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At least 289 records · Page 16

All sources NASA NTRS DOE OSTI

DOE OSTI2014

Crystal structures of type III{sub H} NAD-dependent D-3-phosphoglycerate dehydrogenase from two thermophiles

Highlights: • Determined the crystal structures of PGDH from two thermophiles. • Monomer is composed of nucleotide binding domain and substrate binding domain. • Crystal structures of type III{sub H} PGDH. - Abstract: In the L-Serine biosynthesis, D-3-phosphoglycerate dehydrogenase (PGDH) catalyzes the inter-conversion of D-3-phosphoglycerate to phosphohydroxypyruvate. PGDH belongs to 2-hydroxyacid dehydrogenases family. We have determined the crystal structures of PGDH from Sulfolobus tokodaii (StPGDH) and Pyrococcus horikoshii (PhPGDH) using X-ray diffraction to resolution of 1.77 Å and 1.95 Å, respectively. The PGDH protomer from both species exhibits identical structures, consisting of substrate binding domain and nucleotide binding domain. The residues and water molecules interacting with the NAD are identified. The catalytic triad residues Glu-His-Arg are highly conserved. The residues involved in the dimer interface and the structural features responsible for thermostability are evaluated. Overall, structures of PGDHs with two domains and histidine at the active site are categorized as type III{sub H} and such PGDHs structures having this type are reported for the first time.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Structural insights into the binding of lauric acid to CYP107L2 from Streptomyces avermitilis

Streptomyces avermitilis is an actinobacterium known to produce clinically useful macrolides including avermectins. CYP107L2 from S. avermitilis shares a high sequence similarity with the PikC (CYP107L1) from S. venezuelae. To elucidate the structural features of CYP107L2, we conducted biochemical and structural characterization of CYP107L2 from S. avermitilis. The CYP107L2 gene was cloned, and its recombinant protein was expressed and purified. The CYP107L2 showed a low-spin state of heme, and the reduced form yielded the CO difference spectra with a maximal absorption at 449 nm. Binding of pikromycin and lauric acid yielded the typical type I spectra with K{sub d} values of 4.8 ± 0.3 and 111 ± 9 μM, respectively. However, no metabolic product was observed in the enzyme reaction. X-ray crystal structures of the ligand-free CYP107L2 and its complex with lauric acid were determined at the resolution of 2.6 and 2.5 Å, respectively. CYP107L2 showed a well-conserved CYP structure with a wide-open substrate-binding cavity. The lauric acid is bound mainly via hydrophobic interactions with the carboxylate group of lauric acid coordinated to the heme of P450. Glu-40 and Leu-382 residues in the CYP107L2 complex with lauric acid showed significant conformational changes to provide plentiful room for the lauric acid in the substrate-binding site. - Highlights: • CYP107L2 from S. avermitilis shares a high sequence similarity with the PikC. • Purified CYP107L2 yielded a typical type I binding spectra to pikromycin and lauric acid. • Crystal structure of CYP107L2 complex with lauric acid was determined at 2.5 Å resolution. • Laurate is bound mainly via hydrophobic interactions in the substrate binding cavity of CYP107L2.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Macroscale properties and atomic-scale mechanisms of ash removal in low-temperature hydrothermal carbonization

Biogenic ash is a significant impediment to the utilization of agricultural residues in biofuel production. Such challenge can be addressed by various treatments, as demonstrated in this study on the experimental and computational mechanisms involved in the hydrothermal treatment (HT) of wheat straw. A combination of classical (all-atom) molecular dynamics simulations of cellulose carrying silica and calcium species, along with first principles quantum chemical calculations, indicates the dissociation of inorganics from the cellulose with increased HT temperature. Here, this observation is confirmed by experimental evidence of effective ash removal by HT, showing at least 50% removal of sulfur, chlorine, potassium, and calcium, and 12.5% of silica, leading to a reduced total ash content (from 6.7% to 4.2%).Changes in structural features upon HT, such as surface cellular structure and porosity, were revealed, accompanied by an increased specific surface area (from 1.17 to 6.34 m 2 /g). Our simulations suggest that silica binds tightly to the hydrophobic face of cellulose at room temperature, but HT significantly reduces the binding free energy of association with both hydrophobic and hydrophilic surfaces. Most significantly, ash removal leads to an increased calorific value, rising from approximately 16 MJ/kg to about 19 MJ/kg, along with improved thermal behavior. The improved integration combustion index parameter S indicates that the combustion properties improve with ash removal efficiency. The proposed atomic-level mechanism for the observed removal of inorganics during mild HT underscores the potential of such treatment in producing energy-dense wheat straw, a widely available agricultural residue.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

