| | Contents | |
| | | |
| |
| | Preface | XIII |
| | List of Contributors | XV |
| 1 | Introduction
Christoph A. Schalley | 1 |
| 1.1 | Some Historical Remarks on Supramolecular Chemistry | 1 |
| 1.2 | The Noncovalent Bond: A Brief Overview | 2 |
| 1.3 | Basic Concepts in Supramolecular Chemistry | 4 |
| 1.3.1 | Molecular Recognition: Molecular Complementarity | 5 |
| 1.3.2 | Chelate Effects and Preorganization: Entropy Factors | 5 |
| 1.3.3 | Cooperativity and Multivalency | 7 |
| 1.3.4 | Self-assembly and Self-organization | 8 |
| 1.3.5 | Template Effects | 10 |
| 1.3.6 | Self-replication and Supramolecular Catalysis | 11 |
| 1.3.7 | Molecular Devices and Machines: Implementing Function | 13 |
| 1.4 | Conclusions: Diverse Methods for a Diverse Research Area | 14 |
| | References and Notes | 15 |
| 2 | Determination of Binding Constants
Keiji Hirose | 17 |
| 2.1 | Theoretical Principles | 17 |
| 2.1.1 | The Binding Constants and Binding Energies | 17 |
| 2.1.2 | A General View on the Determination of Binding Constants | 18 |
| 2.1.3 | Guideline for Experiments | 19 |
| 2.2 | A Practical Course of Binding Constant Determination by UV/vis Spectroscopy | 19 |
| 2.2.1 | Determination of Stoichiometry | 19 |
| 2.2.2 | Evaluation of Complex Concentration | 23 |
| 2.2.3 | Precautions to be Taken when Setting Up Concentration Conditions of the Titration Experiment | 25 |
| 2.2.3.1 | Correlation between [H]0, [G]0, x and K | 25 |
| 2.2.3.2 | How to Set Up [H]0 | 27 |
| 2.2.3.3 | How to Set Up [G]0 | 27 |
| 2.2.4 | Data Treatment | 32 |
| 2.2.4.1 | General View | 32 |
| 2.2.4.2 | Rose--Drago Method for UV/vis Spectroscopy | 33 |
| 2.2.4.3 | Estimation of Error | 35 |
| 2.2.5 | Conclusion for UV/vis Spectroscopic Method | 35 |
| 2.3 | Practical Course of Action for NMR Spectroscopic Binding Constant Determination | 36 |
| 2.3.1 | Determination of Stoichiometry | 37 |
| 2.3.2 | Evaluation of Complex Concentration | 39 |
| 2.3.3 | Data Treatment for NMR Method | 39 |
| 2.3.3.1 | Rose--Drago Method for NMR Spectroscopy | 39 |
| 2.3.3.2 | Estimation of Error for NMR Method | 40 |
| 2.3.3.3 | Nonlinear Least Square Data Treatment of NMR Titration Method | 40 |
| 2.3.3.4 | Estimation of Error for Nonlinear Least Square Method of NMR Spectroscopy | 44 |
| 2.4 | Conclusion | 45 |
| | References and Notes | 54 |
| 3 | Isothermal Titration Calorimetry in Supramolecular Chemistry
Franz P. Schmidtchen | 55 |
| 3.1 | Introduction | 55 |
| 3.2 | The Thermodynamic Platform | 56 |
| 3.3 | Acquiring Calorimetric Data | 60 |
| 3.4 | Extending the Applicability | 70 |
| 3.5 | Perspectives | 75 |
| | Acknowledgement | 76 |
| | References | 77 |
| 4 | Extraction Methods
Holger Stephan, Stefanie Juran, Bianca Antonioli, Kerstin Gloe and Karsten Gloe | 79 |
| 4.1 | Introduction | 79 |
| 4.2 | The Extraction Technique | 80 |
| 4.3 | The Technical Process | 83 |
| 4.4 | The Extraction Equilibrium | 84 |
| 4.5 | Principles of Supramolecular Extraction | 87 |
| 4.6 | Examples of Supramolecular Extraction | 89 |
| 4.7 | Conclusions and Future Perspectives | 100 |
