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At least 1,459 records · Page 81
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Groundwater characterization and monitoring at a complex industrial waste site using electrical resistivity imaging

A contaminated industrial waste site in Washington State (USA) containing buried, metallic-waste storage tanks, pipes, and wells, was evaluated to determine the feasibility of monitoring groundwater remediation activities associated with an underlying perched aquifer system using electrical resistivity tomography. The perched aquifer, located ~65 m below ground surface and ~10 m above the regional water table, contains high concentrations of nitrate, uranium, and other contaminants of concern from past tank leaks and intentional releases of wastes to surface disposal sites. The extent of the perched water aquifer is not well known, and the effectiveness of groundwater extraction for contaminant removal is uncertain, so supplemental characterization and monitoring technologies are being evaluated. Numerical simulations of subsurface flow and contaminant transport were performed with a highly resolved model of the hydrogeologic system and waste site infrastructure, and these simulations were used as the physical basis for electrical resistivity tomography modeling. The modeling explicitly accounted for metallic infrastructure at the site. The effectiveness of using surface electrodes versus surface and horizontal subsurface electrodes, for imaging groundwater extraction from the perched water aquifer, was investigated. Although directional drilling is a mature technology, its use for electrode emplacement in the deep subsurface under a complex industrial waste site via horizontal wells has not yet been demonstrated. Results from this study indicate that using horizontal subsurface electrode arrays could significantly improve the ability of electrical resistivity tomography to image deep subsurface features and monitor remediation activities under complex industrial waste sites.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Sorption testing and generalized composite surface complexation models for determining uranium sorption parameters at a proposed in-situ recovery site

Solid-phase iron concentrations and generalized composite surface complexation models were used to evaluate procedures in determining uranium sorption on oxidized aquifer material at a proposed U in situ recovery (ISR) site. At the proposed Dewey Burdock ISR site in South Dakota, USA, oxidized aquifer material occurs downgradient of the U ore zones. Solid-phase Fe concentrations did not explain our batch sorption test results,though total extracted Fe appeared to be positively correlated with overall measured U sorption. Batch sorption test results were used to develop generalized composite surface complexation models that incorporated the full genericsorption potential of each sample, without detailed mineralogiccharacterization. The resultant models provide U sorption parameters (site densities and equilibrium constants) for reactive transport modeling. The generalized composite surface complexation sorption models were calibrated to batch sorption data from three oxidized core samples using inverse modeling, and gave larger sorption parameters than just U sorption on the measured solidphase Fe. These larger sorption parameters can significantly influence reactive transport modeling, potentially increasing U attenuation. Because of the limited number of calibration points, inverse modeling required the reduction of estimated parameters by fixing two parameters. The best-fit models used fixed values for equilibrium constants, with the sorption site densities being estimated by the inversion process. While these inverse routines did provide best-fit sorption parameters, local minima and correlated parameters might require further evaluation. Despite our limited number of proxy samples, the procedures presented provide a valuable methodology to consider for sites where metal sorption parameters are required. Furthermore, these sorption parameters can be used in reactive transport modeling to assess downgradient metal attenuation, especially when no other calibration data are available, such as at proposed U ISR sites.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

The C-terminal region of Rad52 is essential for Rad52 nuclear and nucleolar localization, and accumulation at DNA damage sites immediately after irradiation

