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At least 379 records · Page 21

Search for solid conductors of Na(+) and K(+) ions: Five new conductors

Five conductors of three structure types were discovered which, as solids, can transport Na(+) or K(+) ions with conductivities of approximately .00001/(omega cm) at 300 K. These compounds are: (1) the pyrochlores NaTaWO6 and NaTa2O5F, both with an activation energy for conduction delta E of 21 kJ/mole; (2) the bodycentered cubic form of NaSbO3, with delta E = 42 kJ/mole; and (3) the niobates 2Na2O with 3Nb2O5 and 2K2O with 3Nb2O5, with the alkali ions probably in open layers of the incompletely determined structure; delta E = 17 kJ/mole. On the basis of approximately 40 structure types, some generalizations were made regarding the relation between structure and ionic transport.

Singer, J.↗

Calculations of the radiative and dynamical state of the Venus atmosphere

Results are reported for accurate multiple-scattering calculations to determine the solar-energy deposition profile in the atmosphere of Venus. It is found that most of the absorbed energy is deposited in the main cloud-layer region, located at altitudes above 35 km, and that the ground receives approximately 3% of the energy absorbed in toto by Venus. Using these results, vertical temperature profiles are computed under conditions of pure radiative equilibrium and radiative-convective equilibrium. Since the latter results satisfactorily match the temperature structure determined from various spacecraft observations, it is inferred that the greenhouse effect can account for the high surface temperature. Aerosols make an important contribution to the infrared opacity in these calculations. Preliminary three-dimensional calculations of the general circulation of the atmosphere are discussed which incorporate the results of the radiative calculations.

Pollack, J. B.↗

Changes in an enzyme ensemble during catalysis observed by high-resolution XFEL crystallography

Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp 17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.

59 BASIC BIOLOGICAL SCIENCES↗

Synthesis, Structure, and Properties of the Complex Zintl Phase Eu 9 Zn 4.5 As 9 : A Candidate Topological Insulator and Thermoelectric Material

Reported are the synthesis and detailed analysis of the crystal and electronic structure of the novel Zintl phase Eu 9 Zn 4.5 As 9 . This material was identified in the densely populated Eu–Zn–As compositional space. For structure determination and for property measurements, suitable single crystals of this compound were grown from either Sn- or Pb-flux. Single-crystal X-ray diffraction methods indicate that Eu 9 Zn 4.5 As 9 crystallizes in the orthorhombic crystal system with the space group Pnma (a = 12.1953(7) Å, b = 4.3730(2) Å, c = 42.674(2) Å) and is formally isostructural to Ca 9 Mn 4+x Sb 9 , the less common “9–4–9” type. The structure is heavily disordered, with multiple partially occupied sites, yet, according to the Zintl-Klemm formalism, a charge-balanced composition (Eu 2+ ) 9 (Zn 2+ ) 4.5 (As 3− ) 9 is attained. Electronic structure calculations for a model, disorder-free structure indicate no energy gap between the valence and the conduction bands and suggest (semi)metallic behavior. Preliminary susceptibility measurements confirm the expected divalent nature of Eu 2+ ([Xe] 4 f 7 ground state).

Zintl phases↗

Ligand‐Mediated Quantum Yield Enhancement in 1‐D Silver Organothiolate Metal–Organic Chalcogenolates

X-ray free electron laser (XFEL) microcrystallography and synchrotron single-crystal crystallography are used to evaluate the role of organic substituent position on the optoelectronic properties of metal–organic chalcogenolates (MOChas). MOChas are crystalline 1D and 2D semiconducting hybrid materials that have varying optoelectronic properties depending on composition, topology, and structure. While MOChas have attracted much interest, small crystal sizes impede routine crystal structure determination. A series of constitutional isomers where the aryl thiol is functionalized by either methoxy or methyl ester are solved by small molecule serial femtosecond X-ray crystallography (smSFX) and single crystal rotational crystallography. While all the methoxy examples have a low quantum yield (0-1%), the methyl ester in the ortho position yields a high quantum yield of 22%. Here, the proximity of the oxygen atoms to the silver inorganic core correlates to a considerable enhancement of quantum yield. Four crystal structures are solved at a resolution range of 0.8–1.0 Å revealing a collapse of the 2D topology for functional groups in the 2- and 3- positions, resulting in needle-like crystals. Further analysis using density functional theory (DFT) and many-body perturbation theory (MBPT) enables the exploration of complex excitonic phenomena within easily prepared material systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Single-Crystal-to-Single-Crystal Post-Synthetic Modifications

