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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.  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
5.  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
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.  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
8.  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
9.  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
10.  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
11.  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
12.  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
13.  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
14.  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
15.  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
16.  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
17.  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
18.  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
19.  Polarizable atomic multipole X-ray refinement: application to peptide crystals 
A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time.
Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussian multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of inter­atomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered R free by 20–40% relative to the original spherically symmetric scattering model.
doi:10.1107/S0907444909022707
PMCID: PMC2733883  PMID: 19690373
scattering factors; aspherical; anisotropic; force fields; multipole; polarization; AMOEBA; bond density; direct summation; FFT; SGFFT; Ewald; PME
20.  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
21.  [Bis­(diphenyl­phosphino)methane-κ2 P,P′]dichloridopalladium(II) 
The title complex, [PdCl2(C25H22P2)], is a slightly distorted square-planar bis­(diphenyl­phosphino)methane cis-complex of PdCl2. The structure of a polymorph of the title compound has been described earlier, but the arrangement of the mol­ecules observed in the current structure is distinctively different from that previously reported [Steffen & Palenik (1976 ▶). Inorg. Chem. 15, 2432–2439]. The earlier report describes a structure with individual well separated mol­ecules crystallizing in space group P21/n. The polymorph described here, which is isostructrural to its Pt analogue [Babai et al. (2006 ▶). Z. Anorg. Allg. Chem. 632, 639–644], crystallizes in C2/c with chains of C2-symmetric mol­ecules stretching parallel to the b axis. The Pd atoms and the bis­phosphino­methane units are located on two different positions created by a non-crystallographic mirror operation with an occupancy of 0.6677 (11) for the major (PCH2P)Pd moiety. The positions of the Cl atoms of the minor moiety do coincide perfectly with those of the next mol­ecule along the chain parallel to b, and they are thus not included in the disorder. The phenyl rings also do not take part in the disorder and are common to both the major and minor moieties of the (PCH2P)PdCl2 units. Assuming no defects, mol­ecules in each chain will thus have to be oriented the same way and the effect of the disorder of the (PCH2P)Pd unit is thus a reversal in direction of the chains parallel to b. The presence of light streaks of intensity between actual Bragg peaks indicates that a somehow ordered arrangement not resolved in the Bragg diffraction data may be present (i.e. an incommensurate superstructure) rather than a random or domain arrangement of the chains.
doi:10.1107/S1600536808042980
PMCID: PMC2968394  PMID: 21581770
22.  Reversible Loss of Bernal Stacking during the Deformation of Few-Layer Graphene in Nanocomposites 
ACS Nano  2013;7(8):7287-7294.
The deformation of nanocomposites containing graphene flakes with different numbers of layers has been investigated with the use of Raman spectroscopy. It has been found that there is a shift of the 2D band to lower wavenumber and that the rate of band shift per unit strain tends to decrease as the number of graphene layers increases. It has been demonstrated that band broadening takes place during tensile deformation for mono- and bilayer graphene but that band narrowing occurs when the number of graphene layers is more than two. It is also found that the characteristic asymmetric shape of the 2D Raman band for the graphene with three or more layers changes to a symmetrical shape above about 0.4% strain and that it reverts to an asymmetric shape on unloading. This change in Raman band shape and width has been interpreted as being due to a reversible loss of Bernal stacking in the few-layer graphene during deformation. It has been shown that the elastic strain energy released from the unloading of the inner graphene layers in the few-layer material (∼0.2 meV/atom) is similar to the accepted value of the stacking fault energies of graphite and few layer graphene. It is further shown that this loss of Bernal stacking can be accommodated by the formation of arrays of partial dislocations and stacking faults on the basal plane. The effect of the reversible loss of Bernal stacking upon the electronic structure of few-layer graphene and the possibility of using it to modify the electronic structure of few-layer graphene are discussed.
doi:10.1021/nn402830f
PMCID: PMC3789269  PMID: 23899378
graphene; Bernal stacking; nanocomposites; Raman spectroscopy; deformation
23.  Macrophages Sequester Clofazimine in an Intracellular Liquid Crystal-Like Supramolecular Organization 
PLoS ONE  2012;7(10):e47494.
