High-pressure phase transformation of carbonate malachite Cu2(CO3)(OH)2 driven by [CuO6] regularization and [CO3] rotation
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99 GENERAL AND MISCELLANEOUS↗
SEARCH · Engineering Papers
Results for “crystallographic structures”
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Crystallographic snapshots of ternary complexes of thermophilic secondary alcohol dehydrogenase from
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Dinh, Tung↗
Characterization of a Molecule Partially Confined at the Pore Mouth of a Zeotype
Abstract We investigate the interaction between a molecule and a pore mouth—a critical step in adsorption processes—by characterizing the conformation of a macrocyclic calix[4]arene‐Ti IV complex, which is grafted on the external surface of a zeotype (*‐SVY). X‐ray absorption and 13 C{ 1 H} CPMAS NMR spectroscopies independently detect a unique conformation of this complex when it is grafted at crystallographically equivalent locations that lie at the interface of 7 Å hemispherical microporous cavities and the external surface. Electronic structure calculations support the presence of this unique conformation, and suggest that it is brought about by a specific orientation of the macrocycle that maximizes non‐covalent interactions between calix[4]arene upper‐rim tert ‐butyl substituents and the microporous‐cavity walls. Our comparative study provides a rare “snapshot” of a molecule partially confined at a pore mouth, an essential intermediate for adsorption into micropores, and demonstrates how surrounding environment controls this confinement in a sensitive fashion.
Grosso‐Giordano, Nicolás A.↗
Characterization of a Molecule Partially Confined at the Pore Mouth of a Zeotype
Not provided.
Chemistry↗
A Quick Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors**
The COVID-19 pathogen, SARS-CoV-2, requires its main protease (SC2M Pro ) to digest two of its translated long polypeptides to form a number of mature proteins that are essential for viral replication and pathogenesis. Inhibition of this vital proteolytic process is effective in preventing the virus from replicating in infected cells and therefore provides a potential COVID-19 treatment option. Guided by previous medicinal chemistry studies about SARS-CoV-1 main protease (SC1M Pro ), we have designed and synthesized a series of SC2M Pro inhibitors that contain β-(S-2-oxopyrrolidin-3-yl)-alaninal (Opal) for the formation of a reversible covalent bond with the SC2M Pro active-site cysteine C145. All inhibitors display high potency with K i values at or below 100 nM. The most potent compound, MPI3, has as a K i value of 8.3 nM. Crystallographic analyses of SC2M Pro bound to seven inhibitors indicated both formation of a covalent bond with C145 and structural rearrangement from the apoenzyme to accommodate the inhibitors. Virus inhibition assays revealed that several inhibitors have high potency in inhibiting the SARS-CoV-2-induced cytopathogenic effect in both Vero E6 and A549/ACE2 cells. Two inhibitors, MPI5 and MPI8, completely prevented the SARS-CoV-2-induced cytopathogenic effect in Vero E6 cells at 2.5-5 μM and A549/ACE2 cells at 0.16-0.31 μM. Their virus inhibition potency is much higher than that of some existing molecules that are under preclinical and clinical investigations for the treatment of COVID-19. Our study indicates that there is a large chemical space that needs to be explored for the development of SC2M Pro inhibitors with ultra-high antiviral potency.
3C-like protease↗
A missense variant remote from the active site impairs stability of human phosphoglucomutase 1
Abstract Missense variants of human phosphoglucomutase 1 (PGM1) cause the inherited metabolic disease known as PGM1 deficiency. This condition is categorised as both a glycogen storage disease and a congenital disorder of glycosylation. Approximately 20 missense variants of PGM1 are linked to PGM1 deficiency, and biochemical studies have suggested that they fall into two general categories: those affecting the active site and catalytic efficiency, and those that appear to impair protein folding and/or stability. In this study, we characterise a novel variant of Arg422, a residue distal from the active site of PGM1 and the site of a previously identified disease‐related variant (Arg422Trp). In prior studies, the R422W variant was found to produce insoluble protein in a recombinant expression system, precluding further in vitro characterisation. Here we investigate an alternative variant of this residue, Arg422Gln, which is amenable to experimental characterisation presumably due to its more conservative physicochemical substitution. Biochemical, crystallographic, and computational studies of R422Q establish that this variant causes only minor changes in catalytic efficiency and 3D structure, but is nonetheless dramatically reduced in stability. Unexpectedly, binding of a substrate analog is found to further destabilise the protein, in contrast to its stabilising effect on wild‐type PGM1 and several other missense variants. This work establishes Arg422 as a lynchpin residue for the stability of PGM1 and supports the impairment of protein stability as a pathomechanism for variants that cause PGM1 deficiency. Synopsis Biochemical and structural studies of a missense variant far from the active site of human PGM1 identify a residue with a key role in enzyme stability.