Highlights: •Rad52 might play a key role in the repair of DSB immediately after irradiation. •EYFP-Rad52 accumulates rapidly at DSB sites and colocalizes with Ku80. •Accumulation of Rad52 at DSB sites is independent of the core NHEJ factors. •Localization and recruitment of Rad52 to DSB sites are dependent on the Rad52 CTR. •Basic amino acids in Rad52 CTR are highly conserved among vertebrate species. -- Abstract: Rad52 plays essential roles in homologous recombination (HR) and repair of DNA double-strand breaks (DSBs) in Saccharomyces cerevisiae. However, in vertebrates, knockouts of the Rad52 gene show no hypersensitivity to agents that induce DSBs. Rad52 localizes in the nucleus and forms foci at a late stage following irradiation. Ku70 and Ku80, which play an essential role in nonhomologous DNA-end-joining (NHEJ), are essential for the accumulation of other core NHEJ factors, e.g., XRCC4, and a HR-related factor, e.g., BRCA1. Here, we show that the subcellular localization of EYFP-Rad52(1–418) changes dynamically during the cell cycle. In addition, EYFP-Rad52(1–418) accumulates rapidly at microirradiated sites and colocalizes with the DSB sensor protein Ku80. Moreover, the accumulation of EYFP-Rad52(1–418) at DSB sites is independent of the core NHEJ factors, i.e., Ku80 and XRCC4. Furthermore, we observed that EYFP-Rad52(1–418) localizes in nucleoli in CHO-K1 cells and XRCC4-deficient cells, but not in Ku80-deficient cells. We also found that Rad52 nuclear localization, nucleolar localization, and accumulation at DSB sites are dependent on eight amino acids (411–418) at the end of the C-terminal region of Rad52 (Rad52 CTR). Furthermore, basic amino acids on Rad52 CTR are highly conserved among mammalian, avian, and fish homologues, suggesting that Rad52 CTR is important for the regulation and function of Rad52 in vertebrates. These findings also suggest that the mechanism underlying the regulation of subcellular localization of Rad52 is important for the physiological function of Rad52 not only at a late stage following irradiation, but also at an early stage.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Six independent fucose-binding sites in the crystal structure of Aspergillus oryzae lectin

The crystal structure of AOL (a fucose-specific lectin of Aspergillus oryzae) has been solved by SAD (single-wavelength anomalous diffraction) and MAD (multi-wavelength anomalous diffraction) phasing of seleno-fucosides. The overall structure is a six-bladed β-propeller similar to that of other fucose-specific lectins. The fucose moieties of the seleno-fucosides are located in six fucose-binding sites. Although the Arg and Glu/Gln residues bound to the fucose moiety are common to all fucose-binding sites, the amino-acid residues involved in fucose binding at each site are not identical. The varying peak heights of the seleniums in the electron density map suggest that each fucose-binding site has a different carbohydrate binding affinity. - Highlights: • The six-bladed β-propeller structure of AOL was solved by seleno-sugar phasing. • The mode of fucose binding is essentially conserved at all six binding sites. • The seleno-fucosides exhibit slightly different interactions and electron densities. • These findings suggest that the affinity for fucose is not identical at each site.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Molecular dynamics simulations of Zika virus NS3 helicase: Insights into RNA binding site activity

America is still suffering with the outbreak of Zika virus (ZIKV) infection. Congenital ZIKV syndrome has already caused a public health emergency of international concern. However, there are still no vaccines to prevent or drugs to treat the infection caused by ZIKV. The ZIKV NS3 helicase (NS3h) protein is a promising target for drug discovery due to its essential role in viral genome replication. NS3h unwinds the viral RNA to enable the replication of the viral genome by the NS5 protein. NS3h contains two important binding sites: the NTPase binding site and the RNA binding site. Here, we used molecular dynamics (MD) simulations to study the molecular behavior of ZIKV NS3h in the presence and absence of ssRNA and the potential implications for NS3h activity and inhibition. Although there is conformational variability and poor electron densities of the RNA binding loop in various apo flaviviruses NS3h crystallographic structures, the MD trajectories of NS3h-ssRNA demonstrated that the RNA binding loop becomes more stable when NS3h is occupied by RNA. Our results suggest that the presence of RNA generates important interactions with the RNA binding loop, and these interactions stabilize the loop sufficiently that it remains in a closed conformation. This closed conformation likely keeps the ssRNA bound to the protein for a sufficient duration to enable the unwinding/replication activities of NS3h to occur. In addition, conformational changes of this RNA binding loop can change the nature and location of the optimal ligand binding site, according to ligand binding site prediction results. These are important findings to help guide the design and discovery of new inhibitors of NS3h as promising compounds to treat the ZIKV infection. - Highlights: • Ligand binding site predictions could provide useful insights into design of compounds to block ZIKV helicase activities. • Insights into dynamic features of NS3h and its interactions with ssRNA are provided through molecular dynamics simulations. • Presence of RNA generates stabilizing interactions with RNA binding loop of NS3h, which holds it in a closed conformation. • Closed conformation of the RNA binding loop keeps the ssRNA bound to the protein to enable the activity of NS3h.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Identification of a DYRK1A-mediated phosphorylation site within the nuclear localization sequence of the hedgehog transcription factor GLI1

