of HOBr to an alkene. conjugated molecules having 4n 2 electrons (n an
integer) are aromatic.
Hammond postulate (Section 6.9): A postulate stating
that we can get a picture of what a given transition state Hunds rule (Section 1.3): If two or more empty orbitals of
looks like by looking at the structure of the nearest stable equal energy are available, one electron occupies each,
species. Exergonic reactions have transition states that with their spins parallel, until all are half-full.
resemble reactant; endergonic reactions have transition
Hybrid orbital (Section 1.6): An orbital derived from
states that resemble product.
a combination of atomic orbitals. Hybrid orbitals,
Heat of hydrogenation (Section 6.5): The amount of such as the sp3, sp2, and sp hybrids of carbon, are strongly
heat released when a carboncarbon double bond is directed and form stronger bonds than atomic orbitals do.
hydrogenated.
Hydration (Section 7.4): Addition of water to a molecule,
Heat of reaction (Section 5.7): An alternative name for the such as occurs when alkenes are treated with aqueous sul-
enthalpy change in a reaction, H. furic acid to give alcohols.
Hydride shift (Section 6.10): The shift of a hydrogen atom number of each kind of proton in a molecule. Integrated
and its electron pair to a nearby cationic center. peak areas are superimposed over the spectrum as a stair-
step line, with the height of each step proportional to the
Hydroboration (Section 7.4): Addition of borane (BH3) or
area underneath the peak.
an alkylborane to an alkene. The resultant trialkylborane
products can be oxidized to yield alcohols. Intermediate (Section 5.10): A species that is formed dur-
ing the course of a multistep reaction but is not the final
Hydrocarbon (Section 3.2): A compound that contains
product. Intermediates are more stable than transition
only carbon and hydrogen.
states but may or may not be stable enough to isolate.
Hydrogen bond (Sections 2.12, 13.2): A weak attraction
Intramolecular, intermolecular (Section 17.7): A reac-
between a hydrogen atom bonded to an electronegative
tion that occurs within the same molecule is intramolec-
atom and an electron lone pair on another electro-
ular; a reaction that occurs between two molecules is
negative atom.
intermolecular.
Hydrogenation (Section 7.5): Addition of hydrogen to a
Intron (Section 24.4): A section of DNA that does not con-
double or triple bond to yield a saturated product.
tain genetic information.
Hydrogenolysis (Section 19.7): Cleavage of a bond by
Ion pair (Section 10.7): A loose complex between two
reaction with hydrogen. Benzylic ethers and esters, for
ions in solution. Ion pairs are implicated as intermediates
instance, are cleaved by hydrogenolysis.
in SN1 reactions to account for the partial retention of
Hydrophilic (Sections 2.12, 23.2): Water-loving; attracted stereochemistry that is often observed.
to water.
Isoelectric point, pI (Section 19.2): The pH at which the
Hydrophobic (Sections 2.12, 23.2): Water-fearing; not number of positive charges and the number of negative
attracted to water. charges on a protein or an amino acid are equal.
Hydroquinone (Section 13.5): A 1,4-dihydroxybenzene. Isomers (Section 3.2): Compounds that have the same
molecular formula but different structures.
Hydroxylation (Section 7.7): Addition of two OH groups
to a double bond. Isoprene rule (Chapter 6 Lagniappe): An observation to
the effect that terpenoids appear to be made up of isoprene
Hyperconjugation (Section 6.5): An interaction that
(2-methylbuta-1,3-diene) units connected head-to-tail.
results from overlap of a vacant p orbital on one atom with
a neighboring CH bond. Hyperconjugation is impor- Isotopes (Section 1.1): Atoms of the same element that
tant in stabilizing carbocations and in stabilizing substi- have different mass numbers.
tuted alkenes.
IUPAC system of nomenclature (Section 3.4): Rules for
naming compounds, devised by the International Union
of Pure and Applied Chemistry.
Imine (Section 14.7): A compound with the R2CUNR
functional group; also called a Schiff base.
Inductive effect (Sections 2.1, 6.8, 8.8): The electron- Kekul structure (Section 1.4): A method of representing
attracting or electron-withdrawing effect transmitted molecules in which a line between atoms indicates a bond.
through bonds. Electronegative elements have an
Ketoenol tautomerism (Section 17.1): The rapid equili-
electron-withdrawing inductive effect.
bration between a carbonyl form and vinylic alcohol form
Infrared (IR) spectroscopy (Section 11.6): A kind of opti- of a molecule.
cal spectroscopy that uses infrared energy. IR spec-
Ketogenic amino acid (Section 20.4): An amino acid that
troscopy is particularly useful in organic chemistry for
is metabolized into an intermediate that can enter fatty-
determining the kinds of functional groups present in
acid biosynthesis.
molecules.
Ketone (Chapter 14 Introduction): A compound with two
Initiator (Section 5.3): A substance with an easily broken
organic substituents bonded to a carbonyl group, R2CUO.
bond that is used to initiate a radical chain reaction. For
example, radical chlorination of alkanes is initiated Ketone body (Section 20.4): One of the substances aceto-
when light energy breaks the weak ClCl bond to form Cl acetate, -hydroxybutyrate, or acetone resulting from
radicals. amino acid catabolism.
Integration (Section 12.10): A technique for measuring Ketose (Section 21.1): A carbohydrate with a ketone func-
the area under an NMR peak to determine the relative tional group.
Kinetics (Section 10.5): Referring to reaction rates. Lone-pair electrons (Section 1.4): Nonbonding valence-
Kinetic measurements are useful for helping to determine shell electron pairs. Lone-pair electrons are used by
reaction mechanisms. nucleophiles in their reactions with electrophiles.
Krebs cycle (Section 22.4): An alternative name for the LUMO (Section 11.9): The lowest unoccupied molecular
citric acid cycle, by which acetyl CoA is degraded to CO2. orbital.
Lagniappe: A word in the Creole dialect of southern Magnetic resonance imaging, MRI (Chapter 12 Lagniappe):
Louisiana meaning an extra benefit or a little something A medical diagnostic technique based on nuclear magnetic
extra. See the Lagniappes at the end of each chapter. resonance.
L Sugar (Section 21.3): A sugar whose hydroxyl group at Major groove (Section 24.2): The larger of two grooves in
the chirality center farthest from the carbonyl group the DNA double helix.
points to the left when drawn in Fischer projection.
MALDI (Section 11.4): Matrix-assisted laser desorption
Lactam (Section 16.7): A cyclic amide. ionization, a soft ionization method used for mass spec-
trometry of biological samples of very high molecular
Lactone (Section 16.6): A cyclic ester.
weight.
LD50 (Chapter 1 Lagniappe): The amount of a substance
Malonic ester synthesis (Section 17.4): The synthesis of a
per kilogram body weight that is lethal to 50% of test
carboxylic acid by alkylation of an alkyl halide, followed
animals.
by hydrolysis and decarboxylation.
Leaving group (Section 10.5): The group that is replaced
Markovnikovs rule (Section 6.7): A guide for determin-
in a substitution reaction.
ing the regiochemistry (orientation) of electrophilic addi-
Levorotatory (Section 9.3): An optically active substance tion reactions. In the addition of HX to an alkene, the
that rotates the plane of polarization of plane-polarized hydrogen atom bonds to the alkene carbon that has fewer
light in a left-handed (counterclockwise) direction. alkyl substituents.
Lewis acid (Section 2.11): A substance with a vacant low- Mass number, A (Section 1.1): The total of protons plus
energy orbital that can accept an electron pair from a base. neutrons in an atom.
All electrophiles are Lewis acids.
Mass spectrometry (Section 11.1): A technique for mea-
Lewis base (Section 2.11): A substance that donates an elec- suring the mass, and therefore the molecular weight
tron lone pair to an acid. All nucleophiles are Lewis bases. (MW), of ions.
Lewis structure (Section 1.4): A representation of a mole- McLafferty rearrangement (Section 11.3): A mass-
cule showing valence electrons as dots. spectral fragmentation pathway for carbonyl compounds.
Lindlar catalyst (Section 7.12): A hydrogenation catalyst Mechanism (Section 5.2): A complete description of how
used to convert alkynes to cis alkenes. a reaction occurs. A mechanism must account for all start-
ing materials and all products and must describe the
Line-bond structure (Section 1.4): A representation of a
details of each individual step in the overall reaction
molecule showing covalent bonds as lines between atoms.
process.
134 Link (Section 21.8): An acetal link between the C1
Mercapto group (Section 13.1): An alternative name for
OH group of one sugar and the C4 OH group of another
the thiol group, SH.
sugar.
Meso compound (Section 9.7): A compound that contains
Lipid (Chapter 23 Introduction): A naturally occurring sub-
chirality centers but is nevertheless achiral because it
stance isolated from cells and tissues by extraction with a
contains a symmetry plane.
nonpolar solvent. Lipids belong to many different struc-
tural classes, including fats, terpenes, prostaglandins, and Messenger RNA (Section 24.2): A kind of RNA formed by
steroids. transcription of DNA and used to carry genetic messages
from DNA to ribosomes.
Lipid bilayer (Section 23.3): The ordered lipid structure
that forms a cell membrane. Meta, m- (Section 8.1): A naming prefix used for
1,3-disubstituted benzenes.
Lipoprotein (Chapter 23 Lagniappe): A complex molecule
with both lipid and protein parts that transports lipids Metabolism (Section 20.1): A collective name for the many
through the body. reactions that go on in the cells of living organisms.
Methylene group (Section 6.2): A CH2 or CH2 group. Natural gas (Chapter 3 Lagniappe): A naturally occurring
hydrocarbon mixture consisting chiefly of methane, along
Micelle (Section 23.2): A spherical cluster of soaplike
with smaller amounts of ethane, propane, and butane.
molecules that aggregate in aqueous solution. The ionic
heads of the molecules lie on the outside, where they are Natural product (Chapter 5 Lagniappe; Chapter 25): A
solvated by water, and the organic tails bunch together on catchall term generally taken to mean a small molecule
the inside of the micelle. found in bacteria, plants, or other living organisms.*
Michael reaction (Section 17.10): The conjugate addition Neopentyl group (Section 10.6): The 2,2-dimethylpropyl
reaction of an enolate ion to an unsaturated carbonyl group, (CH3)3CCH2.
compound.
Neuraminidase (Chapter 22 Lagniappe): An enzyme pres-
Minor groove (Section 24.2): The smaller of two grooves ent on the surface of viral particles that cleaves the bond
in the DNA double helix. holding the newly formed viral particles to host cells.
Molar absorptivity (Section 11.9): A quantitative measure New molecular entity, NME (Chapter 5 Lagniappe):
of the amount of UV light absorbed by a sample. A new biologically active chemical substance approved for
sale as a drug by the U.S. Food and Drug Administration.
Molecular ion (Section 11.1): The cation produced in the
mass spectrometer by loss of an electron from the parent Newman projection (Section 3.6): A means of indicating
molecule. The mass of the molecular ion corresponds to stereochemical relationships between substituent groups
the molecular weight of the sample. on neighboring carbons. The carboncarbon bond is
viewed end-on, and the carbons are indicated by a circle.
Molecular mechanics (Chapter 4 Lagniappe): A computer-
Bonds radiating from the center of the circle are attached
based method for calculating the minimum-energy confor-
to the front carbon, and bonds radiating from the edge of
mation of a molecule.
the circle are attached to the rear carbon.
Molecular orbital (MO) theory (Section 1.11): A descrip-
Nitration (Section 8.6): The substitution of a nitro group
tion of covalent bond formation as resulting from a math-
onto an aromatic ring.
ematical combination of atomic orbitals (wave functions)
to form molecular orbitals. Nitrile (Section 15.1): A compound containing the CN
functional group.
Molecule (Section 1.4): A neutral collection of atoms held
together by covalent bonds. Nitrogen rule (Section 18.10): A compound with an odd
number of nitrogen atoms has an odd-numbered molecu-
Monomer (Section 7.8): The simple starting unit from
lar weight.
which a polymer is made.
Node (Section 1.2): A surface of zero electron density
Monosaccharide (Section 21.1): A simple sugar.
within an orbital. For example, a p orbital has a nodal
Monoterpene (Chapter 6 Lagniappe): A ten-carbon lipid. plane passing through the center of the nucleus, perpen-
dicular to the axis of the orbital.
Multiplet (Section 12.11): A pattern of peaks in an NMR
spectrum that arises by spinspin splitting of a single Nonbonding electrons (Section 1.4): Valence electrons
absorption because of coupling between neighboring that are not used in forming covalent bonds.
magnetic nuclei.
Noncovalent interaction (Section 2.12): One of a variety
Mutarotation (Section 21.5): The change in optical rota- of nonbonding interactions between molecules, such as
tion observed when a pure anomer of a sugar is dissolved dipoledipole forces, dispersion forces, and hydrogen
in water. Mutarotation is caused by the reversible opening bonds.
and closing of the acetal linkage, which yields an equilib-
Nonessential amino acid (Section 20.5): One of the eleven
rium mixture of anomers.
amino acids that are biosynthesized by humans.
Nonribosomal polypeptide (Section 25.1): A peptidelike
n 1 rule (Section 12.11): A hydrogen with n other compound biosynthesized from an amino acid without
hydrogens on neighboring carbons shows n 1 peaks in direct RNA transcription. The penicillins are examples.*
its 1H NMR spectrum.
Normal alkane (Section 3.2): A straight-chain alkane, as
N-terminal amino acid (Section 19.4): The amino acid opposed to a branched alkane. Normal alkanes are
with a free NH2 group at the end of a protein chain. denoted by the suffix n, as in n-C4H10 (n-butane).
Nuclear magnetic resonance, NMR (Chapter 12 Intro- Ortho, o- (Section 8.1): A naming prefix used for 1,2-disub-
duction): A spectroscopic technique that provides infor- stituted benzenes.
mation about the carbonhydrogen framework of a
Oxidation (Section 7.6): A reaction that causes a decrease
molecule. NMR works by detecting the energy absorp-
in electron ownership by carbon, either by bond forma-
tion accompanying the transition between nuclear spin
tion between carbon and a more electronegative atom
states that occurs when a molecule is placed in a strong
(usually oxygen, nitrogen, or a halogen) or by bond break-
magnetic field and irradiated with radiofrequency
ing between carbon and a less electronegative atom (usu-
waves.
ally hydrogen).
Nucleophile (Section 5.4): A nucleus-lover, or species
Oxidative deamination (Section 20.2): The conversion of
that donates an electron pair to an electrophile in a polar
a primary amine into a ketone by oxidation to an imine
bond-forming reaction. Nucleophiles are also Lewis
followed by hydrolysis.
bases.
Oxidative decarboxylation (Section 22.3): A decarboxy-
Nucleophilic acyl substitution reaction (Section 16.2): A
lation reaction, usually of an -keto acid, that is accom-
reaction in which a nucleophile attacks a carbonyl com-
panied by a change in oxidation state of the carbonyl
pound and substitutes for a leaving group bonded to the
carbon from that of a ketone to that of a carboxylic acid or
carbonyl carbon.
ester.
Nucleophilic addition reaction (Section 14.4): A reaction
Oxirane (Section 7.6): An alternative name for an epoxide.
in which a nucleophile adds to the electrophilic carbonyl
group of a ketone or aldehyde to give an alcohol. Oxymercuration (Section 7.4): A method for double-bond
hydration using aqueous mercuric acetate as the reagent.
Nucleophilic substitution reaction (Section 10.4): A reac-
tion in which one nucleophile replaces another attached
to a saturated carbon atom.
Para, p- (Section 8.1): A naming prefix used for 1,4-disub-
Nucleoside (Section 24.1): A nucleic acid constituent, stituted benzenes.
consisting of a sugar residue bonded to a heterocyclic
Paraffin (Section 3.5): A common name for alkanes.
purine or pyrimidine base.
Parent peak (Section 11.1): The peak in a mass spectrum
Nucleotide (Section 24.1): A nucleic acid constituent,
corresponding to the molecular ion. The mass of the par-
consisting of a sugar residue bonded both to a hetero-
ent peak therefore represents the molecular weight of the
cyclic purine or pyrimidine base and to a phosphoric
compound.
acid. Nucleotides are the monomer units from which
DNA and RNA are constructed. Pauli exclusion principle (Section 1.3): No more than two
electrons can occupy the same orbital, and those two must
Nylon (Section 16.9): A synthetic polyamide step-growth
have spins of opposite sign.
polymer.
Peptide (Chapter 19 Introduction): A short amino acid
polymer in which the individual amino acid residues are
Olefin (Chapter 6 Introduction): An alternative name for linked by amide bonds.
an alkene.
Peptide bond (Section 19.4): An amide bond in a peptide
Optical isomers (Section 9.4): An alternative name for chain.
enantiomers. Optical isomers are isomers that have a
Periplanar (Section 10.11): A conformation in which
mirror-image relationship.
bonds to neighboring atoms have a parallel arrangement.
Optically active (Section 9.3): A substance that rotates the In an eclipsed conformation, the neighboring bonds are
plane of polarization of plane-polarized light. syn periplanar; in a staggered conformation, the bonds
are anti periplanar.
Orbital (Section 1.2): A wave function, which describes
the volume of space around a nucleus in which an elec- Peroxyacid (Section 7.6): A compound with the CO3H
tron is most likely to be found. functional group.
Organic chemistry (Chapter 1 Introduction): The study of Petroleum (Chapter 3 Lagniappe): A complex mixture of
carbon compounds. naturally occurring hydrocarbons derived from the
decomposition of plant and animal matter.
Organophosphate (Section 1.10): A compound that con-
tains a phosphorus atom bonded to four oxygens, with Phenol (Chapter 13 Introduction): A compound with an
one of the oxygens also bonded to carbon. OH group directly bonded to an aromatic ring, ArOH.
Phenoxide ion (Section 13.2): The anion of a phenol, ArO. electrophile and in which bonds are broken when one
fragment leaves with both electrons from the bond.
Phenyl group (Section 8.1): The name for the C6H5 unit
when the benzene ring is considered as a substituent. A Polarity (Section 2.1): The unsymmetrical distribution of
phenyl group is abbreviated as Ph. electrons in a molecule that results when one atom
attracts electrons more strongly than another.
Phosphite (Section 24.7): A compound with the structure
P(OR)3. Polarizability (Section 5.4): The measure of the change in
a molecules electron distribution in response to changing
Phospholipid (Section 23.3): A lipid that contains a phos-
electric interactions with solvents or ionic reagents.
phate residue. For example, glycerophospholipids con-
tain a glycerol backbone linked to two fatty acids and a Polycyclic compound (Section 4.9): A compound that
phosphoric acid. contains more than one ring.
Phosphoramidite (Section 24.7): A compound with the Polycyclic aromatic compound (Section 8.5): A com-
structure R2NP(OR)2. pound with two or more benzene-like aromatic rings
fused together.
Phosphoric acid anhydride (Section 20.1): A substance
that contains PO2PO link, analogous to the CO2CO link in Polyketide (Section 25.1): A natural product biosynthe-
carboxylic acid anhydrides. sized from simple acyl precursors such as acetyl CoA,
propionyl CoA, and methylmalonyl CoA by a large multi-
Physiological pH (Section 15.3): The pH of 7.3 that exists
functional enzyme complex.*
inside cells.
Polymer (Section 7.8): A large molecule made up of repeat-
Pi () bond (Section 1.8): The covalent bond formed by
ing smaller units. For example, polyethylene is a synthetic
sideways overlap of atomic orbitals. For example,
polymer made from repeating ethylene units, and DNA is a
carboncarbon double bonds contain a bond formed by
biopolymer made of repeating deoxyribonucleotide units.
sideways overlap of two p orbitals.
Polymerase chain reaction, PCR (Section 24.8): A method
PITC (Section 19.6): Phenylisothiocyanate, used in the
for amplifying small amounts of DNA to produce larger
Edman degradation of proteins.
amounts.
pKa (Section 2.8): The negative common logarithm of the
Polysaccharide (Section 21.9): A carbohydrate that is made
Ka; used to express acid strength.
of many simple sugars linked together by acetal bonds.
Plane of symmetry (Section 9.2): A plane that bisects a
Polyunsaturated fatty acid (Section 23.1): A fatty acid
molecule such that one half of the molecule is the mirror
containing two or more double bonds.
image of the other half. Molecules containing a plane of
symmetry are achiral. Primary, secondary, tertiary, quaternary (Section 3.3):
Terms used to describe the substitution pattern at a specific
Plane-polarized light (Section 9.3): Ordinary light that
site. A primary site has one organic substituent attached to
has its electromagnetic waves oscillating in a single plane
it, a secondary site has two organic substituents, a tertiary
rather than in random planes. The plane of polarization is
site has three, and a quaternary site has four.
rotated when the light is passed through a solution of a
chiral substance.
Carbo-
Plasticizer (Section 16.6): A small organic molecule added Carbon cation Hydrogen Alcohol Amine
to polymers to act as a lubricant between polymer chains.
Primary RCH3 RCH2 RCH3 RCH2OH RNH2
Polar aprotic solvent (Section 10.6): A polar solvent that
Secondary R2CH2 R2CH R2CH2 R2CHOH R2NH
cant function as a hydrogen ion donor. Polar aprotic
solvents such as dimethyl sulfoxide (DMSO) and Tertiary R3CH R3C R3CH R3COH R3N
dimethylformamide (DMF) are particularly useful in SN2
reactions because of their ability to solvate cations. Quaternary R4C
Polar covalent bond (Section 2.1): A covalent bond in Primary structure (Section 19.8): The amino acid sequence
which the electron distribution between atoms is unsym- in a protein.
metrical.
pro-R configuration (Section 9.13): One of two identical
Polar reaction (Section 5.2): A reaction in which bonds atoms in a compound, whose replacement leads to an
are made when a nucleophile donates two electrons to an R chirality center.
pro-S configuration (Section 9.13): One of two identical R configuration (Section 9.5): The configuration at a chi-
atoms in a compound whose replacement leads to an rality center as specified using the CahnIngoldPrelog
S chirality center. sequence rules.
Prochiral (Section 9.13): A molecule that can be Racemate (Section 9.8): A mixture consisting of equal
converted from achiral to chiral in a single chemical parts () and () enantiomers of a chiral substance.
step.
Radical (Section 5.2): A species that has an odd number of
Prochirality center (Section 9.13): An atom in a com- electrons, such as the chlorine radical, Cl.
pound that can be converted into a chirality center by
Radical reaction (Section 5.2): A reaction in which bonds
changing one of its attached substituents.
are made by donation of one electron from each of two
Propagation step (Section 5.3): The step or series of steps reactants and in which bonds are broken when each frag-
in a radical chain reaction that carry on the chain. The ment leaves with one electron.
propagation steps must yield both product and a reactive
intermediate. Rate constant (Section 10.5): The constant k in a rate
equation.
Prostaglandin (Section 23.7): A lipid derived from arachi-
donic acid. Prostaglandins are present in nearly all body Rate equation (Section 10.5): An equation that expresses
tissues and fluids, where they serve many important hor- the dependence of a reactions rate on the concentration of
monal functions. reactants.
Protecting group (Sections 19.7, 21.9): A group that is Rate-limiting step (Section 10.7): The slowest step in a
introduced to protect a sensitive functional group toward multistep reaction sequence. The rate-limiting step acts as
reaction elsewhere in the molecule. After serving its pro- a kind of bottleneck in multistep reactions.
tective function, the group is removed. Re face (Section 9.13): One of two faces of a planar,
Protein (Chapter 19 Introduction): A large peptide con- sp2-hybridized atom.
taining 50 or more amino acid residues. Proteins serve Reaction energy diagram (Section 5.9): A representation
both as structural materials and as enzymes that control of the course of a reaction, in which free energy is plotted
an organisms chemistry. as a function of reaction progress. Reactants, transition
Protein Data Bank (Chapter 19 Lagniappe): A worldwide states, intermediates, and products are represented, and
online repository of X-ray and NMR structural data for their appropriate energy levels are indicated.
biological macromolecules. To access the Protein Data Reaction intermediate (See Intermediate; Section 5.10)
Bank, go to http://www.rcsb.org/pdb/.
Reaction mechanism (See Mechanism; Section 5.2)
Protic solvent (Section 10.6): A solvent such as water or
alcohol that can act as a proton donor. Rearrangement reaction (Section 5.1): What occurs when
a single reactant undergoes a reorganization of bonds and
Pyramidal inversion (Section 18.2): The rapid inversion atoms to yield an isomeric product.
of configuration of an amine.
Reducing sugar (Section 21.6): A sugar that reduces silver
Pyranose (Section 21.5): The six-membered-ring form of a ion in the Tollens test or cupric ion in the Fehling or Bene-
simple sugar. dict tests.
Reduction (Section 7.5): A reaction that causes an increase
Quartet (Section 12.11): A set of four peaks in an NMR of electron ownership by carbon, either by bond breaking
spectrum, caused by spinspin splitting of a signal by between carbon and a more electronegative atom or by bond
three adjacent nuclear spins. formation between carbon and a less electronegative atom.
Quaternary (see Primary) Reductive amination (Sections 18.6, 19.3): A method for
preparing an amine by reaction of an aldehyde or ketone
Quaternary structure (Section 19.8): The highest level of
with ammonia and a reducing agent.
protein structure, involving a specific aggregation of indi-
vidual proteins into a larger cluster. Refining (Chapter 3 Lagniappe): The process by which
petroleum is converted into gasoline and other useful
Quinone (Section 13.5): A cyclohexa-2,5-diene-1,4-dione.
products.
Regiospecific (Section 6.7): A term describing a reaction
R group (Section 3.3): A generalized abbreviation for an that occurs with a specific regiochemistry to give a single
organic partial structure. product rather than a mixture of products.
Replication (Section 24.3): The process by which double- Sanger dideoxy method (Section 24.6): A biochemical
stranded DNA uncoils and is replicated to produce two method for sequencing DNA strands.
new copies.
Saponification (Section 16.6): An old term for the base-
Replication fork (Section 24.3): The point of unraveling induced hydrolysis of an ester to yield a carboxylic acid salt.
in a DNA chain where replication occurs.
Saturated (Section 3.2): A molecule that has only single
Residue (Section 19.4): An amino acid in a protein chain. bonds and thus cant undergo addition reactions. Alkanes
are saturated, but alkenes are unsaturated.
Resolution (Section 9.8): The process by which a racemic
mixture is separated into its two pure enantiomers. Sawhorse structure (Section 3.6): A manner of represent-
ing stereochemistry that uses a stick drawing and gives a
Resonance form (Section 2.4): An individual Lewis struc- perspective view of the conformation around a single bond.
ture of a resonance hybrid.
Schiff base (Section 22.2): An alternative name for an
Resonance effect (Section 8.8): The donation or with- imine, R2CUNR, used primarily in biochemistry.
drawal of electrons through orbital overlap with neigh-
boring bonds. For example, an oxygen or nitrogen Second-order reaction (Section 10.5): A reaction whose
substituent donates electrons to an aromatic ring by over- rate-limiting step is bimolecular and whose kinetics
lap of the O or N orbital with the aromatic ring p orbitals. are therefore dependent on the concentration of two
reactants.
Resonance hybrid (Section 2.4): A molecule, such as ben-
zene, that cant be represented adequately by a single Secondary (see Primary)
Kekul structure but must instead be considered as an Secondary metabolite (Chapter 25 Introduction): A small
average of two or more resonance structures. The reso- naturally occurring molecule that is not essential to the
nance structures themselves differ only in the positions of growth and development of the producing organism and
their electrons, not their nuclei. is not classified by structure.*
Restriction endonuclease (Section 24.6): An enzyme that Secondary structure (Section 19.8): The level of protein
is able to cleave a DNA molecule at points in the chain substructure that involves organization of chain sections
where a specific base sequence occurs. into ordered arrangements such as -pleated sheets or
Retrosynthetic (Section 8.10): Planning an organic synthe- -helices.
sis by working backward from product to starting material. Semiconservative replication (Section 24.3): The process
Ribonucleic acid, RNA (Section 24.1): The biopolymer by which DNA molecules are made containing one strand
found in cells that serves to transcribe the genetic infor- of old DNA and one strand of new DNA.
mation found in DNA and uses that information to direct Sense strand (Section 24.4): The coding strand of double-
the synthesis of proteins. helical DNA that contains the gene.
Ribosomal RNA (Section 24.4): A kind of RNA used in the Sequence rules (Sections 6.4, 9.5): A series of rules for
physical makeup of ribosomes. assigning relative priorities to substituent groups on a
Ring-flip (Section 4.6): A molecular motion that converts double-bond carbon atom or on a chirality center.
one chair conformation of cyclohexane into another chair Sesquiterpene (Chapter 6 Lagniappe): A 15-carbon lipid.
conformation. The effect of a ring-flip is to convert an
axial substituent into an equatorial substituent. Sharpless epoxidation (Chapter 14 Lagniappe): A method
for enantioselective synthesis of a chiral epoxide by
RNA (See Ribonucleic acid; Section 24.1) treatment of an allylic alcohol with tert-butyl hydro-
peroxide, (CH3)3CXOOH, in the presence of titanium
tetraisopropoxide and diethyl tartrate.
S configuration (Section 9.5): The configuration at a chi-
Shell (electron) (Section 1.2): A group of an atoms elec-
rality center as specified using the CahnIngoldPrelog
trons with the same principal quantum number.
sequence rules.
Shielding (Section 12.2): An effect observed in NMR that
Saccharide (Section 21.1): A sugar.
causes a nucleus to absorb toward the right (upfield) side
Salt bridge (Section 19.8): The ionic attraction between of the chart. Shielding is caused by donation of electron
two oppositely charged groups in a protein chain. density to the nucleus.
Si face (Section 9.13): One of two faces of a planar, Staggered conformation (Section 3.6): The three-
sp2-hybridized atom. dimensional arrangement of atoms around a carboncarbon
single bond in which the bonds on one carbon bisect the
Side chain (Section 19.1): The substituent attached to the
bond angles on the second carbon as viewed end-on.
carbon of an amino acid.
Step-growth polymer (Section 16.9): A polymer in which
Sigma () bond (Section 1.5): A covalent bond formed by
each bond is formed independently of the others. Poly-
head-on overlap of atomic orbitals.
esters and polyamides (nylons) are examples.
Silyl ether (Section 21.9): A substance with the structure
Stereochemistry (Section 3.6; Chapters 3, 4, and 9):
R3SiXOXR. The silyl ether acts as a protecting group for
The branch of chemistry concerned with the three-
alcohols.
dimensional arrangement of atoms in molecules.
Simple sugar (Section 21.1): A carbohydrate that cannot
Stereoisomers (Section 4.2): Isomers that have their
be broken down into smaller sugars by hydrolysis.
atoms connected in the same order but have different
Skeletal structure (Section 1.12): A shorthand way of three-dimensional arrangements. The term stereoisomer
writing structures in which carbon atoms are assumed to includes both enantiomers and diastereomers.
be at each intersection of two lines (bonds) and at the end
of each line. Steric strain (Sections 3.7, 4.7): The strain imposed on a
molecule when two groups are too close together and try
SN1 reaction (Section 10.7): A unimolecular nucleophilic to occupy the same space. Steric strain is responsible both
substitution reaction. for the greater stability of trans versus cis alkenes and for
SN2 reaction (Section 10.5): A bimolecular nucleophilic the greater stability of equatorially substituted versus axi-
substitution reaction. ally substituted cyclohexanes.
Solid-phase synthesis (Section 19.7): A technique of syn- Steroid (Section 23.9): A lipid whose structure is based on a
thesis whereby the starting material is covalently bound to tetracyclic carbon skeleton with three 6-membered and one
a solid polymer bead and reactions are carried out on the 5-membered ring. Steroids occur in both plants and animals
bound substrate. After the desired transformations have and have a variety of important hormonal functions.
been effected, the product is cleaved from the polymer. Stork enamine reaction (Section 17.11): The conjugate
Solvation (Section 10.6): The clustering of solvent mole- addition of an enamine to an ,-unsaturated carbonyl com-
cules around a solute particle to stabilize it. pound, followed by hydrolysis to yield a 1,5-dicarbonyl
product.
sp Hybrid orbital (Section 1.9): A hybrid orbital derived
from the combination of an s and a p atomic orbital. The STR loci (Chapter 24 Lagniappe): Short, tandem repeat
two sp orbitals that result from hybridization are oriented sequences of noncoding DNA that are unique to every
at an angle of 180 to each other. individual and allow DNA fingerprinting.
sp2 Hybrid orbital (Section 1.8): A hybrid orbital derived Straight-chain alkane (Section 3.2): An alkane whose
by combination of an s atomic orbital with two p atomic carbon atoms are connected without branching.
orbitals. The three sp2 hybrid orbitals that result lie in a Substitution reaction (Section 5.1): What occurs when
plane at angles of 120 to each other. two reactants exchange parts to give two new products.
sp3 Hybrid orbital (Section 1.6): A hybrid orbital derived SN1 and SN2 reactions are examples.
by combination of an s atomic orbital with three p atomic Sulfide (Chapter 13 Introduction): A compound that has two
orbitals. The four sp3 hybrid orbitals that result are organic substituents bonded to the same sulfur atom, RSR.
directed toward the corners of a regular tetrahedron at
angles of 109 to each other. Sulfonation (Section 8.6): The substitution of a sulfonic
acid group onto an aromatic ring.
Specific rotation, []D (Section 9.3): The optical rotation
of a chiral compound under standard conditions. Sulfone (Section 13.10): A compound of the general struc-
ture RSO2R.
Sphingomyelin (Section 23.3): A phospholipid that has
sphingosine as its backbone. Sulfoxide (Section 13.10): A compound of the general
structure RSOR.
Spinspin splitting (Section 12.11): The splitting of an
NMR signal into a multiplet because of an interaction Symmetry plane (Section 9.2): A plane that bisects a mol-
between nearby magnetic nuclei whose spins are cou- ecule such that one half of the molecule is the mirror
pled. The magnitude of spinspin splitting is given by the image of the other half. Molecules containing a plane of
coupling constant, J. symmetry are achiral.
Syn periplanar (Section 10.11): Describing a stereochem- Transfer RNA (Section 24.4): A kind of RNA that trans-
ical relationship in which two bonds on adjacent carbons ports amino acids to the ribosomes, where they are joined
lie in the same plane and are eclipsed. together to make proteins.
Syn stereochemistry (Section 7.4): The opposite of anti. A Transition state (Section 5.9): An activated complex
syn addition reaction is one in which the two ends of the between reactants, representing the highest energy point
double bond react from the same side. A syn elimination on a reaction curve. Transition states are unstable com-
is one in which the two groups leave from the same side of plexes that cant be isolated.
the molecule.
Translation (Section 24.5): The process by which the
genetic information transcribed from DNA onto mRNA is
read by tRNA and used to direct protein synthesis.
Tautomer (Section 17.1): Isomers that are rapidly
interconverted. Tree diagram (Section 12.12): A diagram used in NMR to
sort out the complicated splitting patterns that can arise
Template strand (Section 24.4): The strand of double-
from multiple couplings.
helical DNA that does not contain the gene.
Triacylglycerol (Section 23.1): A lipid, such as that found
Terpenoid (Chapter 6 Lagniappe, Section 23.8): A lipid
in animal fat and vegetable oil, that is a triester of glycerol
that is formally derived by head-to-tail polymerization of
with long-chain fatty acids.
isoprene units.
Tricarboxylic acid cycle (Section 22.4): An alternative
Tertiary (see Primary)
name for the citric acid cycle by which acetyl CoA is
Tertiary structure (Section 19.8): The level of protein degraded to CO2.
structure that involves the manner in which the entire
Triplet (Section 12.11): A symmetrical three-line splitting
protein chain is folded into a specific three-dimensional
pattern observed in the 1H NMR spectrum when a proton
arrangement.
has two equivalent neighbor protons.
Thioester (Chapter 16 Introduction): A compound with
Turnover number (Section 19.9): The number of substrate
the RCOSR functional group.
molecules acted on by an enzyme per unit time.
Thiol (Chapter 13 Introduction): A compound containing
Twist-boat conformation (Section 4.5): A conformation of
the SH functional group.
cyclohexane that is somewhat more stable than a pure
TMS (Section 12.3): Tetramethylsilane, used as an NMR boat conformation.
calibration standard.
TOF (Section 11.4): A time-of-flight mass spectrometer.
Ultraviolet (UV) spectroscopy (Section 11.9): An optical
Tollens reagent (Section 21.6): A solution of Ag2O in spectroscopy employing ultraviolet irradiation. UV spec-
aqueous ammonia; used to oxidize aldehydes to car- troscopy provides structural information about the extent
boxylic acids. of electron conjugation in organic molecules.
Torsional strain (Section 3.6): The strain in a molecule Unimolecular reaction (Section 10.7): A reaction that
caused by electron repulsion between eclipsed bonds. occurs by spontaneous transformation of the starting
Torsional strain is also called eclipsing strain. material without the intervention of other reactants. For
example, the dissociation of a tertiary alkyl halide in the
Tosylate (Section 10.4): A p-toluenesulfonate ester.
SN1 reaction is a unimolecular process.
Transamination (Section 20.2): The exchange of an amino
Unsaturated (Section 6.1): A molecule that has one or
group and a keto group between reactants.
more multiple bonds.
Transimination (Section 20.2): The exchange of an amino
Upfield (Section 12.3): The right-hand portion of the NMR
group and an imine group between reactants.
chart.
Transcription (Section 24.4): The process by which the
Urea cycle (Section 20.3): The metabolic pathway for con-
genetic information encoded in DNA is read and used to
verting ammonia into urea.
synthesize RNA in the nucleus of the cell. A small portion
of double-stranded DNA uncoils, and complementary Uronic acid (Section 21.6): The monocarboxylic acid
ribonucleotides line up in the correct sequence for RNA formed by oxidizing the CH2OH end of a sugar without
synthesis. affecting the CHO end.
Valence bond theory (Section 1.5): A bonding theory that tion is inversely proportional to frequency and inversely
describes a covalent bond as resulting from the overlap of proportional to energy.
two atomic orbitals.
Wavenumber, (Section 11.6): The reciprocal of the
Valence shell (Section 1.4): The outermost electron shell wavelength in centimeters.
of an atom.
Wax (Section 23.1): A mixture of esters of long-chain car-
Van der Waals forces (Section 2.12): Intermolecular boxylic acids with long-chain alcohols.
forces that are responsible for holding molecules together
Williamson ether synthesis (Section 13.8): A method for
in the liquid and solid states.
synthesizing ethers by SN2 reaction of an alkyl halide
Vegetable oil (Section 23.1): A liquid triacylglycerol with an alkoxide ion.
derived from a plant source.
Wittig reaction (Section 14.9): The reaction of a phospho-
Vinyl group (Section 6.2): An H2CUCHX substituent. rus ylide with an aldehyde or ketone to yield an alkene.
Vinyl monomer (Section 7.8): A substituted alkene
monomer used to make chain-growth polymers.
X-ray crystallography (Chapter 17 Lagniappe): A tech-
Vinylic (Section 8.7): A term that refers to a substituent at nique using X rays to determine the structure of
a double-bond carbon atom. For example, chloroethylene molecules.
is a vinylic chloride.
Virion (Chapter 22 Lagniappe): A viral particle.
Ylide (Sections 14.9, 22.3): A neutral species with adja-
Vitamin (Section 19.9): A small organic molecule that cent and charges, such as the phosphoranes used in
must be obtained in the diet and is required in trace Wittig reactions.
amounts for proper growth and function.
Vulcanization (Chapter 7 Lagniappe): A technique for
Z geometry (Section 6.4): A term used to describe the
cross-linking and hardening a diene polymer by heating
stereochemistry of a carboncarbon double bond. The two
with a few percent by weight of sulfur.
groups on each carbon are assigned priorities according to
the CahnIngoldPrelog sequence rules, and the two car-
bons are compared. If the high-priority groups on each
Walden inversion (Section 10.4): The inversion of configu-
carbon are on the same side of the double bond, the bond
ration at a chirality center that accompanies an SN2 reaction.
has Z geometry.
Wave equation (Section 1.2): A mathematical expression
Zaitsevs rule (Section 10.10): A rule stating that E2 elim-
that defines the behavior of an electron in an atom.
ination reactions normally yield the more highly substi-
Wave function (Section 1.2): A solution to the wave equa- tuted alkene as major product.
tion for defining the behavior of an electron in an atom.
Zwitterion (Section 19.1): A neutral dipolar molecule
The square of the wave function defines the shape of an
in which the positive and negative charges are not
orbital.
adjacent. For example, amino acids exist as zwitterions,
Wavelength, (Section 11.5): The length of a wave from H3NXCHRXCO2.
peak to peak. The wavelength of electromagnetic radia-
Appendix D
Answers to In-Text Problems
The following answers are meant only as a quick 1.9 H H H H H H

