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CMS WORKSHOP LECTURES

Volume 19

ADVANCED APPLICATIONSOF SYNCHROTRON

RADIATION IN CLAY SCIENCE

THE CLAY MINERALS SOCIETY

Joseph W. Stucki, Series Editor and Editor in Chief

University of Illinois

Urbana, IL 61801-4798, USA

Glenn A. Waychunas, Volume Editor

Earth Sciences Division, Lawrence Berkeley National Laboratory,

Berkley, CA 94720, USA

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CMS WORKSHOP LECTURES

VOLUME 19

ADVANCED APPLICATIONS OF SYNCHROTRON

RADIATION IN CLAY SCIENCE

Organized By

Glenn A. Waychunas

Lawrence Berkeley National Laboratory

Lectures Presented By

Glenn A. Waychunas, Earth Sciences Division, Lawrence Berkeley National Laboratory, One

Cyclotron Road, Berkeley 94720, California, USA

John B. Parise, Geosciences Department and Department of Chemistry, SUNY at Stony Brook,

Stony Brook, NY 11794, USA

Valeri Petkov, Department of Physics, Central Michigan University Dow 203, Mt. Pleasant MI-

48859, USA

F. Marc Michel, Department of Geosciences, Virginia Tech, Blacksburg, Virginia 24061 USA

Mark L. Rivers, Department of Geophysical Sciences and Center for Advanced Radiation

Sources, University of Chicago, Building 434A, Argonne National Laboratory, 9700 South

Cass Avenue, Lemont, IL 60439, USA

Matthew Newville, Center for Advanced Radiation Sources, University of Chicago, Chicago, Illi-

nois, USA

Antonio Lanzirotti, The University of Chicago – GeoSoilEnviroCARS, 9700 S. Cass Ave., Bldg.

434A, Argonne, IL 60439, USA

Satish C.B. Myneni, Department of Geosciences, Princeton University, Princeton, NJ 08544, USA

Published by

The Clay Minerals Society

3635 Concorde Pkwy Suite 500

Chantilly, VA 20151-1125, USA


Copyright # 2014 The Clay Minerals Society

All rights reserved. No part of this book may be reproduced by any mechanical, photographic, or

electronic process or in the form of photographic recording, nor may it be stored in a retrieval

system, transmitted, or otherwise copied for public or private use without written permission

from the publisher. For information on this and other volumes in the CMS Workshop Lectures

Series, write The Clay Minerals Society, 3635 Concorde Pkwy Suite 500, Chantilly, VA

20151-1125 USA or go to www.clays.org.

Citations of articles in this volume are properly referenced as follows:

Author, X.Y. (2014) Title. Pp. xx–xx in: Advanced Applications of Synchrotron Radiation in

Clay Science. CMS Workshop Lectures, 19 (G.A. Waychunas, editor). The Clay Minerals

Society, Chantilly, Virginia, USA.

Library of Congress Catalog Number

ISBN - 978-1-881208-40-2


THE CLAY MINERALS SOCIETY

The Clay Minerals Society (CMS) was organized in 1963 to stimulate research and to

disseminate information relating to all aspects of the science and technology of clays

and other fine-grained minerals. It sponsors an annual Clay Conference where research

and invited papers are presented in technical sessions and special symposia. Field trips

are organized to important occurrences of clays in regions near the Conference locations

and to industrial sites of clay production and application. In conjunction with its annual

meetings, workshops are held on technical subjects of interest to clay researchers and

technologists. CMS publishes Clays and Clay Minerals, which is the leading inter-

national journal in the field of clay science. In this journal are presented the latest scien-

tific investigations in all areas of the field and from all parts of the world, along with

timely review articles and announcements of new publications on clays and other

fine-grained minerals.

CMS also sponsors the Source Clays Repository, which is now well established as the

provider of clay samples to a plethora of research groups world wide and to teachers of

clay science. It also offers other clay-related publications to its members at a discount

over publisher’s list prices.

Its multi-disciplinary membership includes agronomists, microbiologists, surface

chemists, physicists, geologists, mineralogists, geochemists, material scientists, soil

scientists, crystallographers, sedimentologists, economic geologists, colloid chemists,

ceramicists, rheologists, petroleum engineers, and geotechnical engineers, thereby offer-

ing members the opportunity to exchange ideas and results with fellow researchers

having widely different backgrounds and expertise.

