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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Theoretical search for possible Li–Ni–B crystal structures using an adaptive genetic algorithm

The structural diversity of rare-earth and transition metal borides indicates that alkali-transition metal borides (A-T-B) show tremendous promise in exhibiting a variety of crystal structures with different dimensionalities of T-B frameworks. On the other hand, the A-T-B ternary systems are severely underexplored because of the synthetic challenges associated with their preparation. Accurate and efficient computational predictions of low-energy stable and metastable phases can identify the optimal compositions of the hypothetical compounds in the A-T-B systems to guide the synthesis. As such, in this work, we have computationally discovered several new phases in the Li–Ni–B ternary system. The newly discovered LiNiB, Li 2 Ni 3 B, and Li 2 NiB phases expand the existing theoretical database, and the convex-hull surface of Li–Ni–B has been re-constructed. The lowest energy structure of the LiNiB compound has been found by an adaptive genetic algorithm with layered motif, which matches with the experimentally determined structure. According to our electrochemical calculations, LiNiB and another predicted layered Li 2 NiB compounds have great potential as anode materials for lithium batteries. The Li 2 Ni 3 B compound with the space group P4 3 32 was predicted to crystallize in a cubic structure composed of distorted octahedral units of BNi 6 , which is isostructural to two noncentrosymmetric superconductors Li 2 Pd 3 B and Li 2 Pt 3 B. While we were unable to experimentally confirm the Li 2 Ni 3 B compound utilizing the hydride synthetic route, attempts to synthesize this compound by alternate methods remain highly desirable, considering its potential superconducting properties.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Crystal structures and comparisons of potassium rare-earth molybdates KRE(MoO 4 ) 2 (RE = Tb, Dy, Ho, Er, Yb, and Lu)

Six potassium rare-earth molybdates KRE(MoO 4 ) 2 (RE = Tb, Dy, Ho, Er, Yb, and Lu) were synthesized by flux-assisted growth in K 2 Mo 3 O 10 . The crystal structures were determined using single-crystal X-ray diffraction data. The synthesized molybdates crystallize with the orthorhombic Pbcn space group (No. 60). Trendlines for unit-cell parameters were calculated using data from the current study. The unit-cell parameters a and c increase linearly whereas b decreases with larger RE cations, based on crystal radii. The unit-cell volumes increase linearly and the densities decrease linearly with larger RE cations. The average distances between the RE cations and the nearest O atoms increase with larger cations whereas the average distances of Mo—O and K—O do not show specific trends.

36 MATERIALS SCIENCE↗
DOE OSTI2023

High Layer Number ( n = 1–6) 2D Ruddlesden–Popper Lead Bromide Perovskites: Nanosheets, Crystal Structure, and Optoelectronic Properties

2D Ruddlesden–Popper (RP) lead halide perovskites have highly tunable structures, compositions, and properties that enable their promising optoelectronic applications. Among various 2D halide perovskites, the materials chemistry and fundamental optoelectronic properties of high layer number (n) lead-bromide RP perovskites, where n refers to the number of inorganic octahedra layers, have been less studied. Here, we report the synthesis of thin nanosheets of (PEA) 2 Cs n–1 Pb n Br 3n+1 (n = 1–6, PEA = phenylethylammonium) perovskites and study the optical properties, assigning photoluminescence emissions of 486, 496, and 505 nm to n = 4–6 phases, respectively, and reporting the photoluminescence lifetimes. Furthermore, the crystal structure of (PEA) 2 Cs 2 Pb 3 Br 10 was determined to reveal minimal octahedral structural distortions. Ultraviolet photoelectron spectroscopy measurements reveal the positioning of the valence and conduction bands for n = 1–3 phases and confirm the type-I band alignment for the (PEA) 2 Cs n–1 Pb n Br 3n+1 series, laying the foundation for rational heterostructure device design in the future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding

Cobalamin riboswitches encompass a structurally diverse group of cis-acting, gene regulatory elements found mostly in bacterial messenger RNA and are classified into subtypes based on secondary and tertiary characteristics. An unusual variant of the cobalamin riboswitch with predicted structural features was identified in Bacillus subtilis over a decade ago, but its structure and mechanisms of cobalamin selectivity and translational control have remained unsolved. We present the crystal structure of the aptamer domain of this atypical cobalamin riboswitch and a model for the complete riboswitch, including its expression platform domain. We demonstrate that this riboswitch binds to multiple cobalamin derivatives and correlate its promiscuous behavior to its structure and unique arrangement of peripheral elements. Comparative structural analyses between conventional cobalamin riboswitches and the B. subtilis cobalamin riboswitch reveal that the likely basis for this promiscuous ligand binding is intrinsic structural adaptability encoded in the RNA structure. It suggests that cobalamin selectivity might ultimately be viewed as existing on a spectrum of affinity for each derivative rather than as belonging to distinct types based on ligand specificities. Our work provides an interesting and notable example of functional coupling of ligand-sensing and adaptive folding by a structured RNA molecule.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structures of OrfX1, OrfX2 and the OrfX1–OrfX3 complex from the orfX gene cluster of botulinum neurotoxin E1

Botulinum neurotoxins (BoNTs) are among the most lethal toxins known to humans, comprising seven established serotypes termed BoNT/A–G encoded in two types of gene clusters (ha and orfX) in BoNT-producing clostridia. The ha cluster encodes four non-toxic neurotoxin-associated proteins (NAPs) that assemble with BoNTs to protect and enhance their oral toxicity. However, the structure and function of the orfX-type NAPs remain largely unknown. Here, we report the crystal structures for OrfX1, OrfX2, and an OrfX1–OrfX3 complex, which are encoded in the orfX cluster of a BoNT/E1-producing Clostridium botulinum strain associated with human foodborne botulism. These structures lay the foundation for future studies on the potential roles of OrfX proteins in oral intoxication and pathogenesis of BoNTs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The crystal structure of Vibrio cholerae (6-4) photolyase reveals interactions with cofactors and a DNA-binding region

Photolyases (PLs) reverse UV-induced DNA damage using blue light as an energy source. Of these PLs, (6-4) PLs repair (6-4)-lesioned photoproducts. We recently identified a gene from Vibrio cholerae (Vc) encoding a (6-4) PL, but structural characterization is needed to elucidate specific interactions with the chromophore cofactors. Here, we determined the crystal structure of Vc (6-4) PL at 2.5 Å resolution. Our high-resolution structure revealed that the two well-known cofactors, flavin adenine dinucleotide and the photoantenna 6,7-dimethyl 8-ribityl-lumazin (DMRL), stably interact with an α-helical and an α/β domain, respectively. Additionally, the structure has a third cofactor with distinct electron clouds corresponding to a [4Fe-4S] cluster. Moreover, we identified that Asp106 makes a hydrogen bond with water and DMRL, which indicates further stabilization of the photoantenna DMRL within Vc (6-4) PL. Further analysis of the Vc (6-4) PL structure revealed a possible region responsible for DNA binding. The region located between residues 478 to 484 may bind the lesioned DNA, with Arg483 potentially forming a salt bridge with DNA to stabilize further the interaction of Vc (6-4) PL with its substrate. Our comparative analysis revealed that the DNA lesion could not bind to the Vc (6-4) PL in a similar fashion to the Drosophila melanogaster (Dm, (6-4)) PL without a significant conformational change of the protein. The 23rd helix of the bacterial (6-4) PLs seems to have remarkable plasticity, and conformational changes facilitate DNA binding. In conclusion, our structure provides further insight into DNA repair by a (6-4) PL containing three cofactors.

(6-4) lesioned photoproduct↗
DOE OSTI2020

Ammonothermal Synthesis, Crystal Structure, and Vibrational Properties of the Doubly Deprotonated Calcium Guanidinate, CaC(NH) 3

We report the synthesis of the doubly deprotonated calcium guanidinate, CaC(NH) 3 , from liquid ammonia and its crystal structure as determined from powder X‐ray and neutron diffraction, and confirmed using CNH elemental analysis and infrared (IR) spectroscopy data. CaC(NH) 3 crystallizes in the hexagonal system with space group P 6 3 / m (no. 176) with Z = 2 and a = 5.2666(13) Å, c = 6.5881(6) Å and V = 158.25(4) Å 3 . We also compare the structural similarities and differences of this phase with the isotypical strontium and ytterbium compounds.