check while you study. Full answers for all prob- H C C C C C C H
lems are provided in the accompanying Study
Guide and Solutions Manual. H H H H H H
1.10 The CH3 carbon is sp3; the double-bond carbons

CHAPTER 1
are sp2; the CCC and CCH bond angles are
1.1 (a) 1s2 2s2 2p4 (b) 1s2 2s2 2p6 3s2 3p3
approximately 120; other bond angles are near
(c) 1s2 2s2 2p6 3s2 3p4 109.
1.2 (a) 2 (b) 2 ( 7) (c) 6 H H

H C H
1.3 H
C C
C
Cl Cl H H
Cl
1.11 All carbons are sp2, and all bond angles are near
1.4 H HH 120.
C C H H
HH H C C H
H C C
H H
1.5 (a) CH2Cl2 (b) CH3SH (c) CH3NH2
1.6 (a) Cl (b) H 1.12 All carbons except CH3 are sp2.
Cl H
H C Cl H C Cl S H S H H O
Cl
Cl H C C H
C C O
(c) H C C
H H O
C
H C N H H C N H
H H H C
H H O CH3
1.7 C2H7 has too many hydrogens for a compound 1.13 The CH3 carbon is sp3, the triple-bond carbons are
with 2 carbons. sp; the CCC and HCC bond angles are
approximately 180.
1.8 H H
H
H C H All bond angles are H
C C near 109. H C C C
H H H H H
A-31
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 CHAPTER 2
2.1 (a) H (b) Br (c) Cl (d) C
(a) H H H H (b) N
H3C CH3 2.2
C C H 3C
H O H
(a) + (b) + (c) +
H3C Cl H3C NH2 H2N H
sp3tetrahedral sp3tetrahedral
O (d) H3C SH (e) + (f) +
(c) (d) H3C MgBr H3C F
P H3C CH2CH2CHCOH Carbon and sulfur
H H
S
H have identical
NH2
electronegativities.
sp3tetrahedral sp3tetrahedral
2.3 H3CXOH H3CXMgBr H3CXLi

1.15 (a) OH H3CXF H3CXK
0H 1H
1H
HO NHCH3 2.4 The nitrogen is electron-rich, and the carbon is
0H 2H electron-poor.
0H
1H
HO
1H NH
2
AdrenalineC9H13NO3
C
H H
H +
(b) 3H O
2H
1H 0H
2H 2.5 The two CO dipoles cancel because of the sym-
2H metry of the molecule:
0H
1H
2H
0H H H
1H
2H
HO C OH
1H 2H
HO C
0H
H H
EstroneC18H22O2
1.16 There are numerous possibilities, such as: 2.6 (a) H H (b) H
H C C H
(a) C5H12 CH3CH2CH2CH2CH3 CH3 CH3 C
Cl Cl
CH3CH2CHCH3 CH3CCH3 No dipole Cl
moment
CH3
(b) C2H7N CH3CH2NH2 CH3NHCH3
(c) Cl (d)
H C C Cl
H Cl
(c) C3H6O O H2C CHCH2OH H2C CHOCH3 C
H Cl
CH3CH H
(d) C4H9Cl CH3CH2CH2CH2Cl Cl CH3 2.7 (a) For carbon: FC 4 8/2 0 0; for the
middle nitrogen: FC 5 8/2 0 1;
CH3CH2CHCH3 CH3CHCH2Cl for the end nitrogen: FC 5 4/2 4 1
(b) For nitrogen: FC 5 8/2 0 1;
1.17 O for oxygen: FC 6 2/2 6 1
C (c) For nitrogen: FC 5 8/2 0 1;
OH for the end carbon: FC 4 6/2 2 1
H2N
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 0 2.16
H O (a) H
H C O P O +
CH3CH2OH + H Cl CH3CH2OH + Cl
H O -1 H
+
HN(CH3)2 + H Cl HN(CH3)2 + Cl
2.9
+
(a) P(CH3)3 + H Cl H P(CH3)3 + Cl
O O
P P (b)
CH3O O CH3O O
O O +CH
HO + 3 HO CH3

O
HO + B(CH3)3 HO B(CH3)3
P
CH3O O
O

HO + MgBr2 HO MgBr2
(b) O
O O
N+ N+ N+ 2.17
O O
O O O O
(a) More basic (red) Most acidic (blue)
H
(c) +
H2C CH CH2+ H2C CH CH2
N
N H Imidazole
(d) O
O H
C C H
O O (b) H H
H +
N N
A H N H N H

O O H H
H H
C C
O O
H
H
N +
N H
2.10 H NO3 + NH3 NO3 + NH4+ H

H
Acid Base Conjugate Conjugate H H

base acid
N B N
N H N
2.11 Phenylalanine is stronger. H H
2.12 Water is a stronger acid. H H
2.13 Neither reaction will take place. H

2.14 Reaction will take place. N
N
2.15 Ka 4.9 1010
H
H
2.18 Vitamin C is water-soluble (hydrophilic); vitamin A 3.7 CH3CH2CH2CH2CH2 CH3CH2CH2CH

is fat-soluble (hydrophilic).
CH3
CHAPTER 3 CH3CH2CH CH3CH2CHCH2

3.1 (a) Sulfide, carboxylic acid, amine CH2CH3 CH3
(b) Aromatic ring, carboxylic acid CH3
(c) Ether, alcohol, aromatic ring, amide, CC CH3CHCH2CH2 CH3CH2C
bond
CH3 CH3
3.2 (a) CH3OH (b) CH3 (c) O
CH3 CH3
CH3COH
CH3CHCH CH3CCH2
CH3 CH3
(d) CH3NH2 (e) O (f)
CH3CCH2NH2
3.8 (a) p (b) p t p
CH3 CH3CHCH3
3.3 Ester CH3CHCH2CH2CH3 CH3CH2CHCH2CH3
O p t s s p p s t s p
H3C C CH3 (c) p p
N O CH3 CH3
C8H13NO2
CH3CHCH2 C CH
Amine Double bond p t s q p 3
CH3
p
3.4 CH3
CH3CH2CH2CH2CH2CH3 CH3CHCH2CH2CH3 3.9 Primary carbons have primary hydrogens, sec-

ondary carbons have secondary hydrogens, and
CH3 CH3 tertiary carbons have tertiary hydrogens.
CH3CH2CHCH2CH3 CH3CCH2CH3 3.10 (a) CH3 (b) CH3CHCH3
CH3 CH3CHCHCH3 CH3CH2CHCH2CH3
CH3 CH3
CH3CHCHCH3 (c) CH3
CH3 CH3CCH2CH3
CH3
3.5 Part (a) has nine possible answers.
(a) O O O CH3 3.11 (a) Pentane, 2-methylbutane, 2,2-dimethylpropane

CH3CH2CH2COCH3 CH3CH2COCH2CH3 CH3COCHCH3 (b) 3,4-Dimethylhexane
(b) CH3CH2SSCH2CH3 CH3SSCH2CH2CH3 CH3SSCHCH3 (c) 2,4-Dimethylpentane
CH3 (d) 2,2,5-Trimethylheptane
3.12 (a) CH3
3.6 (a) Two (b) Four (c) Four
CH3CH2CH2CH2CH2CHCHCH2CH3
CH3
(b) CH3 3.17 CH3

CH3CH2CH2C CHCH2CH3 H3C H
CH3 CH2CH3 H CH3

CH3
(c) CH2CH2CH3
CH3CH2CH2CH2CHCH2C(CH3)3 3.18 3.8 kJ/mol

CH3
(d) CH3 CH3
H CH3
CH3CHCH2CCH3 3.8 kJ/mol Total: 11.4 kJ/mol
H CH3
CH3 CH3
3.8 kJ/mol
3.13 Pentyl, 1-methylbutyl, 1-ethylpropyl, 2-methyl-
butyl, 3-methylbutyl, 1,1-dimethylpropyl,
1,2-dimethylpropyl, 2,2-dimethylpropyl CHAPTER 4
3.14 4.1 (a) 1,4-Dimethylcyclohexane
3,3,4,5-Tetramethylheptane (b) 1-Methyl-3-propylcyclopentane

(c) 3-Cyclobutylpentane
(d) 1-Bromo-4-ethylcyclodecane
3.15
(e) 1-Isopropyl-2-methylcyclohexane
(f) 4-Bromo-1-tert-butyl-2-methylcycloheptane
4.2 (a) CH3 (b)
Energy
14 kJ/mol
CH3
0 60 120 180 240 300 360

(c) Cl (d) CH3
Angle of rotation
Cl
H3C H3C H3C H3 C H3C H3 C H3 C
H H H H
H H H H H H
HH HHH HHH HHH HHH HHH HHH H H Br Br

H H H
4.3 3-Ethyl-1,1-dimethylcyclopentane
3.16
4.4 (a) trans-1-Chloro-4-methylcyclohexane
(a) CH3 (b) CH3
4.0 kJ/mol H
H H 6.0 kJ/mol (b) cis-1-Ethyl-3-methylcycloheptane
4.5 (a) H3C H (b) H
H CH3 HH H CH3
H CH3
(c), (d) Br CH3

H
H
Energy
16 kJ/mol
(c) CH2CH3
H
0 60 120 180 240 300 360 C(CH3)3

H
4.6 The two hydroxyl groups are cis. The two side 5.3 H
chains are trans. CO2H
O
4.7 (a) cis-1,2-Dimethylcyclopentane
O
(b) cis-1-Bromo-3-methylcyclobutane
4.8 Six interactions; 21% of strain H
4.9 The cis isomer is less stable because the methyl H

H
groups eclipse each other.
O CO2H
4.10 Ten eclipsing interactions; 40 kJ/mol; 35% is
relieved. O
4.11 Conformation (a) is more stable because the H

H
methyl groups are farther apart.
4.12 OH 5.4 (a) Carbon is electrophilic.
a e
OH (b) Sulfur is nucleophilic.
(c) Nitrogens are nucleophilic.
4.13 CH3 (d) Oxygen is nucleophilic; carbon is electrophilic.

a e 5.5 F Electrophilic;
CH3
H3C vacant p orbital
e B
a F F
CH3
5.6 Cyclohexanol (hydroxycyclohexane)

4.14 Before ring-flip, red and blue are equatorial and
5.7 CH3
green is axial. After ring-flip, red and blue are
axial and green is equatorial. C+
H3C CH3
4.15 4.2 kJ/mol
4.16 Cyano group points straight up. 5.8 (a) Cl Cl + NH3 ClNH3+ + Cl
4.17 (a) 2.0 kJ/mol (b) 11.4 kJ/mol

(b) CH3O + H3C Br CH3OCH3 + Br
(c) 2.0 kJ/mol (d) 8.0 kJ/mol

4.18 a CH3
(c) O O
e + Cl
C C
CH3 H3C CH3 H3C OCH3
Less stable chair form Cl
a
Cl
5.9 H
4.19 trans-Decalin is more stable because it has no O

H
1,3-diaxial interactions.
H CO2 H2O+ CO2
C CH2CO2
CHAPTER 5 C C
C O C
5.1 (a) Substitution (b) Elimination (c) Addition O C 2
2 CH2 CO2 H H
5.2 1-Chloro-2-methylpentane, 2-chloro-2-methyl- H
pentane, 3-chloro-2-methylpentane, 2-chloro-
4-methylpentane, 1-chloro-4-methylpentane H +O
H
5.10 Negative G is more favored. 6.6 (a) 2,5-Dimethylhex-3-yne

5.11 Larger Keq is more exergonic. (b) 3,3-Dimethylbut-1-yne
5.12 Lower G is faster. (c) 3,3-Dimethyloct-4-yne
5.13 (d) 2,5,5-Trimethylhept-3-yne
(e) 6-Isopropylcyclodecyne
Intermediate
6.7
G
Energy
6.8 Compounds (c), (e), and (f) have cistrans isomers.

6.9 (a) cis-4,5-Dimethylhex-2-ene
Reactant
(b) trans-6-Methylhept-3-ene
G
6.10 (a) Br (b) Br (c) CH2CH3
Product
(d) OH (e) CH2OH (f) CHO
Reaction progress
6.11 (a) Cl, OH, CH3, H
CHAPTER 6 (b) CH2OH, CHCH2, CH2CH3, CH3

6.1 (a) 2 (b) 3 (c) 3 (d) 5 (e) 5 (f) 3 (c) CO2H, CH2OH, CN, CH2NH2
6.2 (a) 1 (b) 2 (c) 2 (d) CH2OCH3, CN, CCH, CH2CH3
6.3 C16H13ClN2O 6.12 (a) Z (b) E (c) Z (d) E
6.4 (a) 3,4,4-Trimethylpent-1-ene 6.13 CO2CH3
(b) 3-Methylhex-3-ene
Z
(c) 4,7-Dimethylocta-2,5-diene CH2OH
(d) 6-Ethyl-7-methylnon-4-ene
(e) 1,2-Dimethylcyclohexene 6.14 (a) 2-Methylpropene is more stable than but-1-ene.
(f) 4,4-Dimethylcycloheptene (b) trans-Hex-2-ene is more stable than

cis-hex-2-ene.
(g) 3-Isopropylcyclopentene
(c) 1-Methylcyclohexene is more stable than
6.5 (a) CH3 3-methylcyclohexene.
H2C CHCH2CH2C CH2 6.15 (a) Chlorocyclohexane
(b) CH2CH3 (b) 2-Bromo-2-methylpentane
CH3CH2CH2CH CC(CH3)3 (c) 2-Hydroxy-4-methylpentane
(c) CH3 CH3 (d) 1-Bromo-1-methylcyclohexane
CH3CH CHCH CHC C CH2 6.16 (a) Cyclopentene
CH3 (b) 1-Ethylcyclohexene or ethylidenecyclohexane
(d) CH3 CH3 (c) Hex-3-ene (d) Cyclohexylethylene
CH3CH CHCH3 6.17 (a) CH3 CH3 (b) +
C C CH2CH3
CH3CH2CCH2CHCH3
CH3CH CHCH3 +
CH3 CH3
6.18 In the conformation shown, only the methyl- 7.9 (a) 2-Methylpentane
group CH that is parallel to the carbocation
(b) 1,1-Dimethylcyclopentane
p orbital can show hyperconjugation.
7.10 O
6.19 The second step is exergonic; the transition state
resembles the carbocation. C C cis-2,3-Epoxybutane
H H
H3C CH3
6.20 H
H
C
CH2 H Br 7.11 (a) 1-Methylcyclohexene
(b) 2-Methylpent-2-ene (c) Buta-1,3-diene
7.12 (a) H2CUCHOCH3 (b) ClCHUCHCl

H Br H H 7.13 H
H
+ CH2CH2 + CH CH2
+
CH2CH3 + CH CH2
7.14 1,2-Addition: 4-chloropent-2-ene,

Br 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
CHAPTER 7
7.1 2-Methylbut-2-ene and 2-methylbut-1-ene 7.16 (a) 1,1,2,2-Tetrachloropentane
7.2 Five (b) 1-Bromo-1-cyclopentylethylene
7.3 trans-1,2-Dichloro-1,2-dimethylcyclohexane (c) 2-Bromohept-2-ene and 3-bromohept-2-ene
7.4 Cl CH3
CH3 Cl CHAPTER 8
8.1 (a) Meta (b) Para (c) Ortho
and
8.2 (a) m-Bromochlorobenzene
CH3 CH3
H H
(b) (3-Methylbutyl)benzene
(c) p-Bromoaniline
7.5 Markovnikov orientation
(d) 2,5-Dichlorotoluene
7.6 (a) Oxymercuration: 2-methylpentan-2-ol;
hydroboration: 2-methylpentan-3-ol (e) 1-Ethyl-2,4-dinitrobenzene
(b) Oxymercuration: 1-ethylcyclohexanol; (f) 1,2,3,5-Tetramethylbenzene
hydroboration: 1-cyclohexylethanol
8.3 (a) Cl (b) CH3
7.7 (a) From 3-methylbut-1-ene by hydroboration
(b) From 2-methylbut-2-ene by hydroboration or
Br Br
from 3-methylbut-1-ene by oxymercuration
(c) From methylenecyclohexane by hydroboration (c) H3C NH2 (d) H3C Cl
7.8 CH3 CH3
H H
H3C H
and
H H3C CH3
OH OH
H H
8.4 Pyridine has an aromatic sextet of electrons. 8.17

Ortho intermediate:
H H
+ H H
NO2 NO2
N H Pyridine
+
H H Cl Cl
H H
8.5 Cyclodecapentaene is not flat because of steric NO2 NO2
interactions. +
8.6 The thiazolium ring has six electrons. Cl Cl
+
Para intermediate:
H
+
+ H H
R N S
NO2 NO2
R R +
Cl Cl
H H
8.7
NO2 NO2
+
Cl Cl
+
8.8 The three nitrogens in double bonds each con-
tribute one; the remaining nitrogen contributes Meta intermediate:
two.
+ H H
Cl NO2 Cl NO2
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.
H
8.12 No rearrangement: (a), (b), (e) Cl NO2
8.13 tert-Butylbenzene
+
8.14 (a) (CH3)2CHCOCl (b) PhCOCl
8.15 (a) Phenol Toluene Benzene Nitrobenzene 8.18 (a) m-Chlorobenzonitrile
(b) Phenol Benzene Chlorobenzene (b) o- and p-Bromochlorobenzene
Benzoic acid
8.19 (a) m-Nitrobenzoic acid
(c) Aniline Benzene Bromobenzene
Benzaldehyde (b) p-tert-Butylbenzoic acid
8.16 (a) Methyl m-nitrobenzoate 8.20 1. PhCOCl, AlCl3; 2. H2/Pd
(b) m-Bromonitrobenzene 8.21 (a) 1. HNO3, H2SO4; 2. Cl2, FeCl3
(c) o- and p-Chlorophenol (b) 1. CH3COCl, AlCl3; 2. Cl2, FeCl3; 3. H2, Pd
(d) o- and p-Bromoaniline (c) 1. CH3CH2COCl, AlCl3; 2. H2, Pd; 3. Cl2, FeCl3
(d) 1. CH3Cl, AlCl3; 2. SO3, H2SO4; 3. Br2, FeBr3
8.22 (a) The FriedelCrafts reaction in step 1 will not 9.11 S

take place on a cyano-substituted benzene.
9.12 (a) R,R (b) S,R (c) R,S (d) S,S
(b) The FriedelCrafts reaction will occur with a
Compounds (a) and (d) are enantiomers and are
carbocation rearrangement, and the wrong
diastereomeric with (b) and (c).
isomer will be obtained on chlorination.
9.13 S,S
CHAPTER 9 9.14 Five chirality centers; 32 stereoisomers
9.1 Chiral: screw, beanstalk, shoe
9.15 Compounds (a) and (d) are meso.
9.2 (a) CH2CH2CH3 (b) H CH3
* 9.16 Compounds (a) and (c) have meso forms.
* 9.17
N H3C CH3
H
HO *
* Meso
H H
OH
(c) CH3O
9.18 The product retains its S stereochemistry.
9.19 Two diastereomeric salts are formed: (R)-lactic
* * acid plus (S)-1-phenylethylamine and (S)-lactic
* N CH3 acid plus (S)-1-phenylethylamine.
H
9.20 (a) Constitutional isomers (b) Diastereomers
9.21 An optically inactive, non-5050 mixture of two
9.3 CO2H CO2H racemic pairs: (2R,4R) (2S,4S) and (2R,4S)
(2S,4R)
C and C
H CH3 H3C H
H 2N NH2
9.22 Non-5050 mixture of two racemic pairs:
(1S,3R) (1R,3S) and (1S,3S) (1R,3R)
9.23 (a) pro-S H H pro-R
9.4 (a) HO H H (b) F F F F
CHO
HO C * C H * C C HO
C * C O C O H
HO H
H H H OH F Cl
(b) pro-R H H pro-S

9.5 Levorotatory
CO2
9.6 16.1 H3C
9.7 (a) OH, CH2CH2OH, CH2CH3, H H3N H

+
(b) OH, CO2CH3, CO2H, CH2OH
9.24 (a) Re face (b) Re face
(c) NH2, CN, CH2NHCH3, CH2NH2
(d) SSCH3, SH, CH2SCH3, CH3 O H
H3C C C CH2OH
9.8 (a) S (b) R (c) S CH2OH H 3C C
H
9.9 (a) S (b) S (c) R
Si face Si face
9.10 H
HO
C
CH2CH2CH3 9.25 (S)-Lactate
H3C
9.26 The OH adds to the Re face of C2, and H adds to 10.8 CH3 SCH3
the Re face of C3. The overall addition has anti
(S)-2-Bromo-4-methylpentane (R) CH3CHCH2CHCH3
stereochemistry.
10.9 (a) 1-Iodobutane (b) Butan-1-ol

CHAPTER 10
10.1 (a) 1-Iodobutane (b) 1-Chloro-3-methylbutane (c) Butylammonium bromide
(c) 1,5-Dibromo-2,2-dimethylpentane 10.10 (a) (CH3)2N (b) (CH3)3N (c) H2S
(d) 1,3-Dichloro-3-methylbutane 10.11 CH3OTos CH3Cl (CH3)2CHCl CH3NH2
(e) 1-Chloro-3-ethyl-4-iodopentane 10.12 Similar rate to protic solvents because the transi-
tion state is not stabilized
(f) 2-Bromo-5-chlorohexane
10.13 Racemic 1-ethyl-1-methylhexyl acetate
10.2 (a) CH3CH2CH2C(CH3)2CH(Cl)CH3
10.14 Racemic 2-phenylbutan-2-ol
(b) CH3CH2CH2C(Cl)2CH(CH3)2
10.15 H2CUCHCH(Br)CH3
(c) CH3CH2C(Br)(CH2CH3)2
(CH3)3CBr CH3CH(Br)CH3 H2CUCHBr
(d) Br 10.16 The same allylic carbocation intermediate is
formed in both reactions.
Br
10.17 (a) SN1 (b) SN2
10.18 +
OPP PPi
(e)
CH3CHCH2CH3
CH3CH2CH2CH2CH2CHCH2CHCH3
Linalyl diphosphate
Cl
(f) Br
Br
+
H Base
Limonene
10.3 (a) 2-Methylpropan-2-ol HCl
(b) 4-Methylpentan-2-ol PBr3 10.19 (a) Major: 2-methylpent-2-ene;
minor: 4-methylpent-2-ene
(c) 5-Methylpentan-1-ol PBr3
(b) Major: 2,3,5-trimethylhex-2-ene;
(d) 2,4-Dimethylhexan-2-ol HCl minor: 2,3,5-trimethylhex-3-ene and
10.4 Both reactions occur. 2-isopropyl-4-methylpent-1-ene
10.5 React Grignard reagent with D2O. (c) Major: ethylidenecyclohexane;

minor: cyclohexylethylene
10.6 (R)-1-Methylpentyl acetate,
CH3CO2CH(CH3)CH2CH2CH2CH3 10.20 (a) 1-Bromo-3,6-dimethylheptane
10.7 (S)-Butan-2-ol (b) 4-Bromo-1,2-dimethylcyclopentane

10.21 (Z)-1-Bromo-1,2-diphenylethylene
10.22 (Z)-3-Methylpent-2-ene 12.2 The vinylic CH protons are nonequivalent.

