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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Dehydration synthesis and crystal structure of terbium oxychloride, TbOCl

Terbium oxychloride, TbOCl, was synthesized via a simple heat-treatment of TbCl3·6H2O. The structure was determined using X-ray powder diffraction (XRD) data. The TbOCl compound crystallizes within the tetragonal P4/nmm space group, and its crystal structure is composed of alternating layers of (TbO)n and n Cl- anions. The unit cell parameters, volume, and density were compared to the literature data of other isostructural rare-earth oxychlorides in the P4/nmm space group and showed a good agreement when fitted to the calculated trendlines.

oxychloride, rare-earth oxyhalide, powder diffract↗
DOE OSTI2021

Construction, characterization and crystal structure of a fluorescent single-chain Fv chimera

In vitro display technologies based on phage and yeast have a successful history of selecting single-chain variable fragment (scFv) antibodies against various targets. However, single-chain antibodies are often unstable and poorly expressed in Escherichia coli. Here, we explore the feasibility of converting scFv antibodies to an intrinsically fluorescent format by inserting the monomeric, stable fluorescent protein named thermal green, between the light- and heavy-chain variable regions. Our results show that the scTGP format maintains the affinity and specificity of the antibodies, improves expression levels, allows one-step fluorescent assay for detection of binding and is a suitable reagent for epitope binning. We also report the crystal structure of an scTGP construct that recognizes phosphorylated tyrosine on FcεR1 receptor of the allergy pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Influence of Annealing and Composition on the Crystal Structure of Mixed-Halide, Ruddlesden–Popper Perovskites

Mixed-halide two-dimensional (2D) hybrid organic–inorganic perovskites offer an important opportunity to control the band gap for applications in optoelectronic devices. In this study, we focus on phenethylammonium lead halide [(PEA) 2 Pb(I 1– x Br x ) 4 ] films, the pure iodide form of which is one of the most widely studied optically active 2D perovskite systems. Resonant infrared, matrix-assisted pulsed laser evaporation is used to grow films to explore the effects of post-growth annealing and mixed-halide composition. The composition, crystal structure, and optical properties are studied for as-grown and annealed films of (PEA) 2 Pb(I 1– x Br x ) 4 for x = 0, 0.25, 0.5, 0.75, and 1. First-principles calculations are used in conjunction with the experimental data to explain the mixed-halide behavior that does not trend monotonically with the bromide content. Important results of this work are as follows: (i) X-ray diffraction reveals evidence for halide phase separation around x = 0.25, consistent with first-principles calculations, whereas no phase separation is observed for x = 0.5 and above and (ii) a unique photoluminescence (PL) peak splitting is observed for x = 0.75, a composition for which no compositional phase separation is observed. The PL splitting is tentatively explained by the coexistence of two distinct types of halide short-range ordering at x = 0.75. Overall, this study demonstrates that mixed-halide n = 1 Ruddlesden–Popper perovskites are not simple random alloys but that instead, they display distinct sites and ordering preferences of the different halide anions. These preferences are critical to understand and rationally tune the properties of the materials.

36 MATERIALS SCIENCE↗
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↗
NASA NTRS1995

Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere

In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.

NASA Discipline Exobiology↗
NASA NTRS1973

Elasticity of some mantle crystal structures. II.

The single-crystal elastic constants are determined as a function of pressure and temperature for rutile structure germanium dioxide (GeO2). The data are qualitatively similar to those of rutile TiO2 measured by Manghnani (1969). The compressibility in the c direction is less than one-half that in the a direction, the pressure derivative of the shear constant is negative, and the pressure derivative of the bulk modulus has a relatively high value of about 6.2. According to an elastic strain energy theory, the negative shear modulus derivative implies that the kinetic barrier to diffusion decreases with increasing pressure.

Wang, H.↗
NASA NTRS1993

Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes

We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

NASA Discipline Number 52-20↗
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↗
NASA NTRS1999

Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot

Many viruses regulate translation of polycistronic mRNA using a -1 ribosomal frameshift induced by an RNA pseudoknot. A pseudoknot has two stems that form a quasi-continuous helix and two connecting loops. A 1.6 A crystal structure of the beet western yellow virus (BWYV) pseudoknot reveals rotation and a bend at the junction of the two stems. A loop base is inserted in the major groove of one stem with quadruple-base interactions. The second loop forms a new minor-groove triplex motif with the other stem, involving 2'-OH and triple-base interactions, as well as sodium ion coordination. Overall, the number of hydrogen bonds stabilizing the tertiary interactions exceeds the number involved in Watson-Crick base pairs. This structure will aid mechanistic analyses of ribosomal frameshifting.

Non-NASA Center↗