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Book Details
Abstract
The ultra-bright femtosecond X-ray pulses provided by X-ray free electron lasers (XFELs) open up opportunities to study the structure and dynamics of a wide variety of systems beyond what is possible with synchrotron sources. This book introduces the principles and properties of currently operating and future XFELs, before outlining applications in materials science, chemistry and biology. Edited by pioneers in this exciting field, and featuring contributions from leading researchers, this book is ideal for researchers working with XFELs, synchrotron radiation, ultrafast and femtosecond crystallography and femtosecond spectroscopy.
Uwe Bergmann is a Distinguished Staff Scientist at the SLAC National Accelerator Laboratory, USA. His research activities focus on the development and application of novel x-ray spectroscopy techniques.
Vittal Yachandra is a Senior Scientist Lawrence Berkeley National Laboratory, USA. His main research interest has focused on the study of photosynthetic water oxidation and the structure and mechanism of the Mn4Ca cluster by spectroscopy.
Junko Yano is a Senior Scientist at Lawrence Berkeley National Laboratory and a PI of the Joint Center for Artificial Photosynthesis at Berkeley. Her research areas include the water oxidation in natural photosynthesis and artificial photosynthesis, catalytic reactions in metalloenzymes, application of synchrotron X-ray radiation and X-ray free electron laser techniques to biological and inorganic systems.
Table of Contents
| Section Title | Page | Action | Price |
|---|---|---|---|
| Cover | Cover | ||
| X-Ray Free Electron Lasers: Applications in Materials, Chemistry and Biology | i | ||
| Preface | v | ||
| Quote | xiv | ||
| Contents | xv | ||
| Section I - Properties of XFELs | 1 | ||
| Chapter 1 - The Physics and Status of X-ray Free-electron Lasers | 3 | ||
| 1.1 Introduction | 3 | ||
| 1.1.1 Early Work on X-ray Lasers and the Development of XFELs | 3 | ||
| 1.1.2 Undulator Radiation Characteristics | 5 | ||
| 1.1.3 Introduction to FELs | 7 | ||
| 1.1.4 FEL Physics as Collective Instability | 9 | ||
| 1.2 Three-dimensional (3D) FEL Theory | 14 | ||
| 1.2.1 Characteristics of XFELs | 16 | ||
| 1.3 Present Status | 21 | ||
| 1.3.1 Hard X-ray FELs | 22 | ||
| 1.3.1.1 LCLS | 22 | ||
| 1.3.1.2 SACLA | 24 | ||
| 1.3.1.3 Pohang Accelerator Laboratory (PAL) XFEL | 25 | ||
| 1.3.1.4 SwissFEL | 26 | ||
| 1.3.1.5 European XFEL | 28 | ||
| 1.3.2 Soft XFELs | 29 | ||
| 1.3.2.1 FLASH in Hamburg | 30 | ||
| 1.3.2.2 FERMI | 31 | ||
| 1.3.3 Novel Developments | 32 | ||
| 1.3.3.1 Increasing the Longitudinal Coherence of XFEL Radiation | 33 | ||
| 1.3.3.2 Self-seeding | 33 | ||
| 1.3.3.3 Harmonic Lasing | 34 | ||
| 1.3.3.4 Purified SASE (pSASE) | 34 | ||
| 1.3.3.5 High-brightness SASE (HB-SASE) and improved SASE (iSASE) | 35 | ||
| 1.3.3.6 EEHG | 35 | ||
| 1.3.3.7 Hard X-ray FEL Oscillator (XFELO) | 36 | ||
| 1.3.3.8 Compact XFEL Sources | 36 | ||
| 1.4 Conclusion | 37 | ||
| Acknowledgements | 37 | ||
| References | 38 | ||
| Section II - Biological Structure Determination | 45 | ||
| Chapter 2 - Imaging Protein Dynamics by XFELs | 47 | ||
| 2.1 Introduction: Seeing Atoms Without Using Crystals | 47 | ||
| 2.2 Radiation Damage Limits Resolution | 50 | ||