10.23 The cis isomer reacts faster because the bromine
is axial. b H CH3 a
C C
Br c H Cl
12.3 (a) 7.27 (b) 3.05 (c) 3.46 (d) 5.30

(CH3)3C
12.4 (a) 420 Hz (b) 2.1 (c) 1050 Hz
H
12.5 (a) 4 (b) 7 (c) 4 (d) 5 (e) 5 (f) 7
10.24 (a) SN2 (b) E2 (c) SN1 (d) E1cB 12.6 (a) 1,3-Dimethylcyclopentene
(b) 2-Methylpentane
CHAPTER 11 (c) 1-Chloro-2-methylpropane
11.1 C19H28O2
12.7 CH3, 9.3 ; CH2, 27.6 ,
11.2 (a) 2-Methylpent-2-ene (b) Hex-2-ene CO, 174.6 , OCH3, 51.4
11.3 (a) 43, 71 (b) 82 (c) 58 (d) 86 12.8 23, 26 OH
11.4 102 (M), 84 (dehydration), 87 (alpha cleavage),
59 (alpha cleavage)
11.5 X-ray energy is higher. 124 24 18
9.0 106 m is higher in energy. 132 39 68
11.6 (a) 2.4 106 kJ/mol (b) 4.0 104 kJ/mol

12.9 DEPT-135 ()
(c) 2.4 103 kJ/mol (d) 2.8 102 kJ/mol O DEPT-135 (+)
(e) 6.0 kJ/mol (f) 4.0 102 kJ/mol DEPT-135 (+) H3C O C CH2 CH3
11.7 (a) Ketone or aldehyde (b) Nitro compound C C

DEPT-135 (+) H3C H DEPT-90, DEPT-135 (+)
(c) Carboxylic acid
11.8 (a) CH3CH2OH has an OH absorption.
12.10 CH3
(b) Hex-1-ene has a double-bond absorption.
CH2 C CH3
(c) CH3CH2CO2H has a very broad OH absorption.
CH3
11.9 (a) 1715 cm1 (b) 1730, 2100, 3300 cm1
(c) 1720, 25003100 cm1, 34003650 cm1 12.11 A DEPT-90 spectrum would show two absorp-
tions for the non-Markovnikov product
11.10 1690, 1650, 2230 cm1
(RCHUCHBr) but no absorptions for the
11.11 300600 kJ/mol; UV energy is greater than Markovnikov product (RBrCUCH2).
IR energy.
12.12 (a) Enantiotopic (b) Diastereotopic
11.12 1.46 105 M
(c) Diastereotopic (d) Diastereotopic
11.13 All except (a) have UV absorptions.
(e) Diastereotopic (f) Homotopic
12.13 (a) 2 (b) 4 (c) 3 (d) 4 (e) 5 (f) 3
CHAPTER 12
12.1 7.5 105 kJ/mol for 19F; 12.14 4
8.0 105 kJ/mol for 1H
12.15 (a) 1.43 (b) 2.17 (c) 7.37 13.2 (a) CH2OH (b)
OH
(d) 5.30 (e) 9.70 (f) 2.12 CH3CH C
12.16 Seven kinds of protons CH2CH3
12.17 Two peaks; 32 ratio

(c) H OH (d) SH
12.18 (a) CHBr2, quartet; CH3, doublet Cl H
CH3CHCH2CH2CH2SH
(b) CH3O, singlet; OCH2, triplet;
CH2Br, triplet
(c) ClCH2, triplet; CH2, quintet
(e) CH3 (f) OH
(d) CH3, triplet; CH2, quartet;
CH, septet; (CH3)2, doublet OH CH2CH2OH
(e) CH3, triplet; CH2, quartet;
CH, septet; (CH3)2, doublet H3C
(f) CH, triplet, CH2, doublet;
aromatic CH, two multiplets 13.3 (a) p-Methylphenol Phenol
12.19 (a) CH3OCH3 (b) CH3CH(Cl)CH3 p-(Trifluoromethyl)phenol
(c) ClCH2CH2OCH2CH2Cl (b) Benzyl alcohol Phenol

p-Hydroxybenzoic acid
(d) CH3CH2CO2CH3 or CH3CO2CH2CH3
13.4 The electron-withdrawing nitro group stabilizes
12.20 CH3CH2OCH2CH3 an alkoxide ion, but the electron-donating
12.21 J12 16 Hz; J23 8 Hz methoxyl group destabilizes the anion.
13.5 Thiophenol is more acidic because the anion is
1
H resonance-stabilized.
3
C CH2Br 13.6 (a) Benzaldehyde or benzoic acid (or ester)
C
J12 = 16 Hz (b) Acetophenone
2
H
J23 = 8 Hz (c) Cyclohexanone
(d) 2-Methylpropanal or 2-methylpropanoic acid
(or ester)
13.7 (a) 1-Methylcyclopentanol
12.22 1-Chloro-1-methylcyclohexane has a singlet (b) 3-Methylhexan-3-ol
methyl absorption; 1-chloro-2-methylcyclohexane
has a doublet. 13.8 (a) Acetone CH3MgBr, or ethyl acetate
2 CH3MgBr
CHAPTER 13 (b) Cyclohexanone CH3MgBr

13.1 (a) 5-Methylhexane-2,4-diol (c) Butan-2-one PhMgBr, or ethyl phenyl
(b) 2-Methyl-4-phenylbutan-2-ol ketone CH3MgBr, or acetophenone
CH3CH2MgBr
(c) 4,4-Dimethylcyclohexanol
(e) Formaldehyde PhMgBr
(d) trans-2-Bromocyclopentanol
13.9 Cyclohexanone CH3CH2MgBr
(e) 2-Methylheptane-4-thiol
13.10 (a) 2-Methylpent-2-ene
(f) Cyclopent-2-ene-1-thiol
(b) 3-Methylcyclohexene
(c) 1-Methylcyclohexene
13.11 (a) 1-Phenylethanol (b) 2-Methylpropan-1-ol CHAPTER 14

14.1 (a) 2-Methylpentan-3-one
(c) Cyclopentanol
13.12 (a) Hexanoic acid, hexanal (b) Hexan-2-one (b) 3-Phenylpropanal
(c) Hexanoic acid, no reaction (c) Octane-2,6-dione

13.13 1. LiAlH4; 2. PBr3; 3. (H2N)2CUS; 4. H2O, NaOH (d) trans-2-Methylcyclohexanecarbaldehyde
13.14 (a) Diisopropyl ether (e) Hex-4-enal
(b) Cyclopentyl propyl ether (f) cis-2,5-Dimethylcyclohexanone
(c) p-Bromoanisole or 4-bromo-1-methoxybenzene
14.2
(d) 1-Methoxycyclohexene
(a) CH3 (b) Cl O
(e) Benzyl methyl sulfide
CH3CHCH2CHO CH3CHCH2CCH3
(f) Allyl methyl sulfide
13.15 A mixture of diethyl ether, dipropyl ether, and
ethyl propyl ether is formed in a 112 ratio. (c) CH2CHO (d) H H
(CH3)3C CHO
13.16 (a) CH3CH2CH2O CH3Br
(b) PhO CH3Br
(c) (CH3)2CHO PhCH2Br
(e) CH3 (f) CH3 CH3CHCl
(d) (CH3)3CCH2O CH3CH2Br
H2C CCH2CHO CH3CH2CHCH2CH2CHCHO
13.17 (a) Bromoethane 2-Bromopropane
Bromobenzene
(b) Bromoethane Chloroethane 14.3 (a) 1. CH3COCl, AlCl3; 2. Br2, FeBr3
1-Iodopropene (b) 1. Mg; 2. CH3CHO, then H3O; 3. PCC
13.18 (a)
(c) 1. BH3, then H2O2, NaOH; 2. PCC
Br + CH3OH 14.4 CN
OH
(b) CH3
+ CH3CH2CH2Br
CH3CH2CHOH
14.5 The electron-withdrawing nitro group in
13.19 Protonation of the oxygen atom, followed by p-nitrobenzaldehyde polarizes the carbonyl
E1 reaction group.
14.6 CCl3CH(OH)2
PREVIEW OF CARBONYL CHEMISTRY
1. Acetyl chloride is more electrophilic than acetone. 14.7 Labeled water adds reversibly to the carbonyl
group.
2. O CN O
H3O+
C 14.8 NCH2CH3 N(CH2CH3)2
C
H3C CH3 H 3C CN
H3C and
OH
14.9 The steps are the exact reverse of the forward
C reaction.
H3C CN
H3C
14.10
3. (a) Nucleophilic acyl substitution
(b) Nucleophilic addition O + (CH3CH2)2NH N(CH2CH3)2
(c) Carbonyl condensation
14.11 The mechanism is identical to that between a CHAPTER 15

ketone and 2 equivalents of a monoalcohol (see 15.1 (a) 3-Methylbutanoic acid
Figure 14.10, p. 573).
(b) 4-Bromopentanoic acid
14.12 CH3
(c) 2-Ethylpentanoic acid
CH3O2C
CHO (d) cis-Hex-4-enoic acid
+ CH3OH
(e) 2,4-Dimethylpentanenitrile
(f) cis-Cyclopentane-1,3-dicarboxylic acid
14.13 (a) Cyclohexanone CH3CHUP(Ph)3 15.2
(b) Cyclohexanecarbaldehyde H2CUP(Ph)3 (a) H3C CH3 (b) CH3
(c) Acetone CH3CH2CH2CHUP(Ph)3 CH3CH2CH2CHCHCO2H CH3CHCH2CH2CO2H
(d) Acetone PhCHUP(Ph)3 (c) H (d) CO2H
CO2H
(e) Acetophenone PhCHUP(Ph)3
(f) Cyclohex-2-enone H2CUP(Ph)3 OH
H
14.14 CO2H
(e) CO2H
(f) CH3CH2CH CHCN

2
15.3 Dissolve the mixture in ether, extract with aque-

14.15 Addition of the pro-R hydrogen of NADH takes ous NaOH, separate and acidify the aqueous layer,
place on the Re face of pyruvate. and extract with ether.
14.16 The OH group adds to the Re face at C2, 15.4 43%
and H adds to the Re face at C3, to yield
(2R,3S)-isocitrate. 15.5 (a) 82% dissociation (b) 73% dissociation
14.17 O CN 15.6 Lactic acid is stronger because of the inductive

effect of the OH group.
15.7 The dianion is destabilized by repulsion between
charges.
14.18 Look for the presence or absence of a saturated 15.8 More reactive
ketone absorption in the product.
15.9 (a) 1. Mg; 2. CO2, then H3O
14.19 (a) 1715 cm1 (b) 1685 cm1
(b) 1. Mg; 2. CO2, then H3O or
(c) 1750 cm1 (d) 1705 cm1 1. NaCN; 2. H3O with heat
(e) 1715 cm1 (f) 1705 cm1 15.10 1. NaCN; 2. H3O; 3. LiAlH4 or
Grignard carboxylation, then LiAlH4
14.20 (a) Different peaks due to McLafferty
rearrangement 15.11 1. H3O with heat; 2. LiAlH4
(b) Different peaks due to cleavage and 15.12 A carboxylic acid has a very broad OH absorp-
McLafferty rearrangement tion at 25003300 cm1.
(c) Different peaks due to McLafferty 15.13 4-Hydroxycyclohexanone: HCO absorption near
rearrangement 4 in 1H spectrum and CO absorption near
210 in 13C spectrum. Cyclopentanecarboxylic
14.21 IR: 1750 cm1; MS: 140, 84
acid: CO2H absorption near 12 in 1H spectrum
and CO2H absorption near 170 in 13C spectrum.
CHAPTER 16 16.5 (a) CH3CO2 Na (b) CH3CONH2

16.1 (a) 4-Methylpentanoyl chloride
(c) CH3CO2CH3 CH3CO2 Na
(b) Cyclohexylacetamide
(d) CH3CONHCH3
(c) Isopropyl 2-methylpropanoate
16.6 OCH3
(d) Benzoic anhydride OH
O
(e) Isopropyl cyclopentanecarboxylate
(f) Cyclopentyl 2-methylpropanoate OH
+ OCH
3
(g) N-Methylpent-4-enamide O
(h) (R)-2-Hydroxypropanoyl phosphate
16.7 (a) Acetic acid butan-1-ol
(i) Ethyl 2,3-Dimethylbut-2-enethioate
(b) Butanoic acid methanol
16.2
16.8 O
(a) C6H5CO2C6H5 (b) CH3CH2CH2CON(CH3)CH2CH3
(c) (CH3)2CHCH2CH(CH3)COCl (d) CH3 O

CO2CH3
16.9 (a) Propanoyl chloride methanol
(b) Acetyl chloride ethanol
(e) O O (f) O
(c) Benzoyl chloride ethanol
CH3CH2CCH2COCH2CH3 C
SCH3
16.10 Benzoyl chloride cyclohexanol
Br 16.11 This is a typical nucleophilic acyl substitution

reaction, with morpholine as the nucleophile and
(g) O O (h) H chloride as the leaving group.
COBr
C C 16.12 (a) Propanoyl chloride methylamine
H O CH2CH3
(b) Benzoyl chloride diethylamine
CH3
H
(c) Propanoyl chloride ammonia
16.13 This is a typical nucleophilic acyl substitution
16.3 O O Cl reaction, with p-hydroxyaniline as the nucleo-
C C phile and acetate ion as the leaving group.
Cl OCH3 OCH3
16.14 Monomethyl ester of benzene-1,2-dicarboxylic
acid
16.15 Reaction of a carboxylic acid with an alkoxide ion
O
gives the carboxylate ion.
C
OCH3 16.16 HOCH2CH2CH2CHO
16.17 (a) CH3CH2CH2CH(CH3)CH2OH
(b) PhOH PhCH2OH
16.4 The electron-withdrawing trifluoromethyl group
16.18 (a) H2O, NaOH (b) Product of (a), then LiAlH4
polarizes the carbonyl carbon.
(c) LiAlH4
16.19 1. Mg; 2. CO2, then H3O; 3. SOCl2; 16.24 (a) CH3CH2CH2CO2CH2CH3 and other possibilities
4. (CH3)2NH; 5. LiAlH4
(b) CH3CON(CH3)2
16.20
O O (c) CH3CHUCHCOCl or H2CUC(CH3)COCl
C P
H3C O O Adenosine CHAPTER 17
O
17.1 (a) OH (b) OH
RS H
Base H 2C CSCH3
(c) OH (d) CH3CH CHOH
H 2C COCH2CH3
O O
C P (e) OH
H3C O O Adenosine
S O CH3CH COH
R
(f) OH OH
PhCH CCH3 or PhCH2C CH2

O O
C R + P 17.2
H3C S O O Adenosine
O O O OH
Acetyl CoA
16.21 (a)
O OH O
OCH2CH2CH2OCH2CH2CH2
n Equivalent;
more stable
(b)
O O
O OH
OCH2CH2OC(CH2)6C
n
(c) OH O
O O
NH(CH2)6NHC(CH2)4C
n Equivalent;
less stable
16.22
O O 17.3 (a) CH3CH2CHO (b) (CH3)3CCOCH3
NH NH C C
(c) CH3CO2H (d) PhCONH2
n
(e) CH3CH2CH2CN (f) CH3CON(CH3)2

17.4 CH2C N H2C C N
16.23 (a) Ester (b) Acid chloride (c) Carboxylic acid
(d) Aliphatic ketone or cyclohexanone
17.5 (a) 1. Na OEt; 2. PhCH2Br; 3. H3O 17.14 O CH3

(b) 1. Na OEt; 2. CH3CH2CH2Br; 3. Na OEt;
4. CH3Br; 5. H3O H3C
(c) 1. Na OEt; 2. (CH3)2CHCH2Br; 3. H3O

17.6 1. Na OEt; 2. (CH3)2CHCH2Br;
3. Na OEt; 4. CH3Br; 5. H3O and
17.7 (a) (CH3)2CHCH2Br (b) PhCH2CH2Br O
17.8 None can be prepared.

H3C
17.9 1. 2 Na OEt; 2. BrCH2CH2CH2CH2Br; 3. H3O
17.10 (a) Alkylate phenylacetone with CH3I CH3
(b) Alkylate pentanenitrile with CH3CH2I

17.15 (a) Not an aldol product (b) Pentan-3-one
(c) Alkylate cyclohexanone with H2CUCHCH2Br
17.16 The CH2 position between the two carbonyl
(d) Alkylate cyclohexanone with excess CH3I groups is so acidic that it is completely deproto-
(e) Alkylate C6H5COCH2CH3 with CH3I nated to give a stable enolate ion.
(f) Alkylate methyl 3-methylbutanoate with 17.17 O

CH3CH2I
17.11 (a) OH O
CH3CH2CH2CHCHCH
CH2CH3
17.18 (a) (b)
CH3 O O O O
(b) O HO CH3 CH3CHCH2CCHCOEt PhCH2CCHCOEt
CH(CH3)2 Ph
(c)
O O
(c) O C6H11CH2CCHCOEt
OH
C6H11
17.19 The cleavage reaction is the exact reverse of the

forward reaction.
17.12 The reverse reaction is the exact opposite of the
forward reaction. 17.20 O
17.13
(a) O (b) CH3 O H3C CO2Et
C C
C 17.21 H3C O O
H +
CO2Et CO2Et
(c) O CH3
(CH3)2CHCH2CH CCH
CH(CH3)2
17.22 (a) O CH(COCH3)2 18.3 (a) CH3O (b) H3C

N CH3
N
(b) (CH3CO)2CHCH2CH2CN H
(c) O
(c) N(CH3)2 (d) NH2
(CH3CO)2CHCHCH2COEt N
CH3 N
N
17.23 18.4 (a) CH3CH2NH2 (b) NaOH (c) CH3NHCH3
O O
18.5 Propylamine is stronger; benzylamine pKb 4.67;
(a) (b) O
propylamine pKb 3.29
(EtO2C)2CHCH2CH2CCH3 CH2CH2CCH3
18.6 (a) p-Nitroaniline p-Aminobenzaldehyde
CO2Et
p-Bromoaniline
(b) p-Aminoacetophenone p-Chloroaniline
17.24 p-Methylaniline
(a) O (b) O (c) p-(Trifluoromethyl)aniline
p-(Fluoromethyl)aniline p-Methylaniline
CH2CH2CO2Et CH2CH2CHO
18.7 Pyrimidine is essentially 100% neutral
(unprotonated).
18.8 (a) Propanenitrile or propanamide
(c) O O
(b) N-Propylpropanamide
(c) Benzonitrile or benzamide
(d) N-Phenylacetamide
17.25 (a) Cyclopentanone enamine propenenitrile 18.9 HO CH2CH2Br
NH3
(b) Cyclohexanone enamine methyl propenoate
HO
CHAPTER 18 or
18.1 (a) N-Methylethylamine
(b) Tricyclohexylamine HO CH2Br
1. NaCN
(c) N-Ethyl-N-methylcyclohexylamine 2. LiAlH4
HO
(d) N-Methylpyrrolidine
(e) Diisopropylamine 18.10 H3C CHO
NaBH4
+ (CH3)2NH
(f) Butane-1,3-diamine
18.2 (a) [(CH3)2CH]3N (b) (H2C CHCH2)2NH
18.11 (a) Oct-3-ene and oct-4-ene
(c) NHCH3 (d) CH3 (b) Cyclohexene
NCH2CH3 (c) Hept-3-ene
(d) Ethylene and cyclohexene
(e) NHCH(CH3)2 (f) 18.12 H2CUCHCH2CH2CH2N(CH3)2
N CH2CH3
18.13 1. HNO3, H2SO4; 2. H2/PtO2; 3. (CH3CO)2O;
4. HOSO2Cl; 5. aminothiazole; 6. H2O, NaOH
18.14 (a) 1. HNO3, H2SO4; 2. H2/PtO2; 3. 2 CH3Br 18.18 The side-chain nitrogen is more basic than the
ring nitrogen.
(b) 1. HNO3, H2SO4; 2. H2/PtO2;
3. (CH3CO)2O; 4. Cl2; 5. H2O, NaOH 18.19 Reaction at C2 is disfavored because the aroma-
ticity of the benzene ring is lost
(c) 1. HNO3, H2SO4; 2. Cl2, FeCl3; 3. Sn
18.15 +
H E
E+
N S N H
N
H
H H H
+
18.16 4.1% protonated E E
18.17 H + H
N N
Attack at C2: H H
E+
N CHAPTER 19
19.1 Aromatic: Phe, Tyr, Trp, His;
sulfur-containing: Cys, Met;
+ + alcohols: Ser, Thr;
hydrocarbon side chains: Ala, Ile, Leu, Val, Phe
E E + E
N N N 19.2 The sulfur atom in the CH2SH group of cysteine
H H H
makes the side chain higher in priority than the
Unfavorable CO2H group.
Attack at C3: 19.3 CO2 CO2 CO2

+ S + S R +
H3N H H3N H H NH3
E+ R S R
H OH HO H H OH
N
CH3 CH3 CH3
L-Threonine Diastereomers of L-threonine

E E + E
H H H
19.4 Net positive at pH 5.3; net negative at pH 7.3
+ +
N N N 19.5 (a) (CH3)2CHCH2Br (b) N
CH2Br
N
Attack at C4:
H
(c) CH2Br (d) CH3SCH2CH2Br

E+
N
N
E H E H E H H
+ +
+
N N N
Unfavorable
19.6 19.15 (1) Protect the amino group of leucine.

H CO2H (2) Protect the carboxylic acid group of alanine.
1. H2, [Rh(DiPAMP)(COD)]+ BF4
C C (3) Couple the protected amino acids with DCC.
2. NaOH, H2O
(CH3)2CH NHCOCH3
(4) Remove the leucine protecting group.
CO2 (5) Remove the alanine protecting group.
+ 19.16 (a) Lyase (b) Hydrolase (c) Oxidoreductase

H3N H
CHAPTER 20
19.7 Val-Tyr-Gly (VYG), Tyr-Gly-Val (YGV), 20.1 O O
Gly-Val-Tyr (GVY), Val-Gly-Tyr (VGY), ATP ADP
Tyr-Val-Gly (YVG), Gly-Tyr-Val (GYV) C C
O OH 2O PO OH
3
19.8 O O O O
+
H3NCHC N CHC NHCHC NHCH2CO 20.2 The mechanism is the reverse of that shown in
CH3SCH2CH2 CH(CH3)2
Figure 20.2.
20.3 The Re face
19.9 O O 20.4 +NH NH2

2
HOCCH2 SCH2CHCO O
O C C N
2 N
+ NH N O P O
3
H NH3 H OCH2 N
+ N
O
19.10 O O
N + (CH3)2CHCHO + CO2 OH OH
O O 20.5 The mechanism is the same as that shown in

Figure 20.2.
19.11 Trypsin: Asp-Arg Val-Tyr-Ile-His-Pro-Phe 20.6
Chymotrypsin: Asp-Arg-Val-Tyr Ile-His-Pro-Phe CH3 CH3

H2O +
C H2O C
19.12 Methionine +
H2N CO2 CO2
H2N
19.13 C6H5 O
N C CH3 CH3
H2O
CH2CO2H HO + NH3
C C C H C
S
N H + CO2 O+ CO2
H3N
H
CH3
H3O+ +
19.14 This is a typical nucleophilic acyl substitution C
O CO2
reaction, with the amine of the amino acid as the
nucleophile and tert-butyl carbonate as the leav-
ing group. The tert-butyl carbonate then loses 20.7 The mechanism is essentially the same as that in
CO2 and gives tert-butoxide, which is protonated. Problem 20.6.
20.8 21.6 (a) L-Erythrose; 2S,3S (b) D-Xylose; 2R,3S,4R

(c) D-Xylulose; 3S,4R
N N+
21.7 CHO
NH2 NH2 H OH
C C
HO H L-(+)-Arabinose
H H O H O
HO H
+ +
H NH3 + H NH3 CH2OH
O O
C CO2 C CO2
21.8
OPO32 H + PO43
(a) CHO (b) CHO (c) CHO
HO H HO H HO H
20.9 The nonenzymatic cyclization is an internal
imine formation that occurs by nucleophilic addi- H OH H OH H OH
tion of the amine to the carbonyl group followed HO H H OH HO H
by loss of water. The enzymatic reduction is a
nucleophilic addition to the iminium ion: CH2OH HO H HO H
CH2OH CH2OH
N
H H 21.9 16 D and 16 L aldoheptoses
NH2 N+ 21.10 CHO

C CO2
H OH
H H O H
H OH D-Ribose
H
H OH
N
CH2OH
CO2
H
21.11 HOCH2
O H,
OH
CHAPTER 21
21.1 (a) Aldotetrose (b) Ketopentose
OH OH
(c) Ketohexose (d) Aldopentose
21.2 (a) S (b) R (c) S 21.12 CH2OH OH
21.3 A, B, and C are the same. O OH O CH2OH

OH OH
21.4 H HO HO
HO HO
HOCH2 CH3 R
Cl -D-Fructopyranose -D-Fructopyranose
trans cis
21.5 CHO
* * *
H OH R HOCH2 CH2OH HOCH2 OH
O OH O OH
H OH R
OH CH2OH
CH2OH
OH * OH
-D-Fructofuranose -D-Fructofuranose
21.13 e a 21.22 (a) 1. NaBH4

Cellobiose
HO e HOCH2 OH 2. H2O
a CH2OH e
O O
HO CH2OH CH2OH
HO OH HO OH O H
HO OH
e e OH e e e O
HO HO CH2OH
OH OH
-D-Galactopyranose -D-Mannopyranose
(b) Br2
Cellobiose
21.14 e e H2O
HOCH2 O OH
OH CH2OH CH2OH
e O H
HO e HO OH
HO O
a HO HO CO2H
OH OH
21.15 -D-Allopyranose (see Figure 21.3) (c) CH3COCl
Cellobiose
pyridine
21.16 CH3OCH2 OCH3 AcOCH2 OAc
O O
CH2OAc CH2OAc
AcO O O
O
AcO AcO OAc
OCH3 OCH3 OAc OAc
OAc OAc
21.17 D-Galactitol
has a plane of symmetry and is a
meso compound, whereas D-glucitol is chiral.
CHAPTER 22
21.18 The CHO end of L-gulose corresponds to the 22.1 Steps 7 and 10
CH2OH end of D-glucose after reduction.
22.2 Steps 1, 3: nucleophilic acyl substitutions at
21.19 D-Allaric
acid has a symmetry plane and is a meso phosphorus; steps 2, 5, 7, 8, 10: isomerizations;
compound, but D-glucaric acid is chiral. step 4: retro-aldol reaction; step 6: oxidation
and nucleophilic acyl substitution by phosphate;
21.20 D-Allose and D-galactose yield meso aldaric acids;
step 9: E1cB dehydration
the others yield optically active aldaric acids.
22.3 pro-R
21.21 CO2
22.4
C O N
H2C H Base CO2
C O CONH2
CH2 H H
H O
C H OH
22.5 C1 and C6 of glucose become CH3 groups;
CH3CONH H CH3CONH H C3 and C4 become CO2.
HO H HO H
22.6 Citrate and isocitrate
H OH H OH
22.7 E1cB elimination of water, followed by conjugate
H OH H OH addition
CH2OH CH2OH 22.8 pro-R; anti geometry
22.9 Re face; anti geometry
22.10 The reaction occurs by two sequential nucleo- (b)

philic acyl substitutions, the first by a cysteine
residue in the enzyme, with phosphate as leaving
group, and the second by hydride donation from
NADH, with the cysteine residue as leaving group.
CH2 OPP
CHAPTER 23
23.1 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 88n
Glycerol 2 Sodium oleate Sodium palmitate
23.5 Caprylyl CoA 88n Hexanoyl CoA 88n
Butyryl CoA 88n 2 Acetyl CoA +CH
2
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 O H
R CO2H
R R
S
H H
OH H OH
23.11 The pro-S hydrogen is cis to the CH3 group; the

pro-R hydrogen is trans. +
23.12
(a) OPP
+ B H
+
+ OPP
+ H
Base
-Bisabolene
-Pinene
23.13 24.12 The mechanism was shown in Figure 20.2 on

page 823.
(a) H (b) H
CH3 24.13
e
O O
NADPH, H+
a
H H CH3
H CH3 NADP+ H CH3
N N
23.14 CH3 O N O N
CH3
CH3 H H
CO2H
H2O
O O
H
NH4+
e CH3 O CH3
O CO2 H2O
OH
H2N
H2N N
CHAPTER 24 O
H
24.3 (5
) ACGGATTAGCC (3
)
-Ketoglutarate
24.4 H
O H N N Glutamate
CoASH
N
N H N NAD+
H O C CH3 O C CH3
N N 2 NADH/H+ 2
H O
O H O CoASH
24.5 (3
) CUAAUGGCAU (5
)
24.6 (5
) ACTCTGCGAA (3
) 24.14 The mechanism occurs by (1) phosphorylation
of inosine monophosphate by reaction with GTP,
24.7 (a) GCU, GCC, GCA, GCG (2) acid-catalyzed nucleophilic addition of aspar-
tate to an imine, and (3) loss of phosphate by an
(b) UUU, UUC
E1cB reaction.
(c) UUA, UUG, CUU, CUC, CUA, CUG
24.15 The reaction is an E1cB elimination.
(d) UAU, UAC
24.8 Leu-Met-Ala-Trp-Pro-Stop CHAPTER 25
The answers to the problems in Chapter 25 can be down-
24.9 (5
) TTA-GGG-CCA-AGC-CAT-AAG (3
)
loaded from the web at http://www.thomsonedu.com
24.10 The cleavage is an SN1 reaction that occurs by
protonation of the oxygen atom followed by loss
of the stable triarylmethyl carbocation.
24.11 NH3
O H
RO P O CH2 CHC N E2 reaction

