Equation of state predictions for ScF3 and CaZrF6 with neural network-driven molecular dynamics

In silico property prediction based on density functional theory (DFT) is increasingly performed for crystalline materials. Whether quantitative agreement with experiment can be achieved with current methods is often an unresolved question, and may require detailed examination of physical effects such as electron correlation, reciprocal space sampling, phonon anharmonicity, and nuclear quantum effects (NQE), among others. In this work, we attempt first-principles equation of state prediction for the crystalline materials ScF3 and CaZrF6, which are known to exhibit negative thermal expansion (NTE) over a broad temperature range. We develop neural network (NN) potentials for both ScF3 and CaZrF6 trained to extensive DFT data, and conduct direct molecular dynamics prediction of the equation(s) of state over a broad temperature/pressure range. The NN potentials serve as surrogates of the DFT Hamiltonian with enhanced computational efficiency allowing for simulations with larger supercells and inclusion of NQE utilizing path integral approaches. The conclusion of the study is mixed: while some equation of state behavior is predicted in semiquantitative agreement with experiment, the pressure-induced softening phenomenon observed for ScF3 is not captured in our simulations. We show that NQE have a moderate effect on NTE at low temperature but does not significantly contribute to equation of state predictions at increasing temperature. Overall, while the NN potentials are valuable for property prediction of these NTE (and related) materials, we infer that a higher level of electron correlation, beyond the generalized gradient approximation density functional employed here, is necessary for achieving quantitative agreement with experiment.

Negative Thermal Expansion, Response to Pressure and Phase Transitions in CaTiF6

Strong volume negative thermal expansion over a wide temperature range typically only occurs in ReO₃-type fluorides that retain an ideal cubic structure to very low temperatures, such as ScF₃, CaZrF₆, CaHfF₆, and CaNbF₆. CaTiF₆ was examined in an effort to expand this small family of materials. However, it undergoes a cubic ( Fm3̅ m) to rhombohedral ( R3̅) transition on cooling to ∼120 K, with a minimum volume coefficient of thermal expansion (CTE) close to -42 ppm K^-1 at 180 K and a CTE of about -32 ppm K^-1 at room temperature. On compression at ambient temperature, the material remains cubic to ∼0.25 GPa with K₀ = 29(1) GPa and K'₀ = -50(5). Cubic CaTiF₆ is elastically softer and shows more pronounced pressure induced softening, than both CaZrF₆ and CaNbF₆. In sharp contrast to both CaZrF₆ and CaNbF₆, CaTiF₆ undergoes a first-order pressure induced octahedral tilting transition to a rhombohedral phase ( R3̅) on compression above 0.25 GPa, which is closely related to that seen in ScF₃. Just above the transition pressure, this phase is elastically very soft with a bulk modulus of only ∼4 GPa as octahedral tilting associated with a reduction in the Ca-F-Ti angles provides a low energy pathway for volume reduction. This volume reduction mechanism leads to highly anisotropic elastic properties, with the rhombohedral phase displaying both a low bulk modulus and negative linear compressibility parallel to the crystallographic c-axis for pressures below ∼2.5 GPa. At ∼3 GPa, a further phase transition to a poorly ordered phase occurs.

Synthesis of Defect Perovskites (He2-x□x)(CaZr)F6 by Inserting Helium into the Negative Thermal Expansion Material CaZrF6

Defect perovskites (He_2-x□_x)(CaZr)F₆ can be prepared by inserting helium into CaZrF₆ at high pressure. They can be recovered to ambient pressure at low temperature. There are no prior examples of perovskites with noble gases on the A-sites. The insertion of helium gas into CaZrF₆ both elastically stiffens the material and reduces the magnitude of its negative thermal expansion. It also suppresses the onset of structural disorder, which is seen on compression in other media. Measurements of the gas released on warming to room temperature and Rietveld analyses of neutron diffraction data at low temperature indicate that exposure to helium gas at 500 MPa leads to a stoichiometry close to (He₁□₁)(CaZr)F₆. Helium has a much higher solubility in CaZrF₆ than silica glass or crystobalite. An analogue with composition (H₂)₂(CaZr)F₆ would have a volumetric hydrogen storage capacity greater than current US DOE targets. We anticipate that other hybrid perovskites with small neutral molecules on the A-site can also be prepared and that they will display a rich structural chemistry.

