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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,567 records · Page 87
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DOE OSTI2022

Pseudo-Polymorphism in Layered FeS Intercalates: A Competition between Charged and Neutral Guest Species

Systematic synthesis studies of the formation of tetrahedral FeS-ethylenediamine intercalates resulted in the synthesis of a new compound, [Fe 9.4(2) S 10 ][Fe(en) 3 ] 0.6(1) ·en 0.9 ( 3 ). The composition and complex crystal structure were determined based on a synergistic combination of elemental composition, decomposition behavior, high-resolution synchrotron X-ray diffraction and total scattering, 57 Fe Mössbauer spectroscopy, and electron diffraction. The structural model was derived based on a systematic comparison to the previously reported structures [Fe 8 S 10 ][Fe(en) 3 ] 1 ·en 0.5 and tetragonal FeS. The new compound has flat Fe 9.4 S 10 layers, analogous to those in superconducting binary FeS. In the crystal structure of [Fe 9.4 S 10 ][Fe(en) 3 ] 0.6 ·en 0.9 , the interlayer space is occupied by [Fe(en) 3 ] 2+ complexes and neutral ethylenediamine molecules in a ~2:3 ratio. Interlayer species are not randomly oriented but ordered as evidenced by superstructural diffraction peaks in both high-resolution X-ray diffraction and electron diffraction patterns. Magnetic studies reveal no superconducting transition down to 2 K, indicating that the presence of minute amounts (~6%) of iron vacancies at the Fe-S layer in [Fe 9.4 S 10 ][Fe(en) 3 ] 0.6 ·en 0.9 is still sufficient to shift the position of the Fermi level resulting in an adjustment of the properties. Here, our work shows the importance of detailed characterization of the crystal structure of intercalated compounds to understand the origin of the observed properties and develop proper structure–property relationships.

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

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites

β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a backup against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensable role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand–protein interactions. Herein, we provide a comprehensive comparison of all nonredundant ligand-binding sites available for SARS-CoV2, SARS-CoV, and MERS-CoV Mpro. Extensive adaptive sampling has been used to investigate structural conservation of ligand-binding sites using Markov state models (MSMs) and compare conformational dynamics employing convolutional variational auto-encoder-based deep learning. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-CoV homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structural characterization of an activin class ternary receptor complex reveals a third paradigm for receptor specificity

TGFβ family ligands, which include the TGFβs, BMPs, and activins, signal by forming a ternary complex with type I and type II receptors. For TGFβs and BMPs, structures of ternary complexes have revealed differences in receptor assembly. However, structural information for how activins assemble a ternary receptor complex is lacking. In this paper, we report the structure of an activin class member, GDF11, in complex with the type II receptor ActRIIB and the type I receptor Alk5. The structure reveals that receptor positioning is similar to the BMP class, with no interreceptor contacts; however, the type I receptor interactions are shifted toward the ligand fingertips and away from the dimer interface. Mutational analysis shows that ligand type I specificity is derived from differences in the fingertips of the ligands that interact with an extended loop specific to Alk4 and Alk5. The study also reveals differences for how TGFβ and GDF11 bind to the same type I receptor, Alk5. For GDF11, additional contacts at the fingertip region substitute for the interreceptor interactions that are seen for TGFβ, indicating that Alk5 binding to GDF11 is more dependent on direct contacts. In support, we show that a single residue of Alk5 (Phe 84 ), when mutated, abolishes GDF11 signaling, but has little impact on TGFβ signaling. The structure of GDF11/ActRIIB/Alk5 shows that, across the TGFβ family, different mechanisms regulate type I receptor binding and specificity, providing a molecular explanation for how the activin class accommodates low-affinity type I interactions without the requirement of cooperative receptor interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Monodomain Liquid‐Crystal Elastomer Lattices for Broad Strain‐Rate Mechanical Damping

Designing structures that effectively dissipate energy across a broad range of mechanical loading rates, including those from compression, shock, and vibration, poses a significant engineering challenge. In this study, liquid‐crystal elastomers (LCEs), which possess anisotropic properties due to the alignment of their polymer backbone, are explored. As a result, LCEs exhibit a soft elastic response under mechanical loading, making them ideal for energy dissipation. Advances in additive manufacturing (AM) enable simple fabrication of foamlike dissipative structures with complex lattice geometries. Herein, direct ink write 3D printing, an extrusion AM method, is used to fabricate aligned, monodomain LCE lattice structures for broad strain‐rate mechanical damping. In this work, it is shown that these structures can dissipate strain energy in quasi‐static environments, comparable to traditional elastomeric lattices, and provide improved damping under high strain‐rate drop testing due to LCE soft elasticity. Additionally, under dynamic mechanical vibration, monodomain LCE lattices enhance damping at structural natural frequencies and provide high‐frequency attenuation. Finally, in these findings, a promising method is presented for fabricating mechanical damping devices that effectively dissipate energy across a broad range of loading rates.