OR
Index
The boldfaced references refer to pages reactions with amines, 652 Acetyl coenzyme A, see Acetyl CoA
where terms are defined. synthesis of, 643 Acetyl dihydrolipoamide, acetyl CoA
Acetoacetic ester, alkylation of, from, 904905
, see Alpha 695696 Acetyl group, 559
Abbreviated mechanism, nucleophilic ketones from, 695696 N-Acetyl-D-neuraminic acid, structure
acyl substitution reactions, 840 Acetoacetic ester synthesis, 695696 and function of, 872
Absolute configuration, 330 Acetoacetyl-CoA acetyltransferase, 952 Acetylene, bond angles in, 18
Absorbance, 440 Acetone, enol content of, 683 bond lengths in, 18
Absorption spectrum, 427 hydrate of, 564 bond strengths in, 18
Acesulfame-K, structure of, 881 pKa of, 688 molecular model of, 18
sweetness of, 880 uses of, 557 pKa of, 252
Acetal(s), 572 Acetone anion, electrostatic potential sp hybrid orbitals in, 1718
from aldehydes, 572574 map of, 56, 57, 80, 555 structure of, 18
from ketones, 572574 Acetonitrile, electrostatic potential map N-Acetylglucosamine, biosynthesis of,
hydrolysis of, 572573 of, 615 662663
mechanism of formation of, 572573 pKa of, 690 structure and function of, 872
Acetaldehyde, aldol reaction of, 701, 703 Acetophenone, 13C NMR absorptions of, Acetylide anion(s), 252
bond angles in, 549 585 alkylation of, 412
bond lengths in, 549 structure of, 559 electrostatic potential map of, 253
electrostatic potential map of, 549 Acetyl azide, electrostatic potential map N-Acetylmannosamine, structure and
13C NMR absorptions of, 585 of, 673 function of, 872
1H NMR spectrum of, 584 Acetyl chloride, electrostatic potential Achiral, 322
pKa of, 690 map, 555, 639 Acid, BrnstedLowry, 50
Acetamide, basicity of, 690 pKa of, 690 Lewis, 58
electrostatic potential map of, 639, 673, reaction with alcohols, 652 organic, 5657
743 reaction with amines, 652 strengths of, 5153
Acetaminophen, molecular model of, 28 see also Acid chloride Acid anhydride(s), 633
synthesis of, 652 Acetyl CoA, anion of, 46 amides from, 652
Acetanilide, electrophilic aromatic biosynthesis of, 662 electrostatic potential map of, 639
substitution of, 753754 carboxylation of, 945 esters from, 652
Acetate ion, electrostatic potential map catabolism of, 905910 from acid chlorides, 648
of, 44, 54, 57, 607 citric acid cycle and, 905910 from carboxylic acids, 643
resonance in, 4344 Claisen condensation reactions of, IR spectroscopy of, 667
Acetic acid, dimer of, 605 720 naming, 634
dipole moment of, 39 fat catabolism and, 938942 NMR spectroscopy of, 667668
electrostatic potential map of, 54, 56 fatty acids from, 943947 nucleophilic acyl substitution
hydrogen bonding in, 605 from acetyl dihydrolipoamide, reactions of, 652653
pKa of, 52, 606 904905 reaction with alcohols, 652
properties of, 605 from pyruvate, 901905 reaction with amines, 652
protonation of, 6061 function of, 662663 Acid chloride(s), 633
Acetic acid dimer, electrostatic potential reaction with glucosamine, 662663 acid anhydrides from, 648
map of, 605 reaction with oxaloacetate, 906907 alcoholysis of, 650
Acetic anhydride, electrostatic potential structure of, 819 amides from, 650651
map of, 639 thioester in, 662 aminolysis of, 650651
reaction with alcohols, 652 Acetyl CoA anion, resonance in, 46 carboxylic acids from, 648
I-1
I-2 INDEX
Acid chloride(s) (continued) Acyl-CoA dehydrogenase, 939 carbonyl nucleophilic addition

electrostatic potential map of, 639 Acyl-CoA synthetase, 937 reactions of, 572574
esters from, 650 Acylation (aromatic), see FriedelCrafts carboxylic acids from, 516517
from carboxylic acids, 642643 reaction common names of, 500
hydrolysis of, 648 Adams catalyst, 232 dehydration of, 222, 513515
IR spectroscopy of, 667 1,2-Addition (conjugated carbonyl), 580 electrostatic potential map of, 79
naming, 634 1,2-Addition (diene), 248249 esters from, 515516
NMR spectroscopy of, 667668 1,4-Addition (conjugated carbonyl), 580 ethers from, 523524
nucleophilic acyl substitution reactions 1,4-Addition (diene), 248249 from aldehydes, 506,507, 509510,
of, 648, 650651 Addition reaction, 142 567568
pKa of, 690 Adenine, aromaticity of, 280 from alkenes, 227230, 504505
polarity of, 80 electrostatic potential map of, 983 from carbonyl compounds, 505511
reaction with alcohols, 650 molecular model of, 68 from carboxylic acids, 507508, 647
reaction with amines, 650651 protection of, 993 from epoxides, 505
reaction with ammonia, 650651 structure of, 980 from esters, 507510, 657658
reaction with carboxylate ions, 648 Adenosine, biosynthesis of, 10061007 from ethers, 525526
reaction with water, 648 catabolism of, 9991000 from ketones, 506507, 509510,
Acid halide(s), 633 Adenosine diphosphate (ADP), function 567568
naming, 634 of, 819820 hydrogen bonds in, 501
nucleophilic acyl substitution reactions structure of, 163 IR spectroscopy of, 436, 529
of, 648, 650651 Adenosine triphosphate (ATP), coupled ketones from, 516517
reaction with alcohols, 650 reactions and, 821 mass spectrometry of, 422, 531
reaction with amines, 650651 energy rich bonds in, 162163 mechanism of dehydration of, 513515
see also, Acid chloride function of, 819820 mechanism of oxidation of, 518
Acidity, alcohols and, 501503 hydrolysis of, 163 naming, 499500
amines and, 743 reaction with alcohols, 819820 NMR spectroscopy of, 530
carbonyl compounds and, 689690 reaction with glucose, 821 oxidation of, 516519
carboxylic acids and, 605607 reaction with methionine, 528 polarity of, 79
phenols and, 501503 structure and function of, 163, 802 primary, 499
Acidity constant (Ka), 51 S-Adenosylhomocysteine, from S- properties of, 501503
table of, 52 adenosylmethionine, 390391 reaction with acid, 513514
Acidbase reactions, prediction of, 5354 metabolism of, 411 reaction with acid anhydrides, 652
Aconitase, 907 S-Adenosylmethionine, biological reaction with acid chlorides, 650
ACP, see Acyl carrier protein, 943 methylation with, 390391 reaction with aldehydes, 572574
ACP transacylase, 943 from methionine, 528 reaction with alkyl halides, 524
Acrolein, structure of, 558 SN2 reactions of, 390391 reaction with ATP, 819820
Acrylic acid, pKa of, 606 stereochemistry of, 346 reaction with carboxylic acids,
structure of, 603 structure and function of, 803 644645
Activating group (aromatic substitution), Adenylosuccinate synthetase, 1006 reaction with CrO3, 517518
294 Adipic acid, structure of, 603 reaction with HX, 366, 512
acidity and, 610 ADP, see Adenosine diphosphate reaction with ketones, 572574
explanation of, 294295 Adrenaline, biosynthesis of, 390391 reaction with Na2Cr2O7, 517518
Activation energy, 164 molecular model of, 354 reaction with NaH, 503
magnitude of, 164165 Adrenocortical hormone, 963 reaction with NaNH2, 503
reaction rate and, 164165 -al, aldehyde name ending, 558 reaction with PBr3, 366, 512
Active site (enzyme), 169 Alanine, biosynthesis of, 838 reaction with PCC, 517518
citrate synthase and, 805 catabolism of, 833 reaction with POCl3, 513515
hexokinase and, 169 configuration of, 330 reaction with potassium, 503
urocanase and, 845 electrostatic potential map of, 778 reaction with SOCl2, 366, 512
Acyl adenosyl phosphate, asparagine molecular model of, 28, 777 reactions of, 512518
biosynthesis and, 839840 pyruvate from, 833 secondary, 499
biological reactions of, 648649 structure and properties of, 780 synthesis of, 504511
fatty acid catabolism and, 937 zwitterion of, 778 tertiary, 499
Acyl adenylate, biological reactions of, Alanine zwitterion, electrostatic potential Alcoholysis (nucleophilic acyl
648649 map of, 778 substitution reaction), 640
see also Acyl adenosyl phosphate Alcohol(s), 497 Aldaric acid(s), 871
Acyl carrier protein (ACP), structure and acetals from, 572574 from aldoses, 871
function of, 943 acidity of, 501503 Aldehyde(s), 557
Acyl cation, electrostatic potential map aldehydes from, 516517 acetals from, 572574
of, 290 alkenes from, 223, 513515 alcohols from, 506507, 509510,
FriedelCrafts acylation reaction and, alkoxide ions from, 501503 567568
290 alkyl halides from, 365366, 387, aldol reaction of, 702
resonance in, 290 512 alkenes from, 575577
Acyl group, 290, 547, 559 alpha cleavage of, 422 bromination of, 686687
naming, 603 biological dehydration of, 513514 amines from, 748750
Acyl phosphate, 633 biological oxidation of, 519 biological reduction of, 507, 580
naming, 636 carbonyl compounds from, 516519 Cannizzaro reaction of, 579
INDEX I-3
carbonyl condensation reactions of, oxidation of, 870871 hydroxylation of, 236239
701706 reaction with Br2, 871 hyperconjugation in, 194
carboxylic acids from, 561562 reaction with HNO3, 871 IR spectroscopy of, 434
common names of, 558 reduction of, 868869 Markovnikovs rule and, 198199
conjugate addition reactions of, see also Carbohydrate, Monosaccharide naming, 182184
580583 table of, 860 nucleophilicity of, 152
enamines from, 568571 Tollens test on, 870 organoboranes from, 229
enols of, 682684 uronic acids from, 871 oxymercuration of, 228229
enones from, 705706 Aldosterone, structure and function of, pKa of, 252
from alcohols, 516517 963 polymerization of, 240242
from esters, 560, 658 Algae, chloromethane from, 363 reaction summary of, 221
Grignard reaction of, 509510, 567 Alicyclic, 112 reaction with borane, 229230
hydrates of, 561, 565566 Aliphatic, 82 reaction with Br2, 224225
imines from, 568569 Alitame, structure of, 881 reaction with Cl2, 224225
IR spectroscopy of, 436, 583584 sweetness of, 880 reaction with H2O, 151154
mass spectrometry of, 422, 585586 Alkaloid, 65 reaction with halogen, 224225
McLafferty rearrangement of, 422 Alkane(s), 82 reaction with HBr, 195196
mechanism of hydration of, 565566 boiling points of, 96 reaction with HCl, 195196
naming, 558 branched-chain, 83 reaction with HI, 195196
NMR spectroscopy of, 584585 combustion of, 95 reaction with hydrogen, 232234
oxidation of, 561562 conformations of, 101 reaction with mercuric ion, 229
pKa of, 690 dispersion forces in, 62, 96 reaction with OsO4, 238239
polarity of, 80 from alkyl halides, 368 reaction with peroxyacids, 235236
reaction with alcohols, 572574 from Grignard reagents, 368 reaction with radicals, 240242
reaction with amines, 568571 general formula of, 82 reduction of, 232234
reaction with Br2, 686687 IR spectroscopy of, 434 Sharpless epoxidation of, 587
reaction with CrO3, 561 isomers of, 8283 stability of, 192194
reaction with Grignard reagents, mass spectrometry of, 418419 steric strain in cis isomer, 192
509510, 567 melting points of, 96 synthesis of, 222223
reaction with H2O, 564566 naming, 8485, 8993 Alkoxide ion, 501
reaction with LiAlH4, 506, 568 Newman projections of, 97 Alkoxy group, 522
reaction with NaBH4, 506 568 normal (n), 83 Alkyl group(s), 86
reactivity of versus ketones, 563564 pKa of, 252 directing effect of, 294
reduction of, 506507, 568 properties of, 9596 inductive effect of, 294295
reductive amination of, 748750 reaction with chlorine, 95 naming, 8687, 9293
Wittig reaction of, 575577 sawhorse representations of, 97 orienting effect of, 294
Alditol(s), 868 straight-chain, 83 Alkyl halide(s), 363
from monosaccharides, 868869 Alkene(s), 179 alkenes from, 222
Aldol reaction, 701703 alcohols from, 227230, 504505 amines from, 747748
biological, 718719 biological addition of radicals to, amino acids from, 784785
cyclohexenones from, 707708 243244 carboxylic acids from, 611612
cyclopentenones from, 707708 biological hydration of, 940 dehydrohalogenation of, 222
dehydration in, 705706 biological reduction of, 234235, 947 electrostatic potential map of, 79
equilibrium in, 702 bond rotation in, 186 ethers from, 524
glucose biosynthesis and, 719 bromohydrins from, 226227 from alcohols, 365366, 387, 512
intramolecular, 707708 bromonium ion from, 224225 from ethers, 525526
mechanism of, 702703 cistrans isomerism in, 186187 Grignard reagents from, 367
requirements for, 701702 common names of, 184 malonic ester synthesis with,
reversibility of, 702 1,2-dihalides from, 224225 692694
steric hindrance to, 702 1,2-diols from, 236239 naming, 364365
Aldolase, class I, 718719, 897 electron distribution in, 152 naturally occurring, 402403
class II, 718719, 897 electrophilic addition reactions of, phosphonium salts from, 575576
types of, 718 195196 polarity of, 79
Aldonic acid(s), 870 electrostatic potential map of, 79, 152 polarizability of, 149
from aldoses, 870871 epoxides from, 235237 reaction with alcohols, 524
Aldose(s), 853 E,Z configuration of, 188190 reaction with amines, 747748
aldaric acids from, 871 from alcohols, 223, 513515 reaction with carboxylate ions, 643
alditols from, 868869 from aldehydes, 575577 reaction with HS, 521
aldonic acids from, 870871 from alkyl halides, 222 reaction with sulfides, 527
Benedicts test on, 870 from alkynes, 251 reaction with thiols, 527
configurations of, 859861 from amines, 751752 reaction with thiourea, 521
Fehlings test on, 870 from ketones, 575577 reaction with triphenylphosphine,
Fischer projections of, 854856 general formula of, 180 575576
esters from, 866 halohydrins from, 226227 see also Organohalide
ethers from, 866 hydration of, 227230 synthesis of, 365366
glycosides of, 867868 hydroboration of, 229230 thiols from, 521
names of, 860861 hydrogenation of, 232234 uses of, 363
I-4 INDEX
Alkyl shift, carbocation rearrangements succinyl CoA from, 908 heterocyclic, 738, 755759
and, 207208 transamination of, 825826 Hofmann elimination of, 751752
Alkylamine(s), 736 Alpha pinene, structure of, 179 hydrogen bonding in, 740
basicity of, 740743 Alpha position (carbonyl compounds, IR spectroscopy of, 436, 762
Alkylation (aromatic), see FriedelCrafts 681 mass spectrometry of, 422, 763764
reaction acidity of, 684 naming, 736738
Alkylation (carbonyl), 288 Alpha substitution reaction, 553, 681 nitrogen rule and, 763
acetoacetic ester, 695696 alkylation and, 691700 occurrence of, 735
biological, 700 carbonyl condensation reactions and, odor of, 740
carbonyl compounds and, 691699 704 polarity of, 80
ester, 698 enolate ions and, 691699 primary, 736
ketone, 698 enols and, 685686 properties of, 739740
malonic ester, 692694 mechanism of, 685686 pyramidal inversion in, 739
nitrile, 699 Altrose, configuration of, 860 reaction with acid anhydrides, 652
Alkylbenzene(s), from aryl alkyl ketones, Aluminum chloride, FriedelCrafts reaction with acid chlorides, 650651
299300 reaction and, 288289 reaction with aldehydes, 568571
side-chain oxidation of, 298299 Amantadine, structure of, 139 reaction with alkyl halides, 747748
Alkylthio group, 523 Amide(s), 633 reaction with carboxylic acids and
Alkyne(s), 179 amines from, 660661 DCC, 646
acetylide anions from, 252253 basicity of, 742743 reaction with enones, 582
acidity of, 252253 carboxylic acids from, 659660 reaction with esters, 657
alkenes from, 251 DCC for formation of, 646 reaction with ketones, 568571
electrophilic addition reactions of, electrostatic potential map of, 639 secondary, 736
196 from acid anhydrides, 652 SN2 reactions of, 747748
electrostatic potential map of, 79 from acid chlorides, 650651 structure of, 739
hydrogenation of, 251 from amines, 751 synthesis of, 746750
IR spectroscopy of, 434435 from carboxylic acids, 646647 tertiary, 736
naming, 184 from esters, 657 uses of, 739
pKa of, 252 from nitriles, 616 Amino acid(s), 777
reaction with Br2, 251 hydrolysis of, 659660 abbreviations for, 780781
reaction with Cl2, 251 IR spectroscopy of, 667 acetoacetate from, 832
reaction with HBr, 251 mechanism of hydrolysis of, 659660 acetyl CoA from, 832
reaction with HCl, 251 mechanism of reduction of, 661 acidic, 782
reduction of, 251 naming, 635 -ketoglutarate from, 832
vinylic halides from, 251 nitriles from, 615 amidomalonate synthesis of, 784785
Alkynyl group, 184 NMR spectroscopy of, 667668 amphiprotic behavior of, 778
Allene, heat of hydrogenation of, 214 nucleophilic acyl substitution reactions basic, 782
structure of, 33 of, 659661 biological precursors of, 839
Allinger, Norman Louis, 133 peptide bond and, 787 biosynthesis of, 838844
Allose, configuration of, 860 pKa of, 690 Boc derivatives of, 794
Allyl group, 184 polarity of, 80 C-terminal, 787
Allylic, 249 reaction with LiAlH4, 660661 catabolism of, 822826, 831838
Allylic carbocation, electrostatic reaction with SOCl2, 615 catabolism of carbon chains in,
potential map of, 249, 385 reduction of, 660661 831838
resonance in, 249 restricted rotation in, 788 configuration of, 779, 782
SN1 reaction and, 385386 Amidomalonate synthesis, 784785 deamination of, 822826
stability of, 249 -amine, name ending for amines, 736 electrophoresis of, 784
Allylic halide, SN1 reaction and, 385386 Amine(s), 735 enantioselective synthesis of, 785786
SN2 reaction and, 386 acidity of, 743 essential, 838
Alpha amino acid, see Amino acid, 779 alkenes from, 751752 esters of, 793
Alpha anomer, 863 alpha cleavage of, 422 Fmoc derivatives of, 796
Alpha cleavage, alcohol mass spectrum amides from, 751 from -keto acids, 785
and, 422, 531 basicity of, 740745 from alkyl halides, 784785
aldehyde mass spectrum and, 423, 585 biological, 745746 fumarate from, 832
amine mass spectrum and, 422, 763 carbonyl nucleophilic addition glucogenic, 832
ketone mass spectrum and, 423, 585 reactions of, 568571 HendersonHasselbalch equation and,
Alpha farnesene, structure of, 212 chirality of, 345, 739 746
Alpha-glycosidase, 877, 892 conjugate addition reactions to enones, isoelectric points of, 780781
Alpha helix, molecular model of, 798 582 ketogenic, 832
secondary protein structure and, 798 electrostatic potential map of, 80 molecular weights of, 780781
Alpha-keto acid, amino acids from, 785 from aldehydes, 748750 N-terminal, 787
reductive amination of, 785 from amides, 660661 neutral, 782
transamination of, 822825 from ketones, 748750 nonessential, 838
Alpha-ketoglutarate, from glutamate, 826 from lactams, 661 nonprotein, 779
from oxalosuccinate, 908 from nitriles, 616 oxaloacetate from, 832
glutamate from, 838 HendersonHasselbalch equation and, pIs of, 780781
oxidative decarboxylation of, 908 745746 pKas of, 780781
INDEX I-5
protecting groups for, 793794, 796 Anti stereochemistry, 224 pyrimidine and, 276277
pyruvate from, 832 Antiaromaticity, 273 pyrrole and, 276277
reaction with di-tert-butyl dicarbonate, Antibiotic(s), cephalosporins, 669 requirements for, 273
794 -lactam, 668669 Arrow, electron movement and, 45
reaction with ninhydrin, 789 penicillins, 688669 fishhook, 143
succinyl CoA from, 832 sulfonamides, 285 See also Curved arrow
synthesis of, 784786 vancomycin, 403 Arsenic trioxide, LD50 of, 26
table of, 780781 Antibonding molecular orbital, 22 leukemia therapy and, 26
transimination of, 824 Anticodon (tRNA), 988 Aryl alkyl ketone, reduction of, 299300
zwitterion form of, 778 Antigenic determinants, blood groups Aryl halide, SN2 reaction and, 375376
Amino acid analysis, 789 and, 879 Arylamine(s), 736
Amino acid analyzer, 789 Antisense strand (DNA), 987 basicity of, 741, 743745
Amino group(s), 737 Arabinose, configuration of, 860 electrophilic aromatic substitution of,
directing effect of, 294 Arachidic acid, structure of, 929 753754
inductive effect of, 294295 Arachidonic acid, cyclooxygenase from nitroarenes, 747
orienting effect of, 294 reaction of, 12 resonance in, 744
Amino sugar, 873 prostaglandins from, 12, 243244, synthesis of, 285
p-Aminobenzoic acid, molecular model 948950 Ascorbic acid, see Vitamin C
of, 25 radical reactions of, 146 -ase, enzyme name ending, 801
Aminolysis (nucleophilic acyl structure of, 929 Asparagine, aspartate from, 834
substitution reaction), 640 Arecoline, molecular model of, 81 biosynthesis of, 839840
Aminotransferase, 822824 Arene(s), 269 catabolism of, 834
Ammonia, carbamoyl phosphate from, electrostatic potential map of, 79 from aspartate, 839840
827 see also Aromatic compound fumarate from, 834
dipole moment of, 39 Arginase, 831 oxaloacetate from, 834
electrostatic potential map of, 150 Arginine, biosynthesis of, 828831, structure and properties of, 780
elimination of in animals, 827 840841 Asparagine synthetase, 839
hydrogen bond in, 63 from glutamate, 840841 Aspartame, molecular model of, 29
reaction with acid chlorides, 650651 ornithine from, 831 structure of, 816, 881
reaction with carboxy phosphate, 827 structure and properties of, 781 sweetness of, 880
reaction with carboxylic acids and urea cycle and, 828831 Aspartate, asparagine from, 839840
DCC, 646 Argininosuccinate, arginine from, biosynthesis of, 838
urea cycle and, 827831 830831 catabolism of, 834
Amphetamine, synthesis of, 748749 from citrulline, 828830 from oxaloacetate, 828
Amplitude, 426 metabolism of, 413 fumarate from, 834
-Amylase, 800, 892893 urea cycle and, 828830 homoserine from, 842843
Amylopectin, structure of, 876877 Argininosuccinate lyase, 830 oxaloacetate from, 834
Amylose, structure of, 876877 stereochemistry of, 830 partial reduction of, 842
Anabolism, 818 Argininosuccinate synthetase, 828 reaction with citrulline, 828830
Androgen, 962 epi-Aristolochene, biosynthesis of, 218 threonine from, 842844
function of, 962 Aromatic compound(s), 267 Aspartate semialdehyde, from aspartate,
Androstenedione, structure and function alkylation of, 288289 842
of, 962 biological hydroxylation of, 286287 Aspartic acid, structure and properties of,
Androsterone, structure and function of, bromination of, 282284 781
962 characteristics of, 273275 Asphalt, composition of, 103
-ane, alkane name ending, 86 chlorination of, 283 Aspirin, LD50 of, 26
Angle strain, 118 common names for, 268 molecular model of, 17
Angstrom, 3 electrophilic substitution reactions of, synthesis of, 652
Anhydride, see Acid anhydride 282283 Asymmetric center, 322
Aniline, basicity of, 743745 FriedelCrafts acylation of, 290 -ate, ester name ending, 635
electrostatic potential map of, 744 FriedelCrafts alkylation of, 288289 Atom, atomic mass of, 4
from nitrobenzene, 285 halogenation of, 282284 atomic number of, 4
synthesis of, 285 iodination of, 284 electron configurations of, 56
Anilinium ion, electrostatic potential IR spectroscopy of, 435 electron shells in, 45
map of, 744 naming, 268270 isotopes of, 4
Anilinothiazolinone, Edman degradation nitration of, 284285 orbitals in, 45
and, 790791 oxidation of, 298299 quantum mechanical model of, 45
Anisole, electrostatic potential map of, reduction of, 299300 size of, 3
623 see also Aromaticity structure of, 3
Anomer, 862 sulfonation of, 286 Atomic mass, 4
-, 863 trisubstituted, 300302 Atomic number (Z), 4
-, 863 Aromaticity, heterocycles and, 276277 Atomic weight, 4
Anomeric center, 862 Hckel 4n 2 rule and, 273275 Atorvastatin, structure and function of,
Anthracene, structure of, 278 imidazole and, 276277 1010
Anti conformation, 99 ions and, 315 ATP, see Adenosine triphosphate
Anti periplanar geometry, 396 naphthalene and, 279 Atropine, structure proof of, 773
molecular model of, 396 pyridine and, 276277 ATZ, see Anilinothiazolinone, 790791
I-6 INDEX
Aufbau principle, 5 Benzoquinone, electrostatic potential halohydrin formation, 227

