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At least 1,315 records · Page 73
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Strongly Anisotropic Thermomechanical Response to Shock Wave Loading in Oriented Samples of the Triclinic Molecular Crystal 1,3,5-Triamino-2,4,6-trinitrobenzene

All-atom molecular dynamics (MD) simulations were used to study shock wave loading in oriented single crystals of the highly anisotropic triclinic molecular crystal 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). The crystal structure consists of planar hydrogen-bonded sheets of individually planar TATB molecules that stack into graphitic-like layers. Shocks were studied for seven systematically prepared crystal orientations with limiting cases that correspond to shock propagation exactly perpendicular and exactly parallel to the graphitic-like layers. The simulations were performed for initially defect-free crystals using a reverse-ballistic configuration that generates explicit, supported shocks. Final longitudinal stress components are between ≈8.5 and ≈10.5 GPa for the 1.0 km s –1 impact speed studied. Orientation-dependent properties are reported including shock speeds, stresses, temperatures, compression ratios, and local material strain rates. Spatiotemporal maps of the temperature, stress tensor, material flow, and molecular orientations reveal complicated processes that arise for specific shock directions. Furthermore, the results indicate that TATB shock response is highly sensitive to crystal orientation, with significant qualitative differences for the time evolution of the stress tensor and temperature, elastic/inelastic compression response, defect formation and growth, critical von Mises stress, and strain rates during shock rise that span nearly an order of magnitude. A variety of inelastic deformation mechanisms are identified, ranging from crumpling of graphitic-like layers to dislocation-mediated plasticity to intense shear strain localization. To our knowledge, these are the first systematic MD simulations and analysis of explicit shock wave propagation along nontrivial crystal directions in a triclinic molecular crystal.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Discovery of highly potent and ALK2/ALK1 selective kinase inhibitors using DNA-encoded chemistry technology

Activin receptor type 1 (ACVR1; ALK2) and activin receptor like type 1 (ACVRL1; ALK1) are transforming growth factor beta family receptors that integrate extracellular signals of bone morphogenic proteins (BMPs) and activins into Mothers Against Decapentaplegic homolog 1/5 (SMAD1/SMAD5) signaling complexes. Several activating mutations in ALK2 are implicated in fibrodysplasia ossificans progressiva (FOP), diffuse intrinsic pontine gliomas, and ependymomas. The ALK2 R206H mutation is also present in a subset of endometrial tumors, melanomas, non-small lung cancers, and colorectal cancers, and ALK2 expression is elevated in pancreatic cancer. Using DNA-encoded chemistry technology, we screened 3.94 billion unique compounds from our diverse DNA-encoded chemical libraries (DECLs) against the kinase domain of ALK2. Off-DNA synthesis of DECL hits and biochemical validation revealed nanomolar potent ALK2 inhibitors. Further structure-activity relationship studies yielded center for drug discovery (CDD)-2789, a potent [NanoBRET (NB) cell IC50: 0.54 μM] and metabolically stable analog with good pharmacological profile. Crystal structures of ALK2 bound with CDD-2281, CDD-2282, or CDD-2789 show that these inhibitors bind the active site through Van der Waals interactions and solvent-mediated hydrogen bonds. CDD-2789 exhibits high selectivity toward ALK2/ALK1 in KINOMEscan analysis and NB K192 assay. In cell-based studies, ALK2 inhibitors effectively attenuated activin A and BMP-induced Phosphorylated SMAD1/5 activation in fibroblasts from individuals with FOP in a dose-dependent manner. Thus, CDD-2789 is a valuable tool compound for further investigation of the biological functions of ALK2 and ALK1 and the therapeutic potential of specific inhibition of ALK2.

Jimmidi, Ravikumar↗
DOE OSTI2021

Observation of bound states in the continuum embedded in symmetry bandgaps

In the past decade, symmetry-protected bound states in the continuum (BICs) have proven to be an important design principle for creating and enhancing devices reliant upon states with high-quality (Q) factors, such as sensors, lasers, and those for harmonic generation. However, as we show, current implementations of symmetry-protected BICs in photonic crystal slabs can only be found at the center of the Brillouin zone and below the Bragg diffraction limit, which fundamentally restricts their use to single-frequency applications. By microprinting a three-dimensional (3D) photonic crystal structure using two-photon polymerization, we demonstrate that this limitation can be overcome by altering the radiative environment surrounding the slab to be a 3D photonic crystal. This allows for the protection of a line of BICs by embedding it in a symmetry bandgap of the crystal. This concept substantially expands the design freedom available for developing next-generation devices with high-Q states.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

