High-resolution X-ray Diffraction Data Research Articles

Transferable Aspherical Atom Modeling of Electron Density in Highly Symmetric Crystals: A Case Study of Alkali-Metal Nitrates.

A comparative electron density study (from X-ray diffraction and periodic quantum chemistry) of sodium and potassium nitrates is performed to test the performance of a transferrable aspherical atom model, which is based on the invarioms, to describe chemical bonding features of ions occurring in sites of different symmetry typical of inorganic salts and in different crystal environments. Relying on tabulated entries for the isolated ions (although tailor-made to account for different site symmetries), it takes the same time to employ as the spherical atom model routinely used in X-ray diffraction studies but provides an electron density distribution that faithfully reveals all the interionic interactions-even the weakest ones (such as between the nitrate anions or a K···N interaction found in the metastable form of KNO3) yet important for properties of inorganic materials-as if obtained from high-resolution X-ray diffraction data.

Hydrothermal Synthesis, Structure, and Superconductivity of Simple Cubic Perovskite (Ba0.62K0.38)(Bi0.92Mg0.08)O3 with Tc ∼ 30 K.

We have synthesized a new superconducting perovskite bismuth oxide by a facile hydrothermal route at 220 °C. The choice of starting materials, their mixing ratios, and the hydrothermal reaction temperature was crucial for obtaining products with superior superconducting properties. The structure of the powder sample was investigated using laboratory X-ray diffraction, high-resolution synchrotron X-ray diffraction (SXRD) data, and electron diffraction (ED) patterns [transmission electron microscopy (TEM) analysis]. The refinement of SXRD data confirmed a simple perovskite-type structure with a cubic cell of a = 4.27864(2) Å [space group Pm3̅m (No. 221)]. Elemental analysis detected magnesium in the final products, and a refinement based on SXRD and inductively coupled plasma data yielded an ideal undistorted simple cubic perovskite-type structure, with the chemical composition (Ba0.62K0.38)(Bi0.92Mg0.08)O3. ED patterns also confirmed the simple cubic perovskite structure; the cube-shaped microstructures and compositional homogeneity on the nanoscale were verified by scanning electron microscopy and TEM analyses, respectively. The fabricated compound exhibited a large shielding volume fraction of about 98% with a maximum Tcmag of ∼30 K, which was supported by the measured bismuth valence as well. Its electrical resistivity dropped at ∼21 K, and zero resistivity was observed below 7 K. The compound underwent thermal decomposition above 400 °C. Finally, the calculated band structure showed a metallic behavior for this hydrothermally synthesized bismuth oxide.

Novel sydnone derivatives carrying azidomethyl-1,2, 4-oxadiazole unit and their 1,3-dipolar cycloadditions

ABSTRACTA series of 1,2,4-oxadiazolymethyl sydnones carrying azido group were synthesized and subjected to react with a variety of alkenic and acetylenic dipolarophilic reagents; N-phenyl maleimide, phenyl vinyl sulfone, and phenyl propiolic acid. All the new products are identified by spectral/physical data including high-resolution mass measurements and X-ray diffraction data.

Bonding in Uranium(V) Hexafluoride Based on the Experimental Electron Density Distribution Measured at 20 K.

The electron density distribution of [PPh4][UF6] was obtained from high-resolution X-ray diffraction data measured at 20 K. The electron density was modeled with an augmented Hansen-Coppens multipolar formalism. Topological analysis reveals that the U-F bond is of incipient covalent nature. Theoretical calculations add further support to the bonding description gleaned from the experimental model. The impact of the uranium anomalous dispersion terms on the refinement is also discussed.

High Resolution X-ray Diffraction Dataset for Bacillus licheniformis Gamma Glutamyl Transpeptidase-acivicin complex: SUMO-Tag Renders High Expression and Solubility.