Stiers, Kyle M.↗
Helical spin ordering in room-temperature metallic antiferromagnet Fe 3 Ga 4
Metallic Fe 3 Ga 4 displays a complex magnetic phase diagram that supports an intermediate antiferromagnetic (AFM) helical spin structure (HSS) state at room temperature which lies between two ferromagnetic (FM) phases. Here, magnetic measurements along the three crystallographic axes were performed in order to develop a model for the temperature and field dependence of the HSS state. These results show that the AFM state is a helically ordered spiral propagating along the c-axis with the magnetic moments rotating in the ab-plane. Under applied magnetic field, the AFM state exhibits a metamagnetic transition to conical ordering before entering a fully field-polarized FM state at high fields. The conical ordering in the AFM state is anisotropic even within the ab-plane and may gives rise to Berry phase effects in transport measurements. Metallic conductivity from density of states computations was confirmed through resistivity measurements and no anomalous behavior was observed through the various magnetic transitions.
36 MATERIALS SCIENCE↗
Stoichiometric Lanthanide Compounds with Diglycolamides: A Synthetic Approach toward Understanding Rare-Earth Speciation in Solution
A fundamental understanding of coordination chemistry across the lanthanide series is essential for explaining the chemical behavior of rare-earth metals in complex liquid–liquid extraction processes. Probing the exact bonding between the extractant and the metal is sometimes done through the synthesis of solid-state compounds that can serve as models for metal speciation in solution. In the case of diglycolamide (DGA), a commonly used neutral diamide extractant, extensive studies identify the stepwise formation of 1:1 [Ln(DGA)(H 2 O) 6 ] 3+ , 1:2 [Ln(DGA) 2 (H 2 O) 3 ] 3+ , and 1:3 [Ln(DGA) 3 ] 3+ complexes in solution. The crystallographic reports, however, exclusively show a 1:3 [Ln(DGA) 3 ] 3+ moiety in the solid state, while the structures of 1:1 and 1:2 complexes are yet to be isolated and comprehensively studied. In this work, we report the synthesis and characterization of three new families of stoichiometric N,N,N′,N’ -tetramethyldiglycolamide (TMDGA) compounds: [Ln(TMDGA)(H 2 O) 5 Cl]Cl 2 ·2H 2 O, [Ln(TMDGA) 2 (H 2 O) 3 ]Cl 3 ·3H 2 O, and [Ln(TMDGA) 3 ]Cl 3 ·7H 2 O, where Ln = Nd, Eu, Gd, with Ln:TMDGA ratios of 1:1, 1:2, and 1:3, respectively. Further, the compounds have been analyzed using vibrational spectroscopy (both Raman and FT-IR), as well as variable temperature fluorescence spectroscopy. A spectrophotometric titration of Eu(III) was performed to confirm the presence of the [Eu(TMDGA) n ] 3+ ( n = 1, 2, and 3) species in solution and to compare the individual solid-state emission spectra to their respective analogues in solution.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ultrathin VO 2 Films on Functional Substrates
The metal–insulator transition (MIT) in vanadium dioxide (VO 2 ) thin films is strongly affected by grain size, thickness, and interfacial properties. Typically, a minimum thickness around 50 nm is required for VO 2 to exhibit a significant MIT when functional substrates like sapphire and silicon are used. Several works have shown that thin films below 20 nm, with up to 2–3 decades of change in the resistance across the MIT, can be achieved but require complex pre- or postprocessing of the samples. We show that predeposition substrate condition control facilitates the direct growth of VO 2 ultrathin 15 nm films, exhibiting a resistance change between 3 and 4 decades across the MIT. Our findings indicate that the interface between the film and the substrate is crucial in determining the initial growth layers and the structural evolution. With appropriate substrate surface treatment, the desired VO 2 MIT can be enhanced regardless of the substrate crystallographic orientation. Moreover, we propose a novel approach to obtain large resistance changes across the MIT in ultrathin VO 2 films by incorporating a predeposited 1.5 nm vanadium oxide buffer layer, thereby eliminating the need to use different materials or complex pre- or postprocessing of the samples. Here we also demonstrate that this method improves the transition of 25–50 nm VO 2 thin films on silicon substrates. Our study reveals a simple approach for direct growth of ultrathin VO 2 films exhibiting a significant MIT, which is commonly accepted unattainable over substrates of technological importance, such as sapphire and silicon.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Observation of an Orientational Glass in a Superlattice of Elliptically-Faceted CdSe Nanocrystals