For information on joining the Society and subscribing to Clays and Clay Minerals,

contact:

The Clay Minerals Society

Society Office

3635 Concorde Pkwy Suite 500

Chantilly, VA 20151-1125

Phone: (703) 652-9960

FAX: (703) 652-9951

www.clays.org

E-mail: [email protected]


Preface

The 2013 Workshop on Advanced Applications of Synchrotron Radiation in Clay

Science was held on Saturday, October 5, 2013 in conjunction with the 50th anniversary

meeting of The Clay Minerals Society at the University of Illinois at Urbana-

Champaign. The one-day workshop was attended by about 50 participants, and there

was active discussion of many of the topics with the nine speakers, eight of whom pro-

vided their lectures in the form of pre-publication notes at the workshop. The lecturers

represented the majority of topics in synchrotron science that are of use to the clay

science community, and it is notable that most of them have been responsible for signi-

ficant development of these methods during their own research careers. The final

versions of these lectures are presented in this volume, and serve not only as significant

statements on the state of these applications, but also as useful primers to potential new

users of synchrotron facilities.

The introductory chapter by Waychunas gives a bit of history on the development of

synchrotron X-ray sources, and explains the important aspects of electron and X-ray

beam characteristics, insertion devices, X-ray beam line optics, and synchrotron oper-

ation. There is also a discussion of the procedure for gaining time at synchrotron

sources, and considerations for appropriate beam line selection.

The chapter by Parise et al. covers many of the considerations for use of synchrotron

sources for powder diffraction and scattering experiments. It includes wide angle X-ray

scattering (WAXS), small angle X-ray scattering (SAXS), and pair distribution function

(PDF) methods, and also discusses in situ and time-resolved studies using these

approaches. Basic scattering theory and data analysis is described with several examples

from a number of past studies.

The chapter by Petkov focuses on the use of PDF methods to gain atomic-scale struc-

tural information from highly disordered minerals, and includes a workup of theory,

experimental considerations, data analysis and practical concerns. PDF analysis of dis-

ordered manganese oxides is treated in detail.

The chapter by Michel describes detailed synchrotron studies of natural and synthetic

ferrihydrite by synchrotron total scattering methods (PDF plus Bragg analysis). This is

recent work concerning a nanoparticle mineral phase the stability field and structure of

which are still in dispute, but where there has been much clarification in recent years due

to the work of Michel and colleagues.

The chapter by Rivers is an excellent introduction to synchrotron-based microtomo-

graphy for earth science applications, and includes a wide range of interesting examples.

Rivers and colleagues have operated a premier microtomography facility at the APS for

many years, and have been responsible for many advances using this methodology.

The chapter by Newville on X-ray spectroscopy covers an introduction to EXAFS

theory and describes complete data analysis, as well as experimental concerns. An

additional section treats interpretation of XANES spectra for extracting valence and

coordination information. Newville has developed extensive and widely used software

for EXAFS analysis.

The chapter by Lanzirotti describes applications of the X-ray microprobe to minera-

logical problems, and includes a discussion of instrumentation and experimental


considerations. Examples include microprobe analysis of clay gels, ferromanganese

nodules, and contaminated Hanford sediments. High-resolution mapping of valence

state and chemistry in microprobe samples is discussed.

The chapter by Myneni et al. describes the use of scanning transmission X-ray

microscopy (STXM) and soft X-ray energies to explore the structure, chemistry and

valences of elements in clay minerals, including determining interactions with

organic species and iron oxides. Myneni has greatly enlarged investigations of soils

and sediments using this technology, particularly with respect to organic–mineral

interactions.

G. WaychunasWorkshop organizers

VII


Contents

Chapter 1. Introduction to synchrotron radiation ....................................................1

by GLENN A. WAYCHUNAS

1. X-ray sources – short history ....................................................................................1

1.1 Vacuum-tube high-voltage sources .................................................................... 1

1.2 First-generation synchrotrons and spectrum ...................................................... 2

1.3 Wigglers, undulators, and their spectrum .......................................................... 5

2. Beam parameters ......................................................................................................11

2.1 Beam brightness and flux ................................................................................ 11

2.2 Polarization ...................................................................................................... 11

2.3 Beam coherency .............................................................................................. 11

2.4 Pulse structure and modes of operation .......................................................... 13

3. New lattices and FELs (LCLS)................................................................................14

3.1 Lattices.............................................................................................................. 14

3.2 FELs.................................................................................................................. 15

4. Synchrotron operation considerations ......................................................................15

4.1 Injection ............................................................................................................ 15

4.2 Long-term beam stability ................................................................................ 16

5. Important beamline elements ..................................................................................16

5.1 Monochromators and mirrors .......................................................................... 16

5.2 Zone-plate optics .............................................................................................. 20

6. Types of experiments (and capabilities) ..................................................................21

6.1 X-ray scattering ................................................................................................ 21

6.1.1 Powder diffraction (high resolution) ...................................................... 21

6.1.2 Diffuse scattering from poorly crystalline materials,

PDF measurements .................................................................................. 22

6.1.3 Single-crystal diffraction (small size) .................................................... 22

6.1.4 Small-angle X-ray scattering (SAXS) (flux and brilliance) .................. 22

6.1.5 Grazing Incidence diffraction and reflectivity

(brilliance)................................................................................................ 22

