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Small molecule – Silica interactions in porous silica structures
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A small-box approach to the local crystal structure of Y 3 NbO 7
The local crystal structure of Y 3 NbO 7 was probed using neutron total scattering. Five different structural models were fit to the experimental pair distribution function of this material up to 15 Å. Fits of defect fluorite (Fm$\overline{3}$m), pyrochlore (Fd$\overline{3}$m), and orthorhombic C weberite models (C222 1 ) were attempted based on prior structural investigations of Y 3 NbO 7 and related fluorite-based materials. Orthorhombic P weberite (P222 1 ) and monoclinic weberite models (P112 1 ) were derived via symmetry reduction of the orthorhombic C weberite structure. All models except monoclinic weberite failed to reproduce the experimental pair distribution function. Misfits were clearly visible for peaks arising from atom pairs within the first coordination shell (defect fluorite and pyrochlore) and beyond (orthorhombic C and P weberite). By contrast, monoclinic weberite (γ ≈ 91.8°) provided an excellent fit, with no major misfits observed. This unit cell features distorted YO 8 dodecahedra, YO 7 monocapped octahedra, and NbO 6 octahedra as building blocks. Comparison between the topologies of the cationic and anionic substructures in monoclinic weberite and its parent orthorhombic C structure revealed displacements of the metal atoms along the [100] direction and a less compact spatial distribution of oxygen atoms along the a axis. In conclusion, the monoclinic weberite model presented herein may serve as a starting point to revisit structural modeling of fluorite-based materials with challenging local structures.
Small Pore Aluminosilicate EMM-37: Synthesis and Structure Determination Using Continuous Rotation Electron Diffraction
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CO adsorption on small Au{sub n} (n = 1–4) structures supported on hematite. I. Adsorption on iron terminated α-Fe{sub 2}O{sub 3} (0001) surface
This is the first of two papers dealing with the adsorption of Au and formation of Au{sub n} nanostructures (n = 1–4) on hematite (0001) surface and adsorption of CO thereon. The stoichiometric Fe-terminated (0001) surface of hematite was investigated using density functional theory in the generalized gradient approximation of Perdew-Burke-Ernzerhof (PBE) form with Hubbard correction U, accounting for strong electron correlations (PBE+U). The structural, energetic, and electronic properties of the systems studied were examined for vertical and flattened configurations of Au{sub n} nanostructures adsorbed on the hematite surfaces. The flattened ones, which can be viewed as bilayer-like structures, were found energetically more favored than vertical ones. For both classes of structures the adsorption binding energy increases with the number of Au atoms in a structure. The adsorption of Au{sub n} induces charge rearrangement at the Au{sub n}/oxide contact which is reflected in work function changes. In most considered cases Au{sub n} adsorption increases the work function. A detailed analysis of the bonding electron charge is presented and the corresponding electron charge rearrangements at the contacts were quantified by a Bader charge analyses. The interaction of a CO molecule with the Au{sub n} nanostructures supported on α-Fe{sub 2}O{sub 3} (0001) and the oxide support was studied. It is found that the CO adsorption binding to the hematite supported Au{sub n} structures is more than twice as strong as to the bare hematite surface. Analysis of the Bader charges on the atoms showed that in each case CO binds to the most positively charged (cationic) atom of the Au{sub n} structure. Changes in the electronic structure of the Au{sub n} species and of the oxide support, and their consequences for the interactions with CO, are discussed.
Structural modeling of proteins by integrating small-angle x-ray scattering data
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Particle-scale structure in frozen colloidal suspensions from small-angle x-ray scattering
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Transverse Nucleon Structure and Regge-Like Dynamics at Small x
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Convection beneath young oceanic lithosphere - Implications for thermal structure and gravity
Small-scale convection under the oceanic lithosphere which begins in the first 5 m.y. of cooling can produce a gravity signal with the amplitude and wavelength observed for large areas of the central Pacific and southern Indian oceans using Seasat altimeter data. The trend of the observed anomalies is parallel to the direction of plate motion as might be expected if they were produced by small-scale convection. Models predict that the wavelengths of gravity anomalies increase more rapidly with age than is observed. The persistence of short relatively uniform wavelength anomalies (less than 200 km) to crustal ages of 50 Ma may indicate that they were produced when the lithosphere was very young and thin and were 'frozen in' as cooling thickened the elastic lithosphere. Small-scale convection which begins under very young lithosphere does not violate other geophysical data such as the rate of seafloor subsidence and variations of geoid height with age. After convection has begun, the subsidence due to thermal contraction within the lithosphere varies linearly with age, in the absence of mantle heat sources, although the rate of change of these quantities is affected by convection. Much of the variation of the geoid height across fracture zones can be fit by a model which includes small-scale convection.