Chalcogenides are the cornerstone of the semiconductor and thermoelectric industries and are up-and-coming materials for superconductors, catalysis, and battery applications. Challenges in synthesizing those materials emerge from the chalcogen's volatility and the tendencies of chalcogenides to react with even trace quantities of oxygen. Many techniques have been applied to the growth of chalcogenide single crystals, which are convenient for structure determinations and intrinsic property measurements. One of the recent advances in chalcogenide chemistry is the intriguing single-crystal-to-single-crystal (SCSC) transformation, leading to new metastable compositions. Post-synthetic transformations are well-known and studied for chalcogenide powders; however, examples of post-synthetic conversions that retain single crystallinity are rare. To date, the scope of SCSC reactions includes (de)intercalation in the layered compositions and ion exchange in open-framework materials, salt-inclusion chalcogenides, and layered structures. This poster will discuss the successful examples of SCSC modifications monitored by single-crystal X-ray diffraction (SC-XRD), emphasizing how post-synthetic transformations affect materials' properties.

chalcogenide↗

Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses

X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter’s correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

De novo design of small beta barrel proteins

Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy–based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 Å rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.

59 BASIC BIOLOGICAL SCIENCES↗

NP-MRD: the Natural Products Magnetic Resonance Database

The Natural Products Magnetic Resonance Database (NP-MRD) is a comprehensive, freely available electronic resource for the deposition, distribution, searching and retrieval of nuclear magnetic resonance (NMR) data on natural products, metabolites and other biologically derived chemicals. NMR spectroscopy has long been viewed as the ‘gold standard’ for the structure determination of novel natural products and novel metabolites. NMR is also widely used in natural product dereplication and the characterization of biofluid mixtures (metabolomics). All of these NMR applications require large collections of high quality, well-annotated, referential NMR spectra of pure compounds. Unfortunately, referential NMR spectral collections for natural products are quite limited. It is because of the critical need for dedicated, open access natural product NMR resources that the NP-MRD was funded by the National Institute of Health (NIH). Since its launch in 2020, the NP-MRD has grown quickly to become the world's largest repository for NMR data on natural products and other biological substances. It currently contains both structural and NMR data for nearly 41,000 natural product compounds from >7400 different living species. All structural, spectroscopic and descriptive data in the NP-MRD is interactively viewable, searchable and fully downloadable in multiple formats. Extensive hyperlinks to other databases of relevance are also provided. The NP-MRD also supports community deposition of NMR assignments and NMR spectra (1D and 2D) of natural products and related meta-data. The deposition system performs extensive data enrichment, automated data format conversion and spectral/assignment evaluation.

59 BASIC BIOLOGICAL SCIENCES↗

Promiscuous G-protein activation by the calcium-sensing receptor

The human calcium-sensing receptor (CaSR) detects fluctuations in the extracellular Ca 2+ concentration and maintains Ca 2+ homeostasis. It also mediates diverse cellular processes not associated with Ca 2+ balance. The functional pleiotropy of CaSR arises in part from its ability to signal through several G-protein subtypes. Here, we determined structures of CaSR in complex with G proteins from three different subfamilies: G q , G i and G s . We found that the homodimeric CaSR of each complex couples to a single G protein through a common mode. This involves the C-terminal helix of each Gα subunit binding to a shallow pocket that is formed in one CaSR subunit by all three intracellular loops (ICL1–ICL3), an extended transmembrane helix 3 and an ordered C-terminal region. G-protein binding expands the transmembrane dimer interface, which is further stabilized by phospholipid. The restraint imposed by the receptor dimer, in combination with ICL2, enables G-protein activation by facilitating conformational transition of Gα. We identified a single Gα residue that determines G q and G s versus G i selectivity. The length and flexibility of ICL2 allows CaSR to bind all three Gα subtypes, thereby conferring capacity for promiscuous G-protein coupling.

36 MATERIALS SCIENCE↗

Recent Advances in Small Angle X-ray Scattering for Superlattice Study

Small-angle x-ray scattering is used for the structure determination of superlattice for its superior resolution, nondestructive nature, and high penetration power of x rays. With the advent of high brilliance x-ray sources and innovative computing algorithms, there have been notable advances in small angle x-ray scattering analysis of superlattices. High brilliance x-ray beams have made data analyses less model-dependent. Additionally, novel data acquisition systems are faster and more competitive than ever before, enabling a more accurate mapping of the superlattices' reciprocal space. Fast and high-throughput computing systems and algorithms also make possible advanced analysis methods, including iterative phasing algorithms, non-parameterized fitting of scattering data with molecular dynamics simulations, and the use of machine learning algorithms. As a result, solving nanoscale structures with high resolutions has become an attainable task. In this review, we highlight new developments in the field and introduce their applications for the analysis of nanoscale ordered structures, including nanoparticle supercrystals, nanoscale lithography patterns, and supramolecular self-assemblies. Particularly, we highlight the reciprocal space mapping techniques and the use of iterative phase retrieval algorithms. We also cover coherent-beam-based small angle x-ray scattering techniques such as ptychography and ptycho-tomography in view of the traditional small angle x-ray scattering perspective.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Supported Metal Pair-Site Catalysts