Avian flu, 920 map of, 519 Hofmann elimination reaction, 752
Axial bonds (cyclohexane), 123 Benzoyl group, 559 hydrolysis, thioester, 678
drawing, 124 Benzoyl peroxide, ethylene hydroxylation (aromatic), 286287
polymerization and, 240241 iodination (aromatic), 284
, see Beta Benzo[a]pyrene, metabolism of, 238 methylation, 390391
Backbone (protein), 787 structure of, 278 nucleophilic acyl substitution, 648649
Backside displacement, SN2 reaction and, Benzyl ester, hydrogenolysis of, 793 oxidations with FAD, 939940
372373 Benzyl group, 269 oxidations with NAD, 519
von Baeyer, Adolf, 118 Benzylic carbocation, electrostatic radical reaction, 146, 243244
Baeyer strain theory, 118 potential map of, 385 energy diagram of, 167
Banana, esters in, 653 resonance in, 385 reductions ( alkene), 234235
Base, BrnstedLowry, 50 SN1 reaction and, 385386 reduction (aldehyde), 580
Lewis, 58 Benzylic halide, SN1 reaction and, reduction (ketone, 580
organic, 57 385386 reduction (thioester), 663
strengths of, 5153 SN2 reaction and, 386 reduction with NADH, 507
Base pair (DNA), 982984 Benzylic radical, resonance in, 299 reduction with NADPH, 507
electrostatic potential maps of, 983 Benzylpenicillin, discovery of, 668 reductive amination, 750
hydrogen bonding in, 983 Beta anomer, 863 SN1 reaction, 390391
Base peak (mass spectrum), 416 Beta-carotene, structure of, 179, 951 SN2 reaction, 390391
Basicity, alkylamines, 740743 industrial synthesis of, 577 Biot, Jean Baptiste, 325
amides, 742743 UV spectrum of, 442 Biotin, carboxylation with, 913, 916, 945
amines, 740745 Beta-diketone, Michael reactions and, mechanism of carboxylation with, 916,
arylamines, 741, 743745 715 945
heterocyclic amines, 742 Beta-keto acid, decarboxylation of, 693 stereochemistry of, 356
nucleophilicity and, 377 Beta-keto ester, alkylation of, 696 structure and function of, 803, 913,
Basicity constant (Kb), 741 cyclic, 711713 916, 945
Beeswax, 928 decarboxylation of, 696 bis, name prefix, 662
Benedicts test, 870 Michael reactions and, 715 1,3-Bisphosphoglycerate, from
Bent bond, cyclopropane, 119120 pKa of, 690 glyceraldehyde 3-phosphate, 898
Benzaldehyde, electrophilic aromatic synthesis of, 708710 reaction with ADP, 899
substitution of, 296297 Beta-lactam antibiotics, 668669 Blood groups, antigenic determinants in,
electrostatic potential map of, 294 Beta-oxidation pathway, 938942 879
IR spectrum of, 584 mechanism of, 938942 compatibility of, 879
13C NMR absorptions of, 585 Beta-pleated sheet, molecular model of, types of, 879
Benzene, alkylation of, 288289 798 Boc (tert-butoxycarbonyl amide), 794
bond lengths in, 271 secondary protein structure and, 797 amino acid protection with, 794
bromination of, 282284 Bextra, prostaglandin synthesis and, 2 Bombykol, 538
chlorination of, 283 structure of, 313 Bond, covalent, 1011
discovery of, 269 Bimolecular, 372 pi, 15
electrostatic potential map of, 44, 271, Biodegradable polymers, 665666 sigma, 10
294 Biological amine(s), Bond angle, 13
FriedelCrafts reactions of, 288290 HendersonHasselbalch equation Bond dissociation energy (D), 161
heat of hydrogenation of, 271 and, 745746 table of, 162
Hckel 4n 2 rule and, 274275 protonation of, 745746 Bond length, 11
iodination of, 284 Biological carboxylic acid(s), dissociation Bond strength, 11
molecular orbitals of, 272273 of, 608609 Bonding molecular orbital, 22
nitration of, 284285 HendersonHasselbalch equation and, Borane, electrophilicity of, 229
reaction with Br2, 282283 608609 reaction with alkenes, 229230
reaction with Cl2, 283 Biological mass spectrometry, 424425 Borneol, rearrangement of, 977
reaction with HNO3, 284285 Biological reactions Boron trifluoride, electrostatic potential
reaction with I2, 284 alcohol dehydration, 513514 map of, 59, 151
resonance in, 44, 271 aldol reaction, 718719 Branched-chain alkane, 83
stability of, 271 alkylation, 700 Breathalyzer test, 532
structure of, 270273 benzylic oxidation, 299 BRENDA enzyme database, 807
sulfonation of, 285286 characteristics of, 168170 Bridgehead atom, 131
toxicity of, 267 Claisen condensation reaction, 720 Broadband-decoupled NMR, 467
UV absorption of, 441 comparison with laboratory reactions, Bromine, reaction with alkenes, 224225
Benzenesulfonic acid, synthesis of, 168170 reaction with aromatic compounds,
286 conjugate nucleophilic addition 282284
Benzodiazepine, combinatorial library reaction, 582 Bromo group, directing effect of, 294
of, 306 conventions for writing, 169, 197 p-Bromoacetophenone, molecular model
Benzoic acid, 13C NMR absorptions in, dehydration, 513514 of, 465
618 elimination reaction, 400 13C NMR spectrum of, 465
pKa of, 606, 609 epoxidation, 236237 symmetry plane in, 465
substituent effects on acidity of, 609 FriedelCrafts alkylation, 290291 Bromocyclohexane, molecular model of,
Benzophenone, structure of, 559 halogenation (alkene), 225 125
INDEX I-7
Bromoethane, 1H NMR spectrum of, Camphor, specific rotation of, 326 Carbonyl group(s), 547
476 structure of, 951 directing effect of, 294
spinspin splitting in, 476478 Cannizzaro reaction, 579 inductive effect of, 294295
Bromohydrin(s), 226 mechanism of, 579 orienting effect of, 294
from alkenes, 226227 Capsaicin, structure of, 81 resonance effect of, 294295
mechanism of formation of, 226227 -carbaldehyde, aldehyde name ending, 558 -carbothioate, thioester name ending,
Bromomethane, electrostatic potential Carbamoyl phosphate, biosynthesis of, 635
map of, 150 827 -carboxamide, amide name ending, 635
Bromonium ion, 224 reaction with ornithine, 828829 Carboxy phosphate, mechanism of
electrostatic potential map of, 225 Carbamoyl phosphate synthetase, 827 formation, 945
from alkenes, 224 Carbanion, 393, 567 reaction with ammonia, 827
2-Bromopropane, 1H NMR spectrum of, stability of, 253 Carboxylate ion, reaction with acid
478 Carbinolamine, 569 chlorides, 648
spinspin splitting in, 478 Carbocation(s), 153 reaction with alkyl halides, 643
BrnstedLowry acid, 50 alkyl shift in, 207208 resonance in, 607
conjugate base of, 50 aromatic substitution and, 282 Carboxylation, 612
strengths of, 5153 E1 reaction and, 399 biological, 913, 916, 945
BrnstedLowry base, 50 electronic structure of, 202203 -carboxylic acid, name ending for
conjugate acid of, 50 electrophilic addition reactions and, carboxylic acids, 602
strengths of, 5153 153, 195196 Carboxylic acid(s), 601
cis-But-2-ene, heat of hydrogenation of, FriedelCrafts reaction and, 289 acid anhydrides from, 643
194 Hammond postulate and, 204206 acid chlorides from, 642643
molecular model of, 186, 192 hydride shift in, 207208 acidity of, 605607
steric strain in, 192 hyperconjugation in, 202203 alcohols from, 507508, 647
trans-But-2-ene, heat of hydrogenation of, Markovnikovs rule and, 199 amides from, 646647
194 molecular orbital of, 203 biological, 608609
molecular model of, 186, 192 rearrangements of, 206208, 289 biological nucleophilic acyl
But-3-en-2-one, electrostatic potential SN1 reactions and, 382383 substitutions of, 647648
map of, 581 solvation of, 388 common names of, 603
UV absorption of, 441 stability of, 202203, 386 dimers of, 605
Buta-1,3-diene, 1,2 addition reactions of, steroid biosynthesis and, 968969 dissociation of, 605606
248249 Carbohydrate(s), 851 dissociation of in cells, 608609
1,4 addition reactions of, 248249 anomers of, 863864 esters from, 643645
electrophilic addition reactions of, catabolism of, 893900 from acid halides, 648
248249 classification of, 853 from alcohols, 516517
electrostatic potential map of, 248 complex, 852 from aldehydes, 561562
heat of hydrogenation of, 245 Fischer projections of, 854856 from alkyl halides, 611612, 692694
molecular orbitals in, 247 glycosides of, 867868 from amides, 659660
reaction with HBr, 248249 14-links in, 874875 from esters, 654656
stability of, 245247 origin of name, 851 from Grignard reagents, 612
UV spectrum of, 440 photosynthesis of, 852 from malonic ester, 692694
Butan-1-ol, mass spectrum of, 531 see also Aldose, Monosaccharide from nitriles, 611612, 616
Butan-2-one, 13C NMR spectrum of, 465, Carbon, ground-state electron HendersonHasselbalch equation and,
585 configuration of, 6 608609
Butane, anti conformation of, 99100 Carbon atom, 3 dimensionality of, 7 hydrogen bonding in, 605
bond rotation in, 99100 tetrahedral geometry of, 7 inductive effects in, 609
conformations of, 99100 -carbonitrile, nitrile name ending, 604 IR spectroscopy of, 617
gauche conformation of, 99100 Carbonyl chemistry, overview of, naming, 602603
molecular model of, 83 547555 NMR spectroscopy of, 618
Butanoic acid, IR spectrum of, 617 Carbonyl compound(s), acidity of, nucleophilic acyl substitution reactions
tert-Butoxycarbonyl amide, amino acid 689690 of, 642645
protection with, 794 alcohols from, 505511 occurrence of, 601
Butter, composition of, 929 alkylation of, 691699 pKa table of, 606
tert-Butyl alcohol, pKa of, 502 classification of, 548549 polarity of, 80
tert-Butyl carbocation, molecular model electrophilicity of, 549 properties of, 605
of, 202 electrostatic potential map of, 80, 150 protonation of in cells, 745746
Butyl group, 87 from alcohols, 516519 reaction with alcohols, 644645
Butyllithium, reaction with general reactions of, 550555 reaction with amines and DCC, 646
alkyltriphenylphosphonium salts kinds of, 80 reaction with ammonia and DCC, 646
reaction with diisopropylamine, 689 mass spectrometry of, 422423 reaction with diazomethane, 677
name endings for, 548 reaction with Grignard reagents, 510
c (Speed of light), 426 polarity of, 80 reaction with LiAlH4, 507508, 647
C-terminal amino acid, 787 table of, 548 reaction with SOCl2, 642643
Cadaverine, odor of, 740 Carbonyl condensation reaction, 554, 681 reactions of, 613
Caffeine, structure of, 33 -substitution reactions and, 704 reduction of, 507508, 647
CahnIngoldPrelog sequence rules, biological, 718720 substituent effects on acidity of, 609
188190, 328 mechanism of, 701 synthesis of, 611612
I-8 INDEX
Carboxylic acid derivative(s), 663 Chirality center, 322 Coconut oil, composition of, 929
electrostatic potential maps of, 639 detection of, 323 Coding strand (DNA), 987
interconversions of, 640 R,S configuration of, 328330 Codon (mRNA), 988
IR spectroscopy of, 666667 Chloral hydrate, structure of, 566 table of, 988
kinds of, 663 Chloramphenicol, structure of, 357 Coenzyme, 170, 802
naming, 634636 Chlorine, reaction with alkanes, 95 functions of, 802803
NMR spectroscopy of, 667668 reaction with alkenes, 224 table of, 802803
nucleophilic acyl substitution reactions reaction with aromatic compounds, 283 Coenzyme A, structure and function of,
of, 640641 reaction with methane, 145 802
polarity of, 639 Chloro group, directing effect of, 294 see also Acetyl CoA
relative reactivity of, 639640 Chlorobenzene, electrostatic potential Coenzyme Q, 520
Cardiolipin, structure of, 973 map of, 294 function of, 1004
Carvone, structure of, 24 Chloroform, LD50 of, 26 Cofactor (enzyme), 802
Caryophyllene, structure of, 975 Chloromethane, dipole moment of, 39 Color, perception of, 442443
Catabolism, 818 electrostatic potential map of, 147 UV spectroscopy and, 442443
acetyl CoA, 905910 natural sources of, 363 Combinatorial chemistry, 306307
amino acids, 822826, 831838 Chloronium ion, 224 kinds of, 307
carbohydrates, 893900 Chlorosulfite, 643 Combinatorial library, 306
fats, 934942 leaving group ability of, 378 Common cold, vitamin C and, 619
fatty acids, 937942 Cholestanol, structure of, 334 Complex carbohydrate, 852
glucose, 893900 Cholesterol, biosynthesis of, 964969 biological hydrolysis of, 892893
glycerol, 934937 heart disease and, 970 Concanavalin A, sheet in, 798
nucleic acids, 9971002 molecular model of, 961 ribbon model of, 798
pyruvate, 901905 specific rotation of, 326 Condensed structure, 22
triacylglycerols, 934942 statin drugs and, 1009 1010 rules for drawing, 2223
Catalytic cracking, 103 Cholic acid, molecular model of, 602 Cone cells, vision and, 443
Catalytic hydrogenation, see Choline, synthesis of, 772 Configuration, 328
Hydrogenation Chromate, alcohol oxidation and, 518 assignment of, 328330
Cation radical, mass spectrometry and, Chromatography, 444 chirality centers and, 328330
416 explanation of, 444445 Fischer projections and, 855
Celebrex, prostaglandin synthesis and, 2 high-pressure, 444 inversion of, 368370
Cell membrane, lipid bilayer in, 934 liquid, 444 R, 329
Cellobiose, molecular model of, 874 Chrysanthemic acid, structure of, 111 S, 329
mutarotation of, 874 Chymotrypsin, peptide cleavage with, 792 Conformation (cyclohexane), 97
Cellulose, function of, 876 trans-Cinnamaldehyde, 1H NMR calculating energy of, 133
structure of, 876 spectrum of, 482 E2 reactions and, 397
uses of, 876 synthesis of, 729 Conformational analysis (cyclohexane),
Cellulose nitrate, 876 tree diagram for, 483 128130
Cephalexin, structure of, 669 Cistrans isomers, 116 Coniine, molecular model of, 28
Cephalosporin, structure of, 669 alkenes and, 186187 Conjugate acid, 50
Chain, Ernst, 668 cycloalkanes and, 115116 Conjugate base, 50
Chain-growth polymer, 240242, 664 requirements for, 187 Conjugate nucleophilic addition reaction,
Chain reaction (radical), 145 Citrate, biosynthesis of, 804805, 580583
Chair conformation (cyclohexane), 122 906907 biological, 582
drawing, 122 Citrate synthase, active site in, 805 mechanism of, 581
molecular model of, 122 function of, 804 Michael reactions and, 713715
see also Cyclohexane mechanism of, 806 Conjugated diene(s), 245
Chemical Abstracts, 75 molecular model of, 805 1,2 addition reactions of, 248249
Chemical reactions, conventions for Citric acid, molecular model of, 28 1,4 addition reactions of, 248249
writing, 197 Citric acid cycle, 819, 905910 allylic carbocations from, 249
Chemical shift (NMR), 461 requirements for, 905 electrophilic addition reactions of,
13C NMR spectroscopy and, 464 result of, 910 248249
1H NMR spectroscopy and, 473474 steps in, 906 electrostatic potential map of, 248
Chemical structure, drawing, 2224 Citrulline, argininosuccinate from, heats of hydrogenation of, 245
Chemical waste, green chemistry and, 828830 molecular orbitals in, 247
764765 from ornithine, 828829 reaction with HBr, 248249
Chiral, 321 reaction with aspartate, 828830 stability of, 245248
Chiral drugs, 351352 Claisen condensation reaction, 708710 Conjugation, 245
Chiral methyl group, 414 -oxidation and, 941 ultraviolet spectroscopy and, 441
Chirality, amines and, 345, 739 biological, 718719 Constitutional isomers, 83
amino acids and, 782 fatty acid biosynthesis and, 720 kinds of, 84
carbohydrates and, 858859 intramolecular, 711713 Contraceptive, steroid, 963
cause of, 322 mechanism of, 709710 Copper(II) chloride, aromatic iodination
naturally occurring molecules and, requirements for, 709 and, 284
349351 Cocaine, specific rotation of, 327 Coprostanol, structure of, 334
phosphines and, 345, 785786 structure of, 735 Corn oil, composition of, 929
sulfonium salts and, 346 synthesis of, 733 Coronene, structure of, 278
INDEX I-9
Cortisone, structure of, 111 Cyclohexanol, IR spectrum of, 529 Deamination, 822
Couper, Archibald Scott, 6 13C NMR spectrum of, 530 amino acids and, 822826
Coupled reactions, ATP and, Cyclohexanone, aldol reaction of, 702 mechanism of, 823825
820821 enol content of, 683 PLP and, 823825
Coupling (NMR), 477 enolate ion of, 689 Debye (D), 38
see also Spinspin splitting IR spectrum of, 584 cis-Decalin, conformation of, 132
Coupling constant, 478 13C NMR absorptions of, 585 molecular model of, 132, 960
size of, 478 Cyclohexene, heat of hydrogenation of, trans-Decalin, conformation of, 132
use of, 478 271 molecular model of, 132, 960
Covalent bond, 8 IR spectrum of, 449 Decane, molecular model of, 101
molecular orbital theory of, 2122 Cyclohexenones, from 1,5-diketones, Decarboxylation, 693
polar, 36 707708 acetoacetic ester synthesis and, 696
rotation around, 115 Cyclohexylamine, IR spectrum of, 762 malonic ester synthesis and, 693694
valence bond theory of, 1020 Cyclohexylmethanol, 1H NMR spectrum orotidine monophosphate and, 1005
COX-2, see Cyclooxygenase of, 484 thiamin diphosphate and, 901903
COX-2 inhibitors, 2 Cyclononane, strain energy of, 118 DEET, structure of, 677
Crick, Francis H. C., 982 Cyclooctane, strain energy of, 118 Degenerate orbitals, 273
Crotonaldehyde, structure of, 558 Cyclooctatetraene dianion, aromaticity Degree of unsaturation, 180
Crotonic acid, 13C NMR absorptions in, of, 315 calculation of, 180181
618 electrostatic potential map of, 274 Dehydration, alcohols, 222
Crum Brown, Alexander, 7 Hckel 4n 2 rule and, 274 alcohol mass spectrum and, 531
Crystallization, fractional, 338 reactivity of, 274 aldol reaction and, 705706
Curved arrow, electron movement Cyclooxygenase, 12 biological, 513514
and, 45 function of, 948, 950 Dehydrohalogenation, 222
guidelines for using, 154156 types of, 948 Delocalization (electron), 248
polar reactions and, 149, 154156 Cyclooxygenase reaction, arachidonic Delta scale (NMR), 461
meaning of, 5859 acid and, 12 Denature (protein), 799
Cyanocobalamin, structure of, 1009 Cyclopenta-1,3-diene, electrostatic Deoxy sugar, 873
Cyanocycline A, structure of, 614 potential map of, 756 Deoxyguanosine, catabolism of, 9971000
Cyanogenic glycoside, 614 Cyclopentadienyl anion, aromaticity of, Deoxyribonucleic acid (DNA), 979982
Cycloalkane(s), 112 315 antisense strand of, 987
angle strain in, 118 Cyclopentane, angle strain in, 120121 base-pairing in, 982984
Baeyer strain theory and, 118 conformation of, 120121 bases in, 980
cistrans isomerism in, 115116 molecular model of, 121 cleavage of, 991
naming, 112114 strain energy of, 118 coding strand of, 987
representation of, 112 torsional strain in, 120121 double helix in, 982984
strain energies of, 118 Cyclopentanone, IR absorption of, 583 3 end of, 982
Cycloalkene, naming, 183 Cyclopentenones, from 1,4-diketones, 5 end of, 982
Cyclobutadiene, antiaromaticity of, 707708 exons in, 987
274 Cyclopropane, angle strain in, 119120 fingerprinting with, 10101011
electrostatic potential map of, 274 bent bonds in, 119120 introns in, 987
Hckel 4n 2 rule and, 274 bond strength in, 120 major groove in, 983984
Cyclobutane, angle strain in, 120 molecular model of, 115, 119 minor groove in, 983984
conformation of, 120 strain energy of, 118 polymerase chain reaction and,
molecular model of, 120 torsional strain in, 119120 995997
strain energy of, 118 Cystathionine, cysteine from, 849 promotor sites in, 987
torsional strain in, 120 Cysteine, biosynthesis of, 849 replication fork in, 986
Cyclodecane, strain energy of, 118 disulfide bridges from, 788 replication of, 985986
Cyclodecapentaene, molecular model of, structure and properties of, 780 sense strand of, 987
275 Cytidine, biosynthesis of, 1006 sequencing of, 990992
Cycloheptane, strain energy of, 118 catabolism of, 1002 size of, 980
Cycloheptatrienyl cation, aromaticity of, Cytosine, electrostatic potential map of, structure of, 981984
315 983 synthesis of, 992995
Cyclohexa-1,3-diene, heat of molecular model of, 68 template strand of, 987
hydrogenation of, 271 protection of, 993 transcription of, 986987
UV absorption of, 441 structure of, 980 WatsonCrick model of, 982984
Cyclohexane, axial bonds in, 123125 Deoxyribonucleotide(s), structures of,
barrier to ring flip in, 125 D (Debye), 38 981
chair conformation of, 122125 D (Bond dissociation energy), 161 2-Deoxyribose, structure of, 980
conformational analysis of, 126130 D Sugar, 858 1-Deoxyxylulose 5-phosphate,
1,3-diaxial interactions in, 126128 Fischer projections of, 858 isopentenyl diphosphate from, 952
drawing chair form of, 122 Dacron, structure of, 665 DEPT-NMR, 467468
equatorial bonds in, 123125 DCC, see Dicyclohexylcarbodiimide uses of, 467468
IR spectrum of, 448 Deactivating group (aromatic DEPT-NMR spectrum, 6-methylhept-5-en-
ring-flip in, 125 substitution), 294 2-ol, 468
strain energy of, 118 acidity and, 610 Detectors, mass spectrometry and, 416
twist-boat conformation of, 123 explanation of, 294295 Detergent, structure of, 932
I-10 INDEX
Deuterium isotope effect, 395 Dimethylallyl diphosphate (DMAPP), E configuration, 188

