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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Structural and molecular dynamics studies of a C1-oxidizing lytic polysaccharide monooxygenase from Heterobasidion irregulare reveal amino acids important for substrate recognition

Lytic polysaccharide monooxygenases (LPMOs) are a group of recently discovered enzymes that play important roles in the decomposition of recalcitrant polysaccharides. Here, we report the biochemical, structural, and computational characterization of an LPMO from the white-rot fungus Heterobasidion irregulare (HiLPMO9B). This enzyme oxidizes cellulose at the C1 carbon of glycosidic linkages. The crystal structure of HiLPMO9B was determined at 2.1 A resolution using X-ray crystallography. Unlike the majority of the currently available C1-specific LPMO structures, the HiLPMO9B structure contains an extended L2 loop, connecting ..beta..-strands ..beta..2 and ..beta..3 of the ..beta..-sandwich structure. Molecular dynamics (MD) simulations suggest roles for both aromatic and acidic residues in the substrate binding of HiLPMO9B, with the main contribution from the residues located on the extended region of the L2 loop (Tyr20) and the LC loop (Asp205, Tyr207, and Glu210). Asp205 and Glu210 were found to be involved in the hydrogen bonding with the hydroxyl group of the C6 carbon of glucose moieties directly or via a water molecule. Two different binding orientations were observed over the course of the MD simulations. In each orientation, the active-site copper of this LPMO preferentially skewed toward the pyranose C1 of the glycosidic linkage over the targeted glycosidic bond. This study provides additional insight into cellulose binding by C1-specific LPMOs, giving a molecular-level picture of active site substrate interactions.

09 BIOMASS FUELS↗
DOE OSTI2019

Electronic and Molecular Structures of the CeB 6 Monomer

The electronic and molecular structure of the CeB 6 molecular unit has been probed by anion PE spectroscopy and DFT calculations to gain insight into structural and electronic relaxation on edge and corner sites of this ionic material. While boron in bulk lanthanide hexaboride materials assumes octahedral B 6 3– units, the monomer assumes a less compact structure to delocalize the charge. Two competitive molecular structures were identified for the anion and neutral species, which include a boat-like structure and a planar or near-planar teardrop structure. Ce adopts different orbital occupancies in the two isomers; the boat-like structure has a 4f superconfiguration while the teardrop favors a 4f 6s occupancy. The B 6 ligand in these structures carries a charge of –4 and –3, respectively. The teardrop structure, which was calculated to be isoenergetic with the boat structure, was most consistent with the experimental spectrum. B 6 -local orbitals crowd the energy window between the Ce 4f and 6s (HOMO) orbitals. A low-lying transition from the B-based orbitals is observed slightly less than 1 eV above the ground state. Here, the results suggest that edge and corner conductivity involves stabilized, highly diffuse 6s orbitals or bands rather than the bulk-favored 5d band. High-spin and open-shell low-spin states were calculated to be very close in energy for both the anion and neutral, a characteristic that reflects how decoupled the 4f electron is from the B 6 2p- and Ce 6s-based molecular orbitals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2012

Structural Verification of the First Orbital Wonder of the World - The Structural Testing and Analysis of the International Space Station (ISS)

The International Space Station (ISS) can be considered one of the structural engineering wonders of the world. On par with the World Trade Center, the Colossus of Rhodes, the Statue of Liberty, the Great Pyramids, the Petronas towers and the Burj Khalifa skyscraper of Dubai, the ambition and scope of the ISS structural design, verification and assembly effort is a truly global success story. With its on-orbit life projected to be from its beginning in 1998 to the year 2020 (and perhaps beyond), all of those who participated in its development can consider themselves part of an historic engineering achievement representing all of humanity. The structural design and verification of the ISS could be the subject of many scholarly papers. Several papers have been written on the structural dynamic characterization of the ISS once it was assembled on-orbit [1], but the ground-based activities required to assure structural integrity and structural life of the individual elements from delivery to orbit through assembly and planned on-orbit operations have never been totally summarized. This paper is intended to give the reader an overview of some of the key decisions made during the structural verification planning for the elements of the U.S. On-Orbit Segment (USOS) as well as to summarize the many structural tests and structural analyses that were performed on its major elements. An effort is made for this paper to be summarily comprehensive, but as with all knowledge capture efforts of this kind, there are bound to be errors of omission. Should the reader discover any of these, please feel free to contact the principal author. The ISS (Figure 1) is composed of pre-integrated truss segments and pressurized elements supplied by NASA, the Russian Federal Space Agency (RSA), the European Space Agency (ESA) and the Japanese Aerospace Exploration Agency (JAXA). Each of these elements was delivered to orbit by a launch vehicle and connected to one another either robotically or autonomously. The primary structure of each element was assembled and verified by teams of responsible structural engineers within and among their respective agencies and agency contractors.

