Applications of synchroton radiation in low-temperature geochemistry and environmental sciences / ed. by. P.A.Fenter et al. - Washington: Geochemical Society; Mineralogical Society of America, 2002. - 579 p.: ill. - (Reviews in mineralogy and geochemistry; vol.49). - Bibliogr. at the end of the art. - ISBN 0939950-54-5; ISSN 1529-6466  Место хранения:   018 | Институт нефтегазовой геологии и геофизики им. А.А.Трофимука | Новосибирск | Библиотека

Оглавление / Contents

1 An Overview of Synchrotron Radiation Applications to Low Temperature Geochemistry and Environmental Science Gordon E. Brown, Jr. and Neil С. Sturchio INTRODUCTION .................................................... 1 IMPORTANT ISSUES IN LOW TEMPERATURE GEOCHEMISTRY AND ENVIRONMENTAL SCIENCE ........................................... 3 Water and atmospheric or soil gases are ubiquitous in low temperature geochemical and environmental systems ............ 3 Knowledge of the molecular-level speciation of trace elements and environmental contaminants and pollutants is critical for understanding their behavior .................... 3 Earth and environmental materials are complex ................ 4 Complementary characterization methods are necessary ......... 5 Parallel studies of real and model systems are essential ..... 7 The nature of the solid/water interface and of sorbed species must be known ........................................ 7 Nanoscale earth and environmental materials play a major role in interfacial chemical reactions ....................... 9 Reaction pathways and kinetics of environmental and low temperature geochemical reactions are of critical importance .................................................. 11 Computational chemistry can play an important role in studies of interfacial reactions ............................ 11 Inorganic and organic ligands and coatings can have a major impact on the sorption behavior of metal ions as well as on mineral dissolution .............................. 11 Biota can have a major effect on the speciation and sorption of contaminant and pollutant species ............... 13 Molecular-scale mechanisms of bioremediation and phytoremediation of environmental toxins are typically not known ....................................................... 13 Scaling of molecular-level observations to mesoscopic and macroscopic phenomena: the "Holy Grail" of low temperature geochemistry and environmental science ...................... 13 AN OVERVIEW OF SYNCHROTRON RADIATION METHODS USEFUL IN LOW TEMPERATURE GEOCHEMISTRY AND ENVIRONMENTAL SCIENCE ............. 15 X-ray absorption fine structure (XAFS) spectroscopy ......... 15 X-ray microprobe, spectromicroscopy, and microtomography methods ..................................................... 23 X-ray scattering ............................................ 26 X-ray standing wave methods ................................. 27 X-ray photoemission spectroscopy, X-ray photoelectron diffraction, and X-ray emission spectroscopy ................ 28 SR-based infrared spectroscopy .............................. 30 Comments on sample damage from high intensity synchrotron radiation ................................................... 30 WATER AND METAL IONS IN AQUEOUS SOLUTIONS ...................... 31 CHEMISTRY AT MINERAL/AQUEOUS SOLUTION INTERFACES ............... 35 The initial reaction of water with clean metal oxide surfaces .................................................... 36 The structure of hydrated mineral surfaces .................. 38 In situ X-ray reflectivity studies of water structure at mineral/water interfaces .................................... 40 Comments on the structure and properties of water at solid/aqueous solution interfaces ........................... 41 XSW and X-ray reflectivity studies of adions and the EDL at mineral/water interfaces ................................. 43 Sorption reactions of aqueous metal ions with mineral surfaces - the XAFS perspective ............................. 45 EXAFS studies of metal ion coordination sites in bacterial and fungal cell walls ....................................... 46 Heavy metal speciation and catalysis at biofilm/mineral interfaces .................................................. 47 Examples of SR-based studies of complex environmental samples ..................................................... 51 FUTURE SR DEVELOPMENTS AND THEIR POTENTIAL IMPACT ON RESEARCH IN LOW TEMPERATURE GEOCHEMISTRY AND ENVIRONMENTAL SCIENCE ...... 64 ACKNOWLEDGMENTS ................................................ 69 REFERENCES ..................................................... 69 APPENDIX - TABLES 1 AND 2 ..................................... 107 2 A Brief Overview of Synchrotron Radiation T.K. Sham and Mark L. Rivers ABSTRACT ...................................................... 117 INTRODUCTION .................................................. 117 How does an electron emit light? ........................... 118 Figures of merit ........................................... 