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1.  A look inside epitaxial cobalt-on-fluorite nanoparticles with three-dimensional reciprocal space mapping using GIXD, RHEED and GISAXS 
Journal of Applied Crystallography  2013;46(Pt 4):874-881.
Three-dimensional reciprocal space mapping by X-ray and electron diffraction [namely grazing-incidence X-ray diffraction (GIXD), reflection high-energy electron diffraction (RHEED) and grazing-incidence small-angle X-ray scattering (GISAXS)] was used to explore the internal structure and shape of differently oriented epitaxial Co/CaF2 facetted nanoparticles.
In this work epitaxial growth of cobalt on CaF2(111), (110) and (001) surfaces has been extensively studied. It has been shown by atomic force microscopy that at selected growth conditions stand-alone faceted Co nanoparticles are formed on a fluorite surface. Grazing-incidence X-ray diffraction (GIXD) and reflection high-energy electron diffraction (RHEED) studies have revealed that the particles crystallize in the face-centered cubic lattice structure otherwise non-achievable in bulk cobalt under normal conditions. The particles were found to inherit lattice orientation from the underlying CaF2 layer. Three-dimensional reciprocal space mapping carried out using X-ray and electron diffraction has revealed that there exist long bright 〈111〉 streaks passing through the cobalt Bragg reflections. These streaks are attributed to stacking faults formed in the crystal lattice of larger islands upon coalescence of independently nucleated smaller islands. Distinguished from the stacking fault streaks, crystal truncation rods perpendicular to the {111} and {001} particle facets have been observed. Finally, grazing-incidence small-angle X-ray scattering (GISAXS) has been applied to decouple the shape-related scattering from that induced by the crystal lattice defects. Particle faceting has been verified by modeling the GISAXS patterns. The work demonstrates the importance of three-dimensional reciprocal space mapping in the study of epitaxial nanoparticles.
doi:10.1107/S0021889813008777
PMCID: PMC3769055  PMID: 24046491
cobalt-on-fluorite nanoparticles; grazing-incidence X-ray diffraction (GIXD); reflection high-energy electron diffraction (RHEED); grazing-incidence small-angle X-ray scattering (GISAXS); epitaxial growth; three-dimensional reciprocal space mapping
2.  THE STRUCTURE OF ACTIN-RICH FILAMENTS OF MUSCLES ACCORDING TO X-RAY DIFFRACTION 
From analysis of moderate- to small-angle x-ray diffraction patterns, in the light of similar experience with paramyosin, has been derived the following description for the structure of actin-rich filaments in "tinted" portions of the adductor muscle of the clam, Venus mercenaria: 1. Some 11 diffraction maxima, widely streaked along layer lines and occurring at moderate diffraction angles (spacings 7 to 60 A) appear to be accounted for as (hk) reflections of a net whose cell elements are, for dry material: a ≑ 82 A, b = 406 A (filament axis identity period), and γ ≑ 82° (angle between a and b axes). These reflections follow a selection rule which indicates that the net cell is non-primitive and contains 15 equivalent locations (nodes) arranged as shown in Fig. 5. An alternative net has b' = 351 A and 13 nodes per cell. 2. Another interpretation rolls the net into a large-scale helix and places the 15 (or 13) nodes along 7 (or 6) turns of a helical locus projecting 406 (or 351) A along the filament axis. Whether considered to be built of planar-net or helix-net cells, the individual filament contains a single cell width transverse to its axis. Transverse filament dimensions are, therefore, in either case similar (50 to 100 A). 3. Consideration of existing electron-optical, physicochemical, and x-ray diffraction data regarding isolated actin suggests that the net cell is built of rods, each containing in cross-section from one to four actin molecules which run parallel to or twisted about rod axes that extend at 12° to the filament axis along the (21) diagonals of the cell. Depending on monomer shape, 2 to 15 monomers furnish length to reach across two cells, and the actin molecules are built into each rod in such a way as to repeat (or nearly repeat) structure 15 (or 13) times along the double cell length. Further details of intra-rod structure cannot be suggested because of lack of wide-angle diffraction information. 4. The actin system is sensitive to treatment of the muscle with ethanol. Concentrations of 5 per cent or greater abolish the net reflections. Other solvents—water, benzene, ether, pyridine, acetone—do not alter the pattern materially. 5. Two other reflections, occurring at the first and second layer lines of an axial periodicity of about 400 A, do not clearly belong to the actin-net system. They represent either a superstructure built upon the filaments by parts of the actin molecules themselves or by incorporated other molecular species, or they arise from an additional macromolecular component (possibly myosin, or its homologues or fractions) of similar axial periodicity.
PMCID: PMC2223960  PMID: 13295312
3.  Three-dimensional electron crystallography of protein microcrystals 
eLife  2013;2:e01345.
We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1–1° and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 Å resolution. This proof of principle paves the way for the implementation of a new technique, which we name ‘MicroED’, that may have wide applicability in structural biology.
DOI: http://dx.doi.org/10.7554/eLife.01345.001
eLife digest
X-ray crystallography has been used to work out the atomic structure of a large number of proteins. In a typical X-ray crystallography experiment, a beam of X-rays is directed at a protein crystal, which scatters some of the X-ray photons to produce a diffraction pattern. The crystal is then rotated through a small angle and another diffraction pattern is recorded. Finally, after this process has been repeated enough times, it is possible to work backwards from the diffraction patterns to figure out the structure of the protein.