A cautionary tale on the use of GE-7031 varnish: low-temperature thermal expansion studies of ScF3

GE-7031 varnish, a commonly used low-temperature adhesive and electrical insulator owing to its high thermal conductivity and mechanical strength at low temperatures, was used as a sample matrix for low-temperature powder X-ray diffraction measurements of the negative thermal expansion (NTE) material ScF3. When ScF3powder was mixed with GE-7031 varnish, an unexpected cubic to rhombohedral phase transition in the ScF3sample was observed at ∼50 K, and it exhibited smaller low-temperature unit-cell volumes than samples without the varnish matrix. Experimental observations and quantitative estimates suggest that these anomalies are the result of stress induced by a thermal expansion mismatch between the varnish matrix (large positive coefficient of thermal expansion, CTE) and ScF3(quite large negative CTE). The use of GE-7031 varnish as a sample matrix for low-temperature measurements should be approached with caution if a large thermal expansion mismatch is expected.

Reducing the background from pressure vessels using a BRIM

A collimator and beam-stop assembly that can be inserted inside a temperature-controlled pressure vessel, to reduce dramatically the parasitic Bragg scattering from the vessel, has been designed and evaluated. High-energy X-ray powder diffraction data, suitable for the Rietveld refinement of simple crystal structures, were collected using this background-reducing internal mask (BRIM). ZrW2O8was examined at up to 540 K and 124 MPa, using quite large pressure and temperature steps. No pressure dependence of the order–disorder transition temperature of this material was apparent. An orthorhombic to monoclinic phase transition (onset ∼83 MPa) was observed for Al2W3O12. Upon going through the transition, the bulk modulus of the material decreased from 41.8 to 20.8 GPa. Bulk moduli estimated for CaF2and α-Al2O3, from data collected at up to 280 MPa, were in good agreement with prior literature.

Optimizing high-pressure pair distribution function measurements in diamond anvil cells

Pair distribution function (PDF) methods have great potential for the study of diverse high-pressure phenomena. However, the measurement of high-quality, high-resolution X-ray PDF data (toQmax > 20 Å−1) remains a technical challenge. An optimized approach to measuring high-pressure total scattering data for samples contained within a diamond anvil cell (DAC) is presented here. This method takes into account the coupled influences of instrument parameters (photon energy, detector type and positioning, beam size/shape, focusing), pressure-cell parameters (target pressure range, DAC type, diamonds, pressure-transmitting media, backing plates, pressure calibration) and data reduction on the resulting PDF. The efficacy of our approach is demonstrated by the high-quality, high-pressure PDFs obtained for representative materials spanning strongly and weakly scattering systems, and crystalline and amorphous samples. These are the highest-resolution high-pressure PDFs reported to date and include those for α-alumina (toQmax  =  20 Å−1), BaTiO3(toQmax= 30 Å−1) and pressure-amorphized zeolite (toQmax  =  20 Å−1).

Determining metal ion distributions using resonant scattering at very high-energy K-edges: Bi/Pb in Pb5Bi6Se14

Powder diffraction data collected at ∼86 keV, and just below both the Pb and the Bi K-edges, on an imaging plate detector using synchrotron radiation from the Advanced Photon Source have been used to examine the Pb/Bi distribution over the 11 crystallographically distinct sites in Pb5Bi6Se14 [space group P21/m, a = 16.0096 (2) Å, b = 4.20148 (4) Å, c = 21.5689 (3) Å and β = 97.537 (1)°]. The scattering factors needed for the analyses were determined both by Kramers–Kronig transformation of absorption spectra and by analyses of diffraction patterns from reference compounds. Even with the relatively low scattering contrast that is available at the K-edges, it was possible to determine the Pb/Bi distribution and probe the presence of cation site vacancies in the material. The current results indicate that resonant scattering measurements at high-energy K-edges are a viable, and perhaps preferable, route to site occupancies when absorption from the sample or sample environment/container is a major barrier to the acquisition of high-quality resonant scattering data at lower-energy edges.