3D printings↗
DOE OSTI2025

Acetylcholinesterase: Structure, dynamics, and interactions with organophosphorus compounds

Acetylcholinesterase (AChE) is an enzyme that hydrolyzes the neurotransmitter acetylcholine (ACh), removing it from the synaptic cleft after the transmission of an electrical signal, making it an essential component of chemical neurotransmission. AChE is a serine hydrolase, containing a catalytic triad of Ser/His/Glu. AChE is a prime target for pharmaceuticals treating a variety of neurological disorders. It is also the target of synthetic organophosphorus (OP) compounds that have been used as pesticides and chemical warfare agents. OP compounds contain a potent leaving group, such as fluorine, and act by forming a covalent adduct with the catalytic serine of the AChE active site. A wealth of structural information is available for AChE, including over 300 structures, including a subset of structures in complex with drugs as well as OP compounds. This review will highlight the interactions between OP compounds and AChE from a structural and computational perspective, with a discussion of access to the active site, as well as side reactions that lead to dealkylation of the OP-catalytic serine adduct, a process known as aging. We conclude that while the majority of the conformational changes needed to accommodate the OP compounds are localized to the acyl loop in the crystal structures, molecular dynamics simulations highlight the potential for a far more dynamic enzyme.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

High-Resolution Structure of ClpC1-Rufomycin and Ligand Binding Studies Provide a Framework to Design and Optimize Anti-Tuberculosis Leads

Addressing the urgent need to develop novel drugs against drug-resistant Mycobacterium tuberculosis (M. tb) strains, ecumicin (ECU) and rufomycin I (RUFI) are being explored as promising new leads targeting cellular proteostasis via the caseinolytic protein ClpC1. Details of the binding topology and chemical mode of (inter)action of these cyclopeptides help drive further development of novel potency-optimized entities as tuberculosis drugs. ClpC1 M. tb protein constructs with mutations driving resistance to ECU and RUFI show reduced binding affinity by surface plasmon resonance (SPR). Despite certain structural similarities, ECU and RUFI resistant mutation sites did not overlap in their SPR binding patterns. SPR competition experiments show ECU prevents RUFI binding, whereas RUFI partially inhibits ECU binding. The X-ray structure of the ClpC1-NTD-RUFI complex reveals distinct differences compared to the previously reported ClpC1-NTD-cyclomarin A structure. Surprisingly, the complex structure revealed that the epoxide moiety of RUFI opened and covalently bound to ClpC1-NTD via the sulfur atom of Met1. Furthermore, RUFI analogues indicate that the epoxy group of RUFI is critical for binding and bactericidal activity. Overall, the outcomes demonstrate the significance of ClpC1 as a novel target and the importance of SAR analysis of identified macrocyclic peptides for drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Shock Compression of Fluorapatite to 120 GPa

Apatite is a phosphate mineral relevant to shock metamorphism in planetary materials. Here, we report on the response of natural fluorapatite from Durango, Mexico under shock wave loading between 14.5 and 119.5 GPa. Wave profile measurements were obtained in plate-impact experiments conducted on [0001]-oriented fluorapatite single crystals. To GPa peak stresses, we observed a two-wave structure indicating an elastic-inelastic response with elastic wave amplitudes of 10.5–13.1 GPa. Between 39.1 and 62.1 GPa, a complex wave structure was observed involving the propagation of three waves. At and above 73.7 GPa, only a single shock wave was observed. The data above 73.7 GPa provided the following linear shock velocity – particle velocity relationship: U s = 6.5(2) + 0.78(6) u p , (mm/μs). Above 80 GPa, the densities in the shocked state exceed both the extrapolated 300-K density of fluorapatite and the predicted 300-K density for a mixture of the high-pressure assemblage, tuite and CaF 2 . Furthermore, this result indicates that fluorapatite undergoes a transition to a denser structure under shock loading at these conditions. The shock response of fluorapatite is observed to be similar to enstatite but stiffer than quartz and albite at the stresses examined in this work.