E1 reaction and, 399 from isopentenyl diphosphate, 956 assignment of, 188190
E2 reaction and, 395 terpenoid biosynthesis and, 956958 E1 reaction, 393, 398
Dextromethorphan, structure of, 324 Dimethylamine, electrostatic potential carbocations and, 399
Dextrorotatory, 326 map of, 740 deuterium isotope effect and, 399
Dialkyl phthalates, plasticizers and, cis-1,2-Dimethylcyclohexane, kinetics of, 399
653654 conformational analysis of, 128130 mechanism of, 398399
Dialkylamine, pKa of, 690 trans-1,2-Dimethylcyclohexane, rate-limiting step in, 399
Diastereomers, 334 conformational analysis of, 128130 stereochemistry of, 399
kinds of, 341 cis-1,2-Dimethylcyclopropane, molecular E1cB reaction, 393, 400
Diastereotopic (NMR), 472 model of, 116 biological, 400
1,3-Diaxial interactions, 126128 trans-1,2-Dimethylcyclopropane, carbanion intermediate in, 400
table of, 128 molecular model of, 116 mechanism of, 400
Diazepam, structure of, 182, 267, 283 Dimethylformamide, SN2 reaction and, rate-limiting step in, 400
Diazomethane, reaction with carboxylic 379 requirements for, 400
acids, 677 2,2-Dimethylpropane, mass spectrum of, E2 reaction, 393, 394
DIBAH, see Diisobutylaluminum hydride 418 alcohol oxidation and, 518
Dibromophosphite, leaving group ability molecular model of, 83 cyclohexane conformation and, 397
of, 378 N,N-Dimethyltryptamine, molecular deuterium isotope effect and, 395
cis-1,2-Dichloroethylene, electrostatic model of, 761 kinetics of, 395
potential map of, 67 Diol, 236 mechanism of, 394395
trans-1,2-Dichloroethylene, electrostatic from alkenes, 236239 menthyl chloride and, 397
potential map of, 67 from epoxides, 236238 neomenthyl chloride and, 397
Dicyclohexylcarbodiimide (DCC), amide DiPAMP ligand, amino acid synthesis periplanar geometry of, 395397
bond formation with, 646 and, 785786 rate law for, 395
peptide synthesis with, 794 Dipole moment (), 38 rate-limiting step in, 395
Dideoxy DNA sequencing, 991992 polar covalent bonds and, 3839 stereochemistry of, 397
2,3-Dideoxyribonucleotide, 991 table of, 39 Ebonite, structure of, 254
Dieckmann cyclization, 711713 Dipoledipole forces, 62 Eclipsed conformation, 97
mechanism of, 711712 Disaccharide, 873876 molecular model of, 97
Diene, conjugated, 245 14-links in, 874875 Edman degradation, 790792
Diene polymers, 253254 synthesis of, 878 mechanism of, 790791
vulcanization of, 254 Disparlure, 543 Eicosanoid, 948950
Diethyl ether, synthesis of, 523 Dispersion forces, 62 biosynthesis of, 948950
uses of, 498 alkanes and, 96 naming of, 948949
Diethyl malonate, alkylation of, 692694 Distortionless enhancement by Elaidic acid, structure of, 930
carboxylic acids from, 692694 polarization transfer, see DEPT-NMR Electromagnetic radiation, 425
Michael reactions and, 715 Disulfide, 521 amplitude of, 426
pKa of, 690 electrostatic potential map of, 80 characteristics of, 425426
Diethyl propanedioate, see Diethyl from thiols, 521 energy of, 427
malonate polarity of, 80 frequency of, 426
Diffraction limit, light waves and, 720 reduction of, 521 kinds of, 425
Digestion, 819 thiols from, 521 speed of, 426
Digitoxin, structure of, 868 Disulfide bridge, peptides and, 788 wavelength of, 426
Dihedral angle, 98 Diterpene, 209 Electromagnetic spectrum, 425
Dihydrogen phosphate ion, pKa of, 52 Diterpenoid, 951 regions in, 425
Dihydrolipoamide, oxidation by FAD, 904 DMAPP, see Dimethylallyl diphosphate, Electron, delocalization of, 248
Dihydroorotase, 1003 956 lone-pair, 9
Dihydroorotate dehydrogenase, 1004 DMF, see Dimethylformamide nonbonding, 9
Dihydroxyacetone phosphate, fructose DMSO, see Dimethyl sulfoxide spin of, 6
1,6-bisphosphate from, 917918 DMT (dimethoxytrityl ether), 993 Electron configuration, ground
isomerization of, 897898 DNA, see Deoxyribonucleic acid state, 5
Diisobutylaluminum hydride, reaction DNA fingerprinting, 10101011 rules for assigning, 56
with esters, 560, 658 reliability of, 10101011 Table of, 6
Diisopropylamine, pKa of, 690, 743 STR loci and, 10101011 Electron-dot structure, 8
reaction with butyllithium, 689 DNA polymerase, 991 Electron-impact mass spectrometry,
1,3-Diketone, pKa of, 690 Dopamine, molecular model of, 748 416417
Dimethyl ether, electrostatic potential Double bond, electronic structure of, 1416 Electron movement, curved arrows
map of, 59, 523 length of, 1516 and, 5859
Dimethyl sulfide, bond angle in, 20 molecular orbitals in, 22 Electron shell, 4
molecular model of, 20 see also Alkene Electron-transport chain, 819
sp3 hybrid orbitals in, 20 strength of, 1516 Electronegativity, 36
structure of, 20 Double helix (DNA), 982984 inductive effects and, 37
Dimethyl sulfoxide, electrostatic Doublet (NMR), 478 polar covalent bonds and, 3637
potential map of, 41 Downfield (NMR), 460 table of, 36
formal charges in, 4042 Drugs, approval procedure for, 171 Electrophile, 149150
skin penetration by, 528 chiral, 351352 characteristics of, 155
SN2 reaction and, 379 origin of, 171 curved arrows and, 154156
INDEX I-11
electrostatic potential maps of, 150 chlorobenzene, 294 vinylic anion, 253
examples of, 150 chloromethane, 37, 147 water, 54, 150
Electrophilic addition reaction, 195196 conjugated diene, 248 zwitterion, 778
carbocation rearrangements in, cyclobutadiene, 274 Elimination reaction(s), 142
206208 cyclooctatetraene, 274 mechanisms of, 393400
energy diagram of, 164167 cyclopenta-1,3-diene, 756 summary of, 401
Hammond postulate and, 204206 cytosine, 983 EmbdenMeyerhof pathway, 893900
intermediate in, 166 cis-1,2-dichloroethylene, 67 see also Glycolysis
Markovnikovs rule and, 198199 trans-1,2-dichloroethylene, 67 Enamido acid, amino acids from,
mechanism of, 152154, 195196 dimethyl ether, 59, 523 785786
regiospecificity of, 198199 dimethyl sulfoxide, 41 Enamine, 568
stereochemistry and, 342344 dimethylamine, 740 conjugate addition reactions of, 717
Electrophilic aromatic substitution disulfide, 80 electrostatic potential map of, 716
reaction, 281 DNA base pairs, 983 from aldehydes, 568571
arylamines and, 753754 electrophiles, 150 from ketones, 568571
inductive effects in, 294295 enamine, 716 mechanism of formation of, 570
kinds of, 281 enol, 682, 685 Michael reactions of, 717
pyridine and, 758 enolate ion, 688, 692 nucleophilicity of, 716
pyrrole and, 756757 ester, 639 reaction with enones, 717
resonance effects in, 294295 ethane, 152 Enantiomeric excess, 587
substituent effects in, 292297 ether, 79 Enantiomers, 320
Electrophoresis, 784 ethoxide ion, 607 discovery of, 327328
DNA sequencing and, 992 ethylene, 78, 152 resolution of, 338340
Electrospray ionization mass fatty-acid carboxylate, 932 Enantioselective synthesis, 352, 587
spectrometry, see ESI mass formaldehyde, 173 Enantiotopic (NMR), 471472
spectrometry formate ion, 607 Endergonic reaction, 158
Electrostatic potential map, 37 Grignard reagent, 367 Hammond postulate and, 205
acetaldehyde, 549 guanine, 983 Endothermic reaction, 159
acetamide, 639, 673, 743 histidine, 782 -ene, alkene name ending, 182
acetate ion, 44, 54, 57, 607 HOSO2, 286 Energy diagram, see also Reaction energy
acetic acid, 54, 56 hydrogen bond, 63, 501 diagram, 163164
acetic acid dimer, 605 hydronium ion, 150 Energy-rich bonds, explanation of,
acetic anhydride, 639 hydroxide ion, 54, 150 161162
acetone, 56, 57, 80, 555 imidazole, 61, 276 Enethiol, 497
acetone anion, 57 menthene, 78 Enflurane, molecular model of, 325
acetonitrile, 615 methanethiol, 173 Enol, 497, 682
acetyl azide, 673 methanol, 37, 56, 57, 148, 501 -substitution reaction and, 685686
acetyl chloride, 555, 639 methoxide ion, 57 electrostatic potential map of, 682, 685
acetylide anion, 253 methyl acetate, 639 from aldehydes, 682684
acid anhydride, 639 methyl anion, 253 from ketones, 682684
acid chloride, 639 methyl thioacetate, 639 mechanism of acid-catalyzed formation
acyl cation, 290 methylamine, 38, 57, 743 of, 683
adenine, 983 methyllithium, 37, 147 mechanism of base-catalyzed formation
alanine, 778 methylmagnesium chloride, 567 of, 684
alanine zwitterion, 778 methylmagnesium iodide, 367 reactivity of, 685687
alcohol, 79 naphthalene, 279 Enolase, 900
alkene, 79, 152 nitronium ion, 285 Enolate ion, 553, 684
alkyl halide, 79 nucleophiles, 150 alkylation of, 691699
alkyne, 79 nucleophilic addition reaction, 562 electrostatic potential map of, 688, 692
allyl carbocation, 249, 385 penta-1,4-diene, 248 reactivity of, 691692
amide, 639 phenol, 294 resonance in, 688
amine, 80 phosphate, 79 Enone, conjugate addition reactions of
ammonia, 150 polar covalent bonds and, 37 amines, 582
aniline, 744 protonated methanol, 148 conjugate addition reactions of water,
anilinium ion, 744 purine, 761 582
anisole, 623 pyridine, 276 from aldehydes, 705706
arene, 79 pyrimidine, 276 from aldol reaction, 705706
benzaldehyde, 294 pyrrole, 276, 756 from ketones, 705706
benzene, 44, 271, 294 pyrrolidine, 756 IR absorption of, 583
benzoquinone, 519 SN2 reaction, 373 molecular orbitals of, 706
benzyl carbocation, 385 sulfide, 80 reaction with amines, 582
boron trifluoride, 59, 151 thioanisole, 623 reaction with water, 582
bromomethane, 150 thioester, 639 stability of, 705706
bromonium ion, 225 thiol, 80 synthesis of, 688
but-3-en-2-one, 581 thymine, 983 Enoyl-CoA hydratase, 940
buta-1,3-diene, 248 toluene, 311 Entgegen, E configuration and, 188
carbonyl compound, 80, 150 trifluoromethylbenzene, 311 Enthalpy change (H), 159
carboxylic acid derivatives, 639 trimethylamine, 740 explanation of, 159
I-12 INDEX
EntnerDouderoff pathway, 923 mechanism of Grignard reaction of, 658 Ethyl acetate, ethyl acetoacetate from,
Entropy change (S), 160 mechanism of reduction of, 657 709710
explanation of, 160 naming, 635 1H NMR spectrum of, 667
Enzyme, 168169, 800801 NMR spectroscopy of, 667668 Ethyl acetoacetate, see Malonic ester
active site in, 169 nucleophilic acyl substitution reactions Ethyl acrylate, 13C NMR absorptions in,
classification of, 801 of, 654658 466
naming, 801 occurrence of, 653 Ethyl alcohol, see Ethanol
rate enhancements in, 800 partial reduction of, 560 Ethyl benzoate, 13C NMR spectrum of,
specificity of, 800 pKa of, 690 492
stereochemistry of reactions, 350351 polarity of, 80 Ethyl cation, molecular orbital of, 203
substrates for, 800 reaction with amines, 657 Ethyl group, 86
transition state stabilization by, 800 reaction with DIBAH, 560, 658 Ethylcyclopentane, mass spectrum of,
turnover number of, 800 reaction with Grignard reagents, 420
visualization of, 844845 509510, 658 Ethylene, bond angles in, 1516
Ephedrine, structure of, 65 reaction with LDA, 698 bond lengths in, 1516
Epibatidine, molecular model of, 363 reaction with LiAlH4, 507508, 657 bond strengths in, 1516
Epimers, 334 reduction of, 507508, 657658 electrostatic potential map of, 78, 152
Epinephrine, biosynthesis of, 390391 saponification of, 654655 ethanol from, 227
Epoxide(s), 235 uses of, 653 heat of hydrogenation of, 194
acid-catalyzed cleavage of, 236238 Estradiol, structure and function of, hormonal activity of, 179
alcohols from, 505 962963 molecular model of, 15
base-catalyzed cleavage of, 526 Estrogen, 962963 molecular orbitals in, 22
1,2-diols from, 236238 function of, 962 pKa of, 252
from alkenes, 235237 Estrone, structure and function of, polymerization of, 240241
from halohydrins, 236 962963 reaction with H2O, 151154
mechanism of cleavage of, 237238 Ethane, bond angles in, 1314 sp2 hybrid orbitals in, 1416
reaction with acids, 236238 bond lengths in, 1314 structure of, 1416
reaction with base, 526 bond rotation in, 9698 Ethylene dichloride, synthesis of, 224
reaction with HCl, 378 bond strengths in, 1314 Ethylene glycol, acetals from, 574
SN2 reactions of, 378 conformations of, 9698 manufacture of, 237
synthesis of, 235237 eclipsed conformation of, 97 uses of, 237
Equations, conventions for writing, 197 electrostatic potential map of, 152 N-Ethylpropylamine, mass spectrum of,
Equatorial bonds (cyclohexane), 123 molecular model of, 9, 14, 83 764
drawing, 124 rotational barrier in, 97 Ethynylestradiol, structure and function
Equilibrium constant, Keq, 157 sp3 hybrid orbitals in, 1314 of, 963
free-energy change and, 159 staggered conformation of, 97 Exergonic reaction, 158
Ergosterol, UV absorption of, 451 structure of, 14 Hammond postulate and, 205
Erlenmeyer, Emil, 7 torsional strain in, 97 Exon (DNA), 987
Erythronolide B, structure of, 355 Ethanol, from pyruvate, 923 Exothermic reaction, 159
Erythrose, configuration of, 860 history of, 532
ESI mass spectrometry, 424 industrial synthesis of, 227, 498 FAD, see Flavin adenine dinucleotide
Essential amino acid, 838 IR spectrum of, 427 FADH2, see Flavin adenine dinucleotide
biological precursors of, 839 LD50 of, 26 (reduced),
Essential monosaccharide, 872873 metabolism of, 532 Faraday, Michael, 269
biosynthesis of, 873 physiological effects of, 532 Farnesyl diphosphate, biosynthesis of,
Essential oil, 209 pKa of, 52, 502 957958
Ester(s), 633 toxicity of, 532 squalene from, 957, 964
acid-catalyzed hydrolysis of, 655656 U.S. production of, 498 Farnesyl diphosphate synthase, 957
alcohols from, 507510, 657658 Ether(s), 497 Fat(s), 928
aldehydes from, 560, 658 alcohols from, 525526 biological hydrolysis of, 656657,
alkylation of, 698 alkyl halides from, 525526 934937
amides from, 657 bond angles in, 523 catabolism of, 934942
aminolysis of, 657 cleavage of with HI, 525526 energy content of, 928
-keto esters from, 711713 cleavage of with trifluoroacetic acid, saponification of, 931
base-catalyzed hydrolysis of, 654655 526 table of, 929
carbonyl condensation reactions of, electrostatic potential map of, 79 Fatty acid(s), 928
708710 from alcohols, 523524 acetyl CoA from, 937942
carboxylic acids from, 654656 from alkyl halides, 524 biosynthesis of, 943947
electrostatic potential map of, 639 IR spectroscopy of, 529 catabolism of, 937942
from acid anhydrides, 652 naming, 522 Claisen reactions in biosynthesis of,
from acid chlorides, 650 NMR spectroscopy of, 530 720
from alcohols, 515516 polarity of, 79 fatty acyl CoAs from, 937
from carboxylate ions, 643 properties of, 523 mechanism of biosynthesis, 943947
from carboxylic acids, 643645 reaction with HI, 525526 melting point trends in, 930
Grignard reaction of, 509510, 658 uses of, 498 polyunsaturated, 928
IR spectroscopy of, 436437, 667 Ethoxide ion, electrostatic potential map table of, 929
mechanism of hydrolysis of, 654656 of, 607 trans, 234, 930
INDEX I-13
Fatty acyl CoA, formation of, 649, 937 N-Formiminoglutamate, reaction with Geranyl diphosphate, biosynthesis of,
Fatty acid biosynthesis, differences from tetrahydrofolate, 836837 957958
fatty acid catabolism, 943 Formyl group, 559 terpenoids from, 958
loading reaction in, 945 Fourier-transform NMR spectroscopy Gibbs free-energy change (G), 158
overall result of, 947 (FT-NMR), 462463 equilibrium constant and, 159
priming reactions in, 943944 Fractional crystallization, 338 Globo H hexasaccharide, structure of, 880
Fatty acid carboxylate, electrostatic Fragmentation (mass spectrum), 417420 Globular protein, 797
potential map of, 932 Free-energy change (G), 158 Glucitol, structure of, 869
Fatty acid catabolism, differences from Free radical, 144 Glucocorticoid, 963
fatty acid biosynthesis, 943 Fremys salt, 519 Glucogenic amino acid, 832
Fatty acid synthase, 943 Frequency (), 426 Gluconeogenesis, 913919
Favorskii reaction, 629 FriedelCrafts acylation reaction, 290 comparison with glycolysis, 919
Fehlings test, 870 acyl cations in, 290 steps in, 914915
Fenoprofen, synthesis of, 611 arylamines and, 753754 summary of, 919
Fibrous protein, 797 mechanism of, 290 -D-Glucopyranose, molecular model of,
Fingerprint region (IR), 430 FriedelCrafts alkylation reaction, 863
First-order reaction, 381 288289 -D-Glucopyranose, molecular model of,
Fischer, Emil, 853 arylamines and, 753754 863
Fischer esterification reaction, 644645 carbocation rearrangements in, 289 Glucosamine, biosynthesis of, 924
limitations of, 644 limitations of, 288289 Glucose, anomers of, 863
mechanism of, 644645 mechanism of, 288 biosynthesis of, 912919
Fischer projection, 853856 Fructose, anomers of, 863864 catabolism of, 893900
carbohydrates and, 854856 furanose form of, 864 chair conformation of, 123
D sugars, 858 phosphorylation of, 896 configuration of, 860
L, sugars, 858859 pyranose form of, 864 ethers from, 524
rotation of, 854855 sweetness of, 880 Fischer projection of, 856
R,S configuration of, 855 Fructose 1,6-bisphosphatase, 918 from starch, 892893
conventions for, 854 FT-NMR, 462463 glycosides of, 867
Fishhook arrow, radical reactions and, L-Fucose, biosynthesis of, 926 isomerization of, 895896
143144 structure and function of, 872 molecular model of, 130
Flavin adenine dinucleotide (FAD), Fumarase, 909 mutarotation of, 863864
mechanism of, 939940 Fumarate, from succinate, 909 oxidation of, 870871
structure and function of, 803, 939 malate from, 909 pentaacetyl ester of, 866
Flavin adenine dinucleotide (reduced), Fumaric acid, structure of, 603 pentamethyl ether of, 866
structure of, 939 Functional group(s), 75 phosphorylation of, 895
Flavin hydroperoxide, alkene carbonyl compounds and, 80 pyranose form of, 863
epoxidation with, 236237, 965 electronegative atoms in, 7980 reaction with acetic anhydride, 866
Flavin mononucleotide (FMN), importance of, 78 reaction with ATP, 821
mechanism of, 1004 IR spectroscopy of, 430437 reaction with iodomethane, 866
Flavin mononucleotide (reduced), multiple bonds in, 7879 reduction of, 869
function of, 1001, 1004 polarity patterns of, 148 sweetness of, 880
Fleming, Alexander, 668 table of, 7677 Williamson ether synthesis with, 866
Flexibilene, structure of, 975 Furan, industrial synthesis of, 755 Glucose 6-phosphate, hydrolysis of, 918
Florey, Howard, 668 Furanose, 863 Glucose-6-phosphate isomerase, 895
(S)-Fluoxetine, molecular model of, Fused-ring heterocycle, 759761 Glutamate, arginine from, 840841
350 biosynthesis of, 838
stereochemistry of, 350 , see Gamma glutamine from, 840
FMN, see Flavin mononucleotide Galactose, biosynthesis of, 923 ornithine from, 841
Fmoc, amino acid protection with, 796 configuration of, 860 oxidative deamination of, 826
cleavage of, 813 metabolism of, 543 partial reduction of, 840841
Food, catabolism of, 818819 Gamma-aminobutyric acid, structure of, proline from, 841
Food and Drug Administration (FDA), 779 transamination and, 822825
171 Gamma rays, electromagnetic spectrum Glutamate dehydrogenase, 826
Formal charge, 4042 and, 425 Glutamate 5-semialdehyde, from
calculation of, 42 Gasoline, composition of, 103 glutamate, 841
summary table of, 42 octane number of, 103 proline from, 750
Formaldehyde, dipole moment of, 39 GattermanKoch reaction, 317 Glutamic acid, structure and properties
electrostatic potential map of, 173 Gauche conformation, 99 of, 781
hydrate of, 565 steric strain in, 99 Glutamine, biosynthesis of, 839840
reaction with Grignard reagents, Gel electrophoresis, DNA sequencing from glutamate, 840
509510 and, 992 structure and properties of, 780
U.S. production of, 557 Gem (geminal), 564 Glutamine synthetase, 839
uses of, 557 Geminal (gem), 564 Glutaric acid, structure of, 603
Formate ion, bond lengths in, 607 Gene, 986 Glutathione, oxidation of, 522
electrostatic potential map of, 607 number of in humans, 1, 992 prostaglandin biosynthesis and, 948,
Formic acid, bond lengths in, 607 Genome, human, 986 950
pKa of, 606 Geraniol, biosynthesis of, 390391 structure of, 522
I-14 INDEX
Glycal, 878 Griseofulvin, synthesis of, 732 High-pressure liquid chromatography, 445
Glycal assembly method, 878 Guanine, aromaticity of, 280 Highest occupied molecular orbital
()-Glyceraldehyde, configuration of, 330 biological hydrolysis of, 999 (HOMO), 439
(R)-Glyceraldehyde, Fischer projection catabolism of, 9971000 UV spectroscopy and, 439
of, 854 electrostatic potential map of, 983 Histidine, basicity of, 757
molecular model of, 855 phosphorolysis of, 998 catabolism of, 835837
Glyceraldehyde 3-phosphate, from protection of, 993 electrostatic potential map of, 782
dihydroxyacetone phosphate, structure of, 980 structure and properties of, 781
897898 xanthine from, 997998 trans-urocanate from, 835836
fructose 1,6-bisphosphate from, Guanine deaminase, 998 Histidine ammonia lyase, 835
917918 Guanosine, biosynthesis of, 10071008 HMG-CoA, see 3-Hydroxy-3-
Glyceraldehyde-3-phosphate catabolism of, 9971000 methylglutaryl CoA, 954
dehydrogenase, 917 Gulose, configuration of, 860 HMG-CoA reductase, cholesterol
Glyceric acid, structure of, 603 Guncotton, 876 biosynthesis and, 1009
Glycerol, biological oxidation of, 937 Hoffmann-LaRoche Co., vitamin C
catabolism of, 934937 H5N1 virus, 920 synthesis and, 619
sn-Glycerol 3-phosphate, naming of, 937 Halo group, inductive effect of, 294295 Hofmann elimination reaction, 414,
Glycerophospholipid, 933 Haloalkane, see Alkyl halide 751752
Glycine, structure and properties of, 780 Halogen, directing effect of, 294 biological, 752
Glycoconjugate(s), 868 inductive effect of, 294295 mechanism of, 752
biosynthesis of, 868869 orienting effect of, 294 regiochemistry of, 752
mechanism of formation of, 868869 resonance effect of, 294295 Zaitsevs rule and, 752
Glycogen, function of, 877 Halohydrin(s), 226 HOMO, see Highest occupied molecular
structure of, 877878 epoxides from, 236 orbital, 439
Glycol, 236 reaction with base, 236 homo-, as naming prefix, 842
Glycolic acid, pKa of, 606 Haloperoxidase, biological halogenations Homocysteine, structure of, 779
structure of, 603 with, 225 Homoserine, biosynthesis of, 842843
Glycolipid(s), 868 biological halohydrin formation with, from aspartate, 842843
Glycolysis, 893900 227 threonine from, 843844
comparison with gluconeogenesis, 919 Hammond postulate, 204206 Homotopic (NMR), 471
steps in, 894895 SN1 reaction and, 385 Honey, sugars in, 875
summary of, 900 Handedness, 319320 Hormone, 962
Glycoprotein(s), 868 HDL, heart disease and, 970 adrenocortical, 963
biosynthesis of, 868869 Heart disease, cholesterol and, 970 sex, 962963
Glycosidase, 800, 877, 892 Heat of hydrogenation, 193 HPLC, 445
-, 877, 892 table of, 194 Hckel, Erich, 273
mechanism of, 892893 Heat of reaction, 159 Hckel 4n 2 rule, 273275
Glycoside, 867 Helminthogermacrene, structure of, 972 cyclobutadiene and, 274
hydrolysis of, 868 Heme, cyclooxygenase reaction and, 12 cycloheptatrienyl cation and, 315
naming, 868 structure of, 755 cyclooctatetraene and, 274
occurrence of, 868869 Hemiacetal, 572 cyclopentadienyl anion and, 315
Glyoxalate cycle, 922 Hemithioacetal, 898 explanation of, 274275
GMP synthetase, 1007 HendersonHasselbalch equation, imidazole and, 276277
GPP, see Geranyl diphosphate 608609 molecular orbitals and, 274275
Green chemistry, 764765 carboxylic acids and, 608609 pyridine and, 276277
principles of, 764765 amines and, 745746 pyrimidine and, 276277
Grignard, Franois Auguste Victor, 367 Hertz (Hz), 426 pyrrole and, 276277
Grignard reaction, aldehydes and, Heterocycle, 275 Hughes, Edward Davies, 372
509510, 567 aromatic, 275277 Human fat, composition of, 929
esters and, 509510, 658 fused-ring, 759761 Human genome, size of, 986, 992
formaldehyde and, 509510 Heterocyclic amine, 738, 755759 Humulene, structure of, 209
ketones and, 509510, 567 basicity of, 742 Hunds rule, 6
mechanism of, 567 names of, 738 Hybrid orbitals, 1220
strategy for using, 511 HETPP, see Hydroxyethylthiamin sp, 1718
Grignard reagent, 367 diphosphate sp2, 15
alkanes from, 368 Hevea brasieliensis, rubber from, 253 sp3, 1214
carboxylation of, 612 Hex-1-ene, IR spectrum of, 432 Hydrate (carbonyl), 561
carboxylic acids from, 612 Hex-2-ene, mass spectrum of, 421 from aldehydes, 564566
electrostatic potential map of, 367 Hex-1-yne, IR spectrum of, 432 from ketones, 564566
from alkyl halides, 367 Hexa-1,3,5-triene, UV absorption of, 441 Hydration (alkene), 227230
reaction with acids, 368 Hexane, IR spectrum of, 432 Hydride shift, carbocation
reaction with aldehydes, 509510, 567 mass spectrum of, 419 rearrangements and, 207208
reaction with carboxylic acids, 510 molecular model of, 14 Hydroboration, 229230
reaction with CO2, 612 Hexokinase, 895 mechanism of, 229230
reaction with esters, 509510, 658 active site in, 169 regiochemistry of, 229230, 484
reaction with formaldehyde, 509510 function of, 169 stereochemistry of, 229230
reaction with ketones, 509510, 567 molecular model of, 169 Hydrocarbon, 82
INDEX I-15
Hydrochloric acid, pKa of, 52 Hypoxanthine, biological oxidation of, Infrared spectrum, benzaldehyde, 584
Hydrocortisone, structure and function 1000 butanoic acid, 617
of, 963 from adenosine, 1000 cyclohexane, 448
Hydrocyanic acid, pKa of, 52 cyclohexanol, 529
Hydrogen bond, 63 Ibuprofen, chirality and, 352 cyclohexanone, 584
alcohols and, 501 green synthesis of, 765 cyclohexene, 449
amines and, 740 molecular model of, 352 cyclohexylamine, 762
ammonia and, 63 stereochemistry of, 352 ethanol, 427
carboxylic acids and, 605 Idose, configuration of, 860 hex-1-ene, 432
DNA and, 63 Imidazole, aromaticity of, 276277 hex-1-yne, 432
DNA base pairs and, 983 basicity of, 742, 757 hexane, 432
electrostatic potential map, 63, 501 electrostatic potential map of, 61, interpretation of, 430437
phenols and, 501 276 phenol, 529
water and, 63 Hckel 4n 2 rule and, 276277 phenylacetaldehyde, 437
Hydrogen iodide, ether cleavage with, Imidazolone 5-propionate, from trans- toluene, 435
525526 urocanate, 836837 Ingold, Christopher Kelk, 372
Hydrogen molecule, bond length in, 11 hydrolysis of, 836 Initiation step (radical), 145
bond strength in, 11 Imine(s), 568 Inosine, biosynthesis of, 10061007
molecular orbitals in, 2122 from aldehydes, 568569 Inosine monophosphate, oxidation of,
Hydrogen peroxide, reaction with from ketones, 568569 10071008
organoboranes, 229230 mechanism of formation of, 569 Integration (1H NMR), 476
Hydrogenation, 232 Schiff base and, 897 Intermediate, See Reaction intermediate
alkenes and, 232234 IMP dehydrogenase, 1007 Intoxilyzer test, 532
alkyne, 251 IND, see Investigational new drug, 171 Intramolecular aldol reaction, 707708
catalysts for, 232 Indole, aromaticity of, 279 mechanism of, 707708
mechanism of, 232233 electrophilic substitution reaction of, Intramolecular Claisen reaction, 711713
stereochemistry of, 232233 761 mechanism of, 711712
trans fatty acids and, 234, 930 structure of, 760 Intron (DNA), 987
vegetable oil, 930 Indolmycin, biosynthesis of, 700 Invert sugar, 875
Hydrolase, 801 Inductive effect, 37, 294295 Investigational new drug (IND), 171
Hydrolysis (nucleophilic acyl carboxylic acid strength and, 609 Iodination (aromatic), 284
substitution reaction), 640 electronegativity and, 37 thyroxine biosynthesis and, 284
amides, 659660 electrophilic aromatic substitution and, Iodoform reaction, 680
esters, 654656 294295 Ion pair, 384
fats, 656657 Influenza pandemics, 920 SN1 reaction and, 384
nitriles, 616 Influenza virus, spread of, 920 Ionic bond, 8
proteins, 660 Infrared radiation, electromagnetic Ionization sources, mass spectrometry
Hydronium ion, electrostatic potential spectrum and, 425426 and, 416
map of, 150 energy of, 428429 IPP, see Isopentenyl diphosphate, 951
Hydrophilic, 64 frequencies of, 429 IPP isomerase, 956
Hydrophobic, 64 wavelengths of, 429 IR, see Infrared
Hydroquinone, 519 Infrared spectroscopy, 428429 Iron, reaction with nitroarenes, 747
from quinones, 519520 acid anhydrides, 667 Iron(III) bromide, aromatic bromination
Hydroxide ion, electrostatic potential acid chlorides, 667 and, 282
map of, 54, 150 alcohols, 436, 529 Iron sulfate, LD50 of, 26
3-Hydroxy-3-methylglutaryl-CoA, aldehydes, 436, 583584 Isoamyl group, 93
reduction of, 954 alkanes, 434 Isoborneol, structure of, 976
3-Hydroxy-3-methylglutaryl-CoA alkenes, 434 Isobutane, molecular model of, 83
reductase, 954 alkynes, 434435 Isobutyl group, 87
3-Hydroxy-3-methylglutaryl-CoA amides, 667 Isocitrate, from citrate, 906907
synthase, 954 amines, 436, 762 oxalosuccinate from, 908
Hydroxyacetic acid, pKa of, 606 aromatic compounds, 435 oxidation of, 908
L-3-Hydroxyacyl-CoA dehydrogenase, bond stretching in, 429 Isocitrate dehydrogenase, 908
mechanism of, 940 carbonyl compounds, 436437 Isoelectric point (pI), 783
Hydroxyethylthiamin diphosphate, from carboxylic acid derivatives, 666667 calculation of, 783
pyruvate, 903 carboxylic acids, 617 Isoleucine, metabolism of, 728
reaction with lipoamide, 904 esters, 436437, 667 molecular model of, 335
Hydroxyl group, directing effect of, ethers, 529 structure and properties of, 780
294296 explanation of, 429 Isomerase, 801
inductive effect of, 294295 fingerprint region in, 430 Isomers, 83
orienting effect of, 294296 ketones, 436, 583584 alkanes, 8283
resonance effect of, 294295 molecular motions in, 429 cistrans, 116, 186187
Hydroxylation, alkene, 237239 nitriles, 617 constitutional, 83
Hydroxylation, aromatic, 286287 phenols, 529 epimers, 334
Hyperconjugation, 194 regions in, 430 kinds of, 341
alkenes and, 194 table of absorptions in, 431 review of, 340342
carbocation stability and, 202203 vibrations in, 429 stereoisomers, 116
I-16 INDEX
Isonitrile, 412 IR spectroscopy of, 436, 583584 Leaving group, 372

Isopentenyl diphosphate, biosynthesis of, mass spectrometry of, 422, 585586 reactivity of, 377378
952955 McLafferty rearrangement of, 422, SN1 reaction and, 386387
dimethylallyl diphosphate from, 956 585586 SN2 reactions and, 377378
mevalonate pathway for, 952955 naming, 559 LeBlanc process, 931
terpenoids from, 956958 NMR spectroscopy of, 584585 Leucine, biosynthesis of, 731
Isoprene, heat of hydrogenation of, 245 pKa of, 690 metabolism of, 728
structure of, 184 polarity of, 80 structure and properties of, 780
Isoprene rule, terpenes and, 209210 reaction with alcohols, 572574 Leukotriene, naming of, 948949
Isopropyl group, 87 reaction with amines, 568571 Levorotatory, 326
Isoquinoline, aromaticity of, 279 reaction with Br2, 686687 Lewis acid, 58
electrophilic substitution reaction of, reaction with Grignard reagents, examples of, 59
760 509510, 567 reactions of, 5859
Isotope, 4 reaction with H2O, 564566 Lewis base, 58
Isoxazole, aromaticity of, 313 reaction with LDA, 698 examples of, 60
IUPAC system of nomenclature, 89 reaction with LiAlH4, 506, 568 reactions of, 5961
reaction with NaBH4, 506, 568 Lewis structure, 8
J, see Coupling constant, 478 reactivity versus aldehydes, 563564 resonance and, 4344
Jefferson, Thomas, DNA fingerprinting reduction of, 299300, 506507, 568 Lidocaine, molecular model of, 104
and, 10101011 reductive amination of,748750 Ligase, 801
Wittig reaction of, 575577 Light, plane-polarized, 325
Ka (acidity constant), 51 Ketone bodies, 832 speed of, 426
Kb, basicity constant, 741 Ketose, 853 Limit dextrin, from starch, 892
Keq (equilibrium constant), 157 KilianiFischer reaction, 887 Limonene, biosynthesis of, 218, 958
KEGG biosynthesis database, 807 Kilojoule (kJ), 11 molecular model of () enantiomer, 349
Kekul, Friedrich August, 6 Kinetics, 371 molecular model of () enantiomer,
Kekul structure, 8 E1 reaction and, 399 349
Kelp, chloromethane from, 403 E2 reaction and, 395 odor of, 349
Kerosene, composition of, 103 SN1 reaction and, 381382 Linalyl diphosphate, biosynthesis of, 958
Ketal, see Acetal, 572 SN2 reaction and, 371372 Lindlar catalyst, 251
-Keto acid, transamination of, Knowles, William S., 587, 786 Line-bond structure, 8
822825 Krebs, Hans Adolf, 905 14-Link, 874
Ketoenol tautomerism, 682684 Krebs cycle, see Citric acid cycle Linoleic acid, structure of, 929
-Keto thioester reductase, 946 Linolenic acid, molecular model of, 930
-Ketoacyl-CoA thiolase, mechanism of, LAmino acid, 779, 782 structure of, 929
941 LSugar, 858 Lipase, 934
Ketogenic amino acid, 832 Fischer projections of, 858859 mechanism of, 935
-Ketoglutarate, from glutamate, 826 Labetalol, structure of, 739 Lipid, 927
from oxalosuccinate, 908 synthesis of, 739 classification of, 927
glutamate from, 838 Laboratory reactions, comparison with Lipid bilayer, 934
oxidative decarboxylation of, 908 biological reactions, 168170 structure of, 934
succinyl CoA from, 908 Lactam(s), 661 Lipitor, structure and function of, 1010
transamination of, 825826 cyclic amines from, 661 Lipoamide, structure and function of, 904
Ketone(s), 557 reaction with LiAlH4, 661 Lipoic acid, structure and function of,
bromination of, 686687 Lactic acid, configuration of () 803, 904
acetals from, 572574 enantiomer, 330 Lipoprotein, heart disease and, 970
acidity of, 690 configuration of () enantiomer, Liquid chromatography, 444
alcohols from, 506507, 509510, 330 Lithium aluminum hydride, danger of,
567568 enantiomers of, 320321 506
aldol reaction of, 702 molecular model of, 321 reaction with carboxylic acids, 647
alkenes from, 575577 resolution of, 338340 reaction with ketones and aldehydes,
alkylation of, 698 Lactone(s), 654 506, 567
amines from, 748750 alkylation of, 698 Lithium diisopropylamide (LDA),
biological reduction of, 507, 580 reaction with LDA, 698 formation of, 689
carbonyl condensation reactions of, Lactose, molecular model of, 875 properties of, 689
701706 occurrence of, 875 reaction with cyclohexanone, 689
common names of, 559 structure of, 875 reaction with esters, 698
conjugate addition reactions of, sweetness of, 880 reaction with ketones, 698
580583 Lanosterol, biosynthesis of, 964969 reaction with lactones, 698
enamines from, 568571 Lard, composition of, 929 reaction with nitriles, 699
enols of, 682684 Latex, rubber from, 253254 Lithocholic acid, structure of, 628, 962
enones from, 705706 Lauric acid, structure of, 929 Loading reaction, fatty acid biosynthesis
from acetoacetic ester, 695696 LD50, 26 and, 945
from alcohols, 516517 table of, 26 Locant (nomenclature), 91
Grignard reaction of, 509510, 567 LDA, see Lithium diisopropylamide position of in chemical names, 183
hydrates of, 564566 LDL, heart disease and, 970 Lone-pair electrons, 9
imines from, 568569 Le Bel, Joseph Achille, 7 Loratidine, structure of, 213
INDEX I-17
Lotaustralin, structure of, 614 alpha cleavage of ketones in, 423, 585 base-catalyzed epoxide cleavage, 526
Lowest unoccupied molecular orbital amines, 422, 763764 base-catalyzed ester hydrolysis,
(LUMO), 439 base peak in, 416 654655
LUMO, see Lowest unoccupied molecular biological, 424425 biological alkene epoxidation, 236237
orbital, 439 carbonyl compounds and, 422423 biological alkene reductions with
Lyase, 801 cation radicals in, 416 NADPH, 234235
Lysine, catabolism of, 849 dehydration of alcohols in, 422 biological epoxidation, 964965
saccharopine from, 849 electron-impact, 416417 biological hydroxylation of aromatic
structure and properties of, 781 ESI source in, 424 compounds, 286287
Lysozyme, isoelectric point of, 784 fragmentation in, 417420 biological carbonyl reduction with
MALDI-TOF mass spectrum of, 425 ketones, 422423, 585586 NADH, 507
Lyxose, configuration of, 860 MALDI source in, 424425 biological carbonyl reduction with
McLafferty rearrangement in, 422 NADPH, 507
Magnetic field, NMR spectroscopy and, molecular ion in, 417 biotin-mediated carboxylation, 945
456457 nitrogen rule and, 447, 763 bromohydrin formation, 226227
Magnetic resonance imaging, 485 parent peak in, 417 bromonium ion formation, 224
uses of, 485 time-of-flight, 424425 Cannizzaro reaction, 579
Major groove (DNA), 983984 Mass spectrum, 416 carbonyl condensation reaction, 701
Malate, oxaloacetate from, 910 butan-1-ol, 531 citric acid cycle, 905910
oxidation of, 910 2,2-dimethylpropane, 418 Claisen condensation reaction,
Malate dehydrogenase, 910 ethylcyclopentane, 420 709710
MALDITOF mass spectrometry, 424425 hex-2-ene, 421 conjugate nucleophilic additions to
MALDI-TOF mass spectrum, lysozyme, hexane, 419 enones, 581
425 lysozyme, 425 deamination, 823825
Maleic acid, structure of, 603 methylcyclohexane, 420 Dieckmann cyclization reaction,
Malic acid, structure of, 603 2-methylpent-2-ene, 421 711712
Walden inversion of, 368369 2-methylpentan-2-ol, 423 DNA replication, 985986
Malonic ester, carboxylic acids from, 2-methylpentane, 447 DNA transcription, 986987
692694 5-methylhexan-2-one, 586 E1 reaction, 399
decarboxylation of, 693 N-ethylpropylamine, 764 E1cB reaction, 400
pKa of, 690 propane, 417 E2 reaction, 394395
Malonic ester synthesis, 692694 Matrix-assisted laser-desorption Edman degradation, 790791
intramolecular, 694 ionization mass spectrometry, see electrophilic addition reaction,
Malonyl CoA, from acetyl CoA, 945 MALDI 152154, 195196
Maltose, molecular model of, 874 MaxamGilbert DNA sequencing, 991 electrophilic aromatic substitution,
mutarotation of, 874 McLafferty rearrangement, 422, 585 282283
Maltotriose, from starch, 892 Mechanism (reaction), 143 enamine formation, 570
Mannich reaction, 733 acetal formation, 572573 ester reduction, 657
Mannose, biosynthesis of, 924 acid-catalyzed enol formation, 683 ether cleavage with HI, 525526
configuration of, 860 acid-catalyzed epoxide cleavage, FAD reactions, 939940
molecular model of, 130 237238, 526 fat hydrolysis, 934937
Margarine, manufacture of, 930 acid-catalyzed ester hydrolysis, fatty acid biosynthesis, 943947
Markovnikov, Vladimir Vassilyevich, 198 655656 fatty acyl CoA biosynthesis, 649, 937
Markovnikovs rule, 198199 alcohol dehydration with acid, Fischer esterification reaction, 644645
alkyne additions and, 251 513514 FriedelCrafts acylation reaction, 290
carbocation stability and, 199 alcohol dehydration with POCl3, FriedelCrafts alkylation reaction, 288
hydroboration and, 229230 513515 geranyl diphosphate biosynthesis,
oxymercuration and, 229 alcohol oxidation, 518 957958
Mass analyzers, mass spectrometry and, aldehyde hydration, 565566 glycoconjugate biosynthesis, 868869
416 aldehyde oxidation, 561562 glycolysis, 894895
Mass number (A), 4 aldol reaction, 702703 Grignard carboxylation, 612
Mass spectrometer, detectors in, 416 alkene epoxidation, 236 Grignard reaction, 567
double-focusing, 418 alkene hydration, 227 Hofmann elimination reaction, 752
exact mass measurement in, 418 alkene polymerization, 240241 hydroboration, 229230
ionization sources in, 416 bromination of aldehydes, 686687 hydrogenation, 232233
kinds of, 416 bromination of ketones, 686687 imine formation, 569
mass analyzers in, 416 -substitution reaction, 685686 intramolecular aldol reaction, 707708
operation of, 416417 amide hydrolysis, 659660 isopentenyl diphosphate biosynthesis,
soft ionization in, 418, 424425 amide reduction, 661 952955
Mass spectrometry (MS), 415 amide synthesis with DCC, 646 ketone hydration, 565566
alcohols, 422, 531 aromatic bromination, 282283 lipase, 935
aldehydes, 422423, 585586 aromatic chlorination, 283 mevalonate decarboxylation, 955
alkanes and, 418419 aromatic iodination, 284 Michael reaction, 714
alpha cleavage of alcohols in, 422, 531 aromatic nitration, 285 mutarotation, 863864
alpha cleavage of aldehydes in, 423, aromatic sulfonation, 286 nitrile hydrolysis, 616
585 -oxidation pathway, 938942 nucleophilic acyl substitution reaction,
alpha cleavage of amines in, 422, 763 base-catalyzed enol formation, 684 637638
I-18 INDEX
Mechanism (reaction) (continued) pKa of, 502 5-Methylhexan-2-one, mass spectrum of,
nucleophilic addition reaction, 562 polar covalent bond in, 3637 586
orotidine monophosphate sp3 hybrid orbitals in, 19 4-Methylideneimidazol-5-one, formation
decarboxylase, 1005 structure of, 19 of, 836
oxidative deamination, 826 toxicity of, 497 histidine catabolism and, 835836
oxymercuration, 229 U.S. production of, 497 Methyllithium, electrostatic potential
phosphorylation with ATP, 820 uses of, 497 map of, 37, 147
pyruvate decarboxylation, 901903 Methionine, biosynthesis of, 593 polar covalent bond in, 37
reductive amination, 749 molecular model of, 333 Methylmagnesium chloride, electrostatic
saponification, 654655 reaction with ATP, 528 potential map of, 567
SN1 reaction, 382, 387 S-adenosylmethionine from, 528 Methylmagnesium iodide, electrostatic
SN2 reaction, 372373 structure and properties of, 780 potential map of, 367
steroid biosynthesis, 964969 Methoxide ion, electrostatic potential 2-Methylpent-2-ene, mass spectrum of,
Stork enamine reaction, 717 map of, 57 421
transamination, 823825 p-Methoxybenzoic acid, pKa of, 609 2-Methylpentan-3-ol, mass spectrum of,
transimination, 824 p-Methoxypropiophenone, 1H NMR 423
Williamson ether synthesis, 524 spectrum of, 480 2-Methylpentane, mass spectrum of, 447
Wittig reaction, 575576 Methyl acetate, electrostatic potential p-Methylphenol, pKa of, 502
MeerweinPonndorfVerley reaction, 595 map of, 639 2-Methylpropane, molecular model of, 83
Menthene, electrostatic potential map of, 13C NMR spectrum of, 458 2-Methylpropene, heat of hydrogenation
78 1H NMR spectrum of, 458 of, 194
functional groups in, 78 pKa of, 690 Mevaldehyde, biosynthesis of, 663
Menthol, molecular model of, 121 Methyl anion, electrostatic potential map Mevalonate, biosynthesis of, 952954
structure of, 324 of, 253 decarboxylation of, 954955
Menthyl chloride, E2 reaction of, 397 Methyl 2,2-dimethylpropanoate, 1H NMR isopentenyl diphosphate from,
Mercapto group, 500 spectrum of, 475 952955
Mercurinium ion, 229 Methyl group, 86 Mevalonate-5-diphosphate
Merrifield solid-phase synthesis, 794796 chiral, 414 decarboxylase, 955
Fmoc protecting group in, 796 directing effect of, 294 Mevalonate kinase, 955
PAM resin in, 796 inductive effect of, 294295 Micelle, 932
steps in, 795796 orienting effect of, 294 Michael reaction, 713715
Wang resin in, 796 Methyl phosphate, bond angle in, 20 acceptors in, 715
Meso compound, 336 molecular model of, 20 donors in, 715
plane of symmetry in, 336 sp3 hybrid orbitals in, 20 mechanism of, 714
Messenger RNA, 986 structure of, 20 Stork enamine reaction and, 717
codons in, 988 Methyl propanoate, 13C NMR spectrum Microwaves, electromagnetic spectrum
translation of, 987989 of, 466 and, 425
Mestranol, structure of, 261 Methyl thioacetate, electrostatic potential Mineralocorticoid, 963
Meta (m), 269 map of, 639 Minor groove (DNA), 983984
Meta-directing group, 293 pKa of, 690 MIO, see 4-Methylideneimidazol-5-one,
Metabolic cycle, reasons for, 910911 Methylamine, bond angles in, 19 836
Metabolic pathways, kinds of, 910 dipole moment of, 39 Mobile phase, chromatography and, 444
Metabolism, 818 electrostatic potential map of, 38, 57, Molar absorptivity, 440
overview of, 818 743 Molecular ion (M), 417
Methandrostenolone, structure and molecular model of, 19 Molecular mechanics, 133
function of, 963 sp3 hybrid orbitals in, 19 Molecular model, helix, 798
Methane, bond angles in, 13 structure of, 19 acetaminophen, 28
bond lengths in, 13 2-Methylbutan-2-ol, 1H NMR spectrum acetylene, 18
bond strengths in, 13 of, 481 adenine, 68
molecular model of, 7, 13, 83 2-Methylbutane, molecular model of, 83 adrenaline, 354
pKa of, 252 Methylcyclohex-1-ene, 13C NMR alanine, 28, 777
reaction with Cl2, 145 spectrum of, 470 p-aminobenzoic acid, 25
sp3 hybrid orbitals in, 1213 Methylcyclohexane, conformations of, anti periplanar geometry, 396
structure of, 13 126127 arecoline, 81
Methanethiol, bond angle in, 20 1,3-diaxial interactions in, 126127 aspartame, 29
dipole moment of, 39 mass spectrum of, 420 aspirin, 17
electrostatic potential map of, 173 molecular model of, 323 -D-glucopyranose, 863
molecular model of, 20 1-Methylcyclohexanol, 1H NMR -D-glucopyranose, 863
pKa of, 502 spectrum of, 484 p-bromoacetophenone, 465
sp3 hybrid orbitals in, 20 2-Methylcyclohexanone, chirality of, 323 bromocyclohexane, 125
structure of, 20 molecular model of, 323 butane, 83
Methanol, bond angle in, 19 N-Methylcyclohexylamine, 13C NMR cis-but-2-ene, 186
dipole moment of, 39 spectrum of, 763 trans-but-2-ene, 186
electrostatic potential map of, 37, 56, 1H NMR spectrum of, 763 cellulose, 874
57, 148, 501 Methylene group, 184 chair cyclohexane, 122
industrial synthesis of, 497 6-Methylhept-5-en-2-ol, DEPT-NMR cholesterol, 961
molecular model of, 19 spectra of, 468 cholic acid, 602
INDEX I-19
citrate synthase, 805 testosterone, 132 N-terminal amino acid, 787

