High-resolution X-ray Diffraction Data Research Articles

Late-Holocene coastal depositional environments and climate changes in the Gulf of Corinth, Greece

Multidisciplinary studies in coastal systems of the eastern Mediterranean region have proven to be excellent tools in understanding paleoenvironmental, paleoecological, and paleoclimatic changes that took place during the Holocene period, and how these changes interacted with urban development and growth. This paper presents sedimentological, high-resolution x-ray fluorescence (XRF scanning), micropaleontological, and x-ray diffraction (XRD) data from three shallow sediment cores that were retrieved from Aliki (ancient Siphai or Tipha) salt pond. The study area is located in a unique, highly tectonic geographical region, at the northeast part of the Gulf of Corinth in Greece. Beachrock deposits that form a barrier between the salt pond and the marine environment seem to play an important role in the evolution of the area. The chronological framework was set at around 3100 cal. BP by four 14C radiocarbon dates, and the evolutionary model that was established indicates four different changes taking place during this period at the study area. From around 3100 to 1600 cal. BP, a transition from a closed to an open lagoonal environment was identified, interrupted by a fluvial terrestrial deposit at around 2500 cal. BP. A shift toward a closed lagoonal system at around 1600 cal. BP and the establishment of a salt pond environment seem to correlate with tectonic activity. The study provides important information about the evolution of coastal landscape in such a tectonic active region and points the interaction between regional human activity and climatic changes during the late-Holocene period.

Effects of disorder activated scattering and defect-induced phase on the ferroelectric properties of BaSnxTi1-xO3 (0≤x≤0.28) ceramics

BaSnxTi1-xO3 solid solutions with varying Sn content (x = 0.0–0.28) have been characterized for their structural, dielectric and ferroelectric properties. Rietveld analysis of high resolution X-ray diffraction (HRXRD) data reveals the coexistence of (tetragonal+orthorhombic) phases for x = 0.05, and (rhombohedral+cubic) phases for x = 0.12, and a single phase for the remaining compositions. Raman spectroscopy at room temperature reveals composition induced structural changes, and exhibits disorder-activated scattering at ∼110 cm−1 due to coexisting SnO6 and TiO6 octahedra in BaSnxTi1-xO3 compositions with Sn content x ≥ 0.1. Presence of SnO6 is confirmed both by Raman and infrared (IR) absorption spectroscopy. Incipient growth of a defect-induced semiconducting phase (BaSnO3) builds-up with increasing Sn content (x ≥ 0.05), but remains undetected by X-ray diffraction. It is prominently revealed by the high frequency Raman mode at ∼752 cm−1, which upon de-convolution shows the involvement of two overlapped modes. A decreasing intensity ratio of the two modes with increasing Sn content (x = 0.05–0.15) correlates with the observed decrease in remnant polarization, and a complete overlapping of the modes at a higher level of Sn content (x = 0.27) signifies the onset of relaxor behavior in the dielectric characteristics.

Crystal Chemistry of Birefringent Uvarovite Solid Solutions

The crystal chemistry of five optically anisotropic uvarovite samples from different localities (California, Finland, Russia, and Switzerland) were studied with electron-probe microanalysis (EPMA) and the Rietveld method. Monochromatic synchrotron high-resolution powder X-ray diffraction (HRPXRD) data were used, and Rietveld refinement was carried out with the cubic space group, I a 3 ¯ d . The general formula for garnet is [8]X3[6]Y2[4]Z3[4]O12. Uvarovite has the ideal formula, Ca3Cr2Si3O12, which may be written as Ca3{Cr,Al,Fe}Σ2[Si3O12] because of solid solutions. HRPXRD traces show multiple cubic garnet phases in each sample that has a heterogeneous chemical composition. The optical and back-scattered electron (BSE) images and elemental maps contain lamellar and concentric zoning as well as patchy intergrowths. With increasing a unit-cell parameter for uvarovite solid solutions, the Z–O distance remains constant, and the average <X–O> distance increases slightly in response to the Cr3+ ⇔ Al3+ cation substitution in the Y site. The Y–O distance increases most because Cr3+ (radius = 0.615 Å) is larger than Al3+ (radius = 0.545 Å) cations. The Fe3+ (radius = 0.645 Å) cation is also involved in this substitution. Structural mismatch between the cubic garnet phases in the samples gives rise to strain-induced optical anisotropy.

