Mechanical Catalysis: Methods of Enzymatic, Homogeneous, and Heterogeneous Catalysis

MECHANICAL CATALYSIS......Page 3
CONTENTS......Page 9
PREFACE......Page 23
CONTRIBUTORS......Page 27
GLOSSARY......Page 29
1.1 Thermodynamic (Energy-Dependent) and Mechanical (Time-Dependent) Processes......Page 33
1.2 What Is a Thermodynamic Process?......Page 37
1.3 What Is a Mechanical Process?......Page 39
1.4.1 Time-Dependent (Mechanical) Processes Are Path-Reliant and Spatiotemporal in Character......Page 41
1.4.2 Time-Dependent (Mechanical) Processes Have a Flat Underlying Energy Landscape (or Are Unaffected by the Energy Landscape)......Page 42
1.4.3 Time-Dependent (Mechanical) Processes Display Deterministic Chaos; This Causes Them to be Stochastic and Complex......Page 43
1.4.4 Time-Dependent (Mechanical) Processes Often Involve Synergies of Action......Page 46
1.4.5 Time-Dependent (Mechanical) Processes Characterize Numerous Aspects of Human Experience......Page 47
1.5.1 The Origin of Time- and Energy-Dependent Processes in Chemistry......Page 49
1.5.2 Examples of Time-Dependent Processes in Chemistry......Page 51
1.5.3 Time- and Energy-Dependent Processes in Catalysis......Page 54
1.5.4 Is There Such a Thing as a Time-Dependent Process in Catalysis?......Page 56
1.6.1 Summary of the Key Finding: Many Enzymes Seem to be Time-Dependent Catalysts......Page 57
1.6.2 The Aims and Structure of this Series. Summary: Other Major Findings of this Series......Page 60
References......Page 66
2.1 Introduction: The Problem of Conceptually Unifying Heterogeneous, Homogeneous, and Enzymatic Catalysis? Trends in Catalysis Science......Page 69
2.2.1 Homogeneous and Heterogeneous Catalysis......Page 70
2.2.2 Hybrid Homogeneous–Heterogeneous Catalysts......Page 72
2.2.3 Enzymatic Catalysis......Page 73
2.2.4 Theories and Mimicry of Enzymatic Catalysis......Page 74
2.3.1 Single-Centered Homogeneous Catalysts. Most Manmade Homogeneous Catalysts Are Single-Centered Catalysts......Page 76
2.3.2 Multicentered Homogeneous Catalysts: Most Enzymes Are Multicentered Homogeneous Catalysts......Page 78
2.5 The Alternative of Time-Dependence in Catalysis......Page 80
References......Page 84
3.1 Introduction......Page 87
3.2.1 Reactions as Collisions Between Molecules......Page 88
3.2.2 The Fundamental Origin of Energy-Dependent and Time-Dependent Reactions......Page 89
3.2.3 Time-Dependent and Energy-Dependent Domains Were First Observed in Unimolecular Gas-Phase Reactions......Page 90
3.2.4 The Pathway of the Reaction Is also Controlled by the Least-Likely Step in the Sequence......Page 91
3.2.5 Transition State Theory (TST) Describes the Pathway and Rate of Energy-Dependent Reactions. Transition State Theory Corresponds to the High-Pressure Limit of Hinshelwood–RRK Theory......Page 93
3.2.6 Time-Dependent Reactions in the Liquid Phase: Some Examples......Page 95
3.2.7 The Transition between Energy-Dependence and Time-Dependence as a Function of Temperature. Curvature in Arrhenius Plots......Page 97
3.2.8 Methods of Creating Time-Dependent Reactions......Page 99
3.3.1 Catalyzed Reactions Are More Likely to be Time-Dependent than Are Uncatalyzed Reactions......Page 100
3.3.2 Catalysis Changes the Reaction Processes......Page 101
3.3.4 The Distinction Between Time-Dependent Catalysis and Diffusion-Controlled Catalysis......Page 104
3.3.5 Energy-Dependent and Time-Dependent Control of Catalysis......Page 105
3.3.6 The Influence of the Product Release Step......Page 106
Acknowledgments......Page 107
References......Page 108