The Structure of Maltooctaose-Bound Escherichia coli Branching Enzyme Suggests a Mechanism for Donor Chain Specificity

Glycogen is the primary storage polysaccharide in bacteria and animals. It is a glucose polymer linked by α-1,4 glucose linkages and branched via α-1,6-linkages, with the latter reaction catalyzed by branching enzymes. Both the length and dispensation of these branches are critical in defining the structure, density, and relative bioavailability of the storage polysaccharide. Key to this is the specificity of branching enzymes because they define branch length. Herein, we report the crystal structure of the maltooctaose-bound branching enzyme from the enterobacteria E. coli. The structure identifies three new malto-oligosaccharide binding sites and confirms oligosaccharide binding in seven others, bringing the total number of oligosaccharide binding sites to twelve. In addition, the structure shows distinctly different binding in previously identified site I, with a substantially longer glucan chain ordered in the binding site. Using the donor oligosaccharide chain-bound Cyanothece branching enzyme structure as a guide, binding site I was identified as the likely binding surface for the extended donor chains that the E. coli branching enzyme is known to transfer. Furthermore, the structure suggests that analogous loops in branching enzymes from a diversity of organisms are responsible for branch chain length specificity. Together, these results suggest a possible mechanism for transfer chain specificity involving some of these surface binding sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Microstructural characterization of nuclear graphite: from the microscale to the nanoscale

Multiple reactor designs use graphite as a moderator of the nuclear reactions and as structural support. During the lifetime of the reactor, multiple aging factors such as neutron irradiation, oxidation, and temperature along with others induce changes in the microstructure and crystal lattice of graphite components. The pore morphology and crystal structure of some phases in graphite can be used to trace the evolution of irradiation defects and mechanical properties of graphite. We present a combination of results from several microscopy techniques to investigate the differences between nuclear graphite grades and the effects of neutron irradiation and oxidation at multiple length scales. This multiscale approach is needed to understand the microstructural variations caused by the raw materials and manufacturing processes as well as how the different phases of graphite are affected by the reactor environment. The results provide insight into the oxidation- and radiation-induced changes of graphite and create a robust baseline of microstructure information that can be used for the selection of materials for the next generation of nuclear power stations. Moreover, the experiments conducted in this work provide an overview of the advantages and limitations of the most common techniques used to characterize nuclear graphite and how these techniques might be applied to study other carbon-based materials used in the nuclear industry.

Arregui Mena, Jose'↗
DOE OSTI2024

Exploring the Links between Structural Distortions, Orbital Ordering, and Multipolar Magnetic Ordering in Double Perovskites Containing Re(VI) and Os(VII)

A combination of high-resolution powder diffraction techniques and solid-state NMR has been employed to explore the links between crystal structure, orbital ordering, and magnetism in three isostructural double perovskites containing transition metal ions with a 5d 1 configuration. In Ba 2 ZnReO 6 , both neutron and synchrotron X-ray powder diffraction data reveal a cubic-to-tetragonal transition at 23 K that breaks the degeneracy of the t 2g orbitals and leads to a pattern of orbital ordering that stabilizes magnetic ordering when the sample is cooled below 16 K. Similar behavior is observed in Ba 2 MgReO 6 , with an orbital ordering temperature of 33 K and a magnetic ordering temperature of 18 K. Prior theoretical works suggest that the pattern of orbital order seen in the P42/mnm space group is needed to stabilize the heavily canted antiferromagnetism of these compounds. Unfortunately, powder diffraction data is not sensitive enough to differentiate between the I4/mmm and P42/mnm structural models, as the distortions are too subtle to be unambiguously identified from either neutron or synchrotron X-ray powder diffraction methods. In contrast, both diffraction and 7 Li NMR data indicate that Ba 2 LiOsO 6 retains the cubic structure down to 1.7 K. The antiferromagnetic ground state and lack of any sign of orbital ordering in Ba 2 LiOsO 6 provide compelling evidence that the electronically driven tetragonal distortion seen in Ba2ZnReO6, and Ba2MgReO6 is intimately linked to the magnetic ordering seen in those compounds. The absence of magnetic reflections in high intensity neutron powder diffraction data collected on Ba 2 MgReO 6 strongly suggests ordering of multipolar moments on Re(VI), likely ferro-octupolar ordering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Structure and regulation of human epithelial cell transforming 2 protein

