Structural analysis of Mycobacterium tuberculosis M13 metalloprotease Zmp1 open states
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Phosphinodiboranates (H 3 BPR 2 BH 3 – ) are a class of borohydrides that have merited a reputation as weakly coordinating anions, which is attributed in part to the dearth of coordination complexes known with transition metals, lanthanides, and actinides. We recently reported how K(H 3 BP t Bu 2 BH 3 ) exhibits sluggish salt elimination reactivity with f-metal halides in organic solvents such as Et 2 O and THF. Here we report how this reactivity appears to be further attenuated in solution when the t Bu groups attached to phosphorus are exchanged for R = Ph or H, and we describe how mechanochemistry was used to overcome limited solution reactivity with K(H 3 BPPh 2 BH 3 ). Grinding three equivalents of K(H 3 BPPh 2 BH 3 ) with UI 3 (THF) 4 or LnI 3 (Ln = Ce, Pr, Nd) allowed homoleptic complexes with the empirical formulas U(H 3 BPPh 2 BH 3 ) 3 (1), Ce(H 3 BPPh 2 BH 3 ) 3 (2), Pr(H 3 BPPh 2 BH 3 ) 3 (3), and Nd(H 3 BPPh 2 BH 3 ) 3 (4) to be prepared and subsequently crystallized in good yields (50–80%). Single-crystal XRD studies revealed that all four complexes exist as dimers or coordination polymers in the solid-state, whereas 1 H and 11 B NMR spectra showed that they exist as a mixture of monomers and dimers in solution. Treating 4 with THF breaks up the dimer to yield the monomeric complex Nd(H 3 BPPh 2 BH 3 ) 3 (THF) 3 (4-THF). XRD studies revealed that 4-THF has one chelating and two dangling H 3 BPPh 2 BH 3 – ligands bound to the metal to accommodate binding of THF. In contrast to the results with K(H 3 BPPh 2 BH 3 ), attempting the same mechanochemical reactions with Na(H 3 BPH 2 BH 3 ) containing the simplest phosphinodiboranate were unsuccessful; only the partial metathesis product U(H 3 BPH 2 BH 3 )I 2 (THF) 3 (5) was isolated in poor yields. Here, despite these limitations, our results offer new examples showing how mechanochemistry can be used to rapidly synthesize molecular coordination complexes that are otherwise difficult to prepare using more traditional solution methods.
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XRD and XAS were used to characterize the bulk structure, while XPS was used to characterize the surface structure, of commercially obtained nominally K 4 Fe(CN) 6 ·3H 2 O, K 3 Fe(CN) 6 and our synthesized Prussian Blue (PB) material. K 4 Fe(CN) 6 ·3H 2 O was found to consist of a fully hydrated phase, which crystallizes in the monoclinic form and a less hydrated or anhydrous phase which crystallizes in the orthorhombic form. K 3 Fe(CN) 6 was found to consist of the well-established orthorhombic form rather than the monoclinic form. The structure of our synthesized Prussian Blue (PB) was found to be consistent with that reported for (KOH) 0.7 Fe(III) 1.33 Fe(II)(CN) 6 ·4.0H 2 O which crystallizes in the cubic form. XPS and XAS confirmed the presence of ferrous Fe(II) at the surface and bulk levels in K 4 Fe(CN) 6 ·xH 2 O. However, XPS revealed the presence of Fe(II) (~30%) and Fe(III) (~70%) in the surface region of K 3 Fe(CN) 6 while XAS confirmed the presence of mostly Fe(III) at the bulk level. Both XPS and XANES confirmed the presence of Fe(II) and Fe(III) in the surface and bulk regions of PB. We report that this ex situ XAS study will be used to support the analysis of an in situ XAS data collected on a PB containing supercapacitor to understand the mechanistic origin of pseudocapacitance in these devices.
The structure–property relationship of single-atom alloy catalysts is reviewed from the perspective of atomic structure analysis, electronic properties, and catalytic activities.
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Current practices for structural analysis of extremely large-molecular-weight polysaccharides via solution-state nuclear magnetic resonance (NMR) spectroscopy incorporate partial depolymerization protocols that enable polysaccharide solubilization in suitable solvents. Non-specific depolymerization techniques utilized for glycosidic bond cleavage, such as chemical degradation or ultrasonication, potentially generate structural fragments that can complicate complete and accurate characterization of polysaccharide structures. Utilization of appropriate enzymes for polysaccharide degradation, on the other hand, requires prior structural knowledge and optimal enzyme activity conditions that are not available to an analyst working with novel or unknown compounds. Herein, we describe an application of a permethylation strategy that allows the complete dissolution of intact polysaccharides for NMR structural characterization. This approach is utilized for NMR analysis of Xylella fastidiosa extracellular polysaccharide (EPS), which is essential for the virulence of the plant pathogen that affects multiple commercial crops and is responsible for multibillion dollar losses each year.
