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At least 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Crystal Structure of an Anisotropic Pyrope Garnet That Contains Two Cubic Phases

The crystal structure of two different samples of pyrope garnet, ideally Mg 3 Al 2 Si 3 O 12 , from South Africa was refined using the Rietveld method, space group Ia3¯d, and monochromatic synchrotron high-resolution powder X-ray diffraction (HRPXRD) data. Sample 1 from Wesselton Mine is a single cubic phase and is optically isotropic. Electron-probe microanalysis (EPMA) provided an average composition {Mg 2.30 Fe 2+ 0.26 Ca 0.42 Mn 2+ 0.02 } Σ3 [Al 1.53 Fe 3+ 0.06 Cr 3+ 0.40 Ti 4+ 0.01 Fe 2+ 0.01 ] Σ2 Si 3 O 12 , which contains a significant amount of Cr cations. The unit-cell parameter (Å) and bond distances (Å) are a = 11.56197(1) Å, average = 2.2985, Al-O = 1.9101(4), and Si-O = 1.6343(3) Å. Sample 2 from De Beers Diamond Mine has an average composition {Mg 2.33 Fe 2+ 0.33 Ca 0.33 Mn 2+ 0.01 } Σ3 [Al 1.73 Fe 3+ 0.12 Cr 3+ 0.06 Ti 4+ 0.05 Fe 2+ 0.05 ] Σ2 Si 3 O 12 and is a fine-scale intergrowth of two cubic phases. The weight percentage, unit-cell parameter (Å), and bond distances (Å) for phase 2a are 62.2(1)%, a = 11.56185(1) Å, average = 2.3006, Al-O = 1.9080(4), Si-O = 1.6334(4) Å. The corresponding values for phase 2b are 37.8(1)%, a = 11.53896(1) Å, average = 2.2954, Al-O = 1.9020(6), Si-O = 1.6334(6) Å. The two cubic phases in sample 2 cause the crystal to be optically anisotropic because of strain induce birefringence. The unit-cell parameter and bond distances for sample 1 are similar to those in phase 2a.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Synthesis of Zn2NbN3 ternary nitride semiconductor with wurtzite-derived crystal structure

Binary III-N nitride semiconductors with wurtzite crystal structure such as GaN and AlN have been long used in many practical applications ranging from optoelectronics to telecommunication. The structurally related ZnGeN2 or ZnSnN2 derived from the parent binary compounds by cation mutation (elemental substitution) have recently attracted attention, but such ternary nitride materials are mostly limited to II-IV-N2 compositions. This paper demonstrates synthesis and characterization of zinc niobium nitride (Zn2NbN3) – a previously unreported II2-V-N3 ternary nitride semiconductor. The Zn2NbN3 thin films are synthesized using a one-step adsorption-controlled growth, and a two-step deposition/annealing method that suppresses the loss of Zn and N. Measurements indicate that this sputtered Zn2NbN3 crystalizes in cation-disordered wurtzite-derived structure, in contrast to chemically related rocksalt-derived Mg2NbN3 compound, also synthesized here for comparison using the two-step method. The estimated wurtzite lattice parameter ratio of Zn2NbN3 is 1.55, and the optical absorption onset is at 2.1 eV. Both of these values are lower compared to published Zn2NbN3 computational values of c/a = 1.62 and Eg = 3.5 - 3.6 eV. Additional theoretical calculations indicate that this difference is due to cation disorder in experimental samples, suggesting a way to tune the structural parameters and the resulting properties of heterovalent ternary nitride materials. Overall, this work expands the wurtzite family of nitride semiconductors to include Zn2NbN3, and suggests that related II2-V-N3 and other ternary nitrides should be possible to synthesize.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2013

The crystal structure of human protein α1M reveals a chromophore-binding site and two putative protein–protein interfaces

Highlights: •We determined the first structure of human α1M with heavy electron density of the chromophore. •We proposed a new structural model of the chromophore. •We first revealed that the two conserved surface regions of α1M are proposed as putative protein–protein interface sites. -- Abstract: Lipocalin α1-microglobulin (α1M) is a conserved glycoprotein present in plasma and in the interstitial fluids of all tissues. α1M is linked to a heterogeneous yellow–brown chromophore of unknown structure, and interacts with several target proteins, including α1-inhibitor-3, fibronectin, prothrombin and albumin. To date, there is little knowledge about the interaction sites between α1M and its partners. Here, we report the crystal structure of the human α1M. Due to the crystallization occurring in a low ionic strength solution, the unidentified chromophore with heavy electron density is observed at a hydrophobic inner tube of α1M. In addition, two conserved surface regions of α1M are proposed as putative protein–protein interface sites. Further study is needed to unravel the detailed information about the interaction between α1M and its partners.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Synthesis, crystal structure and magnetic properties of a new B-site ordered double perovskite Sr{sub 2}CuIrO{sub 6}

