Preface ...................................................... xiii
List of Contributors ......................................... xvii
1 Reaction Control by Molecular Recognition - A Survey
from the Photochemical Perspective ........................... 1
Cheng Yang, Chenfeng Ke, Yu Liu, and Yoshihisa Inoue
1.1 Introduction ............................................ 1
1.2 Photochemical Reactions Mediated by Macrocyclic
Compounds ............................................... 2
1.2.1 Supramolecular Photoreactions with Crown
Ethers ........................................... 2
1.2.2 Supramolecular Photoreactions with Calixarenes ... 3
1.2.3 Supramolecular Photoreactions with
Cyclodextrins .................................... 6
1.2.4 Supramolecular Photoreactions with
Cucurbiturils ................................... 12
1.3 Photochemical Reactions with Biomolccules .............. 15
1.3.1 Photochemical Reactions Templated by
Deoxyribonucleic Acid (DNA) ..................... 15
1.3.2 Photochemical Reactions Mediated by Proteins .... 18
1.4 Photochemical Reactions with Confined Cages Based on
Inorganic and Organic-Inorganic Hybrid Materials ....... 21
1.4.1 Photochemical Reactions with Zeolites ........... 21
1.4.2 Photochemical Reactions in Mesoporous
Materials ....................................... 25
1.4.3 Photochemical Reaction with Sell-Assembled
Molecular Cages ................................. 26
1.5 Photochemical Reactions with other Artificial Hosts .... 28
1.5.1 Photochemical Reactions with Dendrimers ......... 28
1.5.2 Photochemical Reactions with Hydrogen-Bonding
Templates ....................................... 30
1.5.3 Photochemical Reactions Templated by Cationic
Ion ............................................. 32
1.6 Photoreaction Control by External Variants ............. 34
1.7 Conclusions ............................................ 36
Acknowledgements ............................................ 37
References .................................................. 37
2 Cyclodextrins ............................................... 43
Ronald Breslow
2.1 Introduction ........................................... 43
2.2 Acylations of the Cyclodextrins by Bound Substrates .... 44
2.3 Catalytic Reactions in Cyclodextrin Cavities:
Aromatic Substitution .................................. 46
2.3.1 Catalytic Reactions in Cyclodextrin Cavities:
Diels-Alder Reactions ........................... 47
2.4 Other Solvents than Water .............................. 47
2.5 Catalytic Reactions Produced by Cyclodextrins With
Covalently Attached Catalytic Groups ................... 48
2.5.1 Catalysed Hydrolysis Reactions .................. 48
2.5.2 Ribonuclease Mimics ............................. 49
2.6 Binding by Cyclodextrins and their Dimers and
Trimers ................................................ 53
2.6.1 Transaminase Mimics ............................. 54
2.7 Mimics of Enzymes that Use Thiamine Pyrophosphate as
a Co-Enzyme ............................................ 57
2.8 Aldol Condensations Catalysed by Cyclodextrin
Derivatives ............................................ 59
2.9 Mimics of Enzymes Using Coenzyme В12 as a Cofactor ..... 61
2.10 Mimics of Cytochrome P-450 ............................. 61
Acknowledgements ............................................ 65
References .................................................. 65
3 Cyclodextrins as Molecular Reactors ......................... 71
Christopher J. Easton and Hideki Onagi
3.1 Introduction ........................................... 71
3.2 Regiocontrolled Electrophilic Aromatic Substitutions ... 73
3.3 Catalysis of Hydrolytic Reactions ...................... 75
3.4 A Molecular Reactor lor the Synthesis of Indigoid
Dyes ................................................... 77
3.5 Manipulation of Cycloadditions ......................... 80
3.6 Conclusion ............................................. 86
Acknowledgements ............................................ 87
References .................................................. 87
4 Reactions Mediated by Cyclodextrins ......................... 91
Keiko Takahashi
4.1 Introduction ........................................... 91
4.2 The Inclusion Phenomena of Cyclodextrins ............... 92
4.3 Origin of Microvessels as Molecular Flasks ............. 93
4.3.1 Ternary Complex Formation with γ-CD ............. 93
4.3.2 Organic Reactions Mediated by γ-CD .............. 93
4.3.3 Ternary Complex Formation with β-CD ............. 95
4.4 Organic Reactions Mediated by CD in Water .............. 99
4.4.1 Catalytic Systems Based on Metal Complexes ...... 99
4.4.2 Ring Opening Reactions ......................... 101
4.4.1 Addition ....................................... 105
4.4.4 Oxidation and Reduction ........................ 108
4.5 Conclusion ............................................ 110
References ................................................. 111
5 Reactions in Zeolites ...................................... 117
Stéphane Walspurger and Jean Sommer
5.1 The Confinement Effect ................................ 121