Phase composition depth profiles using spatially resolved energy dispersive X-ray diffraction

Spatially resolved energy dispersive X-ray diffraction, using high-energy synchrotron radiation (∼35–80 keV), was used nondestructively to obtain phase composition profiles along the radii of cylindrical cement paste samples to characterize the progress of the chemical changes associated with sulfate attack on the cement. Phase distributions were acquired to depths of ∼4 mm below the specimen surface with sufficient spatial resolution to discern features less than 200 µm thick. The experimental and data analysis methods employed to obtain quantitative composition profiles are described. The spatial resolution that could be achieved is illustrated using data obtained from copper cylinders with a thin zinc coating. The measurements demonstrate that this approach is useful for nondestructively visualizing the sometimes complex transformations that take place during sulfate attack on cement-based materials. These transformations can be spatially related to microstructure as seen by computed microtomography.

Strategies for solving neighboring-element problems: a case study using resonant X-ray diffraction and pulsed neutron diffraction to examine Sr8Ga16Ge30

The distribution of gallium and germanium over the available framework sites in the type-I clathrate Sr8Ga16Ge30(Pm\bar{3}n) has been determined by powder diffraction using several different combinations of resonant scattering data sets, collected at energies close to both the Ga and GeK-edges, and time-of-flight (TOF) neutron diffraction data. Based on a combined refinement using three X-ray data sets and a composition restraint, the fractional occupancies of the 6c, 16iand 24ksites by gallium are estimated to be 0.705 (5), 0.181 (3) and 0.376 (2), respectively. The required resonant scattering factors were determined by Kramers–Kronig transformation from X-ray absorption spectra. The results from refinements using single data sets and various combinations of data sets are compared. The high degree of scattering contrast that resonant diffraction can provide leads to very precise site occupancies. However, systematic errors in the resonant diffraction intensity data can considerably degrade the accuracy of the results. The use of a carefully chosen multiple-data-set strategy can minimize bias in the refinement results by reducing the correlations between site occupancies, atomic displacement parameters and histogram scale factors. The effect of errors in the resonant scattering factors on the refinement results was also examined.

Hydrolysis by lactase phlorizin hydrolase is the first step in the uptake of daidzein glucosides by rat small intestine in vitro

1. Isoflavones are naturally occurring oestrogenic compounds found in plants, where they exist in the glycosylated form. A proportion of ingested glycosides appears to be absorbed in the upper gastrointestinal tract, where enterocytes play an important role in their metabolism. 2. One hypothesis is that ingestion may involve hydrolysis by the luminally exposed enzyme lactase phlorizin hydrolase (LPH), an enzyme expressed specifically at the small intestinal brush border. 3. Using an everted sac preparation of rat jejunum and an inhibitor of LPH, we investigated the absorption of daidzein-O(7)-glucoside (daidzin) and the effect of LPH inhibition on this process. It was demonstrated that LPH plays a major role in the deglycosylation of daidzin. 4. The hydrolysis product, daidzein, is absorbed by epithelial cells and glucuronidated to daidzein-O(7)-glucuronide, which is subsequently exported primarily to the serosal (vascular) side of the tissue rather than to the luminal side. 5. A small but significant proportion of the intact glycoside is also transferred to the serosal compartment, and in the presence of an LPH inhibitor this was enhanced with a corresponding reduction in deglucosylation and glucuronidation. 6. The results indicate that that LPH plays an important role in the metabolism of glycosylated phytochemicals, and that the expression and activity of this enzyme in the small intestine can modify the profile of metabolites appearing in the circulation.

Identification and quantification of polyphenol phytoestrogens in foods and human biological fluids

We review the methods used to measure phytoestrogens (genistein, daidzein, lignans and their derivatives) in foods and biological fluids, and discuss advantages and disadvantages of each. The range of detection limits reported varies widely between individual laboratories, but generally the best reported sensitivity is as follows: immunoassay>HPLC-mass spectrometry=HPLC-multichannel electrochemical detection (coularray)>GC-single ion monitoring-mass spectrometry>HPLC-UV diode array>HPLC-single channel electrochemical detection. The best sensitivity reported so far is 0.002 pmol per assay for daidzein by radioimmunoassay. HPLC with UV diode array detection is the most commonly employed, but is the least sensitive and specific. GC and HPLC coupled with mass spectrometry or electrochemical detection are the most accurate and reproducible methods for a wide variety of analytes. Generally most methods, with the exception of immunoassay, have not been correlated with other methods. Recoveries from extraction methods, limits of detection, nature of compounds analysed and the internal standards used are summarised for more than 90 reports in the literature. From this data, it is clear that an inter-laboratory validation and correlation between a wide range of methods for phytoestrogen analysis is required. One underdeveloped area that requires particular attention is the analysis of plant lignans.