citric acid, 28 threose, 325 NADH, see Nicotinamide adenine
coniine, 28 trimethylamine, 739 dinucleotide (reduced)
cyclobutane, 120 twist-boat cyclohexane, 123 NADPH, see Nicotinamide adenine
cyclodecapentaene, 275 vitamin C, 619 dinucleotide phosphate (reduced)
cyclohexane ring flip, 125 Molecular orbital, 21 Naming, acid anhydrides, 634
cyclopentane, 121 antibonding, 22 acid chlorides, 634
cyclopropane, 115, 119 bonding, 22 acid halides, 634
cytosine, 68 buta-1,3-diene, 247 acyl groups, 603
cis-decalin, 132, 960 Molecular orbital (MO) theory, 2122 acyl phosphates, 636
trans-decalin, 132, 960 benzene and, 272275 alcohols, 499500
decane, 101 conjugated dienes and, 246247 aldehydes, 558
dimethyl sulfide, 20 Hckel 4n 2 rule and, 274275 aldoses, 860861
cis-1,2-dimethylcyclopropane, 116 Molecular weight, determination of, alkanes, 8993
trans-1,2-dimethylcyclopropane, 116 418 alkenes, 182184
dimethylpropane, 83 Molecule, 8 alkyl groups, 8687, 9293
N,N-dimethyltryptamine, 761 electron-dot structures of, 89 alkyl halides, 364365
dopamine, 748 lone-pair electrons in, 9 alkynes, 184
eclipsed ethane conformation, 97 Monomer, 239 alphabetization and, 93
enflurane, 325 Monosaccharide(s), 852 amides, 635
epibatidine, 363 aldaric acids from, 871 amines, 736738
ethane, 9, 14, 83 alditols from, 868869 aromatic compounds, 268270
ethylene, 15 aldonic acids from, 870871 carboxylic acid derivatives,
(S)-fluoxetine, 350 anomers of, 863864 634636
glucose, 130 configurations of, 859861 carboxylic acids, 602603
(R)-glyceraldehyde, 855 cyclic forms of, 863864 cycloalkanes, 112114
hexane, 14 essential, 872873 cycloalkenes, 183
(S)-ibuprofen, 352 esters of, 866 eicosanoids, 948949
isobutane, 83 ethers of, 866 enzymes, 801
isoleucine, 335 Fischer projections of, 854856 esters, 635
lactic acid, 321 glycosides of, 867868 ethers, 522
lactose, 875 hemiacetal forms of, 863864 heterocyclic amines, 738
lidocaine, 104 osazones from, 888 ketones, 559
()-limonene, 349 oxidation of, 870871 leukotrienes, 948949
()-limonene, 349 phosphorylation of, 868 nitriles, 604
linolenic acid, 930 reaction with acetic anhydride, 866 phenols, 500
maltose, 874 reaction with iodomethane, 866 prostaglandins, 948949
mannose, 130 reaction with NaBH4, 868869 sulfides, 523
menthol, 121 reactions of, 866871 thioesters, 635
meso-tartaric acid, 336 reduction of, 868869 thiols, 500
methane, 7, 13, 83 see also Aldose thromboxanes, 948949
methanethiol, 20 uronic acids from, 871 Naphthalene, aromaticity of, 279
methanol, 19 Monoterpene, 209 electrostatic potential map of, 279
methionine, 333 Monoterpenoid, 951 Hckel 4n 2 rule and, 279
methyl phosphate, 20 Morphine, specific rotation of, 326 molecular model of, 67
methylamine, 19 structure of, 65 orbitals of, 279
2-methylbutane, 83 MRI, see Magnetic resonance imaging, reaction with Br2, 279
2-methylcyclohexanone, 323 485 resonance in, 278
methylcyclohexane, 323 mRNA, see Messenger RNA Natural gas, composition of, 103
2-methylpropane, 83 MS, see Mass spectrometry thiols in, 521
naphthalene, 61 Mullis, Kary Banks, 995 Natural products, drugs from, 171
Newman projections, 97 Multiplet (NMR), 476 Natural rubber, structure of, 254
oseltamivir, 133 table of, 479 NDA, see New drug application, 171
pentane, 83 Mutarotation, 864 Neomenthyl chloride, E2 reaction of, 397
phenylalanine, 104 glucose and, 863864 Neopentyl group, 93
piperidine, 753 mechanism of, 863864 SN2 reaction and, 375
pleated sheet, 798 Mycomycin, stereochemistry of, 361 Neuraminic acid, biosynthesis of, 873
propane, 83 Mylar, structure of, 665 Neuraminidase, influenza virus and, 920
propane conformations, 98 myo-Inositol, structure of, 138 New drug application (NDA), 171
pseudoephedrine, 354 Myoglobin, helix in, 798 New molecular entity (NME), number of,
staggered ethane conformation, 97 ribbon model of, 798 171
stearic acid, 929 Myrcene, structure of, 209 Newman projection, 97
steroid, 960 Myristic acid, catabolism of, 942 molecular model of, 97
sucrose, 876 structure of, 929 Nicotinamide adenine dinucleotide
syn periplanar geometry, 396 (NAD), biological oxidations with,
Tamiflu, 133 n- (normal), 84 518
tert-butyl carbocation, 202 n 1 rule (NMR), 478 mechanism of oxidation with, 518
I-20 INDEX
Nicotinamide adenine dinucleotide Nonequivalent protons, spinspin cyclohexanol, 530

(reduced), biological reductions splitting and, 482483 cyclohexanone, 585
with, 507, 580 tree diagram in NMR of, 483 ethyl benzoate, 492
mechanism of reduction with, 507, 580 Nonessential amino acid, 838 methyl acetate, 458
structure of, 170, 507 biological precursors of, 839 methyl propanoate, 466
Nicotinamide adenine dinucleotide Norepinephrine, biosynthesis of, 299 1-methylcyclohexene, 470
phosphate (reduced), biological Norethindrone, structure and function of, N-methylcyclohexylamine, 763
reductions with, 235, 507 963 pentan-1-ol, 463
mechanism of reduction with, 235, 507 Normal (n) alkane, 83 propanenitrile, 618
Nicotine, structure of, 30, 735 Noyori, Ryoji, 587 propanoic acid, 618
Ninhydrin, reaction with amino acids, Nuclear magnetic resonance propionic acid, 618
789 spectrometer, field strength of, 456 1H Nuclear magnetic resonance
Nitration (aromatic), 284285 operation of, 459 spectrum, acetaldehyde, 584
Nitric acid, pKa of, 52 Nuclear magnetic resonance spectroscopy bromoethane, 476
Nitrile(s), 604 (NMR), 455 2-bromopropane, 478
alkylation of, 699 acid anhydrides, 667668 trans-cinnamaldehyde, 482
amides from, 616 acid chlorides, 667668 cyclohexylmethanol, 484
amines from, 616 alcohols, 530 ethyl acetate, 667
carboxylic acids from, 611612, 616 aldehydes, 584585 methyl acetate, 458
from amides, 615 amides, 667668 methyl 2,2-dimethylpropanoate, 475
hydrolysis of, 611612, 616 amines, 762763 2-methylbutan-2-ol, 481
IR spectroscopy of, 617 13C chemical shifts in, 464 1-methylcyclohexanol, 484
mechanism of hydrolysis of, 616 calibration peak for, 461 N-methylcyclohexylamine, 763
naming, 604 carboxylic acids, 618 p-methoxypropiophenone, 480
naturally occurring, 614 carboxylic acid derivatives, 667668 phenylacetic acid, 618
NMR spectroscopy of, 618 chart of absorptions in, 461 propan-1-ol, 530
nucleophilic additions to, 615 coupling constants in, 478 toluene, 482
pKa of, 690 delta scale for, 461 Nuclear spin, common nuclei and,
reaction with LDA, 699 DEPT-NMR and, 467468 457
reaction with LiAlH4, 616 diastereotopic protons and, 472 NMR and, 455457
reactions of, 615616 enantiotopic protons and, 471472 Nuclease, 997
reduction of, 616 energy levels in, 456457 Nucleic acid, 979982
synthesis of, 615 esters, 667668 biosynthesis of, 10031008
Nitrile group, directing effect of, 294 ethers, 530 catabolism of, 9971002
inductive effect of, 294295 field strength and, 456457 hydrolysis of, 997
orienting effect of, 294 FT-NMR and, 462463 see also Deoxyribonucleic acid,
resonance effect of, 294295 H chemical shifts in, 473474 Ribonucleic acid
Nitro group, directing effect of, 294 homotopic protons and, 471 structure of, 981982
inductive effect of, 294295 integration of 1H spectra, 475476 Nucleophile, 149150
orienting effect of, 294 ketones, 584585 characteristics of, 155
resonance effect of, 294295 multiplets in, 478479 curved arrows and, 154156
Nitroarene, arylamines from, 747 n 1 rule and, 478 electrostatic potential maps of, 150
catalytic reduction of, 747 nitriles, 618 examples of, 150
reaction with iron, 747 overlapping signals in, 482 SN1 reaction and, 387
reaction with tin, 747 peak assigning in 13C spectra, 464, SN2 reaction and, 376377
reduction of, 747 467468 Nucleophilic acyl substitution reaction,
Nitrobenzene, aniline from, 285 peak size in 13C spectra, 465 552, 637638
reduction of, 285 peak size in 1H spectra, 475476 abbreviated mechanism for, 840
synthesis of, 285 phenols, 531 acid anhydrides, 652653
p-Nitrobenzoic acid, pKa of, 609 principle of, 455457 acid chlorides, 648, 650651
Nitrogen rule (mass spectrometry), 447, proton equivalence and, 470472 acid halides, 648, 650651
763 radiofrequency energy and, 456457 amides, 659661
Nitronium ion, 284285 shielding in, 458 biological, 648649
electrostatic potential map of, 285 signal averaging in, 462463 carboxylic acids and, 642645
p-Nitrophenol, pKa of, 502 spin-flips in, 456 esters, 654658
p-Nitrophenoxide ion, resonance in, 503 spinspin splitting in, 476480 kinds of, 640641
NME, see New molecular entity, 171 time scale of, 460 mechanism of, 637638
NMR, see Nuclear magnetic resonance uses of 13C spectra in, 469470 reactivity in, 639640
Node, 5 uses of 1H spectra in, 484 Nucleophilic carbonyl addition reaction,
Nomenclature, see Naming 13C Nuclear magnetic resonance 550551, 562
Nonbonding electrons, 9 spectrum, acetaldehyde, 585 acid catalysis of, 565566
Noncovalent interaction(s), 62 acetophenone, 585 base catalysis of, 565
dipoledipole forces and, 62 benzaldehyde, 585 electrostatic potential map of, 562
dispersion forces and, 62 benzoic acid, 618 kinds of, 563
hydrogen bonds and, 63 p-bromoacetophenone, 465 mechanism of, 562
kinds of, 6264 butan-2-one, 465, 585 steric hindrance in, 563
van der Waals forces and, 62 crotonic acid, 618 trajectory of, 563564
INDEX I-21
Nucleophilic substitution reaction, 369 Organoborane, from alkenes, 229 PAM resin, peptide synthesis and, 796
biological examples of, 390391 reaction with H2O2, 229230 Para (m), 269
summary of, 401 Organohalide(s), biological uses of, Paraffin, 95
Nucleophilicity, 377 402403 Parallel synthesis, 307
basicity and, 377 function of, 403 Parent peak (mass spectrum), 417
table of, 376 naturally occurring, 402403 Partial charge, 36
trends in, 377 Organometallic compound, 367 Pasteur, Louis, 327
Nucleosidase, 997 polarity of, 147 enantiomers and, 327328
Nucleoside, 979982 Organophosphate, sp3 hybrid orbitals in, Patchouli alcohol, structure of, 951
Nucleoside phosphorylase, 998 20 Pauli exclusion principle, 6
Nucleotidase, 997 structure of, 20 Pauling, Linus Carl, 12
Nucleotide, 979982 Ornithine, biosynthesis of, 841 PCC, see Pyridinium chlorochromate
biosynthesis of, 10031008 citrulline from, 828829 PCR, see Polymerase chain reaction,
catabolism of, 9971002 from arginine, 831 995997
3 end of, 982 reaction with carbamoyl phosphate, PDB, see Protein Data Bank
5 end of, 982 828829 Peanut oil, composition of, 929
Nucleus, size of, 3 urea cycle and, 828 Penicillin, discovery of, 668
Nylon, 664 Ornithine transcarbamoylase, 828 Penicillin V, specific rotation of, 326
naming, 664 Orotate, biosynthesis of, 10031006 stereochemistry of, 351
uses of, 664 Orotate phosphoribosyltransferase, 1004 Penta-1,4-diene, electrostatic potential
Nylon 6, structure of, 664 Orotidine, biosynthesis of, 10031005 map of, 248
Nylon 66, structure of, 664 Orotidine monophosphate, Pentan-1-ol, 13C NMR spectrum of, 463
decarboxylation of, 1005 Pentane, molecular model of, 83
Ocimene, structure of, 212 Orotidine monophosphate decarboxylase, Pentane-2,4-dione anion, resonance
Octane number (fuel), 103 1005 forms of, 4748
Octet rule, 7 rate acceleration in, 1005 pKa of, 690
-oic acid, name ending for carboxylic Ortho (m), 269 Pentose phosphate pathway, 924, 925
acids, 602 Ortho- and para-directing group, 293, PEP, see Phosphoenolpyruvate
-ol, alcohol name ending, 499 295296 Pepsin, isoelectric point of, 784
Olefin, 179 Osazone, 888 Peptide, 777
Oleic acid, structure of, 929 -ose, carbohydrate name ending, 853 amino acid analysis of, 789
Oligonucleotide, 992 Oseltamivir, molecular model of, 133 backbone of, 787
synthesis of, 992995 Oseltamivir phosphate, mechanism of, covalent bonding in, 788
Olive oil, composition of, 929 920 disulfide bonds in, 788
-one, ketone name ending, 559 -oside, glycoside name ending, 868 Edman degradation of, 790792
-onitrile, nitrile name ending, 604 Osmium tetroxide, reaction with alkenes, reaction with phenylisothiocyanate,
Optical activity, measurement of, 238239 790791
325326 Oxalic acid, structure of, 603 sequencing of, 790792
Optical isomers, 328 Oxaloacetate, aspartate from, 828, 838 solid-phase synthesis of, 794796
Optically active, 325 decarboxylation of, 913 synthesis of, 793796
Orbital, 4 from malate, 910 Peptide bond, 787
energies of, 5 from pyruvate, 913, 916 DCC formation of, 794
hybridization of, 1220 phosphoenolpyruvate from, 913 restricted rotation in, 788
shapes of, 45 reaction with acetyl CoA, 906907 Periplanar geometry, 395
d Orbital, shape of, 4 Oxaloacetic acid, structure of, 603 E2 reactions and, 395397
p Orbital, lobes of, 5 Oxalosuccinate, decarboxylation of, 908 Perlon, structure of, 664
nodes in, 5 from isocitrate, 908 Peroxyacid, 235
shape of, 45 Oxidation, alcohols and, 516519 reaction with alkenes, 235236
s Orbital, shape of, 4 aldehydes, 561562 Petroleum, catalytic cracking of, 103
Organic chemicals, elements found FAD and, 939949 composition of, 103
in, 3 NAD and, 519 gasoline from, 103
number of, 75 organic, 235 refining of, 103
size of, 2 phenols, 519 Pfu DNA polymerase, 996
toxicity of, 26 Oxidative deamination, 826 PGA, see Polyglycolic acid, 665666
Organic chemistry, 2 mechanism of, 826 PGH synthase, 948
foundations of, 2 Oxidative decarboxylation, 901 Pharmaceuticals, approval procedure for,
Organic molecule, polar covalent bonds Oxidoreductase, 801 171
in, 147149 Oxidosqualene : lanosterol cyclase, 965 origin of, 171
Organic reactions, conventions for Oxirane, 235 PHB, see Polyhydroxybutyrate, 665666
writing, 197 Oxo group, 559 Phenol(s), 497
kinds of, 142143 Oxymercuration, 228 acidity of, 501503
stereochemistry and, 342344 mechanism of, 229 electrophilic aromatic substitution of,
Organic synthesis, enantioselective, 587 regiochemistry of, 229 295296
strategy for, 300306 Oxytocin, structure of, 815 electrostatic potential map of, 294
Organodiphosphate, Friedel-Crafts hydrogen bonds in, 501
reactions and, 290291 Palmitic acid, structure of, 929 IR spectroscopy of, 529
SN1 reactions and, 390391 Palmitoleic acid, structure of, 929 IR spectrum of, 529
I-22 INDEX
Phenol(s) (continued) Phosphorylation, ATP and, 819820 Polymerization, mechanism of, 240241
naming, 500 mechanism of, 820 radical, 240242
NMR spectroscopy of, 531 Photon, 426 Polysaccharide(s), 852, 876878
oxidation of, 519 energy of, 427 synthesis of, 878
phenoxide ions from, 501503 Photosynthesis, 852 Polyunsaturated fatty acid, 928
pKa of, 502, 606 Phthalic acid, structure of, 603 Porphobilinogen, biosynthesis of, 772
properties of, 501503 Phylloquinone, biosynthesis of, 291 Potassium nitrosodisulfonate, reaction
quinones from, 519 Physiological pH, 608 with phenols, 519
uses of, 498 Pi () bond, 15 Preeclampsia, Viagra and, 171
Phenoxide ion, 501 acetylene and, 1718 Prelaureatin, biosynthesis of, 264
resonance in, 503 ethylene and, 1416 Priestley, Joseph, 253
Phenyl group, 269 molecular orbitals in, 22 Primary alcohol, 499
Phenylacetaldehyde, aldol reaction of, Picometer, 3 Primary amine, 736
702 Pinacol rearrangement, 542 Primary carbon, 88
IR spectrum of, 437 Pineapple, esters in, 653 Primary hydrogen, 88
Phenylacetic acid, 1H NMR spectrum of, Piperidine, molecular model of, 753 Primary protein structure, 797
618 PITC, see Phenylisothiocyanate, 790791 Priming reaction, fatty acid biosynthesis
Phenylalanine, molecular model of, 104 pKa, 52 and, 943944
structure and properties of, 780 table of, 52 pro-R prochirality center, 347
Phenylisothiocyanate, Edman PLA, see Polylactic acid, 665666 pro-S prochirality center, 347
degradation and, 790791 Plane of symmetry, 321322 Problems, how to work, 27
Phenylthiohydantoin, Edman meso compounds and, 336 Procaine, structure of, 32
degradation and, 790791 Plane-polarized light, 325 Prochirality, 346348
Phosphate, electrostatic potential map of, Plasmalogen, structure of, 972 assignment of, 346348
79 Plasticizer, 653654 biological reactions and, 348
polarity of, 79 Plexiglas, 263 Re descriptor for, 346
Phosphatidic acid, structure of, 933 Plocamium cartilagineum, alkyl halides Si descriptor for, 347
Phosphatidylcholine, structure of, 933 in, 225 structure and function of, 962963
Phosphatidylethanolamine, structure of, PLP, see Pyridoxal phosphate Prochirality center, 347
933 PMP, see Pyridoxamine phosphate pro-R, 347
Phosphatidylserine, structure of, 933 Poison ivy, urushiols in, 498 pro-S, 347
Phosphine(s), chirality of, 345 Polar aprotic solvent, 379 Progestin, 962963
Phosphite, 994 SN1 reaction and, 388 function of, 962
oxidation of, 994 SN2 reaction and, 379 Proline, biosynthesis of, 750, 840841
Phosphoenolpyruvate (PEP), from Polar covalent bond, 36 catabolism of, 848
2-phosphoglycerate, 900 dipole moments and, 3839 from glutamate, 841
from oxaloacetate, 913 electronegativity and, 3637 structure and properties of, 780
2-phosphoglycerate from, 915 electrostatic potential maps and, 37 Promotor site (DNA), 987
pyruvate from, 900 Polar reaction, 144 Propagation step (radical), 145
Phosphoenolpyruvate carboxykinase, characteristics of, 147150 Propan-1-ol, 1H NMR spectrum of, 530
913 curved arrows in, 149, 154156 Propane, bond rotation in, 98
Phosphofructokinase, 896 electrophiles in, 149150 molecular model of, 98
2-Phosphoglycerate, from example of, 151154 conformations of, 98
phosphoenolpyruvate, 915 nucleophiles in, 149150 mass spectrum of, 417
from 3-phosphoglycerate, 899 Polarimeter, 325 molecular model of, 83
3-Phosphoglycerate, from 1,3- Polarizability, 149 Propanenitrile, 13C NMR absorptions in,
bisphosphoglycerate, 899 Poly(vinyl pyrrolidone), 263 618
isomerization of, 899 Polyamide, 664 Propanoic acid, 13C NMR absorptions in,
Phosphoglycerate kinase, 899 Polycyclic aromatic compound, 618
Phosphoglycerate mutase, 899 278280 Propionic acid, 13C NMR absorptions in,
Phosphohomoserine, elimination Polycyclic compound(s), 131 618
reaction of, 844 conformations of, 131132 Propionyl CoA, catabolism of, 942
Phospholipid, 933934 Polyester, 664 Propyl group, 87
abundance of, 934 uses of, 665 Propylene, heat of hydrogenation of, 194
classification of, 933 Polyethylene, synthesis of, 240241 Prostaglandin(s), 948
Phosphopantetheine, structure of, 662, Polyglycolic acid, 665666 biological activity of, 2, 948
819 Polyhydroxybutyrate, 665666 biosynthesis of, 12, 243244
Phosphoramidite, 994 Polylactic acid, 665666 structure of, 1, 117, 948949
Phosphorane, 575 Polymer, 239 functions of, 948
Phosphoric acid, pKa of, 52 biodegradable, 665666 naming of, 948949
Phosphoric acid anhydride, 819 biological, 239240 number of, 948
Phosphorus, ground-state electron chain-growth, 240242, 664 Prostaglandin H2, biosynthesis of, 12,
configuration of, 6 step-growth, 664 146
Phosphorus oxychloride, alcohol Polymerase chain reaction (PCR), structure of, 1
dehydration with, 513515 995997 Protein(s), 777
Phosphorus tribromide, reaction with amplification factor in, 997 helix in, 798
alcohols, 366, 512 taq DNA polymerase in, 996 backbone of, 787
INDEX I-23
biosynthesis of, 987989 Pyrimidine, aromaticity of, 276277 Radio waves, electromagnetic spectrum
classification of, 797 basicity of, 742, 759 and, 425
denaturing, 799 biosynthesis of, 10031006 Radiofrequency energy, NMR
electrophoresis of, 784 catabolism of, 10001002 spectroscopy and, 456457
fibrous, 797 electrostatic potential map of, 276 Rate equation, 372
globular, 797 Hckel 4n 2 rule and, 276277 Rate-determining step, 381
hydrolysis of, 660, 789 Pyrrole, aromaticity of, 276277, 756 Rate-limiting step, 381
isoelectric point of, 784 basicity of, 742, 756 Rayon, 876
number of in humans, 817 electrophilic substitution reactions of, Re prochirality, 346
primary structure of, 797 756757 Reaction (polar), 144, 147150
purification of, 784 electrostatic potential map of, 276, 756 Reaction (radical), 144146
quaternary structure of, 797 Hckel 4n 2 rule and, 276277 Reaction coordinate, 163
secondary structure of, 797 industrial synthesis of, 755 Reaction energy diagram, 163164
see also Peptide Pyrrolidine, electrostatic potential map biological reactions and, 167
tertiary structure of, 797 of, 756 electrophilic addition reactions and,
X-ray crystallography of, 721 Pyrrolysine, structure of, 779 164167
Protein Data Bank, 807 Pyruvate, acetyl CoA from, 901905 endergonic reactions and, 165
uses of, 807 alanine from, 838 exergonic reactions and, 165
visualizing enzyme structures and, carboxylation of, 913, 916 intermediates and, 166167
844845 catabolism of, 901905 Reaction intermediate, 166
X-ray crystallographic structures in, decarboxylation of, 901903 Reaction mechanism, 143
721 ethanol from, 923 Reaction rate, activation energy and,
Protic solvent, SN1 reaction and, 388 from alanine, 833 164165
SN2 reaction and, 379 from phosphoenolpyruvate, 900 Rearrangement reaction, 142
Proton equivalence, 1H NMR from serine, 833834 Reducing sugar, 870
spectroscopy and, 470472 oxaloacetate from, 913, 916 Reduction, aldehydes, 506507, 568
Protonated methanol, electrostatic reaction with thiamine diphosphate, alkenes, 232234
potential map of, 148 901903 alkynes, 251
Protosteryl cation, steroid biosynthesis Pyruvate carboxylase, 913 amides, 660661
and, 968 Pyruvate dehydrogenase complex, 901 aromatic compounds and,
Prozac, structure of, 350 Pyruvate kinase, 900 299300
PRPP synthetase, 1005 Pyruvic acid, structure of, 603 carboxylic acids, 507508
Pseudoephedrine, molecular model of, esters, 507508, 657658
354 Quantum mechanical model, 45 ketones, 506507, 568
PTH, see Phenylthiohydantoin, 790791 Quartet (NMR), 476 lactams, 661
PUFA, see Polyunsaturated fatty acid, Quaternary ammonium salt, 736 nitriles, 616
928 Hofmann elimination of, 751752 organic, 232
Purification, organic compounds, Quaternary carbon, 88 quinones, 519520
444445 Quaternary protein structure, 797 Reductive amination, 748750
Purine, aromaticity of, 279 Quinine, structure of, 280, 760 biological, 750
basicity of, 761 Quinoline, aromaticity of, 279 mechanism of, 749
biosynthesis of, 10061008 electrophilic substitution reaction of, 760 Refining (petroleum), 103
catabolism of, 9971000 Quinone, 519 Regiospecific, 198
electrostatic potential map of, 761 from phenols, 519 Replication (DNA), 985986
Purine nucleoside phosphorylase, 998 hydroquinones from, 519520 Replication fork (DNA), 986
Pyramidal inversion, amines and, 739 reduction of, 519520 Reserpine, structure of, 65
energy barrier to, 739 Residue (protein), 787
Pyran, structure of, 863 R configuration, 329 Resolution (enantiomers), 338340
Pyranose, 862 assignment of, 328330 Resonance, acetate ion and, 4344
Pyridine, aromaticity of, 276277 R group, 88 acetyl CoA anion and, 46
basicity of, 742, 758 Racemate, 338 acyl cations and, 290
bond lengths in, 758 Racemic mixture, 338 allylic carbocations and, 249
dipole moment of, 759 Radical, 144 arylamines and, 744
electrophilic substitution reactions of, addition reactions of, 144 benzene and, 271, 44
758 biological addition reactions of, benzylic carbocation and, 385
electrostatic potential map of, 276 243244 benzylic radical and, 299
Hckel 4n 2 rule and, 276277 reaction with alkenes, 240242 carboxylate ions and, 607
Pyridinium chlorochromate, reaction reactivity of, 144146 enolate ions and, 688
with alcohols, 517518 substitution reactions of, 144145 naphthalene and, 278
Pyridoxal phosphate, 803 Radical polymerization, 240242 p-nitrophenoxide ion and, 503
deamination and, 823825 Radical reaction, 144146 pentane-2,4-dione anion and,
from PMP, 825826 biological, 146 4748
imine formation from, 568, 824 characteristics of, 144146 phenoxide ion and, 503
Pyridoxamine phosphate, structure of, fishhook arrows and, 143144 see also Resonance form,
825 initiation steps in, 145 Resonance effect, 294295
transamination of, 825826 propagation steps in, 145 electrophilic aromatic substitution
Pyridoxine, structure of, 822 termination steps in, 145 and, 294295
I-24 INDEX
Resonance form, 44 Secondary hydrogen, 88 SN2 reaction, 372