4.1 Introduction......Page 109
4.2.1 Volcano Plots......Page 111
4.2.3.1 How Is Time-Dependence Created on the Left-Hand Side of the Volcano Plot?......Page 114
4.2.3.2 Why Do Volcano Plots Slope Upward on the Left......Page 116
4.2.3.3 The Rate-Determining Step in a Time-Dependent Catalyst......Page 118
4.2.3.4 The Physical Manifestation of Time-Dependent Catalysis. “Saturation” of a Time-Dependent Catalyst......Page 119
4.2.4.2 Why Do Volcano Plots Slope Downward on the Right?......Page 120
4.2.5 The Physical Origin of Sabatier’s Principle......Page 121
4.2.6 Other Plots Illustrating Sabatier’s Principle......Page 122
4.2.7 Modeling of Volcano Plots......Page 123
4.2.8 Reaction Pathway as a Function of the Most-Favored Transition State......Page 124
4.4 Sabatier’s Principle in Homogeneous Catalysis......Page 125
4.5 Conclusions. Sabatier’s Principle Two Independent Catalytic Domains: Energy- and Time-Dependent Catalysis......Page 126
References......Page 127
5.1 Introduction......Page 129
5.2 Historical Background: Are Enzymes Generally Energy-Dependent or Time-Dependent Catalysts?......Page 131
5.3 The Methodology of This Chapter: Identify, Contrast, and Rationalize the Common Processes Present in Biological and Nonbiological Homogeneous Catalysts......Page 132
5.4.1 Michaelis–Menten Kinetics......Page 133
5.4.2 Kinetics in Most Nonbiological Catalysts......Page 134
5.4.4 Saturation in Time- and Energy-Dependent Catalysts. Saturation Kinetics Is Necessarily an Indication of Time-Dependence......Page 135
5.4.5 Physical Studies of the Rate Processes in Enzymes Are Consistent with a Time-Dependent Action......Page 137
5.4.6 A Time-Dependent Catalyst Cannot Become an Energy-Dependent Catalyst, or vice versa, Without Changing the Temperature or Chemically Altering the Reactivity of the Reactants......Page 138
5.4.7 The Current View of Michaelis–Menten Kinetics Is Flawed by an Unwarranted Assumption......Page 139
5.5 Other General Characteristics of Catalysis by Enzymes and Comparable Nonbiological Homogeneous Catalysts......Page 141
5.5.1 Enzymes Employ Weak and Dynamic Individual Binding Interactions with Their Substrates. Nonbiological Catalysts Do Not......Page 142
5.5.3 Enzymatic Catalysis Is “Structure-Sensitive.” Nonbiological Catalysis Is “Structure-Insensitive”......Page 143
5.5.4 Enzymes Transform Catalytically Unconventional Groups into Potent Catalysts. Nonbiological Catalysts Use Only Conventional Catalytic Groups......Page 144
5.5.5 Enzymes Catalyze Forward and Reverse Reactions. Nonbiological Catalysts Do Not......Page 145
5.5.7 Enzymes Display Convergent Synergies. Nonbiological Catalysts Display Complementary Synergies......Page 146
5.6.1 Common Processes in Multicentered Homogeneous Catalysts......Page 148
5.6.2 The Influence of the Strength of the Individual Catalyst–Reactant Binding Interactions......Page 150
5.6.3 The Coexistence of Transition State Complementarity, Structure-Sensitive Catalysis, and Unconventional Catalytic Groups in Enzymes Is Caused by their Weak Individual Binding Interactions......Page 153
5.6.4 The Origin of the Time-Dependence and the Synergies of Enzymes......Page 154
5.6.5 The Mechanism of Time-Dependence in Enzymes Resolves the Contradiction of a Kinetically Observed Rapidly Forming and Dissociating Intermediate in the Face of Strong Overall Substrate Binding......Page 156
5.6.7 Summary: The Origin of the General Properties of Enzymes......Page 157
5.6.9 Enzymatic Selectivity and Synergies Derive from Time-Dependence......Page 159
