Iron Oxides -  - E-Book

Iron Oxides E-Book

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Compiling all the information available on the topic, this ready reference covers all important aspects of Iron Oxides. Following a preliminary overview chapter discussing iron oxide minerals along with their unique structures and properties, the text goes on to deal with the formation and transformation of Iron Oxides, covering geological, synthetic, and biological formation, as well as various physicochemical aspects. Subsequent chapters are devoted to characterization techniques, with a special focus on X-ray-based methods, magnetic measurements, and electron microscopy alongside such traditional methods as IR/Raman and Mössbauer spectroscopy. The final section mainly concerns exciting new applications of magnetic Iron Oxides, for example in medicine as microswimmers or as water filtration systems, while more conventional uses as pigments or in biology for magnetoreception illustrate the full potential. A must-read for anyone working in the field.

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Table of Contents

Cover

Related Titles

Title Page

Copyright

List of Contributors

Foreword

Preface

Chapter 1: Introduction

1.1 Iron Oxides: From Nature to Applications

1.2 A Very Brief Overview of the Iron Oxides and How They Found Names

References

Part I: Formation, Transformation

Chapter 2: Geological Occurrences and Relevance of Iron Oxides

2.1 Introduction

2.2 Elemental Iron: From the Universe to the Earth

2.3 Residency of Elemental Iron on Earth

2.4 Mineral Forms of Iron Oxides

2.5 Occurrence and Geological Relevance of Iron Oxides

2.6 Iron Oxides in Continental Dust Deposits

2.7 Concluding Remarks

Acknowledgments

References

Chapter 3: Reductive Dissolution and Reactivity of Ferric (Hydr)oxides: New Insights and Implications for Environmental Redox Processes

3.1 Introduction

3.2 The Classical Perspective on Reductive Dissolution

3.3 Electron Transfer at Ferric (Hydr)oxides Surfaces: The Role of Fe(II)

3.4 Energetics at the Ferric (Hydr)oxide Interface

3.5 Rate Control: Surface versus Structural Properties

3.6 Interaction between Dissolved Sulfide and Ferric Hydroxides

3.7 Implications

References

Chapter 4: Formation and Transformation of Iron-Bearing Minerals by Iron(II)-Oxidizing and Iron(III)-Reducing Bacteria

4.1 Introduction

4.2 Biomineralization of Iron through Microbial Fe(II) Oxidation

4.3 Iron(III) Minerals: Electron Acceptors for Iron-Reducing Bacteria

4.4 Specific Properties of Iron Biominerals

4.5 Microbial Fe Redox Cycling: Past, Present, and Future

4.6 Conclusion

References

Chapter 5: Controlled Biomineralization of Magnetite in Bacteria

5.1 Introduction

5.2 Magnetotactic Bacteria

5.3 Organization and Role of Magnetosomes

5.4 Biomineralization of Magnetosomes

5.5 Mineral Phase of Magnetosomes

Acknowledgments

References

Chapter 6: Ferritin Iron Mineralization and Storage: From Structure to Function

6.1 Introduction

6.2 Basic Structure of Ferritins

6.3 Iron Storage and Mineralization

6.4 NMR and MRI Studies of the Ferritin Iron Core

6.5 Magnetoferritin

6.6 Ferritin as a Biotechnological Tool

6.7 Protocol Annexes

References

Chapter 7: Iron Oxides in the Human Brain

7.1 Introduction

7.2 Iron Oxides Observed in the Human Brain

7.3 Properties of Iron Oxides in the Brain

7.4 Stored and Sequestered Iron Oxide in the Human Brain

7.5 Methods to Detect Iron Oxides in the Brain

7.6 Tools and Treatments: Manipulating Iron Oxides in the Brain

7.7 Concluding Remarks

Acknowledgments

References

Chapter 8: The Chiton Radula: A Model System for Versatile Use of Iron Oxides*

8.1 Functional Anatomy of the Mollusk Radula

8.2 Development of the Radula: Organic Matrix

8.3 The Discovery of Biominerals in the Radula

8.4 The Microarchitecture of Chiton Radula Teeth

8.5 Development of the Chiton Radula: Stages of Biomineralization

8.6 Development of the Radula: Biological Control

8.7 Role of Acidic Macromolecules in the Insoluble Organic Matrix

8.8 Soluble Organic Matrix Composition

8.9 Selective Deposition of Ferrihydrite in Stage II

8.10 Conversion of Ferrihydrite to Magnetite in Stage III

8.11 Phase Transformations in Stage IV

8.12 Final Functional Architecture

8.13 Concluding Remarks

Acknowledgments

References

Chapter 9: Mineralization of Goethite in Limpet Radular Teeth

9.1 Introduction

9.2 Structure, Properties, and Function of the Limpet Radula

9.3 Goethite Produced in the Laboratory

9.4 Goethite Produced in Limpets

9.5 Conclusion

References

Chapter 10: Synthetic Formation of Iron Oxides

10.1 Introduction

10.2 Iron Oxide and Oxyhydroxide from Aqueous Ferric Solution

10.3 Iron Oxide and Oxyhydroxide from Aqueous Ferrous Solution

10.4 Iron Oxide Synthesis Using Microfluidic Process

References

Chapter 11: Oriented Attachment and Nonclassical Formation in Iron Oxides

11.1 Introduction

11.2 OA in Iron Oxides in the Literature

11.3 OA and Phase Transformation

11.4 Detection and Characterization of Growth by OA

11.5 Kinetics of Growth by OA

11.6 Thermodynamics

11.7 Morphology and Surface Chemistry

11.8 Forces Governing Assembly

11.9 Future Work

References

Chapter 12: Thermodynamics of Iron Oxides and Oxyhydroxides in Different Environments

12.1 Introduction

12.2 Magnetic Transformations

12.3 Polymorphic Transformations

12.4 Summary

References

Part II: Characterization Techniques

Chapter 13: Introduction to Standard Spectroscopic Methods: XRD, IR/Raman, and Mössbauer

13.1 Introduction

13.2 X-Ray Diffraction (XRD)

13.3 Vibrational Spectroscopy

13.4 Mössbauer Spectroscopy

Acknowledgments

References

Chapter 14: TEM and Associated Techniques

Common Abbreviations

14.1 Introduction

14.2 Nanoscale Analysis of Iron Oxides

14.3 Electron Holography

14.4 The Near

In Situ

Approach

14.5

In Situ

Analysis with a Liquid Cell

Acknowledgment

References

Chapter 15: Magnetic Measurements and Characterization

15.1 Introduction

15.2 Summary of Magnetic Properties of Iron Oxides and Iron Hydroxides

15.4 Remanent Magnetization

15.5 Usage of Magnetic Properties

15.6 Summary

References

Chapter 16: Total X-Ray Scattering and Small-Angle X-ray Scattering for Determining the Structures, Sizes, Shapes, and Aggregation Extents of Iron (Hydr)oxide Nanoparticles

16.1 Introduction

16.2 Determination of Particle Structures: Total X-Ray Scattering with PDF Analysis

16.3 Determination of Particle Sizes, Shapes, and Aggregation Extents: SAXS and GISAXS

16.4 Outlook

Acknowledgments

References

Chapter 17: X-Ray Absorption Fine Structure Spectroscopy in Fe Oxides and Oxyhydroxides

17.1 Brief Introduction to XAFS

17.2 XANES spectroscopy

17.3 EXAFS Spectroscopy

17.4 Conclusion and Perspectives

References

Part III: Applications

Chapter 18: Medical Applications of Iron Oxide Nanoparticles

18.1 Introduction

18.2 IONPs for Imaging

18.3 Magnetic Drug Targeting

18.4 IONPs and Tissue Engineering

18.5 Activation of IONPs with Time-Dependent Magnetic Fields

18.6 Life Cycle of IONPs

18.7 Conclusion

References

Chapter 19: Iron Nanoparticles for Water Treatment: Is the Future Free or Fixed?