| | Acknowledgements | 100 |
| | References | 101 |
| 5 | Mass Spectrometry and Gas Phase Chemistry of Supramolecules
Michael Kogej and Christoph A. Schalley | 104 |
| 5.1 | Introduction | 104 |
| 5.2 | Instrumentation | 105 |
| 5.2.1 | Ionization Techniques Suitable for Noncovalent Species | 106 |
| 5.2.1.1 | Matrix-assisted Laser Desorption/Ionization (MALDI) | 106 |
| 5.2.1.2 | Electrospray Ionization (ESI) | 108 |
| 5.2.1.3 | Resonance-enhanced Multiphoton Ionization (REMPI) | 110 |
| 5.2.1.4 | Ionization of Noncovalent Species | 110 |
| 5.2.2 | Mass Analyzers | 111 |
| 5.2.2.1 | Quadrupole Instruments and Quadrupole Ion Traps | 111 |
| 5.2.2.2 | Time-of-flight (TOF) | 113 |
| 5.2.2.3 | Ion Cyclotron Resonance (ICR) | 115 |
| 5.3 | Particuliarities and Limitations of Mass Spectrometry | 117 |
| 5.4 | Beyond Analytical Characterization: Tandem MS Experiments for the Examination of the Gas-phase Chemistry of Supramolecules | 119 |
| 5.4.1 | Collision-induced Decay (CID) | 120 |
| 5.4.2 | Infrared-multiphoton Dissociation (IRMPD) | 120 |
| 5.4.3 | Blackbody Infrared Dissociation (BIRD) | 121 |
| 5.4.4 | Electron-capture Dissociation (ECD) and Electron Transfer Dissociation (ETD) | 122 |
| 5.4.5 | Bimolecular Reactions: H/D-exchange and Gas-phase Equilibria | 122 |
| 5.5 | Selected Examples | 123 |
| 5.5.1 | Analytical Characterization: Exact Mass, Isotope Patterns, Charge State, Stoichiometry, Impurities | 125 |
| 5.5.2 | Structural Characterization of Supramolecules | 126 |
| 5.5.2.1 | The Mechanical Bond: How to Distinguish Molecules with Respect to Their Topology | 126 |
| 5.5.2.2 | Encapsulation of Guest Molecules in Self-assembling Capsules | 127 |
| 5.5.3 | Ion Mobility: A Zwitterionic Serine Octamer? | 138 |
| 5.5.4 | Mass Spectrometry for the Detection of Chirality | 140 |
| 5.5.5 | Reactivity Studies of Supramolecules in Solution | 142 |
| 5.5.6 | Reactivity in the Gas Phase: Isolated Species instead of Dynamic Interconverting Complexes | 147 |
| 5.5.6.1 | Metallosupramolecular Squares: A Supramolecular Equivalent to Neighbor Group Assistance | 147 |
| 5.5.6.2 | A Surprising Dendritic Effect: Switching Fragmentation Mechanisms | 151 |
| 5.5.7 | Determining Thermochemical Data: The Influence of the Environment | 154 |
| 5.5.7.1 | Crown Ether -- Alkali Complexes: Questioning the Best-fit Model | 154 |
| 5.5.7.2 | BIRD: Arrhenius Kinetics of Oligonucleotide Strand Separation in the Gas Phase | 157 |
| 5.6 | Conclusions | 157 |
| | References and Notes | 159 |
| 6 | Diffusion NMR in Supramolecular Chemistry
Yoram Cohen, Liat Avram, Tamar Evan-Salem and Limor Frish | 163 |
| 6.1 | Introduction | 163 |
| 6.2 | Concepts of Molecular Diffusion | 164 |
| 6.3 | Measuring Diffusion with NMR | 164 |
| 6.3.1 | The Basic Pulse Sequence | 164 |
| 6.3.2 | The Stimulated Echo (STE) Diffusion Sequence | 168 |
| 6.3.3 | Technical Issues in Diffusion NMR | 169 |
| 6.3.4 | The LED and BPLED Sequences | 171 |
| 6.3.5 | DOSY -- Diffusion Ordered Spectroscopy | 173 |