Origin and Evolution of Deep Plasmaspheric Notches
Deep plasmaspheric notches can extend over more than 2 R(sub E) in radial distance and 3 hours MLT in the magnetic equatorial plane, as observed by the extreme ultraviolet (EUV) imager on the IMAGE mission. They are among the largest evacuated features in the exterior plasmaspheric boundary. They can last for days and exhibit a variety of shapes. It appears that weak convection and limited erosion precedes notch formation at the westward, near-Earth edge of the convection plume. Eighteen clear notch events were found and analyzed in 2000. Among these events, notches were found to drift as slowly as 44% of corotation. In only one case was a notch found to drift at the corotation rate within measurement error. On average, these notches drift at about 21.5 h d(sup -1) or 90% of the corotational rate. Notches sometimes exhibit an interior structure that appears as an extended prominence of dense plasma, which forms a W- or M-like feature in IMAGE/EUV images, depending on viewing perspective. Initial modeling suggests that notches and notch prominences may be caused in part by intense small-scale potential structures that result from the localized injection of ring current plasma. Plasma filling rates during recovery are examined in three L shell ranges from L = 2 to L = 3.5 with rates ranging from 5 to 140 cm(sup -3) d(sup -1). Plasma loss during a minor substorm is found to extend to surprisingly low L shell with rates ranging from 100 to 130 cm(sup -3) d(sup -1) across the L shells examined.
Small molecule inhibitors reveal PTK6 kinase is not an oncogenic driver in breast cancers
Protein tyrosine kinase 6 (PTK6, or BRK) is aberrantly expressed in breast cancers, and emerging as an oncogene that promotes tumor cell proliferation, migration and evasion. Both kinase-dependent and -independent functions of PTK6 in driving tumor growth have been described, therefore targeting PTK6 kinase activity by small molecule inhibitors as a therapeutic approach to treat cancers remains to be validated. In this study, we identified novel, potent and selective PTK6 kinase inhibitors as a means to investigate the role of PTK6 kinase activity in breast tumorigenesis. We report here the crystal structures of apo-PTK6 and inhibitor-bound PTK6 complexes, providing the structural basis for small molecule interaction with PTK6. The kinase inhibitors moderately suppress tumor cell growth in 2D and 3D cell cultures. However, the tumor cell growth inhibition shows neither correlation with the PTK6 kinase activity inhibition, nor the total or activated PTK6 protein levels in tumor cells, suggesting that the tumor cell growth is independent of PTK6 kinase activity. Furthermore, in engineered breast tumor cells overexpressing PTK6, the inhibition of PTK6 kinase activity does not parallel the inhibition of tumor cell growth with a >500-fold shift in compound potencies (IC 50 values). Overall, these findings suggest that the kinase activity of PTK6 does not play a significant role in tumorigenesis, thus providing important evidence against PTK6 kinase as a potential therapeutic target for breast cancer treatment.
Structural investigation of cellobiose dehydrogenase IIA: Insights from small angle scattering into intra- and intermolecular electron transfer mechanisms
Background: Cellobiose dehydrogenases have gained interest due to their potential applications in sectors from biofuel production to biomedical devices. The CDHIIA variant is comprised of a cytochrome domain (CYT), a dehydrogenase domain (DH), and a carbohydrate-binding module (CBM) that are connected by two flexible linkers. Upon cellobiose oxidation at the DH, intramolecular electron transfer (IaET) occurs from the DH to the CYT. In vivo, CDHIIA CYT subsequently performs intermolecular electron transfer (IeET) to a lytic polysaccharide monooxygenase (LPMO). The relevant solution-state CDH domain conformations for IaET and IeET have not been fully characterized.Methods: Small-angle X-ray and neutron scattering measurements of oxidized CDHIIA from Myriococcum thermophilum and Neurospora crassa were performed to investigate the structural landscape explored in solution by MtCDHIIA and NcCDHIIA in response to cations, pH, and the presence of an electron acceptor, LPMO9D from N. crassa.Results: The scattering data complemented by modeling show that, under oxidizing conditions, MtCDHIIA undergoes global conformational rearrangement in the presence of Ca2+. Oxidized NcCDHIIA exhibits conformational changes upon pH variation and, in the presence of NcLPMO9D, primarily adopts a compact conformation.Conclusions: These results demonstrate different conformational responses of oxidized MtCDHIIA and NcCDHIIA to changes in environment. The results also reveal a shift in the oxidized NcCDHIIA conformational landscape toward interdomain compaction upon co-incubation with NcLPMO9D.General significance: The present study is the first report on the structural landscapes explored in solution by oxidized cellobiose dehydrogenases under various cation concentrations, pH conditions and in the presence of an electron-accepting LPMO.