Gamma glutamyl transpeptidase, (GGT) is a ubiquitous protein which plays a central role in glutathione metabolism and has myriad clinical implications. It has been shown to be a virulence factor for pathogenic bacteria, inhibition of which results in reduced colonization potential. However, existing inhibitors are effective but toxic and therefore search is on for novel inhibitors, which makes it imperative to understand the interactions of various inhibitors with the protein in substantial detail. High resolution structures of protein bound to different inhibitors can serve this purpose. Gamma glutamyl transpeptidase from Bacillus licheniformis is one of the model systems that have been used to understand the structure-function correlation of the protein. The structures of the native protein (PDB code 4OTT), of its complex with glutamate (PDB code 4OTU) and that of its precursor mimic (PDB code 4Y23) are available, although at moderate/low resolution. In the present study, we are reporting the preliminary analysis of, high resolution X-ray diffraction data collected for the co-crystals of B. licheniformis, Gamma glutamyl transpeptidase, with its inhibitor, Acivicin. Crystals belong to the orthorhombic space group P212121 and diffract X-ray to 1.45Å resolution. This is the highest resolution data reported for all GGT structures available till now. The use of SUMO fused expression system enhanced yield of the target protein in the soluble fraction, facilitating recovery of protein with high purity. The preliminary analysis of this data set shows clear density for the inhibitor, acivicin, in the protein active site.

Charge density analysis of metformin chloride, a biguanide anti-hyperglycemic agent

The experimental charge density analysis of the anti-hyperglycemic agent metformin chloride with high-resolution X-ray diffraction data at low temperature (100 K) has been performed and these experimental results were compared with that derived from the corresponding periodic theoretical calculations at the B3LYP/6-31G** level of theory. The experimental and theoretical multipolar charge-density analyses of metformin chloride have been accomplished in order to understand its structural and electronic properties. The C and N atoms of the molecular backbone adopt a near trigonal geometry due to the occurrence of extensive delocalization/resonance of C—N bonds, as confirmed by topological analysis and also found by Natural Resonance Theory calculations performed in the isolated metformin cation. The molecule contains six C—N bonds and the topological bond order analysis shows that four bonds have bond orders close to 4/3 and two bonds can be considered as single. The analysis of numerical parameters of the valence shell charge concentration reports that the N3 atom, which forms two bonds with C atoms, possesses one non-bonding valence-shell charge concentration (VSCC) in the direction of the electron lone pair. Among the intermolecular interactions of the chloride atom with the H—C and H—N atoms, eight have been found to be shorter than the sum of van der Waals radii. The analysis of contacts on the Hirshfeld surface reveals that the H—N...Cl hydrogen bonds are enriched (over-represented) and act as the driving force in the crystal packing formation. The metformin cations form favorable electrostatic interactions with the chloride anions which have globally a stronger energy than the unfavorable cation/cation interactions.

Crystallization of a fungal lytic polysaccharide monooxygenase expressed from glycoengineered Pichia pastoris for X-ray and neutron diffraction.

Lytic polysaccharide monooxygenases (LPMOs) are carbohydrate-disrupting enzymes secreted by bacteria and fungi that break glycosidic bonds via an oxidative mechanism. Fungal LPMOs typically act on cellulose and can enhance the efficiency of cellulose-hydrolyzing enzymes that release soluble sugars for bioethanol production or other industrial uses. The enzyme PMO-2 from Neurospora crassa (NcPMO-2) was heterologously expressed in Pichia pastoris to facilitate crystallographic studies of the fungal LPMO mechanism. Diffraction resolution and crystal morphology were improved by expressing NcPMO-2 from a glycoengineered strain of P. pastoris and by the use of crystal seeding methods, respectively. These improvements resulted in high-resolution (1.20 Å) X-ray diffraction data collection at 100 K and the production of a large NcPMO-2 crystal suitable for room-temperature neutron diffraction data collection to 2.12 Å resolution.

Crystal Structure of Colocasia esculenta Tuber Agglutinin at 1.74 Å Resolution and Its Quaternary Interactions