| 6.4 | Applications of Diffusion NMR in Supramolecular Chemistry: Selected Examples | 175 |
| 6.4.1 | Binding and Association Constants | 175 |
| 6.4.2 | Encapsulation and Molecular Capsules | 181 |
| 6.4.3 | Molecular Size, Shape and Self-aggregation | 193 |
| 6.4.4 | Diffusion as a Filter: Virtual Separation and Ligand Screening | 203 |
| 6.4.5 | From Organometallics to Supercharged Supramolecular Systems | 207 |
| 6.5 | Advantages and Limitations of Diffusion NMR | 209 |
| 6.6 | Diffusion NMR and Chemical Exchange | 210 |
| 6.7 | Summary and Outlook | 215 |
| | References and Notes | 216 |
| 7 | Photophysics and Photochemistry of Supramolecular Systems
Bernard Valeur, Mário Nuno Berberan-Santos and Monique M. Martin | 220 |
| 7.1 | Introduction | 220 |
| 7.2 | Spectrophotometry and Spectrofluorometry | 221 |
| 7.2.1 | Determination of the Stoichiometry and Association Constant of Supramolecular Complexes from Spectrophotometric or Spectrofluorometric Titrations | 221 |
| 7.2.2 | Cooperativity and Anticooperativity | 224 |
| 7.2.3 | Possible Differences in Binding Constants in the Ground State and in the Excited State | 226 |
| 7.2.4 | Information on Photoinduced Processes from Fluorescence Spectra | 227 |
| 7.2.4.1 | Photoinduced Electron Transfer in a Calixarene-based Supermolecule Designed for Mercury Ion Sensing [10] | 227 |
| 7.2.4.2 | Excitation Energy Transfer in an Inclusion Complex of a Multichromophoric Cyclodextrin with a Fluorophore | 229 |
| 7.3 | Time-resolved Fluorescence Techniques | 230 |
| 7.3.1 | General Principles | 231 |
| 7.3.2 | Pulse Fluorometry | 233 |
| 7.3.3 | Phase-modulation Fluorometry | 235 |
| 7.3.3.1 | Phase Fluorometers using a Continuous Light Source and an Electro-optic Modulator | 235 |
| 7.3.3.2 | Phase Fluorometers using the Harmonic Content of a Pulsed Laser | 237 |
| 7.3.4 | Data Analysis | 237 |
| 7.3.5 | Examples | 238 |
| 7.3.5.1 | Photoinduced Electron Transfer in a Self-assembled Zinc Naphthalocyanine--Fullerene Diad | 238 |
| 7.3.5.2 | Excitation Energy Transfer in a Self-assembled Zinc Porphyrin--Free Base Porphyrin Diad | 240 |
| 7.3.5.3 | Excitation Energy Transfer in an Inclusion Complex of a Multichromophoric Cyclodextrin with a Fluorophore | 241 |
| 7.3.5.4 | Excimer Formation of Cyanobiphenyls in a Calix[4]resorecinarene Derivative | 241 |
| 7.4 | Fluorescence Anisotropy | 243 |
| 7.4.1 | Principles | 244 |
| 7.4.2 | Examples | 249 |
| 7.4.2.1 | Supramolecular Polymer Length | 249 |
| 7.4.2.2 | Excitation Energy Hopping in Multichromophoric Cyclodextrins | 251 |
| 7.5 | Transient Absorption Spectroscopy | 253 |
| 7.5.1 | General Principles | 253 |
| 7.5.2 | Pump-probe Spectroscopy with Subpicosecond Laser Excitation | 254 |
| 7.5.2.1 | White Light Continuum Generation | 254 |
| 7.5.2.2 | Subpicosecond Pump-continuum Probe Set-up | 255 |
| 7.5.2.3 | Time-resolved Differential Absorption Measurements | 257 |
| 7.5.2.4 | Data Analysis | 257 |
| 7.5.3 | Examples of Application | 258 |
| 7.5.3.1 | Charge Separation in Porphyrin--Fullerene Diads | 258 |
