Modern Physical Organic Chemistry

Front Cover
University Science Books, 2006 - Science - 1099 pages
"The twentieth century saw the birth of physical organic chemistry - the study of the interrelationships between structure and reactivity in organic molecules - and the discipline matured to a brilliant and vibrant field. Some would argue that the last century also saw the near death of the field. In our opinion, physical organic chemistry is alive and well in the early twenty-first century. New life has been breathed into the field because it has embraced newer chemical disciplines, such as bioorganic, organometallic, materials, and supramolecular chemistries. These newer disciplines have given physical organic chemists fertile ground in which to study the interrelationships of structure and reactivity. Yet, even while these new fields have been developing, remarkable advances in our understanding of basic organic chemical reactivity have continued to appear, exploiting classical physical organic tools and developing newer experimental and computational techniques. Importantly, the techniques of physical organic chemistry and the intellectual approach to problems embodied by the discipline remain as relevant as ever to organic chemistry. Therefore, a course in physical organic chemistry will be essential for students for the foreseeable future. This book is meant to capture the state of the art of physical organic chemistry in the early twenty-first century, and, within the best of our ability, to present material that will remain relevant as the field evolves in the future. A student must know the fundamentals, such as the essence of structure and bonding in organic molecules, the nature of the basic reactive intermediates, and organic reaction mechanisms. However, students should also have an appreciation of the current issues and challenges in the field, so that when they inspect the modern literature they will have the necessary background to read and understand current research efforts. Therefore, while treating the fundamentals, we have wherever possible chosen examples and highlights from modern research areas."--adapted from Preface, page xxiii.
 

Contents

PART I
1
Introduction to Structure and Models of Bonding
3
CHAPTER
7
Scaling Electrostatic Surface Potentials
15
Particle in a Box
21
A Brief Look at Symmetry and Symmetry Operations
29
Groups as Perturbations of Allyl
49
CH5Not Really a WellDefined Structure
55
Stereoelectronics in an Acyl Transfer Model
579
Gas Phase Eliminations
588
AconitaseAn Enzyme that Catalyzes Dehydration
595
The Catalytic Triad
604
Summary and Outlook
617
FURTHER READING
624
Enolate Aggregation
631
SUBSTITUTIONS ON ALIPHATIC CENTERS
637

