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At least 1,423 records · Page 79

Full-wavefield inversion of surface waves for mapping embedded low-velocity zones in permafrost

Surface waves are advantageous for mapping seismic structures of permafrost, in which irregular velocity gradients are common and thus the effectiveness of refraction methods are limited. Nevertheless, the complex velocity structures that are common in permafrost environments often yield unusual dispersion spectra, in which higher-order and leaky modes are dominant. Such unusual dispersion spectra were prevalent in the multichannel surface-wave data acquired from our permafrost study site at Barrow, Alaska. Owing to the difficulties in picking and identifying dispersion curves from these dispersion spectra, conventional surface-wave inversion methods become problematic to apply. Here, to overcome these difficulties, we adopted a full-wavefield method to invert for velocity models that can best fit the dispersion spectra instead of the dispersion curves. The inferred velocity models were consistent with collocated electric resistivity results and with subsequent confirmation cores, which indicated the reliability of the recovered seismic structures. The results revealed embedded low-velocity zones underlying the ice-rich permafrost at our study site — an unexpected feature considering the low ground temperatures of - 10 ° C to - 8 ° C . The low velocities in these zones ( ~ 70 % – 80 % lower than the overlying ice-rich permafrost) were most likely caused by saline pore-waters that prevent the ground from freezing, and the resultant velocity structures are vivid examples of complex subsurface properties in permafrost terrain. Finally, we determined that full-wavefield inversion of surface waves, although carrying higher computational costs than conventional methods, can be an effective tool for delineating the seismic structures of permafrost.

58 GEOSCIENCES↗

Effect of LPBF Processing Parameters on Inconel 718 Lattice Structures: Geometrical Characteristics, Surface Morphology, and Mechanical Properties

Laser Powder Bed Fusion (LPBF) enables the additive manufacturing of complex lattice structures. However, the fabrication of lattice structures via LPBF poses challenges in achieving the intended geometrical accuracy due to their inherent complexity. This study investigates the effects of LPBF processing parameters, specifically laser power and scanning speed, on the geometrical characteristics, surface quality, and mechanical behavior of Inconel 718 lattices structures. The results reveal that processing parameters required for the fabrication of near-full dense structures do not translate effectively to lattice configurations, as variations in energy input influence lattice geometry and surface quality. In this work, strut thickness, open-pore size, open-cell porosity, and surface roughness were measured, and the mechanical properties of the lattices were evaluated under shear loading. The findings indicate that lower energy inputs, achieved by reducing laser power and increasing scanning speed, yield porous structures but lead to mechanical degradation. In contrast, high energy inputs lead to lattices with enhanced strength but result in undesirable open-pore blockage and dimensional inaccuracies. These findings provide insights into tailoring LPBF parameters for dimensional accuracy in lattices and correlating the processing parameters to mechanical performance and surface roughness.

36 MATERIALS SCIENCE↗

Electron Tomography and Machine Learning for Understanding the Highly Ordered Structure of Leafhopper Brochosomes

Insects known as leafhoppers (Hemiptera: Cicadellidae) produce hierarchically structured nanoparticles known as brochosomes that are exuded and applied to the insect cuticle, thereby providing camouflage and anti-wetting properties to aid insect survival. Although the physical properties of brochosomes are thought to depend on the leafhopper species, the structure–function relationships governing brochosome behavior are not fully understood. Brochosomes have complex hierarchical structures and morphological heterogeneity across species, due to which a multimodal characterization approach is required to effectively elucidate their nanoscale structure and properties. In this work, we study the structural and mechanical properties of brochosomes using a combination of atomic force microscopy (AFM), electron microscopy (EM), electron tomography, and machine learning (ML)-based quantification of large and complex scanning electron microscopy (SEM) image data sets. This suite of techniques allows for the characterization of internal and external brochosome structures, and ML-based image analysis methods of large data sets reveal correlations in the structure across several leafhopper species. Our results show that brochosomes are relatively rigid hollow spheres with characteristic dimensions and morphologies that depend on leafhopper species. Nanomechanical mapping AFM is used to determine a characteristic compression modulus for brochosomes on the order of 1–3 GPa, which is consistent with crystalline proteins. Altogether, this work provides an improved understanding of the structural and mechanical properties of leafhopper brochosomes using a new set of ML-based image classification tools that can be broadly applied to nanostructured biological materials.