5.6.10 Enzymatic Activity Is Consistent with Time-Dependence......Page 160
5.7 All Generalizations Support Time-Dependence in Enzymes......Page 161
5.8 Time-Dependence in a Nonbiological Catalyst Generates the Distinctive Properties of Enzymes......Page 162
5.9 Conclusion: Many Enzymes Are Time-Dependent Catalysts......Page 165
References......Page 166
6.1 Introduction......Page 169
6.2 Time- and Energy-Dependent, Multicentered Homogeneous Catalysts......Page 171
6.3 The Action of Energy-Dependent, Multicentered Homogeneous Catalysts......Page 173
6.4 The Action of Time-Dependent, Multicentered Homogeneous Catalysts......Page 178
6.4.1 The Activation Energy E(a) Does Not Provide a True Measure of the Threshold Energy in Time-Dependent Catalysts......Page 180
6.4.2 Weak and Dynamic Binding and Activation Is Sufficient to Fulfill the Threshold Energy in Time-Dependent Catalysts......Page 181
6.4.4 Time-Dependent Catalysts Are Machine-Like (Mechanical) in Their Catalytic Action......Page 182
6.4.5 The Origin of Michaelis–Menten Kinetics in Time-Dependent Catalysts......Page 183
6.4.6 Time-Dependent Catalysts like Many Enzymes Display All of the Characteristic Hallmarks of Mechanical Processes......Page 185
6.4.7 Additional Insights into Enzymatic Catalysis: The Bidirectionality of Enzymatic Catalysis Originates from the Mechanical Nature of the Catalytic Action......Page 186
6.5 The Importance of Recognizing Time-Dependent Catalysis......Page 187
6.6 Time-Dependent Catalysis Is Very Different to Energy-Dependent Catalysis and Therefore Seems Unfamiliar......Page 188
6.8 Conclusions for Homogeneous Catalysis......Page 189
6.10 Conclusions for the Conceptual Unity of the Field of Catalysis......Page 190
References......Page 191
7.1 Introduction......Page 193
7.2.2 “Lock-and-Key” Theory......Page 195
7.2.3 Haldane’s Strain Theory......Page 196
7.2.6 Intramolecularity......Page 197
7.2.7 Orbital Steering......Page 199
7.2.10 “Coupled” Protein Motions......Page 200
7.3 Theories Explaining Enzymatic Catalysis Fall into Two Camps: Energy-Dependent and Time-Dependent Catalysis......Page 201
7.3.1 Haldane’s Strain Theory and Fersht’s Concept of Stress and Strain Are Valid Explanations for Rate Accelerations but Do Not Seem to be Responsible for the Rate Accelerations of Many Enzymes......Page 203
7.3.3 Experiments Studying Intramolecular Reaction Rates Were Probably Often Conceptually Contradictory......Page 204
7.3.4 Theories of “Coupled” Protein Motions and Machine-Like Catalytic Actions Seem to Be Generally Accurate Descriptions of Enzymatic Catalysis......Page 205
7.4 Studies Verifying Pauling’s Theory in Model Systems Are Correct, but Describe Energy-Dependent and not Time-Dependent Catalysis......Page 206
7.5 The Anomaly Described in the Spatiotemporal Hypothesis Originates, in Part, from the Onset of Time-Dependence......Page 208
References......Page 209
8.1 Introduction......Page 213
8.2 Synergy in Heterogeneous Catalysts......Page 215
8.3.1 Facial Selectivity in Single-Centered Catalysts......Page 216
8.3.2 Energy-Dependent, Single-Centered Homogeneous Catalysts Display ‘Mutually Enhancing’ Synergies......Page 219
8.3.3 The Synergies in Time-Dependent, Single-Centered Homogeneous Catalysts......Page 220
8.3.4 The Selectivity of Single-Centered Catalysts......Page 221
8.4 Multicentered, Energy-Dependent Homogeneous Catalysts and Their Functionally Complementary Synergies......Page 222
8.5 Enzymes and Their Functionally Convergent Synergies......Page 226