High-rate and long-life lithium-ion battery performance of hierarchically hollow-structured NiCo 2 O 4 /CNT nanocomposite

In this paper, 3D-transition binary metal oxides have been considered as promising anode materials for lithium-ion batteries with improved reversible capacity, structural stability and electronic conductivity compared with single metal oxides. Here, carbon nanotube supported NiCo 2 O 4 nanoparticles (NiCo 2 O 4 /CNT) with 3D hierarchical hollow structure are fabricated via a simple one-pot method. The NiCo 2 O 4 nanoparticles with interconnected pores are consists of small nanocrystals. When used as anode material for the lithium-ion battery, NiCo 2 O 4 /CNT exhibits enhanced electrochemical performance than that of Co 3 O 4 /CNT and NiO/CNT. Moreover, ultra-high discharge/charge stability was obtained for 4000 cycles at a current density of 5 A g –1 . The superior battery performance of NiCo 2 O 4 nanoparticles is probably attributed to the special structural features and physical characteristics, including integrity, hollow structure with interconnected pores, which providing sufficient accommodation for the volume change during charge/discharge process. Besides, the consisting of ultra-small crystals enhanced the utility of active material, and intimate interaction with CNTs improved the electron-transfer rate.

36 MATERIALS SCIENCE↗

DOE OSTI2013

The new Hg-rich barium indium mercurides BaIn{sub x}Hg{sub 7−x} (x=3.1) and BaIn{sub x}Hg{sub 11−x} (x=0–2.8)

The title compounds BaIn{sub x}Hg{sub 7−x} (x=3.1(1)) and BaIn{sub x}Hg{sub 11−x} (x=0–2.8) were synthesized from stoichiometric ratios of the elements in Ta crucibles. Their crystal structures have been determined using single crystal X-ray data. BaIn{sub x}Hg{sub 7−x} (x=3.1(1)) crystallizes in a new structure type (orthorhombic, oC16, space group Cmmm: a=512.02(1), b=1227.68(3), c=668.61(2) pm, Z=2, R1=0.0311). In the structure, the atoms of the three crystallographically different mixed In/Hg positions form planar nets of four-, six- and eight-membered rings. These nets are shifted against each other such that the four-membered rings form empty distorted cubes. The cubes are connected via common edges, corners and folded ladders, which are also found in BaIn{sub 2}/BaHg{sub 2} (KHg{sub 2} structure type) and BaIn (α-NaHg type). The Ba atoms are centered in the eight-membered rings and exhibit an overall coordination number of 20. The [BaM{sub 20}] polyhedra and twice as many distorted [M{sub 8}] cubes tesselate the space. BaIn{sub 2.8}Hg{sub 8.2} (cubic, cP36, space group Pm3{sup ¯}m, a=961.83(1) pm, Z=3, R1=0.0243) is the border compound of the phase width BaIn{sub x}Hg{sub 11−x} of the rare BaHg{sub 11} structure type. In the structure, ideal [M{sub 8}] cubes (at the corners of the unit cell) and BaM{sub 20} polyhedra (at the edges of the unit cell) represent the building blocks comparable to the other new In mercuride. In accordance with the increased In/Hg content, additional M-pure regions appear: the center of the unit cell contains a huge [Hg(1)M(2){sub 12}M(3,4){sub 32}] polyhedron, a Hg-centered cuboctahedron of In/Hg atoms surrounded by a capped cantellated cube of 32 additional M atoms. For both structure types, the bonding situation and the ‘coloring’, i.e. the In/Hg distribution of the polyanionic network, are discussed considering the different sizes of the atoms and the charge distribution (Bader AIM charges), which have been calculated within the framework of FP-LAPW density functional theory. - Graphical abstract: BaIn{sub 2.6}Hg{sub 4.4}: distorted cubes [(In/Hg){sub 8}] (green, like in BaHg{sub 11}), folded ladders (violet, like in BaIn, BaHg{sub 2} and BaIn{sub 2}) and Ba coordination polyhedra [Ba(In/Hg){sub 20}] (blue, like in BaHg{sub 11}). - Highlights: • The Hg-rich In-mercuride BaIn{sub 3.1}Hg{sub 3.9} crystallizes with a singular structure type. • The phase width of the BaHg{sub 11} structure in BaIn{sub x}Hg{sub 11-x} ends at x=2.8. • The relations of both compounds with other alkaline-earth mercurides are outlined. • The Hg/In coloring of the polyanion is discussed considering the structure features. • Bonding aspects are explored using band structure calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2011