58 GEOSCIENCES↗
DOE OSTI2017

Cluster formation in precompound nuclei in the time-dependent framework

Background: Modern applications of nuclear time-dependent density functional theory (TDDFT) are often capable of providing quantitative description of heavy ion reactions. However, the structures of precompound (preequilibrium, prefission) states produced in heavy ion reactions are difficult to assess theoretically in TDDFT as the single-particle density alone is a weak indicator of shell structure and cluster states. Purpose: We employ the time-dependent nucleon localization function (NLF) to reveal the structure of precompound states in nuclear reactions involving light and medium-mass ions. We primarily focus on spin saturated systems with N = Z . Furthermore, we study reactions with oxygen and carbon ions, for which some experimental evidence for α clustering in precompound states exists. Method: We utilize the symmetry-free TDDFT approach with the Skyrme energy density functional UNEDF1 and compute the time-dependent NLFs to describe 16 O + 16 O, 40 Ca + 16 O, 40 Ca + 40 Ca , and 16,18 O + 12 C collisions at energies above the Coulomb barrier. Results: We show that NLFs reveal a variety of time-dependent modes involving cluster structures. For instance, the 16 O + 16 O collision results in a vibrational mode of a quasimolecular α - 12 C - 12 C- α state. For heavier ions, a variety of cluster configurations are predicted. For the collision of 16,18 O + 12 C, we showed that the precompound system has a tendency to form α clusters. This result supports the experimental findings that the presence of cluster structures in the projectile and target nuclei gives rise to strong entrance channel effects and enhanced α emission. Conclusion: The time-dependent nucleon localization measure is a very good indicator of cluster structures in complex precompound states formed in heavy-ion fusion reactions. Finally, the localization reveals the presence of collective vibrations involving cluster structures, which dominate the initial dynamics of the fusing system.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Heavy Anionic Complex Creates a Unique Water Structure at a Soft Charged Interface

Ion hydration and interfacial water play crucial roles in numerous phenomena ranging from biological to industrial systems. Although biologically relevant (and mostly smaller) ions have been studied extensively in this context, very little experimental data exist about molecular scale behavior of heavy ions and their complexes at interfaces, especially under technologically significant conditions. It has recently been shown that PtCl 6 2- complexes adsorb at positively charged interfaces in a two-step process that cannot fit into well-known empirical trends, such as Hofmeister series (J. Phys. Chem. C, 121, 25377). Here, a combined vibrational sum frequency generation and molecular dynamics study reveals that a unique interfacial water structure is connected to this peculiar adsorption behavior. A novel sub-ensemble analysis of MD simulation results show that after adsorption, PtCl 6 2- complexes partially retain their first and second hydration spheres, and it is possible to identify three different types of water molecules around them based on their orientational structures and hydrogen bonding strengths. These results have important implications for relating interfacial water structure and hydration enthalpy to the general understanding of specific ion effects. This in turn influences interpretation of heavy metal ion distribution across and reactivity within, liquid interfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

The three cellulose synthase isoforms for secondary cell wall make specific contributions to microfibril synthesis

Cellulose is synthesized at the plasma membrane by the cellulose synthase complex, a structure that contains three distinct isoforms of the catalytic subunit, cellulose synthase A (CESA). The division into three subunits appears early in land plant evolution and is highly conserved, particularly for the secondary cell wall. However, what if any unique roles each isoform plays in the complex remain unclear. Here, we assessed the contributions of specific isoforms to microfibril synthesis. First, we expressed CESA isoforms of the primary cell wall or the moss Physcomitrium patens in Arabidopsis thaliana backgrounds missing a secondary cell wall CESA. While the primary cell wall isoforms rescued the cesa knockout phenotype with partial isoform specificity, those from the moss rescued with fewer restrictions. Then, we recreated various CESA missense mutations in all three of the secondary cell wall isoforms; while results are consistent with isoform specificity, they are difficult to interpret further without molecular structures. Finally, we show that catalytically inactive CESA isoforms restore growth and cellulose content in the corresponding knockout in an isoform-specific manner; along with partial rescue of the growth and cellulose content of the inflorescence stem, the replacement lines have fiber cells with partially disorganized microfibrils and secondary cell wall cellulose with narrow crystal width. Generally, effects were more pronounced in lines where CESA8 was inactivated compared with inactivating CESA4 or 7, which tended to have similar phenotypes to each other. Here, we account for these results with a model for cellulose synthase structure with the isoforms assigned specific localization within the cellulose synthase complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The highly disordered Zintl phase Ca 10 GdCdSb 9 – New example of a p-type semiconductor with remarkable thermoelectric properties