Epithelial cell transforming 2 (Ect2) protein activates Rho GTPases and controls cytokinesis and many other cellular processes. Dysregulation of Ect2 is associated with various cancers. Here, we report the crystal structure of human Ect2 and complementary mechanistic analyses. The data show the C-terminal PH domain of Ect2 folds back and blocks the canonical RhoA-binding site at the catalytic center of the DH domain, providing a mechanism of Ect2 autoinhibition. Ect2 is activated by binding of GTP-bound RhoA to the PH domain, which suggests an allosteric mechanism of Ect2 activation and a positive-feedback loop reinforcing RhoA signaling. Furthermore this bimodal RhoA binding of Ect2 is unusual and was confirmed with Förster resonance energy transfer (FRET) and hydrogen–deuterium exchange mass spectrometry (HDX-MS) analyses. Several recurrent cancer-associated mutations map to the catalytic and regulatory interfaces, and dysregulate Ect2 in vitro and in vivo. Together, our findings provide mechanistic insights into Ect2 regulation in normal cells and under disease conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The anti-aromatic dianion and aromatic tetraanion of [18]annulene

π-Conjugated macrocycles behave differently from analogous linear chains because their electronic wavefunctions resemble a quantum particle on a ring, leading to aromaticity or anti-aromaticity. [18]Annulene, (CH) 18 , is the archetypal non-benzenoid aromatic hydrocarbon. Molecules with circuits of 4 n +2 π electrons, such as [18]annulene ( n =4), are aromatic, with enhanced stability and diatropic ring currents (magnetic shielding inside the ring), whereas those with 4 n π electrons, such as the dianion of [18]annulene, are expected to be anti-aromatic and exhibit the opposite behaviour. Here we use 1 H NMR spectroscopy to re-evaluate the structure of the [18]annulene dianion. We also show that it can be reduced further to an aromatic tetraanion, which has the same shape as the dianion. The crystal structure of the tetraanion lithium salt confirms its geometry and reveals a metallocene-like sandwich, with five Li + cations intercalated between two [18]annulene tetraanions. We also report a heteroleptic sandwich, with [18]annulene and corannulene tetraanion decks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Ab initio prediction of an order-disorder transition in Mg 2 Ge O 4 : Implication for the nature of super-Earth's mantles

Here we present an ab initio prediction of an order-disorder transition (ODT) from a I¯42d-type to Th 3 P 4 -type phase in the cation sublattices of Mg 2 GeO 4 , a post-post-perovskite phase. This uncommon type of prediction is achieved by carrying out a high-throughput sampling of atomic configurations in a 56-atom supercell followed by a Boltzmann ensemble statistics calculation. Mg 2 GeO 4 is a low-pressure analog of I¯42d-type Mg 2 SiO 4 , a predicted major planet-forming phase of super-Earths' mantles. Therefore, a similar ODT is anticipated in I¯42d-type Mg 2 SiO 4 as well, which should impact the internal structure and dynamics of these planets. Furthermore, the prediction of this Th 3 P 4 -type phase in Mg 2 GeO 4 further enhances the relationship between the crystal structures of Earth/planet-forming silicates and oxides at extreme pressures and those of rare-earth sesquisulfides at low pressures.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Structural mechanism for modulation of functional amyloid and biofilm formation by Staphylococcal Bap protein switch

The Staphylococcal Bap proteins sense environmental signals (such as pH, [Ca 2+ ]) to build amyloid scaffold biofilm matrices via unknown mechanisms. We here report the crystal structure of the aggregation-prone region of Staphylococcus aureus Bap which adopts a dumbbell-shaped fold. The middle module (MM) connecting the N-terminal and C-terminal lobes consists of a tandem of novel double-Ca 2+ -binding motifs involved in cooperative interaction networks, which undergoes Ca 2+ -dependent order-disorder conformational switches. The N-terminal lobe is sufficient to mediate amyloid aggregation through liquid-liquid phase separation and maturation, and subsequent biofilm formation under acidic conditions. Such processes are promoted by disordered MM at low [Ca 2+ ] but inhibited by ordered MM stabilized by Ca 2+ binding, with inhibition efficiency depending on structural integrity of the interaction networks. Furthermore, these studies illustrate a novel protein switch in pathogenic bacteria and provide insights into the mechanistic understanding of Bap proteins in modulation of functional amyloid and biofilm formation, which could be implemented in the anti-biofilm drug design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural and biochemical analyses of the nuclear IκBζ protein in complex with the NF-κB p50 homodimer

As part of the efforts to understand nuclear IκB function in NF-κB-dependent gene expression, we report an X-ray crystal structure of the IκBζ ankyrin repeat domain in complex with the dimerization domain of the NF-κB p50 homodimer. IκBζ possesses an N-terminal α helix that conveys domain folding stability. Affinity and specificity of the complex depend on a small portion of p50 at the nuclear localization signal. The model suggests that only one p50 subunit supports binding with IκBζ, and biochemical experiments confirm that IκBζ associates with DNA-bound NF-κB p50:RelA heterodimers. Comparisons of IκBζ:p50 and p50:κB DNA complex crystallographic models indicate that structural rearrangement is necessary for ternary complex formation of IκBζ and p50 with DNA.