Many members of the monocot mannose-binding lectin family, characterized by specificity towards mannose have been characterized and cloned. A majority of these lectins molecules contain 1-4 polypeptides of about 110 residues each. From the previously solved crystal structures of a few such lectins, mostly from non-edible plants, these lectins are thought to possess a common β-prism II fold structure. The major tuber storage protein of Colocasia esculenta is a monocot mannose-binding, widely used, dietary lectin. This tuber agglutinin contains two polypeptides of 12.0 and 12.4 kDa by matrix assisted laser desorption ionisation time-of-flight mass spectrometry. By gel filtration at pH 7.2, the purified lectin has a α2β2 form of apparent molecular mass of 48.2 kDa in solution but at pH 3, it has the heterodimeric αβ form. Lectin crystals were obtained by hanging-drop, vapor-diffusion method at room temperature and high-resolution X-ray diffraction data were collected using a home X-ray source. Among previously solved crystal structures of this family are garlic, Solomon’s seal, snowdrop, daffodil and Spanish blue-bell lectins, but the protein sequence of the Colocasia esculenta tuber agglutinin was found to be closest to that of the Remusatia vivipara lectin having no simple mannose-binding property. Using the previously solved 2.4A crystal structure of the Remusatia vivipara lectin, that of Colocasia esculenta has been solved by molecular replacement and subsequent crystallographic refinement and root mean square deviations between various lectins are tabulated and rationalized. The asymmetric unit in our lectin crystal structure contains four β-prism II domains or two αβ heterodimers, each forming a α2β2 heterotetramer with a symmetry related unit. The tetrameric interface obtained from our crystal structure is used to explain the conversion to dimers in acidic pH. Five ordered magnesium ions were located in the asymmetric unit and the presence of magnesium verified by atomic absorption spectroscopy.

Two cubic phases in kimzeyite garnet from the type locality Magnet Cove, Arkansas.

The crystal structure of an optically anisotropic kimzeyite garnet from Magnet Cove, Arkansas, USA, where it was first discovered, was refined with the Rietveld method, cubic space group, Ia\overline 3 d, and monochromatic [λ = 0.41422 (2) Å] synchrotron high-resolution powder X-ray diffraction (HRPXRD) data. The Rietveld refinement reduced χ2 and overall R(F2) values are 1.840 and 0.0647, respectively. The sample, with the general garnet formula [8]X3[6]Y2[4]Z3[4]O12, contains an intergrowth of two cubic phases that occur initially as oscillatory growth zoning, and patchy intergrowths arise later from fluid-enhanced dissolution and re-precipitation. The two compositions obtained with electron-probe microanalyses (EPMA) are Ca3.00(Zr1.31Ti4+0.46Fe3+0.22Mn3+0.01)∑2[Al0.76Fe3+1.01Si1.23]∑3O12 for phase 1a and Ca2.99(Zr1.48Ti4+0.37Fe3+0.15)∑2[Al0.87Fe3+0.98Si1.15]∑3O12 for phase 1b. The weight percentage, unit-cell parameter (Å), distances (Å), and site occupancy factors (s.o.f.s) for phase 1a are as follows: 42.6 (2)%, a = 12.46553 (3) Å, average 〈X-O〉 = 2.482, Y-O = 2.059 (2), Z-O = 1.761 (2) Å, Ca (X s.o.f.) = 0.960 (4), Zr (Y s.o.f.) = 0.809 (3), and Fe (Z s.o.f.) = 0.623 (2). The corresponding values for phase 1b are 57.4 (2)%, a = 12.47691 (2) Å, average 〈X-O〉 = 2.482, Y-O = 2.062 (1), Z-O = 1.762 (1) Å, Ca (X s.o.f.) = 0.957 (3), Zr (Y s.o.f.) = 0.828 (2) and Fe (Z s.o.f.) = 0.617 (2). The main structural differences between the two phases are in the unit-cell parameter, Δa = 0.01138 Å, Y(s.o.f.), and Y-O distance. Structural mismatch between the two cubic phases in a crystal gives rise to strain-induced optical anisotropy.

Observation of anisotropic distribution of microstructure in GaP/GaAs epitaxial layers

