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"Beyond the basics" physical organic chemistry textbook, written for advanced undergraduates and beginning graduate students
Based on the author's first-hand classroom experience, Perspectives on Structure and Mechanism in Organic Chemistry uses complementary conceptual models to give new perspectives on the structures and reactions of organic compounds, with the overarching goal of helping students think beyond the simple models of introductory organic chemistry courses. Through this approach, the text better prepares readers to develop new ideas in the future.
In the 3rd Edition, the author thoroughly updates the topics covered and reorders the contents to introduce computational chemistry earlier and to provide a more natural flow of topics, proceeding from substitution, to elimination, to addition. About 20% of the 438 problems have been either replaced or updated, with answers available in the companion solutions manual.
To remind students of the human aspect of science, the text uses the names of investigators throughout the text and references material to original (or accessible secondary or tertiary) literature as a guide for students interested in further reading.
Sample topics covered in Perspectives on Structure and Mechanism in Organic Chemistry include:
A comprehensive yet accessible reference on the subject, Perspectives on Structure and Mechanism in Organic Chemistry is an excellent learning resource for students of organic chemistry, medicine, and biochemistry. The text is ideal as a primary text for courses entitled Advanced Organic Chemistry at the upper undergraduate and graduate levels.
Felix A. Carroll, PhD is the Joseph R. Morton Professor of Chemistry Emeritus at Davidson College. His research focuses on organic photochemistry and photophysics, kinetics, the synthesis and characterization of insect pheromone analogues, the correlation of molecular structure with physical properties, the combustion characteristics of organic compounds, and chemical education. Dr. Carroll has published extensively in the peer-reviewed literature and was awarded a patent in the field of insect pheromones.
Preface xi
Chapter 1 Fundamental Models of Organic Chemistry 1
1.1 Atoms and Molecules 1
Basic Concepts 1
Molecular Dimensions 5
1.2 Heats of Formation and Reaction 8
Experimental Determination of Heats of Formation 8
Bond Increment Calculation of Heats of Formation 10
Group Increment Calculation of Heats of Formation 11
Heats of Formation and the Concept of Protobranching 13
Homolytic and Heterolytic Bond Dissociation Energies 15
1.3 Bonding Models 18
Electronegativity and Bond Polarity 20
Complementary Theoretical Models of Bonding 23
Pictorial Representations of Bonding Concepts 27
sp3 Hybridization 28
Are There sp3 Hybrid Orbitals in Methane? 30
Hybridization and Molecular Geometry 34
Variable Hybridization 35
1.4 Complementary Models for the Double Bond 41
The s,p Description of Ethene 41
The Bent Bond Description of Ethene 42
Predictions of Physical Properties with the Two Models 42
1.5 The Role of Complementary Models in Organic Chemistry 46
Problems 47
Chapter 2 Introduction to Computational Chemistry 53
2.1 Hückel Molecular Orbital Theory 53
Correlation of Physical Properties with Results of HMO Calculations 63
Other Parameters Generated Through HMO Theory 67
Properties of Odd Alternant Hydrocarbons 69
The Frost Circle 74
2.2 Aromaticity 75
Benzene 77
Other Aromatic Systems 81
Polycyclic Conjugated Systems 85
Larger Annulenes 90
Dewar Resonance Energy and Absolute Hardness 93
2.3 Contemporary Computational Methods 95
Extended Hückel Theory 95
Semiempirical Methods 96
Ab Initio Theory 97
2.4 Localized Molecular Orbitals 100
Perturbational Molecular Orbital Theory 104
Atoms in Molecules 108
2.5 Density Functional Theory 112
2.6 Another Look at Valence Bond Theory 114
Resonance Structures and Resonance Energies 114
Interpreting Computational Results 117
Problems 119
Chapter 3 Stereochemistry 127
3.1 Representations of Three-Dimensional Structures 127
3.2 Stereoisomerism 130
Isomerism 130
Symmetric, Asymmetric, Dissymmetric, and Nondissymmetric Molecules 133
Fischer Projections 146