The crystals used for X-ray crystallography must be large to withstand the damage caused by repeated exposure to the X-ray beam. However, some proteins do not form crystals at all, and others only form small crystals. It is possible to overcome this problem by using extremely short pulses of X-rays, but this requires a very large number of small crystals and ultrashort X-ray pulses are only available at a handful of research centers around the world. There is, therefore, a need for other approaches that can determine the structure of proteins that only form small crystals.
Electron crystallography is similar to X-ray crystallography in that a protein crystal scatters a beam to produce a diffraction pattern. However, the interactions between the electrons in the beam and the crystal are much stronger than those between the X-ray photons and the crystal. This means that meaningful amounts of data can be collected from much smaller crystals. However, it is normally only possible to collect one diffraction pattern from each crystal because of beam induced damage. Researchers have developed methods to merge the diffraction patterns produced by hundreds of small crystals, but to date these techniques have only worked with very thin two-dimensional crystals that contain only one layer of the protein of interest.
Now Shi et al. report a new approach to electron crystallography that works with very small three-dimensional crystals. Called MicroED, this technique involves placing the crystal in a transmission electron cryo-microscope, which is a fairly standard piece of equipment in many laboratories. The normal ‘low-dose’ electron beam in one of these microscopes would normally damage the crystal after a single diffraction pattern had been collected. However, Shi et al. realized that it was possible to obtain diffraction patterns without severely damaging the crystal if they dramatically reduced the normal low-dose electron beam. By reducing the electron dose by a factor of 200, it was possible to collect up to 90 diffraction patterns from the same, very small, three-dimensional crystal, and then—similar to what happens in X-ray crystallography—work backwards to figure out the structure of the protein. Shi et al. demonstrated the feasibility of the MicroED approach by using it to determine the structure of lysozyme, which is widely used as a test protein in crystallography, with a resolution of 2.9 Å. This proof-of principle study paves the way for crystallographers to study protein that cannot be studied with existing techniques.
DOI: http://dx.doi.org/10.7554/eLife.01345.002
doi:10.7554/eLife.01345
PMCID: PMC3831942  PMID: 24252878
electron crystallography; electron diffraction; electron cryomicroscopy (cryo-EM); microED; protein structure; microcrystals; None
4.  Redetermination of Ce[B5O8(OH)(H2O)]NO3·2H2O 
The crystal structure of Ce[B5O8(OH)(H2O)]NO3·2H2O, cerium(III) aqua­hydroxidoocta­oxidopenta­borate nitrate dihydrate, has been redetermined from single-crystal X-ray diffraction data. In contrast to the previous determination [Li et al. (2003 ▶). Chem. Mater. 15, 2253–2260], the present study reveals the location of all H atoms, slightly different fundamental building blocks (FBBs) of the polyborate anions, more reasonable displacement ellipsoids for all non-H atoms, as well as a model without disorder of the nitrate anion. The crystal structure is built from corrugated polyborate layers parallel to (010). These layers, consisting of [B5O8(OH)(H2O)]2− anions as FBBs, stack along [010] and are linked by Ce3+ ions, which exhibit a distorted CeO10 coordination sphere. The layers are additionally stabilized via O—H⋯O hydrogen bonds between water mol­ecules and nitrate anions, located at the inter­layer space. The [BO3(H2O)]-group shows a [3 + 1] coordination and is considerably distorted from a tetra­hedral configuration. Bond-valence-sum calculation shows that the valence sum of boron is only 2.63 valence units (v.u.) when the contribution of the water mol­ecule (0.49 v.u.) is neglected.
doi:10.1107/S1600536812016169
PMCID: PMC3344287  PMID: 22590053
5.  Complementary ab initio and X-ray nanodiffraction studies of Ta2O5 
Acta Materialia  2015;83:276-284.
The complex structure of Ta2O5 led to the development of various structural models. Among them, superstructures represent the most stable configurations. However, their formation requires kinetic activity and long-range ordering processes, which are hardly present during physical vapor deposition. Based on nano-beam X-ray diffraction and concomitant ab initio studies, a new metastable orthorhombic basic structure is introduced for Ta2O5 with lattice parameters a = 6.425 Å, b = 3.769 Å and c = 7.706 Å. The unit cell containing only 14 atoms, i.e. two formula unit blocks in the c direction, is characterized by periodically alternating the occupied oxygen site between two possible positions in succeeding 002-planes. This structure can be described by the space group 53 (Pncm) with four Wyckoff positions, and exhibits an energy of formation of −3.209 eV atom−1. Among all the reported basic structures, its energy of formation is closest to those of superstructures. Furthermore, this model exhibits a 2.5 eV band gap, which is closer to experimental data than the band gap of any other basic-structure model. The sputtered Ta2O5 films develop only a superstructure if annealed at temperatures >800 °C in air or vacuum. Based on these results and the conveniently small unit cell size, it is proposed that the basic-structure model described here is an ideal candidate for both structure and electronic state descriptions of orthorhombic Ta2O5 materials.
doi:10.1016/j.actamat.2014.10.006
PMCID: PMC4308001  PMID: 25642136
Ta2O5; Structure; Nanobeam diffraction; Ab initio; DOS
6.  Ionothermal synthesis of open-framework metal phosphates with a Kagomé lattice network exhibiting canted anti-ferromagnetism† †Electronic supplementary information (ESI) available: Cif files, atomic parameters, X-ray diffraction patterns, IR spectra, TG curves, and thermal ellipsoid plot and atomic label schemes of compound 1–4. See DOI: 10.1039/c4tc00290c Click here for additional data file.  