drawing, 4749 Secondary protein structure, 797 allylic halides in, 386
electron movement and, 45 helix in, 798 amines and, 747748
rules for, 4546 sheet in, 798 benzylic halides in, 386
stability of, 46 Selenocysteine, structure of, 779 biological, 390391
three-atom groupings in, 4749 Semiconservative replication (DNA), characteristics of, 374380
Resonance hybrid, 44 985 electrostatic potential maps of, 373
Restriction endonuclease, 991 Sense strand (DNA), 987 inversion of configuration in, 372373
Retinal, vision and, 443444 Sequence rules, 188190, 328 kinetics of, 371372
Rhodopsin, isomerization of, alkenes and, 188190 leaving groups and, 377378
443444 enantiomers and, 328330 mechanism of, 372373
vision and, 443444 Serine, catabolism of, 833834, 847 nucleophiles in, 376377
Ribavirin, structure of, 313 pyruvate from, 833834 rate law for, 372
Ribonucleic acid, 979982 structure and properties of, 781 solvent effects and, 379
bases in, 980 Serine dehydratase, 833 stereochemistry of, 372373
biosynthesis of, 986987 Serum lipoprotein, table of, 970 steric hindrance in, 374375
catabolism of, 9971002 Sesquiterpene, 209 substrate structure and, 374376
3 end of, 982 Sesquiterpenoid, 951 summary of, 380
5 end of, 982 Sex hormone, 962963 table of, 376
kinds of, 986 Sharpless, K. Barry, 587 Williamson ether synthesis and, 524
messenger, 986 Sharpless epoxidation, 587 epoxide cleavage and, 526
ribosomal, 986 Shell (electron), 4 Soap, 931932
size of, 980 capacity of, 5 history of, 931
structure of, 981982 Shielding (NMR), 458 manufacture of, 931
transfer, 986 Si prochirality, 347 mechanism of action of, 932
translation of, 987989 Sialic acid, 873 micelles in, 932
Ribonucleotide, biosynthesis of, Side chain (amino acid), 779 Sodium amide, reaction with alcohols,
10031008 Sigma () bond, 10 503
catabolism of, 9971002 cylindrical symmetry of, 10 Sodium bisulfite, osmate reduction with,
structures of, 981 Signal averaging, FT-NMR spectroscopy 238239
Ribose, configuration of, 860 and, 462463 Sodium borohydride, reaction with
Ribosomal RNA, 986 Sildenafil, structure of, 755 aldehydes, 506, 568
function of, 987989 see also Viagra reaction with ketones, 506, 568
Ricinoleic acid, structure of, 929 Silver oxide, Hofmann elimination reaction with organomercury
Ring-flip (cyclohexane), 125 reaction and, 752 compounds, 229
energy barrier to, 125 Simple sugar, 852 reductive amination with, 749
molecular model of, 125 Simvastatin, structure and function of, Sodium chloride, dipole moment of, 39
Risk, chemicals and, 26 1010 Sodium cyclamate, LD50 of, 26
RNA, see Ribonucleic acid Single bond, electronic structure of, Sodium hydride, reaction with alcohols,
Rod cells, vision and, 443 1314 503
rRNA, see Ribosomal RNA length of, 1314 Solid-phase synthesis, DNA, 992995
Rubber, history of, 253254 see also Alkane peptides, 794796
vulcanization of, 254 strength of, 1314 see also, Merrifield, 794796
Skeletal structure, 23 Solvation, 379
S configuration, 329 rules for drawing, 2324 carbocations and, 388
assignment of, 328330 Skunk scent, cause of, 520 SN2 reaction and, 379
Saccharin, structure of, 881 sn-, naming prefix Solvent, polar aprotic, 379
sweetness of, 880 SN1 reaction, 381 SN1 reaction and, 388
Saccharopine, from lysine, 849 allylic halides in, 385386 SN2 reaction and, 379
SAH, see S-Adenosylhomocysteine benzylic halides in, 385386 Soot, carcinogenic compounds in, 238
Salt bridge (protein), 799 biological, 390391 Sorbitol, structure of, 869
SAM, see S-Adenosylmethionine carbocation stability and, 385386 Specific rotation, 326
Sanger, Frederick, 991 characteristics of, 385389 table of, 326
Sanger dideoxy DNA sequencing, energy diagram for, 383 Sphingomyelin, 933934
991992 ion pairs in, 384 Sphingosine, structure of, 934
Saponification, 654 931 kinetics of, 381382 Spin-flip, NMR spectroscopy and, 456
mechanism of, 654655 leaving groups in, 386387 Spinspin splitting, 477
Saturated, 82 mechanism of, 382, 387 alcohols and, 530
Sawhorse representation, 97 nucleophiles and, 387 bromoethane and, 476478
Schiff base, 897 racemization in, 382384 2-bromopropane and, 478
see also Imine rate law for, 381 n 1 rule and, 478
Scurvy, vitamin C and, 619 rate-limiting step in, 381382 13C NMR spectroscopy and, 480
sec-Butyl group, 87 solvent effects on, 388 1H NMR spectroscopy and, 476480
Second-order reaction, 372 stereochemistry of, 382384 nonequivalent protons and, 478479
Secondary alcohol, 499 substrate structure and, 385386 origin of, 477478
Secondary amine, 736 summary of, 388389 rules for, 479
Secondary carbon, 88 epoxide cleavage and, 526 tree diagrams and, 483
INDEX I-25
Split synthesis, 307 Structure, condensed, 22 Table sugar, see Sucrose

Squalene, biological epoxidation of, electron-dot, 8 Talose, configuration of, 860
236237, 964965 Kekul, 8 Tamiflu, avian flu virus and, 920
from farnesyl diphosphate, 964 Lewis, 8 mechanism of, 920
steroid biosynthesis and, 964969 line-bond, 8 molecular model of, 133
Squalene epoxidase, 964 skeletal, 23 Tamoxifen, synthesis of, 595
Staggered conformation, 97 Strychnine, LD50 of, 26 Taq DNA polymerase, PCR and, 996
molecular model of, 97 Substituent effect, additivity of, Tartaric acid, stereoisomers of, 335336
Standard state, biological, 159 301302 meso-Tartaric acid, molecular model of,
thermodynamic, 159 electrophilic aromatic substitution and, 336
Starch, digestion of, 877 292297 Tautomer, 682
glucose from, 892893 summary of, 297 Tautomerism, 682
hydrolysis of, 892893 Substitution reaction, 142 Template strand (DNA), 987
maltotriose from, 892 Substrate (enzyme), 800 Termination step (radical), 145
structure of, 876877 Succinate, dehydrogenation of, 909 Terpene, 209, 950
Statins, mechanism of, 1010 from succinyl CoA, 908909 biosynthesis of, 209210
Stationary phase, chromatography and, fumarate from,909 Terpene cyclase, 957
444 Succinate dehydrogenase, 909 Terpenoid, 209, 950958
Stearic acid, molecular model of, 929 Succinic acid, structure of, 603 biosynthesis of, 951958
structure of, 929 Succinyl CoA, from -ketoglutarate, classification of, 951
Step-growth polymer, 664 908 occurrence of, 951
Stereochemistry, 96 succinate from, 908909 -Terpineol, biosynthesis of, 959
absolute configuration and, 330 Succinyl CoA synthetase, 908 tert-Amyl group, 93
alkene addition reactions and, 342344 Sucralose, structure of, 881 tert-Butyl group, 87
cistrans isomers and, 115116, sweetness of, 880 Tertiary alcohol, 499
186187 Sucrose, molecular model of, 876 Tertiary amine, 736
cycloalkenes and, 188190 specific rotation of, 326 Tertiary carbon, 88
diastereomers and, 334 structure of, 876 Tertiary hydrogen, 88
E1 reaction and, 399 sweetness of, 880 Tertiary protein structure, 797
E2 reactions and, 397 Sugar, D, 858 hydrophilic interactions in, 799
enantiomers and, 320322 L, 858 hydrophobic interactions in, 799
epimers and, 334 simple, 852 noncovalent interactions in, 799
R,S configuration and, 328330 see also Aldose, Carbohydrate, salt bridges in, 799
SN1 reaction and, 382384 Monosaccharide Testosterone, conformation of, 132
SN2 reactions and, 372373 Sulfa drugs, 754 molecular model of, 132
Stereogenic center, 322 synthesis of, 285 structure and function of, 962
Stereoisomers, 116 Sulfanilamide, structure of, 285 Tetrahedral geometry, conventions for
cistrans isomers and, 115116, synthesis of, 754 drawing, 7
186187 Sulfathiazole, structure of, 754 Tetrahydrofolate, histidine catabolism
diastereomers and, 334 Sulfide(s), 497 and, 836837
enantiomers and, 320322 electrostatic potential map of, 80 structure and function of, 803, 837
epimers and, 334 from thiols, 527 Tetrahydrofuran, as reaction solvent, 223
kinds of, 341 naming, 523 Tetramethylsilane, NMR spectroscopy
properties of, 336 occurrence of, 498 and, 461
Stereospecific numbering (sn-), 937 oxidation of, 528 Tetraterpenoid, 951
Steric hindrance, SN2 reaction and, polarity of, 80 Tetrazole, DNA synthesis and, 994
374375 reaction with alkyl halides, 527 Thermodynamic quantities, 160
Steric strain, 99 sp3 hybrid orbitals in, 20 Thermodynamic standard state, 159
cis alkenes and, 192 structure of, 20 Thiamin, aromaticity of, 278
substituted cyclohexanes and, 126128 sulfoxides from, 528 basicity of, 757
Steroid(s), 959969 Sulfonamides, synthesis of, 285 Thiamin diphosphate, decarboxylations
adrenocortical, 963 Sulfonation (aromatic), 285286 with, 901903
anabolic, 963 Sulfone(s), 528 pKa of, 903
biosynthesis of, 964969 from sulfoxides, 528 reaction with pyruvate, 901903
classification of, 962 Sulfonium salt(s), 346 structure and function of, 803, 903
conformations of, 132, 960961 chirality of, 346 ylide from, 903
hormones and, 962963 Sulfoxide(s), 528 Thiazole, basicity of, 757
molecular model of, 960 from sulfides, 528 Thiazolium ring, aromaticity of, 278
numbering of, 960 oxidation of, 528 pKa of, 901
shape of, 960 Sutures, absorbable, 666 Thioacetal, synthesis of, 594
synthetic, 963 Sweeteners, synthetic, 880881 Thioanisole, electrostatic potential map
Stork enamine reaction,717 Symmetry plane, 321322 of, 623
mechanism of, 717 Syn periplanar geometry, 395396 -thioate, thioester name ending, 635
STR loci, DNA fingerprinting and, molecular model of, 396 Thioester(s), 633
10101011 Syn stereochemistry, 229 biological hydrolysis of, 678
Straight-chain alkane, 83 Synthesis, trisubstituted aromatic biological reactivity of, 662
Strecker synthesis, 775 compounds, 300306 biological reduction of, 663
I-26 INDEX
Thioester(s) (continued) Transcription (DNA), 986987 interpretation of, 441

electrostatic potential map of, 639 Transfer RNA, 986 molar absorptivity and, 440
naming, 635 anticodons in, 988989 Ultraviolet spectrum, benzene, 441
pKa of, 690 function of, 988989 -carotene, 442
polarity of, 80 shape of, 989 but-3-en-2-one, 441
Thiol(s), 497 Transferase, 801 buta-1,3-diene, 440
acidity of, 502 Transimination, 824 cyclohexa-1,3-diene, 441
disulfides from, 521 amino acids and, 824 ergosterol, 451
electrostatic potential map of, 80 mechanism of, 824 hexa-1,3,5-triene, 441
from alkyl halides, 521 Transition state, 164 Unimolecular, 381
naming, 500 Hammond postulate and, 204206 Unsaturated, 180
occurrence of, 498 Translation (RNA), 988989 Unsaturated aldehyde, conjugate addition
odor of, 520 Tree diagram (NMR), 483 reactions of, 580583
oxidation of, 521 Triacylglycerol, 928 Unsaturated ketone, conjugate addition
polarity of, 80 catabolism of, 934942 reactions of, 580583
polarizability of, 149 Trialkylsulfonium salt, alkylations with, Unsaturation, degree of, 180
reaction with alkyl halides, 527 528 Upfield (NMR), 460
reaction with Br2, 521 from sulfides, 527528 Uracil, biological reduction of, 1001
reaction with NaH, 527 1,2,4-Triazole, aromaticity of, 313 catabolism of, 10011002
sp3 hybrid orbitals in, 20 Tricarboxylic acid cycle, see Citric acid structure of, 980
structure of, 20 cycle Urea, from ammonia, 827831
sulfides from, 527 Trichodiene, biosynthesis of, 978 Urea cycle, 828831
thiolate ions from, 527 Trifluoroacetic acid, ether cleavage with, steps in, 829
-thiol, thiol name ending, 500 526 Uric acid, from xanthine, 999
Thionyl chloride, reaction with alcohols, pKa of, 606 pKa of, 625
366, 512 Trifluoromethylbenzene, electrostatic structure of, 625, 827
reaction with amides, 615 potential map of, 311 Uridine, biosynthesis of, 10031006
reaction with carboxylic acids, Triglyceride, see Triacylglycerol, 928 catabolism of, 10001002
642643 Trimethylamine, bond angles in, 739 from orotidine, 1005
Thiophene, aromaticity of, 277 electrostatic potential map of, 740 phosphorolysis of, 10001001
Thiophenol, 497 molecular model of, 739 Uridine phosphorylase, 1001
Thiourea, reaction with alkyl halides, 521 Trimetozine, synthesis of, 651 Uridine triphosphate, glycoconjugate
Threonine, biosynthesis of, 842844 Triose phosphate isomerase, 898 biosynthesis and, 868869
catabolism of, 847 Triphenylphosphine, reaction with alkyl Urocanase, active site of, 845
from aspartate, 842844 halides, 575576 histidine catabolism and, 835
from homoserine, 843844 Triple bond, electronic structure of, ribbon model of, 844
stereoisomers of, 333 1718 trans-Urocanate, from histidine, 835836
structure and properties of, 781 length of, 18 hydration of, 836837
Threonine synthase, 843 see also Alkyne imidazolone 5-propionate from,
Threose, configuration of, 860 strength of, 18 836837
molecular model of, 325 Triplet (NMR), 476 Uronic acid, 871
Thromboxane, naming of, 948949 Trisubstituted aromatic compound, from aldoses, 871
Thymidine, catabolism of, 1002 synthesis of, 300306 Urushiols, structure of, 498
Thymine, electrostatic potential map of, Triterpenoid, 951 UV, see Ultraviolet
983 tRNA, see Transfer RNA
structure of, 980 Trypsin, peptide cleavage with, 792 Valence bond theory, 1020
Thyroxine, biosynthesis of, 284 Tryptophan, structure and properties of, orbital hybridization and, 1220
structure of, 779 781 Valence shell, 7
Time-of-flight (TOF) mass spectrometry, Tswett, Mikhail, 444 Valine, structure and properties of, 781
424425 Turnover number, enzyme, 800 Valium, see Diazepam
sensitivity of, 424 Twist-boat conformation, cyclohexane, 123 Van der Waals forces, 62
Tin, reaction with nitroarenes, 747 molecular model of, 123 alkanes and, 96
TMS, see Tetramethylsilane, 461 Tyrosine, biological iodination of, 284 Vancomycin, structure of, 403
Tollens test, 870 biosynthesis of, 514 uses of, 403
Toluene, electrostatic potential map of, catabolism of, 848 vant Hoff, Jacobus Hendricus, 7
311 structure and properties of, 781 Vasopressin, structure of, 788
IR spectrum of, 435 Vegetable oil, 928
1H NMR spectrum of, 482 Ubiquinones, function of, 520 hydrogenation of, 233234, 930
Torsional strain, 97 structure of, 520 table of, 929
Tosylate, 369 Ultraviolet light, electromagnetic Vent DNA polymerase, 996
Toxicity, chemicals and, 26 spectrum and, 425 Viagra, structure of, 755
TPP, see, Thiamin diphosphate wavelength of, 438439 preeclampsia and, 171
Trans fatty acid, formation of, 234 Ultraviolet spectroscopy, 438440 Vinyl group, 184
from hydrogenation of fats, 930 absorbance and, 440 Vinyl monomer, 241
Transamination, 822 conjugation and, 441 Vinylic anion, electrostatic potential map
PMP and, 825826 HOMOLUMO transition in, 439 of, 253
INDEX I-27
Vinylic halide, SN2 reaction and, electrophilicity of, 150 X rays, electromagnetic spectrum and, 425
375376 electrostatic potential map of, 54, 150 X-ray crystallography, 720721
Vioxx, prostaglandin synthesis and, 2 hydrogen bond in, 63 X-ray diffractometer, 721
Visible light, electromagnetic spectrum nucleophilic addition reactions of, Xanthine, biological oxidation of, 999
and, 425 564566 from guanine, 998999
Vision, chemistry of, 443444 nucleophilicity of, 150 Xanthine oxidase, 999
retinal and, 443444 pKa of, 52 Xanthosine, biosynthesis of, 10071008
Vitamin, 802 reaction with aldehydes, 564566 Xylose, configuration of, 860
chromatography of, 445 reaction with enones, 582
coenzymes from, 802 reaction with ketones, 564566 Yeast alcohol dehydrogenase,
Vitamin B6, structure of, 822 Watson, James Dewey, 982 stereochemistry of, 348
Vitamin B12, structure of, 1009 WatsonCrick DNA model, 982984 -yl, alkyl group name ending, 86
Vitamin C, history of, 618 Wave equation, 4 Ylide, 575
industrial synthesis of, 619 Wave function, 4 synthesis of, 575576
molecular model of, 619 molecular orbitals and, 2122 -yne, alkyne name ending, 184
scurvy and, 619 Wavelength ( ), 426
uses of, 618 Wavenumber, 428 Z configuration, 188
Vitamin K1, biosynthesis of, 291 Wax, 928 assignment of, 188190
VLDL, heart disease and, 970 Whale blubber, composition of, 929 Zaitsev, Alexander M., 392
Volcano, chloromethane from, 363 Williamson ether synthesis, 524 Zaitsevs rule, 392
Vulcanization, 254 Ag2O in, 524 alcohol dehydration and, 513
carbohydrates and, 866 Hofmann elimination and, 752
Walden, Paul, 368 mechanism of, 524 NMR proof for, 470
Walden inversion, 368370 Wittig reaction, 575577 Zocor, structure and function of, 1010
Wang resin, peptide synthesis and, 796 mechanism of, 575576 Zusammen, Z configuration and, 188
Water, acidbase behavior of, 5051 uses of, 577 Zwitterion, 778
conjugate addition reactions to enones, ylides in 575576 amino acids and, 778
582 Wohl degradation, 887 Zwitterion, electrostatic potential map of,
dipole moment of, 39 Wood alcohol, 497 778
Periodic Table of the Elements
Key
Atomic number Metals
79
Au Symbol Semimetals
Gold Name
196.9665 Nonmetals
Atomic mass
Group number, An element
U.S. system
IUPAC system 1A
(1) 8A
1 (18)
Period H 2
1 Hydrogen He
number
1.0079 3A 4A 5A 6A 7A Helium 1
2A
(2) (13) (14) (15) (16) (17) 4.0026
3 4 5 6 7 8 9 10
Li Be B C N O F Ne
2 Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon 2
6.941 9.0122 10.811 12.011 14.0067 15.9994 18.9984 20.1797
11 12 13 14 15 16 17 18
Na Mg Al Si P S Cl Ar
3 Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon
3
3B 4B 5B 6B 7B 8B 8B 8B 1B 2B
22.9898 24.3050 (3) (4) (5) (6) (7) (8) (9) (10) (11) (12) 26.9815 28.0855 30.9738 32.066 35.4527 39.948
19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
4 Potassium Calcium Scandium Titanium Vanadium Chromium Manganese Iron Cobalt Nickel Copper Zinc Gallium Germanium Arsenic Selenium Bromine Kyrpton 4
39.0983 40.078 44.9559 47.88 50.9415 51.9961 54.9380 55.847 58.9332 58.693 63.546 65.39 69.723 72.61 74.9216 78.96 79.904 83.80
37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
5 Rubidium Strontium Yttrium Zirconium Niobium Molybdenum Technetium Ruthenium Rhodium Palladium Silver Cadmium Indium Tin Antimony Tellurium Iodine Xenon
5
85.4678 87.62 88.9059 91.224 92.9064 95.94 (98) 101.07 102.9055 106.42 107.8682 112.411 114.82 118.710 121.757 127.60 126.9045 131.29
55 56 57 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86
Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
6 Cesium Barium Lanthanum Hafnium Tantalum Tungsten Rhenium Osmium Iridium Platinum Gold Mercury Thallium Lead Bismuth Polonium Astatine Radon 6
132.9054 137.327 138.9055 178.49 180.9479 183.85 186.207 190.2 192.22 195.08 196.9665 200.59 204.3833 207.2 208.9804 (209) (210) (222)
87 88 89 104 105 106 107 108 109 110 111

Fr Ra Ac Rf Db Sg Bh Hs Mt Ds Rg
7 7
Francium Radium Actinium Rutherfordium Dubnium Seaborgium Bohrium Hassium Meitnerium Darmstadtium Roentgenium
(223) 227.0278 (227) (261) (262) (263) (262) (265) (266) (269) (272)
58 59 60 61 62 63 64 65 66 67 68 69 70 71
Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu
Lanthanides 6 Cerium Praseodymium Neodymium Promethium Samarium Europium Gadolium Terbium Dysprosium Holmium Erbium Thulium Ytterbium Lutetium
6
140.115 140.9076 144.24 (145) 150.36 151.965 157.25 158.9253 162.50 164.9303 167.26 168.9342 173.04 174.967
Numbers in parentheses
are mass numbers of 90 91 92 93 94 95 96 97 98 99 100 101 102 103
Actinides
Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr
radioactive isotopes. 7 Thorium Protactinium Uranium Neptunium Plutonium Americium Curium Berkelium Californium Einsteinium Fermium Mendelevium Nobelium Lawrencium
7
232.0381 231.0359 238.00289 (237) (244) (243) (247) (247) (251) (252) (257) (258) (259) (260)
Structures of Some Common Functional Groups
Name Structure Name ending Name Structure Name ending
Alkene -ene Sulfide S sulfide

(double bond) C C C C
Alkyne XCmCX -yne Disulfide disulfide

(triple bond) S C
C S
Arene None
(aromatic ring) Sulfoxide O sulfoxide
S+
C C
Halide X None Aldehyde O -al

C
C
H
(X F, Cl, Br, I)
Alcohol OH -ol Ketone O -one

C
C
C C
Ether O ether
C C
Carboxylic acid O -oic acid
C
C OH
Monophosphate O phosphate
C P
O O
Ester O -oate
O
C C
C O
Amine -amine
N
C
Thioester O -thioate
C C
C S
Imine None
N
(Schiff base)
C
C C Amide O -amide
C
C N
Nitrile XCmN -nitrile
Acid chloride O -oyl chloride

SH -thiol
Thiol C C
C Cl

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Structures of Common Coenzymes

Adenosine triphosphateATP (phosphorylation)

Coenzyme A (acyl transfer)

Nicotinamide adenine dinucleotideNAD+ (oxidation/reduction)

Flavin adenine dinucleotideFAD (oxidation/reduction)

Tetrahydrofolate (transfer of C1 units)

S-Adenosylmethionine (methyl transfer)

Lipoic acid (acyl transfer) Pyridoxal phosphate

Thiamin diphosphate Biotin (carboxylation)

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Organic Chemistry: A Biological Approach

Publisher, Physical Sciences: David Harris Permissions Editor: Joohee Lee

Assistant Editor: Ellen Bitter Text Designer: Jeanne Calabrese

Editorial Assistant: Lauren Oliviera Photo Researcher: Dena Digilio Betz

Marketing Assistant: Michele Colella Cover Designer: Lee Friedman

Printed in the United States of America

Library of Congress Control Number: 2006920388

Student Edition: ISBN 0-495-01525-3

Key to Sequence of Topics (chapter numbers are color coded as follows):

1 Structure and Bonding 1

1.1 Atomic Structure: The Nucleus 3

2 Polar Covalent Bonds; Acids and Bases 35

2.11 Acids and Bases: The Lewis Definition 58

3 Organic Compounds: Alkanes

4 Organic Compounds: Cycloalkanes

5 An Overview of Organic Reactions 141

5.4 Polar Reactions 147

6 Alkenes and Alkynes 179

7 Reactions of Alkenes and Alkynes 221

Lagniappe: Natural Rubber 253

8 Aromatic Compounds 267

10 Alkyl Halides: Nucleophilic Substitutions

Structure Determination: Mass

12 Structure Determination: Nuclear Magnetic

13 Alcohols, Phenols, and Thiols;

A Preview of Carbonyl Chemistry 547

I. Kinds of Carbonyl Compounds 547

14 Aldehydes and Ketones:

15 Carboxylic Acids and Nitriles 601

16 Carboxylic Acid Derivatives: Nucleophilic

17.1 KetoEnol Tautomerism 682

18 Amines and Heterocycles 735

18.1 Naming Amines 736

19 Biomolecules: Amino Acids,

20 Amino Acid Metabolism 817

20.1 An Overview of Metabolism and Biochemical Energy 818

Lagniappe: Visualizing Enzyme Structures 844

21 Biomolecules: Carbohydrates 851

21.1 Classification of Carbohydrates 852

22 Carbohydrate Metabolism 891

22.1 Hydrolysis of Complex Carbohydrates 892

23 Biomolecules: Lipids and Their Metabolism 927

23.1 Waxes, Fats, and Oils 928

23.9 Steroids 959

24 Biomolecules: Nucleic Acids

25 Secondary Metabolites: An Introduction

Companions to This Text

To further student understanding, the text features sensi-

Pushing Electrons: A Guide for Students of Organic Chemistry, third edition