Extensive prior work has shown that colloidal inorganic nanocrystals coated with organic ligand shells can behave as artificial atoms and, as such, form superlattices with different crystal structures and packing densities. Although ordered superlattices present a high degree of long-range positional order, the relative crystallographic orientation of the inorganic nanocrystals with respect to each other tends to be random. Recent works have shown that superlattices can achieve orientational alignment through combinations of nanocrystal faceting and ligand modification, as well as selective metal particle attachment to particular facets. These studies have focused on the assembly of high-symmetry nanocrystals, such as cubes and cuboctahedra. In this work, we study the assembly of elliptically faceted CdSe/CdS core/shell nanocrystals with one distinctive crystallographic orientation along the major elliptical axis. We show that the nanocrystals form an unexpectedly well-ordered translational superlattice, with a degree of order comparable to that achieved with higher-symmetry nanocrystals. Additionally, we show that, due to the particles' faceted shape, the superlattice is characterized by an orientational glass phase in which only certain orientations are possible due to entropically frustrated crystallization. In this phase, the nanocrystals do not exhibit a local orientational ordering but rather have distinct orientations that emerge at different locations within the same domain. The distinct orientations are a result of a facet-to-facet lock-in mechanism that occurs during the self-assembly process. These facet-to-facet alignments force the nanocrystals to tilt on different lattice planes forming different projections that we termed apparent polydispersity. Our experimental realization of an orientational glass phase for multifaceted semiconducting nanocrystals can be used to investigate how this phase is formed and how it can be utilized for potential optical, electrical, and thermal transport applications.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Computational design of thermoelectric alloys through optimization of transport and dopability
Alloying is a common technique to optimize the functional properties of materials for thermoelectrics, photovoltaics, energy storage etc. Designing thermoelectric (TE) alloys is especially challenging because it is a multi-property optimization problem, where the properties that contribute to high TE performance are interdependent. In this work, we develop a computational framework that combines first-principles calculations with alloy and point defect modeling to identify alloy compositions that optimize the electronic, thermal, and defect properties. We apply this framework to design n-type Ba 2(1–x) Sr 2x CdP 2 Zintl thermoelectric alloys. Our predictions of the crystallographic properties such as lattice parameters and site disorder are validated with experiments. To optimize the conduction band electronic structure, we perform band unfolding to sketch the effective band structures of alloys and find a range of compositions that facilitate band convergence and minimize alloy scattering of electrons. Here, we assess the n-type dopability of the alloys by extending the standard approach for computing point defect energetics in ordered structures. Through the application of this framework, we identify an optimal alloy composition range with the desired electronic and thermal transport properties, and n-type dopability. Such a computational framework can also be used to design alloys for other functional applications beyond TE.
36 MATERIALS SCIENCE↗
Magnetic phase transitions in Eu(Co 1-x Nix) 2-y As 2 single crystals
The effects of Ni doping in Eu(Co 1-x Ni x ) 2-y As 2 single crystals with x = 0 to 1 grown out of self flux are investigated via crystallographic, electronic transport, magnetic, and thermal measurements. All compositions adopt the body-centered-tetragonal ThCr 2 Si 2 structure with space group I 4= mmm . Here, we also find 3-4% of randomly-distributed vacancies on the Co/Ni site. Anisotropic magnetic susceptibility $\chi$α (α = ab; c) data versus temperature T show clear signatures of an antiferromagnetic (AFM) c-axis helix structure associated with the Eu +2 spins-7/2 for x = 0 and x = 1 as previously reported. The $\chi$α (T) data for x = 0.03 and 0.10 suggest an anomalous 2 q magnetic structure containing two helix axes along the c axis and in the ab plane, respectively, whereas for x = 0.75, 0.82, and 1 a c-axis helix is inferred as previously found for x = 1. At intermediate compositions x = 0:2, 0.32, 0.42, 0.54, and 0.65 a magnetic structure with a large ferromagnetic (FM) c-axis component is found from magnetization versus fi eld isotherms, suggested to be an incommensurate FM cone structure associated with the Eu spins, which consists of both AFM and FM components. In addition, the $\chi$ (T) and heat capacity C p (T) data for x = 0.2-0.65 indicate the occurrence of itinerant FM order associated with the Co/Ni atoms with Curie temperatures from 60 K to 25 K, respectively. Electrical resistivity ρ(T) measurements indicate metallic character for all compositions with abrupt increases in slope on cooling below the Eu AFM transition temperatures. In addition to this panoply of magnetic transitions, 151 Eu Mössbauer measurements indicate that ordering of the Eu moments proceeds via an incommensurate sine amplitude-modulated structure with additional transition temperatures associated with this effect.
