Search NASA⌕ Search

SEARCH · Search NASA

Results for “structural modification”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly

Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene (“BMIE”), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu ++ and Zn ++ in bidentate (N 2 ) and tridentate (N 2 S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn ++ , Cu ++ , and Co ++ . EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu ++ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H 2 O/HO – , tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn ++ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. Finally, these features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Structural mechanisms of the Ih–II and II → Ic transitions between the crystalline phases of aqueous ice

Structural mechanisms are proposed for experimentally observed phase transitions between crystalline modifications of aqueous ice, Ih and II, as well as II and Ic. It is known that the Ih–II transition occurs with the conservation of large structural units (hexagonal channels) common for these ices. It is shown that the Ih → II transition may occur with the conservation of 5/6 of all hydrogen bonds in crystal, including all hydrogen bonds in the retained channels (3/4 of the total number of bonds in crystal) and 1/3 of the bonds between these channels (1/12 of the total number). The transformation of other hydrogen bonds between the retained channels leads to the occurrence of proton order in ice II. A structural mechanism is proposed to explain the transformation of single crystals of ice Ih either into single crystals of ice II or into crystalline twins of ice II with c axes rotated by 180° with respect to each other, which is often observed at the Ih → II transition. It is established that up to 7/12 of all hydrogen bonds are retained at the irreversible cooperative II → Ic transition.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Correlated oxide Dirac semimetal in the extreme quantum limit

Quantum materials (QMs) with strong correlation and nontrivial topology are indispensable to next-generation information and computing technologies. Exploitation of topological band structure is an ideal starting point to realize correlated topological QMs. Here, we report that strain-induced symmetry modification in correlated oxide SrNbO 3 thin films creates an emerging topological band structure. Dirac electrons in strained SrNbO 3 films reveal ultrahigh mobility (μ max ≈ 100,000 cm 2 /Vs), exceptionally small effective mass (m* ~ 0.04m e ), and nonzero Berry phase. Strained SrNbO 3 films reach the extreme quantum limit, exhibiting a sign of fractional occupation of Landau levels and giant mass enhancement. Our results suggest that symmetry-modified SrNbO 3 is a rare example of correlated oxide Dirac semimetals, in which strong correlation of Dirac electrons leads to the realization of a novel correlated topological QM.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Mycobacterium tuberculosis CitA activity is modulated by cysteine oxidation and pyruvate binding

As an adaptation for survival during infection, Mycobacterium tuberculosis becomes dormant, reducing its metabolism and growth. Two types of citrate synthases have been identified in Mycobacterium tuberculosis, GltA2 and CitA. Previous work shows that overexpression of CitA, the secondary citrate synthase, stimulates the growth of Mycobacterium tuberculosis under hypoxic conditions without showing accumulation of triacylglycerols and makes mycobacteria more sensitive to antibiotics, suggesting that CitA may play a role as a metabolic switch during infection and may be an interesting TB drug target. To assess the druggability and possible mechanisms of targeting CitA with small-molecule compounds, the CitA crystal structure was solved to 2.1 Å by X-ray crystallography. The solved structure shows that CitA lacks an NADH binding site that would afford allosteric regulation, which is atypical of most citrate synthases. However, a pyruvate molecule is observed within the analogous domain, suggesting pyruvate may instead be the allosteric regulator for CitA. Further, the R149 and R153 residues forming the charged portion of the pyruvate binding pocket were mutated to glutamate and methionine, respectively, to assess the effect of mutations on activity. Protein thermal shift assay shows thermal stabilization of CitA in the presence of pyruvate compared to the two CitA variants designed to decrease pyruvate affinity. Solved crystal structures of both variants show no significant structural changes. However, the catalytic efficiency of the R153M variant increases by 2.6-fold. Additionally, we show that covalent modification of C143 of CitA by Ebselen completely arrests enzyme activity. Similar inhibition is observed using two spirocyclic Michael acceptor containing compounds, which inhibit CitA with IC app 50 values of 6.6 and 10.9 μM. A crystal structure of CitA modified by Ebselen was solved, but significant structural changes were lacking. Considering that covalent modification of C143 inactivates CitA and the proximity of C143 to the pyruvate binding site, this suggests that structural and/or chemical changes in this sub-domain are responsible for regulating CitA enzymatic activity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1