GLI1 is a key downstream transcription effector of the Hedgehog (Hh) signaling pathway that is involved in promoting cell growth, differentiation and tissue patterning in embryonic development. GLI1 over-activation and its nuclear localization has also been linked to the increased aggressiveness of a number of cancers. It has previously been demonstrated that DYRK1A (dual-specificity tyrosine-regulated kinase 1A) can phosphorylate GLI1 and promote GLI1 nuclear localization and its transcriptional activity. Utilizing recombinant human GLI1 and DYRK1A proteins and phospho-peptide mass spectrometry, we demonstrated that GLI1 is phosphorylated by DYRK1A at Ser408, a phospho-site that falls within the putative nuclear localization sequence (NLS) of GLI1, suggesting a possible mechanistic role in modulating its translocation. Further, we showed that the Ser408 site on GLI1 was not phosphorylated in the presence of the selective DYRK1A inhibitor harmine. The data described herein provide the first identification of a DYRK1A-mediated site of phosphorylation on GLI1 within its NLS and may serve as a valuable mechanism for further understanding Hh signaling modulation. - Highlights: • We describe a novel direct DYRK1A phosphorylation site on GLI1 at Ser408. • Harmine a selective DYRK1A inhibitor, blocks DYRK1A-mediated GLI1 phosphorylation. • The Ser408 phospho-site is within the GLI1 nuclear localization sequence (380–420). • This phosphorylation site provides a potential anti-Hh therapeutic target.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

A spatially based area–time inundation index model developed to assess habitat opportunity in tidal–fluvial wetlands and restoration sites

The hydrodynamics of tidal wetland areas in the lower Columbia River floodplain and estuary directly affect habitat opportunity for endangered salmonid fishes. Physical and biological structures and functions in the system are directly affected by inundation patterns influenced by tidal cycles, hydropower operations, river discharge, upriver water withdrawals, climate, and physical barriers such as dikes, culverts, and tide gates. Ongoing ecosystem restoration efforts are intended to increase the opportunity for salmon to access beneficial habitats by hydrologically reconnecting main-stem river channels and diked areas within the historical floodplain. To address the need to evaluate habitat opportunity, a geographic information system-based Area-Time Inundation Index Model (ATIIM) was developed. Additionally, the ATIIM integrates in situ or modeled hourly water-surface elevation (WSE) data and advanced terrain processing of high-resolution elevation data. The ATIIM uses a spatially based wetted-area algorithm to determine site average bankfull elevation, two- and three-dimensional inundation extent, and other site metrics. Hydrological process metrics such as inundation frequency, duration, maximum area, and maximum frequency area can inform evaluation of proposed restoration sites; e.g., determine trade-offs between WSE and habitat opportunity, contrast alternative restoration designs, predict impacts of altered flow regimes, and estimate nutrient and biomass fluxes. In an adaptive management framework, this model can be used to provide standardized site comparisons and effectiveness monitoring of changes in the developmental trajectories of restoration sites. Overall, results are presented for 11 wetlands representative of tidal marshes, tidal forested wetlands, and restoration sites.