Conventional approaches for the structural health monitoring of infrastructures often rely on physical sensors or targets attached to structural members, which require considerable preparation, maintenance, and operational effort, including continuous on-site adjustments. This paper presents an image-driven hybrid structural analysis technique that combines digital image processing (DIP) and regression analysis with a continuum point cloud method (CPCM) built on a particle-based strong formulation. Polynomial regressions capture the boundary shape change due to the structural loading and precisely identify the edge and corner coordinates of the deformed structure. The captured edge profiles are transformed into essential boundary conditions. This allows the construction of a strongly formulated boundary value problem (BVP), classified as the Dirichlet problem. Capturing boundary conditions from the digital image is novel, although a similar approach was applied to the point cloud data. It was shown that the CPCM is more efficient in this hybrid simulation framework than the weak-form-based numerical schemes. Unlike the finite element method (FEM), it can avoid aligning boundary nodes with regression points. A three-point bending test of a rubber beam was simulated to validate the developed technique. The simulation results were benchmarked against numerical results by ANSYS and various relevant numerical schemes. The technique can effectively solve the Dirichlet-type BVP, yielding accurate deformation, stress, and strain values across the entire problem domain when employing a linear strain model and increasing the number of CPCM nodes. In addition, comparative analysis with conventional displacement tracking techniques verifies the developed technique’s robustness. The proposed technique effectively circumvents the inherent limitations of traditional monitoring methods resulting from the reliance on physical gauges or target markers so that a robust and non-contact solution for remote structural health monitoring in real-scale infrastructures can be provided, even in unfavorable experimental environments.
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In the current work, we have performed multiscale structural analysis of a Pb-free sodium niobate-based smart system, i.e., 0.9NaNbO 3 –0.1Ba 0.9 Ca 0.1 TiO 3 (NN-10BCT) reported earlier for its high ferroelectric response. We have investigated the temperature-dependent evolution of crystal structure at long, medium, and short ranges using synchrotron x-ray diffraction (SXRD), Raman scattering, and pair distribution function(PDF) techniques in conjunction with dielectric studies. Temperature-dependent synchrotron x-ray diffraction data combined with dielectric analysis suggest two unique polymorphic phase boundaries (PPB) with two coexisting ferroelectric phases stable in the wide temperature ranges. These PPBs are stable in different regions viz. (i) cryogenic temperatures with coexisting R3c and Pmc2 1 phases (ii) vicinity of room temperatures with coexisting Pmc2 1 and Amm2 phases. In contrast to the conclusions drawn from SXRD, PDF reveals structures having lower symmetry (with coexisting Cc+ Pmc2 1 phases at 1.7 ≤r≤ 20 Å) at short ranges for these PPBs. In conclusion, the presence of different long- and short-range symmetries (accommodating tilt-oriented ferroelectric phases) in the unique polymorphic phase boundaries makes them thermally stable and advantageous for technological applications.
There is a growing need in the AEC industry for the digitalization of model-based data exchange in BIM workflows. However, users continue to face difficulties exchanging data between BIM-based computer-aided design (CAD) and computer-aided engineering (CAE) software, even with the open, non-proprietary data exchange format called Industry Foundation Classes (IFC). Proposed solutions in academic research focus primarily on building systems, with comparatively little attention to piping models. Therefore, this paper introduces an interoperability tool for enabling piping model data exchange between architectural and structural analysis domains. The tool is tested using a piping model created in Autodesk Revit and shows marked improvement for IFC-based CAD-to-CAE interoperability over existing practice.
The objective of this analysis is to estimate and assess the stresses in the passive plates caused by a limiting plasma disruption. The objective of this calculation is also to address observed damage to mounting hardware after completion of NSTX operation. These observations initiated diagnostic efforts during the Upgrade project to monitor the severity of the disruptions that were causing the damage, and planned instrumentation to trend the behavior of the mounting hardware. The Recovery Project mission for the passive plate hardware is to appropriately reinforce the passive plates with stainless steel ribs mounted on the back of the plate to reduce their flexure and stress and reinforcements of the “biscuit” components of the bracketry to transfer loads without damage to bolts, biscuits, and bracket plates and welds. Mid-plane disruptions and quenches were manageable with NSTX vintage hardware. The Vertical Displacement Event (VDE) disruptions position the plasma closer to the passive plates and are more severe than the centered plasma. Earlier work pointed to the P1-P5 VDE as limiting. This has been confirmed by A. Brooks work in support of the load generation effort in reference. During vertical displacement large counter currents are generated in the plate as the plasma approaches it. - as would be expected from passive plates. When the plasma disrupts the currents in the plates are reversed, which also reverses the loading on the plates. This report documents the methodology and results of transient structural analysis on the plasma, passive plates support brackets. The loads induced by eddy and halo currents have been considered, and were generated using a separate electromagnetic analysis (NSTXU_1_11_2_1_CALC_051). The structural model also incorporates the effects from preload. Calculation was performed with the assumption that existing biscuits are not participating in the load bearing except the biscuits connected to jumper bolts, which are fully engaged. Results show that with the planned reinforcements, Passive plates and mounting structures satisfy static and fatigue criteria in all areas except welds, where separate analysis was performed. Both symmetric and asymmetric (with locating block) designs were analyzed, and although stresses were higher without locating block they still satisfy NSTX design criteria.
Direct electron detectors in scanning transmission electron microscopy give unprecedented possibilities for structure analysis at the nanoscale. In electronic and quantum materials, this new capability gives access to, for example, emergent chiral structures and symmetry-breaking distortions that underpin functional properties. Quantifying nanoscale structural features with statistical significance, however, is complicated by the subtleties of dynamic diffraction and coexisting contrast mechanisms, which often results in a low signal-to-noise ratio and the superposition of multiple signals that are challenging to deconvolute. Here we apply scanning electron diffraction to explore local polar distortions in the uniaxial ferroelectric Er(Mn,Ti)O 3 . Using a custom-designed convolutional autoencoder with bespoke regularization, we demonstrate that subtle variations in the scattering signatures of ferroelectric domains, domain walls, and vortex textures can readily be disentangled with statistical significance and separated from extrinsic contributions due to, e.g., variations in specimen thickness or bending. The work demonstrates a pathway to quantitatively measure symmetry-breaking distortions across large areas, mapping structural changes at interfaces and topological structures with nanoscale spatial resolution.
Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662–C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662–C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662–C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus.