Advanced Fluorescence Reporters in Chemistry and Biology I (eBook)

Advanced Fluorescence Reporters in Chemistry and Biology I 3
Fundamentals and Molecular Design 3
Series Editor 5
Aims and Scope 5
Preface 7
Contents 9
Part I: 
11 
Comparative Analysis of Fluorescence Reporter Signals Based on Intensity, Anisotropy, Time-Resolution, and Wavelength-Ratiometry 12
1 Why Fluorescence? 13
2 Sensing Based on Emission Intensity 15
3 Variation of Emission Anisotropy 16
4 Time-Resolved and Time-Gated Detection 19
5 Wavelength Ratiometry with Two Emitters 20
5.1 Intensity Sensing with the Reference 21
5.2 Formation of Excimers 22
5.3 Förster Resonance Energy Transfer 23
6 Wavelength Ratiometry with Single Emitter 25
6.1 Transitions Between Ground-State Forms 26
6.2 Transitions Between Excited-State Forms 27
6.3 Multiparametric Reporters Combining the Transitions Between Ground-State and Excited-State Forms 28
7 Concluding Remarks 29
References 30
Part II: 
34 
Optimized UV/Visible Fluorescent Markers 35
1 Introduction 36
2 Coumarin Markers 36
3 Benzoxadiazole, Acridone, and Acridine Markers 42
4 Polyaromatic Markers 46
5 Fluorescein Markers 51
6 Rhodamine Markers 57
7 Concluding Remarks 62
References 63
Long-Wavelength Probes and Labels Based on Cyanines and Squaraines 73
1 Introduction 74
2 Cyanines: Fluorescent Labels for Low- and High-Molecular-Weight Analytes 75
3 Oxo-Squaraines: Microenvironment-Sensitive Dyes 80
3.1 Oxo-Squaraine Probes 83
3.1.1 Probes for Cellular Imaging, Proteins, and Other High-Molecular-Weight Analytes 83
3.1.2 Metal Cation Chemosensors 89
3.1.3 Chemosensor for Carbohydrates 91
3.1.4 pH Sensor 91
3.1.5 Chemosensors for Thiols 92
3.2 Oxo-Squaraine Labels 93
4 Ring-Substituted Squaraines: Probes and Labels with High Sensitivity and Photostability 95
4.1 Probes 96
4.2 Labels 101
5 Fluorescence Lifetime Dyes 103
6 Norcyanines and Norsquaraines: pH-Sensitive Probes and Labels 104
7 Concluding Remarks 106
References 107
Two-Photon Absorption in Near-IR Conjugated Molecules: Design Strategy and Structure-Property Relations 113
1 Introduction 114
1.1 Brief Historical Account of Two-Photon Absorption and pi-Conjugated Systems 115
1.2 Nonlinear Mechanisms in pi-Conjugated Molecules 116
1.2.1 Two-Photon Absorption 116
1.2.2 Excited State Absorption (ESA) 120
1.2.3 Excited State Absorption via Two-Photon Absorption 122
1.3 Linear pi-Conjugated Molecular Systems 122
2 Experimental Methodologies for Linear and Nonlinear Optical Characterization 124
2.1 Linear Optical Characterization 124
2.2 Nonlinear Optical Characterization 127
2.2.1 Pump-Probe Technique 127
2.2.2 Z-Scan Technique 129
2.2.3 Two-Photon Fluorescence (2PF) Technique 131
3 Trends in Dye Design and Structure-Property Relations 134
3.1 Extending Absorption into the NIR 134
3.2 Symmetrical pi-Conjugated Cyanine-Like Systems 139
3.2.1 Cationic D-pi-D Dyes 139
3.2.2 Neutral D-pi-A-pi-D Dyes 140
3.2.3 Anionic A-pi-A Dyes 141
3.3 Asymmetrical pi-Conjugated Cyanine-Like Systems 143
3.4 Enhancement of 2PA Cross Sections 148
4 Conclusions and Future Directions 149
References 150