120 SYNCHROTRON STORAGE RINGS ..................................... 120 History of synchrotron radiation ........................... 123 Bending magnet radiation ................................... 128 INSERTION DEVICES ............................................. 130 Wiggler radiation .......................................... 130 Undulator radiation ........................................ 131 Important storage ring parameters .......................... 134 BEAMLINE AND EXPERIMENTAL STATIONS ............................ 139 Beamline design ............................................ 139 Synchrotron beamlines: general ............................. 139 OTHER CHARACTERISTICS OF SYNCHROTRON RADIATION ................ 140 Polarization ............................................... 140 Time structure ............................................. 142 THE INTERACTION OF LIGHT WITH MATTER .......................... 142 Scattering ................................................. 142 Absorption ................................................. 143 The overall picture ........................................ 145 ACKNOWLEDGMENTS ............................................... 147 REFERENCES .................................................... 147 3 X-ray Reflectivity as a Probe of Mineral-Fluid Interfaces: A User Guide Paul A. Fenter INTRODUCTION .................................................. 149 Review of relevant literature .............................. 150 ELEMENTARY SCATTERING THEORY: INTERFERENCE AND BRAGG'S LAW .... 151 Interference and reciprocal space .......................... 151 SCATTERING INTENSITY AND REFLECTIVITY ......................... 162 Intrinsic factors .......................................... 164 Sample- and cell-dependent factors ......................... 167 Spectrometer-dependent factors ............................. 172 Absolute specular reflectivity ............................. 176 PRACTICAL ISSUES .............................................. 177 Measuring reflectivity signals ............................. 177 Surface inhomogeneities .................................... 182 The spatial resolution of a CTR, or how many data are needed? .................................................... 183 EXAMPLES ...................................................... 185 Deconstructing a CTR: the orthoclase(001)-water interface .................................................. 185 Probing large molecule adsorption: stearate monolayers on calcite .................................................... 195 Water structure near the muscovite-water interface ......... 198 DEFECT STRUCTURES AT BARITE-WATER INTERFACES ............... 201 Observing dissolution reactions in real-time ............... 204 SUMMARY, CONCLUSIONS, AND PERSPECTIVES ........................ 211 Non-specular reflectivity .................................. 211 Anomalous reflectivity ..................................... 212 Microbeams ................................................. 212 Temporal resolution ........................................ 212 Direct methods ............................................. 213 ACKNOWLEDGMENTS ............................................... 213 REFERENCES .................................................... 213 APPENDIX 1 COMPLEX NUMBERS .................................... 217 APPENDIX 2 TERMINOLOGY, SYMBOLS AND DEFINITIONS ............... 217 APPENDIX 3 STRUCTURE FACTORS .................................. 219 APPENDIX 4 SPECTROMETER ANGLES AND RECIPROCAL SPACE ........... 220 4 X-ray Standing Wave Studies of Minerals and Mineral Surfaces: Principles and Applications Michael J. Bedzyk and Likwan Cheng INTRODUCTION .................................................. 221 X-RAY STANDING WAVES BY BRAGG DIFFRACTION FROM A SINGLE CRYSTAL .............................................. 222 The X-ray standing wave field .............................. 222 XSW-induced yields from photo-effect ....................... 227 Extinction effect and evanescent-wave emission ............. 228 Structure determination using coherent fraction and coherent position .......................................... 229 "Ideal crystals" vs. "real crystals" in Bragg diffraction XSW ........................................................ 232 The special case of back-reflection XSW .................... 233 The special case of thin-film Bragg diffraction XSW ........ 234 X-RAY STANDING WAVES GENERATED BY TOTAL EXTERNAL REFLECTION ... 235 XSW generated by total external reflection ................. 235 X-RAY STANDING WAVES FROM LAYERED SYNTHETIC MICROSTRUCTURES ... 238 EXPERIMENTAL CONSIDERATIONS OF X-RAY STANDING WAVE MEASUREMENTS .................................................. 238 XSW setup at the Advanced Photon Source .................... 239 The postmonochromator for XSW experiments .................. 239 LOCATING IMPURITY LATTICE SITES IN MINERALS WITH X-RAY STANDING WAVES ................................................ 243 Impurities in minerals ..................................... 243 Mn2+ lattice sites in calcite .............................. 