THE CARNEGIE-IRVINE GALAXY SURVEY. I. OVERVIEW AND ATLAS OF OPTICAL IMAGES

The Carnegie-Irvine Galaxy Survey (CGS) is a long-term program to investigate the photometric and spectroscopic properties of a statistically complete sample of 605 bright (B{sub T} < 12.9 mag), southern ({delta} < 0 Degree-Sign ) galaxies using the facilities at Las Campanas Observatory. This paper, the first in a series, outlines the scientific motivation of CGS, defines the sample, and describes the technical aspects of the optical broadband (BVRI) imaging component of the survey, including details of the observing program, data reduction procedures, and calibration strategy. The overall quality of the images is quite high, in terms of resolution (median seeing {approx}1''), field of view (8.'9 Multiplication-Sign 8.'9), and depth (median limiting surface brightness {approx}27.5, 26.9, 26.4, and 25.3 mag arcsec{sup -2} in the B, V, R, and I bands, respectively). We prepare a digital image atlas showing several different renditions of the data, including three-color composites, star-cleaned images, stacked images to enhance faint features, structure maps to highlight small-scale features, and color index maps suitable for studying the spatial variation of stellar content and dust. In anticipation of upcoming science analyses, we tabulate an extensive set of global properties for the galaxy sample. These include optical isophotal and photometric parameters derived from CGS itself, as well as published information on multiwavelength (ultraviolet, U-band, near-infrared, far-infrared) photometry, internal kinematics (central stellar velocity dispersions, disk rotational velocities), environment (distance to nearest neighbor, tidal parameter, group, or cluster membership), and H I content. The digital images and science-level data products will be made publicly accessible to the community.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2015

The unusual and dynamic character of PX-DNA

PX-DNA is a four-stranded DNA structure that has been implicated in the recognition of homology, either continuously, or in an every-other-half-turn fashion. Some of the structural features of the molecule have been noted previously, but the structure requires further characterization. Here, we report atomic force microscopic characterization of PX molecules that contain periodically placed biotin groups, enabling the molecule to be labeled by streptavidin molecules at these sites. In comparison with conventional double stranded DNA and with antiparallel DNA double crossover molecules, it is clear that PX-DNA is a more dynamic structure. Moreover, the spacing between the nucleotide pairs along the helix axis is shorter, suggesting a mixed B/A structure. Circular dichroism spectroscopy indicates unusual features in the PX molecule that are absent in both the molecules to which it is compared.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

The Influence of Modification on Crystal Lattice Stability of Austenite in Stainless Steel

Using the methods of electron diffraction microscopy and X-ray diffraction analysis, the influence of alloying of the austenitic steel, Grade 110H13, with chromium and vanadium, as well as high-melting, ultrafine-grained TiO{sub 2}, ZrO{sub 2} powders and Na{sub 3}AlF{sub 6} cryolite on its structural-phase state and microstructure is investigated. It is shown that the matrix of non-modified steel is completely austenitic and consists of an iron-based solid solution and the interstitial (C, N, O and other) and substitutional (Cr, V and other) atoms simultaneously. Alloying with chromium and vanadium changes neither its phase composition nor defect structure, while alloy modification results in qualitatively new structural features: γ → ε-transformation, high-intensity microtwinning, defect structure changes, and a sharp increase in the scalar dislocation density. The features of the deformation-induced microtwinning and ε-martensite plates identified in the modified steel promote revealing additional microtwin systems in the matrix γ-phase, which result in structural changes making it possible to classify it as a γ′-phase. It is found out that an introduction of modifying additions gives rise to the following sequence of structural-phase transformations: γ→γ′→(γ′ +ε). The experimental data obtained demonstrate that as a result of modification the crystal lattice transits into a low-stability state. This transition is accompanied by marked structural-phase changes consisting in the formation of several microtwin systems and γ → ε-transformation. These structural-phase changes in the modified steel are due to the crystal-lattice transition into the low-stability state, followed by new structural-phase alterations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2019

Computationally Driven Discovery of a Family of Layered LiNiB Polymorphs

Abstract Two novel lithium nickel boride polymorphs, RT ‐LiNiB and HT ‐LiNiB, with layered crystal structures are reported. This family of compounds was theoretically predicted by using the adaptive genetic algorithm (AGA) and subsequently synthesized by a hydride route with LiH as the lithium source. Unique among the known ternary transition‐metal borides, the LiNiB structures feature Li layers alternating with nearly planar [NiB] layers composed of Ni hexagonal rings with a B–B pair at the center. A comprehensive study using a combination of single crystal/synchrotron powder X‐ray diffraction, solid‐state 7 Li and 11 B NMR spectroscopy, scanning transmission electron microscopy, quantum‐chemical calculations, and magnetism has shed light on the intrinsic features of these polymorphic compounds. The unique layered structures of LiNiB compounds make them ultimate precursors for exfoliation studies, thus paving a way toward two‐dimensional transition‐metal borides, MBenes.