42 ENGINEERING↗
DOE OSTI2015

Agreement of central site measurements and land use regression modeled oxidative potential of PM{sub 2.5} with personal exposure

Oxidative potential (OP) of ambient particulate matter (PM) has been suggested as a health-relevant exposure metric. In order to use OP for exposure assessment, information is needed about how well central site OP measurements and modeled average OP at the home address reflect temporal and spatial variation of personal OP. We collected 96-hour personal, home outdoor and indoor PM{sub 2.5} samples from 15 volunteers living either at traffic, urban or regional background locations in Utrecht, the Netherlands. OP was also measured at one central reference site to account for temporal variations. OP was assessed using electron spin resonance (OP{sup ESR}) and dithiothreitol (OP{sup DTT}). Spatial variation of average OP at the home address was modeled using land use regression (LUR) models. For both OP{sup ESR} and OP{sup DTT}, temporal correlations of central site measurements with home outdoor measurements were high (R>0.75), and moderate to high (R=0.49–0.70) with personal measurements. The LUR model predictions for OP correlated significantly with the home outdoor concentrations for OP{sup DTT} and OP{sup ESR} (R=0.65 and 0.62, respectively). LUR model predictions were moderately correlated with personal OP{sup DTT} measurements (R=0.50). Adjustment for indoor sources, such as vacuum cleaning and absence of fume-hood, improved the temporal and spatial agreement with measured personal exposure for OP{sup ESR}. OP{sup DTT} was not associated with any indoor sources. Our study results support the use of central site OP for exposure assessment of epidemiological studies focusing on short-term health effects. - Highlights: • Oxidative potential (OP) of PM was proposed as a health-relevant exposure metric. • We evaluated the relationship between measured and modeled outdoor and personal OP. • Temporal correlations of central site with personal OP are moderate to high. • Adjusting for indoor sources improved the agreement with personal OP. • Our results support the use of central site OP for short-term health effect studies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Siting bioenergy facilities in the United States: Measuring participation in decisions and distribution of effects

Scientists and stakeholders can inform the process of siting renewable energy facilities in ways that do not perpetuate socioeconomic disparities associated with fossil fuel industries or create new ones. Procedural justice indicators and distributional justice indicators that incorporate environmental, social, and economic objectives can be used to site energy facilities in ways that increase benefits and reduce negative impacts to disadvantaged and underserved populations. A generic list of potential energy justice indicators for siting bioenergy facilities was developed collaboratively between U.S. bioenergy researchers and diverse agriculture, energy, and energy and environmental justice stakeholders and experts. From this list smaller numbers of indicators can be selected or modified with communities for local siting of bioenergy facilities. Groups of indicators can be used to guide biorefinery or biopower siting and permitting decisions, e.g., to compare siting options, to draw early attention to key problems, or to track progress toward justice-related targets.

09 BIOMASS FUELS↗
DOE OSTI2012

Atomic-level studies of the depletion in reactive sites during clay mineral dissolution

Environmental weathering is typically viewed as a macroscopic phenomenon that is based on a number of competing atomic- or molecular-level processes. One important process is the release of metal or metalloid elements into solution at the water-rock interface. To both explain and predict environmental weathering, the atomic-level “reactive sites” on the surfaces of minerals must be characterized and quantified. Whether these sites are atomic in nature, represented by a chemical bond, or comprise a more complex assemblage of covalently or ionically linked atoms or molecules, the kinetic rate of atomic release (dissolution) depends on the available reactive surface. For one important class of materials, clay minerals, their reactive surface areas are a challenge to quantify as it is well recognized that there are two distinct types of surfaces: edge sites and basal planes1-3. Clay dissolution rates continuously decrease over time as reactive edge sites are preferentially depleted4. Changes in reactive surface area and the difficulties in quantifying this elusive variable have often been cited as one key reason for the complexity in developing accurate rate equations3,5,6. In this work, we demonstrate a solid-state nuclear magnetic resonance (SSNMR) method for counting the number of reactive surface sites on a defined quantity of a clay mineral. Using this SSNMR proxy7-9, changes in reactive surface area were monitored for a series of batch dissolution experiments of low-defect kaolinite KGa-1b at 21 ºC and pH 3 over the course of 80 days. While no changes (within error) were observed for specific surface area (as determined from BET gas isotherm data), the SSNMR proxy revealed decreases in the number of reactive surface sites per gram of kaolinite as a function of dissolution time. This observation can be tied to a concomitant decrease in the rates of release of Si and Al into solution. These results further highlight the need to account for changes in reactive surface area when developing and using dissolution rate models for clay minerals and other heterogeneous materials in the environment.