| 2.3 Serial Crystallography at XFELs for Structural Biology | 54 | ||
| 2.4 Molecular Machines and Single-particle Imaging | 55 | ||
| 2.5 Time-resolved Serial Crystallography, Optical Pump-probe Methods and Photosynthesis | 58 | ||
| 2.6 Time-resolved SFX for Slower Processes: Mixing Jets and Other Excitations | 60 | ||
| 2.7 Fast Solution Scattering and Angular Correlation Methods | 61 | ||
| 2.8 Data Analysis | 63 | ||
| 2.9 Summary | 65 | ||
| Acknowledgements | 65 | ||
| References | 66 | ||
| Chapter 3 - Overcoming Data Processing Challenges for Breakthrough Crystallography | 70 | ||
| 3.1 Introduction | 70 | ||
| 3.2 Data Measurement Challenges Intrinsic to SFX Experiments | 71 | ||
| 3.3 Data Processing Tools Aimed at Still-shot Signal Integration | 73 | ||
| 3.3.1 The Universal Approach of Modelling the Lattice | 73 | ||
| 3.3.2 The Difficulty of Deducing the Lattice Model from Partial Spots | 74 | ||
| 3.3.3 An Approach to Compensate for Missetting | 76 | ||
| 3.3.4 Models of Crystal Imperfection | 76 | ||
| 3.3.5 Post-refinement | 78 | ||
| 3.3.6 Outlier Rejection and Consistent Lattice Alignment | 79 | ||
| 3.3.7 Lessons from Validation | 80 | ||
| 3.3.8 Detector Geometry | 83 | ||
| 3.4 Future Outlook | 84 | ||
| Acknowledgements | 85 | ||
| References | 85 | ||
| Chapter 4 - 3D Imaging Using an X-ray Free Electron Laser | 88 | ||
| 4.1 Background | 88 | ||
| 4.2 The Challenge | 89 | ||
| 4.3 Methods to Orient Diffraction Patterns | 91 | ||
| 4.4 Expand, Maximize and Compress | 92 | ||
| 4.4.1 Updating the Orientations | 93 | ||
| 4.4.2 Updating the Model | 95 | ||
| 4.4.3 Choosing the Similarity Function d | 96 | ||
| 4.4.4 Photon Fluency | 97 | ||
| 4.5 Validation | 98 | ||
| 4.6 The 3D Reconstruction of the Mimivirus Particle | 100 | ||
| 4.7 The Resolution Limit | 102 | ||
| 4.8 Dynamics | 103 | ||
| Acknowledgements | 103 | ||
| References | 103 | ||
| Section III - Photochemistry in Biological Systems | 105 | ||
| Chapter 5 - Dynamic and Static X-ray Scattering from Biological Systems on the Femtosecond to Nanosecond Time Scale | 107 | ||
| 5.1 Introduction | 107 | ||
| 5.1.1 The Biological Part | 107 | ||
| 5.1.2 The Physical Part | 109 | ||
| 5.1.3 Structure and Dynamics | 112 | ||
| 5.1.4 Dynamic X-ray Crystallography | 117 | ||
| 5.2 Example: Dynamic Structural Studies of the Photocycle of the Bacterial Blue Light Photoreceptor, PYP | 121 | ||
| 5.3 Summary | 125 | ||
| Acknowledgements | 125 | ||
| References | 125 | ||
| Chapter 6 - Elucidating Ultrafast Structural Motions in Photosynthetic Reaction Centers with XFEL Radiation | 128 | ||
| 6.1 Photosynthetic Reaction Centers | 128 | ||
| 6.2 Conformational Stabilization of the Charge Separated State | 130 | ||
| 6.3 Evidence for Structural Changes Using Synchrotron Radiation | 130 | ||
| 6.4 Ultrafast Structural Gating in Photosynthetic RCs | 132 | ||
| 6.5 Studies of Protein Structure Using X-ray Free Electron Laser (XFEL) Radiation | 133 | ||
| 6.6 Time-resolved SFX | 134 | ||
| 6.7 Time-resolved Wide Angle X-ray Scattering Using XFEL Radiation | 136 | ||
| 6.8 Concluding Remarks | 138 | ||
| References | 138 | ||
| Chapter 7 - Damage-free Electronic and Geometric Structure Determination of Metalloproteins | 141 | ||
| 7.1 Introduction | 141 | ||
| 7.2 Methods | 143 | ||