Additional Stereochemical Designations 149
3.3 Physical Manifestations of Chirality 159
Optical Activity 159
Configuration and Optical Activity 161
Other Physical Properties of Stereoisomers 166
3.4 Stereotopicity 167
Stereochemical Relationships of Substituents 167
Chirotopicity and Stereogenicity 171
Problems 172
Chapter 4 Molecular Geometry and Steric Energy 183
4.1 Designation of Molecular Conformation 183
4.2 Conformational Analysis 187
Torsional Strain 187
van der Waals Strain 191
Angle Strain and Baeyer Strain Theory 193
Application of Conformational Analysis to Cycloalkanes 194
Conformational Analysis of Substituted Cyclohexanes 198
4.3 Molecular Mechanics 204
4.4 Anomeric Effect 221
4.5 Strain and Molecular Stability 225
Problems 237
Chapter 5 Reactive Intermediates 243
5.1 Reaction Coordinate Diagrams 243
5.2 Radicals 244
Early Evidence for the Existence of Radicals 244
Detection and Characterization of Radicals 246
Structure and Bonding of Radicals 251
Thermochemical Data for Radicals 253
Generation of Radicals 255
Radical Chain Reactions 256
5.3 Carbenes 263
Structure and Geometry of Carbenes 263
Generation of Carbenes 267
Reactions of Carbenes 268
5.4 Carbocations 272
Carbonium Ions and Carbenium Ions 272
Structure and Geometry of Carbocations 274
The 2-Norbornyl Cation 281
Carbocation Rearrangements 283
Radical Cations 285
5.5 Carbanions 290
Generation of Carbanions 294
Stability of Carbanions 296
Reactions of Carbanions 296
5.6 Choosing Models of Reactive Intermediates 298
Problems 299
Chapter 6 Determining Reaction Mechanisms 305
6.1 Reaction Mechanisms 305
6.2 Methods to Determine Reaction Mechanisms 306
Identification of Reaction Products 306
Determination of Intermediates 306
Crossover Experiments 311
Isotopic Labeling 313
Stereochemical Studies 314
Solvent Effects 315
Computational Studies 317
6.3 Applications of Kinetics in Studying Reaction Mechanisms 319
6.4 Arrhenius Theory and Transition State Theory 326
6.5 Reaction Barriers and Potential Energy Surfaces 337
6.6 Kinetic Isotope Effects 348
Primary Kinetic Isotope Effects 349
Secondary Kinetic Isotope Effects 354
Tunneling and Isotope Effects 359
Solvent Isotope Effects 362
6.7 Substituent Effects 363
6.8 Linear Free Energy Relationships 368
Problems 383
Chapter 7 Acid and Base Catalysis of Organic Reactions 393
7.1 Acidity and Basicity of Organic Compounds 393
Acid-Base Measurements in Solution 393
Acid-Base Reactions in the Gas Phase 402
Comparison of Gas Phase and Solution Acidities 408
Acidity Functions 410
7.2 Acid and Base Catalysis of Chemical Reactions 413
Specific Acid Catalysis 413
General Acid Catalysis 414
Brønsted Catalysis Law 417
7.3 Acid and Base Catalysis of Reactions of Carbonyl Compounds and Carboxylic
Acid Derivatives 418
Addition to the Carbonyl Group 418
Enolization of Carbonyl Compounds 422
Hydrolysis of Acetals 426
Acid-Catalyzed Hydrolysis of Esters 428
Alkaline Hydrolysis of Esters 431
Hydrolysis of Amides 437
Problems 441
Chapter 8 Substitution Reactions 449
8.1 Introduction 449
8.2 Nucleophilic Aliphatic Substitution 450
8.3 The SN1 Reaction 453
Kinetics 453
Structural Effects in SN1 Reactions 454
Solvent Polarity and Nucleophilicity 455
Solvated Ions and Ion Pairs 459
Anchimeric Assistance in SN1 Reactions 464
Nonclassical Carbocations in SN1 Reactions 469
8.4 The SN2 Reaction 471
Stereochemistry 471
Solvent Effects 473
Substrate Effects 477
8.5 Quantitative Measures of Nucleophilicity 480
Brønsted Correlations 481
Hard-Soft Acid-Base Theory and Nucleophilicity 482
Edwards Equations 483
Swain-Scott Equation 484
Mayr Equations 485
The a-Effect 488
Leaving Group Effects in SN2 Reactions 489
Aliphatic Substitution and Single Electron Transfer 490
8.6 Electrophilic Aromatic Substitution 495
The SEAr Reaction 495
Quantitative Measurement of SEAr Rate Constants: Partial Rate Factors 498
Lewis Structures as Models of Reactivity in SEAr Reactions 500
8.7 Nucleophilic Aromatic and Vinylic Substitution 504
Nucleophilic Aromatic Substitution 504
Nucleophilic Vinylic Substitution 509
8.8 Substitution Involving Benzyne Intermediates 511
8.9 Radical-Nucleophilic Substitution 518
8.10 The Impermanence of Mechanistic Labels 521
Problems 521
Chapter 9 Elimination Reactions 529
