Comment on "Regulating the valence level arrangement of high-Al-content AlGaN quantum wells using additional potentials with Mg doping" by W. Lin, J. Kang et al., Phys. Chem. Chem. Phys., 2022, 24, 5529.

Lu et al. (2022), 24, 5529 uses incorrect explanations for their findings based on an incorrect application of ideas from tight-binding methods. An alternative qualitative explanation based on strain variations and a tight-binding model based on nearest neighbor interactions is provided.

Intestinal anastomotic healing models during experimental colitis.

BACKGROUND: Anastomotic leakage represents a major complication following resections in colorectal surgery. Among others, intestinal inflammation such as in inflammatory bowel disease is a significant risk factor for disturbed anastomotic healing. Despite technical advancements and several decades of focused research, the underlying mechanisms remain incompletely understood. Animal experiments will remain the backbone of this research in the near future. Here, instructions on a standardized and reproducible murine model of preoperative colitis and colorectal anastomosis formation are provided to amplify research on anastomotic healing during inflammatory disease. METHODS: We demonstrate the combination of experimental colitis and colorectal anastomosis formation in a mouse model. The model allows for monitoring of anastomotic healing during inflammatory disease through functional outcomes, clinical scores, and endoscopy and histopathological examination, as well as molecular analysis. DISCUSSION: Postoperative weight loss is used as a parameter to monitor general recovery. Functional stability can be measured by recording bursting pressure and location. Anastomotic healing can be evaluated macroscopically from the luminal side by endoscopic scoring and from the extraluminal side by assessing adhesion and abscess formation or presence of dehiscence. Histologic examination allows for detailed evaluation of the healing process. CONCLUSION: The murine model presented in this paper combines adjustable levels of experimental colitis with a standardized method for colorectal anastomosis formation. Extensive options for sample analysis and evaluation of clinical outcomes allow for detailed research of the mechanisms behind defective anastomotic healing.

Optoelectronic Dichotomy of Mixed Halide CH3NH3Pb(Br1- xCl x)3 Single Crystals: Surface versus Bulk Photoluminescence.

In this work, the spatially dependent recombination kinetics of mixed-halide hybrid perovskite CH3NH3Pb(Br1- xCl x)3 (0 ≤ x ≤ 0.19) single crystals are investigated using time-resolved photoluminescence spectroscopy with one- and two-photon femtosecond laser excitation. The introduction of chloride by substituting a fraction of the bromide leads to a decreased lattice constant compared to pure bromide perovskite ( x = 0) and a higher concentration of surface defects. The measured kinetics under one-photon excitation (1PE) shows that increasing the chloride addition quenches the photoluminescence (PL) lifetimes, due to substitution-induced surface defects. In stark contrast, upon 2PE, the PL lifetimes measured deeper in the bulk become longer with increasing chloride addition, until the halide substitution reaches the critical concentration of ∼19%. At x = 19% Cl concentration, a significant reversal of this behavior is observed indicating a change in crystal structure beyond the continuous trends observed at lower percentages of halide substitution ( x ≤ 11%). The observed opposing trends, based on 1PE versus 2PE, highlight a dichotomy between extrinsic (surface) and intrinsic (bulk) effects of chloride substitution on the carrier dynamics in lead bromide perovskites. We discuss the physical relation between halide exchange and bulk carrier lifetimes in CH3NH3PbBr3 in terms of the Rashba effect. We propose that the latter is suppressed at the surface due to disorder in the alignment of the MA and that it increases in the bulk with Cl concentration because of the reduction in lattice parameters, which compresses the space available for the MA orientational degrees of freedom.

Effects of the van der Waals Interactions on Structural and Electronic Properties of CH3NH3(Pb,Sn)(I,Br,Cl)3 Halide Perovskites.

In hybrid perovskite materials like CH3NH3PbI3, methylammonium (MA) lead iodide (MAPI), the orientation of the MA+ cations and their ordering can significantly affect the structure of the inorganic framework. Although the states near the band edges are known to be primarily derived from the Pb and halogen orbitals rather than from the organic ion, the latter may have an indirect effect through their impact on the structural relaxation. In this work, we investigate both the structural relaxation effects of the inorganic framework in response to the MA+ orientation and their impact on the electronic structure near the band edges. Calculations are performed for MA(Pb,Sn)X 3 with (X = I, Br, and Cl) materials for both Pb- and Sn-based compounds. The work focuses on the high-temperature α-phase, which is nominally cubic if averaged over all possible MA orientations and in which no alternating rotations of the octahedral occur, so that the unit cell is the smallest possible. The effects of van der Waals (vdW) corrections to density functional theory on the structural relaxation are investigated. Our results reveal that the vdW interactions between the MA+ cation and the inorganic framework can strongly affect the optimized orientation and position of the molecule and the resulting distortion of the inorganic framework. Consequently, it also affects the electronic properties of the materials and specifically can change the band structure from direct to indirect band gaps. The robustness of this result is studied by comparing hybrid functional calculations and quasiparticle self-consistent GW calculations as well as spin-orbit coupling.