Chemical structure↗

Adsorption Behavior of Organic Molecules: A Study of Benzotriazole on Cu(111) with Spectroscopic and Theoretical Methods

The adsorption of organic molecules on solid substrates is important to applications in fields such as catalysis, photovoltaics, corrosion inhibition, adhesion, and sensors. The molecular level description of the surface–molecule interaction and of the adsorption structures in these complex systems is crucial to understand their properties and function. Here, we present an investigation of one such system, benzotriazole (BTAH) on single-crystal Cu(111) in vacuum conditions. BTAH is the most widely used corrosion inhibitor for copper and thus a molecule of great industrial relevance. We show that the co-application of a wide range of spectroscopic techniques with theoretical methods provides unique insight in the description of the atomistic details of the adsorbed structures. Specifically, spectroscopic photoemission, absorption, and standing wave experiments combined with ab initio computational modeling allowed us to identify that benzotriazole forms overlayers of intact BTAH when deposited at low temperature, and it dissociates into BTA and H at room temperature and above. The dissociated molecule then forms complex structures of mixed chains and dimers of BTA bound to copper adatoms. Our work also reveals that copper adatoms at low concentrations, such as the theoretically predicted superstructures, cannot be resolved by means of current X-ray photoelectron spectroscopy as the modeled Cu 2p spectra are practically indistinguishable from those for a Cu surface without adatoms. Overall this study significantly deepens understanding of BTAH on Cu, a system studied for more than 50 years, and it highlights the benefits of combining spectroscopic and computational methods to obtain a complete picture of a complex adsorption system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure of 6-diazo-5-oxo-norleucine-bound human gamma-glutamyl transpeptidase 1, a novel mechanism of inactivation

Intense efforts are underway to identify inhibitors of the enzyme gamma–glutamyl transpeptidase 1 (GGT1) which cleaves extracellular gamma–glutamyl compounds and contributes to the pathology of asthma, reperfusion injury and cancer. The glutamate analog, 6–diazo–5–oxo–norleucine (DON), inhibits GGT1. DON also inhibits many essential glutamine metabolizing enzymes rendering it too toxic for use in the clinic as a GGT1 inhibitor. We investigated the molecular mechanism of human GGT1 (hGGT1) inhibition by DON to determine possible strategies for increasing its specificity for hGGT1. DON is an irreversible inhibitor of hGGT1. The second order rate constant of inactivation was 0.052 m M –1 min –1 and the K i was 2.7 ± 0.7 m M . The crystal structure of DON–inactivated hGGT1 contained a molecule of DON without the diazo–nitrogen atoms in the active site. The overall structure of the hGGT1–DON complex resembled the structure of the apo–enzyme; however, shifts were detected in the loop forming the oxyanion hole and elements of the main chain that form the entrance to the active site. The structure of hGGT1–DON complex revealed two covalent bonds between the enzyme and inhibitor which were part of a six membered ring. The ring included the OG atom of Thr381, the reactive nucleophile of hGGT1 and the α–amine of Thr381. As a result, the structure of DON–bound hGGT1 has led to the discovery of a new mechanism of inactivation by DON that differs from its inactivation of other glutamine metabolizing enzymes, and insight into the activation of the catalytic nucleophile that initiates the hGGT1 reaction.

