Organic Chemistry: With Biological Applications

1158 Pages·2010·15.48 MB·English

by  John E. McMurry

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Structures of Common Coenzymes
The reactive parts of the molecules are darkened, while nonreactive parts are ghosted.
Adenosine triphosphate—ATP (phosphorylation)
NH2
N
N
O O O
–O P O P O P OCH2 N N
O
– – –
O O O
OH OH
Coenzyme A (acyl transfer)
NH2
N
N
O O CH3 O O
HSCH2CH2NHCCH2CH2NHCCHCCH2OPOPOCH2 N N
O
– –
HO CH3 O O
2–O3PO OH
+
Nicotinamide adenine dinucleotide—NAD (oxidation/reduction)
+
(NADP )
NH2
CONH2 N
N
O O
+N CH2OPOPOCH2 N N
O
OH HO O–O–
O
OH OH (OPO32–)
Flavin adenine dinucleotide—FAD (oxidation/reduction)
NH2
N
N
HO OH O O
HO CHCHCHCH2OPOPOCH2 N N
O
– –
CH2 O O
H3C N N O
OH OH
N
H3C N H
O
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Tetrahydrofolate (transfer of C1 units)
H
H2N N N
H
N N
H N CO2– O
H
O H NHCHCH2CH2C O–
1–5
O
S-Adenosylmethionine (methyl transfer)
NH2
N
N
O CH3
–OCCHCH2CH2 S+ CH2 O N N
+
NH3
OH OH
Lipoic acid (acyl transfer) Pyridoxal phosphate
(amino acid metabolism)
S S CH2OPO32–
– CHO
CH2CH2CH2CH2CO2
+
N
H OH
CH3
Thiamin diphosphate Biotin (carboxylation)
(decarboxylation)
H NH2 O
+
H H
S N N N N
O O
H H
–OPOPOCH2CH2 CH3 N CH3 H
–
O–O– S CH2CH2CH2CH2CO2
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John McMurry
All royalties from Organic Chemistry with Biological Applicationswill be donated to the Cystic Fibrosis (CF) Foundation. This
book and donation are dedicated to the author’s eldest son and to the thousands of others who daily fight this disease.
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Organic Chemistry
with Biological Applications 2e
John McMurry
Cornell University
Australia • Brazil • Japan • Korea • Mexico • Singapore • Spain • United Kingdom • United States
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Organic Chemistry with Biological © 2011, 2007 Brooks/Cole, Cengage Learning
Applications 2e
ALL RIGHTS RESERVED. No part of this work covered by the copyright herein
John McMurry
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data for the following fi gures: 10.12, 10.14, 10.16,
10.17, 13.9, 13.10, 13.7, 14.15, 18.5; and data for
the spectra in Problems 10.31, 10.45, 10.46,
13.72, 15.54, and 16.62 (http://riodb01
.ibase.aist.go.jp/sdbs/, National Institute of
Advanced Industrial Science and Technology,
8/26/05, 2/7/09, 2/13/09, 3/10/09).
Printed in Canada
1 2 3 4 5 6 7 13 12 11 10 09
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Brief Contents
1 Structure and Bonding 1
2 Polar Covalent Bonds; Acids and Bases 33
3 Organic Compounds: Alkanes and Their Stereochemistry 70
4 Organic Compounds: Cycloalkanes and Their Stereochemistry 105
5 Stereochemistry at Tetrahedral Centers 134
6 An Overview of Organic Reactions 175
7 Alkenes and Alkynes 212
8 Reactions of Alkenes and Alkynes 251
9 Aromatic Compounds 309
10 Structure Determination:
Mass Spectrometry, Infrared Spectroscopy, and Ultraviolet Spectroscopy 367
11 Structure Determination: Nuclear Magnetic Resonance Spectroscopy 404
12 Organohalides: Nucleophilic Substitutions and Eliminations 444
13 Alcohols, Phenols, and Thiols; Ethers and Sulfides 501
Preview of Carbonyl Chemistry 555
14 Aldehydes and Ketones: Nucleophilic Addition Reactions 564
15 Carboxylic Acids and Nitriles 610
16 Carboxylic Acid Derivatives: Nucleophilic Acyl Substitution Reactions 643
17 Carbonyl Alpha-Substitution and Condensation Reactions 695
18 Amines and Heterocycles 749
19 Biomolecules: Amino Acids, Peptides, and Proteins 791
20 Amino Acid Metabolism 832
21 Biomolecules: Carbohydrates 862
22 Carbohydrate Metabolism 901
23 Biomolecules: Lipids and Their Metabolism 936
24 Biomolecules: Nucleic Acids and Their Metabolism 987
25 Secondary Metabolites: An Introduction to Natural Products Chemistry 1015
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
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Detailed Contents
11 Structure and Bonding
1
1.1 Atomic Structure: The Nucleus 3
1.2 Atomic Structure: Orbitals 4
1.3 Atomic Structure: Electron Configurations 6
1.4 Development of Chemical Bonding Theory 7
1.5 The Nature of Chemical Bonds: Valence Bond Theory 10
1.6 sp3 Hybrid Orbitals and the Structure of Methane 12
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 18
1.11 The Nature of Chemical Bonds: Molecular Orbital Theory 20
1.12 Drawing Chemical Structures 21
Summary 24
Lagniappe—Chemicals, Toxicity, and Risk 25
Working Problems 26
Exercises 26
22 Polar Covalent Bonds; Acids and Bases
33
2.1 Polar Covalent Bonds: Electronegativity 33
2.2 Polar Covalent Bonds: Dipole Moments 36
2.3 Formal Charges 38
2.4 Resonance 41
2.5 Rules for Resonance Forms 43
2.6 Drawing Resonance Forms 45
2.7 Acids and Bases: The Brønsted–Lowry Definition 48
vi
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