Quasiparticle self-consistent GW electronic band structures of Be-IV-N2 compounds.

The electronic band structures of BeSiN2 and BeGeN2 compounds are calculated using the quasiparticle self-consistent GW method. The lattice parameters are calculated for the wurtzite based crystal structure commonly found in other II-IV-N2 compounds with the Pbn21 space group. They are determined both in the local density approximation and generalized gradient approximation, which provide lower and upper limits. At the GGA lattice constants, which gives lattice constants closer to the experimental ones, BeSiN2 is found to have an indirect band gap of 6.88 eV and its direct gap at [Formula: see text] is 7.77 eV, while in BeGeN2 the gap is direct at [Formula: see text] and equals 5.03 eV. To explain the indirect gap in BeSiN2 comparisons are made with the parent III-N compound w-BN band structure. The effective mass parameters are also evaluated and found to decrease from BeSiN2 to BeGeN2.

V2O5: A 2D van der Waals Oxide with Strong In-Plane Electrical and Optical Anisotropy.

V2O5 with a layered van der Waals (vdW) structure has been widely studied because of the material's potential in applications such as battery electrodes. In this work, microelectronic devices were fabricated to study the electrical and optical properties of mechanically exfoliated multilayered V2O5 flakes. Raman spectroscopy was used to determine the crystal structure axes of the nanoflakes and revealed that the intensities of the Raman modes depend strongly on the relative orientation between the crystal axes and the polarization directions of incident/scattered light. Angular dependence of four-probe resistance measured in the van der Pauw (vdP) configuration revealed an in-plane anisotropic resistance ratio of ∼100 between the a and b crystal axes, the largest in-plane transport anisotropy effect experimentally reported for two-dimensional (2D) materials to date. This very large resistance anisotropic ratio is explained by the nonuniform current flow in the vdP measurement and an intrinsic mobility anisotropy ratio of 10 between the a and b crystal axes. Room-temperature electron Hall mobility up to 7 cm2/(V s) along the high-mobility direction was obtained. This work demonstrates V2O5 as a layered 2D vdW oxide material with strongly anisotropic optical and electronic properties for novel applications.

Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair.

BACKGROUND: Formation of isoaspartyl residues is one of several processes that damage proteins as they age. Protein L-isoaspartate (D-aspartate) O-methyltransferase (PIMT) is a conserved and nearly ubiquitous enzyme that catalyzes the repair of proteins damaged by isoaspartyl formation. RESULTS: We have determined the first structure of a PIMT from crystals of the T. maritima enzyme complexed to S-adenosyl-L-homocysteine (AdoHcy) and refined it to 1.8 A resolution. Although PIMT forms one structural unit, the protein can be divided functionally into three subdomains. The central subdomain closely resembles other S-adenosyl-L-methionine-dependent methyltransferases but bears a striking alteration of topological connectivity, which is not shared by any other member of this family. Rather than arranged as a mixed beta sheet with topology 6 upward arrow7 downward arrow5 upward arrow4 upward arrow1 upward arrow2 upward arrow3 upward arrow, the central sheet of PIMT is reorganized to 7 upward arrow6 downward arrow5 upward arrow4 upward arrow1 upward arrow2 upward arrow3 upward arrow. AdoHcy is largely buried between the N-terminal and central subdomains by a conserved and largely hydrophobic loop on one rim of the binding cleft, and a conserved Ser/Thr-rich beta strand on the other. The Ser/Thr-rich strand may provide hydrogen bonds for specific interactions with isoaspartyl substrates. The side chain of Ile-206, a conserved residue, crosses the cleft, restricting access to the donor methyl group to a deep well, the putative isoaspartyl methyl acceptor site. CONCLUSIONS: The structure of PIMT reveals a unique modification of the methyltransferase fold along with a site for specific recognition of isoaspartyl substrates. The sequence conservation among PIMTs suggests that the current structure should prove a reliable model for understanding the repair of isoaspartyl damage in all organisms.

Observation of an unexpected third receptor molecule in the crystal structure of human interferon-gamma receptor complex.