36 MATERIALS SCIENCE↗

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

59 BASIC BIOLOGICAL SCIENCES↗

Structure of the IFNγ receptor complex guides design of biased agonists

The cytokine interferon-γ (IFNγ) is a central coordinator of innate and adaptive immunity, but its highly pleiotropic actions have diminished its prospects for use as an immunotherapeutic agent. Here, we took a structure-based approach to decoupling IFNγ pleiotropy. We engineered an affinity-enhanced variant of the ligand-binding chain of the IFNγ receptor IFNγR1, which enabled us to determine the crystal structure of the complete hexameric (2:2:2) IFNγ–IFNγR1–IFNγR2 signalling complex at 3.25 Å resolution. The structure reveals the mechanism underlying deficits in IFNγ responsiveness in mycobacterial disease syndrome resulting from a T168N mutation in IFNγR2, which impairs assembly of the full signalling complex. The topology of the hexameric complex offers a blueprint for engineering IFNγ variants to tune IFNγ receptor signalling output. Unexpectedly, we found that several partial IFNγ agonists exhibited biased gene-expression profiles. Here, these biased agonists retained the ability to induce upregulation of major histocompatibility complex class I antigen expression, but exhibited impaired induction of programmed death-ligand 1 expression in a wide range of human cancer cell lines, offering a route to decoupling immunostimulatory and immunosuppressive functions of IFNγ for therapeutic applications.

59 BASIC BIOLOGICAL SCIENCES↗

Structures of chaperone-substrate complexes docked onto the export gate in a type III secretion system

The flagellum and the injectisome enable bacterial locomotion and pathogenesis, respectively. These nanomachines assemble and function using a type III secretion system (T3SS). Exported proteins are delivered to the export apparatus by dedicated cytoplasmic chaperones for their transport through the membrane. The structural and mechanistic basis of this process is poorly understood. Here we report the structures of two ternary complexes among flagellar chaperones (FliT and FliS), protein substrates (the filament-capping FliD and flagellin FliC), and the export gate platform protein FlhA. The substrates do not interact directly with FlhA; however, they are required to induce a binding-competent conformation to the chaperone that exposes the recognition motif featuring a highly conserved sequence recognized by FlhA. The structural data reveal the recognition signal in a class of T3SS proteins and provide new insight into the assembly of key protein complexes at the export gate.

59 BASIC BIOLOGICAL SCIENCES↗

PRINCEPS: A computer-based approach to the structural description and recognition of trends within structural databases, and its application to the Ce-Ni-Si System

Intermetallic crystal structures offer an enormous structural diversity, with an endless array of structural motifs whose connection to stability and physical properties are often mysterious. Making sense of the often complex crystal structures that arise here, developing a clear structural description, and identifying connections to other phases can be laborious and require an encyclopedic knowledge of structure types. In this Article, we present PRINCEPS, an algorithm based on a new coordination environment projection scheme that facilitates the structural analysis and comparison of such crystal structures. We demonstrate the potential of this approach by applying it to the complex Ce-Ni-Si ternary system, whose 17 binary and 21 ternary phases would present a daunting challenge to one seeking to understand the system by manual inspection (but has nonetheless been well-described through the heroic efforts of previous researchers). With the help of PRINCEPS, most of the ternary phases in this system can be rationalized as intergrowths of simple structural fragments, and grouped into a handful of structural series (with some outliers). Lastly, these results illustrate how the PRINCEPS approach can be used to organize a vast collection of crystal structures into structurally meaningful families, and guide the description of complex atomic arrangements.

97 MATHEMATICS AND COMPUTING↗

Enhancing glycan isomer separations with metal ions and positive and negative polarity ion mobility spectrometry-mass spectrometry analyses

Glycomics has become an increasingly important field of research since glycans play critical roles in biology processes ranging from molecular recognition and signaling to cellular communication. Glycans often conjugate with other biomolecules such as proteins and lipids, and alter their properties and functions, so understanding the effect glycans have on cellular systems is essential. However the analysis of glycans is extremely difficult due to their complexity and structural diversity (i.e., the number and identity of monomer units, and configuration of their glycosidic linkages and connectivities). In this work, we coupled ion mobility spectrometry with mass spectrometry (IMS-MS) to characterize glycan standards and biologically important isomers of synthetic αGal-containing O-glycans including glycotopes of the protozoan parasite Trypanosoma cruzi, which is the causative agent of Chagas disease. IMS-MS results showed significant differences for the glycan structural isomers when analyzed in positive and negative polarity and complexed with different metal cations. These results suggest specific metal ions or ion polarities could be used to target and baseline separate glycan isomers of interest with IMS-MS.