9.1 Introduction 529
9.2 Dehydrohalogenation and Related 1,2-Elimination Reactions 534
Potential Energy Surfaces for 1,2-Elimination 534
Competition Between Substitution and Elimination 540
Stereochemistry of 1,2-Elimination Reactions 541
Elimination Reactions to Produce Alkynes 547
Regiochemistry of 1,2-Elimination Reactions 548
9.3 Other 1,2-Elimination Reactions 558
Dehalogenation of Vicinal Dihalides 558
Dehydration of Alcohols 561
Deamination of Amines 568
Pyrolytic Eliminations 572
Problems 578
Chapter 10 Addition Reactions 587
10.1 Introduction 587
10.2 Addition of Halogens to Alkenes 588
Electrophilic Addition of Bromine to Alkenes 588
Role of Charge-Transfer Complexes in Bromine Addition Reactions 592
Kinetics of Bromine Addition Reactions 593
Solvent Effects in Bromine Additions 596
Reversibility of Bromine Addition 598
Intermediates in the Addition of Bromine to Alkyl-Substituted Alkenes 599
Intermediates in the Addition of Bromine to Aryl-Substituted Alkenes 604
Summary of Bromine Addition 608
Addition of Other Halogens to Alkenes 609
10.3 Other Addition Reactions 618
Addition of Hydrogen Halides to Alkenes 618
Hydration of Alkenes 625
Oxymercuration 628
Hydroboration 632
Epoxidation 637
Electrophilic Addition to Alkynes and Cumulenes 639
Nucleophilic Addition to Alkenes and Alkynes 647
Nucleophilic Addition to Carbonyl Compounds 651
Problems 656
Chapter 11 Pericyclic Reactions 661
11.1 Introduction 661
11.2 Electrocyclic Transformations 665
Definitions and Selection Rules 665
MO Correlation Diagrams 670
State Correlation Diagrams 675
11.3 Sigmatropic Reactions 678
Selection Rules for Sigmatropic Reactions 679
Other Examples of Sigmatropic Reactions 687
11.4 Cycloaddition Reactions 691
Introduction 691
Ethene Dimerization 692
The Diels-Alder Reaction 694
Selection Rules for Cycloaddition Reactions 698
11.5 Other Pericyclic Reactions 705
Cheletropic Reactions 705
Double Group Transfer Reactions 707
Ene Reactions 709
11.6 A General Selection Rule for Pericyclic Reactions 711
11.7 Alternative Conceptual Models for Pericyclic Reactions 713
Frontier Molecular Orbital Theory 713
Hückel and Möbius Aromaticity of Transition Structures 719
Synchronous and Nonsynchronous Pericyclic Reactions 725
Potential Energy Surfaces and Ambimodal Reactions 729
11.8 Reaction Dynamics and Potential Energy Surfaces 729
Problems 735
Chapter 12 Organic Photochemistry 745
12.1 Energy and Electronic States 745
12.2 Photophysical Processes 747
Designation of Spectroscopic Transitions 748
Selection Rules for Radiative Transitions 754
Fluorescence and Phosphorescence 756
Energy Transfer and Electron Transfer 759
12.3 Photochemical Kinetics 763
Actinometry and Quantum Yield Determinations 763
Rate Constants for Unimolecular Processes 764
Transient Detection and Monitoring 765
Bimolecular Decay of Excited States: Stern-Volmer Kinetics 768
12.4 Physical Properties of Excited States 770
Acidity and Basicity in Excited States 770
Bond Angles and Dipole Moments of Excited-State Molecules 774
12.5 Representative Photochemical Reactions 777
Photochemical Reactions of Alkenes and Dienes 778
Photochemical Reactions of Carbonyl Compounds 790
Photochemical Reactions of a,ß-Unsaturated Carbonyl Compounds 798
Photochemical Reactions of Aromatic Compounds 800
Photosubstitution Reactions 802
s Bond Photodissociation Reactions 803
Singlet Oxygen and Organic Photochemistry 808
12.6 Applications of Organic Photochemistry 811
Problems 822
References for Selected Problems 831
Index 837
Organic chemists think of atoms and molecules as basic units of matter. We work with mental pictures of atoms and molecules, and we rotate, twist, disconnect, and reassemble physical models in our hands.1,2 Where do these mental images and physical models come from? It is useful to begin thinking about the fundamental models of organic chemistry by asking a simple question: What do we know about atoms and molecules, and how do we know it? As Kuhn pointed out,
Though many scientists talk easily and well about the particular individual hypotheses that underlie a concrete piece of current research, they are little better than laymen at characterizing the established bases of their field, its legitimate problems and methods.3