Four open-framework transition-metal phosphates; (NH4)2Co3(HPO4)2F4 (1), (NH4)Co3(HPO4)2(H2PO4)F2 (2), KCo3(HPO4)2(H2PO4)F2 (3), and KFe3(HPO4)2(H2PO4)F2 (4); are prepared by ionothermal synthesis using pyridinium hexafluorophosphate as the ionic liquid.
Four open-framework transition-metal phosphates; (NH4)2Co3(HPO4)2F4 (1), (NH4)Co3(HPO4)2(H2PO4)F2 (2), KCo3(HPO4)2(H2PO4)F2 (3), and KFe3(HPO4)2(H2PO4)F2 (4); are prepared by ionothermal synthesis using pyridinium hexafluorophosphate as the ionic liquid. Single-crystal X-ray diffraction analyses reveal that the four compounds contain cobalt/iron–oxygen/fluoride layers with Kagomé topology composed of interlinked face-sharing MO3F3/MO4F2 octahedra. PO3OH pseudo-tetrahedral groups augment the [M3O6F4] (1)/[M3O8F2] layers on both sides to give M3(HPO4)2F4 (1) and M3(HPO4)2F2 (2–4) layers. These layers are stacked along the a axis in a sequence AA…, resulting in the formation of a layer structure for (NH4)2Co3(HPO4)2F4(1). In NH4Co3(HPO4)2(H2PO4)F2 and KM3(HPO4)2(H2PO4)F2, the M3(HPO4)2F2 layers are stacked along the a axis in a sequence AAi… and are connected by [PO3(OH)] tetrahedra, giving rise to a 3-D open framework structure with 10-ring channels along the [001] direction. The negative charges of the inorganic framework are balanced by K+/NH4 + ions located within the channels. The magnetic transition metal cations themselves form layers with stair-case Kagomé topology. Magnetic susceptibility and magnetization measurements reveal that all four compounds exhibit a canted anti-ferromagnetic ground state (T c = 10 or 13 K for Co and T c = 27 K for Fe) with different canting angles. The full orbital moment is observed for both Co2+ and Fe2+.
doi:10.1039/c4tc00290c
PMCID: PMC4285085  PMID: 25580250
7.  The Complexity of Hydration of Phloroglucinol: A Comprehensive Structural and Thermodynamic Characterization 
The Journal of Physical Chemistry. B  2012;116(13):3961-3972.
Hydrate formation is of great importance as the inclusion of water molecules affects many solid state properties and hence determines the required chemical processing, handling, and storage. Phloroglucinol is industrially important, and the observed differences in the morphology and diffuse scattering effects with growth conditions have been scientifically controversial. We have studied the anhydrate and dihydrate of phloroglucinol and their transformations by a unique combination of complementary experimental and computational techniques, namely, moisture sorption analysis, hot-stage microscopy, differential scanning calorimetry, thermogravimetry, isothermal calorimetry, single crystal and powder X-ray diffractometry, and crystal energy landscape calculations. The enthalpically stable dihydrate phase is unstable below 16% relative humidity (25 °C) and above 50 °C (ambient humidity), and the kinetics of hydration/dehydration are relatively rapid with a small hysteresis. A consistent atomistic picture of the thermodynamics of the hydrate/anhydrate transition was derived, consistent with the disordered single X-ray crystal structure and crystal energy landscape showing closely related low energy hydrate structures. These structures provide models for proton disorder and show stacking faults as intergrowth of different layers are possible. This indicates that the consequent variability in crystal surface features and diffuse scattering with growth conditions is not a practical concern.
doi:10.1021/jp211948q
PMCID: PMC3320094  PMID: 22390190
8.  Structure cristalline du composé intermétallique Ni18Ge12  
The title compound was synthesized using solid-state reaction and characterized by X-ray diffraction. The structure crystallizes in an own structure type which is a commensurate superstructure of an underlying B8-type substructure.
Single crystals of octa­deca­nickel dodeca­germanide were grown by chemical transport reaction. The inter­metallic compound crystallizes in a superstructure of the hexa­gonal NiAs type (B8 type). All atoms in the asymmetric unit lie on special positions except one Ni atom (two Ni atoms have site symmetry -6.. and another one has site symmetry .2. while the Ge atoms have site symmetries 32., m.. and 3..). In the structure, the Ni atoms are arranged in 11- or 13-vertex polyhedra (CN = 11–13). The coordination polyhedra of the Ge atoms are bicapped square anti­prisms (CN = 10) or 11-vertex polyhedra (CN = 11). The structure exhibits strong Ge⋯Ni inter­actions, but no close Ge⋯Ge contacts are observed. The Ni atoms with CN = 13 form infinite chains along [001] with an Ni—Ni distance of 2.491 (2) Å.
doi:10.1107/S2056989015003680
PMCID: PMC4350741  PMID: 25844198
crystal structure; nickel germanide; inter­metallic compound; B8-type substructure; Ge⋯Ni inter­actions
9.  Epitaxial Structure of (001)- and (111)-Oriented Perovskite Ferrate Films Grown by Pulsed-Laser Deposition 
Crystal Growth & Design  2010;10(4):1725-1729.