Gvozdetskyi, Volodymyr↗

DOE OSTI2019

Computationally Driven Discovery of a Family of Layered LiNiB Polymorphs

Gvozdetskyi, Volodymyr↗

DOE OSTI2016

Hydrothermal synthesis of vanadium pentoxide nanowires

Nanowires of V{sub 2}O{sub 5} were prepared via hydrothermal route using NH{sub 4}VO{sub 3} as precursor in the presence of sulfuric acid at 120°C for 24 h. This synthesis process is free of any templates and reducing agents. Thermal analysis showed a phase change at 350°C and the samples were annealed at 500°C. The XRD analysis showed the monoclinic phase for the as-prepared and orthorhombic phase of V{sub 2}O{sub 5} when annealed at 500°C. Characteristic Raman peaks also expressed the same structural features. Microstructure analysis by SEM showed the nanowire structure of V{sub 2}O{sub 5} with thickness in the range of 20–50 nm and length in micrometers. The possible mechanisms of formation of the nanowires were schematically explained based on the layered structure of V{sub 2}O{sub 5}.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2019

Numerical Simulation of the Structure and Mechanical Properties of Silicene Layers on Graphite during the Lithium Ion Motion

The molecular dynamics method is applied to study structural and mechanical effects appearing during the lithium ion motion in a dc electric field along a planar channel formed by perfect silicene sheets and sheets containing vacancy-type defects. Mono-, di-, tri-, and hexavacancies of rather densely and uniformly filled silicene sheets are arranged one above the other on a graphite substrate. The times of Li{sup +} ion passage through silicene channels with various gaps are determined. The construction of Voronoi polyhedra and truncated polyhedrons, whose centers coincide with the moving ion position allowed revealing the structural features inherent to the two-dimensional layered structure. The nature of stresses appearing in silicene sheets most critical to ion motion over the channel is determined.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2019

Coupled Geomechanical Modeling to Assess Cap Rock Integrity and Mechanical Fault Stability: Application to Farnsworth Field Unit Project

Abstract The SWP project is located in a mature waterflood undergoing conversion to CO2-WAG operations in the Farnsworth, Texas, USA. Anthropogenic CO2 is sourced from a fertilizer and an ethanol plant. This work utilizes Farnsworth’s full-field, history-matched, compositional hydrodynamic coupled geomechanical model for assessing the impact of stress changes observed through the history matched field life. Production and injection induced stress changes, fault stability and caprock integrity investigations are performed to project the potential for fault reactivation and the loss of caprock integrity under shear failure. A static mechanical earth model (MEM) was constructed for use in transient coupled geomechanical model based on the existing Southwest Regional Partnership (SWP) geological model. The static MEM inherits the stratigraphic and structural features of the geologic model and incorporates additional overburden, underburden, and sideburden formations required to impose mechanical boundary conditions. Mechanical properties were distributed in the 3D MEM through integration of geophysical logs and 3-dimensional seismic elastic inversion properties using a combination of Bayesian and stochastic interpolation methods. These data are further enhanced by lab derived strength and failure criteria for the caprock interval. Additionally, interpreted faults and other geological features were included as part of the static structural framework to fully represent subsurface hydraulic and mechanical systems and appropriately integrate heterogeneity. Two-way coupling of hydrodynamic flow and geomechanical simulations incorporates the Kozeny-Carman relationship for updating permeability and is history matched through primary, secondary (waterflooding) and tertiary (CO2 WAG) recovery periods before performing a twenty year forecast. Two-way simulations are performed to understand the effective stress perturbations imposed by field operations: water injection and the more recent implementation of WAG. Evaluation of Mohr circles with liquid production and field pressure charts as well as slip tendency and distance to failure metrics indicate that neither our faults or cap rock are critically stressed. This paper presents the results of the Farnsworth initial attempts to integrate the seismic driven 3D MEM into coupled hydrodynamic geomechanical history match simulation workflow.