Much of what we know in organic chemistry consists of what we were taught. Underlying that teaching are observations that someone has made and someone has interpreted. The most fundamental observations are those that can be made directly with human senses. We note the physical state of a substance-solid, liquid, or gas. We see its color or lack of color. We observe whether it dissolves in a given solvent and whether it evaporates if exposed to the atmosphere. We might get some sense of its density by seeing it float or sink when added to an immiscible liquid. These are qualitative observations, but they provide an important foundation for further experimentation.
It is only a modest extension of direct observation to the use of some simple experimental apparatus for quantitative measurements. A heat source and a thermometer allow determination of melting and boiling ranges. Other equipment allows measurement of indices of refraction, densities, surface tensions, viscosities, and heats of reaction. Classical elemental analysis indicates the elements present in a sample and their mass ratios. In all of these experiments, the experimenter uses some equipment but still makes the actual experimental observations by eyes. These simple techniques can provide essential data, nonetheless. For example, finding that 159.8?grams of bromine will always be decolorized by 82.15?grams of cyclohexene leads to the law of definite proportions. In turn, that suggests a model of matter in which submicroscopic particles combine with each other in characteristic patterns, just as the macroscopic samples do. It is then only a matter of definition to call the submicroscopic particles: atoms or molecules. It is essential, however, to remember that laboratory experiments are conducted with materials. The chemist may talk about the addition of bromine to cyclohexene in terms of individual molecules, but that can only be inferred from experimental data collected with macroscopic samples of the reactants.
Electronic instrumentation opened the door to a variety of investigations that expand the range of observations beyond those of the human senses. These instruments extend our eyes from seeing only a limited portion of the electromagnetic spectrum to detecting practically the entire spectrum, from X-rays to radio waves, and they let us "see" light in other ways (e.g. in polarimetry). They allow us to use entirely new tools, such as electron or neutron beams, magnetic fields, and electrical potential or current. They extend the range of conditions for studying matter from near atmospheric pressure to high vacuum or high pressure. They effectively expand and compress the time scale of the observations, allowing study of events that require eons or that occur in zeptoseconds.4,5,6
The unifying characteristic of modern instrumentation is that we no longer observe the chemical or physical change directly. Instead, it is detected only indirectly, such as through changes in pixels on a computer display. With such instruments, it is essential to recognize the difficulty in freeing the observations from constraints imposed by expectations. To a layperson, a UV-vis spectrum may not seem very different from an upside-down infrared spectrum, and a capillary gas chromatogram of a complex mixture may appear to resemble a mass spectrum. But the chemist sees these images not as lines on a paper or a computer display but as vibrating or rotating molecules, as electrons moving from one place to another, as substances separated from a mixture, or as fragments produced in a mass spectrometer. Thus, implicit assumptions about the origins of experimental data both make the observations interpretable and influence the interpretation of the data.7
With that caveat, what do we know about molecules and how do we know it? The first assumption is that all substances are composed of atoms-indivisible particles that are the smallest units of that particular kind of matter that still retain all its properties.8 As noted, it is convenient to correlate observations that substances combine only in certain proportions with the notion that these submicroscopic entities called atoms combine with each other only in certain ways.