Ca 10 GdCdSb 9 is a new Zintl phase with a large unit cell volume (~2500 Å 3 ) and a very complex, disordered structure, which can drive the realization of ultralow thermal conductivity in this material. The measured Seebeck coefficient, α, for single-crystalline Ca 10 GdCdSb 9 approaches 350 μV/K at 600 K. The experimentally determinedelectrical resistivity of Ca 10 GdCdSb 9 is very low, leading to a remarkably high-power factor PF of 23.2 μW/cm·K 2 at 460 K. Furthermore, the extraordinary PF value in this material, higher than those of the currently known state-of-the-art materials within the same temperature range, suggests that the Ca 10 RECdSb 9 material system (RE = rare earth metal) could serve as a viable playground to harnessing new efficient thermoelectric generators.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Crystal structure of E. coli ZinT with one zinc-binding mode and complexed with citrate

Highlights: • Crystal structure of E. coli ZinT complexed with citrate in one zinc-binding mode. • The bound zinc shows octahedral coordination by histidine residues and citrate. • EcZinT exists as a monomer in solution in the absence and presence of zinc ions. The ZnuABC ATP-binding cassette transporter found in gram-negative bacteria has been implicated in ensuring adequate zinc import into Zn(II)-poor environments. ZinT is an essential component of ZnuABC and contributes to metal transport by transferring metals to ZnuA, which delivers them to ZnuB in periplasmic zinc recruitment. Although several structures of E. coli ZinT have been reported, its zinc-binding sites and oligomeric state have not been clearly identified. Here, we report the crystal structure of E. coli ZinT at 1.76 Å resolution. This structure contains one zinc ion in its calycin-like domain, and this ion is coordinated by three highly conserved histidine residues (His167, His176 and His178). Moreover, three oxygen atoms (O{sub 1}, O{sub 6} and O{sub 7}) from the citrate molecule interact with zinc, giving the zinc ion stable octahedral coordination. Our EcZinT structure shows the fewest zinc ions bound of all reported EcZinT structures. Crystallographic packing and size exclusion chromatography suggest that EcZinT prefers to form monomers in solution. Our results provide insights into the molecular function of ZinT.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Imaging the short-lived hydroxyl-hydronium pair in ionized liquid water

The radiolysis of water is ubiquitous in nature and plays a critical role in numerous biochemical and technological applications. Although the elementary reaction pathways for the ionized water have been studied, the short-lived intermediate complex and structural dynamic response after the proton transfer reaction remain poorly understood. Here, using liquid-phase ultrafast electron diffraction technique to measure the intermolecular O··O and O··H bonds, we captured the short-lived radical-cation complex OH(H 3 O + ) that was formed within 140 femtoseconds through a direct oxygen-oxygen bond contraction and proton transfer, followed by the radical-cation pair dissociation and the subsequent structural relaxation of water within 250 femtoseconds. These measurements provide direct evidence of capturing this metastable radical-cation complex before separation, thereby improving our fundamental understanding of elementary reaction dynamics in ionized liquid water.

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

A high-pressure Raman study of FeTiO 3 ilmenite: Fermi resonance as a manifestation of Fe-Ti charge transfer

In this work, we investigated the 300 K high-pressure behavior of ilmenite using Raman spectroscopy to 54 GPa. Upon compression, we observe a Fermi resonance between the lowest frequency A g symmetry peaks (ν 4 and ν 5 ) between ~ 10 and ~ 30 GPa: bands that involve major components of Ti–O and Fe–O-related displacements, respectively. The peaks’ relative intensities switch at ~ 18 GPa and they also reach their minimum separation at ~ 20 GPa, indicating that their maximum resonance occurs between 18 and 20 GPa. The negative shift of the Ti–O-associated ν 4 vibration under compression is fully consistent with a shift in valence of Ti from 4 + to 3 + under compression. Anomalously small mode shifts of other, more localized vibrations are also consistent with a charge transfer from Fe to Ti under compression. At higher pressures, we have not found definitive evidence for a transition to the perovskite-structure at 300 K, which has been well characterized at high pressures and temperatures. At 40 GPa, we observe an apparent reversible disordering that persists up to our highest pressure. The 300 K mode shifts of the Raman active modes in FeTiO 3 under pressure are notably different from those of other ABO 3 compounds (where A = Mg, Mn and B = Ti, Si); in other ilmenite-structured compounds, the peaks shift at a faster rate and there has not been any observation of Fermi resonance. Thus, iron’s complex electronic structure, and its charge transfer with titanium, appears to play a primary role in the behavior of phonons in FeTiO 3 ilmenite.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Human cytochrome P450 17A1 structures with metabolites of prostate cancer drug abiraterone reveal substrate-binding plasticity and a second binding site