BACKGROUND: Molecular interactions among cytokines and cytokine receptors form the basis of many cell-signaling pathways relevant to immune function. Interferon-gamma (IFN-gamma) signals through a multimeric receptor complex consisting of two different but structurally related transmembrane chains: the high-affinity receptor-binding subunit (IFN-gammaRalpha) and a species-specific accessory factor (AF-1 or IFN-gammaRbeta). In the signaling complex, the two receptors probably interact with one another through their extracellular domains. Understanding the atomic interactions of signaling complexes enhances the ability to control and alter cell signaling and also provides a greater understanding of basic biochemical processes. RESULTS: The crystal structure of the complex of human IFN-gamma with the soluble, glycosylated extracellular part of IFN-gammaRalpha has been determined at 2.9 A resolution using multiwavelength anomalous diffraction methods. In addition to the expected 2:1 complex, the crystal structure reveals the presence of a third receptor molecule not directly associated with the IFN-gamma dimer. Two distinct intermolecular contacts, involving the edge strands of the C-terminal domains, are observed between this extra receptor and the 2:1 receptor-ligand complex thereby forming a 3:1 complex. CONCLUSIONS: The observed interactions in the 2:1 complex of the high-affinity cell-surface receptor with the IFN-gamma cytokine are similar to those seen in a previously reported structure where the receptor chains were not glycosylated. The formation of beta-sheet packing interactions between pairs of IFN-gammaRalpha receptors in these crystals suggests a possible model for receptor oligomerization of Ralpha and the structurally homologous Rbeta receptors in the fully active IFN-gamma signaling complex.

High-resolution macromolecular structure determination using CCD detectors and synchrotron radiation.

BACKGROUND: Synchrotron radiation sources have made impressive contributions to macromolecular crystallography. The delay in development of appropriate X-ray detectors has, however, been a significant limitation to their efficient use. New technologies, based on charge-coupled devices (CCDs), provide capabilities for faster, more accurate, automated data collection. RESULTS: A CCD-based X-ray detector has been developed for use in macromolecular crystallography and has been in operation for about one and a half years at the Cornell High Energy Synchrotron Source. It has been used for a variety of crystallographic projects, including a number of high-resolution structural studies. The statistical quality of the data, the detector's ease and efficiency of use, and the growing number of structural results illustrate the practical utility of this new detector system. CONCLUSIONS: The new detector has enhanced capabilities for measuring diffraction patterns from crystals of macromolecules, especially at high resolution, when the X-ray intensities are weak. The survey of results described here ranges from virus crystallography to weakly diffracting small-molecule structure determination and demonstrates the potential of CCD detectors when combined with synchrotron radiation sources.

Multiple wavelength anomalous diffraction (MAD) crystal structure of rusticyanin: a highly oxidizing cupredoxin with extreme acid stability.

The X-ray crystal structure of the oxidized form of the extremely stable and highly oxidizing cupredoxin rusticyanin from Thiobacillus ferrooxidans has been determined by the method of multiwavelength anomalous diffraction (MAD) and refined to 1.9 A resolution. Like other cupredoxins, rusticyanin is a copper-containing metalloprotein, which is composed of a core beta-sandwich fold. In rusticyanin the beta-sandwich is composed of a six- and a seven-stranded beta-sheet. Also like other cupredoxins, the copper ion is coordinated by a cluster of four conserved residues (His85, Cys138, His143, Met148) arranged in a distorted tetrahedron. Rusticyanin has a redox potential of 680 mV, roughly twice that of any other cupredoxin, and it is optimally active at pH values < or = 2. By comparison with other cupredoxins, the three-dimensional structure of rusticyanin reveals several possible sources of the chemical differences, including more ordered secondary structure and more intersheet connectivity than other cupredoxins. The acid stability and redox potential of rusticyanin may also be enhanced over other cupredoxins by a more extensive internal hydrogen bonding network and by more extensive hydrophobic interactions surrounding the copper binding site. Finally, reduction in the number of charged residues surrounding the active site may also make a major contribution to acid stability. We propose that the resulting rigid copper binding site, which is constrained by the surrounding hydrophobic environment, structurally and electronically favours Cu(I). We propose that the two extreme chemical properties of rusticyanin are interrelated; the same unique structural features that enhance acid stability also lead to elevated redox potential.

Recent advances in atomic-scale spin-polarized scanning tunneling microscopy.