The chemical modification of RNA bases represents a ubiquitous activity that spans all domains of life. Pseudouridylation is the most common RNA modification and is observed within tRNA, rRNA, ncRNA and mRNAs. Pseudouridine synthase or ‘PUS’ enzymes include those that rely on guide RNA molecules and others that function as ‘stand-alone’ enzymes. Among the latter, several have been shown to modify mRNA transcripts. Although recent studies have defined the structural requirements for RNA to act as a PUS target, the mechanisms by which PUS1 recognizes these target sequences in mRNA are not well understood. Here we describe the crystal structure of yeast PUS1 bound to an RNA target that we identified as being a hot spot for PUS1-interaction within a model mRNA at 2.4 Å resolution. The enzyme recognizes and binds both strands in a helical RNA duplex, and thus guides the RNA containing the target uridine to the active site for subsequent modification of the transcript. The study also allows us to show the divergence of related PUS1 enzymes and their corresponding RNA target specificities, and to speculate on the basis by which PUS1 binds and modifies mRNA or tRNA substrates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Theory of two-meson photo- and electroproduction off the nucleon

Using the reaction γN → ππN as the paradigmatic topological framework, a field-theoretical description of the electromagnetic production of two pseudoscalar mesons off the nucleon is derived and applied to photo- and electroproduction processes, assuming only one-photon exchange for the latter. The dynamics of all explicit three-point interaction mechanisms of the ππN system is accounted for by the Faddeev-type ordering structure of the Alt-Grassberger-Sandhas equations. The modifications necessary for incorporating n-meson vertices for n ≥ 4 are discussed. The formulation is valid for hadronic two-point and three-point functions dressed by arbitrary (even nonlinear) internal mechanisms provided all associated electromagnetic currents are constructed to satisfy their respective (generalized) Ward-Takahashi identities. Coupling the photon to the Faddeev structure of the underlying hadronic two-pion production mechanisms results in a natural expansion of the full two-pion photoproduction current $M$$^{μ}_{ππ}$ in terms of multiple dressed loops involving two-body subsystem scattering amplitudes of the ππN system that preserves gauge invariance as a matter of course order by order in the number of (dressed) loops. A closed-form expression is presented for the entire gauge-invariant current $M$$^{μ}_{ππ}$ with complete three-body dynamics. Individually gauge-invariant truncations of the full dynamics most relevant for practical applications at the no-loop, one-loop, and two-loop levels are discussed in detail. An approximation scheme to the full two-meson amplitude for calculational purposes is also presented. It approximates, systematically, the full amplitude to any desired order of expansion in the underlying hadronic two-body amplitude. Furthermore, it allows for the approximate incorporation of all neglected higher-order mechanisms in terms of a locally gauge-invariant phenomenological remainder current.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Interplay of local structure, charge, and spin in bilayered manganese perovskites

Chemical doping is a reliable method of modification of the electronic properties of transition metal compounds. In manganese perovskites, it leads to charge transfer and peculiar ordering phenomena. However, depending on the interplay of the local crystal structure and electronic properties, synthesis of stable compounds in the entire doping range is often impossible. In this paper, we show results of high-energy resolution x-ray absorption and emission spectroscopies on a ${\mathrm{La}}_{2{-}2x}{\mathrm{Sr}}_{1+2x}{\mathrm{Mn}}_{2}{\mathrm{O}}_{7}$ family of bilayered manganites in a broad doping range $(0.5{\le}x{\le}1)$. We established a relation between local Mn charge and Mn-O distances as a function of doping. Finally, based on a comparison of such relation with other manganites, we suggest why stable structures cannot be realized for certain doping levels of bilayered compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria

Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

PDB↗
DOE OSTI2019

Electronic Structure of LiCoO 2 Surfaces and Effect of Al Substitution

The surface properties of LiCoO 2 nanoplatelets, and their chemical modifications with Al 3+ , were studied using combined experimental and theoretical approaches. Our model shows that the electronic structures of several LiCoO 2 surface facets are significantly different from those of bulk LiCoO 2 , due to altered spin states of surface Co 3+ atoms. O K -edge X-ray absorption revealed a prominent splitting of the Co 3d -O 2p states, which is attributed to the presence of intermediate-state and/or high-spin-state Co 3+ . at the surface. In particular, the nonpolar (104) surface with intermediate-spin-state Co 3+ exhibits a strong two-dimensional character of splitting in these states, whereas the polar (001) surface with low-spin-state Co 3+ has a similar electronic structure to bulk LiCoO 2 . Here, partial substitution of Co 3+ by Al 3+ through the formation of core-shell architectures increases the ratio of low-spin-state Co3+, resulting in a distinct change in the intensity ratio of the split Co 3d -O 2p states, as revealed by spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Evolution of Mass Spectrometers for High m / z Biological Ion Formation, Transmission, Analysis and Detection: A Personal Perspective

Mass spectrometry (MS) has become an essential tool in virtually all academic, pharmaceutical, and biopharmaceutical analytical laboratories. The specialized and bespoke area of MS research and application of high m / z ion (> m / z 6000 and high mass, >150 kDa) formation, transmission, analysis, and detection is a relatively new area of focus for MS that has seen dramatic acceleration in interest over the last two decades. Herein we delve into this exciting aspect of MS, discussing how MS instrumentation has been refined and evolved for native-MS analysis. We cover the early groundbreaking experiments showing high m / z ion formation, transmission, and preservation of protein structure in the gas phase. Additionally, we discuss specific instrument optimizations and modifications that have advanced high m / z ion generation, transmission, analysis, and detection, contributing to the research area known as gas-phase structural biology. Native-MS sample introduction methods, emerging technologies, and future perspectives are also examined. Finally, we share personal opinions, observations, and experiences that are new to the community or previously unpublished.

collisions↗
DOE OSTI2022

Enhancing Lifetime and Reducing Costs for Fish Diversion Netting Structures (Abstract)

This effort will focus on technology transfer and commercialization of antifouling coatings with an enthusiastic and engaged industrial team. Environmental requirements and operational demands call for a nontoxic coating/paint to prevent fouling on fish passage guidance netting at hydropower facilities. For example, one netting customer estimated the capital cost for compliance at $\$12$ million to $\$15$ million. This project will build partnerships between PNNL and private companies to optimize, demonstrate, mature, and commercialize a novel PNNL-developed technology that addresses this critical coating need of the hydropower industry. This effort will support modification of existing coatings for application to flexible netting structures. Industrial partners include commercial coating development specialist (Lorama), hydrophobic material manufacturer and paint developer (Dry Surface Technologies), aquatic applications specialists (Prometheus Innovations and River Connectivity Systems), and hydropower netting producer (Pacific Netting Products). Engagement with the U.S. Army Corps of Engineers (USACE) and Bureau of Reclamation (BOR), two hydropower operators, throughout the project will provide expertise and field test sites that will provide crucial proof of real-world performance data (additional details provided in Teaming section). Taylor Shellfish Farms will provide organisms and fouling expertise as well as a perspective of potential broader impacts for the blue economy. Sample netting will demonstrate performance in a range of environments for key hydropower applications. PNNL will work with industrial partners to overcome commercialization barriers as well as resolving any manufacturing or regulatory issues. This Phase 1 effort is focused on technology optimization for application to fish passage guidance netting and technology validation as verified by independent testing (through USACE, BOR, Taylor Shellfish and Prometheus Innovations). Through this effort, SLIC will be demonstrated for netting applications at technology readiness level (TRL) 5. The field test data will allow optimization of SLIC formulation and performance which is key to enabling technology transfer of a mature proven technology to industry and production of a viable commercial product specifically focused for hydropower needs.