Cell Biology↗
DOE OSTI2022

Thermodynamically Driven Synthetic Optimization for Cation-Disordered Rock Salt Cathodes

Relating the synthesis conditions of materials to their functional performance has long been an experience-based trial-and-error process. However, this methodology is not always efficient in identifying an appropriate protocol and can lead to overlooked opportunities for the performance optimization of materials through simple modifications of the synthesis process. In this work, we systematically track the structural evolution in the synthesis of a representative disordered rocksalt (a promising next-generation Li-ion cathode material) at the scale of both the long-range crystal structure and the short-range atomic structure using various in situ and ex situ techniques, including transmission electron microscopy, X-ray diffraction, and pair distribution function analysis. Further, an optimization strategy is proposed for the synthesis protocol, leading to a remarkably enhanced capacity (specific energy) of 313 mAh g –1 (987 Wh kg –1 ) at a low rate (20 mA g –1 ), with a capacity of more than 140 mAh g –1 retained even at a very high cycling rate of 2,000 mA g –1 . This strategy is further rationalized using ab initio calculations, and important opportunities for synthetic optimization demonstrated in this study are highlighted.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Small‐Molecule Mixed Ionic‐Electronic Conductors for Efficient N‐Type Electrochemical Transistors: Structure‐Function Correlations

Abstract The fundamental challenge in electron‐transporting organic mixed ionic‐electronic conductors (OMIECs) is simultaneous optimization of electron and ion transport. Beginning from Y6‐type/U‐shaped non‐fullerene solar cell acceptors, we systematically synthesize and characterize molecular structures that address the aforementioned challenge, progressively introducing increasing numbers of oligoethyleneglycol (OEG; g) sidechains from 1 g to 3 g, affording OMIECs 1gY, 2gY, and 3gY, respectively. The crystal structure of 1gY preserves key structural features of the Y n series: a U‐shaped/planar core, close π–π molecular stacking, and interlocked acceptor groups. Versus inactive Y6 and Y11, all of the new glycolated compounds exhibit mixed ion‐electron transport in both conventional organic electrochemical transistor (cOECT) and vertical OECT (vOECT) architectures. Notably, 3gY with the highest OEG density achieves a high transconductance of 16.5 mS, an on/off current ratio of ~10 6 , and a turn‐on/off response time of 94.7/5.7 ms in vOECTs. Systematic optoelectronic, electrochemical, architectural, and crystallographic analysis explains the superior 3gY‐based OECT performance in terms of denser n gY OEG content, increased crystallite dimensions with decreased long‐range crystalline order, and enhanced film hydrophilicity which facilitates ion transport and efficient redox processes. Finally, we demonstrate an efficient small‐molecule‐based complementary inverter using 3gY vOECTs, showcasing the bioelectronic applicability of these new small‐molecule OMIECs.

Cho, Yongjoon↗
DOE OSTI2024

Small‐Molecule Mixed Ionic‐Electronic Conductors for Efficient N‐Type Electrochemical Transistors: Structure‐Function Correlations

Abstract The fundamental challenge in electron‐transporting organic mixed ionic‐electronic conductors (OMIECs) is simultaneous optimization of electron and ion transport. Beginning from Y6‐type/U‐shaped non‐fullerene solar cell acceptors, we systematically synthesize and characterize molecular structures that address the aforementioned challenge, progressively introducing increasing numbers of oligoethyleneglycol (OEG; g) sidechains from 1 g to 3 g, affording OMIECs 1gY, 2gY, and 3gY, respectively. The crystal structure of 1gY preserves key structural features of the Y n series: a U‐shaped/planar core, close π–π molecular stacking, and interlocked acceptor groups. Versus inactive Y6 and Y11, all of the new glycolated compounds exhibit mixed ion‐electron transport in both conventional organic electrochemical transistor (cOECT) and vertical OECT (vOECT) architectures. Notably, 3gY with the highest OEG density achieves a high transconductance of 16.5 mS, an on/off current ratio of ~10 6 , and a turn‐on/off response time of 94.7/5.7 ms in vOECTs. Systematic optoelectronic, electrochemical, architectural, and crystallographic analysis explains the superior 3gY‐based OECT performance in terms of denser n gY OEG content, increased crystallite dimensions with decreased long‐range crystalline order, and enhanced film hydrophilicity which facilitates ion transport and efficient redox processes. Finally, we demonstrate an efficient small‐molecule‐based complementary inverter using 3gY vOECTs, showcasing the bioelectronic applicability of these new small‐molecule OMIECs.