| 7.5.3.2 | Cation Photorelease from a Crown-ether Complex | 260 |
| 7.6 | Concluding Remarks | 262 |
| | References and Notes | 262 |
| 8 | Circular Dichroism Spectroscopy
Marie Urbanová and Petr Malon | 265 |
| 8.1 | Basic Considerations | 265 |
| 8.1.1 | Circular Dichroism | 265 |
| 8.1.2 | Variants of Chiroptical Methods | 268 |
| 8.1.3 | Advantages and Limits of Circular Dichroism Spectroscopies | 269 |
| 8.1.3.1 | Chiral and Parent Non-chiral Spectroscopies | 269 |
| 8.1.3.2 | Electronic and Vibrational Circular Dichroism | 269 |
| 8.1.3.3 | Instrumentation | 270 |
| 8.1.3.4 | Calculations | 270 |
| 8.2 | Measurement Techniques (Methodology of CD Measurement) | 270 |
| 8.2.1 | Electronic Circular Dichroism Measurements | 272 |
| 8.2.2 | Vibrational Circular Dichroism Measurements | 272 |
| 8.3 | Processing of Circular Dichroism Spectra | 275 |
| 8.3.1 | Intensity Calibration in VCD Spectroscopy | 276 |
| 8.3.2 | Baseline Corrections and Reliability in VCD | 277 |
| 8.3.3 | Advanced Processing of Circular Dichroism Spectra | 277 |
| 8.4 | Theory | 279 |
| 8.4.1 | Rotational Strength | 279 |
| 8.4.2 | Mechanisms Generating Optical Activity | 280 |
| 8.4.3 | Ab initio Calculations | 282 |
| 8.5 | Examples of Vibrational Circular Dichroism Applications | 283 |
| 8.5.1 | Absolute Configuration and Detailed Structural Parameters | 283 |
| 8.5.2 | Solution Structure of Biomolecules | 287 |
| 8.5.3 | Supramolecular Systems | 292 |
| 8.6 | Concluding Remarks | 299 |
| | Abbreviations | 299 |
| | References and Notes | 300 |
| 9 | Crystallography and Crystal Engineering
Kari Rissanen | 305 |
| 9.1 | Introduction | 305 |
| 9.2 | Crystallography | 306 |
| 9.2.1 | Introduction | 306 |
| 9.2.2 | A Walk through a Single Crystal Structural Determination | 308 |
| 9.2.2.1 | The (Single) Crystal | 309 |
| 9.2.2.2 | Mounting of the Crystal | 310 |
| 9.2.2.3 | Unit Cell Determination and Preliminary Space Group Selection | 312 |
| 9.2.2.4 | Data Collection, Data Processing and Final Space Group Determination | 318 |
| 9.2.2.5 | Data Reduction, Structure Solution and Refinement | 322 |
| 9.2.2.6 | Analysis of Structure | 327 |
| 9.3 | Crystal Engineering | 331 |
| 9.3.1 | Introduction | 331 |
| 9.3.2 | Definition | 331 |
| 9.4 | Conclusions | 334 |
| | Acknowledgements | 335 |
| | References and Notes | 335 |
| 10 | Scanning Probe Microscopy
B. A. Hermann | 337 |
| 10.1 | Introduction: What is the Strength of Scanning Probe Techniques? | 337 |
| 10.2 | How do Scanning Probe Microscopes Work? | 339 |
| 10.2.1 | Scanning Tunneling Microscopy (STM) | 341 |
| 10.2.1.1 | Working Principle of STM | 341 |
| 10.2.1.2 | Operation Modes of STM | 344 |
| 10.2.1.3 | Imaging with STM | 346 |
| 10.2.1.4 | Tunneling Spectroscopy | 350 |
| 10.2.1.5 | Manipulating Atoms and Molecules with STM | 359 |
| 10.2.2 | Atomic Force Microscopy (AFM) | 363 |
| 10.2.2.1 | Function Principle of AFM | 363 |
| 10.2.2.2 | Various Operation Modes of AFM | 364 |
| 10.2.2.3 | Single Molecule Force Spectroscopy -- Force-Distance Measurements | 367 |
| 10.3 | Which Molecules can be Studied? | 369 |
