Diffraction Patterns Of Crystals Research Articles

シリコーンゴムにおけるメゾ相の形成と結晶化

Silicone rubber consists of cross-linked poly(dimethyl siloxane)(PDMS). Formation of the mesomorphic phase was found in silicone rubber that is highly stretched at room temperature. The mesomorphic phase is characterized by a pair of sharp equatorial reflections in the wide-angle X-ray diffraction (WAXD) pattern. At low temperature, the stretched silicone rubber crystallizes. The WAXD patterns from the crystallized silicone rubber exhibit totally different features depending on the draw ratio. The author successfully obtained single crystals of linear PDMS. Electron diffraction patterns of the single crystals indicate that at least four different crystal forms exist. The observed WAXD patterns and their peculiar transition scheme could be explained by the combination of the crystal forms.

Structure Determination Using X-Ray Free-Electron Laser Pulses.

The intense X-ray pulses from free-electron lasers, of only femtoseconds duration, outrun most of the processes that lead to structural degradation in X-ray exposures of macromolecules. Using these sources it is therefore possible to increase the dose to macromolecular crystals by several orders of magnitude higher than usually tolerable in conventional measurements, allowing crystal size to be decreased dramatically in diffraction measurements and without the need to cool the sample. Such pulses lead to the eventual vaporization of the sample, which has required a measurement approach, called serial crystallography, of consolidating snapshot diffraction patterns of many individual crystals. This in turn has further separated the connection between dose and obtainable diffraction information, with the only requirement from a single pattern being that to give enough information to place it, in three-dimensional reciprocal space, in relation to other patterns. Millions of extremely weak patterns can be collected and combined in this way, requiring methods to rapidly replenish the sample into the beam while generating the lowest possible background . The method is suited to time-resolved measurements over timescales below 1 ps to several seconds, and opens new opportunities for phasing. Some straightforward considerations of achievable signal levels are discussed and compared with a wide variety of recent experiments carried out at XFEL, synchrotron, and even laboratory sources, to discuss the capabilities of these new approaches and give some perspectives on their further development.

New organic conjugated dye nano-aggregates exhibiting naked-eye fluorescence color switching

In this study, a variety of new conjugated containing strong electron-donating groups were prepared for formation of organic nano-scale aggregates. The properties and aggregation modes of these aggregates were investigated on basis of time dependent absorption, fluorescence emission spectra as well as scanning electron microscope images. The results show that nano organic aggregates could be yielded by the linear dyes in mixed DMF/H2O solvent through a simple re-precipitation method, while no aggregates of the branched dyes were produced. X-ray diffraction of single crystal and X-ray diffraction patterns of the powders results demonstrate that the linear dyes tend to show ordered molecular arrangements, while the armed dyes do not exhibit such a tendency. A remarkable fluorescence switching process under 365 nm lamp was observed for the target aggregates. This study successfully provides real examples of organic aggregates in mixed DMF/H2O solvent which have great capacity to show enhanced fluorescence color switching.

Method for Signals Detection in Single Crystal Diffraction Patterns through a Diffraction Pattern Indexing Software

Method for Signals Detection in Single Crystal Diffraction Patterns through a Diffraction Pattern Indexing Software

Single Crystals of the Frustrated β-Phase and Genesis of the Disordered α'-Phase of Poly(l-lactic acid).

The metastable, frustrated β-phase of poly(l-lactic acid) (PLLA) had been obtained so far only by drawing fibers from amorphous PLLA or the stable α-phase. This phase has now been obtained by crystallization in thin films in the form of snow-flake-like crystals produced at high Tc (140 °C). They display the characteristic single crystal diffraction pattern of frustrated polymers with a three-chains, trigonal unit-cell. Also, hko electron diffraction patterns indicate that crystallization of PLLA at 90 °C takes place in a transient, frustrated βPLLA phase that converts rapidly to α'PLLA. The disorder in α'PLLA stems from the incompatible cell symmetries of the trigonal, three-chains βPLLA and orthorhombic, two-chains αPLLA unit-cells. The disorder in α'PLLA involves shifts of domains along the chain axis and three azimuthal orientations 120° apart that both reflect the initial trigonal/hexagonal symmetry of the parent βPLLA. Recognition of this solid-state transformation provides a logical framework that explains many unusual characteristics of the α'PLLA phase (structural disorder, lamellar thickness and possibly growth rate vs Tc).

Facilitating guest transport in clathrate hydrates by tuning guest-host interactions.