58 GEOSCIENCES↗
DOE OSTI2021

Impact of reservoir parameters and wellbore permeability uncertainties on CO 2 and brine leakage potential at the Shenhua CO 2 Storage Site, China

Here, this paper describes a system-level risk assessment for the Shenhua CO 2 storage site, China, using the National Risk Assessment Partnership Integrated Assessment Model for Carbon Storage (NRAP-IAM-CS). Here, we begin by determining the optimal number of Monte Carlo (MC) simulations to achieve CO 2 and brine leakage result convergence. Then, we calculate mass CO 2 and brine leakage to the atmosphere and a hypothetical shallow aquifer. Finally, we assess the geochemical impacts in the event of leakage as if there were a shallow freshwater aquifer at the Shenhua site. Simulation results show that leakage results tend to stabilize after 300 Monte Carlo simulations. When the three wells on site are assigned a permeability of 10 -11 m 2 (representing significantly leaking wells), moderate CO 2 and brine leakages occur, and the percentage of CO 2 leakage exceeds the threshold value we set based on the Intergovernmental Panel on Climate Change (IPCC). This is, however, unlikely to be the case for the Shenhua site. For all the other scenarios, the CO 2 leakage is trivial although there is still the possibility of CO 2 leakage into the groundwater aquifer exceeding the 1% threshold over 1000 years, assuming constant legacy wellbore permeability. For the significantly leaking scenario, there is a 10% probability to have a moderate (2.7 × 10 7 m 3 ) leakage-affected volume in the shallow aquifer with the pH below 6.5, and a large (1.4 × 10 8 m 3 ) volume with the total dissolved solids (TDS) above 500 ppm, hence pH and TDS may be considered for site monitoring plans. Based on the simulation results, there is a very low probability of significant CO 2 /brine leakage through the existing wells at the Shenhua CO 2 storage site.

58 GEOSCIENCES↗
DOE OSTI2013

Localization Accuracy and Immobilization Effectiveness of a Stereotactic Body Frame for a Variety of Treatment Sites

Purpose: The purpose of this study was to analyze the pretreatment setup errors and intrafraction motion using cone beam computed tomography (CBCT) for stereotactic body radiation therapy patients immobilized and localized with a stereotactic body frame for a variety of treatment sites. Methods and Materials: Localization errors were recorded for patients receiving SBRT for 141 lung, 29 liver, 48 prostate, and 45 spine tumors representing 1005 total localization sessions. All patients were treated in a stereotactic body frame with a large custom-molded vacuum pillow. Patients were first localized to the frame using tattoos placed during simulation. Subsequently, the frame was aligned to the room lasers according to the stereotactic coordinates determined from the treatment plan. Every patient received a pretreatment and an intrafraction CBCT. Abdominal compression was used for all liver patients and for approximately 40% of the lung patients to reduce tumor motion due to respiration. Results: The mean ± standard deviation pretreatment setup errors from all localizations were −2.44 ± 3.85, 1.31 ± 5.84, and 0.11 ± 3.76 mm in the anteroposterior, superoinferior, and lateral directions, respectively. The mean pretreatment localization results among all treatment sites were not significantly different (F test, P<.05). For all treatment sites, the mean ± standard deviation intrafraction shifts were 0.33 ± 1.34, 0.15 ± 1.45, and −0.02 ± 1.17 mm in the anteroposterior, superoinferior, and lateral directions, respectively. The mean unidimensional intrafraction shifts were statistically different for several of the comparisons (P<.05) as assessed by the Tukey-Kramer test. Conclusions: Despite the varied tumor locations, the pretreatment mean localization errors for all sites were found to be consistent among the treatment sites and not significantly different, indicating that the body frame is a suitable immobilization and localization device for a variety of tumor sites. Our pretreatment localization errors and intrafraction shifts compare favorably with those reported in other studies using different types of immobilization devices.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