243 Phengitic ion sites in muscovite ........................... 244 ION ADSORPTION STRUCTURES AT MINERAL SURFACES WITH X-RAY STANDING WAVES ................................................ 244 Ion adsorption at the calcite-water interface .............. 244 Cation adsorption on calcite ............................... 245 Molecular anion adsorption on calcite ...................... 250 Uranyl adsorption on calcite ............................... 251 PROBING METAL DISTRIBUTIONS IN ORGANIC FILMS WITH X-RAY STANDING WAVES ................................................ 252 Metal in organic films at mineral surfaces ................. 252 Zn2+ in a Langmuir-Blodgett multilayer ..................... 253 Br- location and ordering in self-assembled multilayers .... 254 Pb2+ partitioning at biofilm-oxide interfaces .............. 255 PROFILING THE ELECTRICAL DOUBLE LAYER STRUCTURE WITH X-RAY STANDING WAVES .......................................... 256 The electrical double layer at the solid-water interface ... 256 The diffuse layer profiled with long-period X-ray standing waves ............................................. 257 The condensed layer measured with Bragg-diffraction X-ray standing waves ............................................. 261 CONCLUSION .................................................... 262 ACKNOWLEDGMENTS ............................................... 263 REFERENCES .................................................... 263 5 Grazing-incidence X-ray Absorption and Emission Spectroscopy Glenn A. Waychunas INTRODUCTION .................................................. 267 Grazing-incidence X-ray methods ............................ 267 DEFINITIONS ................................................... 268 EARLY STUDIES AND QUANTITATIVE ISSUES ......................... 272 GI X-RAY ABSORPTION SPECTROSCOPY .............................. 272 Geometric considerations ................................... 272 Surface roughness and related effects ...................... 278 Fresnel analysis of total external reflection and sensitivity factors ........................................ 281 SAMPLE CELLS, SURFACE LIQUIDS AND COVER MEMBRANES ............. 283 Sample heating and damage .................................. 287 Surface symmetry and polarized measurements ................ 289 SELF ABSORPTION AND CONTAMINATION PROBLEMS .................... 291 DETECTOR LIMITATIONS .......................................... 291 Examples of GI X-ray absorption spectroscopy ............... 292 EXPERIMENTS AT SOFT X-RAY ENERGIES; ORGANICS ON SURFACES ...... 299 TOTAL REFLECTION X-RAY ANALYSIS (TRXRF) SURFACE CHEMISTRY ANALYSIS ...................................................... 300 Comparison with other methods .............................. 301 Environmental Studies ...................................... 303 Cape Cod aquifer synchrotron TRXRF measurements ............ 305 Depth selective analysis ................................... 308 GRAZING-EXIT X-RAY FLUORESCENCE SPECTROSCOPY (GEXRF) .......... 308 OPPORTUNITIES FOR FUTURE WORK .............................. 308 Redox reactions at surfaces ................................ 308 Lower Z species GI-XAS ..................................... 309 Defects on surfaces ........................................ 310 TRXRF analysis ............................................. 310 CONCLUSIONS ................................................... 310 ACKNOWLEDGMENTS ............................................... 311 REFERENCES .................................................... 311 6 Applications of Storage Ring Infrared Spectromicroscopy and Reflection-Absorption Spectroscopy to Geochemistry and Environmental Science Carol J. Hirschmugl ABSTRACT ...................................................... 317 INTRODUCTION .................................................. 317 INTERACTIONS BETWEEN LIGHT AND MATTER ......................... 319 Dielectric functions, complex indices of refraction and Maxwell's equations ........................................ 319 IR absorption spectroscopy ................................. 320 INFRARED SYNCHROTRON RADIATION PROPERTIES AND CONSIDERATIONS ................................................ 322 IRSR power ................................................. 322 IRSR brightness ............................................ 322 IRSR polarization and pulsed patterns ...................... 323 Conservation of brightness: storage ring emittance and experiment throughput ...................................... 323 Diffraction limited infrared imaging ....................... 326 Spectral reproducibility and signal-to-noise ............... 326 Status of IRSR facilities .................................. 327 APPLICATIONS: IRSR SPECTROMICROSCOPY .......................... 327 Single cell chemistry ...................................... 328 Spatially resolved chemistry in inhomogeneous materials .... 332 APPLICATIONS: VIBRATIONAL SPECTROSCOPY AT SURFACES ............ 336 Fe3O4-water interface ...................................... 