Influence of PEGylation on the Strength of Protein Surface Salt Bridges.

Conjugation of polyethylene glycol (PEGylation) is a well-known strategy for extending the serum half-life of protein drugs and for increasing their resistance to proteolysis and aggregation. We previously showed that PEGylation can increase protein conformational stability; the extent of PEG-based stabilization depends on the PEGylation site, the structure of the PEG-protein linker, and the ability of PEG to release water molecules from the surrounding protein surface to the bulk solvent. The strength of a noncovalent interaction within a protein depends strongly on its microenvironment, with salt-bridge and hydrogen-bond strength increasing in nonpolar versus aqueous environments. Accordingly, we wondered whether partial desolvation by PEG of the surrounding protein surface might result in measurable increases in the strength of a salt bridge near a PEGylation site. Here we explore this possibility using triple-mutant box analysis to assess the impact of PEGylation on the strength of nearby salt bridges at specific locations within three peptide model systems. The results indicate that PEG can increase the nearby salt-bridge strength, though this effect is not universal, and its precise structural prerequisites are not a simple function of secondary structural context, of the orientation and distance between the PEGylation site and salt bridge, or of salt-bridge residue identity. We obtained high-resolution X-ray diffraction data for a PEGylated peptide in which PEG enhances the strength of a nearby salt bridge. Comparing the electron density map of this PEGylated peptide versus that of its non-PEGylated counterpart provides evidence of localized protein surface desolvation as a mechanism for PEG-based salt-bridge stabilization.

Chemical Bonding in Polarised Push-Pull Ethylenes.

1,1-Diamino-2,2-bis(triflyl)ethylenes with both twisted and planar structures around the partial "C=C" bond were synthesised. Bonding properties in these compounds were analysed by an experimental approach using high-resolution X-ray diffraction data treated with X-ray wavefunction refinement (XWR). In the twisted compound, a dominant contribution of the charge-separated resonance structure was revealed. On the contrary, the nearly planar compound still showed π-bonding character, however, with a considerable contribution of the charge-separated resonance structure.

Room temperature crystal structure and high temperature structural and magnetic phase transitions in Sr(Fe0.5Nb0.5)O3 ceramic

The room temperature structure of the perovskite Sr(Fe0.5Nb0.5)O3 ceramic has been investigated by Rietveld structure refinement using high resolution X-ray diffraction (XRD) data. The correct structure is determined to be tetragonal in the space group I4/mcm ruling out orthorhombic (Pbnm), tetragonal (P4 mm), and monoclinic structures previously reported by authors. The high temperature structural phase transition has been studied by Rietveld analysis using the high resolution XRD data in the temperature range of 300–850 K. A high temperature structural phase transition is observed from tetragonal (I4/mcm) to cubic (Pm3̅m) phase around ∼630 K. This phase transition was also confirmed by the heat flow experiment using differential scanning calorimetry. To confirm the nature of phase transition, we have studied the variation of integrated intensity (ISL) of superlattice peak and the oxygen octahedral tilt angle (φ) in a tetragonal structure with temperature. The temperature variations of these two parameters provide evidence for the tricritical nature of the phase transition. A magnetic phase transition is discovered in temperature dependence of magnetization M(T) around ∼708 K, which coincides with the dielectric anomaly temperature in loss tangent.

Reconciling Crystallographic and Physical Property Measurements on Thermoelectric Lead Sulfide.