13 HYDRO ENERGY↗
DOE OSTI2016

Theory of the formation of P4{sub 1}32(P4{sub 3}32)-phase spinels

A group-theoretical, thermodynamic, and structural study of the formation of P4{sub 1}32(P4{sub 3}32) spinel modification has been performed. In particular, the occurrence of unique hyper-kagome atomic order is analyzed. The critical order parameter inducing a phase transition is established. It is shown that the calculated structure of the low-symmetry P4{sub 1}32(P4{sub 3}32) phase is formed as a result of displacements of atoms of all types and due to the cation and anion ordering. The problem of the occurrence of unique hyper-kagome atomic order in the structures of P4{sub 1}32(P4{sub 3}32) spinel modifications is considered theoretically. It is proven within the Landau theory of phase transitions that the P4{sub 1}32(P4{sub 3}32) phase can be formed from the high-symmetry Fd3m phase with an ideal spinel structure only as a result of first-order phase transition. Therefore, the formation of hyper-kagome sublattice in the P4{sub 1}32(P4{sub 3}32) phase is accompanied by a significant transformation of the spinel structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Effect of Polyphenylsulfone and Polysulfone Incompatibility on the Structure and Performance of Blend Membranes for Ultrafiltration

This study deals with the modification of polyphenylsulfone ultrafiltration membranes by introduction of an incompatible polymer polysulfone to the polyphenylsulfone casting solution to improve the permeability. The correlation between properties of the blend polyphenylsulfone/polysulfone solutions and porous anisotropic membranes for ultrafiltration prepared from these solutions was revealed. The blend polyphenylsulfone/polysulfone solutions were investigated using a turbidity spectrum method, optical microscopy and measurements of dynamic viscosity and turbidity. The structure of the prepared blend flat sheet membranes was studied using scanning electron microscopy. Membrane separation performance was investigated in the process of ultrafiltration of human serum albumin buffered solutions. It was found that with the introduction of polysulfone to the polyphenylsulfone casting solution in N-methyl-2-pyrrolidone the size of supramolecular particles significantly increases with the maximum at (40–60):(60:40) polyphenylsulfone:polysulfone blend ratio from 76 nm to 196–354 nm. It was shown that polyphenylsulfone/polysulfone blend solutions, unlike the solutions of pristine polymers, are two-phase systems (emulsions) with the maximum droplet size and highest degree of polydispersity at polyphenylsulfone/polysulfone blend ratios (30–60):(70–40). Pure water flux of the blend membranes passes through a maximum in the region of the most heterogeneous structure of the casting solution, which is associated with the imposition of a polymer-polymer phase separation on the non-solvent induced phase separation upon membrane preparation. The application of polyphenylsulfone/polysulfone blends as membrane-forming polymers and polyethylene glycol (Mn = 400 g·mol -1 ) as a pore-forming agent to the casting solutions yields the formation of ultrafiltration membranes with high membrane pure water flux (270 L·m -2 ·h -1 at 0.1MPa) and human serum albumin rejection of 85%.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Towards an Understanding of Oxidative Damage in an a-L-Arabinofuranosidase of Trichoderma reesei : a Molecular Dynamics Approach