First principles, microkinetic, and experimental analysis of Lewis acid site speciation during ethanol dehydration on Sn-Beta zeolites

Density functional theory calculations are combined with kinetic measurements of ethanol dehydration to diethyl ether to identify the relative catalytic contributions of structurally distinct speciations of Sn sites in zeolite Beta frameworks. The structural complexities of the Beta framework require nonstandard techniques for entropy and energy calculations, including consideration of anharmonic effects in vibrational modes, employment of quasi-harmonic densities of states methods to evaluate entropies, and use of hybrid density functionals to evaluate binding energies. Calculated energies and entropies are used to construct a microkinetic model that is iteratively refined to identify all kinetically and thermodynamically sensitive reaction steps and intermediates which are subsequently treated with the higher-level methods. The rate and equilibrium constants obtained from this tiered approach agree well with measured reaction orders in ethanol and water. Site balances provide evidence for the interconversion of Sn sites between “closed” configurations that are tetra-coordinated to the framework, open configurations formed by hydrolysis that are tri-coordinated to the framework and contain a hydroxyl ligand and proximal silanol group (“hydroxy-open”), and open tri-coordinate configurations formed by reaction with ethanol, yielding an ethoxy ligand and proximal silanol group (“ethoxy-open”). Closed, hydroxy-open, and ethoxy-open Sn sites adsorb ethanol via distinct modes and react via distinct pathways, with the consequence that prevalent dehydration pathways depend on the speciation of Sn sites under reaction conditions. The kinetic modeling indicates that, under the conditions studied (404 K, 0.5–35 kPa ethanol, 0.1–50 kPa water), bimolecular dehydration on the closed Sn site is the sole kinetically-relevant step, and ethanol, ethanol-ethanol dimers, and ethanol-water dimers are the most abundant surface intermediates. In conclusion, these results highlight the importance of considering the distribution of heteroatom coordination modes to zeolite frameworks under reaction conditions, as well as pathways for their interconversion in the presence of reacting molecules, to obtain more robust mechanistic and kinetic interpretations of catalytic pathways in Lewis acid zeolites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2011

Crystal structure of Eu-doped magnetoplumbite-type lanthanum aluminum oxynitride with emission site splitting

Eu-doped lanthanum aluminum oxynitride (LaAl{sub 12}(O,N){sub 19}) with magnetoplumbite structure was prepared by nitridation of the oxide precursor obtained from aluminum glycine gel and subsequent post-annealing. Eu-doped lanthanum aluminum oxynitride exhibited blue light emission at 440 nm with a shoulder at 464 nm under excitation at 254 nm. Isostructural Eu-doped calcium aluminum oxide (CaAl{sub 12}O{sub 19}) exhibited a single emission peak at 415 nm. Structural refinement using neutron powder diffraction indicated that the lanthanum site occupied partially by Eu{sup 2+} splits into 2d and 6h sites in the aluminum oxynitride. The longer emission and the shoulder peak in the former aluminum oxynitride were observed in relation to the increasing covalency as well as crystal field splitting around doped Eu{sup 2+} induced by site splitting involved with the two kinds of anions. - Graphical Abstract: Magnetoplumbite type Eu-doped lanthanum aluminum oxynitride has lanthanum site splitting induced by two kinds of anions, causing two emission peaks. Highlights: > Magnetoplumbite type LaAl{sub 12}(O,N){sub 19} doped with Eu shows emission peak splitting. > ND analysis is performed on La{sub 0.97}Eu{sub 0.03}Al{sub 12}(O,N){sub 19} and Ca{sub 0.97}Eu{sub 0.03}Al{sub 12}O{sub 19}. > La{sub 0.97}Eu{sub 0.03}Al{sub 12}(O,N){sub 19} has lanthanum site splitting. > The lanthanum site splitting is induced by coexisting of two kinds of anions.

