The intrinsic twinning and enigmatic twisting of aragonite crystals.

It is generally accepted that aragonite crystals of biogenic origin are characterized by significantly higher twin densities compared to samples formed during geological processes. Based on our single crystal X-ray diffraction (SCXRD) and transmission electron microscopy (TEM) study of aragonite crystals from various localities, we show that in geological aragonites, the twin densities are comparable to those of the samples from crossed lamellar zones of molluscs shells. The high twin density is consistent with performed calculations, according to which the Gibbs free energy of twin-free aragonite is close to that of periodically twinned aragonite structure. In some cases, high twin densities result in the appearance of diffuse scattering in SCXRD patterns. The obtained TEM and optical micrographs show that besides the twin boundaries (TBs) of growth origin, there are also TBs and especially stacking faults that were likely formed as the result of local strain compensation. SCXRD patterns of the samples from Tazouta, in addition to diffuse scattering lines, show Debye arcs in the [Formula: see text] plane. These Debye arcs are present only on one side of the Bragg reflections and have an azimuthal extent of nearly 30°, making the whole symmetry of the diffraction pattern distinctly chiral, which has not yet been reported for aragonite. By analogy with biogenic calcite crystals, we associate these arcs with the presence of misoriented subgrains formed as a result of crystal twisting during growth.

Ag4B7O12X (X = Cl, Br, I) Heptaborate Family: Comprehensive Crystal Chemistry, Thermal Stability Trends, Topology, and Vibrational Anharmonicity.

Using glass crystallization and solid-state techniques, we were able to complete the family of salt-inclusion silver halide borates, Ag4B7O12X, by the X = Cl and I members. The new compounds are characterized by differential scanning calorimetry, single-crystal and high-temperature powder X-ray diffraction, optical spectroscopy, and density functional theory calculations. In all structures, the silver atoms exhibit strong anharmonicity of thermal vibrations, which could be modeled using Gram-Charlier expansion, and its asymmetry was characterized by the skewness vector. The topology of the silver halide and borate sublattices has been analyzed separately for the first time. Along the I → Br → Cl series, we observe a decrease of the melting point and configuration entropy and an increase of thermal expansion and its anisotropy and thermal vibration anharmonicity, which indicates decreasing stability.

Molecular dynamics study of the competitive binding of hydrogen peroxide and water molecules with DNA phosphate groups.

The interaction of hydrogen peroxide molecules with the DNA double helix is of great interest for understanding the mechanisms of anticancer therapy utilising heavy ion beams. In the present work, a molecular dynamics study of competitive binding of hydrogen peroxide and water molecules with phosphate groups of the DNA double helix backbone was carried out. The system of DNA double helix in a water solution with hydrogen peroxide molecules and Na[Formula: see text] counterions was simulated. The results show that the hydrogen peroxide molecules bind to oxygen atoms of the phosphate groups of the double helix backbone replacing water molecules of its hydration shell. The complexes of hydrogen peroxide molecules with the phosphate groups are stabilized by one or two hydrogen bonds and by Na[Formula: see text] counterions, forming ion-mediated contacts between phosphate groups and hydrogen peroxide molecules. The complex characterized by one H-bond between the hydrogen peroxide molecule and phosphate group is dominant, the other complexes are rare. The hydrogen peroxide molecule bound to the phosphate group of the double helix backbone can inhibit the formation of hydrogen bonds indispensable for the DNA biological functioning.

Probing the Electrolyte Transfer in Ultrathin Polypyrrole Films by In Situ X-ray Reflectivity and Electrochemistry.

This study reports on the potential-induced charge and mass transfer between an ultrathin polypyrrole (PPy) film and an electrolyte by simultaneous in situ X-ray reflectivity (XRR) and electrochemistry (EC) utilizing their sensitivity to electrons. An about 30 nm thin PPy film was deposited on a silicon single crystal by fast potential cycling, providing a dense film of an extraordinary small surface roughness. XRR was recorded from the PPy film in an aqueous 0.1 M perchloric acid at electric potentials between -0.2 V and +0.5 V vs Ag/AgCl. The PPy film shows typical reversible and linear changes in film thickness and electron density arising from the potential-dependent electrolyte incorporation. By introducing EC-XRR, a comprehensive analysis combining in situ XRR and EC, the net number of electrons passing through the PPy-electrolyte interface was deduced along with the potential-induced thickness variations, indicating a complex exchange mechanism. Evidently, along with the anion transfer, parallel charge compensation by protons and a volume and electron compensating counterflow of solvent molecules take place. Complementary time-dependent EC-XRR scans indicate that these exchange mechanisms are individual in two potential ranges. The low actuation along with a high pseudocapacitance suggest the fast potentiodynamically deposited PPy film as a promising supercapacitor material.