Environmental Molecular Sciences Laboratory↗

Improved representation of black carbon mixing structures suggests stronger direct radiative heating

Black carbon significantly influences the Earth system because of its strong solar radiation absorption. However, its direct radiative effect remains poorly understood in current climate models, partly because current climate models oversimplify the diverse structures formed when black carbon mixes with other atmospheric components. Here we show that incorporating more realistic, multi-mixing-structure representations of black carbon increases the direct radiative effect. We find that aged black carbon particles, with thicker coatings and higher embedded fractions, enhance the direct radiative effect more efficiently. Using machine learning alongside the Community Earth System Model, we show that the direct radiative effect at the top of the atmosphere in regions with heavy black carbon pollution is 31.6% greater when multi-mixing structures are considered. These findings highlight the importance of modeling complex mixing structures of particle-resolved black carbon to accurately capture their warming impacts on global atmosphere, particularly in highly polluted regions.

54 ENVIRONMENTAL SCIENCES↗

Two-Dimensional Hybrid Halide Perovskites: Principles and Promises

Hybrid halide perovskites have become the “next big thing” in emerging semiconductor materials as the past decade witnessed their successful application in high-performance photovoltaics. This resurgence has seen enormous and widespread development of the three-dimensional (3D) perovskites, spearheaded by CH 3 NH 3 PbI 3 . The next generation of halide perovskites, however, is characterized by reduced dimensionality perovskites, emphasizing on the two-dimensional (2D) perovskite derivatives which expand as a more diverse subgroup of semiconducting hybrids that possesses even higher tunability and excellent photophysical properties. In this perspective, we start with a histori-cal flashback that traces back to early reports before the “perovskite fever” and we follow this original work to its fruition in the present day, where 2D halide perov-skites are on the spotlight of current research, thriving on several aspects of high-performance optoelectronics. We approach the evolution of 2D halide perovskites from a structural perspective, providing a classification for the diverse structure-types of the materials, which largely dictate the unusual physical properties ob-served. We sort out the 2D hybrid halide perovskite based on two key components: the inorganic layers and their modification and the organic cation diversity. As these two heterogeneous components blend, either by synthetic manipulation (shuffling the organic cations or inorganic elements) or by external stimuli (temperature and pressure), the modular perovskite structure evolves to construct crystallographically defined quantum wells (QW). The complex electronic structure that arises is sensitive to the structural features that could be in turn used as a knob to control the dielectric and optical properties the QWs. We end this perspective with the most notable optoelectronic device achievements that have been demonstrated to date with an eye to-wards future material discovery and potential techno-logical developments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Magnetic tunability in tetragonal Mn–Rh–Ir–Sn inverse Heusler compounds

Abstract Gaining control over magnetic structure has been an ongoing challenge in materials that form complex, nanoscale, and non-collinear magnetic configurations. Recently, it was predicted that tuning the ratio of the Dzyaloshinskii–Moriya interaction to the uniaxial magnetic anisotropy in tetragonal inverse Heuslers through changes in composition could allow a range of interesting magnetic states to be accessed, from simple ferrimagnetism, to helical and antiskyrmionic phases. Here, we show tunability of the magnetic phase behavior in the Mn–Rh–Sn system through Ir substitution on the Rh substructure. Iridium substitution correlates to an increase in the strength of ferromagnetic exchange couplings, at the expense of antiferromagnetic exchange couplings. However, we do not observe the complex non-collinear magnetic phases proposed previously, likely due to the extremely narrow composition window where these phases are predicted to form in a bulk sample. This work highlights the sensitivity of complex magnetic structures to stoichiometry, which makes them difficult to discover empirically.