Discovery of New Fluorescent Dyes: Targeted Synthesis or Combinatorial Approach? 156
1 Introduction 157
2 Coumarin Dyes 157
2.1 Coumarin-Based Targeted Approach 158
2.2 Coumarin-Based Combinatorial Approach 160
3 Xanthene Dyes 163
3.1 Xanthene-Based Targeted Approach 165
3.2 Xanthene-Based Combinatorial Approach 169
4 BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) Dyes 169
4.1 BODIPY-Based Targeted Approach 169
4.2 BODIPY-Based Combinatorial Approach 176
5 Cyanine (Polymethine) Dyes 177
5.1 Cyanine-Based Targeted Approach 179
5.2 Cyanine-Based Combinatorial Approach 181
6 Combinatorial Approach for the Discovery of Novel Fluorescent Dyes 183
7 Conclusion 188
References 189
Part III: 
194 
Physical Principles Behind Spectroscopic Response of Organic Fluorophores to Intermolecular Interactions 195
1 Fluorescence and Main Intermolecular Processes Affecting Fluorescence Properties 196
1.1 Fluorescence and Fluorescence Probes 196
1.2 Main Intermolecular Processes Affecting Fluorescence Properties 198
1.3 Contact Diffusion Controlled Reactions 199
1.4 Reactions with a Change of Chemical Nature of Fluorophore 200
1.5 Noncontact Interactions (Nonradiative and Radiative Energy Transfer) 203
2 Solvation and Solvatochromism 205
2.1 Inhomogeneous Broadening of Electronic Spectra of Dye Molecules in Solutions 205
2.2 Solute Intermolecular Interactions and Inhomogeneous Broadening of Electronic Spectra in Solutions 206
2.3 Effect of Polarity 213
2.3.1 Single-Parameter Approach 214
2.3.2 Multiparameter Approach 214
2.3.3 Theory of Solvatochromic Shifts 216
2.4 Photoinduced Charge Transfer 219
2.5 Effect of Specific Interactions and Viscosity 222
3 Concluding Remarks 225
References 226
Organic Dyes with Excited-State Transformations (Electron, Charge, and Proton Transfers) 230
1 Photoinduced Electron Transfer (PET) 231
1.1 Theoretical Background of Electron Transfer 232
1.2 Adiabatic Versus Nonadiabatic Electron Transfer Across Linear Fused Oligo-Norbornyl Structures 234
1.3 The Application of Electron Transfer Process Toward Visual Detection of Metal Ions 236
1.3.1 The Conjugated D-A Bipolar System 238
1.3.2 The Conjugated D-A-D Assembly 240
1.3.3 Ion Sensor in a Through-Space PET System 240
2 Organic Dyes with Excited-State Proton Transfer Property 241
2.1 Excited-State Intramolecular Proton Transfer 243
2.1.1 ESIPT via Five-Membered-Ring Hydrogen-Bonding System 244
3-Hydroxyflavone 244
2-Pyridyl Pyrazoles 246
2.1.2 ESIPT via Six-Membered-Ring Hydrogen-Bonding System 247
10-Hydroxybenzo[h]quinoline 247
2-(2-Hydroxyphenyl)benzoxazole and 2-(2-Hydroxyphenyl)benzo-thiazole 249
2.1.3 ESIPT via Seven-Membered-Ring Hydrogen-Bonding System 251
3 Solvation Dynamics in the Proton Transfer Coupled Charge Transfer Reaction 253
3.1 Fundamental Background 253
3.2 Excited-State Charge Transfer Coupled Proton Transfer Reaction 255
3.3 Excited-State Proton Transfer Coupled Charge Transfer Reaction 261
References 264
Dyes with Segmental Mobility: Molecular Rotors 272
1 Introduction 273
2 Photophysical Properties of Molecular Rotors 274
3 Chemical Classes of Molecular Rotors 283
3.1 DMABN-Related Fluorescent Probes 284