36 MATERIALS SCIENCE↗
Effects of high temperature and e-beam irradiation on the stability of refractory thin films
Refractory thin films of Al2O3, ZrO2, MgO, ThO2, and BN have been investigated in situ in an UHV transmission electron microscope. The electron transparent refractory films were prepared by electron-beam evaporation, anodization, RF sputtering, and thinning of bulk crystal materials. The study concentrates on monitoring the thermal and mechanical stability of the films, phase and structural changes, and electron irradiation effects as a function of film-preparation conditions. With increasing temperatures, five different crystallographic phases were observed for both anodized and electron-beam-evaporated alumina films. Zirconia films exhibited two phase transitions upon heating to 1200 C and electron-irradiation-induced crystallization of ZrO2 even at room temperature. MgO, ThO2, and BN films did not undergo any noticeable phase transformation but ruptured due to sintering below 1200 C.
Lee, E. H.↗
Technology of GaAs metal-oxide-semiconductor solar cells
The growth of an oxide interfacial layer was recently found to increase the open-circuit voltage (OCV) and efficiency by up to 60 per cent in GaAs metal-semiconductor solar cells. Details of oxidation techniques to provide the necessary oxide thickness and chemical structure and using ozone, water-vapor-saturated oxygen, or oxygen gas discharges are described, as well as apparent crystallographic orientation effects. Preliminary results of the oxide chemistry obtained from X-ray, photoelectron spectroscopy are given. Ratios of arsenic oxide to gallium oxide of unity or less seem to be preferable. Samples with the highest OVC predominantly have As(+3) in the arsenic oxide rather than As(+5). A major difficulty at this time is a reduction in OCV by 100-200 mV when the antireflection coating is vacuum deposited.
Stirn, R. J.↗
Self-inhibited State of Venezuelan Equine Encephalitis Virus (VEEV) nsP2 Cysteine Protease: A Crystallographic and Molecular Dynamics Analysis
The Venezuelan equine encephalitis virus (VEEV) belongs to the Togaviridae family and is pathogenic to both humans and equines. The VEEV non-structural protein 2 (nsP2) is a cysteine protease (nsP2pro) that processes the polyprotein and thus it is a drug target for inhibitor discovery. The atomic structure of the VEEV nsP2 catalytic domain was previously characterized by both X-ray crystallography and computational studies. A modified nsP2pro harboring a N475A mutation in the N terminus was observed to exhibit an unexpected conformation: the N-terminal residues bind to the active site, mimicking binding of a substrate. The large conformational change of the N terminus was assumed to be induced by the N475A mutation, as N475 has an important role in stabilization of the N terminus and the active site. This conformation was first observed in the N475A mutant, but we also found it while determining a crystal structure of the catalytically active nsP2pro containing the wild-type N475 active site residue and K741A/K767A surface entropy reduction mutations. This suggests that the N475A mutation is not a prerequisite for self-inhibition. Here, we describe a high resolution (1.46 Å) crystal structure of a truncated nsP2pro (residues 463–785, K741A/K767A) and analyze the structure further by molecular dynamics to study the active and self-inhibited conformations of nsP2pro and its N475A mutant. A comparison of the different conformations of the N-terminal residues sheds a light on the interactions that play an important role in the stabilization of the enzyme.