| 7.2.1 Triggering Reactions | 143 | ||
| 7.2.2 Diffraction | 144 | ||
| 7.2.3 X-Ray Spectroscopy | 147 | ||
| 7.2.4 Sample Delivery | 149 | ||
| 7.3 Applications | 151 | ||
| 7.3.1 Processes Relevant to Metalloenzyme Systems | 151 | ||
| 7.3.2 Studies on Myoglobin and Related Systems | 153 | ||
| 7.3.3 Studies on Cytochromes and Related Systems | 155 | ||
| 7.3.4 Cu and Non-heme Fe Enzymes | 157 | ||
| 7.3.5 Studies on Photosystem II | 159 | ||
| 7.4 Conclusions | 165 | ||
| Acknowledgements | 166 | ||
| References | 166 | ||
| Section IV - Photochemistry in Materials | 171 | ||
| Chapter 8 - Gas Phase Photochemistry Probed by Free Electron Lasers | 173 | ||
| 8.1 Introduction | 173 | ||
| 8.2 Different Ways of Probing the Molecular Dynamics: Direct vs. Indirect | 174 | ||
| 8.2.1 Indirect Methods | 176 | ||
| 8.2.1.1 Auger Electron Spectroscopy | 176 | ||
| 8.2.1.2 Mass Spectroscopy of Auger Decay-induced Coulomb Explosion of Molecules | 178 | ||
| 8.2.2 Outlook: Direct Methods | 179 | ||
| 8.2.2.1 Time-resolved XPS | 180 | ||
| 8.2.2.2 Time-resolved NEXAFS Spectroscopy | 181 | ||
| 8.3 Future Opportunities | 182 | ||
| Acknowledgements | 182 | ||
| References | 183 | ||
| Chapter 9 - Chemical Dynamics in Liquid Water and at Catalytic Surfaces | 187 | ||
| 9.1 Introduction | 187 | ||
| 9.2 Surface-mediated Catalysis | 188 | ||
| 9.3 Water | 192 | ||
| 9.4 Conclusion | 197 | ||
| Acknowledgements | 198 | ||
| References | 199 | ||
| Chapter 10 - Ultrafast Photochemical Reaction Trajectories Revealed by X-ray Transient Absorption Spectroscopy Using X-ray Free Electron Laser Sources | 201 | ||
| 10.1 Introduction | 201 | ||
| 10.2 Experimental | 205 | ||
| 10.2.1 Characteristics of X-ray Pulses and the XAS Signal at the X-ray Pump-probe (XPP) Station of LCLS | 205 | ||
| 10.2.2 Sample Considerations and Data Collection for XANES Spectra | 206 | ||
| 10.3 Results and Discussion | 209 | ||
| 10.3.1 Excited State Structural Dynamics | 209 | ||
| 10.3.2 Identity of the T′ State: The Transient Ni(i) Center | 213 | ||
| 10.3.3 Implications and Significance | 215 | ||
| 10.4 Conclusion | 218 | ||
| Acknowledgements | 218 | ||
| References | 219 | ||
| Chapter 11 - Tracking Excited State Dynamics in Photo-excited Metal Complexes with Hard X-ray Scattering and Spectroscopy | 225 | ||
| 11.1 Introduction | 225 | ||
| 11.2 Experimental Techniques | 226 | ||
| 11.2.1 XES | 226 | ||
| 11.2.2 XDS | 227 | ||
| 11.2.3 Combined Experimental Setup | 227 | ||
| 11.3 Experimental Results | 228 | ||
| 11.3.1 Characterizing the Decay of Metal-to-ligand Charge Transfer (MLCT) States in Fe-centered Molecular Systems | 228 | ||
| 11.3.2 Characterizing Electron Transfer and Spin State Dynamics of Co-centered Molecular Systems | 232 | ||
| 11.3.3 Characterizing Structural and Solvation Dynamics in Photocatalytic Molecular Systems | 236 | ||
| 11.4 Summary | 238 | ||
| Acknowledgements | 239 | ||
| References | 239 | ||
| Chapter 12 - Orbital-specific Mapping of Chemical Interactions and Dynamics with Femtosecond Soft X-ray Pulses | 242 | ||
| 12.1 Introduction | 242 | ||
| 12.2 Results and Discussion | 246 | ||
| 12.3 Summary and Outlook | 259 | ||
| Acknowledgements | 261 | ||
| References | 261 | ||
| Chapter 13 - Visualizing Chemical Reactions in Solution with Femtosecond X-ray Scattering | 264 | ||