The understanding and eventual control of guest molecule transport in gas hydrates is of central importance for the efficient synthesis and processing of these materials for applications in the storage, separation, and sequestration of gases and natural gas production. Previously, some links have been established between dynamics of the host water molecules and guest-host hydrogen bonding interactions, but direct observation of transport in the form of cage-to-cage guest diffusion is still lacking. Recent calculations have suggested that pairs of different guest molecules in neighboring cages can affect guest-host hydrogen bonding and, therefore, defect injection and water lattice motions. We have chosen two sets of hydrate guest pairs, tetrahydrofuran (THF)-CO2 and isobutane-CO2, that are predicted to enhance or to diminish guest-host hydrogen bonding interactions as compared to those in pure CO2 hydrate and we have studied guest dynamics in each using (13)C nuclear magnetic resonance (NMR) methods. In addition, we have obtained the crystal structure of the THF-CO2 sII hydrate using the combined single crystal X-ray diffraction and (13)C NMR powder pattern data and have performed molecular dynamics-simulation of the CO2 dynamics. The NMR powder line shape studies confirm the enhanced and delayed dynamics for the THF and isobutane containing hydrates, respectively, as compared to those in the CO2 hydrate. In addition, from line shape studies and 2D exchange spectroscopy NMR, we observe cage-to-cage exchange of CO2 molecules in the THF-CO2 hydrate, but not in the other hydrates studied. We conclude that the relatively rapid intercage guest dynamics are the result of synergistic guest A-host water-guest B interactions, thus allowing tuning of the guest transport properties in the hydrates by choice of the appropriate guest molecules. Our experimental value for inter-cage hopping is slower by a factor of 10(6) than a published calculated value.

Non-contact Current Transfer Induces the Formation and Improves the X-ray Diffraction Quality of Protein Crystals

The effect of non-contact current transfer on the crystallization of three model proteins (hen egg white lysozyme, bovine pancreatic ribonuclease A, and human recombinant insulin) was investigated using a prototype ion-generator device. The device can produce an equivalent of microcurrent that can be transmitted in a contactless manner by spraying negatively charged ions and using available air gases (O2) as a transfer medium. From a crystallographic perspective, non-contact current transfer technology clearly enhanced the crystal formation process of these three proteins, as evidenced by the high crystallization speed and crystal quality. The quality and X-ray diffraction patterns of lysozyme crystals grown in the presence and absence of the device’s microcurrent were analyzed. Our results indicate a significant positive effect on the quality of the X-ray diffraction pattern after non-contact current transfer, highlighting the value of this technique in protein crystallization.

Data Validation and Structural Classifications in Powder Diffraction File

The new Powder Diffraction File™, housing more than 760,000 diffraction patterns and 200,000 crystal structures, has a wealth of information that a materials scientist can take advantage of in various ways, from materials identification, characterization to design. Various structural and chemical classifications implemented in the database will be presented in detail. These classifications are important in data mining studies and optimizing pattern search/match methods. While using any database in materials characterization, it is important to know the quality of the crystal structure or diffraction pattern found in the database. With varying quality of published data in the literature, database editorial review processes had to adopt rigorous data evaluation methods to classify data based on its quality. Every entry in the Powder Diffraction File™ has a quality mark and editorial comments describing the error and the correction. Results of the analysis of the quality of the crystal structures (~500,000) published over the years will be discussed along with the most common errors found. The recent developments in Powder Diffraction File will be presented.

In vivo protein crystallization in living insect cells

Spontaneous protein crystallization within living cells has been observed several times in nature, e.g. for storage proteins in seeds. In vivo crystal growth can also occur during gene over-expression, as particularly discovered in baculovirus-infected insect cells [1]. We have recently shown that these in vivo crystals represent valuable targets for structural biology after isolation from the cell. Applying serial crystallography techniques at an X-ray free-electron laser (XFEL) as well as using a highly brilliant synchrotron source, single crystal diffraction pattern were collected and combined to yield high-resolution structural information of the associated fully glycosylated protein [2,3]. So far, the cellular mechanisms involved in the in vivo crystallization process remain to be understood, preventing a more successful application of this novel approach. Thus, our study aims at identifying the parameters crucial for optimal crystal growth within baculovirus-infected Sf9 insect cells. Combining confocal microscopy with live-cell imaging techniques and compartment-specific staining methods, we systematically investigated the impact of the intracellular environment on in vivo crystallization by directing recombinant proteins into different cellular compartments using specific signal sequences. Moreover, the impact of cellular transport mechanisms and induced cellular stress on the quality and size of the in vivo crystals was investigated in detail. The presented results provide important insights into the process of protein crystallization within living cells and will therefore significantly contribute to increase the success rate for spontaneous crystal growth of other proteins. Considering that in vivo crystals represent highly suitable targets for structural biology, this approach offers exciting new possibilities for proteins that do not form crystals suitable for conventional X-ray diffraction in vitro.