Here we synthesize and characterize a new double-perovskite oxide Sr{sub 2}CuIrO{sub 6}. The synthesis requires the use of high oxygen pressure to stabilize the VI oxidation state of iridium. The compound has a tetragonally-distorted crystal structure due to the Jahn–Teller active Cu{sup II} ion, and a high degree of B-site cation order. Magnetic transition is apparent at 15 K, but the zero-field-cooled and field-cooled susceptibilities diverge below this temperature. The high degree of cation order would exclude the possibility of a typical spin-glass, indicating that the divergence is probably due to a frustration of the magnetic interactions between Cu and Ir, with a high frustration factor of f≈25. - Graphical abstract: A new member of the A{sub 2}B′B″O{sub 6} double-perovskite family with JT-active Cu{sup II} at the B′ site and Ir{sup VI} at the B″ site is synthesized through high pressure synthesis and characterized for the structural and magnetic properties. - Highlights: • New member of the A{sub 2}CuB″O{sub 6} double-perovskite family is synthesized with B″=Ir. • Stabilization of Ir{sup VI} requires the use of high oxygen pressure synthesis. • Crystal structure is tetragonally distorted due to JT-active Cu{sup II}. • Divergence of ZFC and FC curves is seen below the T{sub N} of 15 K. • This is presumably due to a frustration effect.

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

Mesoscale Frank–Kasper Crystal Structures from Dendron Assembly by Controlling Core Apex Interactions

Single-component polymeric materials open up a great potential for self-assembly into mesoscale complex crystal structures that are known as Frank-Kasper (FK) phases. Predicting the packing structures of the soft-matter spheres, however, remains a challenge even when the molecular design is precisely known. Here, we investigate the role of the molecules' enthalpic interaction in determining the low-symmetry crystal structures. To this end, we synthesize architecturally asymmetric dendrons by varying their apex functionalities and examine the packing structures of the second-generation (G2) dendritic wedges. Our work shows that weakening the hydrogen bonding of the dendron apex makes the particles softer and smaller, and leads to the formation of various FK structures at lower temperatures, including the new observation of a FK C14 phase in the cone-shaped dendron systems. As a consequence of the free energy balance between the particle's interfacial tension and the chain's stretching, various packing structures are mainly tuned by designing the hydrogen bonding interaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2012

Crystal Structure of the PAC1R Extracellular Domain Unifies a Consensus Fold for Hormone Recognition by Class B G-Protein Coupled Receptors

Pituitary adenylate cyclase activating polypeptide (PACAP) is a member of the PACAP/glucagon family of peptide hormones, which controls many physiological functions in the immune, nervous, endocrine, and muscular systems. It activates adenylate cyclase by binding to its receptor, PAC1R, a member of class B G-protein coupled receptors (GPCR). Crystal structures of a number of Class B GPCR extracellular domains (ECD) bound to their respective peptide hormones have revealed a consensus mechanism of hormone binding. However, the mechanism of how PACAP binds to its receptor remains controversial as an NMR structure of the PAC1R ECD/PACAP complex reveals a different topology of the ECD and a distinct mode of ligand recognition. Here we report a 1.9 {angstrom} crystal structure of the PAC1R ECD, which adopts the same fold as commonly observed for other members of Class B GPCR. Binding studies and cell-based assays with alanine-scanned peptides and mutated receptor support a model that PAC1R uses the same conserved fold of Class B GPCR ECD for PACAP binding, thus unifying the consensus mechanism of hormone binding for this family of receptors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Crystal structure and biochemical features of dye-decolorizing peroxidase YfeX from Escherichia coli O157 Asp{sup 143} and Arg{sup 232} play divergent roles toward different substrates

YfeX from Escherichia coli O157 is a bacterial dye-decolorizing peroxidase that represents both dye-decoloring activity and typical peroxidase activity. We reported the crystal structure of YfeX bound to heme at 2.09 Å resolution. The YfeX monomer resembles a ferredoxin-like fold and contains two domains. The three conserved residues surrounding the heme group are His{sup 215}, Asp{sup 143} and Arg{sup 232}. His{sup 215} functions as the proximal axial ligand of the heme iron atom. Biochemical data show that the catalytic significance of the conserved Asp{sup 143} and Arg{sup 232} depends on the substrate types and that YfeX may adopt various catalytic mechanisms toward divergent substrates. In addition, it is observed that an access tunnel spans from the protein molecular surface to the heme distal region, it serves as the passageway for the entrance and binding of the H{sub 2}O{sub 2}. - Highlights: • We determined the crystal structure of YfeX bound to heme at 2.09 Å resolution. • The conserved Asp{sup 143} and Arg{sup 232} play different roles toward divergent substrates. • The H{sub 2}O{sub 2} access tunnel spans from the protein molecular surface to the heme distal region.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain

Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Molecular and crystal structure of 2-((E)-[(4-Methylphenyl)imino]methyl)-4-nitrophenol: A redetermination

The crystal structure of the title compound, C{sub 14}H{sub 12}N{sub 2}O{sub 3}, was recently determined as a mixture of its neutral (OH containing) and zwitterionic (NH containing) forms, in a 0.60 (4): 0.40 (4) ratio using the X-ray determination. In this study, the title compound has been characterized by FT-IR and X-ray diffraction. The redetermination showed that the title compound has only enol (OH) form because of lack of the NH stretching vibration in FT-IR spectrum. In addition, the molecular structure and tautomerism of the title compound have been discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

An unusual crystal structure of ferric-enterobactin bound FepB suggests novel functions of FepB in microbial iron uptake

Iron acquisition by siderophores is critical for the survival of most bacteria. Enterobactin is a kind of catechol siderophore that exhibits the highest affinity to iron atoms secreted by E. coli and several other species of Enterobacteriaceae. The periplasmic binding protein (PBP) FepB can transport ferric-enterobactin (Fe-Ent) from the outer membrane to the membrane-associated ATP-binding cassette transport system in E. coli. To elucidate this process, we solved the crystal structure of FepB in complex with Fe-Ent at a resolution of 1.8 Å. Consistent with previously reported NMR results, our crystal structure shows that, similar to the other type III PBPs, the FepB structure was folded with separated globular N- and C-termini linked by a long α-helix. Additionally, the structure showed that the Fe-Ent bound to the cleft between the N- and C-terminal domains. Exceptionally, FepB differs from the other known siderophore binding PBPs in that it forms a trimer by capturing four Fe-Ents that can each contribute to FepB trimerization. Dynamic light-scattering experiments are consistent with the structural observations and indicate that FepB forms a trimer in a Fe-Ent-dependent manner.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2010

The first crystal structure of a gramicidin complex with sodium: high-resolution study of a nonstoichiometric gramicidin D-NaI complex

The crystal structure of the nonstoichiometric complex of gramicidin D with NaI has been studied using synchrotron radiation at 100 K. The limiting resolution was 1.25 {angstrom} and the R factor was 16% for 19,883 observed reflections. The general architecture of the antiparallel two-stranded gramicidin dimers in the studied crystal was a right-handed antiparallel double-stranded form that closely resembles the structures of other right-handed species published to date. However, there were several surprising observations. In addition to the significantly different composition of linear gramicidins identified in the crystal structure, including the absence of the gramicidin C form, only two cationic sites were found in each of the two independent dimers (channels), which were partially occupied by sodium, compared with the seven sites found in the RbCl complex of gramicidin. The sum of the partial occupancies of Na{sup +} was only 1.26 per two dimers and was confirmed by the similar content of iodine ions (1.21 ions distributed over seven sites), which was easily visible from their anomalous signal. Another surprising observation was the significant asymmetry of the distributions and occupancies of cations in the gramicidin dimers, which was in contrast to those observed in the high-resolution structures of the complexes of heavier alkali metals with gramicidin D, especially that of rubidium.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2017

In situ determination of crystal structure and chemistry of minerals at Earth's deep lower mantle conditions

Recent advances in experimental techniques and data processing allow in situ determination of mineral crystal structure and chemistry up to Mbar pressures in a laser-heated diamond anvil cell (DAC), providing the fundamental information of the mineralogical constitution of our Earth's interior. This work highlights several recent breakthroughs in the field of high-pressure mineral crystallography, including the stability of bridgmanite, the single-crystal structure studies of post-perovskite and H-phase as well as the identification of hydrous minerals and iron oxides in the deep lower mantle. The future development of high-pressure crystallography is also discussed.