Bridging the Salt-Inclusion and Open-Framework Structures: The Case of Acentric Ag4B4O7X2 (X = Br, I) Borate Halides.

An acentric borate family, Ag4B4O7X2 (X = Br, I), has been prepared by slow cooling stoichiometric melts in evacuated silica ampules. Their crystal structure is comprised of two porous interpenetrating frameworks and demonstrates a further development of the "salt-inclusion" architecture toward a "covalent-inclusion" structure. The (Ag2X)+ sublattice shows strong anharmonic vibrations. Thermal expansion is strongly anisotropic because of the presence of condensed rigid kernite boron-oxygen chains aligned perpendicular to the c axes.

Correction to: Possible scenarios of DNA double-helix unzipping process in single-molecule manipulation experiments.

The original article was published with the following errors.

Possible scenarios of DNA double-helix unzipping process in single-molecule manipulation experiments.

Single-molecule experiments on DNA unzipping are analyzed on the basis of the mobility of nucleic bases in complementary pairs. Two possible scenarios of DNA double-helix unzipping are proposed and studied, using the atom-atom potential function method. According to the first scenario, the base pairs transit into a 'preopened' metastable state and then fully open along the 'stretch' pathway. In this case, the DNA unzipping takes place slowly and as an equilibrium process, with the opening energies being similar to the energies obtained in thermodynamic experiments on DNA melting. The second scenario is characterized by higher opening forces. In this case, the DNA base pairs open directly along the 'stretch' pathway. It follows from our calculations that, in this scenario, the enthalpy difference between the A[Formula: see text]T and G[Formula: see text]C base pairs is much higher than in the first case. The features of the first unzipping scenario show that it can play a key role during the process of DNA genetic information transfer in vivo. It follows from our study that a peculiarity of the second scenario is that it can be used for the development of faster methods for reading genetic information in vitro.

Non-uniform nanosecond gate-delay of hybrid pixel detectors.

A simple experiment to characterize the gating properties of X-ray area detectors using pulsed X-ray sources is presented. For a number of time-resolved experiments the gating uniformity of area detectors is important. Relative gating delays between individual modules and readout chips of PILATUS2 series area X-ray detectors have been observed. For three modules of a PILATUS 300K-W unit the maximum gating offset between the modules is found to be as large as 30 ns. On average, the first photosensor module is found to be triggered 15 ns and 30 ns later than the second and the third modules, respectively.

A γ-cyclodextrin duplex connected with two disulfide bonds: synthesis, structure and inclusion complexes.

Per(2,3,6-tri-O-benzyl)-γ-cyclodextrin was debenzylated by DIBAL-H to produce a mixture of C6(I),C6(IV) and C6(I),C6(V) isomeric diols, which were separated and isolated. The C2-symmetrical C6(I),C6(V) diol was transformed into dithiol and dimerized to produce a γ-cyclodextrin duplex structure. A crystal structure revealed tubular cavity whose peripheries are slightly elliptically distorted. The solvent accessible volume of the cavity of the γ-CD duplex is about 740 Å(3). Due to this large inner space the duplex forms very stable inclusion complexes with steroids; bile acids examined in this study show binding affinities to the γ-cyclodextrin duplex in the range of 5.3 × 10(7) M(-1)-1.9 × 10(8) M(-1).

Correlation between stoichiometry and surface structure of the polar MgAl2O4(100) surface as a function of annealing temperature.