Physics↗

Crystal structure of hypothetical protein PA4202 from Pseudomonas aeruginosa PAO1 in complex with nitroethane as a nitroalkane substrate

Highlights: • Crystal structure of PA4202 protein in complex with FMN and NE was determined. • A kinetic study reveals that the PA4202 enzyme may catalyze a neutral nitroalkane. • Our results provide the first structure-based substrate binding property of PA4202. Nitroalkane oxidase (NAO) and nitronate monooxygenase (NMO) are two different types of nitroalkane oxidizing flavoenzymes identified in nature. A previous study suggested that the hypothetical protein PA4202 from Pseudomonas aeruginosa PAO1 is NMO and utilizes only anionic nitronates. However, the structural similarity between the PA4202 protein and Streptomyces ansochromogenes NAO has motivated investigation for what features of the two enzymes differentiate between the NAO and NMO activities. Herein, we report the crystal structure of PA4202 in a ternary complex with a neutral nitroethane (NE) and flavin mononucleotide (FMN) cofactor to elucidate the substrate recognition mechanism using a site-directed mutagenesis. The ternary complex structure indicates that the NE is bound with an orientation, which is poised for the proton transfer to H183 (which is the essential first catalytic step with nitroalkanes), and subsequent reactions with FMN. Moreover, a kinetic study reveals that the catalytic reactions of the wild type and H183 mutants PA4202s with nitroalkane substrates may yield the products of hydrogen peroxide and nitrite that are specified to NAO, although they show a low catalytic efficiency. Our results provide the first structure-based molecular insight into the substrate binding property of the hypothetical protein PA4202, including the interactions with neutral nitroalkanes as the substrate.

60 APPLIED LIFE SCIENCES↗

Observation of two different fractal structures in nanoparticle, protein and surfactant complexes

Small angle neutron scattering has been carried out from a complex of nanoparticle, protein and surfactant. Although all the components are similarly (anionic) charged, we have observed strong interactions in their complex formation. It is characterized by the coexistence of two different mass fractal structures. The first fractal structure is originated from the protein and surfactant interaction and second from the depletion effect of first fractal structure leading the nanoparticle aggregation. The fractal structure of protein-surfactant complex represents to bead necklace structure of micelle-like clusters of surfactant formed along the unfolded protein chain. Its fractal dimension depends on the surfactant to protein ratio (r) and decreases with the increase in r. However, fractal dimension of nanoparticle aggregates in nanoparticle-protein complex is found to be independent of protein concentration and governed by the diffusion limited aggregation like morphology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Aryl-substituted BIAN complexes of iron dibromide: Synthesis, X-ray and electronic structure, and catalytic hydrosilylation activity

Anhydrous iron dibromide complexes bearing bidentate a-diimine ligands ArN@C(Me)A(Me)C@NAr and ArBIAN (BIAN = bis(imino)acenaphthene; Ar = dpp and Mes; dpp = 2,6-diisopropylphenyl; Mes = 2,4,6-trimethylphenyl) have been prepared and characterized by 1H NMR spectroscopy. The aryl-substituted BIAN complexes were structurally characterized by single-crystal X-ray diffraction, and their metrical parameters are consistent with a redox-innocent chelating ligand. A high-spin iron(II) electronic structure description for the ArBIAN iron complexes is supported by Mössbauer spectroscopy, solution state magnetic measurements, and quantum-chemical calculations. Upon reduction, the iron complexes promote catalytic hydrosilylation of 1-hexene with phenylsilane at 22 _C. Under optimized conditions, 1 mol% of the dppBIANFeBr2 precatalyst was activated in situ to produce 1-hexylphenylsilane in high yield from a 1:1 ratio of 1-hexene:PhSiH3 in solvent-free conditions at 22 _C in 24 h.

Supej, Michael J.↗