58 GEOSCIENCES↗
DOE OSTI2016

Crystal structure of human PCNA in complex with the PIP box of DVC1

In higher eukaryotes, DVC1 (SPRTN, Spartan or C1orf124) is implicated in the translesion synthesis (TLS) pathway. DVC1 localizes to sites of DNA damage, binds to the proliferating cell nuclear antigen (PCNA) via its conserved PCNA-interacting motif (PIP box), and associates with ubiquitin selective segregase p97 and other factors, thus regulating translesion synthesis polymerases. Here, we report the crystal structure of human PCNA in complex with a peptide ({sup 321}SNSHQNVLSNYFPRVS{sup 336}) derived from human DVC1 that contains a unique YF type PIP box. Structural analysis reveals the detailed PIP box-PCNA interaction. Interestingly, substitution of Y331 with Phe severely reduces its PCNA binding affinity. These findings offer new insights into the determinants of PIP box for PCNA binding. -- Highlights: •Crystal structure of PCNA in complex with DVC1{sup PIP} peptide was determined. •The Y331{sup P7}F mutation severely impairs DVC1's PCNA binding affinity. •The intramolecular hydrogen bond N326−Y331 in the 3{sub 10} helix affects DVC1's PCNA binding affinity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

Effect of crystal structure of manganese dioxide on response for electrolyte of ahydrogen sensor operative at room temperature

Sensoring properties of a hydrogen sensor that used electrolytes made of different crystal type manganese dioxides were compared. An electrolyte made of a manganese dioxide, which has a high purity of ramsdellite-type crystal structure, provided the best characteristics for the hydrogen sensor. To explain the sensor property, network model of oxygen-pairs to store protons with a weak covalent bond and to conduct protons along the network in the ideal crystal structure of ramsdellite manganese dioxide was proposed. The inter-atomic distance of those oxygen-pairs in the high purity of ramsdellite manganese dioxide was estimated between 2.57 and 2.60 A using inelastic neutron scattering measurements. The property of the hydrogen sensor supported the unique proton conduction based on the network model.

Koyanaka, Hideki↗
DOE OSTI2010

Crystal structures of truncated alphaA and alphaB crystallins reveal structural mechanisms of polydispersity important for eye lens function

Small heat shock proteins alphaA and alphaB crystallin form highly polydisperse oligomers that frustrate protein aggregation, crystallization, and amyloid formation. Here, we present the crystal structures of truncated forms of bovine alphaA crystallin (AAC{sub 59-163}) and human alphaB crystallin (ABC{sub 68-162}), both containing the C-terminal extension that functions in chaperone action and oligomeric assembly. In both structures, the C-terminal extensions swap into neighboring molecules, creating runaway domain swaps. This interface, termed DS, enables crystallin polydispersity because the C-terminal extension is palindromic and thereby allows the formation of equivalent residue interactions in both directions. That is, we observe that the extension binds in opposite directions at the DS interfaces of AAC{sub 59-163} and ABC{sub 68-162}. A second dimeric interface, termed AP, also enables polydispersity by forming an antiparallel beta sheet with three distinct registration shifts. These two polymorphic interfaces enforce polydispersity of alpha crystallin. This evolved polydispersity suggests molecular mechanisms for chaperone action and for prevention of crystallization, both necessary for transparency of eye lenses.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Spectra from a Photonic Crystal Structure with a Metallic Nanoparticle Monolayer

We have used the transfer matrix (T-matrix) method to calculate the transmission and reflection spectra of a one-dimensional photonic crystal structure with a metallic nanoparticle monolayer insert. We have studied the influence of the monolayer parameters and position on the defect modes for the photonic structure.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2014

Synthesis and crystal structure studies of ethyl 5-methyl-1, 3-diphenyl-1H-pyrazole-4-carboxylate

The title compound, C{sub 19}H{sub 18}N{sub 2}O{sub 2}, was investigated by single crystal X-ray diffraction method. It crystallizes in monoclinic class under the space group P2{sub 1}/c with cell parameters a= 8.4593(4) Å, b=15.6284(6) Å, c=12.4579(5) Å, α=90°, β=98.241(3)°, γ=90° and Z=2. The ethoxycarbonyl group is slightly twisted from the pyrazole ring, and adopts syn-periplanar conformation. The crystal structure is stabilized by intermolecular C-H….O hydrogen bonds, which help in stabilizing the crystal structure.

36 MATERIALS SCIENCE↗
DOE OSTI2011

Locally deformed states of the crystal structure of double semiconductors ZnSe and ZnTe doped with vanadium ions

Specific features of the crystal structure of a lightly doped Zn{sub 1-x}V{sub x}Te crystal (x = 0.0002) were investigated for the first time by thermal neutron diffraction. The experimental results are discussed together with the data of neutron diffraction measurements that were performed previously on Zn{sub 1-x}V{sub x}Se single crystals (x = 0.0018). An enhanced response of the ZnTe lattice (in comparison with ZnSe) to a perturbation introduced by an incorporated 3d ion is found.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