Ogutu, George↗
DOE OSTI2020

Synthesis, Crystal Structure, and Cooperative 3d–5d Magnetism in Rock Salt Type Li 4 NiOsO 6 and Li 3 Ni 2 OsO 6

Two new transition metal oxides with the nominal chemical compositions of Li 4 NiOsO 6 and Li 3 Ni 2 OsO 6 were successfully synthesized. Both compounds crystallize in an ordered rock salt structure type in the monoclinic C2/m space group. The crystal structures were determined using both synchrotron X-ray and time-of-flight neutron, powder diffraction data. In both phases, Ni2+ ions are present while oxidation states of osmium are +6 and +5 in Li 4 NiOsO 6 and Li 3 Ni 2 OsO 6 , respectively. Ni2+ ions in the hypothetical fully ordered phase form a honeycomb arrangement in the ab crystallographic plane and these hexagons are centered by osmium ions. Furthermore, the magnetic layers are separated along the c axis by the octahedra, which are centered by Li+ (or Li+/Ni 2+ , depending on the chemical compositions). Crystal structure refinements reveal that there is some degree of mixed occupancy in cationic positions. Temperature dependent magnetic susceptibility data for both phases show ferrimagnetic transitions with predominant antiferromagnetic (AFM) interactions among 3d electrons of nickel and Sd electrons of osmium. Iso-thermal magnetization loops as a function of the applied magnetic field below the transition temperatures confirm the ferrimagnetic nature in magnetic transitions. Temperature dependent heat capacity data, however, did not exhibit any anomaly in either phase, indicating the absence of long-range magnetic ordering. The lack of long-range order for both Os 5+ and Os 6+ -based compounds was also confirmed by low temperature neutron diffraction data down to 10 K. Temperature dependent AC magnetic susceptibility data in various frequencies for both samples indicate that Li 4 NiOsO 6 exhibits spin-glass-like behavior, while the transition temperature for Li 3 Ni 2 OsO 6 is nearly frequency independent.

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

Crystal structure and magnetic properties of Gd 8 Mn 3 Sb 19

Here, in this study, a novel magnetic semimetal compound, Gd 8 Mn 3 Sb 19 , was synthesized successfully via high-temperature solid-state reaction. The crystal structure of Gd 8 Mn 3 Sb 19 was determined using both single crystal and powder X-ray diffraction techniques, revealing a non-centrosymmetric orthorhombic space group, Pmn2 1 (No. 31). The Sb atoms in Gd 8 Mn 3 Sb 19 form five-atom-wide Sb 5 7− ribbons, narrower three-atom-wide Sb 3 5− ribbons, and single Sb 3− anions. On the other hand, both Gd 3+ and Mn 2+ ions form the distorted Gd 3 and Mn 3 triangular lattices, respectively. The magnetic measurements suggest the complex magnetic interactions contributed by both Gd 3+ and Mn 2+ ions. A sharp peak observed in the magnetic susceptibility plot at approximately 25 K corresponds to the antiferromagnetic-type transition in Gd 8 Mn 3 Sb 19 . Furthermore, the magnetic measurements along different directions indicate the strong magnetic anisotropy present in Gd 8 Mn 3 Sb 19 , which is likely due to the complex magnetic interactions arising from the existence of Gd and Mn ions. Finally, the electrical resistivity measurements of Gd 8 Mn 3 Sb 19 indicate semimetallic behavior with a positive magnetoresistance.

Chemistry↗
DOE OSTI2022

Two distinct rotations of bithiazole DNA intercalation revealed by direct comparison of crystal structures of Co(III)•bleomycin A 2 and B 2 bound to duplex 5'-TAGTT sites

Bleomycins constitute a family of anticancer natural products that bind DNA through intercalation of a C-terminal tail/bithiazole moiety and hydrogen-bonding interactions between the remainder of the drug and the minor groove. The clinical utility of the bleomycins is believed to result from single- and double-strand DNA cleavage mediated by the HOO-Fe(III) form of the drug. The bleomycins also serve as a model system to understand the nature of complex drug-DNA interactions that may guide future DNA-targeted drug discovery. In this study, the impact of the C-terminal tail on bleomycin-DNA interactions was investigated. Toward this goal, we determined two crystal structures of HOO-Co(III)•BLMA 2 “green” (a stable structural analogue of the active HOO-Fe(III) drug) bound to duplex DNA containing 5'-TAGTT, one in which the entire drug is bound (fully bound) and a second with only the C-terminal tail/bithiazole bound (partially bound). The structures reported here were captured by soaking HOO-Co(III)•BLMA 2 into preformed host–guest crystals including a preferred DNA-binding site. While the overall structure of DNA-bound BLMA 2 was found to be similar to those reported earlier at the same DNA site for BLMB 2 , the intercalated bithiazole of BLMB 2 is “flipped” 180° relative to DNA-bound BLMA 2 . Further, this finding highlights an unidentified role for the C-terminal tail in directing the intercalation of the bithiazole. In addition, these analyses identified specific bond rotations within the C-terminal domain of the drug that may be relevant for its reorganization and ability to carry out a double-strand DNA cleavage event.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Crystal structure of a seven-substitution mutant of hydroxynitrile lyase from rubber tree

