Non-resonant inelastic X-ray scattering for discrimination of pigments.

Inelastic X-ray scattering (IXS) spectroscopy has been used in many fields of solid-state physics and theoretical chemistry as an accurate and quantitative probe of elementary excitations. We show that non-resonant IXS spectra in the energy loss range below 100 eV exhibit a strong contrast across a wide range of commercially available pigments, opening new routes for their discrimination. These signatures combine plasmonic transitions, collective excitations and low energy absorption edges. We have performed IXS to discriminate different artists' pigments within complex mixtures and to quantitatively determine rutile and anatase polymorphs of TiO2. The integration of experimental data on pigment powders with suitable ab initio simulations shows a precise fit of the spectroscopic data both in the position of the resonances and in their relative intensity.

The case for data science in experimental chemistry: examples and recommendations.

The physical sciences community is increasingly taking advantage of the possibilities offered by modern data science to solve problems in experimental chemistry and potentially to change the way we design, conduct and understand results from experiments. Successfully exploiting these opportunities involves considerable challenges. In this Expert Recommendation, we focus on experimental co-design and its importance to experimental chemistry. We provide examples of how data science is changing the way we conduct experiments, and we outline opportunities for further integration of data science and experimental chemistry to advance these fields. Our recommendations include establishing stronger links between chemists and data scientists; developing chemistry-specific data science methods; integrating algorithms, software and hardware to 'co-design' chemistry experiments from inception; and combining diverse and disparate data sources into a data network for chemistry research.

Network analysis of synthesizable materials discovery.

Assessing the synthesizability of inorganic materials is a grand challenge for accelerating their discovery using computations. Synthesis of a material is a complex process that depends not only on its thermodynamic stability with respect to others, but also on factors from kinetics, to advances in synthesis techniques, to the availability of precursors. This complexity makes the development of a general theory or first-principles approach to synthesizability currently impractical. Here we show how an alternative pathway to predicting synthesizability emerges from the dynamics of the materials stability network: a scale-free network constructed by combining the convex free-energy surface of inorganic materials computed by high-throughput density functional theory and their experimental discovery timelines extracted from citations. The time-evolution of the underlying network properties allows us to use machine-learning to predict the likelihood that hypothetical, computer-generated materials will be amenable to successful experimental synthesis.

The stability, electronic structure, and optical absorption of boron-nitride diamondoids predicted with first-principles calculations.

Although diamondoids are broadly studied for their fundamental properties and applications, boron-nitride-based diamondoids are scarcely explored. Here we predict the stability, electronic structure, and optical absorption spectra of six boron-nitride (BN) diamondoids with first-principles methods based on pseudopotential density functional theory and many-body perturbation methods implemented with a real-space formalism. We find that four of them are thermodynamically stable at room temperature, while B10N8H24 and B6N4H16 show thermodynamic instability in molecular dynamics simulations. With the GW approximation, we predicted the ionization energies and electron affinities of BN-diamondoids and find that the evolution of the electronic structure with size does not follow the same trend as diamondoids, owing to the unbalanced numbers of boron and nitrogen atoms. We show strong photoabsorption of BN-triamantane and BN-adamantane in the infrared and visible ranges and analyze the features of low-energy absorption by examining the characteristics of related orbitals.

Benchmarking the GW Approximation and Bethe-Salpeter Equation for Groups IB and IIB Atoms and Monoxides.

Energies from the GW approximation and the Bethe-Salpeter equation (BSE) are benchmarked against the excitation energies of transition-metal (Cu, Zn, Ag, and Cd) single atoms and monoxide anions. We demonstrate that best estimates of GW quasiparticle energies at the complete basis set limit should be obtained via extrapolation or closure relations, while numerically converged GW-BSE eigenvalues can be obtained on a finite basis set. Calculations using real-space wave functions and pseudopotentials are shown to give best-estimate GW energies that agree (up to the extrapolation error) with calculations using all-electron Gaussian basis sets. We benchmark the effects of a vertex approximation (ΓLDA) and the mean-field starting point in GW and the BSE, performing computations using a real-space, transition-space basis and scalar-relativistic pseudopotentials. While no variant of GW improves on perturbative G0W0 at predicting ionization energies, G0W0ΓLDA-BSE computations give excellent agreement with experimental absorption spectra as long as off-diagonal self-energy terms are included. We also present G0W0 quasiparticle energies for the CuO-, ZnO-, AgO-, and CdO- anions, in comparison to available anion photoelectron spectra.