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

Boron site preference in ternary Ta and Nb boron silicides

X-ray single crystal (XSC) and neutron powder diffraction data (NPD) were used to elucidate boron site preference for five ternary phases. Ta{sub 3}Si{sub 1-x}B{sub x} (x=0.112(4)) crystallizes with the Ti{sub 3}P-type (space group P4{sub 2}/n) with B-atoms sharing the 8g site with Si atoms. Ta{sub 5}Si{sub 3-x} (x=0.03(1); Cr{sub 5}B{sub 3}- type) crystallizes with space group I4/mcm, exhibiting a small amount of vacancies on the 4a site. Both, Ta{sub 5}(Si{sub 1-x}B{sub x}){sub 3}, x=0.568(3), and Nb{sub 5}(Si{sub 1-x}B{sub x}){sub 3}, x=0.59(2), are part of solid solutions of M{sub 5}Si{sub 3} with Cr{sub 5}B{sub 3}-type into the ternary M-Si-B systems (M=Nb or Ta) with B replacing Si on the 8h site. The D8{sub 8}-phase in the Nb-Si-B system crystallizes with the Ti{sub 5}Ga{sub 4}-type revealing the formula Nb{sub 5}Si{sub 3}B{sub 1-x} (x=0.292(3)) with B partially filling the voids in the 2b site of the Mn{sub 5}Si{sub 3} parent type. - Graphical abstract: The crystal structures of a series of compounds have been solved from X-ray single crystal diffractometry revealing details on the boron incorporation. Highlights: Black-Right-Pointing-Pointer Structure of a series of compounds have been solved by X-ray single crystal diffractometry. Black-Right-Pointing-Pointer Ta{sub 3}(Si{sub 1-x}B{sub x}) (x=0.112) crystallizes with the Ti{sub 3}P-type, B and Si atoms randomly share the 8g site. Black-Right-Pointing-Pointer Structure of Nb{sub 5}Si{sub 3}B{sub 1-x} (x=0.292; Ti{sub 5}Ga{sub 4}-type) was solved from NPD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Photoluminescence of A- and B-site Eu{sup 3+}-substituted (Sr{sub x}Ba{sub 1−x}){sub 2}CaW{sub y}Mo{sub 1−y}O{sub 6} phosphors

The photoluminescence of two series of A- and B-site Eu{sup 3+} substituted (Sr{sub x}Ba{sub 1−x}){sub 2}CaW{sub y}Mo{sub 1−y}O{sub 6} double perovskite phosphor materials, (Sr{sub x}Ba{sub 1−x}){sub 1.96}Eu{sub 0.02}K{sub 0.02}CaW{sub y}Mo{sub 1−y}O{sub 6} and (Sr{sub x}Ba{sub 1−x}){sub 2}Ca{sub 0.96}Eu{sub 0.02}Li{sub 0.02}W{sub y}Mo{sub 1−y}O{sub 6} (x and y=0, 0.25, 0.50, 0.75, and 1), were studied systematically as a function of stoichiometry and crystal structure. The Eu{sup 3+} lattice sites controlled by co-doping with either K or Li were confirmed by Raman spectroscopy. The variation in integrated emission intensity and emission colour over the experimental matrix was examined using statistical tools, and the observed trends were rationalized based on the physical and electronic structure of the phosphors. Phosphors with Eu on B-site with maximum Sr content had remarkably higher emission intensities than all other materials, but the emission was more orange than red due to domination of the {sup 5}D{sub 0}–{sup 7}F{sub 1} (595 nm) transition of Eu{sup 3+}. The relative intensities of the {sup 5}D{sub 0}–{sup 7}F{sub 2} (615 nm) and {sup 5}D{sub 0}–{sup 7}F{sub 1} transitions of Eu{sup 3+}, and thus the red-shift of the emission, decreased linearly with increasing Sr content in the A-site Eu-substituted phosphors, and reached a maximum for Sr{sub 1.96}Eu{sub 0.02}K{sub 0.02}CaW{sub 0.25}Mo{sub 0.75}O{sub 6}. A maximum external quantum efficiency of 17% was obtained for the phosphor Sr{sub 2}Ca{sub 0.7}Eu{sub 0.15}Li{sub 0.15}W{sub 0.5}Mo{sub 0.5}O{sub 6} with Eu on B-site. - Highlights: • Systematic study of the photoluminescence of Eu{sup 3+}-doped (Sr{sub x}Ba{sub 1−x}){sub 2}CaW{sub y}Mo{sub 1−y}O{sub 6}. • The Eu{sup 3+} lattice sites were confirmed by Raman spectroscopy. • A large parameter space was investigated using statistical tools. • A maximum external QE of 17% was obtained for Sr{sub 2}Ca{sub 0.7}Eu{sub 0.15}Li{sub 0.15}W{sub 0.5}Mo{sub 0.5}O{sub 6}.