For many decades the lead chalcogenides PbTe, PbSe, and PbS (and their solid solutions) have been preferred high-performance thermoelectric materials due to their exceptional electronic and thermal properties as well as great stability during operation. However, there is a lack of understanding about the fundamental relation between the reported high-defect crystal structure containing cation disorder and vacancies and the observed transport properties, which follow expectations for an ideal rock salt crystal structure. Here we have studied a series of undoped lead sulfide samples (Pb1- xS) with presumed small chemical variations. Crystallographic refinements of high-resolution synchrotron powder X-ray diffraction data give unphysically low lead occupancies (0.75-0.98), in contradiction with the measured charge carrier concentration, resistivity, mobility, and Seebeck coefficient, which show no signs of lead vacancies. A new Rietveld refinement model including preferred orientation parameters and anisotropic strain gives almost full lead occupancy and improved agreement factors. However, transmission electron microscopy analysis reveals that there is no preferred orientation in this system. Instead it is the diffuse scattering due to directional correlated disorder in the structure that necessitates the additional parameters when modeling Bragg intensities. The present approach is a general method for absorbing effects of direction-dependent correlations in advanced materials.

Unintentional As incorporation into AlSb and interfacial layers within InAs/AlSb superlattices

The InAs/AlSb material system has proven to be an excellent choice for high-performance mid-infrared quantum cascade lasers. In this work, an unintentional displacement of Sb by residual As flux incident on the wafer was studied by direct monitoring of such flux during a simulated molecular beam epitaxy (MBE) growth sequence and dynamical simulations of high-resolution x-ray diffraction data collected on InAs/AlSb periodic structures grown under similar conditions. The results revealed that predominantly Al–As bonds detected at the InAs/AlSb interfaces, which were reported earlier, can be attributed to a residual bypass As flux on the wafer after closing the As shutter. Moreover, the experiments revealed that under typical growth conditions, AlSb binary barriers are converted into AlAsSb ternary layers with appreciable As content. The exact As content in the barriers is proportional to the effective As flux bypassing the closed shutter and thus depends on the particulars of the MBE system design and the exact As flux used for the growth of InAs wells.

Revisiting a Historical Concept by Using Quantum Crystallography: Are Phosphate, Sulfate and Perchlorate Anions Hypervalent?

There are many examples of atoms in molecules that violate Lewis' octet rule, because they have more than four electron pairs assigned to their valence. These atoms are referred to as hypervalent. However, hypervalency may be regarded as an artifact arising from Lewis' description of molecules, which is based on the assumption that electrons are localized in two-center two-electron bonds and lone pairs. In the present paper, the isoelectronic phosphate (PO4 3- ), sulfate (SO4 2- ) and perchlorate (ClO4 - ) anions were examined with respect to the concept of hypervalency. Lewis formulas containing a hypervalent central atom exist for all three anions. Based on X-ray wavefunction refinements of high-resolution X-ray diffraction data of representative crystal structures (MgNH4 PO4 ⋅6 H2 O, Li2 SO4 ⋅H2 O, and KClO4 ), complementary bonding analyses were performed. In this way, experimental information from the new field of quantum crystallography validate long-known facts, or refute long-standing misunderstandings. It is shown that the P-O and S-O bonds are highly polarized covalent bonds and, thus, the increase in the valence population following three-center four-electron bonding is not sufficient to yield hypervalent phosphorus or sulfur atoms, respectively. However, for the highly covalent Cl-O bond, most bonding indicators imply a hypervalent chlorine atom.

Molecular Potential Energies from Experimental Electric Field and Electrostatic Potential at Nuclei.

In this paper, the molecular electrostatic potential energy V is first estimated from the electric field generated by an experimental electron density. Once the high resolution X-ray diffraction data are fitted against the Hansen-Coppens multipole model, the electric field E is analytically computed on every point inside and around the molecule by using our own software FIELD. The potential energy is then obtained by a numerical and robust integration of E2/2. The topological analysis of the electric field is carried out to reveal the specific contribution of atoms in a molecule. Application is made on a set of seven organic molecules of different sizes. The results are compared to those obtained from Politzer's empirical calculations of the molecular energy using the electrostatic potential values at the atomic nuclei (EPN) within the framework of the Thomas-Fermi approximation. In this context, the molecular energy estimates found for the chosen molecules are presented and discussed.

Insights into Single-Molecule-Magnet Behavior from the Experimental Electron Density of Linear Two-Coordinate Iron Complexes.