The correlation between surface structure, stoichiometry and atomic occupancy of the polar MgAl2O4(100) surface has been studied with an interplay of noncontact atomic force microscopy, X-ray photoelectron spectroscopy and surface X-ray diffraction under ultrahigh vacuum conditions. The Al/Mg ratio is found to significantly increase as the surface is sputtered and annealed in oxygen at intermediate temperatures ranging from 1073-1273 K. The Al excess is explained by the observed surface structure, where the formation of nanometer-sized pits and elongated patches with Al terminated step edges contribute to stabilizing the structure by compensating surface polarity. Surface X-ray diffraction reveals a reduced occupancy in the top two surface layers for both Mg, Al, and O and, moreover, vacancies are preferably located in octahedral sites, indicating that Al and Mg ions interchange sites. The excess of Al and high concentration of octahedral vacancies, very interestingly, indicates that the top few surface layers of the MgAl2O4(100) adopts a surface structure similar to that of a spinel-like transition Al2O3 film. However, after annealing at a high temperature of 1473 K, the Al/Mg ratio restores to its initial value, the occupancy of all elements increases, and the surface transforms into a well-defined structure with large flat terraces and straight step edges, indicating a restoration of the surface stoichiometry. It is proposed that the tetrahedral vacancies at these high temperatures are filled by Mg from the bulk, due to the increased mobility at high annealing temperatures.

Magnesium cations as templates for the self-assembly of supramolecular luminescent {Mg@[B18φ34-35]}-clusters.

Solvothermal reaction of magnesium nitrate and boron oxide in N,N-dimethylformamide produced a number of particularly complex supramolecular magnesium borates. Five topologically different types of negatively charged {Mg@[B18φ34-35]}-clusters, φ = O, OH, were observed with the magnesium cation as a core and octadecaborate anions as shells. The clusters assemble via common borate polyhedra forming 1D chains, a 2D mesoporous layer, and 3D mesoporous frameworks with an effective channel width of up to 16 Å. Topological analysis of the clusters in combination with the modular crystallography approach indicates that numerous new functional materials can be obtained by varying their assembly mode. At least one compound containing such clusters exhibits a very strong luminescence.

Texture formation in DNA films with alkali metal chlorides.

The formation of textures in DNA films with LiCl, NaCl, KCl, RbCl, and CsCl salts has been studied. The films are prepared by evaporation of water solution with highly polymerized calf thymus DNA and excess salt of specific type. For DNA solution with 10 mM concentration of NaCl, KCl, and RbCl the films with dendritic textures have been obtained, whereas in case of CsCl the textures in the films appear only at 30 mM concentration of excess salt in the initial solution. In the solution with LiCl, the textures in DNA films have not been observed within the whole range of concentration of excess salt under consideration. The analysis of parameters of DNA films with different salts has showed that evaporation of solution leads to crystallization of salt ions on DNA macromolecule and formation of DNA-salt complexes. Electrostatic energy of the system of crystalline ordered ions and charges of DNA chains has been estimated to study the stability of DNA-salt complexes. The results obtained for different salts have been showed that the presence of DNA macromolecule enhances crystallization as compared with solution without DNA. The property of excess salt to form the crystalline structures has been found to decrease in the following order: KCl > NaCl > RbCl > CsCl > LiCl. The results of estimation are in good agreement with the experimentally observed dependence of texture formation on excess salt type.

Coherent Anti-Stokes Raman Scattering Measurements of Time and Length Scales of Temperature Fluctuations in a Turbulent Flame.

The ability to derive temporal and spatial scales of "instantaneous" local temperature variations in a turbulent flame by means of coherent anti-Stokes Raman scattering (CARS) spectroscopy is demonstrated, for the first time to our knowledge. The measurements employed two CARS spectrometers with synchronized nanosecond pulse-repetitive lasers. The system was enabling to record, with a high temporal resolution of about 10 ns, series of single laser shot CARS spectra of N2 molecules from two spatially overlapped or displaced probe volumes as small as 0.03 × 0.03 × 2 mm3. The spectra were being recorded at a variable delay between two sequential shots, following each other in pairs at a repetition rate of 10 Hz. The series of 500 coupled measurements, at the delays in the range 1 µs-10 ms and the displacements up to 2.5 mm, have been performed in a few points of an open premixed methane-air flame of a laboratory burner with the time-averaged temperatures in the range 1200-1800 K. From the spectra, "instantaneous" temperatures, at the given delay and probe volume distance, have been derived. This allowed the auto-correlation coefficients of temperature fluctuations versus the delay and the displacement to be calculated. These dependences enabled to evaluate temperature correlation times and lengths under various mixture flow rates and equivalence ratios.