337 SYNOPSIS ...................................................... 338 ACKNOWLEDGMENTS ............................................... 338 REFERENCES .................................................... 338 7 Quantitative Speciation of Heavy Metals in Soils and Sediments by Synchrotron X-ray Techniques Alain Manceau, Matthew A. Marcus, and Nobumichi Tamura INTRODUCTION .................................................. 341 Chemical forms of metals in soils .......................... 342 ANALYTICAL APPROACH ........................................... 348 Electrons vs. X-rays ....................................... 348 Synchrotron-based X-ray radiation fluorescence (SXRF) ...... 350 X-ray diffraction (XRD) .................................... 359 Extended X-ray absorption fine structure (EXAFS) spectroscopy ............................................... 365 Tips, tricks and cautions for hard X-ray microprobe users ...................................................... 386 APPLICATION TO HEAVY METAL SPECIATION ......................... 398 Speciation of metal(loid)s in the contaminated environment ................................................ 398 Speciation of trace metal(loid)s in uncontaminated soils ... 409 CONCLUDING REMARKS ............................................ 419 ACKNOWLEDGMENTS ............................................... 420 REFERENCES .................................................... 420 8 Microfluorescence and Microtomography Analyses of Heterogeneous Earth and Environmental Materials Stephen R. Sutton, Paul M. Bertsch, Matthew Newville, Mark Rivers, Antonio Lanzirotti and Peter Eng INTRODUCTION .................................................. 429 X-RAY MICROPROBE ANALYSIS ..................................... 430 Hard X-ray microprobes in the U.S .......................... 430 X-ray fluorescence process ................................. 431 Synchrotron X-ray microprobe instrumentation ............... 432 Sample preparation ......................................... 436 Choice of excitation energy ................................ 436 Detector optimization ...................................... 437 Data collection ............................................ 437 Data analysis .............................................. 439 Current capabilities ....................................... 446 MICROTOMOGRAPHY ............................................... 446 Microtomography facilities in the US ....................... 446 Basic principles ........................................... 446 Instrumentation ............................................ 447 Sample preparation and experiment setup .................... 448 Data collection ............................................ 449 Data processing ............................................ 450 Current capabilities ....................................... 451 APPLICATIONS .................................................. 451 Microbial processes and biomineralization .................. 452 Plant rhizosphere processes ................................ 455 Biota collected from contaminated environments ............. 458 Vadose zone processes ...................................... 464 Fluid transport ............................................ 468 Hydrothermal fluids and seawater ........................... 470 Extraterrestrial materials ................................. 472 FUTURE DIRECTIONS ............................................. 477 ACKNOWLEDGMENTS ............................................... 477 REFERENCES .................................................... 478 9 Soft X-ray Spectroscopy and Spectromicroscopy Studies of Organic Molecules in the Environment Satish С.В. Myneni INTRODUCTION .................................................. 485 SOFT X-RAY SPECTROSCOPY & CHEMICAL BONDING IN ORGANIC MOLECULES ..................................................... 486 INSTRUMENTATION FOR STUDYING ORGANIC MOLECULES ................ 490 Probing the Is electronic transitions of C, N and O ........ 492 Probing the 1 s electronic transitions of P, S and Cl ...... 494 Detection limits ........................................... 495 Soft X-ray spectromicroscopy facilities .................... 495 FUNCTIONAL GROUP CHEMISTRY OF ORGANIC MOLECULES ............... 498 С functional groups ........................................ 498 N functional groups ........................................ 504 O functional groups ........................................ 515 P functional groups ........................................ 515 S functional groups ........................................ 520 Cl functional groups ....................................... 533 APPLICATIONS OF SPECTROMICROSCOPY FOR STUDIES ON ORGANIC MOLECULE AGGREGATES ........................................... 545 SUMMARY AND FUTURE DIRECTIONS ................................. 549 ACKNOWLEDGMENTS ............................................... 549 REFERENCES .................................................... 549 APPENDIX-TABLES 1-5 ........................................... 559