8.6 Biomimetic Chemistry and Its Pseudo-Convergent Synergies......Page 229
8.6.1 Cyclodextrin-Appended Epoxidation Catalysts: Pseudo-Convergence in a Nonbiological, Multicentered Catalyst......Page 230
8.7 The Spectrum of Synergistic Action in Homogeneous Catalysis......Page 232
8.7.1 The Relationship Between Complementary and Convergent Synergies......Page 234
8.7.2 The Ideal Catalyst......Page 235
8.8 Synergy in Catalysis Is Conceptually Related to Other Synergistic Processes in Human Experience......Page 237
References......Page 238
9.1 Introduction......Page 241
9.2 Diffusion-Controlled and Reaction-Controlled Catalysis......Page 242
9.3 The Diversity of Catalytic Action in Heterogeneous Catalysts......Page 243
9.4 The Diversity of Catalytic Action in Nonbiological Homogeneous Catalysts......Page 244
9.6 Heterogeneous Catalysis and Enzymatic Catalysis Has, Effectively, Involved Combinatorial Experiments that Have Produced Time-Dependent Catalysts. Nonbiological Homogeneous Catalysis Has Not......Page 246
9.7 Homogeneous and Enzymatic Catalysts Are the 3-D Equivalent of 2-D Heterogeneous Catalysts......Page 247
9.8 A Conceptual Unification of Heterogeneous, Homogeneous, and Enzymatic Catalysis......Page 248
References......Page 250
10.1 Introduction......Page 251
10.2.1 Design Criteria for a Time-Dependent Homogeneous Catalyst......Page 253
10.2.2 The Problem of Simultaneously Identifying Suitable Catalytic Groups and Their Active Spatial Arrangement......Page 255
10.2.3 Time-Dependent Homogeneous Catalysis May Conceivably Be Achieved by Mimicry of a Natural Time-Dependent Catalyst......Page 257
10.2.4 Time-Dependent Homogeneous Catalysis May Conceivably Be Achieved in the form of a Combinatorial Experiment Involving a “Statistical Proximity” Effect......Page 258
10.2.4.1 A Time-Dependent Combinatorial Catalyst May Display Unique Kinetics......Page 260
10.2.4.2 Previous Attempts at Concentration-Based Biomimetic Catalysis Involved Energy-Dependent Systems......Page 261
10.3.1 Modes of Binding in Multicentered Catalysts......Page 262
10.3.2.1 Intramolecular Catalysts......Page 263
10.3.2.3 Unconventional Approaches to Optimizing the Spatial Organization of Catalytic Groups......Page 265
10.3.3.1 Practical Approaches to Achieving Functionally Convergent Catalysis......Page 266
10.4.1.1 Functionally Convergent Catalysis (Class A Type): Cofacial and Capped Metalloporphyrins as Oxygen Reduction Catalysts......Page 267
10.4.1.2 Functionally Convergent Catalysis (Class B Type): [1.1]Ferrocenophanes and Related Compounds as Hydrogen Generation Catalysts......Page 273
10.4.1.3 Pseudoconvergent Catalysis: Supramolecular, Bifunctional Catalysts of Organic Reactions......Page 277
10.4.1.4 Probable Functionally Convergent Catalysis: Rhodium-Phosphine Hydroformylation Catalysts......Page 279
10.4.1.5 Possible Functionally Convergent Catalysis: Ruthenium-Based Water Oxidation Catalysts......Page 282
10.4.1.6 Functionally Complementary Catalysis: Intramolecular Epoxidation Catalysts......Page 284
10.4.1.7 Metal Clusters in Multicentered Molecular Catalysis: Triruthenium Dodecacarbonyl Hydrogenation Catalysts......Page 285
10.4.1.8 Statistical Approaches to Functionally Convergent Catalysis: Macromolecular Intramolecular Catalysts......Page 286
10.4.2.1 Functionally Complementary Catalysis......Page 291
10.4.2.2 Statistical Approaches to Functionally Convergent Catalysis: Concentration Effects in Intermolecular Catalysts......Page 292
10.4.2.3 Statistical Approaches to Functionally Convergent Catalysis: Self-Assembled, Supramolecular Catalysts......Page 293