Complexes with neighboring metal centers in isolated pairs and their analogues on surfaces are drawing increasing attention as catalysts. These include molecular homogeneous catalysts incorporating various ligands, enzymes, and solids that include pairs of metal atoms mounted on supports. Catalysts in this broad class are active for numerous reactions and offer unexplored opportunities to address challenging reactions, such as oxidation of methane and oxidation of water in artificial photosynthesis. The subject of supported metal pair-site catalysts is in its infancy, facing challenges in (a) precise synthesis, (b) structure determination at the atomic scale, and (c) stabilization in reactive atmospheres. In this Perspective, we summarize key characteristics of molecular and enzymatic catalysts that incorporate neighboring metal centers and build on this foundation to assess the emerging literature of metal pair-site catalysts on various supports. The supported catalysts include those synthesized by anchoring molecular dinuclear precursors to support surfaces and those synthesized by selective formation of dinuclear surface species from mononuclear surface species. Examples of metals in this class are rhodium and iridium, and examples of supports are MgO and Fe 2 O 3 . We summarize characterization of these materials by electron microscopy and spectroscopy, emphasizing atomic-resolution aberration-corrected scanning transmission electron microscopy and spectroscopies that provide atomic-scale structural information and allow characterization of functioning catalysts, especially X-ray absorption spectroscopy. Finally, we list some opportunities for research, including suggestions that might lead to structurally well-defined supported metal pair-sites with new catalytic properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Joint iterative reconstruction and 3D rigid alignment for X-ray tomography

X-ray tomography is widely used for three-dimensional structure determination in many areas of science, from the millimeter to the nanometer scale. The resolution and quality of the 3D reconstruction is limited by the availability of alignment parameters that correct for the mechanical shifts of the sample or sample stage for the images that constitute a scan. In this paper we describe an algorithm for marker-free, fully automated and accurately aligned and reconstructed X-ray tomography data. Our approach solves the tomographic reconstruction jointly with projection data alignment based on a rigid-body deformation model. We demonstrate the robustness of our method on both synthetic phantom and experimental data and show that our method is highly efficient in recovering relatively large alignment errors without prior knowledge of a low resolution approximation of the 3D structure or a reasonable estimate of alignment parameters.

36 MATERIALS SCIENCE↗

Assembly of JAZ–JAZ and JAZ–NINJA complexes in jasmonate signaling

Jasmonates (JAs) are plant hormones with crucial roles in development and stress resilience. They activate MYC transcription factors by mediating the proteolysis of MYC inhibitors called JAZ proteins. In the absence of JA, JAZ proteins bind and inhibit MYC through the assembly of MYC–JAZ–Novel Interactor of JAZ (NINJA)–TPL repressor complexes. However, JAZ and NINJA are predicted to be largely intrinsically unstructured, which has precluded their experimental structure determination. Through a combination of biochemical, mutational, and biophysical analyses and AlphaFold-derived ColabFold modeling, we characterized JAZ–JAZ and JAZ–NINJA interactions and generated models with detailed, high-confidence domain interfaces. We demonstrate that JAZ, NINJA, and MYC interface domains are dynamic in isolation and become stabilized in a stepwise order upon complex assembly. By contrast, most JAZ and NINJA regions outside of the interfaces remain highly dynamic and cannot be modeled in a single conformation. Our data indicate that the small JAZ Zinc finger expressed in Inflorescence Meristem (ZIM) motif mediates JAZ–JAZ and JAZ–NINJA interactions through separate surfaces, and our data further suggest that NINJA modulates JAZ dimerization. This study advances our understanding of JA signaling by providing insights into the dynamics, interactions, and structure of the JAZ–NINJA core of the JA repressor complex.