Reversible Ultrathin PtOx Formation at the Buried Pt/YSZ(111) Interface Studied In Situ under Electrochemical Polarization.

Three different platinum oxides are observed by in situ X-ray diffraction during electrochemical potential cycles of platinum thin film model electrodes on yttria-stabilized zirconia (YSZ) at a temperature of 702 K in air. Scanning electron microscopy and atomic force microscopy performed before and after the in situ electrochemical X-ray experiments indicate that approximately 20% of the platinum electrode has locally delaminated from the substrate by forming pyramidlike blisters. The oxides and their locations are identified as (1) an ultrathin PtOx at the buried Pt/YSZ interface, which forms reversibly upon anodic polarization; (2) polycrystalline ß-PtO2, which forms irreversibly upon anodic polarization on the inside of the blisters; and (3) an ultrathin α-PtO2 at the Pt/air interface, which forms by thermal oxidation and which does not depend on the electrochemical polarization. Thermodynamic and kinetic aspects are discussed to explain the coexistence of multiple phases at the same electrochemical conditions.

Quantification of phosphatides in sunflower oils using a potentiometric e-tongue.

Consisting of two fatty acyl groups, phospholipids are a vital part of vegetable oils and the source of essential fatty acids. Moreover, phospholipids influence oxidative and flavor stability and color evolution of vegetable oils, and their quantification has a significant role in the quality assessment of oils. In this study, we proposed a new highly efficient, affordable, environmentally friendly, and simple approach for the evaluation of phospholipid concentrations based on potentiometric multisensor systems coupled with chemometric data processing. Support vector machines, partial least squares, and multiple linear regressions were used to predict phosphatide concentrations based on potentiometric multisensor system responses. Application of multivariate regression tools yielded the following root mean square errors of prediction: 0.005 mg/100 g of oil in the range 0.0-59.4 mg/100 g for refined oils; 0.008 mg/100 g in the range 0.0-100 mg/100 g for low phosphatide oils and 0.24 mg/100 g in the range 100-2270 mg/100 g for high phosphatide oils. This approach can be considered as a rapid and straightforward method to quantify the phosphatides in sunflower oils.

Fresh-Water Mollusks as Biomonitors for Ecotoxicity of Nanomaterials.

The use of different nanoparticles (NPs) is growing every year since discoveries of their unique properties. The wide use of nanomaterials has raised concerns about their safety and possible accumulation in the aquatic environment. Mussels are being considered as one of the most suitable organisms for bioaccumulation monitoring. Within our study, we focused on developing the method that can be applied in field studies of ecotoxicity and can be nondestructive and informative at early times of exposure, while at the same time being based on changes of physiological parameters of fresh water mussels. The changes in the cardiovascular and neural systems of mollusks (Anodonta anatina and Unio tumidus) were measured as biomarkers of toxic effects. Different monometallic and bimetallic NPs, silicon NPs with various ligands were applied as test substances. Changes in cardiovascular and neural functions were in good correlation with accumulation tests for all tested NPs.

The first bismuth borate oxyiodide, Bi4BO7I: commensurate or incommensurate?

The first bismuth borate oxyiodide, Bi4BO7I, has been prepared by solid-state reaction in evacuated silica ampoules. Its crystal structure [space group Immm(00γ)000] comprises litharge-related layers of edge-sharing OBi4 tetrahedra; the interlayer space is filled by I- and [BO3]3- anions. The wavevector, q = 0.242 (3)c*, is very close to the rational value of c*/4, yet refinement based on commensurate modulation faces serious problems indicating the incommensurate nature of the modulation. The I-/[BO3]3- anions are ordered in a complex sequence along [001], i.e. -<-BO3-BO3-I-I->n = 28-I-I-I-<-BO3-BO3-I-I->n = 28-BO3-BO3-BO3-, leading to a structural modulation. The principal feature of the latter is the presence of -I-I-I- and -BO3-BO3-BO3- sequences that cannot be accounted for in the a × b × 4c supercell. The thermal expansion of Bi4BO7I is weakly anisotropic (αa = 8, αb = 15 and αc = 17 × 10-6 K-1 at 500 K) which is caused by preferential orientation of the borate groups.