A breakthrough in the study of single-molecule magnets occurred with the discovery of zero-field slow magnetic relaxation and hysteresis for the linear iron(I) complex [Fe(C(SiMe3)3)2]- (1), which has one of the largest spin-reversal barriers among mononuclear transition-metal single-molecule magnets. Theoretical studies have suggested that the magnetic anisotropy in 1 is made possible by pronounced stabilization of the iron d z2 orbital due to 3d z2-4s mixing, an effect which is predicted to be less pronounced in the neutral iron(II) complex Fe(C(SiMe3)3)2 (2). However, experimental support for this interpretation has remained lacking. Here, we use high-resolution single-crystal X-ray diffraction data to generate multipole models of the electron density in these two complexes, which clearly show that the iron d z2 orbital is more populated in 1 than in 2. This result can be interpreted as arising from greater stabilization of the d z2 orbital in 1, thus offering an unprecedented experimental rationale for the origin of magnetic anisotropy in 1.

Characterization of the Dog Lipocalin Allergen Can f 6

Allergies to dogs are a critically important clinical problem that affect between 10%-30% of humans worldwide and continue to increase. Four of the seven currently named dog component allergens (Can f 1, Can f 2, Can f 4, and Can f 6) are lipocalins. Sensitization to Can f 6 is linked to the highest likelihood of allergic symptoms. Accurate biochemical and biophysical data for each is limited. The cDNA encoding 6xHis-tagged Can f 6 was cloned, expressed in bacteria, and purified using a HisPur Ni-NTA Superflow Agarose nitrilotriacetic acid (NTA) column, followed by fast protein liquid chromatography (FPLC) size exclusion column, and then pooling fractions of the appropriate molecular weight. Initial crystallization trials were performed at room temperature by hanging drop vapor diffusion. Data were collected on a cryoprotected crystal on the 24-ID-C Synchrotron at the Advanced Photon Source at Argonne National Laboratory, processed, solved, and refined using Phaser and the CCP4 program suite. The purified recombinant Can f 6 protein has been crystalized. The resulting high-resolution x-ray diffraction data was used to solve the tertiary structure of the protein. This is the third dog lipocalin allergen whose structure has been characterized. This Can f 6 structure can now be used to identify potential sites of cross reactivity with other lipocalins and define allergenic epitopes that can be therapeutic targets.

The Color of the Elements: A Combined Experimental and Theoretical Electron Density Study of ScB2 C2.

The chemical or physical control parameters for the onset of superconductivity in MB2 C2 hetero-graphene materials are unclear. This is mainly due to the almost ubiquitous positional B/C disorder, rendering the description of real structures of borocarbides into one of the most challenging problems in materials science. We will show that high-resolution X-ray diffraction data provides all the essential information to decode even complex coloring problems due to B/C disorder. Electron density studies and subsequent analyses of the fine structure of the Laplacian of the electron density resolves the local electronic structure of ScB2 C2 at sub-atomic resolution and allows for an unequivocal identification of all atoms involved in the coloring scenario. This information could finally be used to identify the electron deficient character of the B/C layers in ScB2 C2 and to synthesize the first bimetallic hetero-metallocene with lithium and scandium atoms embedded in the pentagonal and heptagonal voids, respectively.

Charge density distribution in the crystals of N-n-butyltetrachlorophthalimide. Atoms-in-molecules analysis of different types of halogen interactions

The charge density distribution in N-n-butyltetrachlorophthalimide was experimentally determined using high-resolution X-ray diffraction data and the Hansen–Coppens multipole formalism.

Charge density and electrostatic potential of hepatitis C anti-viral agent andrographolide: an experimental and theoretical study

Andrographolide (AGH) is a hepatitis C anti-viral agent which targets the host cell by covalently binding with the NF-κBreceptor. The experimental electron density distribution study of AGH has been carried out from high-resolution X-ray diffraction data collected at 110.2 (3) K. The unit-cell packing of AGH was stabilized by strong O—H...O and weak C—H...O types of intermolecular interactions. The dissociation energy of the strong hydrogen bond O2—H22...O1 is very high, 32 kJ mol−1. The percentage occupancy of H...H interactions is found to be maximum (68.5%) when it comparing with the other types of interactions occurring in the AGH crystalline phase. The atomic valance index (V topo) of the C16 atom is low compared with other carbon atoms; this shows that C16 could be the possible reactive location of the AGH molecule. All atoms in the OH groups have very low V topo values; this indicates their role in strong hydrogen bonding interactions. The electrostatic potential (ESP) surface of AGH shows the polarization of the C16=C17 bond and ESP contour map shows several maxima at the vicinity of the C16 atom; these results strongly demonstrate that the C16 atom is the reactive location of the AGH molecule. The molecular covalent docking analysis of AGH with the NF-κB receptor has been performed and confirmed this result. The highly electronegative region around γ-butyrolactone can be helpful for initial alignment of the AGH molecule in NF-κB receptor active site. The atomic volumes of the hydrogen atoms which participate in the H...H interaction are found to be low.