Improved methodology to induce hyperoxaluria without treatment using hydroxyproline.

The use of hydroxyproline (HP) to generate hyperoxaluria in the rat is a problem because it is impossible to separate the effect of oxalate on renal injury from the effects of HP and the large array of metabolic intermediates formed when HP is converted to oxalate. Previously, the Dahl salt-sensitive (SS) and Brown Norway (BN) rat strains were studied to determine genetic control of resistance or susceptibility to HP-induced renal injury and crystal deposition. To develop a better model to induce hyperoxaluria without causing injury from HP metabolites, animals were fed a diet containing various levels of added oxalate (0, 1, 2, 3, or 5%). After 5 weeks rats were killed and the kidneys were removed for microscopic evaluation of tubule changes and crystal deposition. The 3 and 5% oxalate-fed groups had a substantial increase in urine oxalate, about 50 and 140 µmol/g body weight over controls, respectively. Both the SS and BN 3% oxalate-fed animals showed only slightly elevated tubule area and no crystal deposition. However, BN animals fed 5% oxalate had a dramatic increase in their percent tubule areas compared to control BN rats and treated SS rats. Crystal deposition in the kidneys was only observed in the 5% oxalate-fed groups. The BN kidneys demonstrated a threefold higher crystal deposition compared to oxalate-fed SS rats. We conclude that oxalate-supplemented food is a better method of producing hyperoxaluria in the rat than using HP which may introduce metabolic intermediates injurious to the kidney.

Study of a rat model for calcium oxalate crystal formation without severe renal damage in selected conditions.

BACKGROUND: Although nephrotoxic in high doses, ethylene glycol (EG) has been used with ammonium chloride (NH(4)Cl) or vitamin D(3) to study calcium oxalate stone formation in rat models. In the present study we used EG alone or with NH(4)Cl to study hyperoxaluria, crystaluria, and crystal attachment to renal epithelial cells in rats with minimal renal damage. METHODS: Six-week-old male Sprague-Dawley (SD) rats were given food and special drinking water. In experiment 1 the drinking water contained 1.0% NH(4)Cl plus four different concentrations of EG (0.8%, 0.4%, 0.2%, 0.1%). In experiment 2 the drinking water contained EG alone (0.8%, 0.4%, 0.2%, 0.1%). Urine was collected for 24 h before the rats were sacrificed. In experiment 1 the rats were sacrificed 5-13 days after starting the special water. In experiment 2 the rats were sacrificed 7-21 days after starting the special water. Bladder urine was also obtained. Blood and urine were tested for calcium, phosphorus, and creatinine. In addition, urine was tested for pH, oxalate and N-acetyl-beta-D glucosaminidase (NAG). Kidney sections were stained with hematoxylin-eosin, von Kossa and Pizzolato stain. Crystal morphology was determined using polarizing microscopy, and composition was determined using high-resolution X-ray powder diffraction. RESULTS: Experiment 1: Aggravation of renal function, an increase in urinary oxalate and NAG excretion, and crystals observed in the kidneys all correlated with EG concentration and length of drinking time. In bladder urine, calcium oxalate monohydrate (COM) crystals exceeded calcium oxalate dihydrate (COD) crystals. Experiment 2: Renal function remained unchanged. Oxalate excretion increased and NAG increased slightly. Crystals occurred only in the papillary tip region. Crystals in bladder urine were mostly COD. CONCLUSION: In the current rat model, calcium oxalate crystaluria could be induced without severe renal damage in selected cases. Either and/or both COM and COD might form and interact with kidney epithelium. We propose different experimental conditions to study the various phases of calcium oxalate stone formation in young male SD rats.

A porcine model of calcium oxalate kidney stone disease.