M-F interatomic distances and effective volumes of second and third transition series MF6- and MF6(2-) anions

Synchrotron X-ray powder diffraction data (SPDD) for representative LiMF6 and Li2MF6 salts of the second and third transition series have provided unit-cell parameters and, from Rietveld analysis, M-F interatomic distances. M-F distances have also been obtained from X-ray single-crystal structural analyses of LiOsF6, Li2PtF6, and KRhF6. The LiMF6 all have the LiSbF6 structure type (space group R3). For M = Ta to Au the primitive unit cell volume decreases with increasing nuclear charge (Z), the volumes (sigma = 0.01 A3) being as follows: Ta, 111.26; Os, 102.42; Ir, 100.77; Pt, 99.62; and Au, 99.12 A3. A similar contraction, with increase in Z, occurs from Nb to Rh, the primitive cell volume (sigma = 0.01 A3) being: Nb, 110.92; Ru, 100.51; and Rh, 98.64 A3. For the TaF6- to AuF6- the M-F distances are not significantly different across the series, at approximately 1.87(1) A; also, Nb-F, Ru-F, and Rh-F = 1.86(1) A. In each series, the a and c values of the hexagonal-cell representation for the LiMF6 structure (separate layers of MF6- and Li+ stacked along c) change smoothly. As Z increases, a decreases and c increases. The variation in a, like the volume change, indicates that the size of MF6- is decreasing with Z. The variation in c suggests that the charge on the F-ligand is decreasing with Z. In the trirutile Li2MF6 series, M = Mo to Pd, the formula-unit volume decreases with Z(Mo, 100.92(6); Ru, 98.21(1); Rh, 97.43(1); Pd, 96.83(1) A3) and a shortening in M-F occurs (Mo-F = 1.936(4); Ru-F = 1.921(7); Rh-F = 1.910(7); Pd-F = 1.899(4) A). The less abundant data for MF6(2-) salts of the third transition series indicate similar trends. For both series, M-F distances of MF6(2-) are longer by 0.03-0.09 A than in MF6-.

Structural features of Ag[AuF4] and Ag[AuF6] and the stuctural relationship of Ag[AgF4]2 and Au[AuF4]2 to Ag[AuF4]2

Synchrotron radiation X-ray powder diffraction data (SPDD) have been obtained for Ag[AgF4]2, Au[AuF4]2, Ag[AuF4], and Ag[AuF6]. Ag[AgF4]2 and Au[AuF4]2 are isostructural with Ag[AuF4]2, space group (SG) P2(1)/n, Z = 2, with the following: for Ag[AgF4]2 a = 5.04664(8), b = 11.0542(2), c = 5.44914(9) A, beta = 97.170(2) degrees; for Au[AuF4]2 a = 5.203(2), b = 11.186(3), c = 5.531(2) A, beta = 90.55(2) degrees. The structure of Ag[AgF4]2 was refined successfully (SPDD) applying the Rietveld method, yielding the following interatomic distances (A): AgII-F = 2.056(12), 2.200(13), 2.558(13); AgIII-F = two at 1.846(12), others = 1.887(12), 1.909(13), 2.786-(12), 2.796(12), 2.855(12). AgAuF4, like other AA'F4 salts (A = Na-Rb; A' = Ag, Au), crystallizes in the KBrF4 structure type, SG I4/mcm (140), Z = 4 with a = 5.79109(6), c = 10.81676(7) A. SPDD gave (in A) four AuIII-F = 1.89(1) and eight AgI-F = 2.577(7). SPDD for AgAuF6 confirmed that it has the LiSbF6 structure, SG R3, Z = 3, with a = 5.2840(2), c = 15.0451(6) A.