We report epitaxial growth and structures of SrFeO2.5 (SFO) films on SrTiO3 (STO) (001) and (111) substrates by pulsed-laser deposition. Reflection high-energy electron diffraction intensity oscillations were observed during the initial growth on both substrates, reflecting a layer-by-layer growth mode of the formula unit cell. It was found that the films were stabilized with a monoclinic structure that was derived from the original orthorhombic structure of bulk Brownmillerite. Using an X-ray reciprocal space mapping technique, in-plane domain structures and the orientation relationship were investigated. In addition, the impact of laser spot area on the epitaxial structures was studied. For the films grown on the (001) STO, the orientation relationship was robust against the change of the laser spot area: SFO(001)//STO(001) and SFO(100)//STO(100) for the out-of-plane and the in-plane, respectively, with the [001] axis tilted toward the 4-fold a- and b-axes by ∼1.4°, whereas nearly (111)-oriented films were obtained on the (111) STO, exhibiting a complicated manner of tilting that depended on laser spot area. The observed variation in tilting configurations can be understood in terms of possible atomic arrangements at the SFO/STO interface. These results present a guide to control the heteroepitaxial growth and structure of (111)-oriented noncubic perovskites.
The epitaxial structures of SrFeO2.5 films grown on SrTiO3 (001) and (111) substrates by PLD are reported. A layer-by-layer growth mode was achieved in the initial stage on both substrates. The films were stabilized with a monoclinic structure, where we identified the in-plane domain structures and orientation relationship. Our study presents a guide to control the heteroepitaxy of (111)-oriented noncubic perovskites.
doi:10.1021/cg901355c
PMCID: PMC2851191  PMID: 20383295
10.  Observation of ‘hidden’ planar defects in boron carbide nanowires and identification of their orientations 
The physical properties of nanostructures strongly depend on their structures, and planar defects in particular could significantly affect the behavior of the nanowires. In this work, planar defects (twins or stacking faults) in boron carbide nanowires are extensively studied by transmission electron microscopy (TEM). Results show that these defects can easily be invisible, i.e., no presence of characteristic defect features like modulated contrast in high-resolution TEM images and streaks in diffraction patterns. The simplified reason of this invisibility is that the viewing direction during TEM examination is not parallel to the (001)-type planar defects. Due to the unique rhombohedral structure of boron carbide, planar defects are only distinctive when the viewing direction is along the axial or short diagonal directions ([100], [010], or 1¯10) within the (001) plane (in-zone condition). However, in most cases, these three characteristic directions are not parallel to the viewing direction when boron carbide nanowires are randomly dispersed on TEM grids. To identify fault orientations (transverse faults or axial faults) of those nanowires whose planar defects are not revealed by TEM, a new approach is developed based on the geometrical analysis between the projected preferred growth direction of a nanowire and specific diffraction spots from diffraction patterns recorded along the axial or short diagonal directions out of the (001) plane (off-zone condition). The approach greatly alleviates tedious TEM examination of the nanowire and helps to establish the reliable structure–property relations. Our study calls attention to researchers to be extremely careful when studying nanowires with potential planar defects by TEM. Understanding the true nature of planar defects is essential in tuning the properties of these nanostructures through manipulating their structures.
doi:10.1186/1556-276X-9-30
PMCID: PMC3898527  PMID: 24423258
Boron carbide nanowires; Rhombohedral crystal system; Transmission electron microscopy; Planar defects
11.  Nanoscale characterization of electrical transport at metal/3C-SiC interfaces 
Nanoscale Research Letters  2011;6(1):120.
In this work, the transport properties of metal/3C-SiC interfaces were monitored employing a nanoscale characterization approach in combination with conventional electrical measurements. In particular, using conductive atomic force microscopy allowed demonstrating that the stacking fault is the most pervasive, electrically active extended defect at 3C-SiC(111) surfaces, and it can be electrically passivated by an ultraviolet irradiation treatment. For the Au/3C-SiC Schottky interface, a contact area dependence of the Schottky barrier height (ΦB) was found even after this passivation, indicating that there are still some electrically active defects at the interface. Improved electrical properties were observed in the case of the Pt/3C-SiC system. In this case, annealing at 500°C resulted in a reduction of the leakage current and an increase of the Schottky barrier height (from 0.77 to 1.12 eV). A structural analysis of the reaction zone carried out by transmission electron microscopy [TEM] and X-ray diffraction showed that the improved electrical properties can be attributed to a consumption of the surface layer of SiC due to silicide (Pt2Si) formation. The degradation of Schottky characteristics at higher temperatures (up to 900°C) could be ascribed to the out-diffusion and aggregation of carbon into clusters, observed by TEM analysis.
doi:10.1186/1556-276X-6-120
PMCID: PMC3211166  PMID: 21711619
12.  Nonlinear optical imaging of defects in cubic silicon carbide epilayers 
Scientific Reports  2014;4:5258.
Silicon carbide is one of the most promising materials for power electronic devices capable of operating at extreme conditions. The widespread application of silicon carbide power devices is however limited by the presence of structural defects in silicon carbide epilayers. Our experiment demonstrates that optical second harmonic generation imaging represents a viable solution for characterizing structural defects such as stacking faults, dislocations and double positioning boundaries in cubic silicon carbide layers. X-ray diffraction and optical second harmonic rotational anisotropy were used to confirm the growth of the cubic polytype, atomic force microscopy was used to support the identification of silicon carbide defects based on their distinct shape, while second harmonic generation microscopy revealed the detailed structure of the defects. Our results show that this fast and noninvasive investigation method can identify defects which appear during the crystal growth and can be used to certify areas within the silicon carbide epilayer that have optimal quality.
doi:10.1038/srep05258
PMCID: PMC4052718  PMID: 24918841
13.  Surface Modification and Planar Defects of Calcium Carbonates by Magnetic Water Treatment 
Nanoscale Research Letters  2010;5(12):1982-1991.