19.1 Introduction

19.2 Why Iron?

19.3 INPs: A Versatile Material for Water Treatment

19.4 Operational Drivers for Water Treatment

19.5 Static Nanocomposites

19.6 What Is Holding Back Static Nanocomposites?

19.7 Conclusion

References

Chapter 20: Actuation of Iron Oxide-Based Nanostructures by External Magnetic Fields

20.1 Introduction

20.2 Nanomachines

20.3 Guided Self-Assembly

20.4 Conclusion

References

Chapter 21: Iron Oxide-Based Pigments and Their Use in History

21.1 Introduction

21.2 Chemical Composition and Properties of Iron Oxide-Based Pigments

21.3 Use of Iron Oxide-Based Pigments in History

21.4 Case Studies

References

Chapter 22: Magnetoreception and Magnetotaxis

22.1 Magnetoreception

22.2 Magnetotaxis

References

Index

End User License Agreement

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Guide

Cover

Table of Contents

Foreword

Preface

Begin Reading

List of Illustrations

Chapter 1: Introduction

Figure 1.1 Scheme of the iron oxide occurrences, sources, and applications.

Figure 1.2 Images of agricultural machine left in a field for decades (a). A closer view clearly shows the presence of rust (b).

Figure 1.3 The iron oxides at the core of a multidisciplinary interest.

Chapter 2: Geological Occurrences and Relevance of Iron Oxides

Figure 2.1 Phase diagrams of Fe: red from Tateno

et al.

[27] and green from Anzellini

et al.

[28], both based on static pressure diamond-anvil experiments and fast synchrotron X-ray diffraction. Anzellini

et al.

[28] reinterpret the solid–liquid boundary of Tateno

et al.

as the onset of fast recrystallization rather than melting. Black curve is the geotherm of Anzellini

et al.

[28]; gray area shows uncertainty. UM, upper mantle; IC, inner core; bcc, body-centered cubic (alpha) iron; fcc, face-centered cubic (gamma) iron; hcp, hexagonal close-packed (epsilon) iron.

Figure 2.2 The temperature–composition phase diagram of the iron–oxygen system at a total pressure of 1 atm.

Figure 2.3 Fe–Ti–O phase diagram at 1300 °C. TH, rhombohedral (hematite–ilmenite) solid solutions; TM, spinel (magnetite–ulvöspinel) solid solutions; wü, Fe

1−

x

O wüstite phase; Fe, metallic Fe phase. Vertical lines represent Ti/(Ti + Fe) of magnetite, ulvöspinel, and ilmenite end members.

Figure 2.4 Solid-phase oxygen buffers of the system Fe–Si–O. IW, iron–wüstite; WM, wüstite–magnetite; MH, magnetite–hematite; QIF, quartz–iron–fayalite; FMQ, fayalite–magnetite–quartz, plotted from equations in Myers and Eugster [59].

Figure 2.5 Eh–pH relation for goethite and ferrihydrite at a Fe

2+

activity of 10

−4

M l

−1

and at 100 kPa and 25 °C.

Figure 2.6 Common pathways of iron oxide formation and transformation.

Figure 2.7 Model phase diagram for a nanoparticle system where surface and bulk energy contributions to the total particle free energy change considerably with respect to one another as a function of particle size. For large crystallites the stable polymorph is α. With decreasing particle size the surface energy contribution increases to the point where the β polymorph, with lower surface energy per unit area, becomes favored. With further size reduction, eventually the β phase becomes unstable with respect to an amorphous structure having lower surface energy per unit area. All nanoparticles are metastable with respect to coarsening and adopting the alpha structure.

Chapter 3: Reductive Dissolution and Reactivity of Ferric (Hydr)oxides: New Insights and Implications for Environmental Redox Processes

Figure 3.1 Conceptual model of a redox-driven conveyor belt to explain electron movement from the aqueous Fe

2+

to bulk ferric (hydr)oxides and release to the solution at a separate site (Fe(II)-catalyzed recrystallization). Oxidation of Fe

2

and growth of new oxide at the left surface and reductive dissolution at the opposing surface of the mineral resembles an electron-carrying conveyor belt.

Figure 3.2 Scheme of the positions of energy levels at the interface of an n-type semiconductor (ferric (hydr)oxide) in contact with an aqueous redox couple transferring electrons to the ferric mineral. (Modified with permission from [45], copyright (2000) Mineralogical Society of America.)

E

c

and

E

V

are the positions of the conduction and valence band edges, respectively.

E

F

is the Fermi level.

E

ft

is the flatband potential.

V

H

denotes the potential drop in the Helmholtz layer.

E

redox

is the redox potential of the aqueous redox couple (cf. text for further explanations).

Figure 3.3 Dynamic processes following the reaction between sulfide (

c

= 10 mM) and goethite (

c

= 38.6 mM) (for details cf. text).

Figure 3.4 Dynamic processes following the reaction between sulfide (10 mM) and lepidocrocite as visualized by high-resolution TEM [22]. After 2 h (a) the lepidocrocite crystals are covered with a rim of FeS (mackinawite). After 72 h (b) the mackinawite rim is slightly corrugated and an amorphous area forms between the grains which consists of Fe and S with variable stoichiometry (arrow). After 168 h pyrite starts to form (arrow in (c)) while only relicts of mackinawite can be found. At 336 h, pyrite grains (arrow in (d)) with a diameter of 200–500 nm are present.

Figure 3.5 Temporal change of sulfur mass balance calculated with Eq. (3.7) for a series of experiments in which the ratio between initial surface site concentration of goethite and initial sulfide concentration (SS/S(-II)

diss

ratio) was varied. The numbers behind each time series denote this ratio for each experimental run.

Figure 3.6 Fraction of excess Fe(II) determined for goethite [62] and for lepidocrocite [22] in percentage of total Fe(II) plotted versus the ratio between initial surface site concentration and initial sulfide concentration.

Figure 3.7 Formation rates of pyrite as determined by Mössbauer spectroscopy (Wan [62]).

Chapter 4: Formation and Transformation of Iron-Bearing Minerals by Iron(II)-Oxidizing and Iron(III)-Reducing Bacteria

Figure 4.1 Interactions between iron bacteria and Fe-bearing minerals: (a) confocal laser scanning microscopy 2D image of cell–goethite (Gt) aggregates from the phototrophic IOB

Rhodovulum iodosum

(green: DNA, red: Fe(III), blue: EPS, gray: reflection signal). (Reprinted with permission from Wu

et al

. [58], © 2014 Federation of European Microbiological Societies.) (b)

Acidovorax

sp. strain BoFeN1 cells encrusted by periplasmic lepidocrocite (L) and surrounded by extracellular magnetite (M) [59]. (c)

Klebsiella mobilis

cell mineralized by goethite (Gt) neighboring hydroxycarbonate green rust (GR) particles [60]. (d) Stalk attachment to

Mariprofundus ferroxydans

composed of individual filaments templating lepidocrocite (L) precipitation. (Reprinted by permission from Chan

et al

. [61], © 2010 McMillan Publisher Ltd: The ISME Journal.) (e)

Gallionella

stalk (right) and

Leptothrix

sheath (left) mineralized by akaganeite (Ak) and/or ferrihydrite (Fh). (Reprinted from Chan

et al

. [12], with permission from Elsevier.) (f)

Ferrovum myxofaciens

strain EHS6 associated with jarosite (J) and schwertmannite (Sch). (Adapted with permission from Hedrich

et al

. [62], © 2011 American Chemical Society.) (g)

Shewanella oneidensis

covered with hematite (Hm) nanoparticles. (Reprinted from Bose

et al

. [63], with permission from Elsevier.) (h) Hydroxycarbonate green rust crystal (GR, blue) associated with

Shewanella putrefaciens

cells (green). (Reprinted with permission from Zegeye

et al

. [64], © 2010 Wiley.)

Figure 4.2 Contribution of IOB and IRB to the (trans)formation of Fe-bearing minerals. “<CH

2

O>”, “HCOO

”, “CH

3

COO

” and “C

3

H

5

O

3

” stand for biomass, methanoate, acetate and lactate, respectively. “o.n.” means average oxidation number of Fe. Fe-bearing minerals were abbreviated as follows: ferrihydrite (Fh), lepidocrocite (L), mössbauerite (Mb), goethite (Gt), hematite (Hm), maghemite (Mh), magnetite (M), green rusts (GRs), siderite (S), chukanovite (Ck), and vivianite (V). Formulae of Fe-bearing minerals are established without water molecules as Fe

2+

4

Fe

3+

2

(OH)

12

CO

3

and Fe

2+

3

(PO4)

2

. Microbial reactions presented here are mass balances of several bacterial metabolisms that do not necessarily reflect their stoichiometry nor the precise nature of reactants and products.