PURPOSE: The pig has been extensively used in biomedical research because of the similarities in organ structure and function to humans. It is desirable to have an animal model of oxaluria and urolithiasis with physiological, anatomical and nutritional characteristics that more closely resemble those of man. In this study we determined if feeding pigs trans-4-hydroxy-l-proline (HP) increased urine oxalate levels and if it would serve as a model for human hyperoxaluria and stone disease. MATERIALS AND METHODS: Male Yorkshire-Durox cross-bred pigs were fed HP for up to 20 days. Urine was periodically collected and analyzed for oxalate levels and the presence of crystalluria. After 20 days of feeding the kidneys were removed and examined grossly and microscopically for indications of injury, crystal deposition and stone formation. RESULTS: Feeding pigs 10% HP (weight per weight HP/food) produced hyperoxaluria, which reached a maximum and leveled off by day 6. Urine oxalate remained near this level until the study ended at 20 days regardless of the further increase in HP to 20% of the weight of the food. When the kidneys were removed and grossly examined, calcium oxalate encrustations were observed on multiple papillary tips. Histopathological observation of the papillary tissue showed tissue injury and crystal deposition. CONCLUSIONS: Pigs fed HP have hyperoxaluria and calcium oxalate crystalluria, and calcium oxalate papillary deposits form that may be precursors of kidney stones. The use of the pig as a model of human hyperoxaluria and stone formation should prove ideal for studies of these human diseases.

Crystal attachment to injured renal collecting duct cells: influence of urine proteins and pH.

BACKGROUND: The attachment of crystals to injured kidney epithelium is thought to be a necessary event in the development of urolithiasis. In vivo, the crystals are coated with urinary macromolecules that define the surface properties of the crystals. The present study examines the influence of coating of calcium oxalate crystals with urinary macromolecules on their attachment to both healthy (polarized) and injured (nonpolarized) primary inner medullary collecting duct (IMCD) cells. METHODS: Calcium oxalate monohydrate (COM) and calcium oxalate dihydrate (COD) crystals were coated with urine macromolecules by incubating the crystals in urine from normal healthy volunteers at pH 5, 6, and 7. The level of attachment of the coated crystals to IMCD cells was also determined at pH 5, 6, and 7. The adsorbed proteins were extracted from the crystal surfaces and separated by gel electrophoresis. RESULTS: The coating of calcium oxalate crystals with urine proteins greatly reduced the attachment of crystals to both control and injured IMCD cells. At pH levels below 6, the crystals readily attached to injured cells. Extraction and separation of the adsorbed proteins showed that both COM and COD crystals adsorbed a similar array of proteins. At pH 5 and 6, several trace proteins were adsorbed to the crystals and were not apparent at pH 7. CONCLUSION: The coating of crystals with urine macromolecules greatly reduces the attachment of the crystals to normal healthy epithelia. The coating and attachment of the crystals below pH 6 enhances the attachment to injured cells. The enhanced crystal attachment could possibly be associated with one or more proteins adsorbed to the crystal surface that are not adsorbed to the crystals at higher pH.

Calcium oxalate monohydrate crystal binding substance produced from Madin-Darby canine kidney cells.

BACKGROUND: The interaction between kidney urothelium and crystals is a critical event in the growth of renal calculi. When studying calcium oxalate monohydrate (COM) crystal binding to Madin-Darby canine kidney (MDCK) cells in culture, we observed that crystals also attached to areas on the coverslips devoid of cells. This phenomenon could be the result of substances produced by the cells that adhere to the glass and subsequently bind COM crystals. We investigated the characteristics of this COM binding substance. METHODS: Media was collected from cultures of MDCK cells (conditioned media) and proteins were separated by high performance liquid chromatography. The molecular weights and purity of isolated proteins were determined by polyacrylamide gel electrophoresis. The conditioned media and each separated fraction were applied to glass and to MDCK cells and COM-binding ability determined using 14C-labeled crystals. The binding of radio-labelled calcium oxalate dihydrate, brushite, uric acid, and apatite to coverslips were also studied. RESULTS: Fourteen times more COM bound to coverslips incubated with conditioned media than those with control media. The molecular weight of the protein bound to the glass was determined to be 200 kDa. The COM crystals binding to this protein was 1.5 micro g/ng. Other crystals bound to a lesser extent. The incubation of cells with this protein inhibited COM binding by 39%. CONCLUSION: The MDCK cells produce a 200-kDa protein that has a high binding affinity for COM crystals. This protein binds to glass and is responsible for crystal binding to areas devoid of cells. This protein also has an inhibitory effect on COM binding to MDCK cells in culture.