Abiraterone acetate is a first-line therapy for castration-resistant prostate cancer. This prodrug is deacetylated in vivo to abiraterone, which is a potent and specific inhibitor of cytochrome P450 17A1 (CYP17A1). CYP17A1 performs two sequential steps that are required for the biosynthesis of androgens that drive prostate cancer proliferation, analogous to estrogens in breast cancer. Abiraterone can be further metabolized in vivo on the steroid A ring to multiple metabolites that also inhibit CYP17A1. Despite its design as an active-site-directed substrate analog, abiraterone and its metabolites demonstrate mixed competitive/noncompetitive inhibition. To understand their binding, we solved the X-ray structures of CYP17A1 with three primary abiraterone metabolites. Despite different conformations of the steroid A ring and substituents, all three bound in the CYP17A1 active site with the steroid core packed against the I helix and the A ring C3 keto or hydroxyl oxygen forming a hydrogen bond with N202 similar to abiraterone itself. The structure of CYP17A1 with 3-keto, 5α-abiraterone was solved to 2.0 Å, the highest resolution to date for a CYP17A1 complex. This structure had additional electron density near the F/G loop, which is likely a second molecule of the inhibitor and which may explain the noncompetitive inhibition. Mutation of the adjacent Asn52 to Tyr positions its side chain in this space, maintains enzyme activity, and prevents binding of the peripheral ligand. Collectively, our findings provide further insight into abiraterone metabolite binding and CYP17A1 function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Bismuth as a Reactive Solvent in the Synthesis of Multicomponent Transition-Metal-Bearing Bismuthides

Employment of liquid bismuth (Bi) allows the facile single-crystal growth of compounds containing elements with high melting points, provided that these elements have reasonably high solubility in Bi. Utilization of the Bi flux approach yielded two new ternary bismuthides, SrNi 0.17(1) Bi 2 [a defect variant of the BaCuSn 2 type, space group Cmcm , α = 4.879(2) Å, b = 17.580(6) Å, and c = 4.696(2) Å] and CaTi 3 Bi 4 [NdTi 3 (Sn 0.1 Sb 0.9 ) 4 structure type, space group Fmmm , a = 5.6295(7) Å, b = 9.8389(1) Å, and c = 23.905(3) Å]. In addition, the ternary antimonide CaV3Sb4, isostructural with CaTi 3 Bi 4 , was synthesized from antimony (Sb) flux, and analyzed with the goal of validating structural assessment of the bismuthide analogue, where the X-ray crystallographic work proved to be very challenging. All synthesized compounds exhibit complex crystal structures featuring quasi-two-dimensional building blocks of different topologies. First-principle calculations reveal hypervalent bonding in the homoatomic Bi subunits. Lastly, physical property measurements indicate metallic conductivity and the absence of localized magnetism in the studied compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2018

NMR Methodologies for the Detection and Quantification of Nanostructural Defects in Silicone Networks

Here, we present and discuss a sensitive spectroscopic means of detecting and quantifying network defects within a series of polysiloxane elastomers through a novel application of 19F solution state nuclear magnetic resonance (NMR). Polysiloxanes are the most utilized non-carbon polymeric material today. Their final network structure is complex, hierarchical, and often ill-defined due to modification. Characterization of these materials with respect to starting and age-dependent network structure is obfuscated by the intractable nature of polysiloxane network elastomers. We report a synthetic strategy for selectively tagging chain-end silanols with an organofluorine compound, which may then be conveniently and quantitatively measured as a function of structure and environment by means of 19 F NMR. This study represents a new and sensitive means of directly quantifying aspects of network architecture in polysiloxane materials and has the potential to be a powerful new tool for the spectroscopic assessment of structural dynamic response in polysiloxane networks.

36 MATERIALS SCIENCE↗