Figure 4.3 Electron transfer mediated by IRB and iron oxides. Extracellular electron transfer (EET) proceeds either by direct contact (a,b), via electron shuttles (c,d) or nanowires (e–h). Interspecies electron transfer (IET) can be mediated by iron oxyhydroxides (i,j). Inset in (a) displays a proposed structural model for

Shewanella oneidensis

electron transport chain including multiheme cytochromes (see text and, e.g., [149], for more details).

OM

: outer membrane;

IM

: inner membrane. (b) AFM image of

Shewanella

bacteria at the surface of bioreduced hematite. Arrows indicate dissolution features. Scale bar 4 µm. Reprinted from Rosso

et al

. [150], with permission from Elsevier. (c) Proposed model of electron transfer via electron shuttles (S) diffusing from the bacteria toward Fe minerals. (d) Anaerobic growth of wild type (WT) or mutants (H1, H2)

S. putrefaciens

on lactate with AQDS (anthraquinone-2,6-disulfonate) as the electron acceptor. Reduction of AQDS (bright orange color) requires a diffusible molecule (electron shuttle) produced by WT that complements the mutants. (Reprinted by permission from Newman and Kolter [151], © 2000 Macmillan Publishers Ltd: Nature.). (e) Model of electron transfer via nanowires. (f) Correlated atomic force microscopy (AFM) and live-cell membrane fluorescence (inset) of

S. oneidensis

nanowires (Pirbadian

et al

. [149], © 2014). (g,h) Two models of electron flow along microbial nanowires, proceeding either via electron hopping (g) or by metallic-like conduction (h) (for more details see text and, e.g., [152]). (i) Schematic model of IET between

G. sulfurreducens

and

T. denitrificans

. (j) Cumulative curves showing amounts of electrons (millimolar equivalent) transferred depending on the nature of added Fe minerals (Kato

et al

. [153], © 2012, PNAS).

Mt NP

: magnetite nanoparticle.

Figure 4.4 Examples of potential biosignatures of microbial iron oxidation or reduction. (a–e) (

Gallionella

samples: Reprinted by permission from Picard

et al

. [240], © 2015 Macmillan Publishers Ltd: Nature Communications;

Acidovorax

sp. strain BoFeN1 samples: Reprinted from Li

et al

. [2], © 2014, with permission from Elsevier): Fe mineral-organic C assemblages in twisted stalks of

Gallionella

(a) and in the periplasm of

Acidovorax

sp. strain BoFeN1 (ND-IOB) (c). Both structures are perfectly preserved upon heating and/or pressure (b,d). Some spectroscopic signatures of organic carbon molecules are also preserved, as observed on NEXAFS C K-edge spectra recorded before and after experimental fossilization (e). Note that fresh stalks of

Mariprofundus ferrooxydans

exhibit similar patterns as

Gallionella

(Panel (e) reprinted by permission from Chan

et al

. [61], © 2010 McMillan Publisher Ltd: The ISME Journal.) Reference spectra have been measured on 1,2-dipalmitoyl-

sn

-glycero-3-phosphocholine (lipid-fatty acid), albumin (protein), and alginate (polysaccharide) (courtesy of A. Hitchcock). (f,g) Fine ultrastructural details such as protein globules (f, in

Acidovorax

sp. strain BoFeN1 cells observed by cryo-electron microscopy of vitreous sections, Miot

et al

. [103], © 2011), peptidoglycan, and periplasm thickness ((g) Miot

et al

. [103], © 2011) can also be preserved in Fe-mineralized IOB.

PG

: peptidoglycan, IM: inner membrane. (h–k) Fe biominerals sometimes exhibit specific crystallographic orientations, for example, periplasmic lepidocrocite with (0 2 0) axis parallel to the cell wall in

Acidovorax

sp. strain BoFeN1 (Panels (h,i) reprinted from Miot

et al

. [59], © 2014 with permission from Elsevier.), lineations parallel to the sheath in

Leptothrix

sheaths (Panel (j) reprinted from Chan

et al

. [12], with permission from Elsevier), and elongated FeOOH crystals in stalk filaments. (Panel (k) reprinted from Chan

et al

. [12], with permission from Elsevier.) (l, m) Fe redox heterogeneities at the submicrometer scale are widespread in IOB cultures, for example, in cultures of the photoferrotroph

Rhodobacter

sp. strain SW2 (Panel (l) Fe redox gradient along organic fibers templating Fe mineralization, Miot

et al

. [75] © 2009.), and in cultures of

Acidovorax

sp. strain BoFeN1 under conditions promoting the formation of extracellular magnetite and periplasmic lepidocrocite. (Panel (m) reprinted from Miot

et al

. [59] © 2014 with permission from Elsevier.) (n–p) Magnetite produced by IOB and IRB sometimes exhibits specific properties. For instance,

Acidovorax

sp. strain BoFeN1 promotes the transformation of green rust to stable single-domain magnetite, slightly oversaturated with Fe(III). (Panel (n) reprinted from Miot

et al

. [59] © 2014 with permission from Elsevier.) On the contrary, extracellular nanomagnetite produced by

S. oneidensis

MR-1 (Panel (o) composite STXM color map, with organic carbon in red and Fe in blue, Coker

et al

. [241] © 2012 Wiley.) is slightly oversaturated with Fe(II) at the cell contact than onto EPS ((p) X-ray magnetic circular dichroism (XMCD) spectrum (blue) and corresponding Fe L

2,3

edges X-ray Absorption spectrum, Coker

et al

. [241] © 2012 Wiley).

Figure 4.5 Potential role of IOB and IRB in the formation of ancient sedimentary deposits. (a) Schematic model of microbial processes potentially involved in the formation of banded iron formations. Fe

2+

originating from deep-sea hydrothermal vents is oxidized by anoxygenic photosynthetic Fe oxidizers (photoferrotrophs), cyanobacteria (oxygen oases), or ND-IOB (in redox-stratified water columns). Abiotic processes potentially contributing to Fe oxidation or reduction are not depicted in this scheme. More details on these models, alternative abiotic models, and connections with the N cycle can be found in the text and in [245, 258]. (b) Overview of BIF from the Joffre iron formation, Pilbara Craton, North West Australia. (Posth

et al

. [245] © 2013 Wiley.) (c) Core consisting of red microbands (<1 mm) of chert–hematite–riebeckite (bluish bands in upper core) alternating with lighter chert–dolomite–siderite–crocidolite mesobands (≥1 cm) and denser dark magnetite mesobands. (Posth

et al

. [245] © 2013 Wiley.) (d) Light micrograph of 170 Ma Fe–silica deposit showing Fe(III)-oxide microfossil filaments, some of which exhibiting twisting morphology (arrow). (Krepski

et al

. [238] © 2013 Wiley.) (e) Presumed fossilized cells (white arrows) and stalks (yellow arrows) from jasper bands of a Quaternary formation, Milos Island, Greece. (Reprinted by permission from Chi Fru

et al.

[259] © 2013 Macmillan Publishers Ltd: Nature Communications).

Figure 4.6 Several examples of modern environments hosting IOB and/or IRB. (a,b) (Reprinted from Jorand

et al

. [270], © 2011, with permission from Elsevier.) Tropical river ferruginous biofilms from French Guiana (panel (a) optical micrograph; mc: microcolony) exhibit intimate association of bacteria (dominated by IRB) and Fe minerals (mainly lepidocrocite and ferrihydrite) (panel (b) TEM image). (Panels c, d) (Reprinted from Elliott

et al

. [271] © 2014, with permission from Elsevier.) Iron-rich freshwater lacustrine aggregates colonized by Fe-cycling bacteria (panel (c) white arrow: sheathed floc IOB; stars: particulate iron) and model of distribution of IOB within these Fe pelagic flocs (panel (d) Gt: goethite, Am: Amorphous Fe(III)OOH, M: magnetite, S: siderite, and V: vivianite). (e–g) (Reprinted by permission from Templeton

et al.

[111] © 2009 MacMillan Publishers Ltd: Nature Geoscience) Basalt colonization by Fe–Mn associated biofilms. Optical micrograph (e) and Fe–Mn map (f) showing Fe redox state (Fe(II): green and Fe(III): red) and Mn (blue) distributions in surface basalt collected from Loihi seamount, Hawaï. Fe-encrusted cells are observed at the surface of basalt slabs exposed to seawater for 1 year (HRTEM of a FIB section (g)). Accumulation of secondary Fe(III) and Mn(IV) oxides may represent early stages of ferromanganese crust formation.