6.2 X-ray spectroscopy .......................................................................................... 23

6.2.1 X-ray absorption spectroscopy ................................................................ 23

6.2.2 X-ray microprobe (X-ray emission)........................................................ 24

6.2.3 Grazing-incidence X-ray fluorescence and X-ray standing wave

approaches .............................................................................................. 24

6.2.4 X-ray spectromicroscopy and nanoprobe................................................ 24

6.3 Imaging modes ................................................................................................ 27

6.3.1 Phase contrast .......................................................................................... 27

6.3.2 X-ray tomography.................................................................................... 28

7. Sources in the US and access ..................................................................................28

7.1 The US DOE sources ...................................................................................... 28

7.2 User support (scientists and technologists) ...................................................... 29

7.3 Choosing beamlines for experiments .............................................................. 29


Acknowledgements........................................................................................................30

References......................................................................................................................31

Chapter 2. Synchrotron powder diffraction methods andrefinement techniques..................................................................................................33

by JOHN B. PARISE, WILLIAM R. WOERNER and REINHARD B. NEDER

1. Introduction and historical perspective ..................................................................33

2. Coherent elastic scattering ....................................................................................37

3. Small-angle scattering ............................................................................................40

4. Time-resolved SAS ................................................................................................43

5. WAXS from geo-nanoparticles ..............................................................................44

6. Prospects for whole nanoparticle refinement ........................................................47

7. Sample environments ............................................................................................52

8. Versatile high-temperature sample stages..............................................................52

9. Cells for studies of fluid–solid interactions ..........................................................53

10. Acoustic levitation..................................................................................................56

11. Prospects for in situ and time-resolved studies ....................................................57


References......................................................................................................................60

Chapter 3. Atomic-scale structure of substantially disordered minerals

by high-energy X-ray diffraction and atomic pair distributionfunction analysis ..........................................................................................................69

by VALERI PETKOV

1. Introduction ..............................................................................................................69

2. Principles of the atomic PDF method......................................................................71

3. Practical aspects of high-energy XRD aimed at

atomic PDF Analysis ................................................................................................73

3.1. Source of X-ray radiation................................................................................ 73

3.2. XRD data statistics and collection time.......................................................... 74

3.3. Experimental set-up (Q-space) resolution ...................................................... 75

3.4. Background scattering treatment .................................................................... 76

3.5. Sample-related ‘unwanted’ scattering ............................................................ 77

3.6. High-energy XRD data processing into atomic PDFs.................................... 78

4. Structural information that can be extracted from

atomic PDFs..............................................................................................................78

5. Conclusions ..............................................................................................................86


References......................................................................................................................86

IX


Chapter 4. Total scattering studies of natural and synthetic ferrihydrite............89by F. MARC MICHEL

1. Introduction ..............................................................................................................89

2. Common occurrences and importance of ferrihydrite ............................................91

3. Total scattering and the pair distribution function ..................................................92

3.1. Total scattering methodology.......................................................................... 92

3.2. The pair distribution function.......................................................................... 93

3.3. Other terms and concepts ................................................................................ 95

3.3.1. Coherent scattering domain size ............................................................ 95

3.3.2. Short-, intermediate-, and long-range order .......................................... 98

3.3.3. Extracting information from the PDF: Real-space fitting .................. 100

4. Studies of pure synthetic ferrihydrite ....................................................................101

4.1. Laboratory XRD-based scattering ................................................................ 101

4.2. Synchrotron total scattering .......................................................................... 103

4.2.1. Laboratory ferrihydrite ...................................................................... 103

4.2.2. Ferrihydrite transformations .............................................................. 106

4.2.3. Ferritin-derived ferrihydrite................................................................ 112

4.3. Neutron total scattering ................................................................................ 113

5. Studies of impure synthetic ferrihydrite ................................................................115

5.1. Mixed CrxFe1 – x-(oxy)hydroxides.................................................................. 116

5.2. Aluminous ferrihydrite .................................................................................. 118

5.3. Fe3þ oxide/silica co-precipitates .................................................................. 120

5.4. Arsenious ferrihydrite.................................................................................... 121

5.5. Arsenate-sorbed ferrihydrite.......................................................................... 122

6. Recent studies and new data for natural ferrihydrite ............................................123

7. Summary and future work......................................................................................129

Acknowledgements......................................................................................................131

References....................................................................................................................131

Chapter 5. Introduction to computed microtomography and

applications in Earth science....................................................................................137

by MARK L. RIVERS

1. Introduction to computed tomography ..................................................................137

1.1. Overview........................................................................................................ 137

1.2. Microtomography .......................................................................................... 138

1.3. Laboratory X-ray sources .............................................................................. 140

1.4. Synchrotron X-ray sources ............................................................................ 140

1.5. Detectors ........................................................................................................ 141