Cho, Yongjoon↗
DOE OSTI2020

Thermal Properties of the Quaternary Chalcogenide BaCdSnSe 4

The fields of nonlinear optics, photovoltaics, and thermoelectrics have been strongly impacted by materials research, and quaternary chalcogenides are one general class of materials that has recently generated strong interest. An understanding of the thermal properties is paramount in these and other applications of interest. The thermal properties of BaCdSnSe 4 , a quaternary chalcogenide that is of interest for applications in nonlinear optics, are reported. Specifically, the thermal conductivity over a large temperature range and heat capacity are evaluated in light of the structural features of this material. Low thermal conductivity results from the complex unit cell as well as local dynamic disorder from Cd in the CdSe 4 tetrahedra in the crystal structure. Finally, the results and analyses reported herein are presented to enhance the fundamental understanding of the thermal properties of these materials, and can be related and applied to other quaternary chalcogenides that are of interest for energy-related applications.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Developing techniques for crystal growth synthesis and characterization of rare earth-silicon-germanium magnetoresponsive alloys

In this study, a crystal growth technique was developed for the family of intermetallic, magnetoresponsive RE 5 (Si 1-x Ge x ) 4 alloys in order to access the intrinsic and anisotropic properties. Initial bulk properties measured on polycrystalline samples alluded to the properties being obscured or averaged and high-quality, well-characterized, single crystals would clarify this. Successful crystal growth led to development of oriented sample preparation techniques specific for the crystal structures (monoclinic and orthorhombic) and mechanical properties (hard and brittle) of these alloys, and customized for the various measurement techniques undertaken. Here we describe our journey, sometimes circuitous, from crystal growth to sample preparation and cite the scientific discoveries that came about as a result.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Fission yeast Duf89 and Duf8901 are cobalt/nickel-dependent phosphatase–pyrophosphatases that act via a covalent aspartyl–phosphate intermediate

Domain of Unknown Function 89 (DUF89) proteins are metal-dependent phosphohydrolases. Exemplary DUF89 enzymes differ in their metal and phosphosubstrate preferences. Here, we interrogated the activities and structures of two DUF89 paralogs from fission yeast—Duf89 and Duf8901. We find that Duf89 and Duf8901 are cobalt/nickel-dependent phosphohydrolases adept at hydrolyzing p-nitrophenylphosphate and PP i . Crystal structures of metal-free Duf89 and Co 2+ -bound Duf8901 disclosed two enzyme conformations that differed with respect to the position of a three-helix module, which is either oriented away from the active site in Duf89 or forms a lid over the active site in Duf8901. Lid closure results in a 16 Å movement of Duf8901 Asp195, vis-à-vis Asp199 in Duf89, that brings Asp195 into contact with an octahedrally coordinated cobalt. Reaction of Duf8901 with BeCl 2 and NaF in the presence of divalent cations Co 2+ , Ni 2+ , or Zn 2+ generated covalent Duf8901-(Asp248)–beryllium trifluoride (BeF 3 )•Co 2+ , Duf8901-(Asp248)–BeF 3 •Ni 2+ , or Duf8901-(Asp248)–BeF 3 •Zn 2+ adducts, the structures of which suggest a two-step catalytic mechanism via formation and hydrolysis of an enzyme-(aspartyl)–phosphate intermediate. Alanine mutations of Duf8901 Asp248, Asn249, Lys401, Asp286, and Asp195 that interact with BeF 3 •Co 2+ squelched p-nitrophenylphosphatase activity. A 1.8 Å structure of a Duf8901-(Asp248)–AlF 4 –OH 2 •Co 2+ transition-state mimetic suggests an associative mechanism in which Asp195 and Asp363 orient and activate the water nucleophile. Whereas deletion of the duf89 gene elicited a phenotype in which expression of phosphate homeostasis gene pho1 was derepressed, deleting duf8901 did not, thereby hinting that the DUF89 paralogs have distinct functional repertoires in vivo.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