Chapter 5: Controlled Biomineralization of Magnetite in Bacteria

Figure 5.1 Phylogenetic tree based on 16S rRNA gene sequences reflecting the taxonomy of magnetotactic bacteria. The type of magnetosome biomineralized is indicated for each species.

Figure 5.2 Transmission electron micrographs of magnetotactic bacteria isolated from the same sampling bottle collected from the Mediterranean Sea at the Calanque of Mejean near Marseille, France. (a, b, c and f) are coccoid cells, (d and e) are rods, (g, h, i, k and l) are vibrios or curved rods and (j) represents a magnetotactic multicellular prokaryote.

Figure 5.3 Model for magnetosome biomineralization based on recent studies involving the

Magnetospirillum

strains MSR-1 and AMB-1. (a) Membrane invagination, (b) recruitment of proteins and import of iron, (c) initiation of biomineralization to create small crystals of magnetite, and (d) crystal maturation and organization of magnetosomes into chains. The magnetosome island (MAI) of

M. magneticum

AMB-1 is represented with genes colored to identify the localization of encoded proteins necessary for magnetosome formation; nonused open reading frame (ORF) are in gray. OM, outer membrane; CM, cytoplasmic membrane.

Chapter 6: Ferritin Iron Mineralization and Storage: From Structure to Function

Figure 6.1 Overall structures of ferritin (in ribbon representation). (a) Monomeric structure of human H-ferritin showing helices A–D in a sequential way from the N- to C-terminals. (b) Left: the monomeric structure of green algae (PDB code 3VNX) with the extension peptide at its N-terminal. Right: the interaction of the extension peptide (black) with an additional ferritin molecule; interacting hydrophobic residues are represented as black sticks. (c) The interaction of

E. coli

BFR (3E1M) with the heme group located at the dimer interface (black sticks). This picture has been generated using PyMOL (DeLano Scientific LLC, San Carlos, LA; http://www.pymol.org).

Figure 6.2 The quaternary assembly of ferritin into a 24-meric protein nanocage. (a) The twofold axis between two ferritin monomers (in black). (b) The threefold axis between three ferritin monomers (in black). (c) The fourfold axis between four ferritin monomers (in black). (d) The B-channel located at the junction of a ferritin dimer with another ferritin monomer. This picture has been generated using PyMOL (DeLano Scientific LLC, San Carlos, LA; http://www.pymol.org).

Figure 6.3 Close-up views of the ferritin pores. (a) The twofold interface between two monomers of a ferritin dimer; human H-ferritin (green) and

E. coli

BFR (yellow). Residues are shown as sticks and colored according to atom type: N, blue; O, red; C, green, and yellow, respectively. (b) The threefold pore of human H-ferritin (green) in top view (left) and side view (right) and of

E. coli

BFR (yellow). (c) The B-channel pore of

E. coli

BFR in top view. (d) The fourfold axis in top view of human H-ferritin (green) and

E. coli

BFR (yellow). This picture has been generated using PyMOL (DeLano Scientific LLC, San Carlos, LA; http://www.pymol.org).

Figure 6.4 (a–d) The ferroxidase center of human H-ferritin ,

E. coli

BFR, and

E. coli

Ftn. Residues are shown as sticks and colored according to atom type: N, blue; O, red; C, green, yellow, and purple respectively. (e) The nucleation site of human L-ferritin. This picture has been generated using PyMOL (DeLano Scientific LLC, San Carlos, LA; http://www.pymol.org).

Figure 6.5

Phase 1 – demineralization

. In order to allow controlled crystal growth, the first step in the process must be the extraction of a naturally occurring ferrihydrite core. This is achieved by dialysis against a reducing agent (TGA).

Phase 2 – reincorporation

. The second phase of this process includes a slow and controlled addition of Fe

2+

atoms under magnetite synthesis conditions.

Chapter 7: Iron Oxides in the Human Brain

Figure 7.1 Gross neuropathology of superficial siderosis: cerebellar cortex (a,b), brain stem (a), and eighth cranial nerve (VIII in (b)) display a dark brown to orange color of variable intensity. Incrustation of the cerebellum is most severe in the upper vermis, the superior hemispheres, and the cortex surrounding the cerebellopontine angle (a,b). The facial and glossopharyngeal nerves (VII and IX, respectively, in (b)) do not show the intense brown discoloration of the adjacent eighth nerve (VIII in (b)). Siderosis of eighth cranial nerve and spinal cord/iron histochemistry with Perls' stain reveals two types of iron deposits. Densely reactive hemosiderin granules cluster in perivascular spaces (c,d). The more diffuse color is due to pale-staining iron in foamy structures of variable size (∼20 µm in the eighth nerve, arrow in (c), and 10–15 µm in the spinal cord white matter; arrow in (d)). The foamy structures are devoid of nuclei militating against their origin from macrophages. Magnification markers: 20 µm.

Figure 7.2 Magnetic analyses of human hippocampus and tumor samples: (a) hysteresis at 5 K for the meningioma (men) and hippocampi (hipp), (b) hysteresis at 300 K of a meningioma sample (HA1b), and (c) hysteresis at 300 K of a hippocampus (HH) sample. Note the difference in scale between (b) and (c). All curves were corrected for linear contributions from the diamagnetic and paramagnetic phases.

Figure 7.3 (a) TEM image of a dystrophic myelinated axon in the neuropil in an Alzheimer's disease hippocampus section. Panels (b,c) are details of the insets showing the ferritin cores. A short postmortem delay and an appropriate sample preparation allow the observation of ferritin in oligodendrocyte processes and within myelin frayed sheets.

Figure 7.4 Quantitative susceptibility mapping provides excellent sensitivity to iron concentration in iron-rich regions of the brain. The magnitude image (a) and susceptibility map (b) are shown from a volunteer, where the arrows delineate substructures of the basal ganglia (putamen, (PUT), globus pallidus (GP), caudate nucleus, (CN), and the internal cerebral vein (ICV)).

Chapter 8: The Chiton Radula: A Model System for Versatile Use of Iron Oxides*

Figure 8.1 Dorsal (a) and ventral (b) aspect of

Acanthochitona fascicularis

(obsolete:

Chiton fascicularis

Linnaeus, 1767). (Adapted from Savigny [4]). (c) Drawing of the radula of

L. caprearum

(obsolete:

Chiton cinereus

Linnaeus, 1767). (Adapted from Poli [5]). (d) Reflected light microscopy image of the anterior end of the radula of

Chaetopleura apiculata

, showing six intact rows of mature teeth. The major lateral teeth appear bluish black. (Adapted from Gordon and Joester [6]). (e) Drawing of two successive rows of radula teeth of

Katharina tunicata

. (Adapted from [7]). SEM image of two successive major lateral teeth (f) and a side view of a single major lateral tooth (g) of

Acanthopleura hirtosa

showing the hollow tooth stylus (ts), the stylus canal pore (cp), and the mineralized tooth cusp (tc). (Adapted from Shaw and coworkers [8]). (h) Schematic drawing of the body plan of

Acanthopleura echinata

, showing the mouth (mo), radula (ra), odontophore (od), and the radula sac (rs). (Adapted from [9, 10]). (i) Schematic drawing of the radula sac that surrounds the radula. The radula is composed of the radula membrane and the radula teeth anchored on the membrane. The radula sac is composed of odontoblasts at the posterior end and the superior and inferior epithelia.

Figure 8.2 (a) Partial taxon tree of the polyplacophora according to the World Register of Marine Species (WoRMS, marinespecies.org). Note

Acanthopleura

deviates from [91] and that scientific names used follow the “accepted” nomenclature as per WoRMS (data retrieved 10/2015). Numbers given in parentheses after the genus indicate the number of species investigated to date. Biominerals identified in tooth micro-architectural compartments are indicated using the following key: M: magnetite;

t

(M): magnetite present in a narrow tab on the trailing edge; M(): window in the magnetite layer; M?: magnetite inferred but not demonstrated; M**: magnetite present on the distal cusp only; Ap: apatite; Ap*: in several

Acanthopleura

sp., limonite may be present in the core [56]; Lp: lepidocrocite; Lim: limonite; Fh: ferrihydrite; AFP: amorphous, hydrous ferric phosphate; W?: the presence of whitlockite suggested [56]; ?: not known; (b)

Acanthopleura

-type radula teeth with magnetite-mineralized leading edge, iron oxyhydroxides interlayer, and apatite core. Note that the magnetite tab on the trailing edge is not visible in this section. Genera with teeth of this type are given in green color font in (a). (c)

Cryptochiton

-type radula teeth with magnetite on leading and trailing edge, a window in the magnetite layer on the trailing edge, and a core composed of AFP. Genera with teeth of this type are given in red color font in (a). (d,e) SEM image using back scattered electron (BSE) contrast and EDS elemental maps of ground and polished longitudinal sections of major lateral radula teeth of

A. echinata

(d) and

C. stelleri

(e). ts: tooth stylus; sc: stylus canal; jz: junction zone.