Powdery calcium carbonates, predominantly calcite and aragonite, with planar defects and cation–anion mixed surfaces as deposited on low-carbon steel by magnetic water treatment (MWT) were characterized by X-ray diffraction, electron microscopy, and vibration spectroscopy. Calcite were found to form faceted nanoparticles having 3x (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ 0\bar{1} 1 4 $$\end{document}) commensurate superstructure and with well-developed {\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ 1 1\bar{2} 0 $$\end{document}} and {\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ 10\bar{1} 4 $$\end{document}} surfaces to exhibit preferred orientations. Aragonite occurred as laths having 3x (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ 0\bar{1} 1$$\end{document}) commensurate superstructure and with well-developed (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ 0\bar{1} 1 $$\end{document}) surface extending along [100] direction up to micrometers in length. The (hkil)-specific coalescence of calcite and rapid lath growth of aragonite under the combined effects of Lorentz force and a precondensation event account for a beneficial larger particulate/colony size for the removal of the carbonate scale from the steel substrate. The coexisting magnetite particles have well-developed {011} surfaces regardless of MWT.
doi:10.1007/s11671-010-9736-5
PMCID: PMC2991221  PMID: 21170405
Calcium carbonate; Nanoparticle; Magnetic water treatment; Surface modification; Superstructure; TEM
14.  Surface Modification and Planar Defects of Calcium Carbonates by Magnetic Water Treatment 
Nanoscale Research Letters  2010;5(12):1982-1991.
Powdery calcium carbonates, predominantly calcite and aragonite, with planar defects and cation–anion mixed surfaces as deposited on low-carbon steel by magnetic water treatment (MWT) were characterized by X-ray diffraction, electron microscopy, and vibration spectroscopy. Calcite were found to form faceted nanoparticles having 3x () commensurate superstructure and with well-developed {} and {} surfaces to exhibit preferred orientations. Aragonite occurred as laths having 3x () commensurate superstructure and with well-developed () surface extending along [100] direction up to micrometers in length. The (hkil)-specific coalescence of calcite and rapid lath growth of aragonite under the combined effects of Lorentz force and a precondensation event account for a beneficial larger particulate/colony size for the removal of the carbonate scale from the steel substrate. The coexisting magnetite particles have well-developed {011} surfaces regardless of MWT.
doi:10.1007/s11671-010-9736-5
PMCID: PMC2991221  PMID: 21170405
Calcium carbonate; Nanoparticle; Magnetic water treatment; Surface modification; Superstructure; TEM
15.  Dynamic Nanoparticles Assemblies 
Accounts of chemical research  2012;45(11):1916-1926.
CONSPECTUS
Importance
Although nanoparticle (NP) assemblies are at the beginning of their development, their unique geometrical shapes and media-responsive optical, electronic and magnetic properties have attracted significant interest. Nanoscale assembly bridges multiple sizes of materials: individual nanoparticles, discrete molecule-like or virus-like nanoscale agglomerates, microscale devices, and macroscale materials. The capacity to self-assemble can greatly facilitate the integration of nanotechnology with other technologies and, in particular, with microscale fabrication. In this Account, we describe developments in the emerging field of dynamic NP assemblies, which are spontaneously formed superstructures containing more than two inorganic nanoscale particles that display ability to change their geometrical, physical, chemical, and other attributes. In many ways, dynamic assemblies can represent a bottleneck in the ‘bottom-up’ fabrication of NP-based devices because they can produce a much greater variety of assemblies, but they also provide a convenient tool for variation of geometries and dimensions of nanoparticle assemblies.
Classification
Superstructures of NPs (and those held together by similar intrinsic forces) are classified into two groups: Class 1 where media and external fields can alter shape, conformation, and order of stable superstructures with a nearly constant number same. The future development of successful dynamic assemblies requires understanding the equilibrium in dynamic NP systems. The dynamic nature of Class 1 assemblies is associated with the equilibrium between different conformations of a superstructure and is comparable to the isomerization in classical chemistry. Class 2 assemblies involve the formation and/or breakage of linkages between the NPs, which is analogous to the classical chemical equilibrium for the formation of a molecule from atoms. Finer classification of NP assemblies in accord with established conventions in the field may include different size dimensionalities: discrete assemblies (artificial molecules), one-dimensional (spaced chains) and two-dimensional (sheets) and three-dimensional (superlattices, twisted structures) assemblies. Notably, these dimensional attributes must be regarded as primarily topological in nature because all of these superstructures can acquire complex three-dimensional shapes.
Preparation
We discuss three primary strategies used to prepare NP superstructures: (1) anisotropy-based assemblies utilizing either intrinsic force field anisotropy around NPs or external anisotropy associated with templates and/or applied fields; (2) assembly methods utilizing uniform NPs with isotropic interactions; and (3) methods based on mutual recognition of biomolecules, such as DNA and antigen-antibody interactions.