5.2 Superelectrophilic Activation in Zeolites ............. 127
5.3 Huisgen [3+2]-Cycloadditions .......................... 130
5.4 Multicomponent Reactions .............................. 132
5.4.1 H/D Exchange Between Neopentane and Zeolites ... 134
5.4.2 H/D Exchange Between Neopentane and Zirconia ... 135
5.4.3 H/D Exchange and Acidity ....................... 135
5.5 Conclusion ............................................ 137
References ................................................. 138
6 Chemistry in Self-Assembled Nanoreactors ................... 145
Jarl Ivar van der Vlugt, Tehila S. Koblenz, Jeroen
Wassenaar, and Joost N.H. Reek
6.1 Introduction .......................................... 145
6.2 Self-Assembled Nanocapsules ........................... 146
6.3 Encapsulation Effects in Catalysis .................... 147
6.3.1 Encapsulation Effects in Terms of Rate
Equation ....................................... 147
6.3.2 New Reactivities and Selectivities ............. 148
6.3.3 Product Stabilization .......................... 149
6.4 Hydrogen Bonded Capsules .............................. 150
6.4.1 Stoichiometric 1,3-Dipolar Cycloaddition ....... 151
6.4.2 Catalytic Diels-Alder Reaction ................. 152
6.5 Capsules Based on Metal-Ligand Interactions ........... 152
6.6 Tetrahedral Cages Based on Octahedral M3+ Ions ........ 153
6.6.1 Hydrolysis ..................................... 154
6.6.2 Allylic Alcohol Isomerization .................. 156
6.7 Octahedral and Square Pyramidal Cages Based on
Square-Planar M2+ Ions ................................ 157
6.7.1 Diels-Alder Reaction ........................... 158
6.7.2 Olefin Photodimerization ....................... 160
6.8 Hydrophobic Effects as the Driving Force for the
Self-Assembly of Nanocapsules ......................... 161
6.8.1 Photooxidation ................................. 162
6.9 Ligand Template Approach Using Lewis Acid/Base
Interactions .......................................... 164
6.9.1 Hydroformylation ............................... 165
6.10 Virus Capsids, Proteins and Micellar Systems .......... 168
6.11 Micellar Systems ...................................... 169
6.12 Conclusions and Outlook ............................... 170
Acknowledgements ........................................... 171
References ................................................. 171
7 Concave Reagents ........................................... 175
Ulrich Lüning
7.1 Introduction .......................................... 175
7.1.1 Supramolecular Chemistry and Enzymes ........... 175
7.1.2 Reagents and Catalysts ......................... 177
7.2 Classes of Concave Reagents ........................... 180
7.2.1 Strategies for the Construction of
Bimacrocycles .................................. 181
7.2.2 Ring-closure ................................... 182
7.2.3 Concave Acids, Bases and Ligands ............... 185
7.3 Reactions and Catalyses ............................... 189
7.3.1 Reagents ....................................... 189
7.3.2 Catalysts ...................................... 190
7.4 Summary and Outlook ................................... 193
References ................................................. 194
8 Reactivity Control by Calixarenes .......................... 201
Luigi Mandolini, Roberta Cacciapaglia, and Stefano Di
Stefano
8.1 Introduction .......................................... 201
8.2 Calixarenes as Hosts .................................. 202
8.3 Calixarenes as Molecular Platforms .................... 209
8.3.1 Artificial Esterases: Barium(II) Complexes ..... 210
8.3.2 Artificial Esterases: Zinc(II) Complexes ....... 212
8.3.3 Artificial Esterases: Trimetallic Complexes .... 215
8.3.4 Artificial Nucleases: Zinc(II) Complexes ....... 216
8.3.5 Artificial Nucleases: Copper(II) Complexes ..... 217
8.4 Concluding Remarks .................................... 222
References ................................................. 223
9 Reactions Inside Carcerands ................................ 227
Ralf Warmuth
9.1 Introduction .......................................... 227
9.2 Types of Inner Phase Reactions ........................ 230
9.3 Probing the Properties of the Inner Phase ............. 231
9.3.1 Amide C—N Bond Rotation and Ring-Flip of
Cyclohexanes ................................... 231
9.3.2 Spectroscopic Probes ........................... 232
9.4 Through-Shell Reactions ............................... 233
9.4.1 Proton Transfer Reactions ...................... 233
9.4.2 Electron Transfer Reactions .................... 234
9.4.3 Nucleophilic Substitutions and Isotopic
Exchanges ...................................... 235
9.4.4 Nucleophilic Additions ......................... 236
9.5 Intramolecular Thermal Reactions ...................... 238
9.5.1 Diazirine Fragmentation ........................ 238
9.5.2 Fragmentation of 3-Sulfolene ................... 240
9.6 Inner Phase Photochemistry ............................ 241
9.6.1 Inner Phase Stabilization of Reactive