Figure 8.3 (a) Major lateral teeth on

Katharina tunicata

radula in developmental stages I–IV. Note teeth are transparent and nearly colorless in stage I, orange in stage II, brown in stage III, and black in stage IV. (b,c) Distribution of iron in longitudinal sections of major lateral teeth of

K. tunicata

in stages II (b) and III (c), as determined by SEM-EDS. (d) BSE-SEM and SEM-EDS elemental maps of longitudinal section of stage IV (fully mineralized) radula tooth of

K. tunicata

, showing a Fe/P/O-rich core (AFP) and a Fe/O-rich cap (magnetite). (a–d) Adapted from [80]. (e,f) Three-dimensional reconstruction of atom probe tomography data sets from the leading edge of major lateral teeth of

Chaetopleura apiculata

. Note the presence of organic fibers that specifically bind Na

+

(e) or Mg

2+

(f). (g,h). Overlay of Na

+

(g) and Mg

2+

(h) ions on carbon concentration maps integrated over the boxed fiber cross sections indicated in (e) and (f). (i) Model of a chiton tooth organic fiber. (e–i) Adapted from [6]. (k) Composite false-color image based on micro X-ray absorption near-edge structure (μ-XANES) analysis of longitudinal thin sections of

Cryptochiton stelleri

major lateral teeth in stages II–III. Distribution of ferric (blue) and ferrous (red) iron reveals the transformation of ferrihydrite deposited in stage II to magnetite in stage III.

Figure 8.4 (a) Major lateral radula teeth

Acanthopleura hirtosa

(rows 7–18) with associated epithelium in longitudinal section. Note onset (stage II) and subsequent progression of mineralization (brown-black color) in posterior (leading) edge of row 14. ds: dorsal sinus; me: minor epithelium; cs: cusp epithelium; tc: tooth cusp; jz: junction zone; sc: stylus canal; and ts: tooth stylus.

Figure 8.5 Schematic drawing of

Acanthopleura

-type (a) and

Cryptochiton

-type (b) teeth in grazing position. Teeth are shown in longitudinal section. Shading indicates the biomineral type. White lines indicate the principal orientation of organic-wrapped mineral rods. After [64]. (c) Schematic drawing of the rod-and-trough-shaped fibers, showing gingko-shaped cross section and corrugated (fracture) surface parallel to long axis. (Adapted from [139]). (d) Backscattered electron contrast image of cross section of

Acanthopleura echinata

tooth. Note rod-and-trough-shaped motifs appear in slightly oblique section. Organic material appears dark against the minerals. Note continuity of pattern from magnetite through the interlayer into the apatite core. (Adapted from [72]). (e) Hexagonal rods near the trailing tooth surface in longitudinal fracture and cross fracture (inset) of

Acanthochitona rubrolineata

, a

Cryptochiton

-type tooth.

Chapter 9: Mineralization of Goethite in Limpet Radular Teeth

Figure 9.1 (a) Schematic of the limpet radula in action. (b) The anatomy of the limpet tooth depicting the self-sharpening in terms of a conserved angle.

Figure 9.2 Crystal structure of goethite (αFeOOH) viewed almost down the

c

-axis. The iron octahedra are shown in gray and the oxygen atoms in red, omitting hydrogen atoms. (a) The direction of the four {110} planes is denoted by yellow lines. The dihedral angle between (110) and () planes is 130.4°. (b) The direction of the two {100} planes is depicted in orange and the one of the {010} faces in green.

Figure 9.3 (a)–(d) A schematic of the common morphologies and delimiting faces of synthetic goethite.

Figure 9.4 Representative scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images of goethite crystals grouped according to their morphology along with the corresponding assigned morphology. The schematic representation of the particle morphology is drawn in the matching direction to the image (denoted by arrows). (a) Crystals with rhomb-shaped sections delimited by {110} faces. (b) Crystals with square sections delimited by {100} and {010} faces. The crystals shown here are apparently hollow. (c) Crystals with triangular sections delimited by two {110} and one {010} face. The dotted arrow points toward the face, which appear darker in the TEM image.

Figure 9.5 (a) A TEM image of a longitudinal section of a tooth in row 35 of limpet

Patella caerulea

showing a diversity of crystal sizes. The arrows point at extremely thin structures of thickness ∼2 nm. Inset: A hollow crystal with a wall thickness of 2–3 nm with rhomb-shaped ends. (b–d) SEM images of goethite crystals isolated from teeth in rows 40–53 nm by mechanical crushing. Scale bars are 100 nm. (a) A hollow crystal with a square cross section with one of the walls partially broken away due to mechanical milling readily exposing the hollow interior. The thickness of the crystal walls is 10 nm. Panels (c) and (d) show thin platelike crystals together with thicker crystals. Here the crystal thickness is as small as 5 nm. (e) A thicker rectangular platelike crystal. The plates (c–e) may be whole crystals or parts of broken crystals.

Figure 9.6 (a) TEM image of a section of a late maturing tooth of limpet

Cellana toreuma

:

sec

denotes the superior epithelial cell,

c

the tooth cusp, and

b

the tooth base. Microvilli in the trailing region are nicely visible (region between

sec

and

c

along the trailing edge between the arrowheads). The scale bar corresponds to 3 µm. (b) TEM image of an immature tooth together with the superior epithelial cells (

sec

). The arrowhead shows a microtubule (

mt

) reaching the base region of the microvilli (

mv

); Two siderosomes (

s

) are nicely visible near the lower edge of the image. The scale bar corresponds to 3 µm. (c) TEM image of a section of superior epithelial cells (

sec

) containing siderosomes (

s

) and microtubule (

mt

) in the immature region of the radula. The scale bar corresponds to 3 µm. (d) TEM image of goethite crystals (arrow) and organic matrix (arrowheads) in an early-maturing tooth (the scale bar corresponds to 1 µm); (e) electron diffraction pattern of a heavy mineralized deposit.

Figure 9.7 Cryo-TEM images of sections of radula of the limpet

Patella caerulea

. (a, b) Cryo-TEM image of the cells of the radular sac surrounding row 19 (yet unmineralized): (a) Intact siderosomes; inset: electron diffraction pattern showing a faint 1.46 Å reflection (arrow) reflection. (b) Loose ferritin cores (arrow) next to intact siderosomes. (c) TEM image at low magnification of a transverse section of row 29 depicting a heavier mineralization in the leading region of the tooth and siderosomes surrounding the cells (arrows). The section was stained with uranyl acetate. (d) TEM image of early mineral deposits in row 25 showing loose ferritin cores outside the leading edge of the tooth. (e) Magnification of the boxed area in (d) depicting some mineral deposits having a granular appearance (arrowheads). No particles similar to the loose ferritin cores in size and shape were observed inside the tooth.

Chapter 10: Synthetic Formation of Iron Oxides

Figure 10.1 Illustration of the two main morphologies of hematite particles obtained from FeCl

3

aqueous solution in both acidic and basic media by hydrothermal treatment and soda precipitation, respectively.

Figure 10.2 Images of unconventional hematite morphology obtained using different capping agents, namely, (a) truncated hexagonal bipyramid synthesized with carboxymethyl cellulose and hydrazine molecules (with permission from [14], © 2012, American Chemical Society), (b) single-crystalline dodecahedral as hexagonal bipyramidal shape synthesized with the aid of F

anions (with permission from [15], © 2010 WILEY-VCH), (c) nanorods with high aspect ratios synthesized by 1,2-propanediamine-assisted hydrothermal method [16], and (d) single-crystalline hematite nanotubes fabricated by one-step hydrothermal method in an aqueous NH

4

H

2

PO

4

solution [17].

Figure 10.3 Schematic representation of crystal structure of hematite seen from the [001] direction showing the 6 equiv. crystalline directions observed for dodecahedral particles.

Figure 10.4 Pathway to illustrate the growth of akaganeite and goethite by dissolution/crystallization process of thermodynamic unstable ferrihydrite.