Applications
We consider optical, electronic, and magnetic properties of dynamic superstructures, focusing primarily on multiparticle effects in NP superstructures as represented by surface plasmon resonance, NP-NP charge transport, and multibody magnetization. Unique properties of NP superstructures are being applied to biosensing, drug delivery, and nanoelectronics. For both Class 1 and Class 2 dynamic assemblies, biosensing is the most dominant and well-developed area of dynamic nanostructures being successfully transitioned into practice. We can foresee the rapid development of dynamic NP assemblies toward applications in harvesting of dissipated energy, photonics, and electronics. The final part of the review is devoted to the fundamental questions facing dynamic assemblies of NPs in the future.
doi:10.1021/ar200305f
PMCID: PMC3479329  PMID: 22449243
16.  Dark-field transmission electron microscopy and the Debye-Waller factor of graphene 
Graphene's structure bears on both the material's electronic properties and fundamental questions about long range order in two-dimensional crystals. We present an analytic calculation of selected area electron diffraction from multi-layer graphene and compare it with data from samples prepared by chemical vapor deposition and mechanical exfoliation. A single layer scatters only 0.5% of the incident electrons, so this kinematical calculation can be considered reliable for five or fewer layers. Dark-field transmission electron micrographs of multi-layer graphene illustrate how knowledge of the diffraction peak intensities can be applied for rapid mapping of thickness, stacking, and grain boundaries. The diffraction peak intensities also depend on the mean-square displacement of atoms from their ideal lattice locations, which is parameterized by a Debye-Waller factor. We measure the Debye-Waller factor of a suspended monolayer of exfoliated graphene and find a result consistent with an estimate based on the Debye model. For laboratory-scale graphene samples, finite size effects are sufficient to stabilize the graphene lattice against melting, indicating that ripples in the third dimension are not necessary.
doi:10.1103/PhysRevB.87.045417
PMCID: PMC4167771  PMID: 25242882
17.  Diffuse scattering study of aspirin forms (I) and (II) 
Full three-dimensional diffuse scattering data have been recorded for both polymorphic forms [(I) and (II)] of aspirin and these data have been analysed using Monte Carlo computer modelling. The observed scattering in form (I) is well reproduced by a simple harmonic model of thermally induced displacements. The data for form (II) show, in addition to thermal diffuse scattering (TDS) similar to that in form (I), diffuse streaks originating from stacking fault-like defects as well as other effects that can be attributed to strain induced by these defects.
Full three-dimensional diffuse scattering data have been recorded for both polymorphic forms [(I) and (II)] of aspirin and these data have been analysed using Monte Carlo computer modelling. The observed scattering in form (I) is well reproduced by a simple harmonic model of thermally induced displacements. The data for form (II) show, in addition to thermal diffuse scattering (TDS) similar to that in form (I), diffuse streaks originating from stacking fault-like defects as well as other effects that can be attributed to strain induced by these defects. The present study has provided strong evidence that the aspirin form (II) structure is a true polymorph with a structure quite distinct from that of form (I). The diffuse scattering evidence presented shows that crystals of form (II) are essentially composed of large single domains of the form (II) lattice with a relatively small volume fraction of intrinsic planar defects or faults comprising misoriented bilayers of molecular dimers. There is evidence of some local aggregation of these defect bilayers to form small included regions of the form (I) structure. Evidence is also presented that shows that the strain effects arise from the mismatch of molecular packing between the defect region and the surrounding form (II) lattice. This occurs at the edges of the planar defects in the direction only.
doi:10.1107/S0108768110037055
PMCID: PMC2992034  PMID: 21099031
diffuse scattering; polymorphism; aspirin; harmonic model
18.  THE STRUCTURE OF PARAMYOSIN FIBRILS ACCORDING TO X-RAY DIFFRACTION 
From analysis of x-ray diffraction patterns obtained with improved small-angle techniques has been derived the following description for the structure of the fibrils of the fibrous protein, paramyosin, obtained in this case from "white" portions of the adductor muscle of the clam, Venus mercenaria: 1. About 25 significantly different diffraction maxima have been resolved and found accounted for as (hk) reflections of a net whose cell elements are, for the dry material: a = 250 A, b = 720 A (fibril axis identity period), and γ = 90.5° (angle included between a and b axes). For rehydrated material a is larger (ca. 325 A), b is essentially unchanged, and γ is slightly larger. There remains an unresolved discrepancy between the electron-optically derived, cell's a dimension (193 A) and that here reported for dry samples. 2. The h = ±1 row lines are crossed on the diagrams (because γ is not 90°) and thus can be distinguished in spite of natural "rotation" of fibrils (within the massive fibrous specimens) about their commonly oriented axes. The observed reflections are then found to obey a selection rule which indicates that the net cell is non-primitive and contains 5 equivalent locations (nodes) arranged as shown in Fig. 5. The nodal distribution is the same as has been previously photographed electron-optically. 3. Analysis of reflection lengths indicates that the native fibrils are not noticeably ribbon-like, having dimensions normal to the ordered net layers approximating their width across the fibril in the plane of the net layers. Corresponding transverse, interlayer spacings (possibly ca. 100 A) have not been observed, however, and may be hidden in troublesome central scatter. 4. Since paramyosin's wide-angle diffraction is very probably of α-type, supercoiled α-helices must be involved according to current interpretations of α-diagrams. Physicochemical evidence suggests that cables of this type, ca. 1400 A in length, may extend over two cells. Of two possible nodal connections, a favored one is shown in Fig. 5 to join 5 nodes in this way. Considerations of space filling, of transverse distribution of small-angle x-ray scattering, and of nodal significance, suggest that the cable units may be further aggregated into supercables, essentially forming rather solid rods of ca. 100 A diameter. 5. An alternative interpretation of the paramyosin small-angle diffraction, in particular of the observed selection rule, would conclude that large particles are arranged in a helical way, with minimum helix diameter about 150 A (dry). The simplest (genetic) particle connection would have 5 particles in 2 coil turns along 720 A of fibril or helix axis. This view is distinctly different from the arrangement of "rods" in net-like layers as given above, even though the rods are said to be made of supercoils or cables. Reasons are given for preferring the net-of-rods explanation over the particulate-helix model. The helix- vs. true-net ambiguity arises whenever the two types of structure are conceivable, and decision between them is difficult on the basis of the diffraction data alone.