Electronic structure of two isostructural `paddle-wheel' complexes: a comparative study

The experimental electron density distribution in two isostructural and isomorphous complexes, tetrakis(μ2-acetato)diaquadicopper(II) [H2OCu(ac)2Cu(ac)2H2O] (I) and tetrakis(μ2-acetato)diaquadichromium(II), [H2OCr(ac)2Cr(ac)2H2O] (II), has been obtained from high-resolution X-ray diffraction data in order to shed light on the bonding properties in the compounds studied. It has been shown that from accurate X-ray data it is possible to discuss the bonding capability of the metal atom (Cu/Cr) and the ligands in these complexes. A comparison of results obtained from averaged and non-averaged X-ray data demonstrates that using the non-averaged data and introducing an anisotropic correction for secondary extinction errors provides a more detailed distribution of the electron density in the area of the metal atoms. In both complexes studied, the bonding of the acetate oxygen atom to the central metal atom is significantly affected by the formation of hydrogen bonds. The electron density and its Laplacian at the bond critical point of metal–oxygen coordination bonds for those oxygen atoms not involved in the intermolecular hydrogen bonds are approximately 10% larger compared with the case when oxygen atoms take part in hydrogen bonds with the neighboring water molecules. It is shown that metal–oxygen bonds in a quasi-equatorial plane are typical coordination bonds and differ significantly from the apical metal–oxygen bond. Metal–metal interaction with a small positive value of the electron density Laplacian at this bond critical point is mainly of electrostatic character. The metal–metal interaction is definitely not a bond according to the classical definition. Based on a search of the Cambridge Structural Database, it can be argued that there are four typical coordination bonds in the [CuO6] chromophore, similar to the four Cu—O coordination bonds in the basal plane of the CuO5 pyramid in one of the complexes under study.

Crystal structure, interaction energies and experimental electron density of the popular drug ketoprophen.

The crystal and molecular structure of the pure (S)-enantiomer of the popular analgesic and anti-inflammatory drug ketoprophen (α-ket) is reported. A detailed aspherical charge-density model based on high-resolution X-ray diffraction data has been refined, yielding a high-precision geometric description and classification of the O-H⋯O interactions as medium strength hydrogen bonds. The crystal structure of the racemic form of ketoprophen (β-ket) was also redetermined at 100 K, at 0.5 Å resolution. A previously unreported disorder (10% occupancy) was discovered. In contrast to the racemic β-ket case, the (S)-enantiomer crystallizes with two independent molecules in the asymmetric unit with two distinct conformations. The major difference between the β-ket and α-ket crystal forms lies in the formation of distinct hydrogen-bonded motifs: a closed ring motif in β-ket versus infinite chains of hydrogen bonds in the chiral α-ket structure. However, the overall crystal packing of both forms is surprisingly similar, with close-packed layers of antiparallel-oriented benzo-phenone moieties bound by C-H⋯π interactions. Notably, the most important stabilizing term in the total lattice energies in both instances proved to be the dispersion related to these interactions. Both forms of the title compound (α- and β-ket) were additionally characterized by differential scanning calorimetry and thermogravimetric analysis.