Figure 10.5 Schematic representation of the formation of ferrous hydroxide from [Fe(OH)

2

(OH

2

)

4

]

0

zero charge complex.

Figure 10.6 TEM images of lepidocrocite particles obtained by controlled oxidation of ferrous hydroxide (a) and magnetite particles obtained by coprecipitation of ferrous and ferric ions. Variation of magnetite particle size with (b) pH value of reaction solution compared to surface charge of magnetite (c).

Figure 10.7 (a) Mixing of two miscible fluid streams under laminar flow conditions. The component streams mix only by diffusion, creating a dynamic diffusive interface with predictable geometry. Reactions can be studied in two types of segmented flows in microfluidic channels. (Reprinted with permission from [27], © 2005 Nature Publishing Group.) (b) Discrete liquid plugs are encapsulated by an immiscible continuous phase (e.g., a fluorocarbon-based carrier fluid). Reactions occur within the dispersed phase (within the plugs). Owing to the surface properties of the microchannel walls, these walls are preferentially wetted by the continuous phase. (c) Aqueous slugs are separated by another immiscible phase (e.g., discrete gas bubbles). Reactions occur within the continuous phase (i.e., within the slugs).

Figure 10.8 (a) Coaxial flow device operating under laminar regime. The inset image shows the outlet of the inner capillary with the solution of iron + II and iron + III flowing into the stream of TMAOH alkaline solution. (b) TEM image of nanoparticles prepared in the channel (for flow rates

Q

in

= 100 µl min

−1

and

Q

out

= 400 µl min

−1

). The inset shows the electron microdiffraction pattern with the Miller indexes of γ-Fe

2

O

3

. (c) Magnetization curve of a stable suspension in water of nanoparticles produced in the millifluidic device. The inset curves represent the fitting log-normal laws for the number distribution (solid line) and the volume distribution (dotted line) of diameters.

Figure 10.9 (a) Up: pairing module. Two aqueous phases are injected by the outer channels and are synchronously emulsified by the central oil channel. The flow rates are

Q

o

= 800 ml h

−1

for the oil and

Q

x

= 400 ml h

−1

and

Q

y

= 100 ml h

−1

for the aqueous phases. (b) Fusion module. Paired droplets can be coalesced by applying an electrical voltage

U

between the two electrodes.

Q

o

= 650 ml h

−1

,

Q

x

= 100 ml h

−1

,

Q

y

= 60 ml h

−1

. Characterization of the iron oxide particles produced. (b) TEM image of the nanoparticles. Inset: HRTEM image of a particle showing (220) spinel planes. (c) Electron diffraction pattern indicating different planes of the spinel structure. (d) Magnetization M/Ms (Ms is the saturation magnetization) as a function of the magnetic field H.

Figure 10.10 (a) The experimental setup used for the preparation of the ferrihydrite and goethite nanoparticles. TMAOH = tetramethylammonium hydroxide. (b) TEM and HRTEM pictures of the sample taken after precipitation in the microreactor

R

1 (before aging) showing ferrihydrite nanoparticles and after aging for 15 min in the microtubular loop

R

2 showing goethite nnolaths.

Chapter 11: Oriented Attachment and Nonclassical Formation in Iron Oxides

Figure 11.1 “Schematic illustrating oriented aggregation. Primary particles (I) reversibly form loose assemblies (II) analogous to outer sphere complexes. Particles in the random assembly rotate and rearrange via Brownian motion until crystallographic alignment is reached (III). The particles can then irreversibly attach to form a continuous crystal (IV).”

Figure 11.2 Electron micrographs of hematite nanoparticles showcase some of the wide variety of morphologies produced from growth via OA: (a) nanoflowers [40], (b) peanuts [43], (c) nanocubes [44], and (d) spindles [45]. The scale bars in (a) are 100 nm and 50 nm (inset).

Figure 11.3 Low- and high-resolution TEM images showing twin and dislocation structures in nanoparticles grown via OA. (a) A twinned lepidocrocite (γ-FeOOH) nanoparticle prepared by aging six-line ferrihydrite nanoparticles with 2 mM FeCl

2

in pH 7 3-(

N

-morpholino)propanesulfonic acid (MOPS) buffer under anoxic conditions for 21 h. The area outlined in white is shown at higher resolution in (b). Black lines highlight the lattice fringes exhibiting symmetry across the twin boundary. (c) “HRTEM image of three attached TiO

2

particles. Arrowheads mark interfaces between primary particles. The edge dislocation at the upper interface is reproduced (in (d)), with lattice fringes around the terminating plane (arrowhead) highlighted for clarity” [6]. Images (a) and (b) were taken by the authors.

Figure 11.4 (a) TEM image of goethite nanoparticles. (b) HRTEM image of a goethite nanoparticle tip. White arrowheads serve to highlight two of many regions containing defects. (

JEOL 2010, Pacific Northwest National Lab

.)

Figure 11.5 Cryo-TEM images of ferrihydrite nanoparticles prior to aging (a) and structural intermediates (b) formed during the synthesis of goethite from ferrihydrite 24 days at 80 °C. The primary particles comprising the structural intermediates lack direct contact with each other, visible in the lower image. Structural intermediates of V-shaped twinned goethite rods can also be seen. Synthesis and procedure are from [34], images by V. Yuwono.

Chapter 12: Thermodynamics of Iron Oxides and Oxyhydroxides in Different Environments

Figure 12.1 Phase diagram of iron oxides and oxyhydroxides with partial pressures of gases at K. Dash-dotted lines indicate standard pressure (1 atm); the dashed line in (a) indicates formation of water vapor from and with no energy gain or loss. Note the different scales of partial pressures of in (a) and O in (b). (With permission, © 2011 American Physical Society.)

Figure 12.2 Pressure–temperature diagram for the reaction -FeOOH(goethite)(hematite) + (fluid). The curve at lower temperature shows the equilibrium among bulk solid phases and water (fluid implies liquid, vapor, or fluid above the critical ice point), whereas that at higher temperature show equilibrium for 10 nm particles of goethite and hematite combined with water. From Ref. [2]. (With permission from © 2008, AAAS.)

Figure 12.3 Calculated surface energies of three terminations of hematite (001).

Figure 12.4 Shapes of goethite nanocrystals explored in the study described in Ref. [71], including (a) and (b), are {111} bipyramids truncated by {100} facets, (c) is a bipyramid enclosed by {111}, (d) is an elongated and truncated bipyramid (referred to as polyhedron), (e) is an elongated variant of (d) truncated in the lateral directions by {011} facets, and (f) and (g) are rhombohedral prisms. Since the {100} surfaces terminated by OH and by O have different surface energies, the aspect ratios are different in (a) and (b) and (f) and (g).

Figure 12.5 Relative free energies of formation of goethite nanocrystals, as functions of size, showing that the (100)OH-enclosed rhombohedral and truncated bipyramids are the thermodynamically preferred shape. Bipyramid shapes are the least preferred. The shapes are defined in Figure 12.4.

Figure 12.6 Shapes of hematite nanocrystals explored in the study described in Ref. [71], including (a) the pseudocube (rhombohedral that looks like a cube); (b) the dodecagonal prism; (c) and (d) are respective hexagonal prisms enclosed by {100} and {110} (referred to as hexagonal prism and alternate hexagonal prism in the original paper, respectively); (e), (f), and (g) are different types of truncated pseudocubes; (h) and (i) are truncated hexagonal prisms; (j) is the rhombohedron.

Figure 12.7 Relative free energies of formation of hematite nanocrystals, as functions of size, showing that the pseudocube is the thermodynamically preferred shape, hexagonal prisms are higher in energy, and rhombohedron is unstable with respect to all other morphologies. The results are relative to bulk phase hematite, and the shapes are defined in Figure 12.6.

Figure 12.8 Size- and temperature-dependent thermodynamic stability of goethite and hematite nanoparticles in the presence of water. (Reprinted from Ref. [71]).

Figure 12.9 Enthalpy, relative to bulk hematite combined with liquid water at 298 K, of various iron oxide and oxyhydroxide polymorphs as a formation of surface area per mole of FeO, FeOOH, or Fe(OH). Values for ferrihydrite are approximate because of sample variability and are represented as an elliptical area. Values of surface areas are plotted for formula units FeOOH (oxyhydroxides), Fe(OH) (ferrihydrite), and FeO (hematite and maghemite) for thermodynamic consistency when comparing different compositions. From Ref. [2]. (With permission from © 2008, AAAS.)