Clofazimine is a poorly-soluble but orally-bioavailable small molecule drug that massively accumulates in macrophages when administered over prolonged periods of time. To determine whether crystal-like drug inclusions (CLDIs) that form in subcellular spaces correspond to pure clofazimine crystals, macrophages of clofazimine-fed mice were elicited with an intraperitoneal thioglycollate injection. Inside these cells, CLDIs appeared uniform in size and shape, but were sensitive to illumination. Once removed from cells, CLDIs were unstable. Unlike pure clofazimine crystals, isolated CLDIs placed in distilled water burst into small birefringent globules, which aggregated into larger clusters. Also unlike pure clofazimine crystals, CLDIs fragmented when heated, and disintegrated in alkaline media. In contrast to all other organelles, CLDIs were relatively resistant to sonication and trypsin digestion, which facilitated their biochemical isolation. The powder x-ray diffraction pattern obtained from isolated CLDIs was consistent with the diffraction pattern of liquid crystals and inconsistent with the expected molecular diffraction pattern of solid, three dimensional crystals. Observed with the transmission electron microscope (TEM), CLDIs were bounded by an atypical double-layered membrane, approximately 20 nanometers thick. CLDIs were polymorphic, but generally exhibited an internal multilayered organization, comprised of stacks of membranes 5 to 15 nanometers thick. Deep-etch, freeze-fracture electron microscopy of unfixed snap-frozen tissue samples confirmed this supramolecular organization. These results suggest that clofazimine accumulates in macrophages by forming a membrane-bound, multilayered, liquid crystal-like, semi-synthetic cytoplasmic structure.
doi:10.1371/journal.pone.0047494
PMCID: PMC3469554  PMID: 23071814
24.  Calcioferrite with composition (Ca3.94Sr0.06)Mg1.01(Fe2.93Al1.07)(PO4)6(OH)4·12H2O 
Calcioferrite, ideally Ca4MgFe3+ 4(PO4)6(OH)4·12H2O (tetra­calcium magnesium tetrairon(III) hexakis-phosphate tetra­hydroxide dodeca­hydrate), is a member of the calcioferrite group of hydrated calcium phosphate minerals with the general formula Ca4 AB 4(PO4)6(OH)4·12H2O, where A = Mg, Fe2+, Mn2+ and B = Al, Fe3+. Calcioferrite and the other three known members of the group, montgomeryite (A = Mg, B = Al), kingsmountite (A = Fe2+, B = Al), and zodacite (A = Mn2+, B = Fe3+), usually occur as very small crystals, making their structure refinements by conventional single-crystal X-ray diffraction challenging. This study presents the first structure determination of calcioferrite with composition (Ca3.94Sr0.06)Mg1.01(Fe2.93Al1.07)(PO4)6(OH)4·12H2O based on single-crystal X-ray diffraction data collected from a natural sample from the Moculta quarry in Angaston, Australia. Calcioferrite is isostructural with montgomeryite, the only member of the group with a reported structure. The calcioferrite structure is characterized by (Fe/Al)O6 octa­hedra (site symmetries 2 and -1) sharing corners (OH) to form chains running parallel to [101]. These chains are linked together by PO4 tetra­hedra (site symmetries 2 and 1), forming [(Fe/Al)3(PO4)3(OH)2] layers stacking along [010], which are connected by (Ca/Sr)2+ cations (site symmetry 2) and Mg2+ cations (site symmetry 2; half-occupation). Hydrogen-bonding inter­actions involving the water mol­ecules (one of which is equally disordered over two positions) and OH function are also present between these layers. The relatively weaker bonds between the layers account for the cleavage of the mineral parallel to (010).
doi:10.1107/S1600536814004061
PMCID: PMC3998495  PMID: 24764934
25.  Strain-release mechanisms in bimetallic core-shell nanoparticles as revealed by Cs-corrected STEM 
Surface science  2013;609:161-166.
Lattice mismatch in a bimetallic core-shell nanoparticle will cause strain in the epitaxial shell layer, and if it reaches the critical layer thickness misfit dislocations will appear in order to release the increasing strain. These defects are relevant since they will directly impact the atomic and electronic structures thereby changing the physical and chemical properties of the nanoparticles. Here we report the direct observation and evolution through aberration-corrected scanning transmission electron microscopy of dislocations in AuPd core-shell nanoparticles. Our results show that first Shockley partial dislocations (SPD) combined with stacking faults (SF) appear at the last Pd layer; then, as the shell grows the SPDs and SFs appear at the interface and combine with misfit dislocations, which finally diffuse to the free surfaces due to the alloying of Au into the Pd shell. The critical layer thickness was found to be at least 50% greater than in thin films, confirming that shells growth on nanoparticles can sustain more strain due to the tridimensional nature of the nanoparticles.
doi:10.1016/j.susc.2012.12.001
PMCID: PMC3580871  PMID: 23457419

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