02 PETROLEUM↗

DOE OSTI2021

Natural Systems Data Package for the Active Trenches of the Low-Level Burial Grounds, Hanford Site, Washington

This document summarizes the available information regarding the natural system (vadose zone and saturated zone) at the active trenches of the 200 West Area and 200 East Area Low-Level Burial Grounds (LLBGs). This information is relevant for developing the natural system fate and transport model for the update of the active trenches performance assessment. This document presents a description of the major features, events, and processes of the natural system at the active trenches of the 200 West Area and 200 East Area LLBGs that involves the geologic features or framework, and the vadose zone and groundwater flow and transport system. The description of the geologic features includes the following items: geologic setting, major structural features, major hydrostratigraphic units, and geologic framework. The discussion concerning vadose zone flow and transport at the active trenches of the 200 West Area and 200 East Area LLBGs includes the following topics: vadose zone features, events, and processes relevant to the development of the vadose zone conceptual model; hydrogeologic units and conditions; factors affecting moisture movement; and flow and transport properties of major units. The discussion concerning the groundwater flow and transport system in the vicinity of the active trenches of the 200 West Area and 200 East Area LLBGs includes the following topics: saturated zone features, events, and processes relevant to the saturated zone conceptual model; hydrogeologic units; groundwater flow conditions; and flow and transport properties.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2019

Structural Chemistry of Akdalaite, Al[subscript 10]O[subscript 14](OH)[subscript 2], the Isostructural Aluminum Analogue of Ferrihydrite

Abstract not provided

Parise, John B.↗

DOE OSTI2018

Elucidating a role for the cytoplasmic domain in the Mycobacterium tuberculosis mechanosensitive channel of large conductance

Microbial survival in dynamic environments requires the ability to successfully respond to abrupt changes in osmolarity. The mechanosensitive channel of large conductance (MscL) is a ubiquitous channel that facilitates the survival of bacteria and archaea under severe osmotic down-shock conditions by relieving excess turgor pressure in response to increased membrane tension. A prominent structural feature of MscL, the cytoplasmic C-terminal domain, has been suggested to influence channel assembly and function. In this report, we describe the X-ray crystal structure and electrophysiological properties of a C-terminal domain truncation of the Mycobacterium tuberculosis MscL (MtMscLΔC). A crystal structure of MtMscLΔC solubilized in the detergent n-dodecyl-β-D-maltopyranoside reveals the pentameric, closed state-like architecture for the membrane spanning region observed in the previously solved full-length MtMscL. Electrophysiological characterization demonstrates that MtMscLΔC retains mechano-sensitivity, but with conductance and tension sensitivity more closely resembling full length EcMscL than MtMscL. This study establishes that the C-terminal domain of MtMscL is not required for oligomerization of the full-length channel, but rather influences the tension sensitivity and conductance properties of the channel. The collective picture that emerges from these data is that each MscL channel structure has characteristic features, highlighting the importance of studying multiple homologs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Is dimerization a common feature in thioredoxins? The case of thioredoxin from Litopenaeus vannamei

The quaternary structure of the redox protein thioredoxin (Trx) has been debated. For bacterial Trx, there is no question regarding its monomeric state. In humans and other eukaryotes, the presence of a cysteine residue at the crystallographic symmetry axis points to the relevance of dimer formation in solution and in vivo . Crystallographic data for shrimp thioredoxin ( Lv Trx) obtained under different redox conditions reveal a dimeric arrangement mediated by a disulfide bond through residue Cys73 and other hydrophobic interactions located in the crystallographic interface, as reported for human Trx. Through the analysis of five mutants located at the crystallographic interface, this study provides structural and biochemical evidence for the existence in solution of monomeric and dimeric populations of wild-type Lv Trx and five mutants. Based on the results of biochemical assays, SAXS studies and the crystallographic structures of three of the studied mutants (Cys73Ser, Asp60Ser and Trp31Ala), it is clear that the Cys73 residue is essential for dimerization. However, its mutation to Ser produces an enzyme which has similar redox activity in vitro to the wild type. A putative regulatory function of dimerization is proposed based on structural analysis. Nonetheless, the biological role of Lv Trx dimerization needs to be experimentally unveiled. Additionally, the findings of this work reopen the discussion regarding the existence of similar behaviour in human thioredoxin, which shares a Cys at position 73 with Lv Trx, a structural feature that is also present in some Trxs from vertebrates and crustaceans.

Campos-Acevedo, Adam A.↗

DOE OSTI2020

TBDB: a database of structurally annotated T-box riboswitch:tRNA pairs

Abstract T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches, and de novo prediction of binding specificities requires advanced knowledge of computational tools to annotate riboswitch secondary structure features. Here, we present the T-box Riboswitch Annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,535 T-box riboswitch sequences, spanning the major phyla of 3,632 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory targets. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.

59 BASIC BIOLOGICAL SCIENCES↗