Understanding electrochemical switchability of perovskite-type exsolution catalysts.

Exsolution of metal nanoparticles from perovskite-type oxides is a very promising approach to obtain catalysts with superior properties. One particularly interesting property of exsolution catalysts is the possibility of electrochemical switching between different activity states. In this work, synchrotron-based in-situ X-ray diffraction experiments on electrochemically polarized La0.6Sr0.4FeO3-δ thin film electrodes are performed, in order to simultaneously obtain insights into the phase composition and the catalytic activity of the electrode surface. This shows that reversible electrochemical switching between a high and low activity state is accompanied by a phase change of exsolved particles between metallic α--Fe and Fe-oxides. Reintegration of iron into the perovskite lattice is thus not required for obtaining a switchable catalyst, making this process especially interesting for intermediate temperature applications. These measurements also reveal how metallic particles on La0.6Sr0.4FeO3-δ electrodes affect the H2 oxidation and H2O splitting mechanism and why the particle size plays a minor role.

The first silver bismuth borate, AgBi2B5O11.

The first silver bismuth borate, AgBi2B5O11 (silver dibismuth pentaborate), has been prepared via glass crystallization in the Ag2O-Bi2O3-B2O3 system and characterized by single-crystal X-ray diffraction. Its structure is derived from that of centrosymmetric Bi3B5O12 by ordered substitution of one Bi3+ ion for Ag+, which results in the disappearance of the mirror plane and inversion centre. Second harmonic generation (SHG) measurements confirm the acentric crystal structure. It is formed by [Bi2B5O11]∞ layers stretched along c and comprised of vertex-sharing B5O10 and BiO3 groups which incorporate the Ag+ cations. The new compound was characterized by thermal analysis, high-temperature powder X-ray diffraction, and vibrational and UV-Vis-NIR (near infrared) spectroscopy. Its thermal expansion is strongly anisotropic due to the presence of rigid B5O10 groups aligned in a parallel manner. The minimal value is observed along their axis [parallel to c, αc = 3.1 (1) × 10-6 K-1], while maximal values are observed in the ab plane [αa = 20.4 (2) and αb = 7.8 (2) × 10-6 K-1]. Upon heating, AgBi2B5O11 starts to decay above 684 K due to partial reduction of silver; incongruent melting is observed at 861 K. According to density functional theory (DFT) band-structure calculations, the new compound is a semiconductor with an indirect energy gap of 3.57 eV, which agrees with the experimental data (absorption onset at 380 nm).

Operando X-ray Investigation of Electrode/Electrolyte Interfaces in Model Solid Oxide Fuel Cells.

We employed operando anomalous surface X-ray diffraction to investigate the buried interface between the cathode and the electrolyte of a model solid oxide fuel cell with atomic resolution. The cell was studied under different oxygen pressures at elevated temperatures and polarizations by external potential control. Making use of anomalous X-ray diffraction effects at the Y and Zr K-edges allowed us to resolve the interfacial structure and chemical composition of a (100)-oriented, 9.5 mol % yttria-stabilized zirconia (YSZ) single crystal electrolyte below a La0.6Sr0.4CoO3-δ (LSC) electrode. We observe yttrium segregation toward the YSZ/LSC electrolyte/electrode interface under reducing conditions. Under oxidizing conditions, the interface becomes Y depleted. The yttrium segregation is corroborated by an enhanced outward relaxation of the YSZ interfacial metal ion layer. At the same time, an increase in point defect concentration in the electrolyte at the interface was observed, as evidenced by reduced YSZ crystallographic site occupancies for the cations as well as the oxygen ions. Such changes in composition are expected to strongly influence the oxygen ion transport through this interface which plays an important role for the performance of solid oxide fuel cells. The structure of the interface is compared to the bare YSZ(100) surface structure near the microelectrode under identical conditions and to the structure of the YSZ(100) surface prepared under ultrahigh vacuum conditions.