59 BASIC BIOLOGICAL SCIENCES↗
Wake up and retention in zinc magnesium oxide ferroelectric films
Zn 0.64 Mg 0.36 O (ZMO) is a newly discovered ferroelectric oxide with the wurtzite structure. Epitaxial Zn 0.64 Mg 0.36 O films from 0.036 to 0.5 μm in thickness are grown on Pt/sapphire with the crystallographic c-axis out of plane. At room temperature, the remanent polarization is ~80 μC/cm 2 and the coercive field is ~3 MV/cm. The coercive field is strongly temperature dependent up to 240 °C with a pseudo-activation energy of 23 ± 0.3 meV, suggesting that polarization reversal occurs through an extrinsic process such as domain wall motion. ZMO films can be woken up in 20 electric field cycles on driving near the coercive field; they wake up in a single loop at fields in excess of 4 MV/cm. A thermally activated fluid imprint process, with a pseudo-activation energy of 67 ± 8 meV, enlarges the coercive field by several hundred kV cm –1 after switching the polarization. Additionally, ZMO films exhibit excellent retention characteristics; no reduction in the polarization is observed up to 1000 h from room temperature to 200 °C bakes. Here, this current early generation of ZMO films can survive several thousand switching cycles before dielectric breakdown occurs.
36 MATERIALS SCIENCE↗
Raman studies of hydrogen trapped in As 4 O 6 ·2H 2 at high pressure and low temperature
In this work, Raman spectroscopic measurements of the arsenolite–hydrogen inclusion compound As 4 O 6 ·2H 2 were performed in diamond anvil cells at high pressure and variable temperature down to 80 K. The experimental results were complemented by ab initio molecular dynamics simulations and phonon calculations. Observation of three hydrogen vibrons in As 4 O 6 ·2H 2 is reported in the entire temperature and pressure range studied (up to 24 GPa). While the experiments performed with protium and deuterium at variable temperatures allowed for the assignment of two vibrons as Q 1 (1) and Q 1 (0) transitions of ortho and para spin isomers of hydrogen trapped in the inclusion compound, the origin of the third vibron could not be unequivocally established. Low-temperature spectra revealed that the lowest-frequency vibron is actually composed of two overlapping bands of A g and T 2g symmetries dominated by H 2 stretching modes as predicted by our previous density functional theory calculations. We observed low-frequency modes of As 4 O 6 ·2H 2 vibrations dominated by H 2 “librations,” which were missed in a previous study. A low-temperature fine structure was observed for the J = 0 → 2 and J = 1 → 3 manifolds of hydrogen trapped in As 4 O 6 ·2H 2 , indicating the lifting of degeneracy due to an anisotropic environment. A non-spherical distribution was captured by molecular dynamics simulations, which revealed that the trajectory of H 2 molecules is skewed along the crystallographic $\langle$111$\rangle$ direction. Last but not least, low-temperature synchrotron powder x-ray diffraction measurements on As 4 O 6 ·2H 2 revealed that the bulk structure of the compound is preserved down to 5 K at 1.6 GPa.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Correlating Crystallographic Orientation and Ferroic Properties of Twin Domains in Metal Halide Perovskites
Metal halide perovskite (MHP) solar cells have attracted worldwide research interest. Although it has been well established that grain, grain boundary, and grain facet affect MHPs optoelectronic properties, less is known about subgrain structures. Recently, MHP twin stripes, a subgrain feature, have stimulated extensive discussion due to the potential for both beneficial and detrimental effects of ferroelectricity on optoelectronic properties. Furthermore, connecting the ferroic behavior of twin stripes in MHPs with crystal orientation will be a vital step to understand the ferroic nature and the effects of twin stripes. In this work, we studied the crystallographic orientation and ferroic properties of CH 3 NH 3 PbI 3 twin stripes, using electron backscatter diffraction (EBSD) and advanced piezoresponse force microscopy (PFM), respectively. Using EBSD, we discovered that the orientation relationship across the twin walls in CH 3 NH 3 PbI 3 is a 90° rotation about ($\bar{11}0$), with the (030) and (111) directions parallel to the direction normal to the surface. By careful inspection of CH 3 NH 3 PbI 3 PFM results including in-plane and out-of-plane PFM measurements, we demonstrate some nonferroelectric contributions to the PFM responses of this CH 3 NH 3 PbI 3 sample, suggesting that the PFM signal in this CH 3 NH 3 PbI 3 sample is affected by nonferroelectric and nonpiezoelectric forces. If there is piezoelectric response, it is below the detection sensitivity of our interferometric displacement sensor PFM (<0.615 pm/V). Overall, this work offers an integrated picture describing the crystallographic orientations and the origin of PFM signal of MHPs twin stripes, which is critical to understanding the ferroicity in MHPs.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