| 13.1 Introduction | 264 | ||
| 13.2 Experimental | 266 | ||
| 13.2.1 Data Collection | 266 | ||
| 13.2.1.1 Data Collection at SACLA | 268 | ||
| 13.2.1.2 Data Collection at KEK | 270 | ||
| 13.2.2 Data Processing | 270 | ||
| 13.2.2.1 Removal of the Solvent Contribution | 270 | ||
| 13.2.2.2 Sine-fourier Transformation of qΔS(q) | 271 | ||
| 13.2.3 Data Analysis | 271 | ||
| 13.2.3.1 SVD | 271 | ||
| 13.2.3.2 Kinetic Analysis | 272 | ||
| 13.2.3.3 Calculation of Theoretical Radial Distribution Functions | 273 | ||
| 13.2.3.4 Structural Fitting Analysis | 274 | ||
| 13.2.3.5 Determination of RDF of the S0 State | 274 | ||
| 13.3 Results and Discussion | 275 | ||
| 13.4 Conclusion | 279 | ||
| Acknowledgements | 280 | ||
| References | 281 | ||
| Chapter 14 - Perspectives for Ultrafast Light-induced Control of Atomic-scale Structure in Condensed Matter Systems | 284 | ||
| 14.1 Introduction | 284 | ||
| 14.2 Phenomenological Treatment for Classical Control of Order Parameters | 286 | ||
| 14.3 Indirect Control | 287 | ||
| 14.3.1 Via Electronic States | 288 | ||
| 14.3.2 Via Phonon–Phonon Coupling | 296 | ||
| 14.4 Direct Control by THz Excitation | 297 | ||
| 14.5 Prospects for Further Progress | 298 | ||
| Acknowledgements | 299 | ||
| References | 299 | ||
| Chapter 15 - Ultrafast Time Structure Imprints in Complex Chemical and Biochemical Reactions | 301 | ||
| 15.1 Introduction | 301 | ||
| 15.2 The Concept: Filming Chemical Reactions in Real Time Utilizing Ultrafast High-flux X-ray Sources | 304 | ||
| 15.3 Crystallography with Ultra-high Temporal and Ultra-high Spatial Resolution Allows Study of the Photochemical Reactions Beyon... | 305 | ||
| 15.4 Applications in Energy Research | 307 | ||
| 15.5 The “from Local to Global” Approach: Ultrafast X-ray Spectroscopy and Ultrafast X-ray Diffraction Shake Hands and Allow the ... | 309 | ||
| 15.6 Ultrafast X-ray Studies of Solution Chemical Reactions | 311 | ||
| 15.7 Applications in Biophysics | 313 | ||
| 15.8 Ultrafast Imaging of Gas-Phase Chemical Reactions | 313 | ||
| 15.9 Summary | 316 | ||
| Acknowledgements | 318 | ||
| References | 319 | ||
| Section V - Sample Delivery Methods | 323 | ||
| Chapter 16 - Sample Delivery Methods: Liquids and Gases at FELs | 325 | ||
| 16.1 Introduction | 325 | ||
| 16.2 Methods Overview | 326 | ||
| 16.2.1 Liquid Jets | 326 | ||
| 16.2.2 Gas Phase Jets | 332 | ||
| 16.3 Automation | 333 | ||
| 16.3.1 Sample Handling | 333 | ||
| 16.3.2 Injector Automation | 334 | ||
| 16.4 Summary | 334 | ||
| Acknowledgements | 335 | ||
| References | 335 | ||
| Chapter 17 - High Viscosity Microstream Sample Delivery for Serial Femtosecond Crystallography | 337 | ||
| 17.1 Introduction | 337 | ||
| 17.2 Crystal Delivery in a Liquid Stream | 338 | ||
| 17.2.1 Low Viscosity Liquid Streams | 338 | ||
| 17.2.2 High Viscosity Injector | 339 | ||
| 17.2.3 High Viscosity Media | 343 | ||
| 17.3 Results and Discussion | 344 | ||
| 17.4 Conclusion | 346 | ||
| Acknowledgements | 346 | ||
| References | 346 | ||
| Chapter 18 - Acoustic Methods for On-demand Sample Injection into XFEL Beams | 348 | ||
| 18.1 Introduction | 348 | ||
| 18.2 Evolution of Sample Delivery Methods at XFELs | 350 | ||
| 18.3 Acoustic Droplet Ejection (ADE) Method Development | 352 | ||
| 18.4 On-demand Acoustic Injectors at XFELs | 355 | ||