High-resolution synchrotron x-ray powder diffraction study of the incommensurate modulation in the martensite phase ofNi2MnGa: Evidence for nearly 7M modulation and phason broadening

The modulated structure of the martensite phase of Ni2MnGa is revisited using high resolution synchrotron x-ray powder diffraction (SXRPD) measurements, which reveals higher order satellite reflections up to the 3rd order and phason broadening of the satellite peaks. The structure refinement, using the (3+1) dimensional superspace group approach, shows that the modulated structure of Ni2MnGa can be described by orthorhombic superspace group Immm(00$\gamma$)s00 with lattice parameters a= 4.21861(2) {\AA}, b= 5.54696(3) {\AA}, and c= 4.18763(2) {\AA} and an incommensurate modulation wave vector q= 0.43160(3)c*= (3/7+$\delta$)c*, where $\delta$=0.00303(3) is the degree of incommensuration of the modulated structure. Additional satellite peak broadening, which could not be accounted for in terms of the anisotropic strain broadening based on a lattice parameter distribution , has been modeled in terms of phasons using fourth rank covariant strain tensor representation for incommensurate structures. The simulation of single crystal diffraction patterns from the refined structural parameters unambiguously reveals a rational approximant structure with 7M modulation. The inhomogeneous displacement of different atomic sites on account of incommensurate modulation and the presence of phason broadening clearly rule out the adaptive phase model proposed recently by Kaufmann et al.[1] and suggests that the modulation in Ni2MnGa originates from soft-mode phonons.

New schemes for recording electron diffraction patterns of hexagonal and monoclinic crystals

Some new schemes for recording electron diffraction patterns of hexagonal crystals rotating around the axes lying in the (hk0) plane of the reciprocal lattice and monoclinic crystals rotating around the a and b axes of the direct lattice and the a* axis of the reciprocal lattice have been developed. Formulas for interpreting electron diffraction patterns are reported. The electron diffraction patterns obtained based on these schemes were used to solve the 2H and 3R polytypes of CdInGaS4 crystals and the 3R polytype of Zn1.5In3Se6 crystal with the parameters a = 4.046 and c = 59.292 A, sp. gr. R3m.

Studies on growth and characterization of l-alanine strontium chloride trihydrate single crystals for optical applications

The optically transparent nonlinear optical single crystals of l-alanine strontium chloride trihydrate (LASCT) were grown by slow evaporation solution growth method using water as solvent. The purity of the crystals was increased by the method of recrystallization. The grown crystals were analyzed by the single crystal X-ray diffraction pattern which proved that LASCT belongs to monoclinic crystal system. The presence of various functional groups and modes of vibrations were identified by FTIR spectroscopy. The optical absorption study confirms the suitability of the crystal for device applications. The thermal strength and the decomposition of the grown crystals were studied using TG/DTA analyses. The dielectric constant and dielectric loss measurements of the grown crystals at different frequencies of the applied field were measured and reported. The mechanical strength of the crystal is estimated by Vicker's hardness test. The nonlinear optical properties of the grown crystals were confirmed by second harmonic generation test which shows the suitability of NLO applications.

X-ray powder reference patterns of the Fe(Sb2+xTe1−x) skutterudites for thermoelectric applications

The crystal structure and powder X-ray diffraction (XRD) patterns for three skutterudite samples, Fe(Sb2+xTe1−x),x = 0.05, 0.10, 0.20, have been determined. These compounds crystallize in the cubic space group$Im\bar 3$. Te was found to randomly substitute in the Sb site. Because of the fact the covalent radius of Sb is greater than that of Te, a trend of increasing lattice parameter has been observed as thexvalue in Fe(Sb2+xTe1−x) increases [cell parameters range from 9.10432(4) to 9.11120(3) Å forx = 0.0 to 0.2, respectively]. The Fe–Sb/Te bond distance also increases progressively [from 2.5358(4) to 2.5388(4) Å] as the Te content decreases. While average Sb/Te–Sb/Te distances in the four-membered rings are similar in these three compounds, the average Sb/Te–Sb/Te edge distances in the octahedral framework increase progressively from 3.5845(12) to 3.5900(13) Å. Reference XRD patterns of these three phases have been prepared to be included in the Powder Diffraction File (PDF).

LCDiXRay: a user-friendly program for powder diffraction indexing of columnar liquid crystals

The formulation of a standard computerized procedure for the indexing of powder X-ray diffraction (PXRD) patterns of columnar liquid crystals, with the determination of all structural information extracted from a properly indexed PXRD spectrum and the attribution of the columnar mesophase symmetry, is presented. In particular, the proposed program notably accelerates the identification of columnar mesophases together with thein situdetermination of their structural parameters such as mesophase type, space group, cell parameters, cross-section area, intermolecular stacking distance between consecutive discoids and, in the case of ordered mesophases, the estimation of the number of molecules constituting each discoid.

Collagen osteoid-like model allows kinetic gene expression studies of non-collagenous proteins in relation with mineral development to understand bone biomineralization.