Anisotropic distribution of microstructure in GaP/GaAs epitaxial layers is investigated by performing high resolution x-ray diffraction (HRXRD) experiments for symmetric reflections at different azimuths. The observed anisotropy leads to the different values of lattice relaxation along the [011¯] and [01¯1¯] directions as revealed by the reciprocal space maps recorded at 0° and 90° azimuths for (42¯2¯) and (422¯) reflections. The anisotropic relaxation process causes large differences in the full width at half maximum of (400) diffraction peaks of omega scans along the [011¯] and [01¯1¯] directions. It therefore provides large differences in the values of microstructural parameters of the GaP epitaxial layer along the two in-plane orthogonal directions. A systematic Williamson-Hall analysis of HRXRD data confirms the presence of large anisotropy of lattice relaxation process along the [011¯] and [01¯1¯] directions. Due to the large lattice mismatch, the GaP/GaAs epilayer presented here possesses grain boundaries and the broadening of the HRXRD pattern is strongly affected by the anisotropy of microstructure and dislocations. The kinetics of dislocations is discussed where it is observed that the misfit strain is primarily relieved by 90° partial dislocations up to a certain thickness of epilayer and thereafter the nucleation of 60° perfect dislocations dominates the strain relaxation process. The effect of the anisotropic distribution of relaxation process is also seen in the surface topography of GaP epilayer as revealed by atomic force microscopy images. The origin of the anisotropic distribution of dislocations is explained by considering the Burgers vector network, and its consequences are also observed in the cross sectional transmission electron microscopy images.

Structural characterization of natural diamond shocked to 60 GPa; implications for Earth and planetary systems

The possible presence of the high-density carbon polymorph with hexagonal symmetry known as “lonsdaleite” provides an important marker for shock impact events. It is typically considered to form as a metastable phase produced from graphite or other carbonaceous precursors. However, its existence has recently been called into question. Here we collected high-resolution synchrotron X-ray diffraction data for laboratory-shocked and natural impact diamonds that both show evidence for deviations from cubic symmetry, that would be consistent with the appearance of hexagonal stacking sequences. These results show that hexagonality can be achieved by shocking diamond as well as from graphite precursors. The diffraction results are analyzed in terms of a general model that describes intermediate stacking sequences between pure diamond (fully cubic) and “lonsdaleite” (fully hexagonal) phases, with provision made for ordered vs disordered stacking arrangements. This approach provides a “hexagonality index” that can be used to characterize and distinguish among samples that have experienced different degrees of shock or static high pressure-high temperature treatments. We have also examined the relative energetics of diamond and “lonsdaleite” structures using density functional theoretical (DFT) methods. The results set limits on the conditions under which a transformation between diamond and “lonsdaleite” structures can be achieved. Calculated Raman spectra provide an indicator for the presence of extended hexagonal stacking sequences within natural and laboratory-prepared samples. Our results show that comparable crystallographic structures may be developed by impact-generated shockwaves starting from ambient conditions using either of the two different allotropes of carbon (diamond, graphite). This broadens the scope for its occurrence in terrestrial and planetary systems.

Cation distribution in nanocrystalline (Co, Ni)Al2O4 Spinel

In the present study, the cations Co2+/Ni2+ and Al3+ distribution in nanocrystalline (Co, Ni)Al2O4 spinel have been investigated using X-ray and transmission electron microscopy. The nanocrystalline (Co, Ni)Al2O4 spinel has been synthesized using mechanically activated Al70Co15Ni15 quasicrystalline precursor through annealing at 600°C in controlled oxygen atmosphere. The mechanical activation of single phasic decagonal Al70Co15Ni15 quasicrystal was carried out in a high energy attritor ball mill for 40h with 40:1 ball to powder ratio using toluene as a process control agent. The high resolution x-ray diffraction data has been refined by the Rietveld method using JANA2006 and subsequently, the corresponding structure has been constructed using Diamond4.0. The structure was also confirmed by analysis of transmission electron microscopy linearized diffraction pattern profile of d-values and corresponding plane. These analyses indicate that the cations Co2+ and Ni2+ distributed in the tetrahedral coordinated sites are the dominant species in the normal spinel phase.