Intermediates: Concept ......................... 241
9.6.2 Cyclobutadiene ................................. 241
9.6.3 Anti-Bredt Bridgehead Olefins .................. 243
9.6.4 o-Benzyne ...................................... 243
9.6.5 Phenylcarbene Rearrangement .................... 246
9.6.6 Carbenes ....................................... 250
9.6.7 Phenylnitrene .................................. 251
9.6.8 Norrish Type II Photochemistry ................. 253
9.6.9 Incarcerated Excited States .................... 254
9.6.10 Photoelectron and Triplet Energy Transfer ...... 256
9.6.11 Hemicarcerand-based Photoactive Assemblies ..... 259
9.7 Conclusions and Outlook ............................... 260
Acknowledgements ........................................... 260
References ................................................. 261
10 Encapsulation of Reactive Intermediates .................... 269
Jean-Luc Mieusset and Udo H. Blinker
10.1 Introduction .......................................... 269
10.2 Encapsulation of Labile Species ....................... 270
10.3 Isolation of Non-covalently Bonded Aggregates ......... 275
10.4 Inclusion of Reactive Intermediates ................... 278
10.4.1 Viologen Radical Cations ....................... 278
10.4.2 Radicals ....................................... 281
10.4.3 Carbenes ....................................... 283
10.4.3.1 4-Oxocyclohexa-2,5-dienylidene ........ 285
10.4.3.2 2-Methylcyclohexylidene ............... 286
10.4.3.3 3-Nortricyclanylidene ................. 288
10.4.3.4 Adamantanylidene ...................... 289
10.4.3.5 Arylcarbenes .......................... 292
10.4.3.6 Chloro(phenyl)carbene ................. 292
10.4.3.7 Bicyclo|3.2.1 |octan-8-ylidenes ....... 293
10.4.4 Nitrenes ....................................... 295
10.4.4.1 l-Adamantanyl nitrene ................. 296
10.4.4.2 2-Adamantanyl nitrene ................. 296
10.4.4.3 Ferrocenyl nitrene .................... 297
10.4.4.4 Phenylnitrene ......................... 301
References ................................................. 304
11 Dye Encapsulation .......................................... 309
Jeremiah J. Gassensmith, Easwaran Arnnkumar and
Bradley D. Smith
11.1 Introduction .......................................... 309
11.2 Reversible Dye Encapsulation Inside Organic
Container Molecules ................................... 311
11.3 Reversible Dye Encapsulation by Biological
Receptors ............................................. 314
11.4 Permanent Dye Encapsulation Inside Rotaxanes .......... 315
11.5 Permanent Encapsulation Inside Inorganic Matrices ..... 320
11.6 Conclusion ............................................ 322
Acknowledgements ........................................... 322
References ................................................. 322
12 Organic Cations in Constrained Systems ..................... 327
Werner Abraham and Lutz Grubert
12.1 Introduction .......................................... 327
12.1.1 Hosts .......................................... 328
12.1.2 Guests ......................................... 329
12.1.3 Structure-Interaction Relationships ............ 330
12.2 Host-guest Complexes with Organic Cations ............. 330
12.2.1 Cyclophanes .................................... 330
12.2.2 Calix[n]arenes ................................. 332
12.2.3 Charged Calixarenes ............................ 334
12.2.4 Homooxacalixarenes ............................. 339
12.2.5 Resorcinarenes ................................. 341
12.3 Extended Hosts and Capsules ........................... 343
12.4 Cucurbiturils ......................................... 348
12.5 Complex Systems and Applications ...................... 350
12.5.1 Photoresponsive Hosts .......................... 353
12.6 Conclusions ........................................... 355
References ................................................. 357
13 Proteins as Host for Enantioselective Catalysis:
Artificial Metalloenzymes Based on the Biotin-
Streptavidin Technology .................................... 361
Jincheng Mao and Thomas R. Ward
13.1 Introduction .......................................... 361
13.2 The Biotin-Avidin Technology .......................... 363
13.2.1 The Chemical Optimization Dimension ............ 364
13.2.2 The Genetic Optimization Dimension ............. 364
13.3 Artificial Hydrogenases ............................... 365
13.4 Artificial Allylic Alkylases .......................... 367
13.5 Artificial Transfer Hydrogenase ....................... 369
13.6 Enantioselective Sulfoxidation Based on Vanadyl-
loaded Streptavidin ................................... 372
13.7 Conclusions and Outlook ............................... 373
Acknowledgements ........................................... 373
References ................................................. 374
14 Chemical Reactions with RNA and DNA Enzymes ................ 377
Andres Jäschke
14.1 Introduction .......................................... 377
14.2 Catalysis by Naturally Occurring Ribozymes ............ 378