Chapter 13: Introduction to Standard Spectroscopic Methods: XRD, IR/Raman, and Mössbauer

Figure 13.1 Representation commonly used to derive Bragg's condition. It shows the reflection of two waves from a family of crystallographic planes. The reflected beams interact constructively when the difference in their path length is equal to an integer number of wavelengths. Note that if the crystal is rotated around the incident beam axis, the diffraction condition is still satisfied and the reflected beams generate a cone, the Debye–Scherrer cone.

Figure 13.2 Two-dimensional representation of the Ewald sphere. The representation is based on the reciprocal lattice. By placing the wave vector

K

i

of the incident wave with the end on a point of the reciprocal lattice and drawing a circumference centered on the origin of that vector and with a radius

K

i

, any point of the reciprocal lattice contained in the circumference will define a scattering event.

Figure 13.3 (a) X-ray powder spectra of magnetite and maghemite nanoparticles. Particle (and crystal) size was about 50 nm. Adapted with permission from [11]. Copyright 2008 American Chemical Society. (b) XRD spectrum of two-line ferrihydrite synthesized by Smith

et al.

[12]. In this case, the crystallite size was about 2–6 nm.

Figure 13.4 Dependence of the lattice parameter

a

on the oxidation parameter

z

for the magnetite–maghemite solid solution system. Data points from Readman and O-Reilly [8] and polynomial regression from Fischer

et al.

[9].

Figure 13.5 (a) Schematic representation of the absorption of IR radiation, leading to the transition indicated with the solid arrow between

n

= 0 (ground state) and

n

= 1. For the ideal quantum harmonic oscillator, only transitions with Δ

n

= 1 are allowed. Real systems deviate from that behavior, and transitions indicated with broken arrows for Δ

n

= 2 (first overtone) or Δ

n

= 3 (second overtone) can occur, although their intensity is small. (b) Energy diagram representing elastic scattering (also called Raleigh scattering) and inelastic (either Stokes or anti-Stokes) scattering events.

Figure 13.6 Schematic representation of the three vibrational modes of the water molecule.

Figure 13.7 Raman spectra of some irons oxides and oxyhydroxides.

Figure 13.8 (a) Raman spectra of magnetite and maghemite nanoparticles (about 50 nm). (Reprinted with permission from [11]. Copyright 2008 American Chemical Society.) (b) IR spectra of magnetite and maghemite prepared by different methods.

Figure 13.9 (a) Schematic representation of the effect of the isomer shift and the quadrupole splitting on the

I

= 1/2 and

I

= 3/2 levels of the

57

Fe nucleus. (b) Resulting Mössbauer spectrum, with the center shift (δ) and the quadrupole splitting (Δ

Q

S

) indicated.

Figure 13.10 (a) Schematic representation of the magnetic splitting, with and without the effect of quadrupole splitting. (b) Typical sextet observed if the two effects are present. Note the asymmetry of the lines with respect to the center of the spectrum.

Figure 13.11 Mössbauer spectra of chemically pure, natural ferrihydrite taken at different temperatures in the absence of a magnetic field and in an external 5 T field (parallel to the γ-ray beam) at 5 K.

Figure 13.12 Mössbauer spectra of nanosized maghemite (diameter about 39 nm) and commercial maghemite (rods of 40–100 nm of diameter and 1 mm of length), taken in fields of 6 T (nanosized particles) and 8 T (commercial particles).

Chapter 14: TEM and Associated Techniques

Figure 14.1 (a) Typical bright-field transmission electron micrograph of Fe

3

O

4

-γ-Fe

2

O

3

nanoparticles, (b) typical polycrystalline electron diffraction ring indexed to the Fe

3

O

4

structure, and (c) a HRTEM image of a nanoparticle with faceted edges terminating in a layer of enhanced atomic contrast, as indicated by the white arrow.

Figure 14.2 BF and phase contrast TEM images of the rapidly quenched β-FeOOH and α-Fe

2

O

3

hydrothermal synthesis reaction products after 80 min of processing (a) examined at room temperature; (b) during

in situ

heating, revealing the formation of an α-Fe

2

O

3

nanoparticle (arrowed); (c) heated

in situ

to 450 °C, revealing the growth of α-Fe

2

O

3

nanoparticles (arrowed); (d) ∼30 nm long, ∼15 nm wide developing β-FeOOH nanorod identified by lattice fringes and associated indexed FFT (both inset); and (e) high magnification of an α-Fe

2

O

3

nanoparticle grown during

in situ

heating, identified by lattice fringes and associated indexed FFT (both inset).

Figure 14.3 (a) O K-edge and (b) Fe L

2,3

-edge structures acquired from hematite (α-Fe

2

O

3

), akaganeite (β-FeOOH), goethite (α-FeOOH), 2-line-ferrihydrite, and magnetite (Fe

3

O

4

).

Figure 14.4 Schematics of the setup used to generate off-axis electron interferogram (hologram) in the TEM.

Figure 14.5 Magnetic induction maps acquired from two pairs of bacterial magnetite chains (a) at 293 K and (b) at 116 K, just below the Verwey transition temperature. At room temperature, the chains are crystallographically analogous to beads on a string, with their [111] directions constrained to lie parallel to the chain axis with the contours being parallel to each other within the crystals. At 116 K, with a magnetocrystalline easy axis no longer parallel to the chain axis, competition between the new easy axis of magnetization, particle shape, and interparticle interactions cause the magnetic field lines to undulate along the chain length. The small vortex in the lower chain in (b) is likely to be an artifact resulting from diffraction contrast in this crystal.

Figure 14.6 (a) HR image of an isolated faceted 50 nm magnetosome magnetite crystal from a magnetotactic bacterium, (b) isosurface visualization of a HAADF tomographic reconstruction of the same nanocrystal, and (c, d) magnetic induction maps recorded using off-axis electron holography from the same particle, displaying the distribution of the magnetic field within the individual particle at (c) room temperature and at (d) 90 K.

Figure 14.7 Visualized effect of oxidation on the magnetization of an isomorphic Fe

3

O

4

particle. Bright-field TEM images acquired (a) before and (b) after

in situ

heating to 700 °C under 9 mbar of O

2

for 8 h in an ETEM, with associated SAED patterns inset, indexed to Fe

3

O

4

. (c) Associated EEL spectra of the Fe 2p L

2,3

edge acquired from the Fe

3

O

4

particles before (blue) and after (red) annealing within the ETEM. Here black arrows emphasize three differing intensities from the mixed-valence compound of Fe

3

O

4

, while the red arrows highlight formation of pre- and postpeaks that indicate oxidation toward γ-Fe

2

O

3

. (d, e) Magnetic induction maps determined from the magnetic contribution to the phase shift, reconstructed from holograms taken (d) before and (e) after

in situ

heating, revealing the vortex nature of the particles. The contour spacing is 0.79 radians for the magnetic induction maps. The magnetization direction is shown using arrows, as depicted in the color wheel. Scale bars: 100 nm.

Figure 14.8 (a)

In situ

liquid cell STEM schematics. Stabilized iron oxide suspension is sandwiched between the two electron-transparent SiN windows and imaged with a focused STEM probe in the thin liquid layer. (b) Movement of ∼15 nm iron oxide nanoparticles is visualized in liquid using the HAADF mode. Scale bar: 100 nm

3

.

Figure 14.9

M. magneticum,

strain AMB-1 imaged in liquid with the STEM-HAADF. Scale bar: 500 nm. (Reference 3).

Chapter 15: Magnetic Measurements and Characterization

Figure 15.1 Representative hysteresis loop with initial magnetization curve for a ferromagnetic mineral.

Figure 15.2 Example for defining

k

hf

(dashed line) in mixed materials. (a) Diamagnetic brain tissue with magnetite inclusions and (b) crystal of paramagnetic orthoclase with magnetite inclusions.

Figure 15.3 Thermomagnetic curve of a mudstone, in which

k

lf

is shown as a function of heating (solid line) and cooling (dashed line); extracted paramagnetic and ferromagnetic

k

components are shown in the insets.

Figure 15.4 (a) FORC acquisition for a magnetotactic bacteria (strain MSR-1) and (b) resulting FORC diagram.

Figure 15.5 Plot of

M

in

as a function of

H

/

T

at temperature for superparamagnetic particles.