Among persisting questions on bone calcification, a major one is the link between protein expression and mineral deposition. A cell culture system is here proposed opening new integrative studies on biomineralization, improving our knowledge on the role played by non-collagenous proteins in bone. This experimental in vitro model consisted in human primary osteoblasts cultured for 60 days at the surface of a 3D collagen scaffold mimicking an osteoid matrix. Various techniques were used to analyze the results at the cellular and molecular level (adhesion and viability tests, histology and electron microscopy, RT- and qPCR) and to characterize the mineral phase (histological staining, EDX, ATG, SAED and RMN). On long term cultures human bone cells seeded on the osteoid-like matrix displayed a clear osteoblast phenotype as revealed by the osteoblast-like morphology, expression of specific protein such as alkaline phosphatase and expression of eight genes classically considered as osteoblast markers, including BGLAP, COL1A1, and BMP2. Von Kossa and alizarine red allowed us to identify divalent calcium ions at the surface of the matrix, EDX revealed the correct Ca/P ratio, and SAED showed the apatite crystal diffraction pattern. In addition RMN led to the conclusion that contaminant phases were absent and that the hydration state of the mineral was similar to fresh bone. A temporal correlation was established between quantified gene expression of DMP1 and IBSP, and the presence of hydroxyapatite, confirming the contribution of these proteins to the mineralization process. In parallel a difference was observed in the expression pattern of SPP1 and BGLAP, which questioned their attributed role in the literature. The present model opens new experimental possibilities to study spatio-temporal relations between bone cells, dense collagen scaffolds, NCPs and hydroxyapatite mineral deposition. It also emphasizes the importance of high collagen density environment in bone cell physiology.

Purification of L-asparaginase II by crystallization

Here a case study of L-asparaginase II out of a recombinant Escherichia coli is presented. The target protein was obtained by simple cell disintegration and acetone precipitation. The L-asparaginase II has been crystallized in three different forms in the following microbatch crystallization. The rod-shaped crystals (∼400 μm edge length) were obtained at either 8°C or 22°C after 17 h by addition of PEG6000. The rectangular-shaped crystals were obtained after further recrystallization of the rod-shaped crystals. The rhombic-shaped crystals formed at 8°C after 12 days when cold ethanol was used instead of PEG6000. All crystallizations were performed in tris-acetate buffer (50 mmol·L−1, pH 5.1). By crystallization, the specific activity of L-asparaginase II has increased 5-fold. The protein content and the purity of the crystals were evaluated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The more concentrated L-asparaginase II out of an extract mixture and the presence of only less minor proteins after crystallization demonstrates that crystallization is an effective and mild method to purify the target protein. The single crystal X-ray diffraction pattern reveals that the crystals are proteins and the X-ray powder diffraction (XRPD) pattern shows clearly that the crystals forming in PEG6000 and ethanol have different crystal structures.

Assembly and tunable luminescence of lanthanide-organic frameworks constructed from 4-(3,5-dicarboxyphenyl)pyridine-2,6-dicarboxylate ligand

A novel N-heterocycle multicarboxylate ligand 4-(3,5-dicarboxyphenyl)pyridine-2,6-dicarboxylic acid (H4dpda) was synthesized, and then reacted with lanthanide salts to yield a series of lanthanide metal–organic frameworks, [Ln(Hdpda)(H2O)4]·0.5(H2O) (Ln=Eu(1), Gd(2), Tb(3), Dy(4)) and [Tb1−xEux(Hdpda)(H2O)4]·0.5(H2O) (x=0.1–10mol%). Single crystal X-ray diffraction and powder XRD patterns confirm these MOFs are isostructural. Luminescent measurements suggest that the ligand can provide efficient sensitization for the lanthanide ion Tb(III) and Eu(III) in the mixed lanthanide MOFs. Additionally, the luminescence color of the mixed MOFs can be easily tuned from green to green–yellow, yellow, orange, red–orange and red by varying the molar ratio of Eu(III)/Tb(III).

Macrophages Sequester Clofazimine in an Intracellular Liquid Crystal-Like Supramolecular Organization

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.

Mirror symmetries in multiple diffraction patterns of face-centred cubic crystals

In this work, a study of the mirror symmetries appearing in multiple diffraction patterns of face-centred cubic crystals is carried out. Several different X-ray and neutron multiple diffraction patterns have been simulated for different face-centred cubic structures. The patterns were plotted in circular plots which showed that two types of symmetry mirrors coexist in the patterns: isomorphic and anamorphic mirrors. The number and types of mirrors depend on then-fold symmetry of the scattering vector associated with the primary reflection. Forneven, onlynisomorphic mirrors appear in the patterns. Fornodd,nisomorphic mirrors are formed intercalated betweennanamorphic mirrors.

Dynamical Simulation of Electron Backscatter Diffraction (EBSD) Patterns of Imperfect Crystals.

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.