Selenides Based Sodium Superionic Conductors

All-solid-state Na-ion batteries that operate at or close to room temperature are a promising next-generation battery technology with enhanced safety and reduced manufacturing cost. An indispensable component of this technology is the solid state electrolyte that allows rapid shuttling of the mobile cation (i.e., Na+) between the cathode and anode. However, there are very few fast Na-ion conductors with ionic conductivity approaching that of the liquid counterparts (i.e., 1 mS cm-1). Compared to oxides and sulfides, selenides form a huge unexplored chemical space for fast ionic conductor discovery. Based upon ionic size considerations, selenide-based compounds may provide a more suitable structural framework for the rapid diffusion of the much larger Na+ cations compared with Li+. This consideration led us to an extensive search of fast Na-ion conductors in the Se-based chemical space via high-throughput computational screening, and has identified cubic Na3PSe4 as one of the most promising candidates. In this work, we present the synthesis and structural characterization of Na3PSxSe4-x (x = 0, 1, 2, 3, 4). The structures of these phases are determined from high-resolution synchrotron X-ray diffraction data, which allow us to unambiguously identify a tetragonal-to-cubic phase transition with increasing Se concentration in Na3PSxSe4-x. The Na-ion conductivity and activation energy for Na-ion diffusion were further characterized via variable temperature impedance spectroscopy, from which a negative correlation between the activation barrier and Se concentration can be established. Of particular note is that the x = 4 end member (i.e., cubic Na3PSe4) possesses a room-temperature ionic conductivity exceeding 0.1 mS cm-1, and does not require high temperature sintering to minimize grain boundary resistance, making it a promising solid-state electrolyte candidate for all-solid-state Na-ion battery applications. These experimental results were complemented by ab initio computation through which we demonstrate an intriguing interplay between the tetragonal-to-cubic phase transition, defect formation, and Na+ migration. This work has two important implications for future studies in related fields: (1) selenide based compounds represent a promising platform for the discovery of new fast Na-ion conductors; and (2) the current study opens up new opportunities for the exploration of Se and/or S based battery chemistry, such as the construction of all-solid-state Na/Se battery.

Electron density, disorder and polymorphism: high-resolution diffraction studies of the highly polymorphic neuralgic drug carbamazepine.

Analysis of neutron and high-resolution X-ray diffraction data on form (III) of carbamazepine at 100 K using the atoms in molecules (AIM) topological approach afforded excellent agreement between the experimental results and theoretical densities from the optimized gas-phase structure and from multipole modelling of static theoretical structure factors. The charge density analysis provides experimental confirmation of the partially localized π-bonding suggested by the conventional structural formula, but the evidence for any significant C-N π bonding is not strong. Hirshfeld atom refinement (HAR) gives H atom positional and anisotropic displacement parameters that agree very well with the neutron parameters. X-ray and neutron diffraction data on the dihydrate of carbemazepine strongly indicate a disordered orthorhombic crystal structure in the space group Cmca, rather than a monoclinic crystal structure in space group P2(1)/c. This disorder in the dihydrate structure has implications for both experimental and theoretical studies of polymorphism.

Disorder and defects are not intrinsic to boron carbide.

A unique combination of useful properties in boron-carbide, such as extreme hardness, excellent fracture toughness, a low density, a high melting point, thermoelectricity, semi-conducting behavior, catalytic activity and a remarkably good chemical stability, makes it an ideal material for a wide range of technological applications. Explaining these properties in terms of chemical bonding has remained a major challenge in boron chemistry. Here we report the synthesis of fully ordered, stoichiometric boron-carbide B13C2 by high-pressure–high-temperature techniques. Our experimental electron-density study using high-resolution single-crystal synchrotron X-ray diffraction data conclusively demonstrates that disorder and defects are not intrinsic to boron carbide, contrary to what was hitherto supposed. A detailed analysis of the electron density distribution reveals charge transfer between structural units in B13C2 and a new type of electron-deficient bond with formally unpaired electrons on the C–B–C group in B13C2. Unprecedented bonding features contribute to the fundamental chemistry and materials science of boron compounds that is of great interest for understanding structure-property relationships and development of novel functional materials.

A microfluidic-based protein crystallization method in 10 micrometer-sized crystallization space

Protein crystallization and subsequent X-ray diffraction analysis of the three-dimensional structure are necessary for elucidation of the biological functions of proteins and effective rational drug design. Therefore, controlling protein crystallization is important to obtain high resolution X-ray diffraction data. Here, a simple microfluidic method using chips with 10 and 50 μm high crystallization chambers to selectively form suitable single protein crystals for X-ray analysis is demonstrated. As proof of concept, three different types of proteins: lysozyme, glucokinase from Pseudoalteromonas sp. AS-131 (PsGK), and NADPH-cytochrome P450 oxidoreductase–heme oxygenase complex were crystallized. We demonstrate that the crystal growth orientation depends on the height of the crystallization chamber regardless of the protein type. Our results suggest that the confined micro space induces the protein molecules to adhere to a specific crystal face and affects the growth kinetics of each crystal face. The present microfluidic-based protein crystallization method can reform a suitable single protein crystal for X-ray analysis from aggregates of needle-shaped protein crystals.