59 BASIC BIOLOGICAL SCIENCES↗

Magnetic structure and spin dynamics of the quasi-two-dimensional antiferromagnet Zn-doped copper pyrovanadate

We report magnetic properties of the antiferromagnet Zn x Cu 2-x V 2 O 7 (ZnCVO) with x ≈ 0.06 have been thoroughly investigated on powder and single-crystal samples. The crystal structure determination using powder x-ray and neutron diffraction confirms that our ZnCVO samples are isostructural with β-Cu 2 V 2 O 7 (β-CVO) with a small deviation in the lattice parameters. Macroscopic magnetic property measurements also confirm the similarity between the two compounds. The Cu 2+ spins were found to align along the crystallographic c axis, antiparallel to their nearest neighbors connected by the leading exchange interaction J 1 . Spin dynamics reveals a typical symmetric spin-wave dispersion with strong interactions in the bc plane and weak interplane coupling. The exchange interaction analysis indicates that the spin network of ZnCVO is topologically consistent with the previous DFT prediction but the values of leading exchange interactions are contradictory. Furthermore, rather than the predicted 2D honeycomb structure, the spin network in ZnCVO could be better described by the anisotropic 2D spin network composed of J 1 , J 5 , and J 6 interactions, four bonds per one spin site, coupled by weak interplane interactions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Control-structure-thermal interactions in analysis of lunar telescopes

The lunar telescope project was an excellent model for the CSTI study because a telescope is a very sensitive instrument, and thermal expansion or mechanical vibration of the mirror assemblies will rapidly degrade the resolution of the device. Consequently, the interactions are strongly coupled. The lunar surface experiences very large temperature variations that range from approximately -180 C to over 100 C. Although the optical assemblies of the telescopes will be well insulated, the temperature of the mirrors will inevitably fluctuate in a similar cycle, but of much smaller magnitude. In order to obtain images of high quality and clarity, allowable thermal deformations of any point on a mirror must be less than 1 micron. Initial estimates indicate that this corresponds to a temperature variation of much less than 1 deg through the thickness of the mirror. Therefore, a lunar telescope design will most probably include active thermal control, a means of controlling the shape of the mirrors, or a combination of both systems. Historically, the design of a complex vehicle was primarily a sequential process in which the basic structure was defined without concurrent detailed analyses or other subsystems. The basic configuration was then passed to the different teams responsible for each subsystem, and their task was to produce a workable solution without requiring major alterations to any principal components or subsystems. Consequently, the final design of the vehicle was not always the most efficient, owing to the fact that each subsystem design was partially constrained by the previous work. This procedure was necessary at the time because the analysis process was extremely time-consuming and had to be started over with each significant alteration of the vehicle. With recent advances in the power and capacity of small computers, and the parallel development of powerful software in structural, thermal, and control system analysis, it is now possible to produce very detailed analyses of intermediate designs in a much shorter period of time. The subsystems can thus be designed concurrently, and alterations in the overall design can be quickly adopted into each analysis; the design becomes an iterative process in which it is much easier to experiment with new ideas, configurations, and components. Concurrent engineering has the potential to produce efficient, highly capable designs because the effect of one subystem on another can be assessed in much more detail at a very early point in the program. The research program consisted of several tasks: scale a prototype telescope assembly to a 1 m aperture, develop a model of the telescope assembly by using finite element (FEM) codes that are available on site, determine structural deflections of the mirror surfaces due to the temperature variations, develop a prototype control system to maintain the proper shape of the optical elements, and most important of all, demonstrate the concurrent engineering approach with this example. In addition, the software used for the finite element models and thermal analysis was relatively new within the Program Development Office and had yet to be applied to systems this large or complex; understanding the software and modifying it for use with this project was also required. The I-DEAS software by Structural Dynamics Research Corporation (SDRC) was used to build the finite element models, and TMG developed by Maya Heat Transfer Technologies, Ltd. (which runs as an I-DEAS module) was used for the thermal model calculations. All control system development was accomplished with MATRIX(sub X) by Integrated Systems, Inc.

Thompson, Roger C.↗

The three-dimensional construction of leaves is coordinated with water use efficiency in conifers

Conifers prevail in the canopies of many terrestrial biomes, holding a great ecological and economic importance globally. Current increases in temperature and aridity are imposing high transpirational demands and resulting in conifer mortality. Therefore, identifying leaf structural determinants of water use efficiency is essential for predicting physiological impacts due to environmental variation. Here, using synchrotron-generated microtomography imaging, we extracted leaf volumetric anatomy and stomatal traits in 34 species across conifers with a special focus on Pinus , the richest conifer genus. We show that intrinsic water use efficiency (WUE i ) is positively driven by leaf vein volume. Needle-like leaves of Pinus , as opposed to flat leaves or flattened needles of other genera, showed lower mesophyll porosity, decreasing the relative mesophyll volume. This led to increased ratios of stomatal pore number per mesophyll or intercellular airspace volume, which emerged as powerful explanatory variables, predicting both stomatal conductance and WUE i . Our results clarify how the three-dimensional organisation of tissues within the leaf has a direct impact on plant water use and carbon uptake. By identifying a suite of structural traits that influence important physiological functions, our findings can help to understand how conifers may respond to the pressures exerted by climate change.

59 BASIC BIOLOGICAL SCIENCES↗