Zipay, John J.↗
DOE OSTI2019

Layer-Dependent Electronic Structure of Atomically Resolved Two-Dimensional Gallium Selenide Telluride

Alloying two-dimensional (2D) semiconductors provides a powerful method to tune their physical properties, especially those relevant to optoelectronic applications. However, as the crystal structure becomes more complex, it becomes increasingly difficult to accurately correlate response characteristics to detailed atomic structure. We investigate, via annular dark-field scanning transmission electron microscopy, electron energy loss spectroscopy, and second harmonic generation, the layered III-VI alloy GaSe 0.5 Te 0.5 as a function of layer number. The local atomic structure and stacking sequence for different layers is explicitly determined. We complement the measurements with first-principles calculations of the total energy and electronic band structure of GaSe 0.5 Te 0.5 for different crystal structures and layer number. The electronic band gap as well as the π and π + σ plasmons are found to be sensitive to layer number.

2D semiconductor alloys↗
DOE OSTI2018

Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide‐rich de novo designed peptides

Abstract Disulfide‐rich peptides represent an important protein family with broad pharmacological potential. Recent advances in computational methods have made it possible to design new peptides which adopt a stable conformation de novo. Here, we describe a system to produce disulfide‐rich de novo peptides using Escherichia coli as the expression host. The advantage of this system is that it enables production of uniformly 13 C‐ and 15 N‐labeled peptides for solution nuclear magnetic resonance (NMR) studies. This expression system was used to isotopically label two previously reported de novo designed peptides, and to determine their solution structures using NMR. The ensemble of NMR structures calculated for both peptides agreed well with the design models, further confirming the accuracy of the design protocol. Collection of NMR data on the peptides under reducing conditions revealed a dependency on disulfide bonds to maintain stability. Furthermore, we performed long‐time molecular dynamics (MD) simulations with tempering to assess the stability of two families of de novo designed peptides. Initial designs which exhibited a stable structure during simulations were more likely to adopt a stable structure in vitro , but attempts to utilize this method to redesign unstable peptides to fold into a stable state were unsuccessful. Further work is therefore needed to assess the utility of MD simulation techniques for de novo protein design.

Buchko, Garry W.↗
DOE OSTI2016

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed II/IV valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn{sub 3}N{sub 4} spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

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

Interdependence of spin structure, anion height and electronic structure of BaFe{sub 2}As{sub 2}

Superconducting as well as other electronic properties of Fe-based superconductors are quite sensitive to the structural parameters specially, on anion height which is intimately related to z{sub As}, the fractional z co-ordinate of As atom. Due to presence of strong magnetic fluctuation in these Fe-based superconductors, optimized structural parameters (lattice parameters a, b, c) including z{sub As} using density functional theory (DFT) under generalized gradient approximation (GGA) does not match experimental values accurately. In this work, we show that the optimized value of z{sub As} is strongly influenced by the spin structures in the orthorhombic phase of BaFe{sub 2}As{sub 2} system. We take all possible spin structures for the orthorhombic BaFe{sub 2}As{sub 2} system and then optimize z{sub As}. Using these optimized structures we calculate electronic structures like density of states, band structures etc., for each spin configurations. From these studies we show that the electronic structure, orbital order which is responsible for structural as well as related to nematic transition, are significantly influenced by the spin structures.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Efficient Simulation of Welding Distortion in Large Structures and Its Reduction by Jig Constraints

Two large construction machinery structures were welded separately with and without jig constraints. The welding distortion of the entire structure was measured by a 3D coordinate measuring system and simulated by elastic FEM using the inherent deformation method. To obtain an accurate inherent deformation, a thermal elastoplastic FE analysis of simple one-side fillet joints with and without jig constraints was performed. Efficient simulation of welding distortion in large structures was accomplished by applying inherent deformation in a localized region, and the effect of jig constraint on the reduction of welding distortion was clarified. The computation of inherent deformation, the weld zone definition and the conversion of inherent deformation into inherent strain were automated. Measured and computed welding distortions in large structures had a good correspondence with respect to both tendency and magnitude. Further investigation of jig configuration was performed for enhanced reduction of welding distortion. Alternative controlling techniques for common welded structures were also addressed.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Confinement of quasi-atomic structures in Ti 2 N and Ti 3 N 2 MXene electrides