The soil pore structure encountered by roots affects plant‐derived carbon inputs and fate
Summary Plant roots are the main supplier of carbon (C) to the soil, the largest terrestrial C reservoir. Soil pore structure drives root growth, yet how it affects belowground C inputs remains a critical knowledge gap. By combining X‐ray computed tomography with 14 C plant labelling, we identified root–soil contact as a previously unrecognised influence on belowground plant C allocations and on the fate of plant‐derived C in the soil. Greater contact with the surrounding soil, when the growing root encounters a pore structure dominated by small (< 40 μm Ø) pores, results in strong rhizodeposition but in areas of high microbial activity. The root system of Rudbeckia hirta revealed high plasticity and thus maintained high root–soil contact. This led to greater C inputs across a wide range of soil pore structures. The root–soil contact Panicum virgatum , a promising bioenergy feedstock crop, was sensitive to the encountered structure. Pore structure built by a polyculture, for example, restored prairie, can be particularly effective in promoting lateral root growth and thus root–soil contact and associated C benefits. The findings suggest that the interaction of pore structure with roots is an important, previously unrecognised, stimulus of soil C gains.
Subsurface Structure in the Martian Polar Layered Deposits: The Deep Space 2 Impact Accelerometry Experiment
While primarily a technology demonstration mission, the New Millenium Mars Microprobes (also known as Deep Space 2, or simply DS2)will also provide the first in situ science measurements of the martian subsurface. The DS2 impact accelerometry experiment will provide both engineering data about the depth of probe emplacement and science data about the physical nature of the subsurface at the probes' landing sites. Little is known about the detailed physical properties or small-scale vertical structure of the subsurface at the DS2 landing site in the southern martian polar layered deposits. Imaging data from the Viking Orbiters and Mars Global Surveyor reveal alternating bands of light and dark material in this region with thicknesses at least as small as the limit of resolution, about 10 m. The overall composition of these layers is poorly constrained, but generally thought to be a mixture of dust and ice with the layers being caused by variations in the dust/ice ratio, or perhaps by dust deposits of different densities. Low thermal inertias in the region suggest that the top few centimeters of the surface are composed of a mantling of fine-grained dust. However, 3.5-cm radar returns indicate that the maximum depth of this dust is not greater than a few tens of centimeters. Thermal models generally agree that, while the layered deposits do provide a potential near-surface reservoir for ice, the uppermost few centimeters to meters in these regions are likely to be ice-free because of sublimation losses. Finally, while it is generally agreed that the layered deposits are the product of variations in the martian climate, no direct correlation has been made between band sequences and specific climate changes. Our intention is to shed light on some of these questions about the martian polar layered deposits by using the DS2 accelerometry experiment to determine the physical nature of the layered deposits, and to detect the presence of any subsurface layering of dust, ice, and/or rock. In the process, we will also determine the final resting depth of the two microprobes, an important parameter in the interpretation of other DS2 experiments.
Universal Electronic‐Structure Relationship Governing Intrinsic Magnetic Properties in Permanent Magnets
An electronic-structure-centered perspective is presented on permanent-magnet (PM) design, highlighting two key levers, that is, saturation magnetization (M s ), governed by 3d-band filling and exchange physics, and magnetocrystalline anisotropy energy (MAE), arising from spin-orbit coupling (SOC) on anisotropic orbital populations. Reviewing current practices, including DFT-based MAE/J ij extraction, atomistic-spin and micromagnetic modeling, and high-throughput machine learning (ML) pipelines, three bottlenecks limiting predictive discovery is identified that is i) electronic-structure accuracy for small MAE (sensitive to functional choice, Hubbard U, and many-body effects), ii) finite-temperature and kinetic realism (phonon/magnon renormalization, ordering kinetics), and iii) descriptor and multiscale decoupling (lack of SOC-weighted and orbital-resolved fingerprints). Deep dives into the electronic-structure of Nd─Fe─B and Fe─N show how these fingerprints govern magnetic performance, motivating DFT- and quantum-mechanics-based descriptors for discovery. Unbiased, structure-driven exploration, coupled with high-throughput simulations, ML, generative AI, and reasoning models, accelerates candidate identification and propagates insights across scales. Addressing supply-chain risks, on future needs of designing “critical-element-free” magnets with tailored microstructure and high energy products is emphasized. By integrating electronic fingerprints, AI reasoning, and multiscale modeling, a practical roadmap is provided for rare-earth-lean or rare-earth free, high-performance, sustainable PMs.