Figure 15.6 (a) IRM acquisition curve for tissue from human hippocampus and (b) representative IRM acquisition curves for magnetite (solid), hematite (dashed), and goethite (dotted).

Figure 15.7 Examples for (a) a Verwey transition for a topsoil (dashed line) and

M. gryphiswaldense

(solid line) and (b) a Morin transition for a single crystal of hematite (solid line) and Resovist

®

(dashed line).

Figure 15.8 Hematite with maghemite intergrowth showing a wasp-waisted hysteresis loop.

Figure 15.9 IRM acquisition curve for synthetic magnetite nanoparticles measured at 290 K (solid line) and 40 K (dotted line); dashed line shows that IRM is not saturated.

Figure 15.10 Example of thermal demagnetization of a cross-component IRM. Inset shows the IRM acquisition curve.

Figure 15.11 Mass susceptibility as a proxy of total Fe in a podzol profile.

Figure 15.12 (a) IRM acquisition curves for varying concentration of Fe

3

C and (b) concentration as a function of

M

RS

.

Figure 15.13 Langevin fit (dashed line) of initial magnetization curve with the extracted particle size distribution in the inset.

Figure 15.14 (a) Ideal case for the relationship between IRM acquisition and demagnetization in an AC field for noninteracting magnetite and (b) example of interacting magnetic particles in brain tissue.

Figure 15.15 Example of FORC analysis to evaluate particle interaction. FORC diagram and reversible/irreversible contributions f are shown for (a) uncoated magnetic nanoparticles and (b) after coating with DOPA.

Chapter 16: Total X-Ray Scattering and Small-Angle X-ray Scattering for Determining the Structures, Sizes, Shapes, and Aggregation Extents of Iron (Hydr)oxide Nanoparticles

Figure 16.1 Schematic representation of the scale of pair distribution function (PDF) analysis and small angle X-ray scattering (SAXS) measurement domains compared to other complementary techniques. EXAFS, extended X-ray absorption fine structure; WAXS, wide-angle X-ray scattering; XRD, X-ray diffraction; USAXS, ultra small angle X-ray scattering; DLS, dynamic light scattering; SEM, scanning electron microscopy; TEM, transmission electron microscopy; AFM, atomic force microscopy; and STM, scanning tunneling microscopy.

Figure 16.2 (a) The weighted total scattering structure factor

q

[

S

(

q

) − 1] normalized for dried 2, 3, and 6 nm ferrihydrite samples (labeled as Fhyd2, Fhyd3, and Fhyd6, respectively). The three patterns show similar occurrences of diffraction maxima. (b) Fourier transform of the total scattering structure factor generates the PDF,

G

(

r

), versus distance

r

[14].

Figure 16.3 (a) PDF

G

(

r

) versus distance

r

for experimental sample Fhyd6 and the calculated structures of akaganéite and goethite. (b) The PDF,

G

(

r

), plotted out to 65 Å to illustrate the degree of attenuation due to the range of structural coherence for Fhyd2 (top), Fhyd3, and Fhyd6 (bottom) [14].

Figure 16.4 Heterogeneous nucleation and growth of iron oxide at water–quartz interfaces using

in situ

time-resolved simultaneous SAXS/GISAXS technique. (a) Simultaneous SAXS/GISAXS setup geometry.

k

i

and

k

f

are the incident and scattered wave vectors,

α

i

and

α

f

are the incident and exit scattered angles of the X-rays out of the surface plane, 2

θ

f

is the exit angles of X-rays within the surface plane,

D

is the interparticle spacing (≈2

π

/

q

xy

*

, where

q

xy

* is the

q

xy

at the center of the peak), and

d

(= 2

R

g,lateral

) and

h

(= 2

R

g,vertical

) are the diameter and height of nanoparticles, respectively. The scattering vector,

q

, is

k

f

k

i

. (b) Clean () surface of quartz image by AFM. (c)

In situ

time-resolved simultaneous SAXS/GISAXS setup at the Advanced Photon Source, sector 12-ID [22].

Figure 16.5 Time series of 2D GISAXS images after exposure of quartz substrate to ferric solutions ([Fe

3+

] = 0.1 mM, [NaNO

3

] = 10 mM, and pH = 3.6). The shift of the lobe location toward a smaller 2

θ

f

indicates the growth of nanoparticles, and the disappearance of distinct lobes suggests particle coalescence. Iron (hydr)oxide nuclei occur and start to grow with well-defined interparticle spacing. Later, the nuclei coalesce, forming larger particles, and exhibit a more polydisperse distribution. This 2D data can be reduced to 1D by cutting along the dotted lines in (c), and 2

θ

f

is converted to

q

xy

in Figure 16.4 by the relationship of

q

xy

=

4π sin((2

θ

f

)/2)

λ

−1

[22].

Figure 16.6

In situ

simultaneous measurements of homogeneous nucleation and heterogeneous nucleation. (a) Quantitative comparison between homogeneously and heterogeneously nucleated total particle volumes under varied aqueous conditions. At [Fe

3+

] = 10

−4

M at pH = 3.6, heterogeneous nucleation is the dominant nucleation mechanism. The inset in (a) shows an enlarged diagram of homogeneously nucleated total particle volume; the axis labels are the same as in (a). (b–d) In-plane GISAXS scattering at

q

z

= 0.0224 Å

−1

(around the Yoneda wing). Green strips and numbers depict the position of interparticle peaks and the approximate lateral radii of nanoparticles, respectively [22].

Figure 16.7 Sizes and interparticle spacings of iron (hydr)oxide nanoparticles at different ionic strengths.

R

g,lateral

and

R

g,vertical

are the radii of particles in the surface plane and in the normal direction, respectively. (a) [Fe

3+

] = 0.1 mM and [NaNO

3

] = 1 mM. (b) [Fe

3+

] = 0.1 mM and [NaNO

3

] = 10 mM. (c) [Fe

3+

] = 0.1 mM and [NaNO

3

] = 100 mM. (d) Interparticle spacings of nanoparticles as a function of

IS

. The solid lines depict the size trend [22].

Figure 16.8 Proposed dominant mechanisms and topology of heterogeneous nucleation in ferric–quartz–water systems depending on

IS

. Different controlling influences dominate, depending on the

IS

. Debye length (= diffuse layer thickness) calculations are based on the following equation from references [60, 61]: Diffuse layer thickness = 2.32 × 10

9

. Saturation ratios (= IAP/

K

sp

) with respect to ferrihydrite are provided. IAP is the ion activity product and

K

sp

is the solubility product at equilibrium [22].

Figure 16.9 Evolutions of the total volume (a), average radius (b), total number (c), and surface area (d) of the primary particles precipitated on the quartz surfaces and in 10

−4

M Fe

3+

solutions with 10 mM NaNO

3

or NaCl. In (b), the evolution of the hydrodynamic particle sizes of the precipitates formed in 10

−4

M Fe

3+

and 3.42 mM Na

2

SO

4

solution is read from the right

y

-axis [23].

Figure 16.10 Evolutions for primary heterogeneously formed particle volume (a), radius of gyration (

R

g

) (b), and particle number (c) evolution in the 10 mM NaNO

3

with 10

−4

M Fe(III) only, 10

−4

M Fe(III) and 10

−5

M As(V), and 10

−4

M Fe(III) and 10

−5

M phosphate systems. The error bars indicate the approximate range of values observed in replicate samples [24].

Chapter 17: X-Ray Absorption Fine Structure Spectroscopy in Fe Oxides and Oxyhydroxides

Figure 17.1 Schematic representation of the X-ray absorption mechanism of an Fe 1s electron. Fluorescence and Auger effect emission mechanisms are also shown.

Figure 17.2 Standard setup of a XAFS beamline: in the optic hutch, the slit systems define the beam size and shape; the monochromator selects the exit beam energy. Standard XAFS equipment generally allows simultaneous transmission and fluorescence measurements. Also shown is an X-ray absorption spectrum of magnetite biomineralized by bacteria

Magnetospirillum gryphiswaldense

where the two characteristic regions, near-edge (XANES) and extended (EXAFS), are indicated.

Figure 17.3 (a) XANES spectra of several iron oxides and oxyhydroxides taken from Ref. [18], : from Berkeley Advanced Light Source (beamline BL 10.3.2) database https://sites.google.com/a/lbl.gov/microxas-lbl-gov/databases, : measured at Elettra Sincrotrone (Trieste, Italy). (b) Shift to lower energies of the absorption edge when reducing from (ferrihydrite) to (wüstite).