Experimental and theoretical investigation of topological and energy characteristics of electron density in crystals of SbV o-amidophenolate complexes

Experimental and theoretical investigations of electron density in the complexes [4,6-ditert-butyl-N-(2,6-diisopropylphenyl)-1,2-amidophenolato]tricyclohexylantimony(V) (1) and [4,6-di-tert-butyl-N-(2,6-dimethylphenyl)-1,2-amidophenolato]tri-4-fluorophenylantimony(V) (2) were performed based on high-resolution X-ray diffraction data and density functional theory calculations (B3LYP/DGDZVP). The nature of chemical bonding, the energy of intraand intermolecular interactions in the crystals, and the atomic charge distribution were studied.

Facile synthesis of reduced graphene oxide–gold nanohybrid for potential use in industrial waste-water treatment

Here, we report a facile approach, by the photochemical reduction technique, for in situ synthesis of Au-reduced graphene oxide (Au-RGO) nanohybrids, which demonstrate excellent adsorption capacities and recyclability for a broad range of dyes. High-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) data confirm the successful synthesis of Au-RGO nanohybrids. The effect of several experimental parameters (temperature and pH) variation can effectively control the dye adsorption capability. Furthermore, kinetic adsorption data reveal that the adsorption process follows a pseudo second-order model. The negative value of Gibbs free energy (ΔG0) confirms spontaneity while the positive enthalpy (ΔH0) indicates the endothermic nature of the adsorption process. Picosecond resolved fluorescence technique unravels the excited state dynamical processes of dye molecules adsorbed on the Au-RGO surface. Time resolved fluorescence quenching of Rh123 after adsorption on Au-RGO nanohybrids indicates efficient energy transfer from Rh123 to Au nanoparticles. A prototype device has been fabricated using Au-RGO nanohybrids on a syringe filter (pore size: 0.220 μm) and the experimental data indicate efficient removal of dyes from waste water with high recyclability. The application of this nanohybrid may lead to the development of an efficient reusable adsorbent in portable water purification.

On the transferability of electron density in binary vanadium borides VB, V3B4 and VB2.

Binary vanadium borides are suitable model systems for a systematic analysis of the transferability concept in intermetallic compounds due to chemical intergrowth in their crystal structures. In order to underline this structural relationship, topological properties of the electron density in VB, V3B4 and VB2 reconstructed from high-resolution single-crystal X-ray diffraction data as well as derived from quantum chemical calculations, are analysed in terms of Bader's Quantum Theory of Atoms in Molecules [Bader (1990). Atoms in Molecules: A Quantum Theory, 1st ed. Oxford: Clarendon Press]. The compounds VB, V3B4 and VB2 are characterized by a charge transfer from the metal to boron together with two predominant atomic interactions, the shared covalent B-B interactions and the polar covalent B-M interactions. The resembling features of the crystal structures are well reflected by the respective B-B interatomic distances as well as by ρ(r) values at the B-B bond critical points. The latter decrease with an increase in the corresponding interatomic distances. The B-B bonds show transferable electron density properties at bond critical points depending on the respective bond distances.

Neutron and high-resolution room-temperature X-ray data collection from crystallized lytic polysaccharide monooxygenase.

Bacteria and fungi express lytic polysaccharide monooxgyenase (LPMO) enzymes that act in conjunction with canonical hydrolytic sugar-processing enzymes to rapidly convert polysaccharides such as chitin, cellulose and starch to single monosaccharide products. In order to gain a better understanding of the structure and oxidative mechanism of these enzymes, large crystals (1-3 mm(3)) of a chitin-processing LPMO from the Gram-positive soil bacterium Jonesia denitrificans were grown and screened for their ability to diffract neutrons. In addition to the collection of neutron diffraction data, which were processed to 2.1 Å resolution, a high-resolution room-temperature X-ray diffraction data set was collected and processed to 1.1 Å resolution in space group P212121. To our knowledge, this work marks the first successful neutron crystallographic experiment on an LPMO. Joint X-ray/neutron refinement of the resulting data will reveal new details of the structure and mechanism of this recently discovered class of enzymes.