Summary and Outlook
61
CHAPTER 2
67
How Big is 3 kcalmol?
93
Differing Magnitudes of Energy Values
100
The NMR Time Scale
106
A Conformational Effect on the Material Properties
116
Protein Disulfide Linkages
123
Summary and Outlook
137
FURTHER READING
143
CHAPTER 3
149
Solvation Can Affect Equilibria
155
A vant Hoff Analysis of the Formation of
163
Summary and Outlook
201
Molecular Recognition
207
Cooperativity in Drug Receptor Interactions
215
The BenesiHildebrand Plot
221
Preorganization and the Salt Bridge
229
CalixarenesImportant Building Blocks for Molecular
238
A Molecular Recognition
249
Summary and Outlook
292
Summary and Outlook
344
FURTHER READING
350
Reactivity Kinetics and Mechanisms
353
Revisiting
388
Realistic Titrations in Water 265 An Organometallic Example of Using the
395
The Role
401
Summary and Outlook
413
CHAPTER 8
414
Thermodynamics and Kinetics
421
Stereoisomerism and Connectivity 300 The Use of Primary Kinetic Isotope Effects to Probe
425
Chiral Shift Reagents 308 The Use of an Inverse Isotope Effect to Delineate
431
Controlling Polymer TacticityThe Metallocenes 332 Using Fractionation Factors to Characterize Very Strong
439
Catalytic Antibody
450
Where TST May be Insufficient 374 Nucleophilic Assistance in the Solvolysis of Arylvinyl
459
Applying the Principle of Microscopic Reversibility Insight into Transition State Structures
465
Molecularity vs Mechanism Cyclization Reactions and An Example of an Unexpected Product
472
or Trap a Proposed Intermediate
473
Determination of 14Biradical Lifetimes Using
480
Summary and Outlook
482
Catalysis
489
The Application of Figure 9 4 to Enzymes
494
Toward an Artificial Acetylcholinesterase
501
A Model for GeneralAcidGeneralBase Catalysis
514
Cyclodextrins Lead the Way
530
Organic Reaction Mechanisms Part
537
CHAPTER 10
539
Cyclic Forms of Saccharides and Concerted Proton
545
Mechanisms of Asymmetric Epoxidation Reactions
558
Natures Hydride Reducing Agent
566
The Captodative Effect
573
ELIMINATIONS
576
Gas Phase SN2 ReactionsA Stark Difference in Mechanism
641
Contact Ion Pairs vs SolventSeparated Ion Pairs
647
Carbocation Rearrangements in Rings
658
Further Examples of Hypervalent Carbon
666
Brominations Using NBromosuccinimide
673
ISOMERIZATIONS AND REARRANGEMENTS
674
Femtochemistry and Singlet Biradicals
693
Summary and Outlook
695
FURTHER READING
703
CHAPTER 12
709
Electrophilic Aliphatic Substitutions SE2 and SE1
715
CH Activation Part I
722
Summary and Outlook
747
Organic Polymer
753
Monodisperse Materials Prepared Biosynthetically
756
Protein Folding Modeled by a TwoState Polymer
762
Dendrimers Fractals Neurons and Trees
769
SelfAssembling Monolayers
778
FreeRadical Living Polymerizations
787
PMMAOne Polymer with a Remarkable Range
793
Summary and Outlook
800
Electronic Structure Theory and Applications
805
Advanced Concepts in Electronic
807
MethaneMolecular Orbitals or Discrete Single
827
ThroughBond Coupling and Spin Preferences
861
Summary and Outlook
868
FURTHER READING
875
CHAPTER 15
887
Allowed Organometallic 2+2 Cycloadditions
895
Electrocyclization in Cancer Therapeutics
910
The OxyCope
921
EXERCISES
929
Photochemistry
935
CHAPTER 16
937
Physical Properties of Excited States
944
Isosbestic PointsHallmarks of OnetoOne Stoichiometric
949
Sensitization
956
SingleMolecule FRET
961
TransCyclohexene?
967
Summary and Outlook
993
FURTHER READING
999
CHAPTER 17
1011
Scanning Probe Microscopy
1040
Summary and Outlook
1041
Conversion Factors and Other Useful Data
1047
The Organic Structures of Biology
1057
How to Denote Resonance
1064
Pushing Electrons for Radical Reactions
1071
INDEX
1079
Copyright

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About the author (2006)

Eric V. Anslyn received his PhD in Chemistry from the California Institute of Technology under the direction of Robert Grubbs. After completing post-doctoral work with Ronald Breslow at Columbia University, he joined the faculty at the University of Texas at Austin, where he became a Full Professor in 1999. He currently holds four patents and is the recipient of numerous awards and honors, including the Presidential Young Investigator, the Alfred P. Sloan Research Fellow, the Searle Scholar, the Dreyfus Teacher-Scholar Award, and the Jean Holloway Award for Excellence in Teaching. He is also the Associate Editor for the Journal of the American Chemical Society and serves on the editorial boards of Supramolecular Chemistry and the Journal of Supramolecular Chemistry. His primary research is in physical organic chemistry and bioorganic chemistry, with specific interests in catalysts for phosphoryl and glycosyl transfers, receptors for carbohydrates and enolates, single and multi-analyte sensors - the development of an electronic tongue, and synthesis of polymeric molecules that exhibit unique abiotic secondary structure. Dennis A. Dougherty received a PhD from Princeton with Kurt Mislow, followed by a year of postdoctoral study with Jerome Berson at Yale. In 1979 he joined the faculty at the California Institute of Technology, where he is now George Grant Hoag Professor of Chemistry. Dougherty's extensive research interests have taken him to many fronts, but he is perhaps best known for development of the cation-π interaction, a novel but potent noncovalent binding interaction. More recently, he has addressed molecular neurobiology, developing the in vivo nonsense suppression method for unnatural amino acid incorporation into proteins expressed in living cells. This powerful new tool enables "physical organic chemistry on the brain" - chemical-scale studies of the molecules of memory, thought, and sensory perception and the targets of treatments for Alzheimer's disease, Parkinson's disease, schizophrenia, learning and attention deficits, and drug addiction. His group is now working on extensive experimental and computational studies of the bacterial mechanosensitive channels MscL and MscS, building off the crystal structures of these channels recently reported by the Rees group at Caltech.

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