Crystal Chemistry of Three Volcanic K-rich Nepheline Samples From Oldoinyo Lengai, Tanzania and Mount Nyiragongo, Eastern Congo, Africa

Natural nepheline (Nph) samples are intermediate members of solid solutions that extend from the pure Na end-member Na[AlSiO4] to the pure K end-member K[AlSiO4] (= kalsilite, Kls). We examined two volcanic nepheline (ideally, K2Na6[Al8Si8O32] or Nph0.75Kls0.25) samples from Oldoinyo Lengai, Tanzania (samples 1 and 2) and a third sample 3 from Mount Nyiragongo, Eastern Congo. The crystal structure of these three samples was obtained using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and Rietveld structure refinements in space group P63. Satellite reflections were not observed in these samples. The EPMA composition of sample 1 is {K1.50Na0.19Ca0.070.23}Σ2(Na)6[Si8.35Al7.48Fe0.18]Σ16.00O32. The A site contains 0.23 vacancies () with some Na and Ca atoms, whereas the B site is completely filled with only Na atoms. From the EPMA formula, K(sof) = 0.844 and Na(sof) = 1.0. The refinement unit-cell parameters are a = 10.00247(1), c = 8.38396(1) A, V = 726.431(1) A3; K(sof) = 0.779(2) and Na(sof) = 0.988(2). The composition of sample 2 is {K1.670.33}Σ2(Na5.76K0.174Ca0.06)Σ6[Si8.44Al7.37Fe0.20]Σ16.01O32, so K(sof) = 0.835 and Na(sof) = 1.030. Sample 2 has a = 10.01769(2), c = 8.39586(2) A, V = 729.678(1) A3, K(sof) = 0.812(2), and Na(sof) = 0.995(2). Sample 3 is a three-phase (3a, 3b, 3c) intergrowth with an average formula of {K1.770.23}2(Na4.30K1.51Ca0.19)Σ6[Si8.13Al7.76Fe0.11]Σ16.00O32, K(sof) = 0.887, and Na(sof) = 1.208. A large amount of K and Ca atoms occur in the B site. Based on the weight percentages and sofs of the three phases, the Rietveld refinement gives an average K(sof) = 0.859 and Na(sof) = 1.145. The average distances indicate a high degree of Al-Si disorder in samples 1, 2, and phase 3b. These African samples extend natural nepheline solid solutions to about Nph0.55Kls0.45. The average distance increases linearly with Na(sof) and V across nepheline solid solutions because K atoms enter the Na site. K-rich nepheline seems to always contain vacancies in the A site.

Experimental charge density study on FLPs and a FLP reaction product

AbstractThe charge density distribution of the intramolecular frustrated Lewis pair (FLP) Mes2PCH2CH2B(C6F5)2(1), the phosphinimine HNPMes2CH2CH2B(C6F5)2(2), as well as a FLP homologue with nitrogen NEt2CHPhCH2B(C6F5)2(3) were investigated with Bader’s quantum theory of atoms in molecules (QTAIM). The charge densities were derived from both experimental high-resolution X-ray diffraction data (2,3) and theoretical calculations (1,3). The QTAIM analysis for the FLPs1and3showed the prominent B-pnictogen interaction to be weak dative bonds without significant charge-transfer. This holds also true for the B–N–bond of2. The nitrogen atom is negatively charged, due to a charge transfer from phosphorous and shows features of a sp2-hybridization. The bond is therefore best described as a non-hypervalent Pδ+–Nδ−moiety.

Local structure and lattice covalency of complex perovskites BaM0.2Ta0.8O3−xNx (M = Li, Na, Mg) studied by X-ray diffraction and X-ray absorption spectroscopy

Local structural aspects of complex perovskites BaM0.2Ta0.8O3−xNx (M = Li, Na, Mg) were studied by the extended X-ray absorption fine structure (EXAFS) and X-ray absorption near edge structure (XANES) spectroscopies at the Ta L3-edge, and also by the diffraction line broadening analysis of high-resolution synchrotron X-ray diffraction (XRD) data. The line broadening analysis based on the Williamson-Hall method indicated that the lattice periodicity of BaM0.2Ta0.8O3−xNx are disturbed remarkably, with a dependence on the size mismatch between M+/2+ and Ta5+. The Ta L3-edge EXAFS revealed that part of the Ta−O/N bonds are contracted by the existence of the large alkali cation on the shared octahedral site. Meanwhile, the XANES implied the distortion of Ta(O,N)6 from ideal octahedral geometry, where the curve fitting of the spectra provided additional information on the bonding character of Ta.