Trichoderma reesei is a ‘workhorse’ fungus that produces glycosyl hydrolases (e.g., cellulases) at high titers for use in industrial bioprocessing. In this study, we focused on two side-chain hemicellulases, a-L-arabinofuranosidases and a-D-galactosidases, which are important for the treatment of lignocellulosic biomass, but susceptible to oxidative damage that can occur during industrial processing. The molecular details that render these enzymes inactive have not yet been identified. To approach this issue, we used proteomics to identify amino acid residues that were oxidized after a relevant oxidative treatment (Fenton reaction). These oxidative modifications were included in the 3D-protein structures, and using molecular dynamics simulations, we then studied the behaviors of non-modified and oxidized enzymes. These simulations showed significant alterations of the conformational stability of proteins when oxidized, as evidenced by changes in root mean square deviation (RMSD) and principal component analyses (PCA) trajectories. Likewise, enzyme-ligand interactions such as hydrogen bonds were greatly reduced in quantity and quality in the oxidized proteins. Finally, free energy landscape plots showed that there was a more rugged energy surface in the oxidized proteins, implying a less favorable reaction pathway. These results reveal the basis for loss of function in these carbohydrate active enzymes (CAZYs) in T. reesei.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Application of organic- and nanoparticle-modified foams in foamed concrete: Reinforcement and stabilization mechanisms

Highlights: • An ultra-stable foam was fabricated by modifying the gas–liquid interface. • A homogeneous and finer pore structure of foamed concrete was generated. • Stabilization and enhancement mechanisms were investigated. - Abstract: In this study, an ultra-stable foam used for foamed concrete was fabricated by modifying the gas–liquid interface by coupling the effects of an organic surfactant and nanoparticles. A serial of techniques was employed to study the products and microstructure development of foam and foamed concrete, respectively. The results show that nano-silica and hydroxypropyl methylcellulose can slow the coalescence and disproportionation of the bubbles by adsorbing at the air bubble surface and increasing the viscosity of cell wall paste, thus preventing gas transfer and hindering physical drainage between the gaseous and liquid phases. Also, a more homogeneous and finer pore structure is generated with the inclusion of the organic surfactant and nanoparticles. The pozzolanic reaction between the nano-silica and Ca(OH){sub 2} results in an increased C-S-H content and the densification of the cell wall structure. In addition, the stability of foamed concrete with modification and relevant stabilization mechanisms were also investigated.

36 MATERIALS SCIENCE↗
DOE OSTI2019

A facile method to introduce iron secondary metal centers into metal–organic frameworks

In this report, we report the successful incorporation of iron (0) species into a 2, 2'-bipyridine functionalized metal–organic framework (MOF) (UiO-67-bpydc). Considering the limited window size of the MOF, a small molecule, iron pentacarbonyl, was used to introduce iron (0) to coordinate to the backbone of the MOF. The newly generated material contains the iron coordinated linker, Fe(CO) 3 (bpydc), which was supported by a series of characterization techniques. DFT calculation was also used to help understand the structure of the formed complex inside the MOF. The MOF structure remained unchanged after the post-synthetic modification, and the resulted material is a great precursor to generate MOF supported catalyst.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Ambient Synthesis for Fe(II) Polypyridyl Complexes with an Order of Magnitude Increase in Charge-Transfer Excited-State Lifetimes over [Fe(bpy) 3 ] 2+

Replacing precious metals with abundant metals is an important research focus in photochemical energy conversion and storage to meet global energy demands. However, transition metal complexes (TMCs) based on abundant 3d metals typically possess photochemical disadvantages─such as short charge-transfer excited-state lifetimes─and molecular modifications have focused on optimizing the interplay of structure, dynamics, and energetics to overcome their limitations. One strategy to do so is the use of bespoke ligands that can extend the lifetimes of chemically useful excited states. Here, in this study, we report the synthesis and characterization of novel Fe(II) complexes featuring lengthy polypyridyl ligands that can be readily synthesized. Steady-state and transient absorption spectroscopies indicate that these complexes have desirable properties and their excited metal-to-ligand charge-transfer states live an order of magnitude longer than in the benchmark [Fe(bpy) 3 ] 2+ . This lifetime is largely preserved in the heteroleptic complexes, thereby enabling the preparation of asymmetric complexes. Additionally, we apply nonradiative transition theory to explain the long-time decay kinetics. In light of their ease of preparation and reasonable excited-state lifetimes, we suggest the use of these complexes in Fe(II) dye-sensitized solar cells, where the rate of charge injection would be competitive with increased lifetime.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