Effects of cationic charge on three-dimensional structures of intercalative complexes: structure of a bis-intercalated DNA complex solved by MAD phasing

We characterize intercalative complexes as either "high charge" and "low charge". In low charge complexes, stacking interactions appear to dominate stability and structure. The dominance of stacking is evident in structures of daunomycin, nogalamycin, ethidium, and triostin A/echinomycin. By contrast in a DNA complex with the tetracationic metalloporphyrin CuTMPyP4 [copper (II) meso-tetra(N-methyl-4-pyridyl)porphyrin], electrostatic interactions appear to draw the porphyrin into the duplex interior, extending the DNA along its axis, and unstacking the DNA. Similarly, DNA complexes of tetracationic ditercalinium and tetracationic flexi-di show significant unstacking. Here we report x-ray structures of complexes of the tetracationic bis-intercalator D232 bound to DNA fragments d(CGTACG) and d(BrCGTABrCG). D232 is analogous to ditercalinium but with three methylene groups inserted between the piperidinium groups. The extension of the D232 linker allows it to sandwich four base pairs rather than two. In comparison to CuTMPyP4, flexi-di and ditercalinium, stacking interactions of D232 are significantly improved. We conclude that it is not sufficient to characterize intercalators simply by net charge. One anticipates strong electrostatic forces when cationic charge is focused to a small volume or region near DNA and so must consider the extent to which cationic charge is focused or distributed. In sum, ditercalinium, with a relatively short linker, focuses cationic charge more narrowly than does D232. So even though the net charges are equivalent, electrostatic charges are expected to be of greater structural significance in the ditercalinium complex than in the D232 complex.

Monoclonal anti-idiotype antibody mimicking the pesticide binding site of cutinase: potential for broad specificity organophosphate recognition

An anti-idiotype monoclonal antibody (Mab) able to bind the organophosphate pesticides, chlorfenvinphos (CFV), ethyl paraoxon, tetrachlorfenvinphos and demeton-s-methyl, has been produced using as immunogen a Mab which binds to the active site of cutinase. The principle of using an anti-idiotype antibody as the mimic of a site on a protein able to bind a group of ligands has, therefore, been demonstrated, and may have implications for future research on broad specificity immunoanalysis of groups of compounds.

Heterologous gene expression in Aspergillus niger: a glucoamylase-porcine pancreatic prophospholipase A2 fusion protein is secreted and processed to yield mature enzyme

The cDNA gene encoding porcine pancreatic prophospholipase A2 (proPLA2) was cloned into an Aspergillus niger expression vector downstream of the glucoamylase (glaA) gene promoter region. When this construct was transformed into A. niger, no detectable PLA2 was produced. Evidence was obtained showing that the PLA2 gene was transcribed and that PLA2 is extremely susceptible to both intracellular and extracellular proteases of A. niger, thus indicating that translation products would be rapidly degraded. By fusing the proPLA2-encoding sequence to the entire glaA gene, secreted yields of PLA2 up to 10 micrograms/ml were obtained from a transformed protease-deficient strain of A. niger. PLA2 was secreted in young cultures as a fusion protein, but in older cultures, it was processed from the glucoamylase carrier protein. Secreted PLA2 was shown to be enzymatically active and to have the correct N-terminal amino acid (aa) sequence, although another form of processed PLA2 was also produced. This form included two aa of the proregion from PLA2. The potential for improving yields of secreted heterologous proteins from A. niger still further is discussed.

Transplacental transfer of aflatoxin in humans

This study quantified aflatoxin (AFB1, AFG1 and AFQ1) by enzyme-linked immunosorbent assay in human cord sera obtained at birth and in serum obtained immediately after birth from the mother. The subjects of the study were residents of Songkhla, Thailand. Of the 35 samples of cord sera, 17 (48%) contained aflatoxin in concentrations from 0.064 to 13.6, mean 3.1 nmol/ml. By comparison only two (6%) of 35 maternal sera contained aflatoxin (mean 0.62 nmol/ml). These results demonstrate transplacental transfer and concentration of aflatoxin by the feto-placental unit which may be of biological importance. Aflatoxins are mutagenic, carcinogenic and teratogenic and cause immunosuppression in animals. The implications of these findings are potentially profound and deserve further study.