PMCID: PMC2223955  PMID: 13295311
19.  Redetermination of Zn2Mo3O8  
The crystal structure of dizinc trimolybdenum(IV) octa­oxide, Zn2Mo3O8, has been redetermined from single-crystal X-ray data. The structure has been reported previously based on neutron powder diffraction data [Hibble et al. (1999 ▶). Acta Cryst. B55, 683-697] and single-crystal data [McCarroll et al. (1957 ▶). J. Am. Chem. Soc. 79, 5410–5414; Ansell & Katz (1966 ▶) Acta Cryst. 21, 482–485]. The results of the current redetermination show an improvement in the precision of the structural and geometric parameters with all atoms refined with anisotropic displacement parameters. The crystal structure consists of distorted hexa­gonal-close-packed oxygen layers with stacking sequence abac along [001] and is held together by alternating zinc and molybdenum layers. The Zn atoms occupy both tetra­hedral and octa­hedral inter­stices with a ratio of 1:1. The Mo atoms occupy octa­hedral sites and form strongly bonded triangular clusters involving three MoO6 octa­hedra that are each shared along two edges, forming a Mo3O13 unit. All atoms lie on special positions. The Zn atoms are in 2b Wyckoff positions with 3m. site symmetry, the Mo atoms are in 6c Wyckoff positions with . m. site symmetry and the O atoms are in 2a, 2b and 6c Wyckoff positions with 3m. and . m. site symmetries, respectively.
doi:10.1107/S1600536809021928
PMCID: PMC2969349  PMID: 21582645
20.  Surface-treated self-standing curved crystals as high-efficiency elements for X- and γ-ray optics: theory and experiment1  
Journal of Applied Crystallography  2015;48(Pt 3):666-671.
It is demonstrated that crystals with curved diffracting planes made of relatively light elements, such as silicon, germanium and gallium arsenide, in the Laue diffraction geometry and in an energy range between 60 and 600 keV can reach a higher diffraction efficiency than more dense mosaic crystals such as copper, silver and gold. In particular, self-standing curved crystals can be used as elements in γ-ray lenses.
The efficiency of a Laue lens for X- and γ-ray focusing in the energy range 60–600 keV is closely linked to the diffraction efficiency of the single crystals composing the lens. A powerful focusing system is crucial for applications like medical imaging and X-ray astronomy where wide beams must be focused. Mosaic crystals with a high density, such as Cu or Au, and bent crystals with curved diffracting planes (CDPs) are considered for the realization of a focusing system for γ-rays, owing to their high diffraction efficiency in a predetermined angular range. In this work, a comparison of the efficiency of CDP crystals and Cu and Au mosaic crystals was performed on the basis of the theory of X-ray diffraction. Si, GaAs and Ge CDP crystals with optimized thicknesses and moderate radii of curvature of several tens of metres demonstrate comparable or superior performance with respect to the higher atomic number mosaic crystals generally used. In order to increase the efficiency of the lens further, a stack of several CDP crystals is proposed as an optical element. CDP crystals were obtained by a surface-damage method, and a stack of two surface-damaged bent Si crystals was prepared and tested. Rocking curves of the stack were performed with synchrotron radiation at 19 keV to check the lattice alignment: they exhibited only one diffraction peak.
doi:10.1107/S1600576715006809
PMCID: PMC4453971  PMID: 26089758
X-ray focusing lenses; integrated reflectivity; curved crystals; crystal stacks
21.  Signature of dislocations and stacking faults of face-centred cubic nanocrystals in coherent X-ray diffraction patterns: a numerical study1  
Journal of Applied Crystallography  2015;48(Pt 3):621-644.
Crystal defects can be identified by their fingerprint in coherent X-ray diffraction patterns. Realistic defects in face-centred cubic nanocrystals are studied numerically, revealing various signatures in diffraction patterns depending on the Miller indices and providing an identification method.
Crystal defects induce strong distortions in diffraction patterns. A single defect alone can yield strong and fine features that are observed in high-resolution diffraction experiments such as coherent X-ray diffraction. The case of face-centred cubic nanocrystals is studied numerically and the signatures of typical defects close to Bragg positions are identified. Crystals of a few tens of nanometres are modelled with realistic atomic potentials and ‘relaxed’ after introduction of well defined defects such as pure screw or edge dislocations, or Frank or prismatic loops. Diffraction patterns calculated in the kinematic approximation reveal various signatures of the defects depending on the Miller indices. They are strongly modified by the dissociation of the dislocations. Selection rules on the Miller indices are provided, to observe the maximum effect of given crystal defects in the initial and relaxed configurations. The effect of several physical and geometrical parameters such as stacking fault energy, crystal shape and defect position are discussed. The method is illustrated on a complex structure resulting from the simulated nanoindentation of a gold nanocrystal.
doi:10.1107/S1600576715005324
PMCID: PMC4453968  PMID: 26089755
dislocations; stacking faults; face-centred cubic nanocrystals; coherent X-ray diffraction
22.  Three-dimensional electron diffraction as a complementary technique to powder X-ray diffraction for phase identification and structure solution of powders 
IUCrJ  2015;2(Pt 2):267-282.
Two recently developed three-dimensional electron diffraction methods have shown great potential for phase identification and structure determination of polycrystalline powder materials. Their combination with powder X-ray diffraction makes them powerful techniques for phase identification in multiphase samples and the determination of very complex structures from nano- and micron-sized crystals.
Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED) data collection, namely automated diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed. Compared with X-ray diffraction (XRD) and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD) provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni–Se–O–Cl crystals, zeolites, germanates, metal–organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional ED methods will become crucially important in the near future.
doi:10.1107/S2052252514028188
PMCID: PMC4392419  PMID: 25866663
three-dimensional electron diffraction; powder X-ray diffraction; phase identification; structure determination
23.  Peptide model helices in lipid membranes: insertion, positioning, and lipid response on aggregation studied by X-ray scattering 
European Biophysics Journal  2010;40(4):417-436.
Studying membrane active peptides or protein fragments within the lipid bilayer environment is particularly challenging in the case of synthetically modified, labeled, artificial, or recently discovered native structures. For such samples the localization and orientation of the molecular species or probe within the lipid bilayer environment is the focus of research prior to an evaluation of their dynamic or mechanistic behavior. X-ray scattering is a powerful method to study peptide/lipid interactions in the fluid, fully hydrated state of a lipid bilayer. For one, the lipid response can be revealed by observing membrane thickening and thinning as well as packing in the membrane plane; at the same time, the distinct positions of peptide moieties within lipid membranes can be elucidated at resolutions of up to several angstroms by applying heavy-atom labeling techniques. In this study, we describe a generally applicable X-ray scattering approach that provides robust and quantitative information about peptide insertion and localization as well as peptide/lipid interaction within highly oriented, hydrated multilamellar membrane stacks. To this end, we have studied an artificial, designed β-helical peptide motif in its homodimeric and hairpin variants adopting different states of oligomerization. These peptide lipid complexes were analyzed by grazing incidence diffraction (GID) to monitor changes in the lateral lipid packing and ordering. In addition, we have applied anomalous reflectivity using synchrotron radiation as well as in-house X-ray reflectivity in combination with iodine-labeling in order to determine the electron density distribution ρ(z) along the membrane normal (z axis), and thereby reveal the hydrophobic mismatch situation as well as the position of certain amino acid side chains within the lipid bilayer. In the case of multiple labeling, the latter technique is not only applicable to demonstrate the peptide’s reconstitution but also to generate evidence about the relative peptide orientation with respect to the lipid bilayer.
Electronic supplementary material
The online version of this article (doi:10.1007/s00249-010-0645-4) contains supplementary material, which is available to authorized users.
doi:10.1007/s00249-010-0645-4
PMCID: PMC3070074  PMID: 21181143
Peptide lipid interactions; Membrane active peptides; Model helices; X-ray scattering; Hydrophobic mismatch; Lipid chain correlation
24.  Light diffraction from colloidal crystals with low dielectric constant modulation 
We theoretically characterized the diffraction properties of both closed-packed and non-closed-packed crystalline colloidal array (CCA) photonic crystals. A general theory based on single-scattering kinematic approach was developed and used to calculate the diffraction efficiency of CCA of different sphere diameters at different incident light angles. Our theory explicitly relates the scattering properties of individual spheres (calculated by using Mie theory) comprising a CCA to the CCA diffraction efficiency. For a CCA with a lattice constant of 380 nm, we calculated the relative diffraction intensities of the fcc (111), (200), and (220) planes and determined which sphere diameter gives rise to the most efficiently diffracting CCA for each set of crystal planes. The effective penetration depth of the light was calculated for several crystal planes of several CCAs of different sphere diameters at different angles of incidence. The typical penetration depth for a CCA comprised of polystyrene spheres was calculated to be in the range of 10-40 CCA layers. A one-dimensional (1D) model of diffraction from the stack of (111) fcc crystal layers was developed and used to assess the role of multiple scattering and to test our single-scattering approach. The role of disorder was studied by using this 1D scattering model. Our methodology will be useful for the optimization of photonic crystal coating materials.
doi:10.1103/PhysRevB.77.235404
PMCID: PMC2908428  PMID: 20657709
25.  Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals 
eLife  null;4:e05421.
There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.
DOI: http://dx.doi.org/10.7554/eLife.05421.001
eLife digest
Large biological molecules (or macromolecules) have intricate three-dimensional structures. X-ray crystallography is a technique that is commonly used to determine these structures and involves directing a beam of X-rays at a crystal that was grown from the macromolecule of interest. The macromolecules in the crystal scatter the X-rays to produce a diffraction pattern, and the crystal is rotated to provide further diffraction images. It is then possible to work backwards from these images and elucidate the structure of the macromolecule in three dimensions.
X-ray beams are powerful enough to damage crystals, and scientists are developing new approaches to overcome this problem. One recent development uses ‘X-ray free electron lasers’ to circumvent the damage caused to crystals. However, early applications of this approach required many crystals and thousands to millions of diffraction patterns to be collected—largely because methods to process the diffraction data were far from optimal.
Uervirojnangkoorn et al. have now developed a new data-processing procedure that is specifically designed for diffraction data obtained using X-ray free electron lasers. This method was applied to diffraction data collected from crystals of three different macromolecules (which in this case were three different proteins). For all three, the new method required many fewer diffraction images to determine the structure, and in one case revealed more details about the structure than the existing methods.
This new method is now expected to allow a wider range of macromolecules to be studied using crystallography with X-ray free electron lasers, including cases where very few crystals are available.
DOI: http://dx.doi.org/10.7554/eLife.05421.002
doi:10.7554/eLife.05421
PMCID: PMC4397907  PMID: 25781634
X-ray crystallography; free electron laser; data processing; none

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