The α/β-hydrolase fold superfamily includes esterases and hydroxynitrile lyases which, despite catalyzing different reactions, share a Ser–His–Asp catalytic triad. We report a 1.99 Å resolution crystal structure of HNL6V, an engineered variant of hydroxynitrile lyase fromHevea brasiliensis(HbHNL) containing seven amino-acid substitutions (T11G, E79H, C81L, H103V, N104A, G176S and K236M). The structure reveals that HNL6V maintains the characteristic α/β-hydrolase fold while exhibiting systematic shifts in backbone and catalytic atom positions. Compared with wild-typeHbHNL, the C α positions in HNL6V differ by a mean of 0.2 ± 0.1 Å, representing a statistically significant displacement. Importantly, the catalytic triad and oxyanion-hole atoms have moved 0.2–0.8 Å closer to their corresponding positions in SABP2, although they remain 0.3–1.1 Å from fully achieving the configuration of SABP2. The substitutions also increase local flexibility, particularly in the lid domain covering the active site. This structural characterization demonstrates that targeted amino-acid substitutions can systematically shift catalytic geometries towards those of evolutionarily related enzymes.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Crystal Structure Evolution of UCl 3 from Room Temperature to Melting

We report uranium trichloride (UCl 3 ) is actively researched to develop and improve applications ranging from molten salt reactors to actinide processing, including spent fuel reprocessing. Here, we report for the first time the crystal structure evolution between room temperature and melting point from in situ high-temperature neutron diffraction to quantify, for example, the thermal expansion of the hexagonal a and c lattice parameters. The results are compared with density functional theory calculations. The melting point of UCl 3 is determined by differential scanning calorimetry to be 1108.2 ± 0.2 K.

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

Crystal structure and thermal expansion of Ta 2 ⁢O 5 from neutron diffraction

Tantalum pentoxide (Ta 2 ⁢O 5 ) is a component of technologies ranging from photographic lenses to medical implants. Despite more than six decades of interest, however, there is no consensus on the crystal structure of Ta 2 ⁢O 5 . Here, we report the results of neutron diffraction experiments on Ta 2⁢ O 5 powders at temperatures up to 1000⁢°⁢C. Because neutron diffraction is sensitive to the positions of O atoms in the presence of heavy elements, our results provide strong evidence that the orthorhombic L SR structure can account for experimental observations better than any other proposal in the literature. Here, we also determine the anisotropic crystallographic thermal expansion parameters of Ta 2 ⁢O 5 , which are important for modeling the performance of Ta 2⁢ O 5 -bearing technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Crystal structures of Salmonella enterica FraB deglycase reveal a conformational heterodimer with remarkable structural plasticity at the active site

Abstract Thefralocus ofSalmonella entericaencodes five genes for metabolism of fructose‐asparagine, an Amadori product formed by condensation of asparagine with glucose. In the last step of this pathway, the FraB deglycase cleaves 6‐phospho‐fructose‐aspartate into glucose‐6‐phosphate and aspartate. In homology models, FraB forms a homodimer with two equivalent active sites located at the dimer interface. E214 and H230, two invariant residues essential for catalysis, project into each active site cleft from opposing subunits of the dimer. Here, we have determined six crystal structures of FraB, three of a variant containing an N‐terminal His 6 tag and two mutations needed for crystallization (hereafter referred to as WT′), two with additional mutations to active site residues (E214A and P232A), and one of a variant with C‐terminal residues 313–325 deleted. Surprisingly, in the WT′ FraB structure, the two catalytic residues, E214 (general base) and H230 (general acid), are positioned ~22 Å apart. In the E214A and C‐terminus‐truncated FraB variants, however, a conformational change in the E214‐residing helix brings E214 and H230* to ~7 Å (* indicates residue from the second protomer that creates the inter‐subunit catalytic center). The loop bearing H230 also exhibits significant variation, ranging from being completely disordered to adopting open or closed states, with the nearby P232* residue being eithercisortrans. The C‐terminal residues 313–325 form a flexible “C‐tail” that can be fully disordered, bind in the active site to block access of substrate, or angle across the active site to wrap across the other subunit of the dimer and potentially close over substrate. Collectively, these structures reveal that FraB is a conformational heterodimer with two chemically identical subunits that are constrained to adopt different structures as they come together for catalysis. This plasticity likely involves correlated opening and closure of the two active sites for their respective binding and release of substrates and ligands.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Solid breeder material crystal structure evolution due to Li burn up–Loss of crystal stability