3.1.1 Modifications of the Electron Donor Group 284
3.1.2 Modifications of the pi-Conjugation System 285
3.1.3 Modifications of the Electron Acceptor Group 286
3.2 DBMN-Related Structures 287
3.2.1 Julolidines 287
3.2.2 Stilbenes 288
3.2.3 2-dicyanomethylene-3-cyano-2,5-dihydrofuran (DCDHF) Fluorophores 288
3.3 Ionic Dyes 288
4 The Measurement of Molecular Rotor Fluorescence 289
5 Applications of Molecular Rotors 293
5.1 Measurement of Bulk Fluid Viscosity 293
5.2 Probing Polymerization Dynamics with Molecular Rotors 294
5.3 Applications of Molecular Rotors in Protein Sensing and Sensing of Other Macromolecules 296
5.4 Molecular Rotors as Microviscosity Probes in the Cell 299
6 Future Directions 304
7 Conclusion 305
References 306
Electrochromism and Solvatochromism in Fluorescence Response of Organic Dyes: A Nanoscopic View 314
1 Introduction 315
2 Quantum Mechanical-Classical Mechanical (QM-MM) Methods for Solvatochromism and Electrochromism Predictions 316
2.1 Introduction and Background 316
2.2 General Methods and Principles 317
2.3 Analysis Tools 318
3 Indoles and Tryptophan in Proteins 319
3.1 Overview of Results 319
3.2 Orientational Dielectric Compensation 321
3.3 Indole Ring Electronic Polarization 322
3.4 Quantitative Quantum Yield/Lifetime Predictions from Electron Transfer Quenching 322
3.5 Fluctuations, Relaxation, Heterogeneity, and Nonexponential Fluorescence Decay 323
4 Voltage-Sensing Dyes 325
4.1 Introduction and Background 325
4.2 Mechanisms of Voltage Sensitivity 326
4.3 Heterogeneity and Lifetime Studies 328
4.4 Prospect for Molecular Dynamics and QM-MM Studies 329
5 Conclusions 331
Appendix: Notes on Electrostatics 331
References 332
Electric Field Sensitive Dyes 336
1 Slow Dyes 338
2 Fast Dyes 339
3 Dual-Wavelength Ratiometry 343
4 Photostability and Photoxicity 344
5 Surface and Dipole Potential Measurements 345
6 Conclusion 347
References 348
Part IV: 
350 
Photophysics and Spectroscopy of Fluorophores in the Green Fluorescent Protein Family 351
1 Introduction to the Green Fluorescent Protein Family 352
1.1 Discovery, Functions, and Applications 352
1.2 Diversity and Relationships Among the GFP Family 353
1.3 Focus and Plan 355
2 The GFP Chromophore Structure and Properties 356
2.1 Formation and Posttranslational Chemistry of the HBI Chromophore 356
2.2 Multiple Configurations of the HBI Chromophore 357
2.3 Electronic Transitions of HBI in the AvGFP Protein 360
2.4 HBI Excited State Twisting and Radiationless Decay 361
3 Photophysics and Spectroscopy of AvGFP 362
3.1 Absorption and Emission Properties 362
3.2 Ground State Protonation Equilibria of the AvGFP Chromophore 363
3.3 Excited State Proton Transfer (ESPT) from the Neutral Chromophore 365
4 Photoreactions in the GFP Family 368
4.1 Photoconversion of AvGFP 368
4.2 Irreversible Photochemistry in GFPs 369
4.3 Reversible Photochromism 370
4.4 Generality and Complexity of GFP Photoreactions 372
5 Color Control in the GFP Family 373
5.1 General Strategies 373
5.2 Blue and Cyan Variants 374
5.3 Red and Far-Red Emitters 375
6 Conclusions and Prospects 375
References 376
Index 388