10.4.3 Footnote: Unexpected Mechanistic Changes in Multicentered Catalysts......Page 294
References......Page 295
11.1 Introduction......Page 299
11.2.1 Chemical Structures......Page 305
11.2.3 Dioxygen Generation......Page 307
11.2.5 Other Reactions......Page 309
11.3 Nafion Provides a Means of Solubilizing and Immobilizing Hydrophobic Metal Complexes......Page 310
11.4 Photoelectrochemical Cells and Dye-Sensitized Solar Cells for Water-Splitting......Page 311
11.5.1 Solution Electrochemistry......Page 314
11.5.3 Electrocatalytic Effects Are Observed Under CV Conditions......Page 315
11.5.4 A Photo-Electrocatalytic Effect Is Observed at 1.00 V (vs. Ag/AgCl)......Page 316
11.5.5 If the Photocurrent Is Caused by Water Oxidation Catalysis, This Involves a Decrease in the Overpotential of 0.4 V......Page 317
11.5.6 The Photocurrent Is Observed only in the Presence of Water. The System Saturates at Low Water Content, Consistent with a Time-Dependent Catalytic Action......Page 318
11.5.9 The Quantity of Gas Generated Matches the Current Obtained. Notable Turnover Frequencies Are Implied......Page 319
11.5.11 The Photoaction Spectrum of the Catalysis Corresponds to the Main LMCT Absorption Peak of 1b......Page 322
11.6 The Challenge of Dye-Sensitized Water-Splitting......Page 323
11.7 The Mechanism of the Catalysis......Page 324
11.8 Conclusions......Page 325
References......Page 326
12.1 Introduction......Page 329
12.2 Monomer and Polymer Preparation......Page 333
12.3.1 PPy-9 and PPy-12 Display Anodic Shifts in the Most Positive Potential for Hydrogen Generation......Page 334
12.3.2 PPy-9 and PPy-12 Increase the Rate of Hydrogen Generation on Pt by ca. 7-Fold after 12 h at 20.44 V......Page 336
12.3.3 PPy-9 and PPy-12 Increase the Rate of Hydrogen Generation on Pt per Unit Area by ca. 3.5-Fold......Page 339
12.3.4 The Mechanism of Catalysis in PPy-9. Is PPy-9 a Combinatorial (“Statistical Proximity”) Catalyst?......Page 340
12.3.5 Polypyrrole Is Likely Involved in the Catalytic Cycle......Page 341
12.3.6 Other Evidence for the Involvement of Polypyrrole in the Catalytic Cycle......Page 343
12.3.7 The Pyrrole in Polypyrrole Is a Powerful, Time-Dependent, Combinatorial, “Statistical Proximity” Catalyst......Page 345
Acknowledgments......Page 348
References......Page 349
13.1 Introduction......Page 351
13.2 Cofacial Diporphyrin Oxygen-Reduction Catalysts......Page 353
13.3 Vapor-Phase Polymerization of Pyrrole as a Means of Immobilizing High Concentrations of Monomeric Catalytic Groups at an Electrode Surface......Page 355
13.4.2 Electrochemistry of, and Oxygen Reduction by, Polypyrrolle-Co Tetraphenylporphyrin, PPy-3......Page 356
13.4.3 Rotating Disk Electrochemistry (RDE) of Polypyrrolle-Co Tetraphenylporphyrin, PPy-3......Page 358
13.4.4 Rotating Ring Disk Electrochemistry (RRDE) of Polypyrrolle-Co Tetraphenylporphyrin, PPy-3......Page 360
13.4.5 The Product Distribution Relative to the Proportion of 3 in the Polypyrrolle-Co Tetraphenylporphyrin, PPy-3......Page 361
13.5.3 Morphology of the PPy-3 Carbon Fiber Composite Film......Page 362
13.5.4 Oxygen-Reduction Catalysis by the PPy-3 Carbon Fiber Composite Film in Simple Fuel Cell Test Apparatus......Page 363
13.6 Conclusions......Page 366
References......Page 367
Appendix A Why Is Saturation Not Observed in Catalysts that Display Conventional Kinetics?......Page 369
Appendix B Graphical Illustration of the Processes Involved in the Saturation of Molecular Catalysts......Page 373
Index......Page 379