| 18.5 Ongoing Research and Development: Future Outlook | 359 | ||
| Acknowledgements | 361 | ||
| References | 361 | ||
| Section VI - New Directions | 365 | ||
| Chapter 19 - Ultrafast Laser-pumped, X-ray-probed Quantum Dynamics at Short-pulsed Light Sources | 367 | ||
| 19.1 Introduction | 367 | ||
| 19.2 The Pump-probe Method | 368 | ||
| 19.2.1 Basic Properties | 368 | ||
| 19.2.2 The Quantum Description of Pump-probe Methods | 369 | ||
| 19.2.3 Ensemble Effects | 369 | ||
| 19.2.4 Hierarchy of Time Scales in Molecules | 370 | ||
| 19.3 First Example: Impulsive Excitation of Coherent Acoustic Phonons Probed by Ultrafast Picosecond X-rays at 3d Generation Sync... | 371 | ||
| 19.4 Second Example: Impulsive Rotational Raman Excitation | 372 | ||
| 19.5 Third Example: X-ray Production of Molecular Movies | 375 | ||
| 19.6 Conclusion and Outlook: Moving Towards Future X-ray Detection of Attosecond Electron Motion | 376 | ||
| Acknowledgements | 378 | ||
| References | 378 | ||
| Chapter 20 - Photoionisation Inner-shell X-ray Lasers | 380 | ||
| 20.1 Introduction | 380 | ||
| 20.2 The Photoionisation Kα X-ray Laser in Neon | 383 | ||
| 20.3 Molecular Soft X-ray Photoionisation Lasers | 389 | ||
| 20.4 Outlook and Conclusions | 392 | ||
| References | 395 | ||
| Chapter 21 - Opportunities for Structure Determination Using X-ray Free-electron Laser Pulses | 397 | ||
| 21.1 Introduction | 397 | ||
| 21.2 Outrunning Radiation Damage | 399 | ||
| 21.3 Single Shot 3D Incoherent Imaging of Unique Objects | 401 | ||
| 21.4 Imaging Reproducible Objects | 405 | ||
| 21.5 Continuous Diffraction from Single Molecules | 409 | ||
| 21.6 Conclusion | 414 | ||
| Acknowledgements | 415 | ||
| References | 415 | ||
| Chapter 22 - Machine-learning Routes to Dynamics, Thermodynamics and Work Cycles of Biological Nanomachines | 418 | ||
| 22.1 Introduction | 418 | ||
| 22.2 Geometric Machine Learning | 421 | ||
| 22.3 Mapping Conformations of Nanomachines | 423 | ||
| 22.4 Three-dimensional Conformational Movies over Energy Landscapes | 423 | ||
| 22.5 Dynamics Beyond Timing Uncertainty | 427 | ||
| 22.6 Conclusions and Future Prospects | 430 | ||
| Acknowledgements | 431 | ||
| References | 431 | ||
| Chapter 23 - New Science Opportunities and Experimental Approaches Enabled by High Repetition Rate Soft X-ray Lasers | 434 | ||
| 23.1 Introduction | 434 | ||
| 23.2 Fundamental Dynamics of Energy and Charge in Atoms and Molecules | 435 | ||
| 23.2.1 Dynamic Molecular Reaction Microscope | 436 | ||
| 23.2.2 Nonlinear X-ray Approaches for Mapping Valence Charge Dynamics | 438 | ||
| 23.2.3 LCLS Instrument NEH 1.1 | 442 | ||
| 23.3 Photo-catalysis and Coordination Chemistry | 443 | ||
| 23.3.1 Excited-state Charge Dynamics via RIXS | 444 | ||
| 23.3.2 LCLS Instrument NEH 2.2 | 446 | ||
| 23.4 Quantum Materials | 447 | ||
| 23.4.1 Opportunities for Momentum-transfer-dependent RIXS at XFELs | 448 | ||
| 23.4.2 Collective Excitations: Transient Fields and Time-dependent (Pump-probe) Approaches | 450 | ||
| 23.4.3 LCLS Instrument NEH 2.1 | 451 | ||
| 23.5 Coherent Imaging at the Nanoscale | 452 | ||
| 23.5.1 Single Particle Imaging | 452 | ||
| 23.5.2 LCLS instrument NEH 1.2 | 453 | ||
| 23.6 Conclusion | 454 | ||
| Acknowledgements | 455 | ||
| References | 455 | ||
| Subject Index | 458 |