High serum concentrations of aflatoxin in Nepal as measured by enzyme-linked immunosorbent serum assay

1 Sera from 28 Nepalis, both patients and workers in a hospital in Banepa, Nepal were examined for AFB1 by enzyme-linked immunosorbent assay (ELISA). 2 This assay, previously validated using spiked sera, provides a sensitive rapid determination of serum aflatoxin (B1, G1 and Q1). 3 All 28 sera were positive with concentrations from 60 pg ml-1 to 10 ng ml-1. 4 These results suggest that consumption of aflatoxin in Nepal is high (greater than 50-800 ng kg-1 d-1). 5 No reports of the degree of contamination of food, human consumption or body fluid concentrations of aflatoxin in Nepal have been previously published. 6 Aflatoxin may contribute to the development of hepatocellular carcinoma, which is probably a common tumour in Nepal.

An ELISA method for the rapid and simple determination of aflatoxin in human serum

A rapid, simple method for the determination of aflatoxin in human serum using anti-aflatoxin antisera in an indirect, double antibody microtitration plate enzyme-linked immunosorbent assay (ELISA) is described. Direct assay of serum necessitated the availability of a large sample volume, due to the presence of 'non-specific' interference. Addition of methanol to sera removed the interference enabling the analysis to be performed on small volumes (0.5 ml) of serum. The sensitivity of the assay is 20 pg ml-1. Total assay time, including sample preparation, is 4.5 h. No aflatoxin was found in any of the UK samples analysed.

Analysis of UK sera for aflatoxin by enzyme-linked immunosorbent assay

1. Aflatoxins are toxic, carcinogenic secondary fungal metabolites produced by certain moulds that commonly infest foods. Measurement of aflatoxins in human serum would give a direct measurement of exposure. 2. Twenty-seven serum samples from UK blood donors were found to contain aflatoxin levels not greater than 64 pmol/l (20 pg/ml) by an enzyme-linked immunosorbent assay. 3. These findings may indicate that present UK guideline tolerances for aflatoxin in imported food are effective in limiting human exposure to toxic aflatoxins in the UK diet, though further work would be needed to confirm this. In particular, sub-populations suspected of being at higher risk may need special considerations.

Measurement of aflatoxin in Nigerian sera by enzyme-linked immunosorbent assay

Sera from 78 healthy men donating blood in Enugu, Nigeria were examined for aflatoxin by enzyme-linked immunosorbent assay (ELISA). Levels varied from less than 20 pg/ml to 3.1 ng/ml. The ELISA method is simple, sensitive and specific, and therefore well suited to the low-resource tropical environment. Aflatoxin is ingested in considerable amounts in Nigeria and many contribute, with hepatitis B, to the development of hepatocellular carcinoma.

Determination of myrosinase (thioglucoside glucohydrolase) activity by a spectrophotometric coupled enzyme assay

The hexokinase/glucose-6-phosphate dehydrogenase coupled enzyme system was used to assay for plant thioglucoside glucohydrolase (myrosinase, EC 3.2.3.1) by measuring the rate of glucose released during hydrolysis of glucosinolates. This coupled assay was compared with two other assays for myrosinase: a pH-stat assay that measures the rate of acid released during glucosinolate hydrolysis, and a spectrophotometric assay in which the decrease in the absorbance at 227.5 nm is used to measure the disappearance of the substrate, 2-propenylglucosinolate (DSA assay). The coupled and pH-stat assays were found to give comparable activities and were linear with enzyme concentration over the range 0 to 30 micrograms. The DSA assay gave lower myrosinase activity in comparison to the coupled and pH-stat assays. This is due to the lower concentrations of substrate and activator (ascorbate) which must be used in the assay. The DSA assay was found to give a nonlinear relationship with enzyme concentration over the range 2 to 30 micrograms. For these reasons this assay was found to be unsatisfactory. The coupled assay was found to be more sensitive and more widely applicable than the pH-stat assay as a routine continuous assay for myrosinase activity.