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

Calculated vibrational properties of pigments in protein binding sites 2: Semiquinones in photosynthetic proteins

[Q A – – Q A ] Fourier transform infrared difference spectra have previously been obtained using purple bacterial reaction centers from Rhodobacter sphaeroides with unlabeled, 18 O and 13 C isotope labeled phylloquinone (PhQ, also known as vitamin K 1 ) incorporated into the QA protein binding site (Breton, (1997), Proc. Natl. Acad. Sci. USA 94 11318–11323). The nature of the bands in these spectra and the isotope induced band shifts are poorly understood, especially for the phyllosemiquinone anion (PhQ – ) state. Here, to aid in the interpretation of the bands in these experimental spectra, ONIOM type QM/MM vibrational frequency calculations were undertaken. Calculations were also undertaken for PhQ – in solution. Surprisingly, both sets of calculated spectra are similar and agree well with the experimental spectra. This similarity suggests pigment-protein interactions do not perturb the electronic structure of the semiquinone in the Q A binding site. This is not found to be the case for the neutral PhQ species in the same protein binding site. PhQ also occupies the A 1 protein binding site in photosystem I, and the vibrational properties of PhQ – in the Q A and A 1 binding sites are compared and shown to exhibit considerable differences. These differences probably arise because of changes in the degree of asymmetry of hydrogen bonding of PhQ – in the A 1 and Q A binding sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Biophysical Examination of the Calcium-Modulated Nickel-Binding Properties of Human Calprotectin Reveals Conformational Change in the EF-Hand Domains and His 3 Asp Site

Calprotectin (CP, S100A8/S100A9 oligomer, MRP-8/MRP-14 oligomer) is a host-defense protein that sequesters nutrient transition metals from microbes. Each S100A8/S100A9 heterodimer contains four EF-hand domains and two transition-metal-binding sites. We investigate the effect of Ca(II) ions on the structure and Ni(II)-binding properties of human CP. By employing energy dispersive X-ray (EDX) spectroscopy, we evaluate the metal content of Ni(II)-bound CP-Ser [oligomer of S100A8(C42S) and S100A9(C3S)] crystals obtained in the absence and presence of Ca(II). We present a 2.1 Å resolution crystal structure of Ni(II)-bound CP-Ser and compare this structure to a reported Ni(II)- and Ca(II)-bound CP-Ser structure [Nakashige, T. G., et al. (2017) J. Am. Chem. Soc.139, 8828–8836]. This analysis reveals conformational changes associated with coordination of Ca(II) to the EF-hands of S100A9 and that Ca(II) binding affects the coordination number and geometry of the Ni(II) ion bound to the His3Asp site. In contrast, negligible differences are observed for the Ni(II)-His6 site in the absence and presence of Ca(II). Biochemical studies show that, whereas the His6 site has a thermodynamic preference for Ni(II) over Zn(II), the His3Asp site selects for Zn(II) over Ni(II), and relatively rapid metal exchange occurs at this site. Furthermore, these observations inform the working model for how CP withholds nutrient metals in the extracellular space.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