14.3 How to Generate Artificial RNA and DNA Catalysts ...... 380
14.4 The Catalytic Spectrum of Artificial Ribozymes ........ 383
14.5 Deoxyribozymes - DNA Molecules with Catalytic
Properties ............................................ 386
14.6 Catalysis of С—С Bond Formation by Diels-Alderase
Ribozymes ............................................. 387
14.6.1 In Vitro Selection ............................. 387
14.6.2 Overall Catalytic Properties ................... 388
14.6.3 Overall Structure of the Ribozyme .............. 389
14.6.4 Architecture of the Catalytic Pocket ........... 390
14.6.5 Interactions Between the Ribozyme and its
Substrates and Products ........................ 391
14.6.6 Conformational Dynamics and the Roles of
Metal Ions ..................................... 392
14.6.7 Mechanistic Considerations ..................... 393
14.7 Conclusion ............................................ 394
References ................................................. 394
15 Reactions in Supramolecular Systems ........................ 397
Lucia Zakharova, Alia Mirgorodskaya, Elena Zhiltsova,
Ludmila Kudryavtseva, and Alexander Konovalov
15.1 Introduction .......................................... 397
15.2 The Single Micellar Systems: Factors of
Concentration and Micellar Microenvironment ........... 398
15.3 The Role of the Structural Factor in Supramolecular
Catalytic Systems ..................................... 402
15.3.1 The Influence of the 'Sphere-Rod' Micellar
Transition on the Reactivity ................... 402
15.3.2 The Effect of the Clustering of Reverse
Micelles on the Reactivity ..................... 402
15.3.3 The Hydrolysis of Carbonic Acid Esters in
Microemulsions under Phase Inversion
Conditions ..................................... 405
15.4 Binary Surfactant Systems ............................. 405
15.4.1 Aqueous Binary System Ionic-Nonionic
Surfactants .................................... 405
15.4.2 The Binary Surfactant Mixtures in Non-aqueous
Media .......................................... 407
15.5 Polycomponent Catalytic Systems Based on Amphiphiles
and Polymers .......................................... 408
15.5.1 The Conventional Surfactant/Polyethyleneimine
Systems ........................................ 408
15.5.2 The Pyrimidinic Surfactant Based Systems ....... 412
15.5.3 The Calixarene Based Systems ................... 413
15.5.4 The Non-Aqueous Supramolecular Systems ......... 414
15.6 Conclusions ........................................... 416
Acknowledgements ........................................... 417
Dedication ................................................. 417
References ................................................. 417
16 Encapsulation Processes by Bilayer Vesicles ................ 421
Marc C.A. Stuart and Jan В.F.N. Engberts
16.1 Introduction ......................................... 421
16.1.1 Vesicular Aggregates ........................... 421
16.1.2 Solute Encapsulation by Vesicles ............... 426
16.1.3 Binding Locations .............................. 427
16.1.4 Experimental Techniques for Measuring
Encapsulation Processes ........................ 429
16.2 Catalysis by Vesicles. Encapsulation of Reactants ..... 430
16.2.1 Unimolecular Decarboxylation of 6-NBIC ......... 431
16.2.2 The Kemp Elimination: Rate-limiting Proton
Transfer ....................................... 433
16.2.3 Bimolecular Nucleophilic Substitution .......... 434
16.3 Liposomal Encapsulation in Drug Delivery .............. 435
16.3.1 Encapsulated Drugs ............................. 436
16.4 Vesicle-Nucleic Acid Interactions: Gene Transfer
Using Lipoplexes ...................................... 438
16.4.1 Lipoplex Formation ............................. 439
16.4.2 Lipoplex Structure ............................. 440
16.4.3 Future Prospects ............................... 446
References ................................................. 446
17 Reactions in Liposomes ..................................... 455
Pasquale Stano and Pier Luigi Luisi
17.1 Introduction .......................................... 455
17.2 Lipid Vesicles (Liposomes) ............................ 456
17.2.1 What are Liposomes (and Fatty Acid Vesicles) ... 456
17.2.2 Morphology and Methods of Preparation .......... 458
17.2.3 Chemical Compatibility ......................... 461
17.3 Experimental Strategies and Theoretical Aspects ....... 462
17.3.1 Basic Strategies ............................... 462
17.3.2 Theoretical Aspects ............................ 466
17.4 A Theoretical Framework for Complex Reactions in
Liposomes ............................................. 470
17.5 Four Cases of Compartmentalized Reactions ............. 473
17.6 Conclusion ............................................ 485
Acknowledgements ........................................... 485
Abbreviations .............................................. 486
References ................................................. 487
Index ......................................................... 493
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