Metal carbides, nitrides, or carbonitrides of early transition metals, better known as MXenes, possess notable structural, electrical, and magnetic properties. Analyzing electronic structures by calculating structural stability, band structure, density of states, Bader charge transfer, and work functions utilizing first principle calculations, we revealed that titanium nitride MXenes, namely Ti 2 N and Ti 3 N 2 , have excess anionic electrons in their lattice voids, making them MXene electrides. Bulk Ti 3 N 2 has competing antiferromagnetic (AFM) and ferromagnetic (FM) configurations with slightly more stable AFM configuration, while the Ti 2 N MXene is nonmagnetic. Although Ti 3 N 2 favors AFM configuration with hexagonal crystal systems having 6/ mmm point group symmetry, Ti 3 N 2 does not support altermagnetism. The monolayer of the Ti 3 N 2 MXene is a ferromagnetic electride. These unique properties of having non-nuclear interstitial anionic electrons in the electronic structure of titanium nitride MXene have not yet been reported in the literature. Density functional theory calculations show TiN is neither an electride, MXene, or magnetic.

Anionic electrons↗
DOE OSTI2017

Structural variability in Cu(I) and Ag(I) coordination polymers with a flexible dithione ligand: Synthesis, crystal structure, microbiological and theoretical studies

Two new compounds namely [Cu(SCN)(µ-L)]{sub n} (1) and ([Ag (µ{sub 2}-L)](ClO{sub 4})){sub n} (2) have been synthesized at room temperature by one-pot reactions between the 1,1-(1,4-butanediyl)bis(1,3-dihydro-3-methyl-1H-imidazole- 2-thione) (L) and appropriate copper(I) and silver(I) salts. These polymers have been characterized by single crystal X-ray diffraction, XRPD, TGA, elemental analysis, infrared spectroscopy, antibacterial activity and scanning probe microscopy studies. In the crystal structure of 1, copper atoms have a distorted trigonal planar geometry with a CuS{sub 2}N coordination environment. Each of the ligands in the structure of 1 acting as a bidentate S-bridging ligand to form a 1D chain structure. Additionally, the adjacent 1D chains are interconnected by the intermolecular C-H…S interactions to create a 2D network structure. In contrast to 1, in the cationic 3D structure of 2 each of the silver atoms exhibits an AgS{sub 4} tetrahedral geometry with 4-membered Ag{sub 2}S{sub 2} rings. In the structure of 2, the flexible ligand adopts two different conformations; gauche-anti-gauche and anti-anti-anti. The antibacterial studies of these polymers showed that polymer 2 is more potent antibacterial agent than 1. Scanning probe microscopy (SPM) study of the treated bacteria was carried out to investigate the structural changes cause by the interactions between the polymers and target bacteria. Theoretical study of polymer 1 investigated by the DFT calculations indicates that observed transitions at 266 nm and 302 nm in the UV–vis spectrum could be attributed to the π→π* and MLCT transitions, respectively. - Graphical abstract: Two new Cu(I) and Ag(I) coordination polymers have been have been synthesized by one-pot reactions. Copper complex has a 2D non-covalent structure, but silver compound is a 3D coordination compound. These compounds have effective antibacterial activity. - Highlights: • Cu(I) and Ag(I) based coordination polymers have different network structures. • Ag(I) polymer has more antibacterial activity than Cu(I) polymer. • DFT calculations of Cu(I) polymer has been investigated. • Cu(I) and Ag(I) polymers can destroy the structure of chromosomal and plasmid DNA.

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

Two Polymorphs of BaZn 2 P 2 : Crystal Structures, Phase Transition, and Transport Properties