Much fundamental information about molecules has been obtained from spectroscopy.9 For example, a 4000?V electron beam has a wavelength of 0.06?Å, so it is diffracted by objects larger than that size.10 Interaction of the electron beam with gaseous molecules produces characteristic circular patterns that can be interpreted in terms of molecular dimensions.11 We can determine internuclear distance through infrared spectroscopy of diatomic molecules and can use X-ray or neutron scattering to calculate distances of atoms in crystals.
"Pictures" of atoms and molecules may be obtained through atomic force microscopy (AFM) and scanning tunneling microscopy (STM).12,13 For example, investigators reported images of pentacene that displayed individual atoms,14 polycyclic aromatic hydrocarbons that allowed determination of bond order,15 products of single-molecule chemical reactions,16 molecule-gears,17 and a video of a single fullerene molecular shuttling in a vibrating carbon nanotube.18 Investigators also reported visualizing atomic orbitals,19 imaging the lateral profiles of individual sp3 hybrid orbitals, and determining the electronegativity of individual surface atoms.20,21 AFM was used to characterize the strength of intermolecular hydrogen bonds.22 Some investigators reported imaging single organic molecules in motion with transmission electron microscopy,23 and others reported studying electron transfer to single polymer molecules with single-molecule spectroelectrochemistry.24
Even though "seeing is believing," it is important to remember that these experiments do not really show molecules-just computer graphics. Some examples illustrate this point: STM features that had been associated with DNA molecules were later assigned to the surface used to support the DNA.25 An STM image of benzene molecules was reinterpreted as possibly showing groups of acetylene molecules instead.26 AFM images suggesting the visualization of intermolecular hydrogen bonds were questioned when it was shown that similar images could be observed when such hydrogen bonding should not be possible.27,28
Organic chemists also reach conclusions about molecular structure on the basis of logic. For example, the fact that one and only one substance has been found to have the molecular formula CH3Cl is consistent with a structure in which three hydrogen atoms and one chlorine atom are attached to a carbon atom in a tetrahedral arrangement. If methane were a trigonal pyramid, then two different compounds with the formula CH3Cl might be possible-one with chlorine at the apex of the pyramid and another with chlorine in the base of the pyramid. The existence of only one isomer of CH3Cl does not require a tetrahedral arrangement; however, since there could also be only one isomer if the four substituents to the carbon atom were arranged in a square pyramid with a carbon atom at the apex or in a square planar structure with a carbon atom at the center. Since no one has identified more than one CH2Cl2 molecule, the latter two geometries seem unlikely. Therefore, the parent compound, methane, may be tetrahedral as well. This view is reinforced by the existence of two different structures (enantiomers) with the formula CHClBrF. Similarly, we infer the flat, aromatic structure for benzene by noting that there are three and only three isomers of dibromobenzene.29
Organic chemists do not think of molecules only in terms of atoms, however. We often envision molecules as collections of nuclei and electrons and consider the electrons to be constrained to certain regions of space (orbitals) around the nuclei. Thus, we interpret UV-vis absorption and emission spectroscopy in terms of movement of electrons from one orbital to another. These concepts resulted from the development of quantum mechanics. The Bohr model of the atom, the Heisenberg uncertainty principle, and the Schrödinger equation laid the foundation for current ways of thinking about chemistry. Although there may be some truth in the statement that
The why? and how? as related to chemical bonding were in principle answered in 1927; the details have been worked out since that time.30
there are still uncharted frontiers of those details to explore in organic chemistry.
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