The Mn3N2 (010) surface has been studied using spin-polarized scanning tunneling microscopy at the atomic scale. The principle objective of this work is to elucidate the properties and potential of this technique to measure atomic-scale magnetic structures. The experimental approach involves the use of a combined molecular beam epitaxy/scanning tunneling microscopy system that allows the study of atomically clean magnetic surfaces. Several key findings have been obtained. First, both magnetic and non-magnetic atomic-scale information has been obtained in a single spin-polarized image. Magnetic modulation of the height profile having an antiferromagnetic super-period of c = 12.14 A (6 atomic rows) together with a non-magnetic superstructure having a period of c/2 = 6.07 A (3 atomic rows) was observed. Methods of separation of magnetic and non-magnetic profiles are presented. Second, bias voltage-dependent spin-polarized images show a reversal of the magnetic modulation at a particular voltage. This reversal is clearly due to a change in the sign of the magnetic term in the tunnel current. Since this term depends on both the tip's as well as the sample's magnetic local density of states, the reversal can be caused by either the sample or the tip. Third, the shape of the line profile was found to vary with the bias voltage, which is related to the energy-dependent spin contribution from the 2 chemically inequivalent Mn sites on the surface. Overall, the results shown here expand the application of the method of spin-polarized scanning tunneling microscopy to measure atomic-scale magnetic structures.

Levels of toxic metals in marine organisms collected from Southern California coastal waters.

Emission of toxic trace metals into southern California coastal waters has resulted in the extensive accumulation of the elements within marine sediments. The current study was undertaken to evaluate concentrations of trace metals in bottom-dwelling marine fauna collected from two sampling areas. Analyses carried out on muscle samples of the dover sole (Microstomus pacificus) and the crab (Cancer anthonyi) by proton-induced x-ray emission analysis showed considerable concentrations of arsenic and selenium. Samples of gonads, digestive gland, and muscle from the crab Mursia gaudichaudii analyzed by atomic absorption spectroscopy showed elemental concentrations in muscle similar to the crab Cancer anthonyi and much higher metal levels in gonad and digestive gland. These findings suggest the need for further studies concerning the relationship between emission of metals into the marine environment and their abundance in marine fauna.

Effect of bur type on microtensile bond strengths of self-etching systems to human dentin.

PURPOSE: To compare the microtensile bond strength (microTBS) of five adhesives to human dentin prepared with 600-grit SiC abrasive paper (SiC), a diamond rotary instrument, or a carbide bur. The null hypothesis was that different cavity preparation instruments do not affect adhesion of resin adhesives. MATERIALS AND METHODS: Human molars (n = 45) were randomly divided into three groups according to surface treatment. Each group was bonded using a total-etch adhesive (Single Bond, 3M ESPE), one of three self-etching primer systems (Clearfil SE Bond or ABF, Kuraray; Imperva Fluorobond, Shofu), or a self-etching adhesive (One-Up Bond F, Tokuyama). A 4-mm composite crown was built over the bonded surface. Specimens were stored in water for 24 h at 37 degrees C. They were sectioned into 0.7-mm-thick slabs, trimmed to a cross-sectional area of 1 mm2, and loaded to failure at a crosshead speed of 1 mm/min using a tabletop tester (EZ-Test, Shimadzu). Microtensile bond strength data were analyzed using analysis of variance and Fisher's PLSD test. RESULTS: Surface preparation using a carbide bur generally yielded higher bond strengths than preparation using either a diamond rotary instrument or SiC abrasive paper. SE Bond had the highest mean microTBS of the five adhesives tested. CONCLUSION: Resin-dentin bond strengths can be affected by the type of instrument used to prepare the tooth. Specifically, higher bond strengths might be achieved by using carbide burs rather than diamond cutting instruments.

Effect of surface preparation on microtensile bond strength of three adhesive systems to bovine enamel.

PURPOSE: The purpose of this study was to compare the microtensile bond strength (microTBS) of three adhesives to bovine enamel prepared with 600-grit silicon carbide paper, diamond rotary instrument, or carbide bur. MATERIALS AND METHODS: Bovine teeth (n = 36) were randomly divided into three treatment groups and bonded using a total-etch adhesive (Single Bond, 3M ESPE), a self-etching primer system (Clearfil SE Bond, Kuraray), or a self-etching adhesive (One-Up Bond F, Tokuyama). A 4-mm composite crown was built on the bonded surfaces and specimens were stored in water for one day at 37 degrees C. Specimens were sectioned into 0.7-mm-thick slabs, trimmed to a cross-sectional area of 1 mm2, and loaded to failure at a crosshead speed of 1 mm/min using a tabletop tester (EZ-Test, Shimadzu). Microtensile bond strength data were analyzed using ANOVA and Fisher's PLSD test (alpha = 0.05). RESULTS: The bond strength of each self-etching system was lower when the enamel was prepared using a diamond or carbide bur, rather than with 600-grit silicon carbide paper. Differences in microTBS between carbide- and diamond-prepared surfaces were not significant. The surface preparation method did not affect the total-etch system. CONCLUSION: Different preparation instruments are unlikely to affect resin-enamel bond strengths.