Here, the novel α-BaZn 2 P 2 structural polymorph has been synthesized and structurally characterized for the first time. Its structure, elu-cidated from single crystal X-ray diffraction, indicates that the compound crystallizes in the orthorhombic α-BaCu 2 S 2 structure type, with unit cell parameters a = 9.7567(14) Å, b = 4.1266(6) Å, and c = 10.6000(15) Å. With β-BaZn 2 P 2 being previously iden-tified as belonging to the ThCr 2 Si 2 family, and with the precedent of structural phase transitions between the α-BaCu 2 S 2 type and the ThCr 2 Si 2 type, the potential for the pattern to be extended to the two different structural forms of BaZn 2 P 2 was explored. Thermal analysis suggest that a first order phase transition occurs at ~1123 K, whereby the low-temperature orthorhombic α-phase transforms to a high-temperature tetragonal β-BaZn 2 P 2 ; the structure of which was also studied and confirmed by single-crystal X-ray diffraction. Preliminary transport properties and band structure calculations indicate that α-BaZn 2 P 2 is a p-type, narrow-gap semiconductor with a direct bandgap (Eg) of 0.5 eV. The Seebeck coefficient, S(T), for the material increases steadily from the room temperature value of 119 µV/K to 184 µV/K at 600 K. The electrical resistivity of α-BaZn 2 P 2 is relatively high, on the order of 40 mΩ·cm, and the ρ(T) dependence shows gradual decrease upon heating. Such behavior is comparable to those of the typical semimetals or degenerate semiconductors. Although the observed values of the as-synthesized samples are not optimal, the carrier concentration can apparently be tuned to fall between the values of metals and semiconductors, thus providing an open window for optimizing this phase towards achieving an enhanced thermoelectric figure of merit zT. The calculated indirect band gap for the β-BaZn 2 P 2 phase is Eg = 0.03 eV which is about an order of magnitude lower than that of α-BaZn 2 P 2 . It is expected that the cage-like structural motif and layered structure possessed by α-BaZn 2 P 2 and β-BaZn 2 P 2 phases, respectively, would promote the realiza-tion of a low thermal conductivity in both compounds.

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

Protein–Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure

Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na+-montmorillonite (001), Ca2+-montmorillonite (001), goethite (100), and Na+-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, four-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvated structure without these mineral surfaces present. Over the Na+-birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2016

Structural Transitions in Cholesteric Liquid Crystal Droplets

Confinement of cholesteric liquid crystals (ChLC) into droplets leads to a delicate interplay between elasticity, chirality, and surface energy. In this work, we rely on a combination of theory and experiments to understand the rich morphological behavior that arises from that balance. More specifically, a systematic study of micrometer-sized ChLC droplets is presented as a function of chirality and surface energy (or anchoring). With increasing chirality, a continuous transition is observed from a twisted bipolar structure to a radial spherical structure, all within a narrow range of chirality. During such a transition, a bent structure is predicted by simulations and confirmed by experimental observations. Simulations are also able to capture the dynamics of the quenching process observed in experiments. Consistent with published work, it is found that nanoparticles are attracted to defect regions on the surface of the droplets. For weak anchoring conditions at the nanoparticle surface, ChLC droplets adopt a morphology similar to that of the equilibrium helical phase observed for ChLCs in the bulk. As the anchoring strength increases, a planar bipolar structure arises, followed by a morphological transition to a bent structure. The influence of chirality and surface interactions are discussed in the context of the potential use of ChLC droplets as stimuli-responsive materials for reporting molecular adsorbates.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Role of peracetic acid on the disruption of lignin packing structure and its consequence on lignin depolymerisation

Peracetic acid (PAA) is an effective oxidant capable of solubilising lignin and efficiently depolymerising it to selective phenolic compounds; however, the specific role by which PAA initiates the depolymerisation is still elusive. Herein, interaction between PAA and the lignin macromolecule and the consequent structural changes of the latter were studied by characterising the lignin packing structure and its associated changes during the oxidation process. While the lignin packing structure and its changes associated with the PAA-mediated oxidation were probed by X-ray diffraction, the impact of the PAA on different chemical functionalities present in the lignin structure was established by 13 C and 1 H– 13 C heteronuclear single-quantum coherence nuclear magnetic resonance (NMR) spectroscopy. Further, combining the NMR spectroscopy results, and the product distribution, we conclude that the predominant reaction pathway for the oxidative depolymerisation of lignin with PAA is the Baeyer–Villiger oxidation of the ketone formed by the oxidation of the benzylic hydroxyl group adjacent to the β-O-4 linkage. The experimental evidence provided herein corroborated that PAA instigates oxygen insertion to the lignin macromolecule resulting in disruption of its packing structures and facilitates depolymerisation. We also investigated various metal oxide and mixed metal oxide catalysts to identify effective catalysts that further enhance the efficiency of PAA-mediated depolymerisation of lignin and produce selective monomeric phenolic compounds. Techno-economic analysis was also conducted to identify the key parameters associated with this oxidative process that need to be considered for possible commercial application.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