1.6. Computers ...................................................................................................... 142

2. Absorption tomography ..........................................................................................142

2.1. X-ray energy and sample size ...................................................................... 142

2.2. Data collection .............................................................................................. 143

X


2.3. Data normalization ........................................................................................ 145

2.4. Sinograms ...................................................................................................... 146

2.5. Reconstruction .............................................................................................. 147

2.6. Spatial resolution .......................................................................................... 151

2.6.1. Source size .......................................................................................... 151

2.6.2. Sample and detector size.................................................................... 152

2.6.3. Visible-light diffraction limit ............................................................ 153

2.6.4. Scintillator limits ................................................................................ 153

2.6.5. Rotation stage limits .......................................................................... 153

2.7. Contrast resolution ........................................................................................ 154

3. Differential absorption tomography ......................................................................154

4. Phase-constrast tomography ..................................................................................155

5. Fluorescence tomography ......................................................................................158

6. Diffraction tomography ..........................................................................................160

7. Applications of tomography in Earth sciences ......................................................162

7.1. Fluids in porous media .................................................................................. 162

7.2. Soils................................................................................................................ 163

7.3. Other applications.......................................................................................... 163

Acknowledgments ......................................................................................................164

References....................................................................................................................164

Chapter 6. X-ray absorption fine-structure spectroscopy ....................................167

by MATTHEW NEWVILLE

1. Introduction ............................................................................................................167

2. X-ray absorption and fluorescence ........................................................................169

3. A simple theoretical description of XAFS ............................................................174

3.1. The EXAFS equation .................................................................................... 176

4. XAFS measurements: transmission and fluorescence............................................180

4.1. Transmission XAFS measurements .............................................................. 183

4.2. Fluorescence XAFS measurements .............................................................. 184

4.2.1. Dead time............................................................................................ 185

4.2.2. Complicated ........................................................................................ 185

5. XAFS data reduction ..............................................................................................186

5.1. Pre-edge subtraction and normalization........................................................ 187

5.2. Background subtraction ................................................................................ 189

5.3. EXAFS Fourier transforms............................................................................ 190

6. XAFS data modeling ..............................................................................................193

6.1. Running and using FEFF for EXAFS calculations...................................... 193

6.2. First-shell fitting ............................................................................................ 194

6.3. Second-shell fitting ........................................................................................ 196

7. Interpretation of XANES........................................................................................197

References....................................................................................................................200

XI


Chapter 7. Application of hard X-ray microprobe methods toclay-rich materials ....................................................................................................203

by ANTONIO LANZIROTTI

1. Introduction ............................................................................................................203

2. Overview of instrumentation..................................................................................204

2.1. X-ray fluorescence ........................................................................................ 209

2.2. Micro-focused X-ray absorption spectroscopy ............................................ 216

2.3. Micro-focused X-ray diffraction .................................................................. 220

3. Examples ................................................................................................................222

3.1. Characterizing geosynthetic clay liners ........................................................ 222

3.2. Uranium speciation in contaminated Hanford sediments ............................ 223

3.3. Nickel sequestration in soil ferromanganese nodules .................................. 225

3.4. Direct visualization of oriented mesostructures in clay gels........................ 225

3.5. Strontium speciation during reaction of kaolinite with simulated

tank-waste leachate........................................................................................ 226


References....................................................................................................................228

Chapter 8. Applications of scanning transmission X-ray microscopy in

studying clays and their chemical interactions ......................................................231by SATISH C.B. MYNENI, BHOOPESH MISHRA, MICHAEL B. HAY

1. Introduction ............................................................................................................231

2. Scanning transmission X-ray microscopy: introduction

and instrumentation details ....................................................................................232

2.1. Detection limits.............................................................................................. 235

2.2. Imaging of samples ...................................................................................... 236

2.3. Limitations of STXM .................................................................................... 236

3. Applications of STXM in studies of clay minerals ..............................................237

3.1. Detection of clay minerals using STXM ...................................................... 237

3.2 Structural evaluation of clay minerals using STXM and

Al-XANES...................................................................................................... 238

3.3. Sorption of Al on mineral surfaces and neoformation

of clays .......................................................................................................... 241

4. Case studies of STXM on inorganic colloids ........................................................244

4.1. STXM studies of inorganic colloids and biominerals .................................. 244

5. STXM studies on organic colloids ........................................................................250

5.1. Mapping and detecting organic colloids using STXM ................................ 250

5.2. STXM studies on the functional group composition of

organic molecules in colloids........................................................................ 251

5.3. STXM studies on the chemical characteristics of biofilms

and bacterial cell membranes ........................................................................ 252

XII


5.4. Limitations of STXM for organic molecule studies .................................... 254

5.5. Distribution of metals in bacterial and planktonic suspensions .................. 255

6. Summary and future directions ..............................................................................257


References....................................................................................................................258

XIII


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