Solid breeder materials for fusion power plants are subjected to extreme conditions of radiation damage, high temperature and designed component burn-up. Here, the loss of lattice stability of Li 2 TiO 3 due to Li burn-up was investigated using first principles-based approaches to aid evaluation of upper limit of component lifetime. The lattice stability is analyzed using calculated phonon dispersion in the Li 2 TiO 3 supercell, while Li burn-up is modeled by the introduction of Li-vacancies. It has been determined that the studied ceramic can be structurally stable up to ~40% of Li atoms burn-up. At 50% burn-up, the negative frequency branch in the phonon dispersion spectrum appears indicating the loss of lattice dynamical stability. Moreover, the structure obtained by introduction of unstable frozen phonons with minima energy amplitude also results in a phonon dispersion with negative branches in the structure obtained. Therefore, the system completely loses stability when approximately half of Li atoms are consumed.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Combinatorial screening of crystal structure in Ba-Sr-Mn-Ce perovskite oxides with ABO 3 stoichiometry

ABO 3 oxides with the perovskite-related structures are attracting significant interest due to their promising physical and chemical properties for many applications requiring tunable chemistry, including fuel cells, catalysis, and electrochemical water splitting. Here we report on the crystal structure of the entire family of perovskite oxides with ABO 3 stoichiometry, where A and B are Ba, Sr, Mn, Ce. Given the vast size of this chemically complex material system, exploration for stable perovskite-related structures with respect to its constituent elements and annealing temperature is performed by combinatorial pulsed laser deposition and spatially-resolved characterization of composition and structure. As a result of this high-throughput experimental study, we identify hexagonal perovskite-related polytypic transformation as a function of composition in the Ba 1-x Sr x MnO 3 oxides after annealing at different temperatures. Furthermore, a hexagonal perovskite-related polytype is observed in a narrow composition-temperature range of the Ba 1-x Sr x MnO 3 oxides. In contrast, a tetragonally-distorted perovskite is observed across a wider range of compositions and annealing temperatures in the Sr 1-x Ce x MnO 3 oxides. This structure stability is further enhanced along the Ba 1-x Sr x MnO 3 - Sr 1-x Ce x MnO 3 pseudo-binary tie-line at x=0.25 by increasing Ba-incorporation and annealing temperature. These results indicate that the BaCe x Mn 1-x O 3 - Sr 1-x Ce x MnO 3 pseudo-binary oxide alloys (solid solutions) with tetragonal perovskite structure and broad composition-temperature range of stability are promising candidates for thermochemical water splitting applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Crystal Structures of Diaryl Hydrazone and Sulfone Stabilizers in Complex with an Amyloidogenic Light Chain Reveal an Alternate Ligand‐Binding Cavity

Abstract Stabilization of amyloidogenic immunoglobulin light chains (LCs) by binding of small molecule “kinetic stabilizers” is under development as a novel treatment for light chain amyloidosis. From a high‐throughput screen, we previously identified 16 full‐length (FL) LC stabilizers from five distinct chemotypes. We then obtained structural biological information on two classes of hits, coumarins and hydantoins, revealing that both chemotypes bind to a pocket at the V L −V L interface of the FL LC dimer. Here, we report crystal structures of three screening hits from two other chemotypes, diaryl hydrazones and sulfones, in complex with an amyloidogenic FL LC. While two of these hits bind to the previously identified pocket, one diaryl hydrazone binds to a different pocket bisected by the C 2 symmetry axis of the dimer. These data further expand on the FL LC stabilizer‐binding surface that could be used in design of more potent FL LC aggregation inhibitors.

Chemistry↗
DOE OSTI2020

The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold

Exoribonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.

59 BASIC BIOLOGICAL SCIENCES↗