Repairability of a packable resin-based composite using different adhesives.

PURPOSE: To compare the repair potential of a packable composite (Filtek P60) to that of a conventional hybrid composite (Pertac II) using three different adhesives: an unfilled resin (EBS-Multi), a one-bottle, acetone-based adhesive (One-Step), and a self-etching adhesive (Prompt L-Pop). MATERIALS AND METHODS: 30 composite disks (diameter = 8 mm) of each composite material were fabricated, light-cured, and stored in 37 degrees C for 7 days. The specimens were polished to 600-grit, sandblasted (CoJet-System), silanated, and randomly assigned to three groups (n=10). EBS-Multi, One-Step, and Prompt L-Pop were applied to each composite and cured. Pertac II was applied in a #5 gelatin capsule and light-cured. As controls, Pertac II was applied to freshly cured Filtek P60 and Pertac II specimens, with no additional surface treatment. Specimens were loaded in shear using an Instron testing machine at a crosshead speed of 5 mm/minute, 24 hours after bonding, and the peak shear force at failure was converted to MPa (force/area). RESULTS: ANOVA showed a significant difference in means at P<0.001. Tukey's test was used for pairwise comparisons. Mean SBS (+/-SD, MPa) were: P60/control: 25.2 (3.0); P60/EBS-Multi: 18.0 (2.3); P60/One-Step: 16.7 (2.3); P60/Prompt: 10.5 (3.3); Pertac/control: 25.5 (3.6); Pertac/EBS-Multi: 18.8 (3.0); Pertac/One-Step: 18.8 (2.4); Pertac/Prompt: 9.7 (3.5). Repair strengths were all significantly less than their respective controls, and repairs made using Prompt L-Pop had significantly lower mean strengths than the repairs made with EBS-Multi and One-Step (P<0.05).

Universal transition state for high-pressure zinc blende to rocksalt phase transitions.

First-principles density functional calculations show that the high-pressure transitions of different semiconductors from zinc blende to rocksalt go through a transition state, which is universal in the sense that its position along the path and the corresponding geometry is independent of the chemical components of the semiconductor. This is explained using a Landau-like model expansion of the free energy in cosine functions of atomic position.

Proton-induced x-ray emission analysis--a promising technique for studying the metal content of plants and soils.

The ease of employing proton-induced X-ray emission analysis (PIXEA) to studies relating metal content of soils to metal uptake in plants was aptly demonstrated in an investigation concerning the effect of automotive pollution on the abundance of about 16 elements accumulated in ribwort plantain and its surrounding soil. Elemental concentrations were shown to be dependent on the age of the plant leaves, as well as the distance from the roadside.

Purine nucleoside phosphorylase. 2. Catalytic mechanism.

X-ray crystallography, molecular modeling, and site-directed mutagenesis were used to delineate the catalytic mechanism of purine nucleoside phosphorylase (PNP). PNP catalyzes the reversible phosphorolysis of purine nucleosides to the corresponding purine base and ribose 1-phosphate using a substrate-assisted catalytic mechanism. The proposed transition state (TS) features an oxocarbenium ion that is stabilized by the cosubstrate phosphate dianion which itself functions as part of a catalytic triad (Glu89-His86-PO4=). Participation of phosphate in the TS accounts for the poor hydrolytic activity of PNP and is likely to be the mechanistic feature that differentiates phosphorylases from glycosidases. The proposed PNP TS also entails a hydrogen bond between N7 and a highly conserved Asn. Hydrogen bond donation to N7 in the TS stabilizes the negative charge that accumulates on the purine ring during glycosidic bond cleavage. Kinetic studies using N7-modified analogs provided additional support for the hydrogen bond. Crystallographic studies of 13 human PNP-ligand complexes indicated that PNP uses a ligand-induced conformational change to position Asn243 and other key residues in the active site for catalysis. These studies also indicated that purine nucleosides bind to PNP with a nonstandard glycosidic torsion angle (+anticlinal) and an uncommon sugar pucker (C4'-endo). Single point energy calculations predicted the binding conformation to enhance phosphorolysis through ligand strain. Structural data also suggested that purine binding precedes ribose 1-phosphate binding in the synthetic direction whereas the order of substrate binding was less clear for phosphorolysis. Conservation of the catalytically important residues across nucleoside phosphorylases with specificity for 6-oxopurine nucleosides provided further support for the proposed catalytic mechanism.