| 10.3.1 | Differences between STM and AFM | 370 |
| 10.3.2 | Exemplary Results on Smaller Molecules | 371 |
| 10.4 | What Results have been Obtained in the Field of Supramolecular Chemistry? | 374 |
| 10.4.1 | Coronenes, Crown ethers, Cryptands, Macrocycles, Squares, Rectangles | 375 |
| 10.4.2 | Calixarenes, Cyclodextrins, Molecular Sieves and Boxes | 378 |
| 10.4.3 | Porphyrins and Phorphyrin Oligomers | 380 |
| 10.4.4 | Complex Interconnected Supermolecules: Rotaxanes and Catenanes | 382 |
| 10.4.5 | Supramolecular Assemblies, Grids, Arrays, Chains | 382 |
| | Acknowledgements | 384 |
| | References | 384 |
| 11 | The Characterization of Synthetic Ion Channels and Pores
Stefan Matile and Naomi Sakai | 391 |
| 11.1 | Introduction | 391 |
| 11.2 | Methods | 392 |
| 11.2.1 | Planar Bilayer Conductance | 394 |
| 11.2.2 | Fluorescence Spectroscopy with Labeled Vesicles | 396 |
| 11.2.3 | Miscellaneous | 398 |
| 11.3 | Characteristics | 399 |
| 11.3.1 | pH Gating | 399 |
| 11.3.2 | Concentration Dependence | 400 |
| 11.3.3 | Size Selectivity | 402 |
| 11.3.4 | Voltage Gating | 403 |
| 11.3.5 | Ion Selectivity | 404 |
| 11.3.6 | Blockage and Ligand Gating | 407 |
| 11.3.7 | Miscellaneous | 410 |
| 11.4 | Structural Studies | 412 |
| 11.4.1 | Binding to the Bilayer | 413 |
| 11.4.2 | Location in the Bilayer | 414 |
| 11.4.3 | Self-Assembly | 414 |
| 11.4.4 | Molecular Recognition | 415 |
| 11.5 | Concluding Remarks | 415 |
| | Acknowledgement | 416 |
| | References | 416 |
| 12 | Theoretical Methods for Supramolecular Chemistry
Barbara Kirchner and Markus Reiher | 419 |
| 12.1 | Introduction | 419 |
| 12.2 | A Survey of Theoretical Methods | 422 |
| 12.2.1 | First-principles Methods | 424 |
| 12.2.2 | The Supramolecular Approach and Total Interaction Energies | 430 |
| 12.2.3 | The Time Dimension: Molecular Dynamics | 433 |
| 12.2.4 | A Technical Note: Linear Scaling and Multiscale Modeling | 437 |
| 12.2.5 | How to Make the Connection to Experiment? | 439 |
| 12.3 | Standard Classification of Intermolecular Interactions | 443 |
| 12.3.1 | A Complication: Cooperative Effects | 445 |
| 12.3.2 | Distributed Multipoles and Polarizabilities | 446 |
| 12.3.3 | Local Multipole Expansions in MD Simulations | 447 |
| 12.4 | Qualitative Understanding and Decomposition Schemes | 450 |
| 12.4.1 | Interaction Energy Decomposition | 451 |
| 12.4.2 | A Core-electron Probe for Hydrogen Bond Interactions | 452 |
| 12.4.3 | The SEN Approach to Hydrogen Bond Energies | 452 |
| 12.5 | General Mechanism for a Static, Step-wise View on Host--Guest Recognition | 455 |
| 12.5.1 | Template-free Pre-orientation Processes | 457 |
| 12.5.2 | Rearrangement Reactions | 458 |
| 12.5.3 | The Host-controlled Association Reaction | 459 |
| 12.5.4 | The Transformation Step | 460 |
| 12.5.5 | Inclusion of Environmental Effects | 460 |
| 12.5.6 | General Aspects of Template Thermodynamics and Kinetics | 460 |
| 12.6 | Conclusions and Perspective | 462 |
| | Acknowledgments | 463 |
| | References and Notes | 463 |
| | Index | 472 |