Investigation into the effect on structure of oxoanion doping in Na{sub 2}M(SO{sub 4}){sub 2}·2H{sub 2}O
In this paper an investigation into the effect of transition metal ion and selenate/fluorophosphate doping on the structures of Na{sub 2}M(SO{sub 4}){sub 2}·2H{sub 2}O (M=transition metal) materials is reported. In agreement with previous reports, the monoclinic (Kröhnkite) structure is adopted for M=Mn, Fe, Co, Cu, while for the smallest first row divalent transition metal ion, M=Ni, the triclinic (Fairfieldite structure) is adopted. On selenate doping there is a changeover in structure from monoclinic to triclinic for M=Fe, Co, Cu, with the larger Fe{sup 2+} system requiring the highest level of selenate to complete the changeover. Thus the results suggest that the relative stability of the two structure types is influenced by the relative size of the transition metal: oxoanion group, with the triclinic structure favoured for small transition metals/large oxoanions. The successful synthesis of fluorophosphate doped samples, Na{sub 2}M(SO{sub 4}){sub 2−x}(PO{sub 3}F){sub x}·2H{sub 2}O was also obtained for M=Fe, Co, Cu, with the results showing a changeover in structure from monoclinic to triclinic for M=Co, Cu for very low levels (x=0.1) of fluorophosphate. In the case of M=Fe, the successful synthesis of fluorophosphates samples was achieved for x≤0.3, although no change in cell symmetry was observed. Rather in this particular case, the X-ray diffraction patterns showed evidence for selective peak broadening, attributed to local disorder as a result of the fluorophosphate group disrupting the H-bonding network. Overall the work highlights how isovalent doping can be exploited to alter the structures of Na{sub 2}M(SO{sub 4}){sub 2}·2H{sub 2}O systems. - Graphical abstract: Partial substitution of sulfate in Na{sub 2}M(SO{sub 4}){sub 2}0.2H{sub 2}O (M=Co, Cu) by selenate or fluorophosphate leads to a structural change from the monoclinic Kröhnkite to the triclinic Fairfieldite structure. - Highlights: • The successful synthesis of Na{sub 2}M(SO{sub 4}){sub 2}·2H{sub 2}O (M=transition metal) phases doped with selenate and fluorophosphate. • A change in structure is observed on selenate doping for M=Fe, Co, Cu. • This change in structure is also observed on fluorophosphate doping for M=Co, Cu. • The work highlights how isovalent doping can be exploited to alter the structures of Na{sub 2}M(SO{sub 4}){sub 2}·2H{sub 2}O systems.
Determination of the Structures of Lignin Subunits and Nanoparticles in Solution by Small‐Angle Neutron Scattering: Towards Improving Lignin Valorization
Abstract Lignin nanoparticles (LNPs) are usually produced from lignin solution through supersaturation. The structure of the lignin in solution is still poorly understood due to structural variability of isolated lignins. Here, lignins were extracted from different plants to establish a general pattern of their structure in several lignin solvents. Lignin molecules (lignin subunits) and larger aggregates were observed in dimethyl sulfoxide (DMSO), ethylene glycol (EG) and 0.1 N NaOD solutions by small‐angle neutron scattering (SANS). It was proposed that the aggregates were composed of lignin subunits with a higher molecular weight and a higher ratio of the aliphatic to phenolic hydroxyl groups. The size, shape, and compactness are important factors that affect the uses of the LNPs, which were obtained from the SANS data for the first time. A discrepancy in the radius between SANS and DLS was discovered, pointing to a large hydration shell around the LNPs in aqueous solutions. The cytotoxicity of the corncob lignin, kraft lignin, and their LNPs were measured and compared.
An X-ray and Neutron Scattering Study of the Formation of Core-Shell Type Polyoxometalates
A typical type of core-shell polyoxometalates can be obtained through the Keggin-type polyoxometalatetemplated growth of a layer of spherical shell structure of {Mo72Fe30}. Small angle X-ray scattering is used to study the structural features and stability of the core-shell structures in aqueous solutions. Timeresolved small angle X-ray scattering is applied to monitor the synthetic reactions and a three-stage formation mechanism is proposed to describe the synthesis of the core-shell polyoxometalates based on the monitoring results. New protocols have been developed by fitting the X-ray data with customed physical models, which provide more convincing, objective, and completed data interpretation. Quasielastic and inelastic neutron scattering are used to probe the dynamics of water molecules in the core-shell structures and two different types of water molecules, the confined and structured water, are observed. These water molecules play an important role in bridging core and shell structures and stabilizing the cluster structures.